ggnewscale-cited.bib

@misc{2023,
  title = {Study on the Mechanism of Lung Ischemia-Reperfusion Injury Based on Bioinformatics},
  year = {2023},
  month = jul,
  doi = {10.21203/rs.3.rs-3088383/v1},
  urldate = {2023-07-19},
  abstract = {Objective: lung ischemia-reperfusion injury has always been a research hotspot in the field of lung transplantation. The purpose of this study is tantamount to explore the molecular mechanism, key genes and related signal pathways of ischemia-reperfusion in lung transplantatio...},
  howpublished = {https://www.researchsquare.com},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/2023_Study on the mechanism of lung ischemia-reperfusion injury based on.pdf}
}

@misc{2023a,
  title = {Integrated Analysis of Hub Genes and {{miRNA-}} Transcription Factor-Hub Gene Interaction Network in Necrotizing Enterocolitis},
  year = {2023},
  month = apr,
  doi = {10.21203/rs.3.rs-2756663/v1},
  urldate = {2023-04-12},
  abstract = {Background The aim of this study was to identify hub genes, related transcription factors (TFs) and miRNAs from the miRNA\–TF\–gene interaction network in necrotizing enterocolitis (NEC).Methods Three expression data sets from GEO database that compared NEC w...},
  howpublished = {https://www.researchsquare.com},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/2023_Integrated analysis of hub genes and miRNA- transcription factor-hub gene.pdf}
}

@article{akhilprakash2021,
  title = {Dissemination of Multidrug Resistant Bacteria to the Polar Environment - {{Role}} of the Longest Migratory Bird {{Arctic}} Tern ({{Sterna}} Paradisaea)},
  author = {Akhil Prakash, E. and Hrom{\'a}dkov{\'a}, Tereza and Jabir, T. and Vipindas, P. V. and Krishnan, K. P. and Mohamed Hatha, A. A. and Briedis, Martins},
  year = {2021},
  month = dec,
  journal = {Science of The Total Environment},
  pages = {152727},
  issn = {0048-9697},
  doi = {10.1016/j.scitotenv.2021.152727},
  urldate = {2022-01-03},
  abstract = {The ever-increasing prevalence of antibiotic-resistant bacteria, primarily due to the frequent use and misuse of antibiotics, is an issue of serious global concern. Migratory birds have a significant role in dissemination of antibiotic-resistant bacteria (ARB), as they acquire resistant bacteria from reservoirs and transport them to other environments which are relatively less influenced by anthropogenically. We have investigated the prevalence of ARB in a long-distance migratory bird, the Arctic tern (Sterna paradisaea) captured from the Svalbard Archipelago. The birds were tagged with geolocators to track their extraordinary long migration, and the cloacal samples were collected before the migration and after the migration by recapturing the same birds. The tracking of 12 birds revealed that during the annual cycle they underwent a total of 166 stopovers (11--18, mean\,=\,3.8) and recovery points along the Atlantic coast. Twelve major bacterial genera were identified from Arctic tern cloacal samples, which are dominated by Staphylococcus spp. and Aerococcus spp. The bacterial isolates showed resistance against 16 antibiotics (before migration) and 17 antibiotics (after migration) out of 17 antibiotics tested. Resistance to {$\beta$}-lactam and quinolone class of antibiotics were frequent among the bacteria. The study highlights the potential role of Arctic tern in the dissemination of multidrug resistant bacteria across far and wide destinations, especially to the polar environments.},
  langid = {english},
  keywords = {Antibiotic resistance,Arctic,Arctic tern,Bacteria,Bird migration,Wildlife}
}

@article{aminitabrizi2020,
  title = {Controls on {{Soil Organic Matter Degradation}} and {{Subsequent Greenhouse Gas Emissions Across}} a {{Permafrost Thaw Gradient}} in {{Northern Sweden}}},
  author = {AminiTabrizi, Roya and Wilson, Rachel M. and Fudyma, Jane D. and Hodgkins, Suzanne B. and Heyman, Heino M. and Rich, Virginia I. and Saleska, Scott R. and Chanton, Jeffrey P. and Tfaily, Malak M.},
  year = {2020},
  journal = {Front. Earth Sci.},
  volume = {8},
  publisher = {Frontiers},
  issn = {2296-6463},
  doi = {10.3389/feart.2020.557961},
  urldate = {2021-03-03},
  abstract = {Warming-induced permafrost thaw could enhance microbial decomposition of previously stored soil organic matter (SOM) to carbon dioxide (CO2) and methane (CH4), one of the most significant potential feedbacks from terrestrial ecosystems to the atmosphere in a changing climate. The environmental parameters regulating microbe-organic matter interactions and greenhouse gas (GHG) emissions in permafrost peatlands are however still largely unknown. The objective of this work is to understand controls on SOM degradation and its impact on GHG emissions across the Stordalen Mire, a thawing peat plateau in Northern Sweden. Here, we applied high-resolution mass spectrometry to characterize SOM molecular composition in peat soil samples from the active layers of a Sphagnum-dominated bog and rich fen sites in the Mire. Microbe-organic matter interactions and GHG emissions across the thaw gradient were controlled by aboveground vegetation and soil pH. An increasingly high abundance of reduced organic compounds experiencing greater humification rates due to enhanced microbial activity were observed with increasing thaw, in parallel with higher CH4 and CO2 emissions. Bog SOM however contained more Sphagnum-derived phenolics, simple carbohydrates, and organic- acids. The low degradation of bog SOM by microbial communities, the enhanced SOM transformation by potentially abiotic mechanisms, and the accumulation of simple carbohydrates in the bog sites could be attributed in part to the low pH conditions of the system associated with Sphagnum mosses. We show that Gibbs free energy of C half reactions based on C oxidation state for OM can be used as a quantifiable measure for OM decomposability and quality to enhance current biogeochemical models to predict C decomposition rates. We found a direct association between OM chemical diversity and {$\delta$}13C-CH4 in peat porewater; where higher substrate diversity was positively correlated with enriched {$\delta$}13C-CH4 in fen sites. Oxidized sulfur-containing compounds, produced by Sphagnum, were further hypothesized to control GHG emissions by acting as electron acceptors for a sulfate-reducing electron transport chain, inhibiting methanogenesis in peat bogs. These results suggest that warming-induced permafrost thaw might increase organic matter lability, in subset of sites that become wetlands, and shift biogeochemical processes toward faster decomposition with an increasing proportion of Creleased as CH4.},
  langid = {english},
  keywords = {bog,fen,Mass Spectrometry,Peatlands,Permafrost,soil organic matter,Sphagnum},
  file = {/home/user1/Dropbox/Papers/AminiTabrizi et al_2020_Controls on Soil Organic Matter Degradation and Subsequent Greenhouse Gas_.pdf}
}

@article{anbo,
  title = {A Bittersweet Fate: Detection of Serotype Switching in {{Pseudomonas}} Aeruginosa},
  shorttitle = {A Bittersweet Fate},
  author = {Anbo, Mikkel and Jelsbak, LarsYR 2023},
  journal = {Microbial Genomics},
  volume = {9},
  number = {1},
  pages = {000919},
  publisher = {Microbiology Society,},
  issn = {2057-5858,},
  doi = {10.1099/mgen.0.000919},
  urldate = {2023-01-15},
  abstract = {High-risk clone types in Pseudomonas aeruginosa are problematic global multidrug-resistant clones. However, apart from their ability to resist antimicrobial treatment, not much is known about what sets these clones apart from the multitude of other clones. In high-risk clone ST111, it has previously been shown that replacement of the native serotype biosynthetic gene cluster (O4) by a different gene cluster (O12) by horizontal gene transfer and recombination may have contributed to the global success of this clone. However, the extent to which isolates undergo this type of serotype switching has not been adequately explored in P. aeruginosa . In the present study, a bioinformatics tool has been developed and utilized to provide a first estimate of serotype switching in groups of multidrug resistant (MDR) clinical isolates. The tool detects serotype switching by analysis of core-genome phylogeny and in silico serotype. Analysis of a national survey of MDR isolates found a prevalence of 3.9{$\mkern1mu\%$} of serotype-switched isolates in high-risk clone types ST111, ST244 and ST253. A global survey of MDR isolates was additionally analysed, and it was found that 2.3{$\mkern1mu\%$} of isolates had undergone a serotype switch. To further understand this process, we determined the exact boundaries of the horizontally transferred serotype O12 island. We found that the size of the serotype island correlates with the clone type of the receiving isolate and additionally we found intra-clone type variations in size and boundaries. This suggests multiple serotype switch events. Moreover, we found that the housekeeping gene gyrA is co-transferred with the O12 serotype island, which prompted us to analyse this allele for all serotype O12 isolates. We found that 95{$\mkern1mu\%$} of ST111 O12 isolates had a resistant gyrA allele and 86{$\mkern1mu\%$} of all O12 isolates had a resistant gyrA allele. The rates of resistant gyrA alleles in isolates with other prevalent serotypes are all lower. Together, these results show that the transfer and acquisition of serotype O12 in high-risk clone ST111 has happened multiple times and may be facilitated by multiple donors, which clearly suggests a strong selection pressure for this process. However, gyrA-mediated antibiotic resistance may not be the only evolutionary driver.,}
}

@article{baker2023,
  title = {Effects of {{Phycosphere Bacteria}} on {{Their Algal Host Are Host Species-Specific}} and {{Not Phylogenetically Conserved}}},
  author = {Baker, Dylan and Lauer, James and Ortega, Anna and Jackrel, Sara L. and Denef, Vincent J.},
  year = {2023},
  month = jan,
  journal = {Microorganisms},
  volume = {11},
  number = {1},
  pages = {62},
  publisher = {Multidisciplinary Digital Publishing Institute},
  issn = {2076-2607},
  doi = {10.3390/microorganisms11010062},
  urldate = {2022-12-28},
  abstract = {Phytoplankton is fundamental to life on Earth. Their productivity is influenced by the microbial communities residing in the phycosphere surrounding algal cells. Expanding our knowledge on how algal-bacterial interactions affect algal growth to more hosts and bacteria can help elucidate general principles of algal-host interactions. Here, we isolated 368 bacterial strains from phycosphere communities, right after phycosphere recruitment from pond water and after a month of lab cultivation and examined their impacts on growth of five green algal species. We isolated both abundant and rare phycosphere members, representing 18.4\% of the source communities. Positive and neutral effects predominated over negative effects on host growth. The proportion of each effect type and whether the day of isolation mattered varied by host species. Bacteria affected algal carrying capacity more than growth rate, suggesting that nutrient remineralization and toxic byproduct metabolism may be a dominant mechanism. Across-host algal fitness assays indicated host-specific growth effects of our isolates. We observed no phylogenetic conservation of the effect on host growth among bacterial isolates. Even isolates with the same ASV had divergent effects on host growth. Our results emphasize highly specific host-bacterial interactions in the phycosphere and raise questions as to which mechanisms mediate these interactions.},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  langid = {english},
  keywords = {cultivation-dependent,host fitness,host specificity,microbiome,phytoplankton},
  file = {/home/user1/Dropbox/Papers/Baker et al_2023_Effects of Phycosphere Bacteria on Their Algal Host Are Host Species-Specific.pdf}
}

@article{baumgarten2023,
  title = {Pan-{{European}} Study of Genotypes and Phenotypes in the {{Arabidopsis}} Relative {{Cardamine}} Hirsuta Reveals How Adaptation, Demography, and Development Shape Diversity Patterns},
  author = {Baumgarten, Lukas and Pieper, Bjorn and Song, Baoxing and Mane, S{\'e}bastien and Lempe, Janne and Lamb, Jonathan and Cooke, Elizabeth L. and Srivastava, Rachita and Str{\"u}tt, Stefan and {\v Z}anko, Danijela and Casimiro, Pedro GP and Hallab, Asis and Cartolano, Maria and Tattersall, Alexander D. and Huettel, Bruno and Filatov, Dmitry A. and Pavlidis, Pavlos and Neuffer, Barbara and Bazakos, Christos and Schaefer, Hanno and Mott, Richard and Gan, Xiangchao and {Alonso-Blanco}, Carlos and Laurent, Stefan and Tsiantis, Miltos},
  year = {2023},
  month = jul,
  journal = {PLOS Biology},
  volume = {21},
  number = {7},
  pages = {e3002191},
  publisher = {Public Library of Science},
  issn = {1545-7885},
  doi = {10.1371/journal.pbio.3002191},
  urldate = {2023-07-24},
  abstract = {We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species.},
  langid = {english},
  keywords = {Alleles,Arabidopsis thaliana,Europe,Gene mapping,Genomics,Leaves,Quantitative trait loci,Single nucleotide polymorphisms},
  file = {/home/user1/Dropbox/Papers/Baumgarten et al_2023_Pan-European study of genotypes and phenotypes in the Arabidopsis relative.pdf}
}

@article{bosch2024,
  title = {Decomposition of {{Fomes}} Fomentatius Fruiting Bodies -- Transition of Healthy Living Fungus into a Decayed Bacteria-Rich Habitat Is Primarily Driven by {{Arthropoda}}},
  author = {Bosch, Jason and Dobbler, Priscila Thiago and V{\v e}trovsk{\'y}, Tom{\'a}{\v s} and , Vojt{\v e}chTl{\'a}skal and Baldrian, Petr and Brabcov{\'a}, Vendula},
  year = {2024},
  month = mar,
  journal = {FEMS Microbiology Ecology},
  pages = {fiae044},
  issn = {0168-6496},
  doi = {10.1093/femsec/fiae044},
  urldate = {2024-04-05},
  abstract = {Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.},
  file = {/home/user1/Dropbox/Papers/Bosch et al_2024_Decomposition of Fomes fomentatius fruiting bodies – transition of healthy.pdf}
}

@article{botero2023,
  title = {A Phylogenomic and Comparative Genomic Analysis of {{Commensalibacter}}, a Versatile Insect Symbiont},
  author = {Botero, Juliana and Sombolestani, Atena Sadat and Cnockaert, Margo and Peeters, Charlotte and Borremans, Wim and De Vuyst, Luc and Vereecken, Nicolas J. and Michez, Denis and Smagghe, Guy and {Bonilla-Rosso}, German and Engel, Philipp and Vandamme, Peter},
  year = {2023},
  month = apr,
  journal = {Animal Microbiome},
  volume = {5},
  number = {1},
  pages = {25},
  issn = {2524-4671},
  doi = {10.1186/s42523-023-00248-6},
  urldate = {2023-05-02},
  abstract = {To understand mechanisms of adaptation and plasticity of pollinators and other insects a better understanding of diversity and function of their key symbionts is required. Commensalibacter is a genus of acetic acid bacterial symbionts in the gut of honey bees and other insect species, yet little information is available on the diversity and function of Commensalibacter bacteria. In the present study, whole-genome sequences of 12 Commensalibacter isolates from bumble bees, butterflies, Asian hornets and rowan berries were determined, and publicly available genome assemblies of 14 Commensalibacter strains were used in a phylogenomic and comparative genomic analysis.},
  keywords = {Asian hornet,Bumble bee,Butterfly,Commensalibacter,Functional genomics,Insect symbiont,Phylogenomics,Western honey bee},
  file = {/home/user1/Dropbox/Papers/Botero et al_2023_A phylogenomic and comparative genomic analysis of Commensalibacter, a.pdf}
}

@article{botero2024,
  title = {A Comparative Genomic Analysis of {{{\emph{Fructobacillus}}}}{\emph{ Evanidus}} Sp. Nov. from Bumble Bees},
  author = {Botero, Juliana and Peeters, Charlotte and De Canck, Evelien and Laureys, David and Wieme, Anneleen D. and Cleenwerck, Ilse and Depoorter, Eliza and Praet, Jessy and Michez, Denis and Smagghe, Guy and Vandamme, Peter},
  year = {2024},
  month = mar,
  journal = {Systematic and Applied Microbiology},
  pages = {126505},
  issn = {0723-2020},
  doi = {10.1016/j.syapm.2024.126505},
  urldate = {2024-03-29},
  abstract = {The increase in studies on bee microbiomes is prompted by concerns over global pollinator declines. Bumble bees host core and non-core microbiota which may contribute to increased lifetime fitness. The presence of Fructobacillus in the gut microbiomes of bumble bee workers, or the replacement of core symbionts with Fructobacillus bacteria, has been considered a marker of dysbiosis. A phylogenomic analysis and functional genomic characterization of the genomes of 21 Fructobacillus isolates from bumble bees demonstrated that they represented four species, i.e. Fructobacillus cardui, Fructobacillus fructosus, Fructobacillus tropaeoli, and the novel species Fructobacillus evanidus sp. Nov. Our results confirmed and substantiated the presence of two phylogenetically and functionally distinct Fructobacillus species clades that differ in genome size, percentage G\,+\,C content, the number of coding DNA sequences and metabolic characteristics. Clade 1 and clade 2 species differed in amino acid and, to a lesser extent, in carbohydrate metabolism, with F. evanidus and F. tropaeoli genomes featuring a higher number of complete metabolic pathways. While Fructobacillus genomes encoded genes that allow adhesion, biofilm formation, antibacterial activity and detoxification, other bacteria isolated from the bumble bee gut appeared better equipped to co-exist with the bumble bee host. The isolation and identification of multiple Fructobacillus species from several bumble bee gut samples in the present study also argued against a specific partnership between Fructobacillus species and their bumble bee hosts.},
  keywords = {Bumble bees,Comparative genomic analysis,Metabolic differences,Phylogenomics}
}

@article{boys2023,
  title = {Structural Homology Screens Reveal Host-Derived Poxvirus Protein Families Impacting Inflammasome Activity},
  author = {Boys, Ian N. and Johnson, Alex G. and Quinlan, Meghan R. and Kranzusch, Philip J. and Elde, Nels C.},
  year = {2023},
  month = aug,
  journal = {Cell Reports},
  volume = {42},
  number = {8},
  pages = {112878},
  issn = {2211-1247},
  doi = {10.1016/j.celrep.2023.112878},
  urldate = {2023-07-30},
  abstract = {Viruses acquire host genes via horizontal transfer and can express them to manipulate host biology during infections. Some homologs retain sequence identity, but evolutionary divergence can obscure host origins. We use structural modeling to compare vaccinia virus proteins with metazoan proteomes. We identify vaccinia A47L as a homolog of gasdermins, the executioners of pyroptosis. An X-ray crystal structure of A47 confirms this homology, and cell-based assays reveal that A47 interferes with caspase function. We also identify vaccinia C1L as the product of a cryptic gene fusion event coupling a Bcl-2-related fold with a pyrin domain. C1 associates with components of the inflammasome, a cytosolic innate immune sensor involved in pyroptosis, yet paradoxically enhances inflammasome activity, suggesting differential modulation during infections. Our findings demonstrate the increasing power of structural homology screens to reveal proteins with unique combinations of domains that viruses capture from host genes and combine in unique ways.},
  langid = {english},
  keywords = {AlphaFold,divergence,evolution,gasdermin,homology,inflammasome,poxvirus,pyroptosis,vaccinia,virus},
  file = {/home/user1/Dropbox/Papers/Boys et al_2023_Structural homology screens reveal host-derived poxvirus protein families.pdf}
}

@misc{boys2023a,
  title = {Structural Homology Screens Reveal Poxvirus-Encoded Proteins Impacting Inflammasome-Mediated Defenses},
  author = {Boys, Ian N. and Johnson, Alex G. and Quinlan, Meghan and Kranzusch, Philip J. and Elde, Nels C.},
  year = {2023},
  month = feb,
  primaryclass = {New Results},
  pages = {2023.02.26.529821},
  publisher = {bioRxiv},
  doi = {10.1101/2023.02.26.529821},
  urldate = {2023-03-02},
  abstract = {Viruses acquire host genes via horizontal gene transfer and can express them to manipulate host biology during infections. Some viral and host homologs retain sequence identity, but evolutionary divergence can obscure host origins. We used structural modeling to compare vaccinia virus proteins with metazoan proteomes. We identified vaccinia A47L as a homolog of gasdermins, the executioners of pyroptosis. An X-ray crystal structure of A47 confirmed this homology and cell-based assays revealed that A47 inhibits pyroptosis. We also identified vaccinia C1L as the product of a cryptic gene fusion event coupling a Bcl-2 related fold with a pyrin domain. C1 associates with components of the inflammasome, a cytosolic innate immune sensor involved in pyroptosis, yet paradoxically enhances inflammasome activity, suggesting a benefit to poxvirus replication in some circumstances. Our findings demonstrate the potential of structural homology screens to reveal genes that viruses capture from hosts and repurpose to benefit viral fitness.},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {{\copyright} 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Boys et al_2023_Structural homology screens reveal poxvirus-encoded proteins impacting.pdf}
}

@article{bruns2024,
  title = {A Wandering Wedgefish Illustrates the Need for Cooperative Elasmobranch Conservation in the {{Arabian Gulf}}},
  author = {Bruns, Stephan and Al Hameli, Shamsa and Sulanke, Erik and Henderson, Aaron C.},
  year = {2024},
  month = mar,
  journal = {Environ Biol Fish},
  issn = {1573-5133},
  doi = {10.1007/s10641-024-01531-4},
  urldate = {2024-03-09},
  abstract = {The smoothnose wedgefish Rhynchobatus laevis, a shark-like ray classified as Critically Endangered by the International Union for Conservation of Nature, has received limited research attention. To address the knowledge gaps in its spatial behaviour, this study utilised satellite monitoring of a fortuitously captured female over a 51-day period in the Arabian Gulf. Based on the resulting movement track, the individual covered a minimum distance of 712~km, traversing the exclusive economic zones of three different countries. Its track began in the United Arab Emirates, from where it headed north, entering Iranian waters, where it spent most of its time, before continuing westward across the Gulf and eventually reaching Qatari waters. Novel insights into its behaviour revealed an observation of rapid ascents over the study period. Although both diurnal and nocturnal ascents were observed, they occurred predominantly during nocturnal periods. Contrary to the prevailing belief that wedgefish are bottom-associated, the study animal spent a considerable amount of time in the water column. The use of various depths in both nearshore and offshore waters highlights elevated susceptibility to multiple types of fishing gear. This underscores the need for an international cooperative approach to the management and conservation of shark-like rays in the Arabian Gulf.},
  langid = {english},
  keywords = {Chondrichthyes,Critically endangered,Fisheries,Management,Middle East,Spatial ecology},
  file = {/home/user1/Dropbox/Papers/Bruns et al_2024_A wandering wedgefish illustrates the need for cooperative elasmobranch.pdf}
}

@article{buitendijk2023,
  title = {Timing and Intensity of Goose Grazing: {{Implications}} for Grass Height and First Harvest},
  shorttitle = {Timing and Intensity of Goose Grazing},
  author = {Buitendijk, Nelleke H. and Nolet, Bart A.},
  year = {2023},
  month = nov,
  journal = {Agriculture, Ecosystems \& Environment},
  volume = {357},
  pages = {108681},
  issn = {0167-8809},
  doi = {10.1016/j.agee.2023.108681},
  urldate = {2023-07-25},
  abstract = {Grazing birds like geese can have a big impact on agricultural land, potentially causing damage to crops. Their exploitation of agricultural land varies within and between seasons, and these temporal grazing patterns can be influenced by management. Furthermore, management practices using scaring and accommodation aim to influence local grazing pressures. To achieve efficient goose management we need a good understanding of the effects of timing and intensity of grazing on grass development and subsequent yield loss. We performed an exclosure study on twelve fields in Friesland (Frysl{\^a}n), the Netherlands to study the effect of grazing on grass development and potential yield loss. Grazing was prevented either from November or from early April until farmers anticipated their first harvest. Every two weeks we measured grass height and calculated growth in exclosures and in ungrazed plots, and performed dropping counts. The results show that the difference in grass height between grazed and ungrazed plots increases with grazing pressure, but less so for higher grazing pressures. We also find that both winter and spring grazing can result in a larger difference in grass height between grazed and ungrazed plots, and grazing into the growing season delays the start of grass growth. This appears due to the relationship between grass height and growth rate. Because the optimal height for growth increases over the season, spring grazing has a much larger impact on grassland yields than winter grazing. Overall these results show that the amount of yield loss depends on different aspects of grazing, most prominently the recovery time, duration and grazing intensity. We hypothesize that barnacle geese may select fields with denser swards and may stimulate sward density by frequent grazing throughout winter and early spring as well as across consecutive years. Future studies should look into the effect of harvest delays and sward density on the size and quality of yield across the season and especially at the last cut. Management with scaring and accommodation may be able to reduce overall yield losses, but the effect may depend on the timing and location of scaring.},
  langid = {english},
  keywords = {Agricultural damage,Goose management,Grass growth,Grazing pressure,Herbivore farmer conflict,Yield loss},
  file = {/home/user1/Dropbox/Papers/Buitendijk_Nolet_2023_Timing and intensity of goose grazing.pdf}
}

