Skip to content

Commit

Permalink
Merge pull request #60 from khanlab/update_publications
Browse files Browse the repository at this point in the history
[MAINT] Update publications spreadsheet
  • Loading branch information
kaitj authored Nov 1, 2023
2 parents 9b89129 + 2f7d99b commit 18254b7
Show file tree
Hide file tree
Showing 2 changed files with 101 additions and 76 deletions.
2 changes: 2 additions & 0 deletions _data/publications/publications.csv
Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
pmid,pmcid,doi,title,authors,year,month,day,journal,volume,issue,pages
37864501,,10.1111/jnc.15990,Focal acetylcholinergic modulation of the human midcingulo-insular network during attention: Meta-analytic neuroimaging and behavioral evidence,"['Chakraborty S', 'Lee SK', 'Arnold SM', 'Haast RAM', 'Khan AR', 'Schmitz TW']",2023,10,21,J Neurochem,,,
37663773,PMC10474320,10.1016/j.dib.2023.109513,A population-averaged structural connectomic brain atlas dataset from 422 HCP-aging subjects,"['Xiao Y', 'Gilmore G', 'Kai J', 'Lau JC', 'Peters T', 'Khan AR']",2023,10,1,Data Brief,50,,109513
37797434,PMC10568416,10.1016/j.nicl.2023.103519,Subregional analysis of striatum iron in Parkinson's disease and rapid eye movement sleep behaviour disorder,"['Alushaj E', 'Hemachandra D', 'Kuurstra A', 'Menon RS', 'Ganjavi H', 'Sharma M', 'Kashgari A', 'Barr J', 'Reisman W', 'Khan AR', 'MacDonald PA']",2023,9,28,Neuroimage Clin,40,,103519
37615057,,10.1002/hbm.26461,Mapping the macrostructure and microstructure of the in vivo human hippocampus using diffusion MRI,"['Karat BG', 'DeKraker J', 'Hussain U', 'Kohler S', 'Khan AR']",2023,8,24,Hum Brain Mapp,,,
37438367,PMC10338502,10.1038/s41597-023-02330-9,Magnetic resonance imaging datasets with anatomical fiducials for quality control and registration,"['Taha A', 'Gilmore G', 'Abbass M', 'Kai J', 'Kuehn T', 'Demarco J', 'Gupta G', 'Zajner C', 'Cao D', 'Chevalier R', 'Ahmed A', 'Hadi A', 'Karat BG', 'Stanley OW', 'Park PJ', 'Ferko KM', 'Hemachandra D', 'Vassallo R', 'Jach M', 'Thurairajah A', 'Wong S', 'Tenorio MC', 'Ogunsanya F', 'Khan AR', 'Lau JC']",2023,7,12,Sci Data,10,1.0,449
37024500,PMC10079825,10.1038/s41597-023-01946-1,Data and Tools Integration in the Canadian Open Neuroscience Platform,"['Poline JB', 'Das S', 'Glatard T', 'Madjar C', 'Dickie EW', 'Lecours X', 'Beaudry T', 'Beck N', 'Behan B', 'Brown ST', 'Bujold D', 'Beauvais M', 'Caron B', 'Czech C', 'Dharsee M', 'Dugre M', 'Evans K', 'Gee T', 'Ippoliti G', 'Kiar G', 'Knoppers BM', 'Kuehn T', 'Le D', 'Lo D', 'Mazaheri M', 'MacFarlane D', 'Muja N', ""O'Brien EA"", ""O'Callaghan L"", 'Paiva S', 'Park P', 'Quesnel D', 'Rabelais H', 'Rioux P', 'Legault M', 'Tremblay-Mercier J', 'Rotenberg D', 'Stone J', 'Strauss T', 'Zaytseva K', 'Zhou J', 'Duchesne S', 'Khan AR', 'Hill S', 'Evans AC']",2023,4,6,Sci Data,10,1.0,189
Expand Down
175 changes: 99 additions & 76 deletions get_publications.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,10 @@
"id": "74557173",
"metadata": {
"papermill": {
"duration": 0.002789,
"end_time": "2023-10-01T05:10:29.097839",
"duration": 0.003281,
"end_time": "2023-11-01T05:11:05.050395",
"exception": false,
"start_time": "2023-10-01T05:10:29.095050",
"start_time": "2023-11-01T05:11:05.047114",
"status": "completed"
},
"tags": []
Expand Down Expand Up @@ -37,16 +37,16 @@
"id": "e22f3858",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-01T05:10:29.103917Z",
"iopub.status.busy": "2023-10-01T05:10:29.103370Z",
"iopub.status.idle": "2023-10-01T05:10:29.359977Z",
"shell.execute_reply": "2023-10-01T05:10:29.359312Z"
"iopub.execute_input": "2023-11-01T05:11:05.057416Z",
"iopub.status.busy": "2023-11-01T05:11:05.056634Z",
"iopub.status.idle": "2023-11-01T05:11:05.391620Z",