@article{camacho2024,
  title = {Mechanisms Preventing Animals to Achieve Buoyant Flight},
  author = {Camacho, Luis F. and {\'A}vila, Jos{\'e} E. and {Fl{\'o}rez-V}, Camilo},
  year = {2024},
  month = mar,
  journal = {Journal of Natural History},
  volume = {58},
  number = {9-12},
  pages = {440--448},
  publisher = {Taylor \& Francis},
  issn = {0022-2933},
  doi = {10.1080/00222933.2024.2322178},
  urldate = {2024-03-29},
  abstract = {In the 300-million-year evolutionary history of animal flight, fliers have universally evolved to exploit the physical principle of drag, whereby an animal uses wings to achieve lift. However, the treehopper Oeda -- an Amazonian insect exhibiting a grotesquely large balloon-like thorax -- has been described in what may be the only account of an animal engaging in buoyant flight, whereby an animal fills body cavities with low-density air to float, akin to a hot-air balloon. We use Oeda as a study system to conduct a theoretical analysis exploring the biomechanics of buoyant flight and the mechanisms preventing its widespread occurrence in animals. We show that not even an organism with the unique and disproportionate dimensions of Oeda can buoy more than 1\% of its body weight. Instead, our results suggest Oeda's bloated thorax is a hindrance for flight that has selected for larger wings to compensate for the species' disproportionate dimensions. Our analysis illustrates that animals may only achieve buoyant flight by filling cavities thousands of times larger than the body with heated low-density biogases. Still, the evolution of such traits is likely restricted by a variety of developmental and ecological factors that have prevented animals from evolving buoyant flight. Whether any animal has evolved the means to conquer buoyant flight remains to be found in nature.},
  keywords = {Flying,insect,lift,locomotion,Membracidae,Oeda},
  file = {/home/user1/Dropbox/Papers/Camacho et al_2024_Mechanisms preventing animals to achieve buoyant flight.pdf}
}

@article{carey2023,
  title = {Global Diversity and Antimicrobial Resistance of Typhoid Fever Pathogens: {{Insights}} from a Meta-Analysis of 13,000 {{Salmonella Typhi}} Genomes},
  shorttitle = {Global Diversity and Antimicrobial Resistance of Typhoid Fever Pathogens},
  author = {Carey, Megan E and Dyson, Zoe A and Ingle, Danielle J and Amir, Afreenish and Aworh, Mabel K and Chattaway, Marie Anne and Chew, Ka Lip and Crump, John A and Feasey, Nicholas A and Howden, Benjamin P and Keddy, Karen H and Maes, Mailis and Parry, Christopher M and Van Puyvelde, Sandra and Webb, Hattie E and Afolayan, Ayorinde Oluwatobiloba and Alexander, Anna P and Anandan, Shalini and Andrews, Jason R and Ashton, Philip M and Basnyat, Buddha and Bavdekar, Ashish and Bogoch, Isaac I and Clemens, John D and Da Silva, Kesia Esther and De, Anuradha and De Ligt, Joep and Diaz Guevara, Paula Lucia and Dolecek, Christiane and Dutta, Shanta and Ehlers, Marthie M and Francois Watkins, Louise and Garrett, Denise O and Godbole, Gauri and Gordon, Melita A and Greenhill, Andrew R and Griffin, Chelsey and Gupta, Madhu and Hendriksen, Rene S and Heyderman, Robert S and Hooda, Yogesh and Hormazabal, Juan Carlos and Ikhimiukor, Odion O and Iqbal, Junaid and Jacob, Jobin John and Jenkins, Claire and Jinka, Dasaratha Ramaiah and John, Jacob and Kang, Gagandeep and Kanteh, Abdoulie and Kapil, Arti and Karkey, Abhilasha and Kariuki, Samuel and Kingsley, Robert A and Koshy, Roshine Mary and Lauer, Ac and Levine, Myron M and Lingegowda, Ravikumar Kadahalli and Luby, Stephen P and Mackenzie, Grant Austin and Mashe, Tapfumanei and Msefula, Chisomo and Mutreja, Ankur and Nagaraj, Geetha and Nagaraj, Savitha and Nair, Satheesh and Naseri, Take K and {Nimarota-Brown}, Susana and Njamkepo, Elisabeth and Okeke, Iruka N and Perumal, Sulochana Putli Bai and Pollard, Andrew J and Pragasam, Agila Kumari and Qadri, Firdausi and Qamar, Farah N and Rahman, Sadia Isfat Ara and Rambocus, Savitra Devi and Rasko, David A and Ray, Pallab and {Robins-Browne}, Roy and {Rongsen-Chandola}, Temsunaro and Rutanga, Jean Pierre and Saha, Samir K and Saha, Senjuti and Saigal, Karnika and Sajib, Mohammad Saiful Islam and Seidman, Jessica C and Shakya, Jivan and Shamanna, Varun and Shastri, Jayanthi and Shrestha, Rajeev and Sia, Sonia and Sikorski, Michael J and Singh, Ashita and Smith, Anthony M and Tagg, Kaitlin A and Tamrakar, Dipesh and Tanmoy, Arif Mohammed and Thomas, Maria and Thomas, Mathew S and Thomsen, Robert and Thomson, Nicholas R and Tupua, Siaosi and Vaidya, Krista and Valcanis, Mary and Veeraraghavan, Balaji and Weill, Fran{\c c}ois-Xavier and Wright, Jackie and Dougan, Gordon and Argim{\'o}n, Silvia and Keane, Jacqueline A and Aanensen, David M and Baker, Stephen and Holt, Kathryn E and {Global Typhoid Genomics Consortium Group Authorship}},
  year = {2023},
  month = sep,
  journal = {eLife},
  volume = {12},
  pages = {e85867},
  issn = {2050-084X},
  doi = {10.7554/eLife.85867},
  urldate = {2023-09-19},
  abstract = {Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods: This is a meta-\-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch.},
  langid = {english},
  keywords = {antimicrobial resistance,genomics,typhoid conjugate vaccine,typhoid fever},
  file = {/home/user1/Dropbox/Papers/Carey et al_2023_Global diversity and antimicrobial resistance of typhoid fever pathogens.pdf;/home/user1/Zotero/storage/T5IUTZXW/Carey et al. - 2023 - Global diversity and antimicrobial resistance of t.pdf}
}

@article{chen2022,
  title = {The {{E3}} Ubiquitin Ligase {{WWP2}} Regulates Pro-Fibrogenic Monocyte Infiltration and Activity in Heart Fibrosis},
  author = {Chen, Huimei and Chew, Gabriel and Devapragash, Nithya and Loh, Jui Zhi and Huang, Kevin Y. and Guo, Jing and Liu, Shiyang and Tan, Elisabeth Li Sa and Chen, Shuang and Tee, Nicole Gui Zhen and Mia, Masum M. and Singh, Manvendra K. and Zhang, Aihua and Behmoaras, Jacques and Petretto, Enrico},
  year = {2022},
  month = nov,
  journal = {Nat Commun},
  volume = {13},
  number = {1},
  pages = {7375},
  publisher = {Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/s41467-022-34971-6},
  urldate = {2022-12-03},
  abstract = {Non-ischemic cardiomyopathy (NICM) can cause left ventricular dysfunction through interstitial fibrosis, which corresponds to the failure of cardiac tissue remodeling. Recent evidence implicates monocytes/macrophages in the etiopathology of cardiac fibrosis, but giving their heterogeneity and the antagonizing roles of macrophage subtypes in fibrosis, targeting these cells has been challenging. Here we focus on WWP2, an E3 ubiquitin ligase that acts as a positive genetic regulator of human and murine cardiac fibrosis, and show that myeloid specific deletion of WWP2 reduces cardiac fibrosis in hypertension-induced NICM. By using single cell RNA sequencing analysis of immune cells in the same model, we establish the functional heterogeneity of macrophages and define an early pro-fibrogenic phase of NICM that is driven by Ccl5-expressing Ly6chigh monocytes. Among cardiac macrophage subtypes, WWP2 dysfunction primarily affects Ly6chigh monocytes via modulating Ccl5, and consequentially macrophage infiltration and activation, which contributes to reduced myofibroblast trans-differentiation. WWP2 interacts with transcription factor IRF7, promoting its non-degradative mono-ubiquitination, nuclear translocation and transcriptional activity, leading to upregulation of Ccl5 at transcriptional level. We identify a pro-fibrogenic macrophage subtype in non-ischemic cardiomyopathy, and demonstrate that WWP2 is a key regulator of IRF7-mediated Ccl5/Ly6chigh monocyte axis in heart fibrosis.},
  copyright = {2022 The Author(s)},
  langid = {english},
  keywords = {Cardiomyopathies,Gene regulation in immune cells,Monocytes and macrophages,Ubiquitylation},
  file = {/home/user1/Dropbox/Papers/Chen et al_2022_The E3 ubiquitin ligase WWP2 regulates pro-fibrogenic monocyte infiltration and.pdf}
}

@article{chen2024,
  title = {Network Pharmacology to Unveil the Mechanism of Suanzaoren Decoction in the Treatment of Alzheimer's with Diabetes},
  author = {Chen, Tao and Lei, Yining and Li, Manqin and Liu, Xinran and Zhang, Lu and Cai, Fei and Gong, Xiaoming and Zhang, Ruyi},
  year = {2024},
  month = jan,
  journal = {Hereditas},
  volume = {161},
  number = {1},
  pages = {2},
  issn = {1601-5223},
  doi = {10.1186/s41065-023-00301-z},
  abstract = {BACKGROUND: Suanzaoren Decoction (SZRD), a well-known formula from traditional Chinese medicine, has been shown to have reasonable cognitive effects while relaxing and alleviating insomnia. Several studies have demonstrated significant therapeutic effects of SZRD on diabetes and Alzheimer's disease (AD). However, the active ingredients and probable processes of SZRD in treating Alzheimer's with diabetes are unknown. This study aims to preliminarily elucidate the potential mechanisms and potential active ingredients of SZRD in the treatment of Alzheimer's with diabetes. METHODS: The main components and corresponding protein targets of SZRD were searched on the TCMSP database. Differential gene expression analysis for diabetes and Alzheimer's disease was conducted using the Gene Expression Omnibus database, with supplementation from OMIM and genecards databases for differentially expressed genes. The drug-compound-target-disease network was constructed using Cytoscape 3.8.0. Disease and SZRD targets were imported into the STRING database to construct a protein-protein interaction network. Further, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed on the intersection of genes. Molecular docking and molecular dynamics simulations were conducted on the Hub gene and active compounds. Gene Set Enrichment Analysis was performed to further analyze key genes. RESULTS: Through the Gene Expression Omnibus database, we obtained 1977 diabetes related genes and 622 AD related genes. Among drugs, diabetes and AD, 97 genes were identified. The drug-compound-target-disease network revealed that quercetin, kaempferol, licochalcone a, isorhamnetin, formononetin, and naringenin may be the core components exerting effects. PPI network analysis identified hub genes such as IL6, TNF, IL1B, CXCL8, IL10, CCL2, ICAM1, STAT3, and IL4. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that SZRD in the treatment of Alzheimer's with diabetes is mainly involved in biological processes such as response to drug, aging, response to xenobiotic, and enzyme binding; as well as signaling pathways such as Pathways in cancer, Chemical carcinogenesis - receptor activation, and Fluid shear stress and atherosclerosis. Molecular docking results showed that licochalcone a, isorhamnetin, kaempferol, quercetin, and formononetin have high affinity with CXCL8, IL1B, and CCL2. Molecular dynamics simulations also confirmed a strong interaction between CXCL8 and licochalcone a, isorhamnetin, and kaempferol. Gene Set Enrichment Analysis revealed that CXCL8, IL1B, and CCL2 have significant potential in diabetes. CONCLUSION: This study provides, for the first time, insights into the active ingredients and potential molecular mechanisms of SZRD in the treatment of Alzheimer's with diabetes, laying a theoretical foundation for future basic research.},
  langid = {english},
  pmcid = {PMC10762922},
  pmid = {38167125},
  keywords = {Alzheimer Disease,Alzheimer's with diabetes,Diabetes Mellitus,Humans,Isorhamnetin,Kaempferol,Kaempferols,Licochalcone A,Molecular Docking Simulation,Molecular dynamics simulation,Network pharmacology,Network Pharmacology,Quercetin},
  file = {/home/user1/Dropbox/Papers/Chen et al_2024_Network pharmacology to unveil the mechanism of suanzaoren decoction in the.pdf}
}

@article{cowan,
  title = {Soil Seedbank Development of Smoke-Responsive Plant Species in a 23-Year Restoration Chronosequence and Implications for Resilience to Fire},
  author = {Cowan, Ebony L. and Miller, Ben P. and Fontaine, Joseph B. and Enright, Neal J. and Standish, Rachel J.},
  journal = {Applied Vegetation Science},
  volume = {n/a},
  number = {n/a},
  pages = {e12713},
  issn = {1654-109X},
  doi = {10.1111/avsc.12713},
  urldate = {2023-02-07},
  abstract = {Questions Responses of ecological restoration projects to disturbances are rarely explored, yet their capacity to withstand and recover from disturbance (resilience) is a critical measure of restoration success. In many plant communities, the soil seedbank (SSB) provides an important source of propagules for species persistence and community resilience to disturbance. Understanding how SSBs develop with time can inform restoration of resilient ecosystems. Here, in fire-prone Banksia woodland restoration following sand mining, we ask: i. How does the smoke-responsive (dormancy broken by smoke) SSB develop through time, ii. What plant-trait and climate factors influence its development? and, iii. What do the data suggest for the resilience of these restored woodlands to fire? Location Ellenbrook, Swan Coastal Plain, Western Australia (lat. -31.76, lon. 115.95) Methods We used smoke, a key germination cue associated with fire disturbance, to trigger germination of the SSB in Banksia woodland restoration. Using a chronosequence of nine ages between three and 26 years since initiation of restoration, we tested how the SSB develops using counts and richness of germinating native and invasive annuals, and native perennial obligate seeding and resprouting species. To understand the contribution of aboveground restored vegetation to SSB development, we compared S{\o}rensen's similarity of the smoke germinable SSB (`smoked SSB') and untreated germinable SSB (`control SSB') to aboveground vegetation. Results Smoked SSB germinant density decreased with restoration age for both native and invasive annuals but was stable for native perennials. Similarity between smoked SSB and aboveground vegetation was higher for perennial obligate seeders than for resprouters and peaked for perennials at 23 years. Conclusions Post-fire regeneration potential of the SSB was evident across the chronosequence, with restoration age influencing the density of native annuals and overall composition of the SSB. The findings for perennial species suggest an increase in resilience to fire with restoration age.},
  langid = {english},
  keywords = {ecological resilience,fire-prone ecosystems,plant communities,restoration,similarity,smoke,soil seedbank}
}

@article{danlin2024,
  title = {Potential Synergistic Regulation of Hsp70 and Antioxidant Enzyme Genes in {{Pyropia}} Yezoensis under High Temperature Stress},
  author = {Danlin, Huang and Chao, Tian and Zhenjie, Sun and Jianfeng, Niu and Guangce, Wang},
  year = {2024},
  month = jan,
  journal = {Algal Research},
  pages = {103375},
  issn = {2211-9264},
  doi = {10.1016/j.algal.2023.103375},
  urldate = {2024-01-16},
  abstract = {High temperatures have been regarded as one of the main factors limiting Pyropia yezoensis cultivation in recent years. Both the heat shock proteins and antioxidant enzymes genes were activated timely before heat damage to the cell. Here, the activities of different antioxidant enzymes under different conditions, including HSF inhibitor, CaM inhibitor, and HSP70 protein inhibitor were determined. Then, RNA-seq was performed using samples that had been pretreated with corresponding chemicals under high temperature conditions. The principal component analysis inferred that the shift of gene transcription patterns under high temperature conditions was closely related to HSF since the addition of QR suppressed the changes in gene transcription pattern. The hsp70 genes and antioxidant enzyme genes were categorized into three groups by the method of WGCNA. And the HSE sites were identified using plantPAN and FIMO in most genes of the categories showed relationship to HSF. Quantitative RT-PCR analysis of designated genes (FMPK {$>$}10) indicated that the expression of hsp70 and antioxidant enzyme genes in Py. yezoensis showed various transcriptional patterns, including upregulation, downregulation, and no significant changes in response to high temperature stress. The classification between qRT-PCR and WGCNA results showed a certain consistency. Considered the results above together, it was speculated that there were different HSFs regulated the expression of different genes of hsp70 and antioxidant enzymes, and HSP70 might also regulate the expression of anti-oxidase genes under the conditions of long-term stress. Additionally, transcription factors other than HSF might be involved in the high temperature stress response. The results indicated the complexity of heat stress response mechanisms in Py. yezoensis.},
  keywords = {Antioxidant enzymes,Heat shock transcription factor,High temperatures}
}

@article{deng,
  title = {Investigating Potential Ferroptosis-Related Differentially Expressed Genes of {{UVB-induced}} Skin Photodamage},
  author = {Deng, Li and Li, Yi and Wu, Qian and Zeng, QianWen and He, Yuanmin and Chen, AiJun},
  journal = {International Journal of Dermatology},
  volume = {n/a},
  number = {n/a},
  issn = {1365-4632},
  doi = {10.1111/ijd.16472},
  urldate = {2022-12-01},
  abstract = {Objectives Ultraviolet B (UVB) is one of the most dangerous insults for skin, which can cause skin sunburn, pigment disease, photoaging, and photocarcinogenesis. This study aimed to identify pathogenic genes related to ferroptosis in the skin of humans after UVB radiation. Methods The gene expression profiles (GSE41078, GSE54413) were downloaded from the Gene Expression Omnibus (GEO) database, and the ferroptosis-related genes (FRGs) were downloaded from the Genecards database. To identify the differentially expressed genes (DEGs) and obtain differentially expressed FRGs by intersecting DEGs with FRGs. To identify the functional annotation and potential pathways by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Differentially expressed FRGs-associated protein--protein interaction network (PPI) was performed by STRING database and Cytoscape software. Results A total of 628 co-expressed DEGs of the two profiles (GSE41078 and GSE54413) were identified, including 371 upregulated and 257 downregulated DEGs. A total of 32 differentially expressed FRGs were identified. The results of GO analyses showed that, in the biological processes, UVB had a great influence on the response to oxidative stress; in the molecular functions, UVB had a great influence on antioxidant activity; in the cellular components, UVB had a great influence on endocytic vesicle lumen. The key pathways of differentially expressed FRGs were identified by KEGG analyses. The most significant 12 central node genes were identified by PPI network. Conclusion We identified differentially expressed FRGs candidate genes and pathways in UVB-induced skin photodamage, which could contribute to the development of new therapeutic targets for skin photodamage.},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Deng et al_Investigating potential ferroptosis-related differentially expressed genes of.pdf}
}

@article{ding2021,
  title = {Sugar and Organic Acid Availability Modulate Soil Diazotroph Community Assembly and Species Co-Occurrence Patterns on the {{Tibetan Plateau}}},
  author = {Ding, Xiaowei and Liu, Kaihui and Yan, Qingyun and Liu, Xingyu and Chen, Ni and Wang, Guoliang and He, Shuai},
  year = {2021},
  month = oct,
  journal = {Appl Microbiol Biotechnol},
  issn = {1432-0614},
  doi = {10.1007/s00253-021-11629-9},
  urldate = {2021-10-21},
  abstract = {Metabolites can mediate species interactions and the assembly of microbial communities. However, how these chemicals relate to the assembly processes and co-occurrence patterns of diazotrophic assemblages in root-associated soils remains largely unknown. Here, we examined the diversity and assembly of diazotrophic communities and further deciphered their links with metabolites on Tibetan Plateau. We found that the distribution of sugars and organic acids in the root-associated soils was significantly correlated with the richness of diazotrophs. The presence of these two soil metabolites explains the variability in diazotrophic community compositions. The differential concentrations of these metabolites were significantly linked with the distinctive abundances of diazotrophic taxa in same land types dominated by different plants or dissimilar soils by same plants. The assembly of diazotrophic communities is subject to deterministic ecological processes, which are widely modulated by the variety and amount of sugars and organic acids. Organic acids, for instance, 3-(4-hydroxyphenyl)propionic acid and citric acid, were effective predictors of the characteristics of diazotrophic assemblages across desert habitats. Diazotrophic co-occurrence networks tended to be more complex and connected within different land types covered by the same plant species. The concentrations of multiple sugars and organic acids were coupled significantly with the distribution of keystone species, such as Azotobacter, Azospirillum, Bradyrhizobium, and Mesorhizobium, in the co-occurrence network. These findings provide new insights into the assembly mechanisms of root-associated diazotrophic communities across the desert ecosystems of the Tibetan Plateau.},
  langid = {english},
  file = {/home/user1/Zotero/storage/E42BGEJP/Ding et al. - 2021 - Sugar and organic acid availability modulate soil .pdf}
}

@article{drivas2021,
  title = {{{eQTpLot}}: A User-Friendly {{R}} Package for the Visualization of Colocalization between {{eQTL}} and {{GWAS}} Signals},
  shorttitle = {{{eQTpLot}}},
  author = {Drivas, Theodore G. and Lucas, Anastasia and Ritchie, Marylyn D.},
  year = {2021},
  month = jul,
  journal = {BioData Mining},
  volume = {14},
  number = {1},
  pages = {32},
  issn = {1756-0381},
  doi = {10.1186/s13040-021-00267-6},
  urldate = {2021-07-21},
  abstract = {Genomic studies increasingly integrate expression quantitative trait loci (eQTL) information into their analysis pipelines, but few tools exist for the visualization of colocalization between eQTL and GWAS results. Those tools that do exist are limited in their analysis options, and do not integrate eQTL and GWAS information into a single figure panel, making the visualization of colocalization difficult.},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Drivas et al_2021_eQTpLot_.pdf}
}

@article{giannakis2022,
  title = {Evolutionary Inference across Eukaryotes Identifies Universal Features Shaping Organelle Gene Retention},
  author = {Giannakis, Konstantinos and Arrowsmith, Samuel J. and Richards, Luke and Gasparini, Sara and Chustecki, Joanna M. and R{\o}yrvik, Ellen C. and Johnston, Iain G.},
  year = {2022},
  month = sep,
  journal = {Cell Systems},
  issn = {2405-4712},
  doi = {10.1016/j.cels.2022.08.007},
  urldate = {2022-09-19},
  abstract = {Mitochondria and plastids power complex life. Why some genes and not others are retained in their organelle DNA (oDNA) genomes remains a debated question. Here, we attempt to identify the properties of genes and associated underlying mechanisms that determine oDNA retention. We harness over 15k oDNA sequences and over 300 whole genome sequences across eukaryotes with tools from structural biology, bioinformatics, machine learning, and Bayesian model selection. Previously hypothesized features, including the hydrophobicity of a protein product, and less well-known features, including binding energy centrality within a protein complex, predict oDNA retention across eukaryotes, with additional influences of nucleic acid and amino acid biochemistry. Notably, the same features predict retention in both organelles, and retention models learned from one organelle type quantitatively predict retention in the other, supporting the universality of these features---which also distinguish gene profiles in more recent, independent endosymbiotic relationships. A record of this paper's transparent peer review process is included in the supplemental information.},
  langid = {english},
  keywords = {endosymbiosis,genome evolution,mitochondria,mtDNA,plastids,ptDNA},
  file = {/home/user1/Dropbox/Papers/Giannakis et al_2022_Evolutionary inference across eukaryotes identifies universal features shaping.pdf}
}

@article{gorodnichev2023,
  title = {Isolation and {{Characterization}} of the {{First Zobellviridae Family Bacteriophage Infecting Klebsiella}} Pneumoniae},
  author = {Gorodnichev, Roman B. and Kornienko, Maria A. and Malakhova, Maja V. and Bespiatykh, Dmitry A. and Manuvera, Valentin A. and Selezneva, Oksana V. and Veselovsky, Vladimir A. and Bagrov, Dmitry V. and Zaychikova, Marina V. and Osnach, Veronika A. and Shabalina, Anna V. and Goloshchapov, Oleg V. and Bespyatykh, Julia A. and Dolgova, Anna S. and Shitikov, Egor A.},
  year = {2023},
  month = jan,
  journal = {International Journal of Molecular Sciences},
  volume = {24},
  number = {4},
  pages = {4038},
  publisher = {Multidisciplinary Digital Publishing Institute},
  issn = {1422-0067},
  doi = {10.3390/ijms24044038},
  urldate = {2023-02-20},
  abstract = {In order to address the upcoming crisis in the treatment of Klebsiella pneumoniae infections, caused by an increasing proportion of resistant isolates, new approaches to antimicrobial therapy must be developed. One approach would be to use (bacterio)phages and/or phage derivatives for therapy. In this study, we present a description of the first K. pneumoniae phage from the Zobellviridae family. The vB\_KpnP\_Klyazma podovirus, which forms translucent halos around the plaques, was isolated from river water. The phage genome is composed of 82 open reading frames, which are divided into two clusters located on opposite strands. Phylogenetic analysis revealed that the phage belongs to the Zobellviridae family, although its identity with the closest member of this family was not higher than 5\%. The bacteriophage demonstrated lytic activity against all (n = 11) K. pneumoniae strains with the KL20 capsule type, but only the host strain was lysed effectively. The receptor-binding protein of the phage was identified as a polysaccharide depolymerase with a pectate lyase domain. The recombinant depolymerase protein showed concentration-dependent activity against all strains with the KL20 capsule type. The ability of a recombinant depolymerase to cleave bacterial capsular polysaccharides regardless of a phage's ability to successfully infect a particular strain holds promise for the possibility of using depolymerases in antimicrobial therapy, even though they only make bacteria sensitive to environmental factors, rather than killing them directly.},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  langid = {english},
  keywords = {<i>Klebsiella pneumoniae</i>,<i>Zobellviridae</i>,bacteriophage,capsular type,capsule depolymerase,multidrug resistance},
  file = {/home/user1/Dropbox/Papers/Gorodnichev et al_2023_Isolation and Characterization of the First Zobellviridae Family Bacteriophage.pdf}
}

@article{granovetter2020,
  title = {With {{Childhood Hemispherectomy}}, {{One Hemisphere Can Support}}---{{But}} Is {{Suboptimal}} for---{{Word}} and {{Face Recognition}}},
  author = {Granovetter, Michael C. and Ettensohn, Leah and Behrmann, Marlene},
  year = {2020},
  month = nov,
  journal = {bioRxiv},
  pages = {2020.11.06.371823},
  publisher = {Cold Spring Harbor Laboratory},
  doi = {10.1101/2020.11.06.371823},
  urldate = {2021-03-03},
  abstract = {{$<$}h3{$>$}Abstract{$<$}/h3{$>$} {$<$}p{$>$}The left and right cerebral hemispheres are important for word and face recognition, respectively---a specialization that emerges over human development. But children who have undergone a hemispherectomy develop with only one hemisphere. The question is whether this preserved hemisphere, be it left or right, can support both word and face recognition. Here, a large sample of patients with childhood hemispherectomy and age-matched controls performed word- and face-matching tasks. Controls viewed stimuli either in one visual field (restricting initial processing to one hemisphere) or, like the patients, in central vision. Across word and face tasks, patients performed comparably to controls using primarily one hemisphere, but more poorly than controls viewing stimuli centrally with both hemispheres engaged. Additionally, patients showed deficits in low-level visual processing that may explain their word/face recognition deficits relative to controls. Altogether, the findings suggest that either hemisphere alone can support word and face recognition, albeit sub-optimally.{$<$}/p{$>$}},
  chapter = {New Results},
  copyright = {{\copyright} 2020, Posted by Cold Spring Harbor Laboratory. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Granovetter et al_2020_With Childhood Hemispherectomy, One Hemisphere Can Support—But is Suboptimal_.pdf}
}

@article{higgs2023,
  title = {Comparison of Contemporary Invasive and Non-Invasive {{Streptococcus}} Pneumoniae Isolates Reveals New Insights into Circulating Anti-Microbial Resistance Determinants},
  author = {Higgs, Charlie and Kumar, Lamali Sadeesh and Stevens, Kerrie and Strachan, Janet and Korman, Tony and Horan, Kristy and Daniel, Diane and Russell, Madeline and McDevitt, Christopher A. and Sherry, Norelle L. and Stinear, Timothy P. and Howden, Benjamin P. and Gorrie, Claire L.},
  year = {2023},
  month = oct,
  journal = {Antimicrobial Agents and Chemotherapy},
  volume = {0},
  number = {0},
  pages = {e00785-23},
  publisher = {American Society for Microbiology},
  doi = {10.1128/aac.00785-23},
  urldate = {2023-10-23},
  file = {/home/user1/Dropbox/Papers/Higgs et al_2023_Comparison of contemporary invasive and non-invasive Streptococcus pneumoniae.pdf}
}

@article{higgs2023a,
  title = {Population Structure, Serotype Distribution and Antibiotic Resistance of {{Streptococcus}} Pneumoniae Causing Invasive Disease in {{Victoria}}, {{Australia}}},
  author = {Higgs, Charlie and Kumar, Lamali Sadeesh and Stevens, Kerrie and Strachan, Janet and Sherry, Norelle L. and Horan, Kristy and Zhang, Josh and Stinear, Timothy P. and Howden, Benjamin P. and Gorrie, Claire L.},
  year = {2023},
  journal = {Microbial Genomics},
  volume = {9},
  number = {7},
  pages = {001070},
  publisher = {Microbiology Society,},
  issn = {2057-5858},
  doi = {10.1099/mgen.0.001070},
  urldate = {2023-07-25},
  abstract = {Streptococcus pneumoniae is a major human pathogen and can cause a range of conditions from asymptomatic colonization to invasive pneumococcal disease (IPD). The epidemiology and distribution of IPD-causing serotypes in Australia has undergone large changes following the introduction of the 7-valent pneumococcal conjugate vaccine (PCV) in 2005 and the 13-valent PCV in 2011. In this study, to provide a contemporary understanding of the IPD causing population in Victoria, Australia, we aimed to examine the population structure and prevalence of antimicrobial resistance using whole-genome sequencing and comprehensive antimicrobial susceptibility data of 1288 isolates collected between 2018 and 2022. We observed high diversity among the isolates with 52 serotypes, 203 sequence types (STs) and 70 Global Pneumococcal Sequencing Project Clusters (GPSCs) identified. Serotypes contained in the 13v-PCV represented 35.3{$\mkern1mu\%$} (n=405) of isolates. Antimicrobial resistance (AMR) to at least one antibiotic was identified in 23.8{$\mkern1mu\%$} (n=358) of isolates with penicillin resistance the most prevalent (20.3{$\mkern1mu\%$}, n=261 using meningitis breakpoints and 5.1{$\mkern1mu\%$} n=65 using oral breakpoints). Of the AMR isolates, 28{$\mkern1mu\%$} (n=101) were multidrug resistant (MDR) (resistant to three or more drug classes). Vaccination status of cases was determined for a subset of isolates with 34 cases classified as vaccine failure events (fully vaccinated IPD cases of vaccine serotype). However, no phylogenetic association with failure events was observed. Within the highly diverse IPD population, we identified six high-risk sub-populations of public health concern characterized by high prevalence, high rates of AMR and MDR, or serotype inclusion in vaccines. High-risk serotypes included serotypes 3, 19F, 19A, 14, 11A, 15A and serofamily 23. In addition, we present our data validating seroBA for in silico serotyping to facilitate ISO-accreditation of this test in routine use in a public health reference laboratory and have made this data set available. This study provides insights into the population dynamics, highlights non-vaccine serotypes of concern that are highly resistant, and provides a genomic framework for the ongoing surveillance of IPD in Australia which can inform next-generation IPD prevention strategies.},
  file = {/home/user1/Dropbox/Papers/Higgs et al_2023_Population structure, serotype distribution and antibiotic resistance of.pdf}
}

@misc{hill2024,
  title = {Evolutionary Genomics Reveals Variation in Structure and Genetic Content Implicated in Virulence and Lifestyle in the Genus {{Gaeumannomyces}}},
  author = {Hill, Rowena and Grey, Michelle and Fedi, Mariano Olivera and Smith, Daniel and Ward, Sabrina J. and Canning, Gail and Irish, Naomi and Smith, Jade and McMillan, Vanessa E. and Hammond, Jess and Osborne, Sarah-Jane and Chancellor, Tania and Swarbreck, David and Hall, Neil and {Palma-Guerrero}, Javier and {Hammond-Kosack}, Kim E. and McMullan, Mark},
  year = {2024},
  month = feb,
  primaryclass = {New Results},
  pages = {2024.02.15.580261},
  publisher = {bioRxiv},
  doi = {10.1101/2024.02.15.580261},
  urldate = {2024-02-20},
  abstract = {Gaeumannomyces tritici is responsible for take-all disease, one of the most important wheat root threats worldwide. High-quality annotated genome resources are sorely lacking for this pathogen, as well as for the closely related antagonist and potential wheat take-all biocontrol agent, G. hyphopodioides. As such, we know very little about the genetic basis of the interactions in this host-pathogen-antagonist system. Using PacBio HiFi sequencing technology we have generated nine near-complete assemblies, including two different virulence lineages for G. tritici and the first assemblies for G. hyphopodioides and G. avenae (oat take-all). Genomic signatures support the presence of two distinct virulence lineages in G. tritici (types A and B), with A strains potentially employing a mechanism to prevent gene copy-number expansions. The CAZyme repertoire was highly conserved across Gaeumannomyces, while candidate secreted effector proteins and biosynthetic gene clusters showed more variability and may distinguish pathogenic and non-pathogenic lineages. A transition from self-sterility (heterothallism) to self-fertility (homothallism) may also be a key innovation implicated in lifestyle. We did not find evidence for transposable element and effector gene compartmentalisation in the genus, however the presence of Starship giant transposable elements likely contributes to genomic plasticity in the genus. Our results depict Gaeumannomyces as an ideal system to explore interactions within the rhizosphere, the nuances of intraspecific virulence, interspecific antagonism, and fungal lifestyle evolution. The foundational genomic resources provided here will enable the development of diagnostics and surveillance of understudied but agriculturally important fungal pathogens.},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {{\copyright} 2024, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Hill et al_2024_Evolutionary genomics reveals variation in structure and genetic content.pdf}
}

@article{hinsu2021,
  title = {Characterizing Rhizosphere Microbiota of Peanut ({{Arachis}} Hypogaea {{L}}.) from Pre-Sowing to Post-Harvest of Crop under Field Conditions},
  author = {Hinsu, Ankit T. and Panchal, Ketankumar J. and Pandit, Ramesh J. and Koringa, Prakash G. and Kothari, Ramesh K.},
  year = {2021},
  month = aug,
  journal = {Sci Rep},
  volume = {11},
  number = {1},
  pages = {17457},
  publisher = {Nature Publishing Group},
  issn = {2045-2322},
  doi = {10.1038/s41598-021-97071-3},
  urldate = {2021-09-06},
  abstract = {The rhizosphere, a narrow zone of soil near plant roots, is a hot spot for microbial activity. Rhizosphere microbiota directly or indirectly benefit plants by supplementing nutrients, producing beneficial chemicals, or suppressing pathogens. Plants attract and modulate bacteria within the rhizosphere by releasing exudates. Plants also tend to select the rhizosphere microbiota based on their needs; a phenomenon termed as ``rhizosphere effect''. In this study, we characterized the rhizosphere microbiota of peanut plants across the crop development cycle from pre-sowing of seeds to post-harvest of crop under field conditions. The rhizosphere and bulk soil samples from different crop developmental stages were also compared. The composition of bulk soil microbiota resembled microbiota of pre-sowing and post-harvest soil and was markedly different from rhizosphere soil samples. Rhizosphere samples were enriched with multiple organisms mostly from the Proteobacteria, Firmicutes and Bacteroidota phyla. Differences in diversity were observed among the rhizosphere samples but not in bulk soil across different crop development stages. Pseudomonas\_M indica was highly enriched during the germination of seeds. Furthermore, Plant Growth Promoting (PGP) bacteria like Bacillus were enriched during the middle stages of crop development but there was a decline in PGP organisms in the matured crop stage. We also observed a significant association of pH and Electrical Conductivity (EC) with the profiles of microbial community. Overall, this study portrayed the changes in rhizosphere microbiota of peanut during different developmental stages of crop and may help to design stage specific bio-strategies such as bio-fertilizer to improve crop yield.},
  copyright = {2021 The Author(s)},
  langid = {english},
  annotation = {Bandiera\_abtest: a\\
Cc\_license\_type: cc\_by\\
Cg\_type: Nature Research Journals\\
Primary\_atype: Research\\
Subject\_term: Metagenomics;Microbial ecology;Microbiome;Soil microbiology\\
Subject\_term\_id: metagenomics;microbial-ecology;microbiome;soil-microbiology},
  file = {/home/user1/Dropbox/Papers/Hinsu et al_2021_Characterizing rhizosphere microbiota of peanut (Arachis hypogaea L_.pdf}
}

@article{hinzke2022,
  title = {Response {{Patterns}} of {{Fen Sedges}} to a {{Nutrient Gradient Indicate}} Both {{Geographic Origin-Specific Genotypic Differences}} and {{Phenotypic Plasticity}}},
  author = {Hinzke, Tjorven and Tanneberger, Franziska and Aggenbach, Camiel and Bog, Manuela and Dahlke, Sven and Knorr, Klaus-Holger and Kotowski, Wiktor and Kozub, {\L}ukasz and Lange, Jelena and Li, Guixiang and Michaelis, Dierk and Pronin, Eugeniusz and Schnittler, Martin and Seeber, Elke and Kreyling, Juergen},
  year = {2022},
  month = nov,
  journal = {Wetlands},
  volume = {42},
  number = {8},
  pages = {113},
  issn = {1943-6246},
  doi = {10.1007/s13157-022-01629-4},
  urldate = {2022-11-24},
  abstract = {In wet peatlands, plant growth conditions are largely determined by local soil conditions, leading to locally adapted vegetation. Despite that Carex species are often the prevailing vascular plant species in fen peatlands of the temperate zone, information about how these species adapt to local environmental conditions is scarce. This holds true especially for below-ground plant traits and for adaptations to fen-typical nutrient level variations. To address this research gap, we investigated how different geographic origins (Germany, Poland, The Netherlands) of C. acutiformis and C. rostrata relate to their response to varying nutrient availability. We performed a common garden experiment with a controlled gradient of nutrient levels, and analyzed above- and below-ground biomass production of both Carex species from the different geographic origins. We related these traits to environmental conditions of the origins as characterized by vegetation composition-derived indicator values for ecological habitat conditions. While we detected high above-ground phenotypic plasticity of Carex from different origins, our data point to below-ground genotypic differences, potentially indicating local adaptation: Rhizome traits of C. rostrata differed significantly between origins with different nutrient indicator values. These results point towards differences in C. rostrata clonal spread behavior depending on local peatland conditions. Therefore, local adaptations of plant species and below-ground biomass traits should be taken into account when studying peatland vegetation ecology, as key functional traits can differ between genotypes within a single species depending on local conditions.},
  langid = {english},
  keywords = {Azonal vegetation,Carex acutiformis,Carex rostrata,Ecotype,Ellenberg indicator values,Genetic differentiation,Mire,Rhizome growth},
  file = {/home/user1/Dropbox/Papers/Hinzke et al_2022_Response Patterns of Fen Sedges to a Nutrient Gradient Indicate both Geographic.pdf}
}

@article{jenckel2021,
  title = {Distribution and {{Genetic Diversity}} of {{Hepatitis E Virus}} in {{Wild}} and {{Domestic Rabbits}} in {{Australia}}},
  author = {Jenckel, Maria and Smith, Ina and King, Tegan and West, Peter and Taggart, Patrick L. and Strive, Tanja and Hall, Robyn N.},
  year = {2021},
  month = dec,
  journal = {Pathogens},
  volume = {10},
  number = {12},
  pages = {1637},
  publisher = {Multidisciplinary Digital Publishing Institute},
  doi = {10.3390/pathogens10121637},
  urldate = {2021-12-21},
  abstract = {In 2020, Hepatitis E virus (HEV) was detected for the first time in Australian rabbits. To improve our understanding of the genetic diversity and distribution of the virus, 1635 rabbit liver samples from locations across Australia were screened via RT-qPCR for HEV. HEV genomes were amplified and sequenced from 48 positive samples. Furthermore, we tested 380 serum samples from 11 locations across Australia for antibodies against HEV. HEV was detected in rabbits from all states and territories, except the Northern Territory. Seroprevalence varied between locations (from 0\% to 22\%), demonstrating that HEV is widely distributed in rabbit populations across Australia. Phylogenetic analyses showed that Australian HEV sequences are genetically diverse and that HEV was likely introduced into Australia independently on several occasions. In summary, this study broadens our understanding of the genetic diversity of rabbit HEV globally and shows that the virus is endemic in both domestic and wild rabbit populations in Australia.},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  langid = {english},
  keywords = {genomic epidemiology,hepeviridae,Luminex,rabbits,seroepidemiology,serology,whole-genome sequencing},
  file = {/home/user1/Dropbox/Papers/Jenckel et al_2021_Distribution and Genetic Diversity of Hepatitis E Virus in Wild and Domestic_.pdf}
}

@article{jentsch2022,
  title = {Spatio-{{Temporal Analysis}} of {{Valley Wind Systems}} in the {{Complex Mountain Topography}} of the {{Rolwaling Himal}}, {{Nepal}}},
  author = {Jentsch, Helge and Weidinger, Johannes},
  year = {2022},
  month = jul,
  journal = {Atmosphere},
  volume = {13},
  number = {7},
  pages = {1138},
  publisher = {Multidisciplinary Digital Publishing Institute},
  issn = {2073-4433},
  doi = {10.3390/atmos13071138},
  urldate = {2022-08-01},
  abstract = {The diurnal, seasonal, and spatio-temporal characteristics of local wind systems in a steep mountain valley in Nepal are analyzed with the identification of valley wind days (VWDs). Distributed across the Rolwaling Himal valley in Nepal between 3700 and 5100 m a.s.l. at eight automated weather stations (AWSs), meteorological data between October 2017 and September 2018 were examined. VWDs were classified by means of ERA5 reanalysis data and in situ observations, employing established thresholds using precipitation, solar radiation, air pressure, and wind speed data at different pressure levels. Thus, overlying synoptic influences are highly reduced and distinctive diurnal patterns emerge. A strong seasonal component in near-surface wind speed and wind direction patterns was detected. Further analyses showed the diurnal characteristics of slow (approximately 0.5--0.9 m s-1), but gradually increasing wind speeds over the night, transitional periods in the morning and evening, and the highest averaged wind speeds of approximately 4.3 m s-1 around noon during the VWDs. Wind directions followed a 180{$\circ$} shift with nocturnal katabatic mountain winds and inflowing anabatic valley winds during the daytime. With AWSs at opposing hillsides, slope winds were clearly identifiable and thermally driven spatio-temporal variations throughout the valley were revealed. Consequently, varying temporal shifts in wind speed and direction along the valley bottom can be extracted. In general, the data follow the well-known schematic of diurnal mountain--valley wind systems, but emphasize the influence of monsoonal seasonality and the surrounding complex mountain topography as decisive factors.},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  langid = {english},
  keywords = {automated weather station,Central Himalayas,complex terrain,diurnal wind,local wind,valley wind,valley wind days,valley wind system},
  file = {/home/user1/Dropbox/Papers/Jentsch_Weidinger_2022_Spatio-Temporal Analysis of Valley Wind Systems in the Complex Mountain.pdf}
}

@article{jiang2023a,
  title = {{{ITK}} Degradation to Block {{T}} Cell Receptor Signaling and Overcome Therapeutic Resistance in {{T}} Cell Lymphomas},
  author = {Jiang, Baishan and Weinstock, David M. and Donovan, Katherine A. and Sun, Hong-Wei and Wolfe, Ashley and Amaka, Sam and Donaldson, Nicholas L. and Wu, Gongwei and Jiang, Yuan and Wilcox, Ryan A. and Fischer, Eric S. and Gray, Nathanael S. and Wu, Wenchao},
  year = {2023},
  month = apr,
  journal = {Cell Chemical Biology},
  volume = {0},
  number = {0},
  publisher = {Elsevier},
  issn = {2451-9456, 2451-9448},
  doi = {10.1016/j.chembiol.2023.03.007},
  urldate = {2023-04-07},
  langid = {english},
  pmid = {37015223},
  keywords = {GATA-3,ITK,PROTAC,T cell lymphoma,TCR signaling},
  file = {/home/user1/Dropbox/Papers/Jiang et al_2023_ITK degradation to block T cell receptor signaling and overcome therapeutic.pdf}
}

@article{jin2023,
  title = {Culturing of a Complex Gut Microbial Community in Mucin-Hydrogel Carriers Reveals Strain- and Gene-Associated Spatial Organization},
  author = {Jin, Xiaofan and Yu, Feiqiao B. and Yan, Jia and Weakley, Allison M. and Dubinkina, Veronika and Meng, Xiandong and Pollard, Katherine S.},
  year = {2023},
  month = jun,
  journal = {Nat Commun},
  volume = {14},
  number = {1},
  pages = {3510},
  publisher = {Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/s41467-023-39121-0},
  urldate = {2023-06-17},
  abstract = {Microbial community function depends on both taxonomic composition and spatial organization. While composition of the human gut microbiome has been deeply characterized, less is known about the organization of microbes between regions such as lumen and mucosa and the microbial genes regulating this organization. Using a defined 117 strain community for which we generate high-quality genome assemblies, we model mucosa/lumen organization with in vitro cultures incorporating mucin hydrogel carriers as surfaces for bacterial attachment. Metagenomic tracking of carrier cultures reveals increased diversity and strain-specific spatial organization, with distinct strains enriched on carriers versus liquid supernatant, mirroring mucosa/lumen enrichment in vivo. A comprehensive search for microbial genes associated with this spatial organization identifies candidates with known adhesion-related functions, as well as novel links. These findings demonstrate that carrier cultures of defined communities effectively recapitulate fundamental aspects of gut spatial organization, enabling identification of key microbial strains and genes.},
  copyright = {2023 The Author(s)},
  langid = {english},
  keywords = {Bacterial genetics,Microbiome},
  file = {/home/user1/Dropbox/Papers/Jin et al_2023_Culturing of a complex gut microbial community in mucin-hydrogel carriers.pdf}
}