"shell.execute_reply": "2023-11-01T05:11:05.390841Z"
},
"papermill": {
"duration": 0.261622,
"end_time": "2023-10-01T05:10:29.361804",
"duration": 0.340766,
"end_time": "2023-11-01T05:11:05.393858",
"exception": false,
"start_time": "2023-10-01T05:10:29.100182",
"start_time": "2023-11-01T05:11:05.053092",
"status": "completed"
},
"tags": []
Expand All @@ -67,10 +67,10 @@
"id": "d526e19d",
"metadata": {
"papermill": {
"duration": 0.00216,
"end_time": "2023-10-01T05:10:29.366350",
"duration": 0.002808,
"end_time": "2023-11-01T05:11:05.399501",
"exception": false,
"start_time": "2023-10-01T05:10:29.364190",
"start_time": "2023-11-01T05:11:05.396693",
"status": "completed"
},
"tags": []
Expand All @@ -85,16 +85,16 @@
"id": "5d9095c2",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-01T05:10:29.371984Z",
"iopub.status.busy": "2023-10-01T05:10:29.371311Z",
"iopub.status.idle": "2023-10-01T05:10:29.379163Z",
"shell.execute_reply": "2023-10-01T05:10:29.378568Z"
"iopub.execute_input": "2023-11-01T05:11:05.405540Z",
"iopub.status.busy": "2023-11-01T05:11:05.404727Z",
"iopub.status.idle": "2023-11-01T05:11:05.412606Z",
"shell.execute_reply": "2023-11-01T05:11:05.411970Z"
},
"papermill": {
"duration": 0.012318,
"end_time": "2023-10-01T05:10:29.380710",
"duration": 0.012634,
"end_time": "2023-11-01T05:11:05.414268",
"exception": false,
"start_time": "2023-10-01T05:10:29.368392",
"start_time": "2023-11-01T05:11:05.401634",
"status": "completed"
},
"tags": []
Expand All @@ -116,10 +116,10 @@
"id": "da017a87",
"metadata": {
"papermill": {
"duration": 0.001965,
"end_time": "2023-10-01T05:10:29.384741",
"duration": 0.002047,
"end_time": "2023-11-01T05:11:05.418452",
"exception": false,
"start_time": "2023-10-01T05:10:29.382776",
"start_time": "2023-11-01T05:11:05.416405",
"status": "completed"
},
"tags": []
Expand All @@ -134,16 +134,16 @@
"id": "700613de",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-01T05:10:29.389909Z",
"iopub.status.busy": "2023-10-01T05:10:29.389539Z",
"iopub.status.idle": "2023-10-01T05:10:29.393215Z",
"shell.execute_reply": "2023-10-01T05:10:29.392528Z"
"iopub.execute_input": "2023-11-01T05:11:05.424212Z",
"iopub.status.busy": "2023-11-01T05:11:05.423642Z",
"iopub.status.idle": "2023-11-01T05:11:05.427945Z",
"shell.execute_reply": "2023-11-01T05:11:05.427119Z"
},
"papermill": {
"duration": 0.007806,
"end_time": "2023-10-01T05:10:29.394616",
"duration": 0.008833,
"end_time": "2023-11-01T05:11:05.429434",
"exception": false,
"start_time": "2023-10-01T05:10:29.386810",
"start_time": "2023-11-01T05:11:05.420601",
"status": "completed"
},
"tags": []
Expand All @@ -165,16 +165,16 @@
"id": "2ad1de07",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-01T05:10:29.399696Z",
"iopub.status.busy": "2023-10-01T05:10:29.399488Z",
"iopub.status.idle": "2023-10-01T05:10:31.735927Z",
"shell.execute_reply": "2023-10-01T05:10:31.735372Z"
"iopub.execute_input": "2023-11-01T05:11:05.434771Z",
"iopub.status.busy": "2023-11-01T05:11:05.434546Z",
"iopub.status.idle": "2023-11-01T05:11:07.016534Z",
"shell.execute_reply": "2023-11-01T05:11:07.015885Z"
},
"papermill": {
"duration": 2.340754,
"end_time": "2023-10-01T05:10:31.737387",
"duration": 1.586549,
"end_time": "2023-11-01T05:11:07.018045",
"exception": false,
"start_time": "2023-10-01T05:10:29.396633",
"start_time": "2023-11-01T05:11:05.431496",
"status": "completed"
},
"scrolled": true,
Expand All @@ -187,7 +187,7 @@
"text": [
"Total number of publications containing \"Khan AR\"[AUTH] AND (\"2015/01/01\"[PDAT] : \"3000/12/31\"[PDAT]) AND\n",
" (\"Western University\"[AFFL] OR \"University of Western Ontario\"[AFFL] OR\n",
" \"Brain and Mind Institute\"[AFFL] OR \"Robarts Research Institute\"[AFFL]): 69\n"
" \"Brain and Mind Institute\"[AFFL] OR \"Robarts Research Institute\"[AFFL]): 73\n"