@phdthesis{joubert2023,
  title = {Catching up to Fungal Plant Pathogens: {{A}} Characterization of Extrachromosomal Circular {{DNAs}} and Gene Presence Absence Variation in {{Magnaporthe}} Oryzae},
  shorttitle = {Catching up to Fungal Plant Pathogens},
  author = {Joubert, Pierre M.},
  year = {2023},
  urldate = {2023-09-28},
  abstract = {Fungal plant pathogens have major impacts on agriculture and global food security and are likely to have an even greater impact in the future. The current tools that we have available to combat them are insufficient, in part because these fungi can quickly adapt to these tools. Understanding fungal plant pathogen evolution is therefore essential to curbing the threat these pathogens pose. In Chapter 1, I describe the motivations for my dissertation work and the state of the field of fungal plant pathogen evolution. I also introduce the model organism I used in my research, Magnaporthe oryzae, which causes the blast disease. Chapter 2 describes my characterization of the extrachromosomal circular DNAs (eccDNAs) of M. oryzae. EccDNAs are a diverse class of molecules that can contribute to phenotypic and genotypic plasticity in eukaryotes, and I hypothesized that these may be involved in fungal plant pathogen evolution. I show that M. oryzae has a more diverse set of eccDNAs than other organisms and that these are enriched in LTR retrotransposons. I also show that many genes are found on eccDNAs in M. oryzae, and that effectors are enriched on eccDNAs. Finally, I show that eccDNAs are associated with gene presence-absence variation (PAV). Next, in Chapter 3, I discuss in greater detail the results presented in Chapter 2, as well as their implications and potential future directions. I also further discuss evidence in Chapter 2 that led me to believe that eccDNAs do not play a major role in fungal plant pathogen evolution and led me to focus directly on gene PAV in M. oryzae in the remainder of my dissertation. Subsequently, in Chapter 4, I describe my characterization of these events in M. oryzae. I find that genes experiencing PAV between lineages of M. oryzae are enriched in disease-causing and non-self-recognition genes. I describe how gene PAV events in the rice and wheat pathotypes show clear differences in their count and genomic location. Through comparing PAV genes to conserved genes, I show that these had distinct distances to TEs, distances to other genes, lengths, GC content, expression, and epigenetic marks. I also describe how a machine learning model can be trained to take advantage of these features to predict genes prone to PAV in the M. oryzae genome. Finally, in Chapter 5, I further discuss the implications of the results I describe in this dissertation, as well as future directions for implementing machine learning models and general knowledge of fungal plant pathogen evolution to help guide rational disease resistance engineering in crops.},
  langid = {english},
  school = {UC Berkeley},
  file = {/home/user1/Dropbox/Papers/Joubert_2023_Catching up to fungal plant pathogens.pdf}
}

@misc{joubert2023a,
  title = {Distinct Genomic Contexts Predict Gene Presence-Absence Variation in Different Pathotypes of a Fungal Plant Pathogen},
  author = {Joubert, Pierre M. and Krasileva, Ksenia V.},
  year = {2023},
  month = feb,
  primaryclass = {New Results},
  pages = {2023.02.17.529015},
  publisher = {bioRxiv},
  doi = {10.1101/2023.02.17.529015},
  urldate = {2023-02-20},
  abstract = {Background Fungi use the accessory segments of their pan-genomes to adapt to their environments. While gene presence-absence variation (PAV) contributes to shaping these accessory gene reservoirs, whether these events happen in specific genomic contexts remains unclear. Additionally, since pan-genome studies often group together all members of the same species, it is uncertain whether genomic or epigenomic features shaping pan-genome evolution are consistent across populations within the same species. Fungal plant pathogens are useful models for answering these questions because members of the same species often infect distinct hosts, and they frequently rely on gene PAV to adapt to these hosts. Results We analyzed gene PAV in the rice and wheat blast fungus, Magnaporthe oryzae, and found that PAV of disease-causing effectors, antibiotic production, and non-self-recognition genes may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features and data from available datasets for patterns that might help explain these PAV events. We observed that proximity to transposable elements (TEs), gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between PAV genes and conserved genes, among other features. We used these features to construct a random forest classifier that was able to predict whether a gene is likely to experience PAV with high precision (86.06\%) and recall (92.88\%) in rice-infecting M. oryzae. Finally, we found that PAV in wheat- and rice-infecting pathotypes of M. oryzae differed in their number and their genomic context. Conclusions Our results suggest that genomic and epigenomic features of gene PAV can be used to better understand and even predict fungal pan-genome evolution. We also show that substantial intra-species variation can exist in these features.},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {{\copyright} 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Joubert_Krasileva_2023_Distinct genomic contexts predict gene presence-absence variation in different.pdf}
}

@article{jung2019,
  title = {Unified Single-Cell Analysis of Testis Gene Regulation and Pathology in Five Mouse Strains},
  author = {Jung, Min and Wells, Daniel and Rusch, Jannette and Ahmad, Suhaira and Marchini, Jonathan and Myers, Simon R and Conrad, Donald F},
  editor = {Bourc'his, Deborah and Wittkopp, Patricia J and Lukassen, Soeren},
  year = {2019},
  month = jun,
  journal = {eLife},
  volume = {8},
  pages = {e43966},
  publisher = {eLife Sciences Publications, Ltd},
  issn = {2050-084X},
  doi = {10.7554/eLife.43966},
  urldate = {2021-03-03},
  abstract = {To fully exploit the potential of single-cell functional genomics in the study of development and disease, robust methods are needed to simplify the analysis of data across samples, time-points and individuals. Here we introduce a model-based factor analysis method, SDA, to analyze a novel 57,600 cell dataset from the testes of wild-type mice and mice with gonadal defects due to disruption of the genes Mlh3, Hormad1, Cul4a or Cnp. By jointly analyzing mutant and wild-type cells we decomposed our data into 46 components that identify novel meiotic gene-regulatory programs, mutant-specific pathological processes, and technical effects, and provide a framework for imputation. We identify, de novo, DNA sequence motifs associated with individual components that define temporally varying modes of gene expression control. Analysis of SDA components also led us to identify a rare population of macrophages within the seminiferous tubules of Mlh3-/- and Hormad1-/- mice, an area typically associated with immune privilege.},
  keywords = {factor analysis,gene regulation,infertility,meiosis,single-cell,testis},
  file = {/home/user1/Dropbox/Papers/Jung et al_2019_Unified single-cell analysis of testis gene regulation and pathology in five_.pdf}
}

@article{karasaki2023,
  title = {Evolutionary Characterization of Lung Adenocarcinoma Morphology in {{TRACERx}}},
  author = {Karasaki, Takahiro and Moore, David A. and Veeriah, Selvaraju and {Naceur-Lombardelli}, Cristina and Toncheva, Antonia and Magno, Neil and Ward, Sophia and Bakir, Maise Al and Watkins, Thomas B. K. and Grigoriadis, Kristiana and Huebner, Ariana and Hill, Mark S. and Frankell, Alexander M. and Abbosh, Christopher and Puttick, Clare and Zhai, Haoran and {Gimeno-Valiente}, Francisco and Saghafinia, Sadegh and Kanu, Nnennaya and Dietzen, Michelle and Pich, Oriol and Lim, Emilia L. and {Mart{\'i}nez-Ruiz}, Carlos and Black, James R. M. and Biswas, Dhruva and Campbell, Brittany B. and Lee, Claudia and Colliver, Emma and Enfield, Katey S. S. and Hessey, Sonya and Hiley, Crispin T. and Zaccaria, Simone and Litchfield, Kevin and Birkbak, Nicolai J. and Cadieux, Elizabeth Larose and Demeulemeester, Jonas and Van Loo, Peter and Adusumilli, Prasad S. and Tan, Kay See and Cheema, Waseem and {Sanchez-Vega}, Francisco and Jones, David R. and Rekhtman, Natasha and Travis, William D. and Hackshaw, Allan and Marafioti, Teresa and Salgado, Roberto and Le Quesne, John and Nicholson, Andrew G. and McGranahan, Nicholas and Swanton, Charles and {Jamal-Hanjani}, Mariam},
  year = {2023},
  month = apr,
  journal = {Nat Med},
  pages = {1--13},
  publisher = {Nature Publishing Group},
  issn = {1546-170X},
  doi = {10.1038/s41591-023-02230-w},
  urldate = {2023-04-14},
  abstract = {Lung adenocarcinomas (LUADs) display a broad histological spectrum from low-grade lepidic tumors through to mid-grade acinar and papillary and high-grade solid, cribriform and micropapillary tumors. How morphology reflects tumor evolution and disease progression is poorly understood. Whole-exome sequencing data generated from 805 primary tumor regions and 121 paired metastatic samples across 248 LUADs from the TRACERx 421 cohort, together with RNA-sequencing data from 463 primary tumor regions, were integrated with detailed whole-tumor and regional histopathological analysis. Tumors with predominantly high-grade patterns showed increased chromosomal complexity, with higher burden of loss of heterozygosity and subclonal somatic copy number alterations. Individual regions in predominantly high-grade pattern tumors exhibited higher proliferation and lower clonal diversity, potentially reflecting large recent subclonal expansions. Co-occurrence of truncal loss of chromosomes 3p and 3q was enriched in predominantly low-/mid-grade tumors, while purely undifferentiated solid-pattern tumors had a higher frequency of truncal arm or focal 3q gains and SMARCA4 gene alterations compared with mixed-pattern tumors with a solid component, suggesting distinct evolutionary trajectories. Clonal evolution analysis revealed that tumors tend to evolve toward higher-grade patterns. The presence of micropapillary pattern and `tumor spread through air spaces' were associated with intrathoracic recurrence, in contrast to the presence of solid/cribriform patterns, necrosis and preoperative circulating tumor DNA detection, which were associated with extra-thoracic recurrence. These data provide insights into the relationship between LUAD morphology, the underlying evolutionary genomic landscape, and clinical and anatomical relapse risk.},
  copyright = {2023 The Author(s) under exclusive license to Springer Nature America, Inc.},
  langid = {english},
  keywords = {Cancer genomics,Non-small-cell lung cancer,Tumour heterogeneity}
}

@article{khan2022,
  title = {Increasing {{Drought Risks Over}} the {{Past Four Centuries Amidst Projected Flood Intensification}} in the {{Kabul River Basin}} ({{Afghanistan}} and {{Pakistan}})---{{Evidence From Tree Rings}}},
  author = {Khan, Nasrullah and Nguyen, Hung T. T. and Galelli, Stefano and Cherubini, Paolo},
  year = {2022},
  journal = {Geophysical Research Letters},
  volume = {49},
  number = {24},
  pages = {e2022GL100703},
  issn = {1944-8007},
  doi = {10.1029/2022GL100703},
  urldate = {2023-05-09},
  abstract = {Increased flood risks have been projected, but with large uncertainties, in the Kabul River Basin (Afghanistan and Pakistan). To place future changes in a long-term perspective, we produce a 382-year precipitation reconstruction for the basin using seven tree-ring chronologies of old-growth conifers from the Hindu Kush Mountains, a monsoon-shadow area. The reconstruction proves robust over rigorous cross-validations (R2 = 0.60, RE = 0.60, CE = 0.53). The full reconstruction (1637--2018) reveals a steady decline in the low end of the precipitation distribution, implying increasing drought risks. We show that droughts are getting more severe, shorter, and more frequent, interspersed with more frequent pluvials in the past century. Drought risks, compounded with projected flood intensification, pose significant threats for this transboundary river. Therefore, future water management needs to account for both flood and drought risks and be informed by long-term hydroclimatic variability.},
  langid = {english},
  keywords = {climate change,dendrochronology,drought,precipitation reconstruction,water cycle,water resources},
  file = {/home/user1/Dropbox/Papers/Khan et al_2022_Increasing Drought Risks Over the Past Four Centuries Amidst Projected Flood.pdf}
}

@article{kornienko2023,
  title = {{{PCR Assay}} for {{Rapid Taxonomic Differentiation}} of {{Virulent Staphylococcus}} Aureus and {{Klebsiella}} Pneumoniae {{Bacteriophages}}},
  author = {Kornienko, Maria and Bespiatykh, Dmitry and Malakhova, Maja and Gorodnichev, Roman and Kuptsov, Nikita and Shitikov, Egor},
  year = {2023},
  month = jan,
  journal = {International Journal of Molecular Sciences},
  volume = {24},
  number = {5},
  pages = {4483},
  publisher = {Multidisciplinary Digital Publishing Institute},
  issn = {1422-0067},
  doi = {10.3390/ijms24054483},
  urldate = {2023-03-02},
  abstract = {Phage therapy is now seen as a promising way to overcome the current global crisis in the spread of multidrug-resistant bacteria. However, phages are highly strain-specific, and in most cases one will have to isolate a new phage or search for a phage suitable for a therapeutic application in existing libraries. At an early stage of the isolation process, rapid screening techniques are needed to identify and type potential virulent phages. Here, we propose a simple PCR approach to differentiate between two families of virulent Staphylococcus phages (Herelleviridae and Rountreeviridae) and eleven genera of virulent Klebsiella phages (Przondovirus, Taipeivirus, Drulisvirus, Webervirus, Jiaodavirus, Sugarlandvirus, Slopekvirus, Jedunavirus, Marfavirus, Mydovirus and Yonseivirus). This assay includes a thorough search of a dataset comprising S. aureus (n = 269) and K. pneumoniae (n = 480) phage genomes available in the NCBI RefSeq/GenBank database for specific genes that are highly conserved at the taxonomic group level. The selected primers showed high sensitivity and specificity for both isolated DNA and crude phage lysates, which permits circumventing DNA purification protocols. Our approach can be extended and applied to any group of phages, given the large number of available genomes in the databases.},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  langid = {english},
  keywords = {<i>Klebsiella pneumoniae</i>,<i>Staphylococcus aureus</i>,bacteriophage,bacteriophage typing,phage,therapy},
  file = {/home/user1/Dropbox/Papers/Kornienko et al_2023_PCR Assay for Rapid Taxonomic Differentiation of Virulent Staphylococcus aureus.pdf}
}

@article{kudrenko2023,
  title = {Walking on the {{Dark Side}}: {{Anthropogenic Factors Limit Suitable Habitat}} for {{Gray Wolf}} ({{Canis}} Lupus) in a {{Large Natural Area Covering Belarus}} and {{Ukraine}}},
  shorttitle = {Walking on the {{Dark Side}}},
  author = {Kudrenko, Svitlana and Vollering, Julien and Zedrosser, Andreas and Selva, Nuria and Ostapowicz, Katarzyna and Fenchuk, Viktar and Beasley, James C. and Heurich, Marco},
  year = {2023},
  month = jul,
  journal = {Global Ecology and Conservation},
  pages = {e02586},
  issn = {2351-9894},
  doi = {10.1016/j.gecco.2023.e02586},
  urldate = {2023-07-27},
  abstract = {Due to successful conservation initiatives and legislations, the grey wolf (Canis lupus) is re-colonising its historic range in Europe. However, wolves have never been extirpated across large areas in Eastern Europe but are often constrained to remote and inaccessible places due to centuries of persecution. This study aimed to identify the potentially suitable wolf habitats in Polesia, a massive cross-border lowland region extending over southern Belarus and northern Ukraine, which are often neglcted in large carnivore studies at the continental scale. We hypothesized that anthropogenic rather than environmental factors govern wolf habitat suitability. We used a dataset of 4,191 GPS locations obtained from radio-collared wolves (n=26) and confirmed observations (n=231) during 2014-2021 and applied maximum entropy method to estimate relative habitat suitability for wolves in Polesia. Artificial light at night (ALAN), proportion of cropland and tree cover were the most important factors affecting wolf habitat suitability. Road densities contributed poorly to predicting habitat suitability for wolves. Our models predicted a quarter of Polesia as suitable habitat and revealed priority areas connecting the important source populations in the Chornobyl Exclusion Zone in the east and the Bia{\l}owie{\.z}a Forest in the west and thus essential for long-term wolf conservation. Our results provide the bases for effective, long-term wolf monitoring and management programs in both Belarus and Ukraine. However, national and transboundary wolf management in Polesia has been extremely challenging since 2022 due to the ongoing war and subsequent habitat degradation in this part of Europe.},
  langid = {english},
  keywords = {artificial light at night (ALAN),Belarus,Eastern Europe,habitat suitability modelling,Ukraine,wolf},
  file = {/home/user1/Dropbox/Papers/Kudrenko et al_2023_Walking on the Dark Side.pdf}
}

@article{lan2020,
  title = {Fine-Scale {{Population Structure}} and {{Demographic History}} of {{Han Chinese Inferred}} from {{Haplotype Network}} of 111,000 {{Genomes}}},
  author = {Lan, Ao and Kang, Kang and Tang, Senwei and Wu, Xiaoli and Wang, Lizhong and Li, Teng and Weng, Haoyi and Deng, Junjie and Team, WeGene Research and Zheng, Qiang and Yao, Xiaotian and Chen, Gang},
  year = {2020},
  month = jul,
  journal = {bioRxiv},
  pages = {2020.07.03.166413},
  publisher = {Cold Spring Harbor Laboratory},
  doi = {10.1101/2020.07.03.166413},
  urldate = {2021-03-03},
  abstract = {{$<$}h3{$>$}ABSTRACT{$<$}/h3{$>$} {$<$}p{$>$}Han Chinese is the most populated ethnic group across the globe with a comprehensive substructure that resembles its cultural diversification. Studies have constructed the genetic polymorphism spectrum of Han Chinese, whereas high-resolution investigations are still missing to unveil its fine-scale substructure and trace the genetic imprints for its demographic history. Here we construct a haplotype network consisted of 111,000 genome-wide genotyped Han Chinese individuals from direct-to-consumer genetic testing and over 1.3 billion identity-by-descent (IBD) links. We observed a clear separation of the northern and southern Han Chinese and captured 5 subclusters and 17 sub-subclusters in haplotype network hierarchical clustering, corresponding to geography (especially mountain ranges), immigration waves, and clans with cultural-linguistic segregation. We inferred differentiated split histories and founder effects for population clans Cantonese, Hakka, and Minnan-Chaoshanese in southern China, and also unveiled more recent demographic events within the past few centuries, such as \emph{Zou Xikou} and \emph{Chuang Guandong}. The composition shifts of the native and current residents of four major metropolitans (Beijing, Shanghai, Guangzhou, and Shenzhen) imply a rapidly vanished genetic barrier between subpopulations. Our study yields a fine-scale population structure of Han Chinese and provides profound insights into the nation's genetic and cultural-linguistic multiformity.{$<$}/p{$>$}},
  chapter = {New Results},
  copyright = {{\copyright} 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Lan et al_2020_Fine-scale Population Structure and Demographic History of Han Chinese Inferred_.pdf}
}

@article{lapp2021,
  title = {Regional Spread of {{blaNDM-1-containing Klebsiella}} Pneumoniae {{ST147}} in Post-Acute Care Facilities},
  author = {Lapp, Zena and Crawford, Ryan and {Miles-Jay}, Arianna and Pirani, Ali and Trick, William E and Weinstein, Robert A and Hayden, Mary K and Snitkin, Evan S and Lin, Michael Y},
  year = {2021},
  month = may,
  journal = {Clinical Infectious Diseases},
  number = {ciab457},
  issn = {1058-4838},
  doi = {10.1093/cid/ciab457},
  urldate = {2021-05-21},
  abstract = {Carbapenem-resistant Enterobacterales (CRE) harboring blaKPC have been endemic in Chicago-area healthcare networks for more than a decade. During 2016-2019, a series of regional point prevalence surveys identified increasing prevalence of blaNDM-containing CRE in multiple long-term acute care hospitals (LTACHs) and ventilator-capable skilled nursing facilities (vSNFs). We performed a genomic epidemiology investigation of blaNDM-producing CRE to understand their regional emergence and spread.We performed whole-genome sequencing on NDM+ CRE isolates from four point-prevalence surveys across 35 facilities (LTACHs, vSNFs, and acute care hospital medical intensive care units) in the Chicago area and investigated the genomic relatedness and transmission dynamics of these isolates over time.Genomic analyses revealed that the rise of NDM+ CRE was due to the clonal dissemination of an ST147 Klebsiella pneumoniae strain harboring blaNDM-1 on an IncF plasmid. Dated phylogenetic reconstructions indicated that ST147 was introduced into the region around 2013 and likely acquired NDM around 2015. Analyzing the relatedness of strains within and between facilities supported initial increases in prevalence due to intra-facility transmission in certain vSNFs, with evidence of subsequent inter-facility spread among LTACHs and vSNFs connected by patient transfer.We identified a regional outbreak of blaNDM-1 ST147 that began in and disseminated across Chicago area post-acute care facilities. Our findings highlight the importance of performing genomic surveillance at post-acute care facilities to identify emerging threats.},
  file = {/home/user1/Dropbox/Papers/Lapp et al_2021_Regional spread of blaNDM-1-containing Klebsiella pneumoniae ST147 in_.pdf}
}

@article{laptikhovsky,
  title = {The Climate-Induced Changes in the Life History of the Common Cuttlefish in the {{English Channel}}},
  author = {Laptikhovsky, Vladimir and Barrett, Christopher J. and Barry, Peter J. and Firmin, Chris and MacLeod, Eleanor and Stott, Samantha and Vieira, Rui},
  journal = {Marine Ecology},
  volume = {n/a},
  number = {n/a},
  pages = {e12810},
  issn = {1439-0485},
  doi = {10.1111/maec.12810},
  urldate = {2024-05-22},
  abstract = {The population of common cuttlefish Sepia officinalis in the English Channel recently developed two life cycles: annual (spawning 1 y.o.) and biennial (spawning 2 y.o.) instead of the biennial strategy known before, associated with increasing environmental temperatures in recent decades because of climate changes. Both groups differ in the size of mature animals (110--196 mm mantle length vs. 140--262 mm) and the number of chambers in the cuttlebone (60--97 in annual vs. 93--152 in biennial). The annual group represented some 15\%--20\% of the population, and the proportion of early spawners increased during the reproductive period, from 3\%--5\% in February/March to 50\%--70\% in June/July. Among spawning cuttlefish males predominated as 2:1. Such environmentally driven changes in historical ecology as exemplified by the cuttlefish might be a critical link in the adaptation of the cephalopod life cycles to changing ecosystems.},
  copyright = {{\copyright} 2024 Wiley-VCH GmbH. Published by John Wiley \& Sons Ltd},
  langid = {english},
  keywords = {climate change,cuttlefish,English Channel,evolution of life histories,historical ecology,population structure,Sepia officinalis,spawning,stock structure}
}

@article{lee2023,
  title = {Thermal and Humidification Effects of a Swimming Pool in {{Hong Kong}}'s Humid-Subtropical Summer},
  author = {Lee, Louis S. H. and Jim, C. Y.},
  year = {2023},
  month = jul,
  journal = {Sustainable Cities and Society},
  pages = {104816},
  issn = {2210-6707},
  doi = {10.1016/j.scs.2023.104816},
  urldate = {2023-07-25},
  abstract = {The microclimatic effect of small urban water bodies such as swimming pools has received little attention. This study aimed at (1) comparing the microclimate adjacent to a swimming pool against two control sites and (2) quantifying the pool's cooling and humidification effects. We employed high-precision sensors to measure air temperature, humidity, black-globe temperature, and incoming and outgoing radiation at a swimming pool, nearby tennis court and turf sites in Hong Kong's humid-subtropical summer. On sunny days, we found a maximum poolside air temperature of 36.6{$^\circ$}C at 0.15 m height. The highest vapour pressure of 3.14--4.13 kPa occurred on cloudy days. Cooler rainy days lowered vapour pressure. Net short-wave radiation gain peaked at 840 W/m2 on sunny days. The findings suggested that energy stored in the morning retarded surface cooling later in the day. The morning poolside surface temperature was cooler than the turf by 3.8{$^\circ$}C but warmer by 5.7{$^\circ$}C in the afternoon, with lingering nighttime warming. Unexpectedly, the pool had lower vapour pressure than the control sites. The water body does not ameliorate heat stress on the deck in sunny conditions. The findings hinted that larger recreational blue spaces might generate more thermal and humidification effects.},
  langid = {english},
  keywords = {Cooling effect,Humid-subtropical climate,Humidification effect,Swimming pool,Urban blue space,Urban microclimate}
}

@article{liang2023,
  title = {Deciphering the Functional Landscape of Phosphosites with Deep Neural Network},
  author = {Liang, Zhongjie and Liu, Tonghai and Li, Qi and Zhang, Guangyu and Zhang, Bei and Du, Xikun and Liu, Jingqiu and Chen, Zhifeng and Ding, Hong and Hu, Guang and Lin, Hao and Zhu, Fei and Luo, Cheng},
  year = {2023},
  month = sep,
  journal = {Cell Reports},
  volume = {42},
  number = {9},
  publisher = {Elsevier},
  issn = {2211-1247},
  doi = {10.1016/j.celrep.2023.113048},
  urldate = {2023-09-19},
  langid = {english},
  pmid = {37659078},
  keywords = {CP: Genomics,CP: Molecular biology,deep neural network,enzymatic activity,evolutionary features,functional phosphosite,NADK,network embedding,protein-protein interaction (PPI)},
  file = {/home/user1/Dropbox/Papers/Liang et al_2023_Deciphering the functional landscape of phosphosites with deep neural network.pdf}
}

@article{lin2023,
  title = {The {{NSP4 T492I}} Mutation Increases {{SARS-CoV-2}} Infectivity by Altering Non-Structural Protein Cleavage},
  author = {Lin, Xiaoyuan and Sha, Zhou and Trimpert, Jakob and Kunec, Dusan and Jiang, Chen and Xiong, Yan and Xu, Binbin and Zhu, Zhenglin and Xue, Weiwei and Wu, Haibo},
  year = {2023},
  month = jul,
  journal = {Cell Host \& Microbe},
  issn = {1931-3128},
  doi = {10.1016/j.chom.2023.06.002},
  urldate = {2023-07-06},
  abstract = {The historically dominant SARS-CoV-2 Delta variant and the currently dominant Omicron variants carry a T492I substitution within the non-structural protein 4 (NSP4). Based on in silico analyses, we hypothesized that the T492I mutation increases viral transmissibility and adaptability, which we confirmed with competition experiments in hamster and human airway tissue culture models. Furthermore, we showed that the T492I mutation increases the replication capacity and infectiveness of the virus and improves its ability to evade host immune responses. Mechanistically, the T492I mutation increases the cleavage efficiency of the viral main protease NSP5 by enhancing enzyme-substrate binding, which increases production of nearly all non-structural proteins processed by NSP5. Importantly, the T492I mutation suppresses viral-RNA-associated chemokine production in monocytic macrophages, which may contribute to the attenuated pathogenicity of Omicron variants. Our results highlight the importance of NSP4 adaptation in the evolutionary dynamics of SARS-CoV-2.},
  langid = {english},
  keywords = {attenuated pathogenicity,immune evasion,NSP4,replication,T492I},
  file = {/home/user1/Dropbox/Papers/Lin et al_2023_The NSP4 T492I mutation increases SARS-CoV-2 infectivity by altering.pdf}
}

@article{luquet,
  title = {Predicting the Seasonal Flight Activity of {{Myzus}} Persicae, the Main Aphid Vector of {{Virus Yellows}} in Sugar Beet},
  author = {Luquet, Martin and Sylvain, Poggi and Buchard, Christelle and Plantegenest, Manuel and Tricault, Yann},
  journal = {Pest Management Science},
  volume = {n/a},
  number = {n/a},
  issn = {1526-4998},
  doi = {10.1002/ps.7653},
  urldate = {2023-07-13},
  abstract = {Background Virus Yellows (VY), a disease caused by several aphid-borne viruses, is a major threat to the global sugar beet production. Following the ban of neonicotinoid-based seed treatments against aphids in Europe, increased efforts are needed to monitor and forecast aphid population spread during the sugar beet growing season. In particular, predicting aphid flight seasonal activity could allow anticipation of the timing and intensity of crop colonisation and contribute to the proper implementation of management methods. Forecasts should be made early enough to assess risk, but can be updated as the season progresses to refine management. Based on a long-term suction-trap dataset gathered between 1978 to 2014, we built and evaluated a set of models to predict the flight activity features of the main VY vector, Myzus persicae, at any location in the French sugar beet production area (circa 4.105 ha). Flight onset dates, length of flight period and cumulative abundance of flying aphids were predicted using climatic and land-use predictors as well as geographical position. Results Our predictions outperformed current models published in the literature. The importance of the predictor variables varied according to the predicted flight feature but winter and early spring temperature always played a major role. Forecasts based on temperature were made more accurate by adding predictors related to aphid winter reservoirs. In addition, updating the model parameters to take advantage of new weather data acquired during the season improved the flight forecast. Conclusion Our models can be used as a tool for the mitigation in sugar beet crops. This article is protected by copyright. All rights reserved.},
  copyright = {This article is protected by copyright. All rights reserved.},
  langid = {english},
  keywords = {Epidemiological surveillance,Forecasting,Myzus persicae,Regression model,Sugar beet,Virus Yellows}
}

@article{ma2020,
  title = {Identification of Key Genes Associated with Progression and Prognosis for Lung Squamous Cell Carcinoma},
  author = {Ma, Xiaohan and Ren, Huijun and Peng, Ruoyu and Li, Yi and Ming, Liang},
  year = {2020},
  month = may,
  journal = {PeerJ},
  volume = {8},
  pages = {e9086},
  issn = {2167-8359},
  doi = {10.7717/peerj.9086},
  urldate = {2024-02-12},
  abstract = {Background Lung squamous cell carcinoma (LUSC) is a major subtype of lung cancer with limited therapeutic options and poor clinical prognosis. Methods Three datasets (GSE19188, GSE33532 and GSE33479) were obtained from the gene expression omnibus (GEO) database. Differentially expressed genes (DEGs) between LUSC and normal tissues were identified by GEO2R, and functional analysis was employed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Protein--protein interaction (PPI) and hub genes were identified via the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. Hub genes were further validated in The Cancer Genome Atlas (TCGA) database. Subsequently, survival analysis was performed using the Kapla--Meier curve and Cox progression analysis. Based on univariate and multivariate Cox progression analysis, a gene signature was established to predict overall survival. Receiver operating characteristic curve was used to evaluate the prognostic value of the model. Results A total of 116 up-regulated genes and 84 down-regulated genes were identified. These DEGs were mainly enriched in the two pathways: cell cycle and p53 signaling way. According to the degree of protein nodes in the PPI network, 10 hub genes were identified. The mRNA expression levels of the 10 hub genes in LUSC were also significantly up-regulated in the TCGA database. Furthermore, a novel seven-gene signature (FLRT3, PPP2R2C, MMP3, MMP12, CAPN8, FILIP1 and SPP1) from the DEGs was constructed and acted as a significant and independent prognostic signature for LUSC. Conclusions The 10 hub genes might be tightly correlated with LUSC progression. The seven-gene signature might be an independent biomarker with a significant predictive value in LUSC overall survival.},
  pmcid = {PMC7210810},
  pmid = {32411535},
  file = {/home/user1/Dropbox/Papers/Ma et al_2020_Identification of key genes associated with progression and prognosis for lung.pdf}
}

@article{ma2023,
  title = {A Systematic Review, Meta-Analysis and Meta-Regression of the Global Prevalence of Foodborne {{Vibrio}} Spp. Infection in Fishes: {{A}} Persistent Public Health Concern},
  shorttitle = {A Systematic Review, Meta-Analysis and Meta-Regression of the Global Prevalence of Foodborne {{Vibrio}} Spp. Infection in Fishes},
  author = {Ma, Jun-Yang and Zhu, Xin-Kun and Hu, Ren-Ge and Qi, Ze-Zheng and Sun, Wen-Chao and Hao, Zhi-Peng and Cong, Wei and Kang, Yuan-Huan},
  year = {2023},
  month = feb,
  journal = {Marine Pollution Bulletin},
  volume = {187},
  pages = {114521},
  issn = {0025-326X},
  doi = {10.1016/j.marpolbul.2022.114521},
  urldate = {2023-01-10},
  abstract = {Human vibriosis, caused by pathogenic Vibrio spp., such as Vibrio parahaemolyticus, Vibrio cholerae and Vibrio vulnificus, has been increasing worldwide, mediated by increasing consumption of seafood. The present study was conducted to examine the global prevalence of V. vulnificus, V. parahaemolyticus and V. cholerae in fishes. We searched PubMed, Web of Science, Scopus, and CNKI for peer-reviewed articles and dissertations prior to December 31, 2021. A total of 24,831 articles were retrieved, and 82 articles contained 61 fish families were included. The global pooled prevalence of V. cholerae, V. parahaemolyticus and V. vulnificus in fishes was 9.56~\% (95~\% CI: 2.12--20.92), 24.77~\% (95~\% CI: 17.40--32.93) and 5.29~\% (95~\% CI: 0.38--13.61), respectively. Subgroup and meta-regression analyses showed that study-level covariates, including temperature, country, continent, origin and detection methods partly explained the between-study heterogeneity. These heterogeneities were underpinned by differences of the three Vibrio spp. in fishes at geographical and climatic scales. These results reveal a high global prevalence of pathogenic Vibrio spp. in fishes and highlight the need for implementation of more effective prevention and control measures to reduce food-borne infection in humans.},
  langid = {english},
  keywords = {Fish,Global prevalence,Meta-analysis,spp.,Systematic review}
}

@article{maghini2023,
  title = {Quantifying Bias Introduced by Sample Collection in Relative and Absolute Microbiome Measurements},
  author = {Maghini, Dylan G. and Dvorak, Mai and Dahlen, Alex and Roos, Morgan and Kuersten, Scott and Bhatt, Ami S.},
  year = {2023},
  month = apr,
  journal = {Nat Biotechnol},
  pages = {1--11},
  publisher = {Nature Publishing Group},
  issn = {1546-1696},
  doi = {10.1038/s41587-023-01754-3},
  urldate = {2023-05-02},
  abstract = {To gain insight into the accuracy of microbial measurements, it is important to evaluate sources of bias related to sample condition, preservative method and bioinformatic analyses. There is increasing evidence that measurement of the total count and concentration of microbes in the gut, or `absolute abundance', provides a richer source of information than relative abundance and can correct some conclusions drawn from relative abundance data. However, little is known about how preservative choice can affect these measurements. In this study, we investigated how two common preservatives and short-term storage conditions impact relative and absolute microbial measurements. OMNIgene GUT OMR-200 yields lower metagenomic taxonomic variation between different storage temperatures, whereas Zymo DNA/RNA Shield yields lower metatranscriptomic taxonomic variation. Absolute abundance quantification reveals two different causes of variable Bacteroidetes:Firmicutes ratios across preservatives. Based on these results, we recommend OMNIgene GUT OMR-200 preservative for field studies and Zymo DNA/RNA Shield for metatranscriptomics studies, and we strongly encourage absolute quantification for microbial measurements.},
  copyright = {2023 The Author(s), under exclusive licence to Springer Nature America, Inc.},
  langid = {english},
  keywords = {Metagenomics,Microbiome}
}

@article{mehic,
  title = {Genome Sequence and Characterisation of a Freshwater Photoarsenotroph, {{Cereibacter}} Azotoformans Strain {{ORIO}}, Isolated from Sediments Capable of Cyclic Light--Dark Arsenic Oxidation and Reduction},
  author = {Mehi{\'c}, Sanjin and Saltikov, Chad},
  journal = {Environmental Microbiology},
  volume = {n/a},
  number = {n/a},
  issn = {1462-2920},
  doi = {10.1111/1462-2920.16542},
  urldate = {2023-11-21},
  abstract = {A freshwater photosynthetic arsenite-oxidizing bacterium, Cereibacter azotoformans strain ORIO, was isolated from Owens River, CA, USA. The waters from Owens River are elevated in arsenic and serve as the headwaters to the Los Angeles Aqueduct. The complete genome sequence of strain ORIO is 4.8 Mb genome (68\% G + C content) and comprises two chromosomes and six plasmids. Taxonomic analysis placed ORIO within the Cereibacter genus (formerly Rhodobacter). The ORIO genome contains arxB2AB1CD (encoding an arsenite oxidase), arxXSR (regulators) and several ars arsenic resistance genes all co-localised on a 136 kb plasmid, named pORIO3. Phylogenetic analysis of ArxA, the molybdenum-containing arsenite oxidase catalytic subunit, demonstrated photoarsenotrophy is likely to occur within members of the Alphaproteobacteria. ORIO is a mixotroph, oxidises arsenite to arsenate (As(V)) photoheterotrophically, and expresses arxA in cultures grown with arsenite. Further ecophysiology studies with Owens River sediment demonstrated the interconversion of arsenite and As(V) was dependent on light--dark cycling. arxA and arrA (As(V) respiratory reductase) genes were detected in the light--dark cycled sediment metagenomes suggesting syntrophic interactions among arsenotrophs. This work establishes C. azotoformans str. ORIO as a new model organism for studying photoarsenotrophy and light--dark arsenic biogeochemical cycling.},
  copyright = {{\copyright} 2023 The Authors. Environmental Microbiology published by Applied Microbiology International and John Wiley \& Sons Ltd.},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Mehić_Saltikov_Genome sequence and characterisation of a freshwater photoarsenotroph,.pdf}
}

@phdthesis{mehic2022,
  title = {Genomic and {{Physiologic Characterization}} of a {{Freshwater Photoarsenotroph}}, {{Cereibacter}} Azotoformans Str. {{ORIO}}, {{Isolated From Sediments Capable}} of {{Light-Dark Arsenic Redox Cycling}}},
  author = {Mehic, Sanjin},
  year = {2022},
  urldate = {2023-05-09},
  abstract = {Photoarsenotrophy is an anoxygenic photosynthesis-dependent arsenite oxidation pathway encoded by the Arx gene cluster and is linked to light-dark cycling of arsenic in freshwater environments. This dissertation uses techniques from microbiology, molecular genetics, DNA sequencing, and analytical chemistry to characterize photoarsenotrophy in freshwater environments. The hypothesis is that photoarsenotrophy occurs in freshwater environments and is associated with light-dark cycling of arsenic, which may have a different effect on arsenic biogeochemical cycling when compared to Arx-type arsenotrophy. Light-dark arsenic redox cycling is defined herein as variations in arsenic species, arsenite and arsenate, that correlate to light or dark phases.Since the discovery of photoarsenotrophy in 2008, less than a dozen Arx-dependent arsenotrophs have been isolated, and light-dependent arsenite oxidation has only been detected in three genera (Ectothiorhodospira sp. strains MLW-1, PHS-1, BSL-9, Ect. shaposhnikovii strains DSM 243 and DSM 2001, Halorhodospira halophila SL-1, and now Cereibacter azotoformans str. ORIO). The other studied Arx-dependent arsenotrophs couple arsenite oxidation to anaerobic respiration (i.e., nitrate reduction) instead of anoxygenic photosynthesis (Alkalilimnicola ehrlichii str. MLHE-1, Azoarcus sp. CIB, Sterolibacteraceae strain M52, Desulfotomaculum strain TC-1, and Halomonas sp. ANAO440). In this thesis, I define the light requirement by referring to photosynthesis-dependent arsenite-oxidation as photoarsenotrophy, and photosynthesis-independent Arx-type arsenite-oxidation as Arx-type arsenotrophy. This difference in light requirement is important as it introduces the possibility that light-dark cycling of arsenic could occur in environments containing a photoarsenotroph and arsenate reducer, since Arx-type arsenotrophs are able to oxidize arsenite in the dark so long there is availability of a terminal electron acceptor.The first question investigated was: Does photoarsenotrophy occur in freshwater environments? This question was studied through the isolation and genetic characterization of a novel photoarsenotroph from freshwater sediments in Owens River, CA, USA. Our results show the photoarsenotrophs are present in freshwater environments and harbor the Arx genes required for photoarsenotrophy.The second question investigated was: Can arsenic be light-dark cycled in the environment? In other words, do concentrations of different arsenic forms correlate to the light phase or dark phase of a day? To answer this question, we performed anaerobic microcosm studies with sediment collected from Owens River. Arsenic speciation was measured over light-dark cycles and was followed by metagenome sequencing and analysis. The results provide evidence of light-dark cycling in freshwater sediments and the potential genes involved in the cycle. The third question investigated was: Can we develop a new model organism for studying photoarsenotrophy? We successfully determined that Cereibacter azotoformans str. ORIO is genetically malleable using traditional cloning techniques and can serve as a model for studying the biological mechanism underlying photoarsenotrophy. This was achieved by validating the role of the arxA gene in ORIO and characterizing the physiology surrounding arsenite oxidation.Taken together, these studies show photoarsenotrophy occurs in freshwater environments, ORIO can serve as a model organism for studying photoarsenotrophy, and evidence of light-dark arsenic redox cycling in freshwater sediments.},
  langid = {english},
  school = {UC Santa Cruz},
  file = {/home/user1/Dropbox/Papers/Mehic_2022_Genomic and Physiologic Characterization of a Freshwater Photoarsenotroph,.pdf}
}

@article{merinotejero2021,
  title = {Multiscale {{Modeling}} of {{Germinal Center Recapitulates}} the {{Temporal Transition From Memory B Cells}} to {{Plasma Cells Differentiation}} as {{Regulated}} by {{Antigen Affinity-Based Tfh Cell Help}}},
  author = {Merino Tejero, Elena and Lashgari, Danial and {Garc{\'i}a-Valiente}, Rodrigo and Gao, Xuefeng and Crauste, Fabien and Robert, Philippe A. and {Meyer-Hermann}, Michael and Mart{\'i}nez, Mar{\'i}a Rodr{\'i}guez and {van Ham}, S. Marieke and Guikema, Jeroen E. J. and Hoefsloot, Huub and {van Kampen}, Antoine H. C.},
  year = {2021},
  month = feb,
  journal = {Front Immunol},
  volume = {11},
  issn = {1664-3224},
  doi = {10.3389/fimmu.2020.620716},
  urldate = {2021-03-03},
  abstract = {Germinal centers play a key role in the adaptive immune system since they are able to produce memory B cells and plasma cells that produce high affinity antibodies for an effective immune protection. The mechanisms underlying cell-fate decisions are not well understood but asymmetric division of antigen, B-cell receptor affinity, interactions between B-cells and T follicular helper cells (triggering CD40 signaling), and regulatory interactions of transcription factors have all been proposed to play a role. In addition, a temporal switch from memory B-cell to plasma cell differentiation during the germinal center reaction has been shown. To investigate if antigen affinity-based Tfh cell help recapitulates the temporal switch we implemented a multiscale model that integrates cellular interactions with a core gene regulatory network comprising BCL6, IRF4, and BLIMP1. Using this model we show that affinity-based CD40 signaling in combination with asymmetric division of B-cells result in switch from memory B-cell to plasma cell generation during the course of the germinal center reaction. We also show that cell fate division is unlikely to be (solely) based on asymmetric division of Ag but that BLIMP1 is a more important factor. Altogether, our model enables to test the influence of molecular modulations of the CD40 signaling pathway on the production of germinal center output cells.},
  pmcid = {PMC7892951},
  pmid = {33613551},
  file = {/home/user1/Dropbox/Papers/Merino Tejero et al_2021_Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition_.pdf}
}

@article{mokrousov2023,
  title = {Insight into Pathogenomics and Phylogeography of Hypervirulent and Highly-Lethal {{Mycobacterium}} Tuberculosis Strain Cluster},
  author = {Mokrousov, Igor and Vyazovaya, Anna and Shitikov, Egor and Badleeva, Maria and Belopolskaya, Olesya and Bespiatykh, Dmitry and Gerasimova, Alena and Ioannidis, Panayotis and Jiao, Weiwei and Khromova, Polina and Masharsky, Aleksey and Naizabayeva, Dinara and Papaventsis, Dimitrios and Pasechnik, Oksana and Perdig{\~a}o, Jo{\~a}o and Rastogi, Nalin and Shen, Adong and Sinkov, Viacheslav and Skiba, Yuriy and Solovieva, Natalia and Tafaj, Silva and Valcheva, Violeta and Kostyukova, Irina and Zhdanova, Svetlana and Zhuravlev, Viacheslav and Ogarkov, Oleg},
  year = {2023},
  month = jun,
  journal = {BMC Infectious Diseases},
  volume = {23},
  number = {1},
  pages = {426},
  issn = {1471-2334},
  doi = {10.1186/s12879-023-08413-7},
  urldate = {2023-06-28},
  abstract = {. The Mycobacterium tuberculosis Beijing genotype is globally spread lineage with important medical properties that however vary among its subtypes. M. tuberculosis Beijing 14717-15-cluster was recently discovered as both multidrug-resistant, hypervirulent, and highly-lethal strain circulating in the Far Eastern region of Russia. Here, we aimed to analyze its pathogenomic features and phylogeographic pattern.},
  keywords = {Beijing genotype,Drug resistance,Mycobacterium tuberculosis,Virulence,Whole genome sequencing},
  file = {/home/user1/Dropbox/Papers/Mokrousov et al_2023_Insight into pathogenomics and phylogeography of hypervirulent and.pdf}
}

@article{moore2024,
  title = {Fitting {{Power-Law Relations}} in {{Watershed Science}} and {{Analysis}}, with an {{Example Using}} the {{R Language}}},
  author = {Moore, R. Dan},
  year = {2024},
  month = feb,
  journal = {Confluence: Journal of Watershed Science and Management},
  volume = {7},
  number = {1},
  pages = {14 pp-14 pp},
  issn = {2561-1836},
  doi = {10.22230/jwsm.2024v7n1a53},
  urldate = {2024-02-20},
  abstract = {Many quantitative relationships in the environmental sciences, and specifically in watershed science, can effectively be modelled using a power-law function. Such relationships are often estimated using ordinary least squares regression after linearizing the relationship by log-transforming both the x and y variables. Alternative approaches include nonlinear least squares regression and generalized nonlinear least squares regression. However, there are some differences in the underlying characteristics of~ these models that can result in the generation of different relationships and associated prediction limits. This article provides an overview of the statistical models underlying these approaches, then illustrates their application using the R language for an example based on fitting a regional relationship to predict flood quantiles from catchment area. Keywords: law relationships, log-transformation, nonlinear least squares regression, generalized nonlinear least squares regression},
  copyright = {Copyright (c) 2024 R. Dan Moore},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Moore_2024_Fitting Power-Law Relations in Watershed Science and Analysis, with an Example.pdf}
}

@article{navickaite2024,
  title = {Occurrence and Characterization of {{rmtB-harbouring Salmonella}} and {{Escherichia}} Coli Isolates from a Pig Farm in the {{UK}}},
  author = {Navickaite, Indre and Holmes, Harry and Dondi, Letizia and Randall, Luke and Fearnley, Catherine and Taylor, Emma and Fullick, Edward and Horton, Robert and Williamson, Susanna and AbuOun, Manal and Teale, Christopher and Anjum, Muna F},
  year = {2024},
  month = apr,
  journal = {Journal of Antimicrobial Chemotherapy},
  pages = {dkae102},
  issn = {0305-7453},
  doi = {10.1093/jac/dkae102},
  urldate = {2024-04-19},
  abstract = {To characterize and elucidate the spread of amikacin-resistant Enterobacteriaceae isolates from environmental samples on a pig farm in the UK, following the previous identification of index Salmonella isolates harbouring the rmtB gene, a 16S rRNA methylase.Environmental samples were collected during two visits to a pig farm in the UK. Isolates were recovered using selective media (amikacin 128 mg/L) followed by real-time PCR and WGS to analyse rmtB-carrying Salmonella and Escherichia coli isolates.Salmonella and E. coli isolates harbouring the rmtB gene were detected at both farm visits. All Salmonella isolates were found to be monophasic S. enterica serovar Typhimurium variant Copenhagen of ST34. rmtB-harbouring E. coli isolates were found to be one of three STs: ST4089, ST1684 and ST34. Long-read sequencing identified the rmtB gene to be chromosomally located in Salmonella isolates and on IncFII-type plasmids in E. coli isolates. The results showed the rmtB gene to be flanked by IS26 elements and several resistance genes.We report on the occurrence of rmtB-harbouring Enterobacteriaceae on a pig farm in the UK. rmtB confers resistance to multiple aminoglycosides and this work highlights the need for surveillance to assess dissemination and risk.}
}

@article{papacharalampous2021,
  title = {Global-Scale Massive Feature Extraction from Monthly Hydroclimatic Time Series: {{Statistical}} Characterizations, Spatial Patterns and Hydrological Similarity},
  shorttitle = {Global-Scale Massive Feature Extraction from Monthly Hydroclimatic Time Series},
  author = {Papacharalampous, Georgia and Tyralis, Hristos and Papalexiou, Simon Michael and Langousis, Andreas and Khatami, Sina and Volpi, Elena and Grimaldi, Salvatore},
  year = {2021},
  month = may,
  journal = {Science of The Total Environment},
  volume = {767},
  pages = {144612},
  issn = {0048-9697},
  doi = {10.1016/j.scitotenv.2020.144612},
  urldate = {2021-03-03},
  abstract = {Hydroclimatic time series analysis focuses on a few feature types (e.g., autocorrelations, trends, extremes), which describe a small portion of the entire information content of the observations. Aiming to exploit a larger part of the available information and, thus, to deliver more reliable results (e.g., in hydroclimatic time series clustering contexts), here we approach hydroclimatic time series analysis differently, i.e., by performing massive feature extraction. In this respect, we develop a big data framework for hydroclimatic variable behaviour characterization. This framework relies on approximately 60 diverse features and is completely automatic (in the sense that it does not depend on the hydroclimatic process at hand). We apply the new framework to characterize mean monthly temperature, total monthly precipitation and mean monthly river flow. The applications are conducted at the global scale by exploiting 40-year-long time series originating from over 13 000 stations. We extract interpretable knowledge on seasonality, trends, autocorrelation, long-range dependence and entropy, and on feature types that are met less frequently. We further compare the examined hydroclimatic variable types in terms of this knowledge and, identify patterns related to the spatial variability of the features. For this latter purpose, we also propose and exploit a hydroclimatic time series clustering methodology. This new methodology is based on Breiman's random forests. The descriptive and exploratory insights gained by the global-scale applications prove the usefulness of the adopted feature compilation in hydroclimatic contexts. Moreover, the spatially coherent patterns characterizing the clusters delivered by the new methodology build confidence in its future exploitation. Given this spatial coherence and the scale-independent nature of the delivered feature values (which makes them particularly useful in forecasting and simulation contexts), we believe that this methodology could also be beneficial within regionalization frameworks, in which knowledge on hydrological similarity is exploited in technical and operative terms.},
  langid = {english},
  keywords = {Autocorrelation,Entropy,Hydroclimatic signatures,Seasonality,Statistical hydrology,Trends},
  file = {/home/user1/Dropbox/Papers/Papacharalampous et al_2021_Global-scale massive feature extraction from monthly hydroclimatic time series_.pdf}
}

@article{peng2023,
  title = {Viruses in Deep-Sea Cold Seep Sediments Harbor Diverse Survival Mechanisms and Remain Genetically Conserved within Species},
  author = {Peng, Yongyi and Lu, Zijian and Pan, Donald and Shi, Ling-Dong and Zhao, Zhao and Liu, Qing and Zhang, Chuwen and Jia, Kuntong and Li, Jiwei and Hubert, Casey R. J. and Dong, Xiyang},
  year = {2023},
  month = oct,
  journal = {ISME J},
  volume = {17},
  number = {10},
  pages = {1774--1784},
  publisher = {Nature Publishing Group},
  issn = {1751-7370},
  doi = {10.1038/s41396-023-01491-0},
  urldate = {2024-04-11},
  abstract = {Deep sea cold seep sediments have been discovered to harbor novel, abundant, and diverse bacterial and archaeal viruses. However, little is known about viral genetic features and evolutionary patterns in these environments. Here, we examined the evolutionary ecology of viruses across active and extinct seep stages in the area of Haima cold seeps in the South China Sea. A total of 338 viral operational taxonomic units are identified and linked to 36 bacterial and archaeal phyla. The dynamics of host-virus interactions are informed by diverse antiviral defense systems across 43 families found in 487 microbial genomes. Cold seep viruses are predicted to harbor diverse adaptive strategies to persist in this environment, including counter-defense systems, auxiliary metabolic genes, reverse transcriptases, and alternative genetic code assignments. Extremely low nucleotide diversity is observed in cold seep viral populations, being influenced by factors including microbial host, sediment depth, and cold seep stage. Most cold seep viral genes are under strong purifying selection with trajectories that differ depending on whether cold seeps are active or extinct. This work sheds light on the understanding of environmental adaptation mechanisms and evolutionary patterns of viruses in the sub-seafloor biosphere.},
  copyright = {2023 The Author(s)},
  langid = {english},
  keywords = {Microbial ecology,Virology},
  file = {/home/user1/Dropbox/Papers/Peng et al_2023_Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and.pdf}
}

@article{plaza2022a,
  title = {Ecosystem Productivity Has a Stronger Influence than Soil Age on Surface Soil Carbon Storage across Global Biomes},
  author = {Plaza, C{\'e}sar and {Garc{\'i}a-Palacios}, Pablo and Berhe, Asmeret Asefaw and Barquero, Jes{\'u}s and Bastida, Felipe and Png, G. Kenny and Rey, Ana and Bardgett, Richard D. and {Delgado-Baquerizo}, Manuel},
  year = {2022},
  month = oct,
  journal = {Commun Earth Environ},
  volume = {3},
  number = {1},
  pages = {1--8},
  publisher = {Nature Publishing Group},
  issn = {2662-4435},
  doi = {10.1038/s43247-022-00567-7},
  urldate = {2022-10-12},
  abstract = {Interactions between soil organic matter and minerals largely govern the carbon sequestration capacity of soils. Yet, variations in the proportions of free light (unprotected) and mineral-associated (protected) carbon as soil develops in contrasting ecosystems are poorly constrained. Here, we studied 16 long-term chronosequences from six continents and found that the ecosystem type is more important than soil age (centuries to millennia) in explaining the proportion of unprotected and mineral-associated carbon fractions in surface soils across global biomes. Soil carbon pools in highly productive tropical and temperate forests were dominated by the unprotected carbon fraction and were highly vulnerable to reductions in ecosystem productivity and warming. Conversely, soil carbon in low productivity, drier and colder ecosystems was dominated by mineral-protected carbon, and was less responsive to warming. Our findings emphasize the importance of conserving ecosystem productivity to protect carbon stored in surface soils.},
  copyright = {2022 The Author(s)},
  langid = {english},
  keywords = {Carbon cycle,Environmental chemistry},
  file = {/home/user1/Dropbox/Papers/Plaza et al_2022_Ecosystem productivity has a stronger influence than soil age on surface soil.pdf}
}

@article{pottier2022,
  title = {A Comprehensive Database of Amphibian Heat Tolerance},
  author = {Pottier, Patrice and Lin, Hsien-Yung and Oh, Rachel R. Y. and Pollo, Pietro and {Rivera-Villanueva}, A. Nayelli and Valdebenito, Jos{\'e} O. and Yang, Yefeng and Amano, Tatsuya and Burke, Samantha and Drobniak, Szymon M. and Nakagawa, Shinichi},
  year = {2022},
  month = oct,
  journal = {Sci Data},
  volume = {9},
  number = {1},
  pages = {600},
  publisher = {Nature Publishing Group},
  issn = {2052-4463},
  doi = {10.1038/s41597-022-01704-9},
  urldate = {2022-10-08},
  abstract = {Rising temperatures represent a significant threat to the survival of ectothermic animals. As such, upper thermal limits represent an important trait to assess the vulnerability of ectotherms to changing temperatures. For instance, one may use upper thermal limits to estimate current and future thermal safety margins (i.e., the proximity of upper thermal limits to experienced temperatures), use this trait together with other physiological traits in species distribution models, or investigate the plasticity and evolvability of these limits for buffering the impacts of changing temperatures. While datasets on thermal tolerance limits have been previously compiled, they sometimes report single estimates for a given species, do not present measures of data dispersion, and are biased towards certain parts of the globe. To overcome these limitations, we systematically searched the literature in seven languages to produce the most comprehensive dataset to date on amphibian upper thermal limits, spanning 3,095 estimates across 616 species. This resource will represent a useful tool to evaluate the vulnerability of amphibians, and ectotherms more generally, to changing temperatures.},
  copyright = {2022 The Author(s)},
  langid = {english},
  keywords = {Animal physiology,Climate-change ecology,Ecology,Ecophysiology},
  file = {/home/user1/Dropbox/Papers/Pottier et al_2022_A comprehensive database of amphibian heat tolerance.pdf}
}

@article{quilty2022,
  title = {A Stochastic Conceptual-Data-Driven Approach for Improved Hydrological Simulations},
  author = {Quilty, John M. and {Sikorska-Senoner}, Anna E. and Hah, David},
  year = {2022},
  month = jan,
  journal = {Environmental Modelling \& Software},
  pages = {105326},
  issn = {1364-8152},
  doi = {10.1016/j.envsoft.2022.105326},
  urldate = {2022-01-19},
  abstract = {In a companion paper, Sikorska-Senoner and Quilty (2021) introduced the ensemble-based conceptual-data-driven approach (CDDA) for improving hydrological simulations. This approach consists of an ensemble of hydrological model (HM) simulations (generated via different parameter sets) whose residuals are `corrected' by a data-driven model (one per HM parameter set), resulting in an improved ensemble simulation. Through a case study involving three Swiss catchments, it was demonstrated that CDDA generates significantly improved ensemble streamflow simulations when compared to the ensemble HM. In this follow-up study, a stochastic version of CDDA (SCDDA) is developed that, in addition to parameter uncertainty, accounts for input data, input variable selection, and model output uncertainty. Using several deterministic and probabilistic performance metrics, it is shown that SCDDA results in significantly more accurate and reliable ensemble-based streamflow simulations than the CDDA, ensemble and stochastic HMs, and a quantile regression-based approach, improving the mean interval score by 26--79\%.},
  langid = {english},
  keywords = {Data-driven model,Ensemble,Hydrological model,Stochastic,Streamflow simulation,Uncertainty}
}

@article{rios2023,
  title = {Comparative Metatranscriptome Analysis of {{Brazilian}} Milk and Water Kefir Beverages},
  author = {Rios, Diego Lisboa and {da Silva}, Patr{\'i}cia Costa Lima and Moura, C{\'e}sar Silva Santana and Villanoeva, Camila Nair Batista Couto and {da Rocha Fernandes}, Gabriel and Bengoa, Ana Agustina and Garrote, Graciela Liliana and Abraham, Anal{\'i}a Graciela and Nicoli, Jacques Robert and Neumann, Elisabeth and Nunes, {\'A}lvaro Cantini},
  year = {2023},
  month = sep,
  journal = {Int Microbiol},
  issn = {1618-1905},
  doi = {10.1007/s10123-023-00431-4},
  urldate = {2023-10-03},
  abstract = {The present study compared bacterial and fungal diversity of kefir beverages produced using milk (MK) or sugared water (WK) as propagation matrices and grains from the cities of Curitiba (CU) or Salvador (SA), Brazil, by sequencing the complete set of RNA transcripts produced in four products. In Brazil, milk and sugared water are used as matrices to propagate kefir grains. In all beverages, the bacterial community was composed of Lactobacillaceae and Acetobacteraceae. Saccharomycetaceae was the yeast family more abundant in WK, and Dipodascaceae and Pichiaceae in MK. Regarding KEGG mapping of functional orthologs, the four kefir samples shared 70\% of KO entries of yeast genes but only 36\% of bacterial genes. Concerning main metabolic processes, the relative abundance of transcripts associated with metabolism (energy metabolism) and environmental information processing (membrane transport) had the highest water/milk kefir ratio observed in Firmicutes. In contrast, transcripts associated with genetic information processing (protein translation, folding, sorting, and degradation) oppositely had the lowest water/milk ratios. Concluding, milk and water kefir have quite different communities of microorganisms. Still, the main mapped functional processes are similar, with only quantitative variation in membrane transport and energy acquisition in the water kefir and protein synthesis and turnover in the milk kefir.},
  langid = {english},
  keywords = {Acetic acid bacteria,Lactic acid bacteria,Metatranscriptome,Milk kefir,Water kefir,Yeasts}
}

@article{rodenhizer2022,
  title = {Abrupt Permafrost Thaw Accelerates Carbon Dioxide and Methane Release at a Tussock Tundra Site},
  author = {Rodenhizer, Heidi and Belshe, Fay and Celis, Gerardo and Ledman, Justin and Mauritz, Marguerite and Goetz, Scott and Sankey, Temuulen and Schuur, Edward A.G.},
  year = {2022},
  month = dec,
  journal = {Arctic, Antarctic, and Alpine Research},
  volume = {54},
  number = {1},
  pages = {443--464},
  publisher = {Taylor \& Francis},
  issn = {1523-0430},
  doi = {10.1080/15230430.2022.2118639},
  urldate = {2022-10-04},
  abstract = {Abrupt thaw could cause permafrost ecosystems to release more carbon than is predicted from gradual thaw alone. However, thermokarst feature mapping is limited in scope, and observed responses of carbon fluxes to abrupt thaw are variable. We developed a thermokarst detection algorithm that identifies thermokarst features from a single elevation dataset with 71.5 percent accuracy and applied it in Healy, Alaska. Additionally, we investigated the landscape-level variation in carbon dioxide and methane fluxes by extent of abrupt thaw using eddy covariance. Seven percent of the site was classified as thermokarst. Water tracks were the most extensive form of thermokarst, although small pits were much more numerous. Abrupt thaw was positively correlated with carbon uptake during the growing season, when increases in gross primary productivity outpaced increases in ecosystem respiration in vegetation-dense water tracks. However, this was outweighed by higher carbon release in thermokarst features during the nongrowing season. Additionally, abrupt thaw was positively correlated with methane production nearly year-round. Our findings support the hypothesis that abrupt thaw of permafrost carbon will contribute to the permafrost climate feedback above and beyond that associated with gradual thaw and highlights the need to map thermokarst and incorporate abrupt thaw into Earth System Models.},
  keywords = {Arctic,carbon dioxide,methane,permafrost,thermokarst}
}

@article{rutz2021,
  title = {Open {{Natural Products Research}}: {{Curation}} and {{Dissemination}} of {{Biological Occurrences}} of {{Chemical Structures}} through {{Wikidata}}},
  shorttitle = {Open {{Natural Products Research}}},
  author = {Rutz, Adriano and Sorokina, Maria and Galgonek, Jakub and Mietchen, Daniel and Willighagen, Egon and Graham, James and Stephan, Ralf and Page, Roderic and Vondr{\'a}{\v s}ek, Ji{\v r}{\'i} and Steinbeck, Christoph and Pauli, Guido F. and Wolfender, Jean-Luc and Bisson, Jonathan and Allard, Pierre-Marie},
  year = {2021},
  month = mar,
  journal = {bioRxiv},
  pages = {2021.02.28.433265},
  publisher = {Cold Spring Harbor Laboratory},
  doi = {10.1101/2021.02.28.433265},
  urldate = {2021-03-07},
  abstract = {{$<$}p{$>$}As contemporary bioinformatic and chemoinformatic capabilities are reshaping natural products research, major benefits could result from an open database of referenced structure-organism pairs. Those pairs allow the identification of distinct molecular structures found as components of heterogeneous chemical matrices originating from living organisms. Current databases with such information suffer from paywall restrictions, limited taxonomic scope, poorly standardized fields, and lack of interoperability. To ensure data quality, references to the work that describes the structure-organism relationship are mandatory. To fill this void, we collected and curated a set of structure-organism pairs from publicly available natural products databases to yield LOTUS (naturaL prOducTs occUrrences databaSe), which contains over 500,000 curated and referenced structure-organism pairs. All the programs developed for data collection, curation, and dissemination are publicly available. To provide unlimited access as well as standardized linking to other resources, LOTUS data is both hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. The diffusion of these referenced structure-organism pairs within the Wikidata framework addresses many of the limitations of currently-available databases and facilitates linkage to existing biological and chemical data resources. This resource represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.{$<$}/p{$>$}},
  chapter = {New Results},
  copyright = {{\copyright} 2021, Posted by Cold Spring Harbor Laboratory. The copyright holder has placed this preprint in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or adapt this material for any purpose without crediting the original authors.},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Rutz et al_2021_Open Natural Products Research_.pdf;/home/user1/Zotero/storage/GLZM74S7/Rutz et al. - 2021 - Open Natural Products Research Curation and Disse.pdf}
}

@article{saha2023,
  title = {Ecological Factors and Parity Mode Correlate with Genome Size Variation in Squamate Reptiles},
  author = {Saha, Anik and Bellucci, Arianna and Fratini, Sara and Cannicci, Stefano and Ciofi, Claudio and Iannucci, Alessio},
  year = {2023},
  month = dec,
  journal = {BMC Ecology and Evolution},
  volume = {23},
  number = {1},
  pages = {69},
  issn = {2730-7182},
  doi = {10.1186/s12862-023-02180-4},
  urldate = {2023-12-16},
  abstract = {Evidence of correlation between genome size, the nuclear haploid DNA content of a cell, environmental factors and life-history traits have been reported in many animal species. Genome size, however, spans over three orders of magnitude across taxa and such a correlation does not seem to follow a universal pattern. In squamate reptiles, the second most species-rich order of vertebrates, there are currently no studies investigating drivers of genome size variability. We run a series of phylogenetic generalized least-squares models on 227 species of squamates to test for possible relationships between genome size and ecological factors including latitudinal distribution, bioclimatic variables and microhabitat use. We also tested whether genome size variation can be associated with parity mode, a highly variable life history trait in this order of reptiles.},
  keywords = {C-value,Ecology,Life history,Lizards,Microhabitat,Oviparity,Reproduction,Snakes,Vertebrates,Viviparity},
  file = {/home/user1/Dropbox/Papers/Saha et al_2023_Ecological factors and parity mode correlate with genome size variation in.pdf}
}

@misc{scharn2021,
  type = {Research-Article},
  title = {Vegetation Responses to 26 Years of Warming at {{Latnjajaure Field Station}}, Northern {{Sweden}}.},
  author = {Scharn, Mr Ruud and Brachmann, Mr Cole G. and Patchett, Ms Aurora and Reese, Dr Heather and Bjorkman, Dr Anne and Alatalo, Dr Juha and Bj{\"o}rk, Dr Robert G. and J{\"a}gerbrand, Dr Annika K. and Molau, Dr Ulf and Bj{\"o}rkman, Dr Mats P.},
  year = {2021},
  month = apr,
  journal = {https://doi.org/10.1139/AS-2020-0042},
  doi = {10.1139/AS-2020-0042},
  urldate = {2021-04-05},
  abstract = {Climate change is rapidly warming high latitude and high elevation regions influencing plant community composition. Changes in vegetation composition have motivated the coordination of ecological m...},
  howpublished = {https://cdnsciencepub.com/doi/full/10.1139/as-2020-0042},
  langid = {english}
}

@article{seep2021,
  title = {Reaction Lumping in Metabolic Networks for Application with Thermodynamic Metabolic Flux Analysis},
  author = {Seep, Lea and {Razaghi-Moghadam}, Zahra and Nikoloski, Zoran},
  year = {2021},
  month = apr,
  journal = {Scientific Reports},
  volume = {11},
  number = {1},
  pages = {8544},
  publisher = {Nature Publishing Group},
  issn = {2045-2322},
  doi = {10.1038/s41598-021-87643-8},
  urldate = {2021-04-23},
  abstract = {Thermodynamic metabolic flux analysis (TMFA) can narrow down the space of steady-state flux distributions, but requires knowledge of the standard Gibbs free energy for the modelled reactions. The latter are often not available due to unknown Gibbs free energy change of formation \$\$, \{{\textbackslash}Delta \}\_\{f\} G{\textasciicircum}\{0\}\$\$, of metabolites. To optimize the usage of data on thermodynamics in constraining a model, reaction lumping has been proposed to eliminate metabolites with unknown \$\$\{{\textbackslash}Delta \}\_\{f\} G{\textasciicircum}\{0\}\$\$. However, the lumping procedure has not been formalized nor implemented for systematic identification of lumped reactions. Here, we propose, implement, and test a combined procedure for reaction lumping, applicable to genome-scale metabolic models. It is based on identification of groups of metabolites with unknown \$\$\{{\textbackslash}Delta \}\_\{f\} G{\textasciicircum}\{0\}\$\$whose elimination can be conducted independently of the others via: (1) group implementation, aiming to eliminate an entire such group, and, if this is infeasible, (2) a sequential implementation to ensure that a maximal number of metabolites with unknown \$\$\{{\textbackslash}Delta \}\_\{f\} G{\textasciicircum}\{0\}\$\$are eliminated. Our comparative analysis with genome-scale metabolic models of Escherichia coli, Bacillus subtilis, and Homo sapiens shows that the combined procedure provides an efficient means for systematic identification of lumped reactions. We also demonstrate that TMFA applied to models with reactions lumped according to the proposed procedure lead to more precise predictions in comparison to the original models. The provided implementation thus ensures the reproducibility of the findings and their application with standard TMFA.},
  copyright = {2021 The Author(s)},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Seep et al_2021_Reaction lumping in metabolic networks for application with thermodynamic_.pdf;/home/user1/Zotero/storage/MZLH7VER/Seep et al. - 2021 - Reaction lumping in metabolic networks for applica.pdf}
}

@mastersthesis{seppala2020,
  title = {Spatial and Temporal Drivers of Soil Respiration in a Tundra Environment},
  author = {Sepp{\"a}l{\"a}, Outi},
  year = {2020},
  address = {FACULTY OF SCIENCE DEPARTMENT OF GEOSCIENCES AND GEOGRAPHY GEOGRAPHY},
  langid = {english},
  school = {UNIVERSITY OF HELSINKI},
  file = {/home/user1/Zotero/storage/UT26ZFW3/Seppälä - Master’s thesis Geography Physical geography.pdf}
}

@article{shah2022,
  title = {Characterizing Temporal Trends of Meteorological Extremes in {{Southern}} and {{Central Ontario}}, {{Canada}}},
  author = {Shah, Lamees and Arnillas, Carlos Alberto and Arhonditsis, George B.},
  year = {2022},
  month = jan,
  journal = {Weather and Climate Extremes},
  pages = {100411},
  issn = {2212-0947},
  doi = {10.1016/j.wace.2022.100411},
  urldate = {2022-01-29},
  abstract = {Forecasts of increased frequency of meteorological extremes have received considerable attention due to their potential impact on the integrity of biotic communities, stability of terrestrial and aquatic environments, availability of ecosystem services, and broader societal prosperity. Canada is projected to experience greater warming rates than many other regions of the world and changes in meteorological extremes are predicted to be variable across the country. In this context, our goal is to evaluate the long-term trends of extreme meteorological variables (air and dew point temperature, relative humidity, wind speed, and precipitation) in southern and central Ontario (from 42{$^\circ$}N to 50{$^\circ$}N), while considering the role dynamics of large-scale atmospheric oscillations (El Ni{\~n}o--Southern Oscillation, North Atlantic Oscillation, Arctic Oscillation, and Pacific Decadal Oscillation). Air temperature minima increased year-round, while temperature maxima mainly increased during the cooler months of the year. Consistent with recent evidence from the literature, our study identified an increase in the amount of atmospheric water since the 1950s, as shown by the rising trends in dew point temperature maxima and minima during winter and mid-summer/early-autumn, respectively. Likewise, we found a weak decline in the relative humidity during the warm season, and a more discernible declining trend during the cooler part of the year, which could be in turn reflective of the moderate change of temperature maxima and rising minima, respectively. Consistent with the broader evidence of a global terrestrial stilling, our analysis showed a declining occurrence of high wind-speed events across the entire study domain, and frequent slow-wind speeds during both warm and cold periods of the year. Interestingly, a closer examination of temporal trends in calm wind frequency provides evidence of a recent reversal in the latter trend with diminishing prevalence of very calm wind conditions. We generally found a weakly increasing temporal trend with maximum total daily precipitation, but without a coherent spatial pattern within the broader study area. Our analysis showed that large-scale phenomena have a discernible signature mostly on air temperature and humidity variables, but had little impact on low relative humidity, high and low wind-speed, and precipitation variability. Given the modest impact of teleconnections on long-term temporal trends, our study concludes that the meteorological extremes are more directly influenced by regional and local heat and humidity balance processes rather than global-scale atmospheric mechanisms. The observed trends of air temperature, humidity, and wind speed extremes suggest a profound impact on the phenology of aquatic and terrestrial ecosystems and human experience of weather.},
  langid = {english},
  keywords = {Bayesian inference,Climate change,Extreme value theory,Meteorological extremes,Teleconnections},
  file = {/home/user1/Zotero/storage/ZYTIATJ5/Shah et al. - 2022 - Characterizing temporal trends of meteorological e.pdf}
}

@misc{simon2023,
  title = {Dancing the {{Nanopore}} Limbo -- {{Nanopore}} Metagenomics from Small {{DNA}} Quantities for Bacterial Genome Reconstruction},
  author = {Simon, Sophie A. and Schmidt, Katharina and Griesdorn, Lea and Soares, Andr{\'e} R. and Bornemann, Till L. V. and Probst, Alexander J.},
  year = {2023},
  month = feb,
  primaryclass = {New Results},
  pages = {2023.02.16.527874},
  publisher = {bioRxiv},
  doi = {10.1101/2023.02.16.527874},
  urldate = {2023-02-20},
  abstract = {Background While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. Here, we evaluated lower-than-recommended DNA quantities for Nanopore library preparation by determining sequencing quality, community composition, assembly quality and recovery of MAGs. Results We generated 27 Nanopore metagenomes using the commercially available ZYMO mock community and varied the amount of input DNA from 1000 ng (the recommended minimum) down to 1 ng in eight steps. The quality of the generated reads remained stable across all input levels. The read mapping accuracy, which reflects how well the reads match a known reference genome, was consistently high across all libraries. The relative abundance of the species in the metagenomes was stable down to input levels of 50 ng. High-quality MAGs ({$>$} 95\% completeness, {$\leq$} 5\% contamination) could be recovered from metagenomes down to 35 ng of input material. When combined with publicly available Illumina reads for the mock community, Nanopore reads from input quantities as low as 1 ng improved the quality of hybrid assemblies. Conclusion Our results show that the recommended DNA amount for Nanopore library preparation can be substantially reduced without any adverse effects to genome recovery and still bolster hybrid assemblies when combined with short-read data. We posit that the results presented herein will enable studies to improve genome recovery from low-biomass environments, enhancing microbiome understanding.},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {{\copyright} 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Simon et al_2023_Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities.pdf}
}

@article{smertina2024,
  title = {First {{Detection}} of {{Benign Rabbit Caliciviruses}} in {{Chile}}},
  author = {Smertina, Elena and Keller, Luca M. and Huang, Nina and {Flores-Benner}, Gabriela and {Correa-Cuadros}, Jennifer Paola and Duclos, Melanie and Jaksic, Fabian M. and Brice{\~n}o, Crist{\'o}bal and Ramirez, Victor Neira and {D{\'i}az-Gacit{\'u}a}, Miguel and {Carrasco-Fern{\'a}ndez}, Sebasti{\'a}n and Smith, Ina L. and Strive, Tanja and Jenckel, Maria},
  year = {2024},
  month = mar,
  journal = {Viruses},
  volume = {16},
  number = {3},
  pages = {439},
  publisher = {Multidisciplinary Digital Publishing Institute},
  issn = {1999-4915},
  doi = {10.3390/v16030439},
  urldate = {2024-03-20},
  abstract = {Pathogenic lagoviruses (Rabbit hemorrhagic disease virus, RHDV) are widely spread across the world and are used in Australia and New Zealand to control populations of feral European rabbits. The spread of the non-pathogenic lagoviruses, e.g., rabbit calicivirus (RCV), is less well studied as the infection results in no clinical signs. Nonetheless, RCV has important implications for the spread of RHDV and rabbit biocontrol as it can provide varying levels of cross-protection against fatal infection with pathogenic lagoviruses. In Chile, where European rabbits are also an introduced species, myxoma virus was used for localised biocontrol of rabbits in the 1950s. To date, there have been no studies investigating the presence of lagoviruses in the Chilean feral rabbit population. In this study, liver and duodenum rabbit samples from central Chile were tested for the presence of lagoviruses and positive samples were subject to whole RNA sequencing and subsequent data analysis. Phylogenetic analysis revealed a novel RCV variant in duodenal samples that likely originated from European RCVs. Sequencing analysis also detected the presence of a rabbit astrovirus in one of the lagovirus-positive samples.},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  langid = {english},
  keywords = {<i>Oryctolagus cuniculus</i>,European rabbit,invasive species,RCV,RHDV,viral pathogens},
  file = {/home/user1/Dropbox/Papers/Smertina et al_2024_First Detection of Benign Rabbit Caliciviruses in Chile.pdf}
}

@article{smith2020,
  title = {Landscape and {{Selection}} of {{Vaccine Epitopes}} in {{SARS-CoV-2}}},
  author = {Smith, Christof C. and Entwistle, Sarah and Willis, Caryn and Vensko, Steven and Beck, Wolfgang and Garness, Jason and Sambade, Maria and Routh, Eric and Olsen, Kelly and Kodysh, Julia and O'Donnell, Timothy and Haber, Carsten and Heiss, Kirsten and Stadler, Volker and Garrison, Erik and Grant, Oliver C. and Woods, Robert J. and Heise, Mark and Vincent, Benjamin G. and Rubinsteyn, Alex},
  year = {2020},
  month = jun,
  journal = {bioRxiv},
  doi = {10.1101/2020.06.04.135004},
  urldate = {2021-03-03},
  abstract = {There is an urgent need for a vaccine with efficacy against SARS-CoV-2. We hypothesize that peptide vaccines containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation would drive both humoral and cellular immunity with high specificity, potentially avoiding undesired effects such as antibody-dependent enhancement (ADE). Additionally, such vaccines can be rapidly manufactured in a distributed manner. In this study, we combine computational prediction of T cell epitopes, recently published B cell epitope mapping studies, and epitope accessibility to select candidate peptide vaccines for SARS-CoV-2. We begin with an exploration of the space of possible T cell epitopes in SARS-CoV-2 with interrogation of predicted HLA-I and HLA-II ligands, overlap between predicted ligands, protein source, as well as concurrent human/murine coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, viral source protein abundance, sequence conservation, coverage of high frequency HLA alleles and co-localization of CD4+ and CD8+ T cell epitopes. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering to select regions with surface accessibility, high sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. From 58 initial candidates, three B cell epitope regions were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we propose a set of SARS-CoV-2 vaccine peptides for use in subsequent murine studies and clinical trials.,},
  pmcid = {PMC7302209},
  pmid = {32577654},
  file = {/home/user1/Dropbox/Papers/Smith et al_2020_Landscape and Selection of Vaccine Epitopes in SARS-CoV-2_.pdf}
}

@article{st-onge2023,
  title = {Functional Connectome Fingerprinting across the Lifespan},
  author = {{St-Onge}, Fr{\'e}d{\'e}ric and Javanray, Mohammadali and Pichet Binette, Alexa and {Strikwerda-Brown}, Cherie and Remz, Jordana and Spreng, R. Nathan and Shafiei, Golia and Misic, Bratislav and {Vachon-Presseau}, {\'E}tienne and Villeneuve, Sylvia},
  year = {2023},
  month = may,
  journal = {Network Neuroscience},
  pages = {1--55},
  issn = {2472-1751},
  doi = {10.1162/netn_a_00320},
  urldate = {2023-05-09},
  abstract = {Systematic changes have been observed in the functional architecture of the human brain with advancing age. However, functional connectivity (FC) is also a powerful feature to detect unique ``connectome fingerprints'', allowing identification of individuals among their peers. Although fingerprinting has been robustly observed in samples of young adults, the reliability of this approach has not been demonstrated across the lifespan. We applied the fingerprinting framework to the Cambridge Centre for Aging and Neuroscience cohort (n = 483 aged 18 to 89 years). We found that individuals are ``fingerprintable'' (i.e., identifiable) across independent functional MRI scans throughout the lifespan. We observed a U-shape distribution in the strength of ``self-identifiability'' (within-individual correlation across modalities), and ``others-identifiability'' (between-individual correlation across modalities), with a decrease from early adulthood into middle-age, before improving in older age. FC edges contributing to self-identifiability were not restricted to specific brain networks and were different between individuals across the lifespan sample. Self-identifiability was additionally associated with regional brain volume. These findings indicate that individual participant-level identification is preserved across the lifespan despite the fact that its components are changing non-linearly.Important inter-individual differences are increasingly identified in functional connectivity studies. However, most of the work to date has focused on samples of younger adults, ignoring older individuals in which brains undergo significant transformation. Here, we examine individual-level patterns of functional connectivity---i.e., connectome fingerprints---across the adult lifespan. Our results suggest that connectome fingerprints can reliably predict individuals from independent brain scans across the lifespan. Additionally, regions contributing to fingerprints differed from person to person, emphasizing the extent of inter-individual differences in the brain. Specific patterns of brain volume, associated with normative age-related atrophy, may impact the identification of individual-specific functional connectivity patterns. Our findings highlight the importance of inter-individual variability in functional connectivity, regardless of participant age, when assessing individual differences in brain function.},
  file = {/home/user1/Dropbox/Papers/St-Onge et al_2023_Functional connectome fingerprinting across the lifespan.pdf}
}

@article{thiede2022,
  title = {Genomic {{Epidemiology Suggests Community Origins}} of {{Healthcare-Associated USA300 MRSA}}},
  author = {Thiede, Stephanie N and Snitkin, Evan S and Trick, William and Payne, Darjai and Aroutcheva, Alla and Weinstein, Robert A and Popovich, Kyle J},
  year = {2022},
  month = feb,
  journal = {The Journal of Infectious Diseases},
  pages = {jiac056},
  issn = {0022-1899},
  doi = {10.1093/infdis/jiac056},
  urldate = {2022-02-26},
  abstract = {Hospital-onset (HO-) MRSA infections have declined over the past decade due to infection control strategies; community-onset (CO-) and healthcare-associated community-onset (HACO-) MRSA, particularly USA300, have declined less. We examined the role of community strains to explain the difference.We performed whole-genome sequencing (WGS) on MRSA clinical isolates from Cook County Health patients during 2011-2014. We defined infections as CO, HO, or HACO epidemiologically. We integrated genomic, community exposure, and statewide hospital discharge data to infer MRSA origin.Among 1020 individuals with available WGS, most were USA300 wound infections (580 CO, 143 HO, 297 HACO). USA300 HO, CO, and HACO infections were intermixed on the USA300 phylogeny consistent with common strains circulating across community and healthcare settings. Community exposures (e.g. substance abuse, incarceration, homelessness) were associated with HACO and HO infections, and genetically-linked individuals from both groups had little overlap in healthcare facilities, supporting community origins. Most repeat infections---over months-to-years---occurred in individuals persistently carrying their own strains. These individuals were more likely to have genetic linkages, suggesting a role of persistent colonization in transmission.Efforts to reduce presumed nosocomial USA300 spread may require understanding and controlling community sources and transmission networks, particularly for repeat infections.}
}

@article{thorn2023,
  title = {Flankophile: A Bioinformatic Pipeline for Prokaryotic Genomic Synteny Analysis},
  shorttitle = {Flankophile},
  author = {Thorn, Alix Vincent and Aarestrup, Frank M. and Munk, Patrick},
  year = {2023},
  month = dec,
  journal = {Microbiol Spectr},
  pages = {e0241323},
  issn = {2165-0497},
  doi = {10.1128/spectrum.02413-23},
  abstract = {The Flankophile pipeline enables the analysis and visualization of flanking regions of prokaryotic sequences of interest on large data sets in one step and in a consistent manner. A specific tool for flanking region analysis with automated visualization has not been developed before, and Flankophile will make flanking region analysis easier and accessible to more people. Flankophile will be especially useful in the field of genomic epidemiology of acquired antimicrobial resistance genes. Here, information from flanking region sequences can be instrumental in rejecting or supporting the possibility of a recent common source of the same resistance gene found in different samples.},
  langid = {english},
  pmid = {38084973},
  keywords = {antibiotics resistance,bioinformatics,epidemiology,genomics,metagenomics,phylogenetic analysis,sequence analysis,software,veterinary microbiology}
}

@article{torres-espin2021,
  title = {Reproducible Analysis of Disease Space via Principal Components Using the Novel {{R}} Package {{syndRomics}}},
  author = {{Torres-Esp{\'i}n}, Abel and Chou, Austin and Huie, J Russell and Kyritsis, Nikos and Upadhyayula, Pavan S and Ferguson, Adam R},
  editor = {Zaidi, Mone and Barton, Matthias},
  year = {2021},
  month = jan,
  journal = {eLife},
  volume = {10},
  pages = {e61812},
  publisher = {eLife Sciences Publications, Ltd},
  issn = {2050-084X},
  doi = {10.7554/eLife.61812},
  urldate = {2021-03-03},
  abstract = {Biomedical data are usually analyzed at the univariate level, focused on a single primary outcome measure to provide insight into systems biology, complex disease states, and precision medicine opportunities. More broadly, these complex biological and disease states can be detected as common factors emerging from the relationships among measured variables using multivariate approaches. `Syndromics' refers to an analytical framework for measuring disease states using principal component analysis and related multivariate statistics as primary tools for extracting underlying disease patterns. A key part of the syndromic workflow is the interpretation, the visualization, and the study of robustness of the main components that characterize the disease space. We present a new software package, syndRomics, an open-source R package with utility for component visualization, interpretation, and stability for syndromic analysis. We document the implementation of syndRomics and illustrate the use of the package in case studies of neurological trauma data.},
  keywords = {disease pattern discovery,multivariate analysis,nonlinear PCA,principal component analysis pca,R package,syndromics},
  file = {/home/user1/Dropbox/Papers/Torres-Espín et al_2021_Reproducible analysis of disease space via principal components using the novel_.pdf}
}

@article{uneno2024,
  title = {Barriers and {{Facilitators}} to the {{Implementation}} of an {{Electronic Patient-Reported Outcome System}} at {{Cancer Hospitals}} in {{Japan}}},
  author = {Uneno, Yu and Fukuyama, Keita and Nishimura, Ayumi and Eguchi, Kana and Kojima, Hideki and Umino, Takeshi and Miyazaki, Kikuko and Negora, Eiju and Minashi, Keiko and Sugiyama, Osamu and Shimazu, Taichi and Muto, Manabu and Matsumoto, Shigemi and Uneno, Yu and Fukuyama, Keita and Nishimura, Ayumi and Eguchi, Kana and Kojima, Hideki and Umino, Takeshi and Miyazaki, Kikuko and Negora, Eiju and Minashi, Keiko and Sugiyama, Osamu and Shimazu, Taichi and Muto, Manabu and Matsumoto, Shigemi},
  year = {2024},
  month = apr,
  journal = {Cureus},
  volume = {16},
  number = {4},
  publisher = {Cureus},
  issn = {2168-8184},
  doi = {10.7759/cureus.58611},
  urldate = {2024-04-23},
  abstract = {Background and objective Implementing electronic patient-reported outcomes (ePROs) in oncology practice has shown substantial clinical benefits. However, it can be challenging in routine practice, warranting strategies to adapt to different clinical contexts. In light of this, this study aimed to describe the implementation process of the ePRO system and elucidate the provider-level implementation barriers and facilitators to a novel ePRO system at cancer hospitals in Japan. Methods We implemented an ePRO system linked to electronic medical records at three cancer hospitals. Fifteen patients with solid cancers at the outpatient oncology unit were asked to regularly complete the Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE™) questionnaire and European Organization for Research and Treatment Core Quality of Life questionnaire (EORTC QLQ C30) by using the smartphone app between October 2021 and June 2022. Thirteen healthcare professionals were interviewed to identify implementation barriers and facilitators to the ePRO system by using the Consolidated Framework for Implementation Research framework. Results The healthcare professionals identified a lack of clinical resources and a culture and system that emphasizes treatment over care as the main barriers; however, the accumulation of successful cases, the leadership of managers, and the growing needs of patients can serve as facilitators to the implementation. Conclusions Our experience implementing an ePRO system in a few Japanese oncology practices revealed comprehensive barriers and facilitators. Further efforts are warranted to develop more successful implementation strategies.},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Uneno et al_2024_Barriers and Facilitators to the Implementation of an Electronic.pdf}
}

@article{wang2023b,
  title = {Comprehensive Analysis of Immune-Related Genes Associated with the Microenvironment of Patients with Unexplained Infertility},
  author = {Wang, Caiyun and Zhao, Xiaodong and Zhang, Haibin and Bing, Zhitong and Wu, Yu and Li, Rui and Yang, Yongxiu and Yang, Kehu},
  year = {2023},
  month = jan,
  journal = {Annals of Translational Medicine},
  volume = {11},
  number = {2},
  pages = {84--84},
  publisher = {AME Publishing Company},
  issn = {2305-5847, 2305-5839},
  doi = {10.21037/atm-22-5810},
  urldate = {2023-02-12},
  abstract = {Comprehensive analysis of immune-related genes associated with the microenvironment of patients with unexplained infertility},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Wang et al_2023_Comprehensive analysis of immune-related genes associated with the.pdf}
}

@article{weidenauer2021,
  title = {Phosphorylation in the {{Charged Linker Modulates Interactions}} and {{Secretion}} of {{Hsp90$\beta$}}},
  author = {Weidenauer, Lorenz and Quadroni, Manfredo},
  year = {2021},
  month = jul,
  journal = {Cells},
  volume = {10},
  number = {7},
  pages = {1701},
  publisher = {Multidisciplinary Digital Publishing Institute},
  doi = {10.3390/cells10071701},
  urldate = {2021-07-08},
  abstract = {Hsp90{$\beta$} is a major chaperone involved in numerous cellular processes. Hundreds of client proteins depend on Hsp90{$\beta$} for proper folding and/or activity. Regulation of Hsp90{$\beta$} is critical to coordinate its tasks and is mediated by several post-translational modifications. Here, we focus on two phosphorylation sites located in the charged linker region of human Hsp90{$\beta$}, Ser226 and Ser255, which have been frequently reported but whose function remains unclear. Targeted measurements by mass spectrometry indicated that intracellular Hsp90{$\beta$} is highly phosphorylated on both sites (\&gt;90\%). The level of phosphorylation was unaffected by various stresses (e.g., heat shock, inhibition with drugs) that impact Hsp90{$\beta$} activity. Mutating the two serines to alanines increased the amount of proteins interacting with Hsp90{$\beta$} globally and increased the sensitivity to tryptic cleavage in the C-terminal domain. Further investigation revealed that phosphorylation on Ser255 and to a lesser extent on Ser226 is decreased in the conditioned medium of cultured K562 cells, and that a non-phosphorylatable double alanine mutant was secreted more efficiently than the wild type. Overall, our results show that phosphorylation events in the charged linker regulate both the interactions of Hsp90{$\beta$} and its secretion, through changes in the conformation of the chaperone.},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  langid = {english},
  keywords = {chaperone,charged linker,heat shock protein 90,interactome,phosphorylation,proteomics},
  file = {/home/user1/Dropbox/Papers/Weidenauer et al_2021_Phosphorylation in the Charged Linker Modulates Interactions and Secretion of_.pdf}
}

@article{wendisch2021,
  title = {{{SARS-CoV-2}} Infection Triggers Profibrotic Macrophage Responses and Lung Fibrosis},
  author = {Wendisch, Daniel and Dietrich, Oliver and Mari, Tommaso and {von Stillfried}, Saskia and Ibarra, Ignacio L. and Mittermaier, Mirja and Mache, Christin and Chua, Robert Lorenz and Knoll, Rainer and Timm, Sara and Brumhard, Sophia and Krammer, Tobias and Zauber, Henrik and Hiller, Anna Luisa and {Pascual-Reguant}, Anna and Mothes, Ronja and B{\"u}low, Roman David and Schulze, Jessica and Leipold, Alexander M. and Djudjaj, Sonja and Erhard, Florian and Geffers, Robert and Pott, Fabian and Kazmierski, Julia and Radke, Josefine and Pergantis, Panagiotis and Ba{\ss}ler, Kevin and Conrad, Claudia and Aschenbrenner, Anna C. and Sawitzki, Birgit and Landthaler, Markus and Wyler, Emanuel and Horst, David and Hippenstiel, Stefan and Hocke, Andreas and Heppner, Frank L. and Uhrig, Alexander and Garcia, Carmen and Machleidt, Felix and Herold, Susanne and Elezkurtaj, Sefer and Thibeault, Charlotte and Witzenrath, Martin and Cochain, Cl{\'e}ment and Suttorp, Norbert and Drosten, Christian and Goffinet, Christine and Kurth, Florian and Schultze, Joachim L. and Radbruch, Helena and Ochs, Matthias and Eils, Roland and {M{\"u}ller-Redetzky}, Holger and Hauser, Anja E. and Luecken, Malte D. and Theis, Fabian J. and Conrad, Christian and Wolff, Thorsten and Boor, Peter and Selbach, Matthias and Saliba, Antoine-Emmanuel and Sander, Leif Erik},
  year = {2021},
  month = nov,
  journal = {Cell},
  issn = {0092-8674},
  doi = {10.1016/j.cell.2021.11.033},
  urldate = {2021-12-11},
  abstract = {COVID-19-induced `acute respiratory distress syndrome' (ARDS) is associated with prolonged respiratory failure and high mortality, but the mechanistic basis of lung injury remains incompletely understood. Here, we analyzed pulmonary immune responses and lung pathology in two cohorts of patients with COVID-19 ARDS using functional single cell genomics, immunohistology and electron microscopy. We describe an accumulation of CD163-expressing monocyte-derived macrophages that acquired a profibrotic transcriptional phenotype during COVID-19 ARDS. Gene set enrichment and computational data integration revealed a significant similarity between COVID-19-associated macrophages and profibrotic macrophage populations identified in idiopathic pulmonary fibrosis. COVID-19 ARDS was associated with clinical, radiographic, histopathological, and ultrastructural hallmarks of pulmonary fibrosis. Exposure of human monocytes to SARS-CoV-2, but not Influenza A virus or viral RNA analogs, was sufficient to induce a similar profibrotic phenotype in vitro. In conclusion, we demonstrate that SARS-CoV-2 triggers profibrotic macrophage responses and pronounced fibroproliferative ARDS.},
  langid = {english}
}

@article{woyda2023,
  title = {Chicken {{Production}} and {{Human Clinical Escherichia}} Coli {{Isolates Differ}} in {{Their Carriage}} of {{Antimicrobial Resistance}} and {{Virulence Factors}}},
  author = {Woyda, Reed and Oladeinde, Adelumola and Abdo, Zaid},
  year = {2023},
  month = jan,
  journal = {Applied and Environmental Microbiology},
  volume = {0},
  number = {0},
  pages = {e01167-22},
  publisher = {American Society for Microbiology},
  doi = {10.1128/aem.01167-22},
  urldate = {2023-01-25},
  abstract = {Contamination of food animal products by Escherichia coli is a leading cause of foodborne disease outbreaks, hospitalizations, and deaths in humans. Chicken is the most consumed meat both in the United States and across the globe according to the U.S. Department of Agriculture. Although E. coli is a ubiquitous commensal bacterium of the guts of humans and animals, its ability to acquire antimicrobial resistance (AMR) genes and virulence factors (VFs) can lead to the emergence of pathogenic strains that are resistant to critically important antibiotics. Thus, it is important to identify the genetic factors that contribute to the virulence and AMR of E. coli. In this study, we performed in-depth genomic evaluation of AMR genes and VFs of E. coli genomes available through the National Antimicrobial Resistance Monitoring System GenomeTrackr database. Our objective was to determine the genetic relatedness of chicken production isolates and human clinical isolates. To achieve this aim, we first developed a massively parallel analytical pipeline (Reads2Resistome) to accurately characterize the resistome of each E. coli genome, including the AMR genes and VFs harbored. We used random forests and hierarchical clustering to show that AMR genes and VFs are sufficient to classify isolates into different pathogenic phylogroups and host origin. We found that the presence of key type III secretion system and AMR genes differentiated human clinical isolates from chicken production isolates. These results further improve our understanding of the interconnected role AMR genes and VFs play in shaping the evolution of pathogenic E. coli strains. IMPORTANCE Pathogenic Escherichia coli causes disease in both humans and food-producing animals. E. coli pathogenesis is dependent on a repertoire of virulence factors and antimicrobial resistance genes. Food-borne outbreaks are highly associated with the consumption of undercooked and contaminated food products. This association highlights the need to understand the genetic factors that make E. coli virulent and pathogenic in humans and poultry. This research shows that E. coli isolates originating from human clinical settings and chicken production harbor different antimicrobial resistance genes and virulence factors that can be used to classify them into phylogroups and host origins. In addition, to aid in the repeatability and reproducibility of the results presented in this study, we have made a public repository of the Reads2Resistome pipeline and have provided the accession numbers associated with the E. coli genomes analyzed.}
}

@article{wright2021,
  title = {Food or Just a Free Ride? {{A}} Meta-Analysis Reveals the Global Diversity of the {{Plastisphere}}},
  shorttitle = {Food or Just a Free Ride?},
  author = {Wright, Robyn J. and Langille, Morgan G. I. and Walker, Tony R.},
  year = {2021},
  month = mar,
  journal = {The ISME Journal},
  volume = {15},
  number = {3},
  pages = {789--806},
  publisher = {Nature Publishing Group},
  issn = {1751-7370},
  doi = {10.1038/s41396-020-00814-9},
  urldate = {2021-03-03},
  abstract = {It is now indisputable that plastics are ubiquitous and problematic in ecosystems globally. Many suggestions have been made about the role that biofilms colonizing plastics in the environment---termed the ``Plastisphere''---may play in the transportation and ecological impact of these plastics. By collecting and re-analyzing all raw 16S rRNA gene sequencing and metadata from 2,229 samples within 35 studies, we have performed the first meta-analysis of the Plastisphere in marine, freshwater, other aquatic (e.g., brackish or aquaculture) and terrestrial environments. We show that random forest models can be trained to differentiate between groupings of environmental factors as well as aspects of study design, but---crucially---also between plastics when compared with control biofilms and between different plastic types and community successional stages. Our meta-analysis confirms that potentially biodegrading Plastisphere members, the hydrocarbonoclastic Oceanospirillales and Alteromonadales are consistently more abundant in plastic than control biofilm samples across multiple studies and environments. This indicates the predilection of these organisms for plastics and confirms the urgent need for their ability to biodegrade plastics to be comprehensively tested. We also identified key knowledge gaps that should be addressed by future studies.},
  copyright = {2020 The Author(s)},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Wright et al_2021_Food or just a free ride_.pdf}
}

@article{wu,
  title = {Disentangling Ecological Drivers of Interspecific Achromatic Plumage Variation in Birds},
  author = {Wu, Su and Zhang, Kai and Wang, Bin and Que, Pinjia and Yang, Biao and Xu, Yu},
  journal = {Global Ecology and Biogeography},
  volume = {n/a},
  number = {n/a},
  pages = {e13892},
  issn = {1466-8238},
  doi = {10.1111/geb.13892},
  urldate = {2024-07-18},
  abstract = {Aim Understanding the ecological determinants of interspecific achromatic (light-to-dark) plumage variation in birds is crucial yet challenging due to the complex interplay of climatic, habitat-related, and morphological influences. This study aimed to disentangle the effects of temperature, precipitation, habitat openness, body mass and hand-wing index (HWI, a widely used single-parameter proxy for the extent to which a species relies on flight) on shaping achromatic plumage variation among bird species. Location Global. Time Period Contemporary. Major Taxa Studied Birds. Methods Based on data from over 8000 sessile bird species globally, we employed phylogenetic linear regressions to account for achromatic plumage colour in relation to temperature, precipitation, habitat openness, body mass and HWI, while correcting for phylogenetic non-independence between species. Furthermore, we conducted phylogenetic path analyses to decompose direct from indirect effects. Results We found that temperature, precipitation, habitat openness and body mass exerted separate but interactive effects on the variation in achromatic colour across species. Species inhabiting cold, wet or densely vegetated environments were darker coloured, while smaller species were lighter. Darker plumage was more strongly related to higher precipitation in colder regions for nocturnal species. For diurnal species, darker plumage was more closely associated with higher precipitation in more open habitats, whereas lighter plumage was more linked to lower mass in denser habitats. Noteworthy was the identification of a substantial correlation between achromatic colour and HWI. Diurnal species that are more aerial were lighter. Conversely, nocturnal flyers, especially females, tended to be darker. Main Conclusions The findings highlight the multifaceted nature of plumage coloration evolution, with adaptations for thermal efficiency, crypsis, signalling, waterproofing or protection against bacteria. However, the variable relative importance of these factors among groups emphasizes the significance of each factor in different contexts.},
  copyright = {{\copyright} 2024 John Wiley \& Sons Ltd.},
  langid = {english},
  keywords = {achromatic colour,climate,complex interplay,habitat,interspecific variation,morphology,phylogenetic comparative analysis,plumage}
}

@article{wu2023,
  title = {Network {{Pharmacology Study}} of {{Bioactive Components}} and {{Molecular Mechanisms}} of the {{Glycoside Fraction}} from {$<$}em{$>$}{{Picrorhiza}} Scrophulariiflora{$<$}/Em{$>$} {{Against Experimental Colitis}}},
  author = {Wu, Peigen and Chang, Churui and Zhu, Guanglin and Zhai, Lixiang and Zhang, Xu and Huan, Qiuchan and Gao, Zhengxian and Deng, Huan and Liang, Yue and Xiao, Haitao},
  year = {2023},
  month = may,
  journal = {DDDT},
  volume = {17},
  pages = {1531--1546},
  publisher = {Dove Press},
  doi = {10.2147/DDDT.S407339},
  urldate = {2023-05-28},
  abstract = {Exploring the potential mechanism of glycosidic fraction of Picrorhiza scrophulariiflora Pennell extract for the treatment of colitis},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Wu et al_2023_Network Pharmacology Study of Bioactive Components and Molecular Mechanisms of.pdf}
}

@article{wyenberg-henzler2022,
  title = {Ontogenetic Dietary Shifts in {{North American}} Hadrosaurids},
  author = {{Wyenberg-Henzler}, Taia and Patterson, R. Timothy and Mallon, Jordan C.},
  year = {2022},
  month = feb,
  journal = {Cretaceous Research},
  pages = {105177},
  issn = {0195-6671},
  doi = {10.1016/j.cretres.2022.105177},
  urldate = {2022-02-26},
  abstract = {Ontogenetic niche shifts, the phenomenon whereby animals change their resource use with growth, were probably widespread in dinosaurs, but most studies of duck-billed dinosaur ontogeny have so far focused mainly on the development of the cranial ornamentation. Here, we quantify allometry of 13 ecomorphological variables of the skull and examine tooth microwear in a sample of North American hadrosaurids to better understand their ecological functioning with growth. Our results indicate that, consistent with the Jarman-Bell principle relating body size to fibre intake and feeding selectivity, juvenile hadrosaurids were relatively more selective than their adult counterparts and subsisted on softer, low-growing browse cropped using lateral rotations of the neck. Chewing movements of the jaw probably did not differ greatly between growth stages. Our findings invite further investigation relating to cranial ontogenetic allometry in hadrosauromorphs more broadly, and to the possible role of ontogenetic niche shifts in the size structuring of Late Cretaceous herbivore communities.},
  langid = {english},
  keywords = {allometry,dental microwear,diet,Hadrosauridae,Late Cretaceous,ontogenetic niche shift,ontogeny}
}

@article{xie2022,
  title = {Cuproptosis-{{Related MiR-21-5p}}/{{FDX1 Axis}} in {{Clear Cell Renal Cell Carcinoma}} and {{Its Potential Impact}} on {{Tumor Microenvironment}}},
  author = {Xie, Mingyue and Cheng, Bo and Yu, Shuang and He, Yajie and Cao, Yu and Zhou, Tiejun and Han, Kun and Dai, Rongyang and Wang, Ronghao},
  year = {2022},
  month = dec,
  journal = {Cells},
  volume = {12},
  number = {1},
  pages = {173},
  issn = {2073-4409},
  doi = {10.3390/cells12010173},
  abstract = {As a newly identified type of programmed cell death, cuproptosis may have an impact on cancer development, including clear cell renal cell carcinoma (ccRCC). Herein, we first noticed that the expression levels of cuproptosis regulators exhibited a tight correlation with the clinicopathological characteristics of ccRCC. The cuproptosis-sensitive sub-type (CSS), classified via consensus clustering analysis, harbored a higher overall survival rate compared to the cuproptosis-resistant sub-type (CRS), which may have resulted from the differential infiltration of immune cells. FDX1, the cuproptosis master regulator, was experimentally determined as a tumor suppressor in ccRCC cells by suppressing the cell growth and cell invasion of ACHN and OSRC-2 cells in a cuproptosis-dependent and -independent manner. The results from IHC staining also demonstrated that FDX1 expression was negatively correlated with ccRCC tumor initiation and progression. Furthermore, we identified the miR-21-5p/FDX1 axis in ccRCC and experimentally verified that miR-21-5p directly binds the 3'-UTR of FDX1 to mediate its degradation. Consequently, a miR-21-5p inhibitor suppressed the cell growth and cell invasion of ACHN and OSRC-2 cells, which could be compensated by FDX1 knockdown, reinforcing the functional linkage between miR-21-5p and FDX1 in ccRCC. Finally, we evaluated the ccRCC tumor microenvironment under the miR-21-5p/FDX1 axis and noted that this axis was strongly associated with the infiltration of immune cells such as CD4+ T cells, Treg cells, and macrophages, suggesting that this signaling axis may alter microenvironmental components to drive ccRCC progression. Overall, this study constructed the miR-21-5p/FDX1 axis in ccRCC and analyzed its potential impact on the tumor microenvironment, providing valuable insights to improve current ccRCC management.},
  langid = {english},
  pmcid = {PMC9818076},
  pmid = {36611966},
  keywords = {3' Untranslated Regions,Apoptosis,Carcinoma Renal Cell,Cell Proliferation,Copper,cuproptosis,FDX1,Humans,Kidney Neoplasms,microenvironment,MicroRNAs,miR-21-5p,renal cell carcinoma,Tumor Microenvironment},
  file = {/home/user1/Dropbox/Papers/Xie et al_2022_Cuproptosis-Related MiR-21-5p-FDX1 Axis in Clear Cell Renal Cell Carcinoma and.pdf;/home/user1/Zotero/storage/8QKZ4TSW/Xie et al. - 2023 - Cuproptosis-Related MiR-21-5pFDX1 Axis in Clear C.pdf}
}

@article{xie2023,
  title = {Comprehensive Spatiotemporal Mapping of Single-Cell Lineages in Developing Mouse Brain by {{CRISPR-based}} Barcoding},
  author = {Xie, Lianshun and Liu, Hengxin and You, Zhiwen and Wang, Luyue and Li, Yiwen and Zhang, Xinyue and Ji, Xiaoshan and He, Hui and Yuan, Tingli and Zheng, Wenping and Wu, Ziyan and Xiong, Man and Wei, Wu and Chen, Yuejun},
  year = {2023},
  month = jul,
  journal = {Nat Methods},
  pages = {1--12},
  publisher = {Nature Publishing Group},
  issn = {1548-7105},
  doi = {10.1038/s41592-023-01947-3},
  urldate = {2023-07-24},
  abstract = {A fundamental interest in developmental neuroscience lies in the ability to map the complete single-cell lineages within the brain. To this end, we developed a CRISPR editing-based lineage-specific tracing (CREST) method for clonal tracing in Cre mice. We then used two complementary strategies based on CREST to map single-cell lineages in developing mouse ventral midbrain (vMB). By applying snapshotting CREST (snapCREST), we constructed a spatiotemporal lineage landscape of developing vMB and identified six progenitor archetypes that could represent the principal clonal fates of individual vMB progenitors and three distinct clonal lineages in the floor plate that specified glutamatergic, dopaminergic or both neurons. We further created pandaCREST (progenitor and derivative associating CREST) to associate the transcriptomes of progenitor cells in vivo with their differentiation potentials. We identified multiple origins of dopaminergic neurons and demonstrated that a transcriptome-defined progenitor type comprises heterogeneous progenitors, each with distinct clonal fates and molecular signatures. Therefore, the CREST method and strategies allow comprehensive single-cell lineage analysis that could offer new insights into the molecular programs underlying neural specification.},
  copyright = {2023 The Author(s), under exclusive licence to Springer Nature America, Inc.},
  langid = {english},
  keywords = {Development of the nervous system,Genetic models,Neurogenesis,RNA sequencing}
}

@article{xu2023,
  title = {Ecological Predictors of Interspecific Variation in Bird Bill and Leg Lengths on a Global Scale},
  author = {Xu, Yu and Price, Megan and Que, Pinjia and Zhang, Kai and Sheng, Shang and He, Xingcheng and Wen, Zhixin and Wang, Bin},
  year = {2023},
  month = jul,
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  volume = {290},
  number = {2003},
  pages = {20231387},
  publisher = {Royal Society},
  doi = {10.1098/rspb.2023.1387},
  urldate = {2023-07-30},
  abstract = {Bills and legs are two vital appendages for birds, and they exhibit huge interspecific variation in form and function, yet no study has examined the global predictors of this variation. This study examined global gradients in the relative lengths of bird bills and tarsi (i.e. exposed leg parts) to body size across non-migratory birds, while accounting for phylogeny. We found that relative bill length and tarsus length were related to diet, habitat density, latitude, annual mean temperature, temperature variability and hand--wing index (HWI), a proxy for birds' flight efficiency. Among these factors, diet played a primary role in predicting bill length, with nectar-feeding pollinators, vertivores, invertivores and omnivores having longer bills; HWI emerged as the predominant predictor of tarsus length, wherein species with higher HWI had shorter tarsi. However, the effects of these factors differed between passerines and non-passerines, with some temperature-related effects exhibiting opposite trends between these two groups. Our findings highlight the compromise in adaptations for feeding, thermoregulation and flight performance between the two distinct appendages.},
  keywords = {appendage,diet,flight performance,interspecific variation,morphology,thermoregulation}
}

@article{yan2020,
  title = {Virome {{Sequencing}} of the {{Human Intestinal Mucosal}}--{{Luminal Interface}}},
  author = {Yan, Austin and Butcher, James and Mack, David and Stintzi, Alain},
  year = {2020},
  month = oct,
  journal = {Front Cell Infect Microbiol},
  volume = {10},
  issn = {2235-2988},
  doi = {10.3389/fcimb.2020.582187},
  urldate = {2021-03-03},
  abstract = {While the human gut virome has been increasingly explored in recent years, nearly all studies have been limited to fecal sampling. The mucosal--luminal interface has been established as a viable sample type for profiling the microbial biogeography of the gastrointestinal tract. We have developed a protocol to extract nucleic acids from viruses at the mucosal--luminal interface of the proximal and distal colon. Colonic viromes from pediatric patients with Crohn's disease demonstrated high interpatient diversity and low but significant intrapatient variation between sites. Whole metagenomics was also performed to explore virome--bacteriome interactions and to compare the viral communities observed in virome and whole metagenomic sequencing. A site-specific study of the human gut virome is a necessary step to advance our understanding of virome--bacteriome--host interactions in human diseases.},
  pmcid = {PMC7642909},
  pmid = {33194818},
  file = {/home/user1/Dropbox/Papers/Yan et al_2020_Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface_.pdf}
}

@article{zannini2021,
  title = {Sacred Natural Sites and Biodiversity Conservation: A Systematic Review},
  shorttitle = {Sacred Natural Sites and Biodiversity Conservation},
  author = {Zannini, Piero and Frascaroli, Fabrizio and Nascimbene, Juri and Persico, Angela and Halley, John Maxwell and Stara, Kalliopi and Midolo, Gabriele and Chiarucci, Alessandro},
  year = {2021},
  month = sep,
  journal = {Biodivers Conserv},
  issn = {1572-9710},
  doi = {10.1007/s10531-021-02296-3},
  urldate = {2021-10-04},
  abstract = {Sacred natural sites (SNS) have gained recognition from conservationists, and are regarded as the oldest form of habitat protection in human history. Many case studies and literature reviews have been published on the subject. However, an updated and global-level synthesis on the effect of SNS on biodiversity conservation is still lacking. Here, we provide the first systematic review on SNS and biodiversity conservation, aiming to evaluate the effect of SNS across different: (i) continents; (ii) taxa; (iii) metrics. We checked 2750 papers and by applying inclusion criteria we selected 27 relevant papers. From these, we extracted descriptive data and 131 comparisons between SNS and Reference Sites. We applied vote-counting, multinomial and binomial post-hoc tests to the 131 comparisons. We found strong evidence that SNS have a positive effect on biodiversity, but also strong geographical and taxonomical biases, with most research focusing on Asia and Africa and on plants. We found that SNS have mainly positive effects on taxonomical diversity, vegetation structure and cultural uses of biodiversity. Our results strongly support the view that SNS have positive effects on biodiversity across continents and geographical settings, as found in a number of local studies and earlier overviews. These effects should be given official recognition in appropriate conservation frameworks, together with the specific forms of governance and management that characterize SNS. At the same time, further efforts are also required to fill the geographical and taxonomical gaps here highlighted, and to advancing our knowledge of SNS through more systematic research.},
  langid = {english},
  file = {/home/user1/Dropbox/Papers/Zannini et al_2021_Sacred natural sites and biodiversity conservation_.pdf}
}

@article{zhang2022,
  title = {Characterization of Resistance to Newer Antimicrobials among Carbapenem-Resistant {{Klebsiella}} Pneumoniae in the Post--Acute-Care Setting},
  author = {Zhang, Helen L. and Gontjes, Kyle J. and Han, Jennifer H. and Alby, Kevin and Lapp, Zena and Snitkin, Evan and Goldstein, Ellie J. C. and Muldoon, Sean and Tolomeo, Pam and Lautenbach, Ebbing},
  year = {2022},
  month = jul,
  journal = {Infection Control \& Hospital Epidemiology},
  pages = {1--4},
  publisher = {Cambridge University Press},
  issn = {0899-823X, 1559-6834},
  doi = {10.1017/ice.2022.185},
  urldate = {2022-08-01},
  abstract = {We assessed susceptibility patterns to newer antimicrobial agents among clinical carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates from patients in long-term acute-care hospitals (LTACHs) from 2014 to 2015. Meropenem-vaborbactam and imipenem-relebactam nonsusceptibility were observed among 9.9\% and 9.1\% of isolates, respectively. Nonsusceptibility to ceftazidime-avibactam (1.1\%) and plazomicin (0.8\%) were uncommon.},
  langid = {english}
}

@article{zhang2023,
  title = {Network Pharmacology and Bioinformatics to Identify Molecular Mechanisms and Therapeutic Targets of {{Ruyi Jinhuang Powder}} in the Treatment of Monkeypox},
  author = {Zhang, Xi and Yu, Xinping and Yu, Zhichao and Fan, Chengcheng and Li, Yueming and Li, Huan and Shen, Yingkai and Sun, Zijin and Zhang, Shuo},
  year = {2023},
  month = apr,
  journal = {Medicine},
  volume = {102},
  number = {17},
  pages = {e33576},
  doi = {10.1097/MD.0000000000033576},
  urldate = {2023-05-02},
  abstract = {Monkeypox outbreaks across the globe has aroused widespread concern. Ruyi Jinhuang Powder (RJP), a common formula in Chinese medicine, is used to treat pox-like illnesses. This study aimed to identify the molecular mechanisms and therapeutic targets of RJP for the treatment of monkeypox using network pharmacology and bioinformatics techniques. The bioactive substances and potential targets of each component of RJP were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The differentially expressed genes (DEGs) of the monkeypox virus (MPXV) were identified from the GSE24125 by GEO2R. Key signaling pathways, bioactive components, and potential targets were obtained by bioinformatics analysis, including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), disease ontology (DO), and protein-protein interactions (PPI) analyses. Finally, molecular docking was used to predict the interaction between active compounds and core targets. A total of 158 active ingredients and 17 drug-disease-shared targets of RJP were screened. Bioinformatics indicated that wogonin and quercetin might be potential drug candidates. Potential therapeutic targets were identified. Immune-related mechanisms that exerted antiviral effects included signaling pathways like TNF, age-rage, and c-type lectin receptor pathways. Our results illustrated the good therapeutic effect of RJP on monkeypox in terms of biological activity, potential targets, and molecular mechanism. This also offered a promising strategy to reveal the scientific basis and therapeutic mechanism of herbal formulas used to treat the disease.},
  langid = {american}
}

@article{zhu2023,
  title = {Correlated Evolution of Social Organization and Lifespan in Mammals},
  author = {Zhu, Pingfen and Liu, Weiqiang and Zhang, Xiaoxiao and Li, Meng and Liu, Gaoming and Yu, Yang and Li, Zihao and Li, Xuanjing and Du, Juan and Wang, Xiao and Grueter, Cyril C. and Li, Ming and Zhou, Xuming},
  year = {2023},
  month = jan,
  journal = {Nat Commun},
  volume = {14},
  number = {1},
  pages = {372},
  publisher = {Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/s41467-023-35869-7},
  urldate = {2023-02-04},
  abstract = {Discerning the relationship between sociality and longevity would permit a deeper understanding of how animal life history evolved. Here, we perform a phylogenetic comparative analysis of {\textasciitilde}1000 mammalian species on three states of social organization (solitary, pair-living, and group-living) and longevity. We show that group-living species generally live longer than solitary species, and that the transition rate from a short-lived state to a long-lived state is higher in group-living than non-group-living species, altogether supporting the correlated evolution of social organization and longevity. The comparative brain transcriptomes of 94 mammalian species identify 31 genes, hormones and immunity-related pathways broadly involved in the association between social organization and longevity. Further selection features reveal twenty overlapping pathways under selection for both social organization and longevity. These results underscore a molecular basis for the influence of the social organization on longevity.},
  copyright = {2023 The Author(s)},
  langid = {english},
  keywords = {Ageing,Gene expression,Social behaviour,Social evolution,Transcriptomics},
  file = {/home/user1/Dropbox/Papers/Zhu et al_2023_Correlated evolution of social organization and lifespan in mammals.pdf}
}

@misc{zotero-226,
  title = {Using {{Stochastic Point Pattern Analysis}} to {{Track Regional Orientations}} of {{Magmatism During}} the {{Transition}} to {{Cenozoic Extension}} and {{Rio Grande Rifting}}, {{Southern Rocky Mountains}} - {{Rosera}} - 2024 - {{Tectonics}} - {{Wiley Online Library}}},
  urldate = {2024-02-12},
  howpublished = {https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2023TC007902}
}

@misc{zotero-287,
  title = {Application of {{Rapid Diagnostics}} and {{Next-Generation Amplicon Sequencing}} to {{Address Product Quality}} in the {{Food Industry}} - {{ProQuest}}},
  urldate = {2023-06-28},
  abstract = {Explore millions of resources from scholarly journals, books, newspapers, videos and more, on the ProQuest Platform.},
  howpublished = {https://www.proquest.com/openview/3238c502f2c2d6c8bef42493c35d6a47/1?pq-origsite=gscholar\&cbl=18750\&diss=y},
  langid = {english}
}

@misc{zotero-406,
  title = {Rifaximin Prophylaxis Causes Resistance to the Last-Resort Antibiotic Daptomycin {\textbar} {{medRxiv}}},
  urldate = {2023-03-10},
  howpublished = {https://www.medrxiv.org/content/10.1101/2023.03.01.23286614v1}
}

@misc{zotero-454,
  title = {Nutrigonometry {{II}}: {{Experimental}} Strategies to Maximize Nutritional Information in Multidimensional Performance Landscapes - {{Morimoto}} - 2022 - {{Ecology}} and {{Evolution}} - {{Wiley Online Library}}},
  urldate = {2022-08-08},
  howpublished = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.9174}
}