]
},
{
Expand All @@ -201,7 +201,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/tmp/ipykernel_2439/990535001.py:54: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.\n",
"/tmp/ipykernel_2585/990535001.py:54: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.\n",
" df = df_old.append(new_pubs)\n"
]
}
Expand Down Expand Up @@ -275,16 +275,16 @@
"id": "70df731e",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-01T05:10:31.743885Z",
"iopub.status.busy": "2023-10-01T05:10:31.743242Z",
"iopub.status.idle": "2023-10-01T05:10:31.752024Z",
"shell.execute_reply": "2023-10-01T05:10:31.751390Z"
"iopub.execute_input": "2023-11-01T05:11:07.024971Z",
"iopub.status.busy": "2023-11-01T05:11:07.024711Z",
"iopub.status.idle": "2023-11-01T05:11:07.033664Z",
"shell.execute_reply": "2023-11-01T05:11:07.032838Z"
},
"papermill": {
"duration": 0.013681,
"end_time": "2023-10-01T05:10:31.753591",
"duration": 0.014462,
"end_time": "2023-11-01T05:11:07.035191",
"exception": false,
"start_time": "2023-10-01T05:10:31.739910",
"start_time": "2023-11-01T05:11:07.020729",
"status": "completed"
},
"tags": []
Expand All @@ -294,13 +294,17 @@
"name": "stdout",
"output_type": "stream",
"text": [
"64 total articles found.\n",
"1 new articles found.\n",
"66 total articles found.\n",
"2 new articles found.\n",
"\n",
"New publications found:\n",
"Title: A population-averaged structural connectomic brain atlas dataset from 422 HCP-aging subjects (Data Brief)\n",
"Authors: ['Xiao Y', 'Gilmore G', 'Kai J', 'Lau JC', 'Peters T', 'Khan AR']\n",
"Journal (Date): Data Brief (10/1/2023)\n",
"Title: Focal acetylcholinergic modulation of the human midcingulo-insular network during attention: Meta-analytic neuroimaging and behavioral evidence (J Neurochem)\n",
"Authors: ['Chakraborty S', 'Lee SK', 'Arnold SM', 'Haast RAM', 'Khan AR', 'Schmitz TW']\n",
"Journal (Date): J Neurochem (10/21/2023)\n",
"\n",
"Title: Subregional analysis of striatum iron in Parkinson's disease and rapid eye movement sleep behaviour disorder (Neuroimage Clin)\n",
"Authors: ['Alushaj E', 'Hemachandra D', 'Kuurstra A', 'Menon RS', 'Ganjavi H', 'Sharma M', 'Kashgari A', 'Barr J', 'Reisman W', 'Khan AR', 'MacDonald PA']\n",
"Journal (Date): Neuroimage Clin (9/28/2023)\n",
"\n"
]
}
Expand All @@ -327,16 +331,16 @@
"id": "e76e9b21",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-01T05:10:31.759465Z",
"iopub.status.busy": "2023-10-01T05:10:31.759051Z",
"iopub.status.idle": "2023-10-01T05:10:31.774288Z",
"shell.execute_reply": "2023-10-01T05:10:31.773654Z"
"iopub.execute_input": "2023-11-01T05:11:07.041556Z",
"iopub.status.busy": "2023-11-01T05:11:07.041094Z",
"iopub.status.idle": "2023-11-01T05:11:07.059049Z",
"shell.execute_reply": "2023-11-01T05:11:07.058355Z"
},
"papermill": {
"duration": 0.019815,
"end_time": "2023-10-01T05:10:31.775857",
"duration": 0.023112,
"end_time": "2023-11-01T05:11:07.060887",
"exception": false,
"start_time": "2023-10-01T05:10:31.756042",
"start_time": "2023-11-01T05:11:07.037775",
"status": "completed"
},
"tags": []
Expand Down Expand Up @@ -380,35 +384,54 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>37663773</td>\n",
" <td>PMC10474320</td>\n",
" <td>10.1016/j.dib.2023.109513</td>\n",
" <td>A population-averaged structural connectomic b...</td>\n",
" <td>[Xiao Y, Gilmore G, Kai J, Lau JC, Peters T, K...</td>\n",
" <td>37864501</td>\n",
" <td></td>\n",
" <td>10.1111/jnc.15990</td>\n",
" <td>Focal acetylcholinergic modulation of the huma...</td>\n",
" <td>[Chakraborty S, Lee SK, Arnold SM, Haast RAM, ...</td>\n",
" <td>2023</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>Data Brief</td>\n",
" <td>50</td>\n",
" <td>21</td>\n",
" <td>J Neurochem</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>37797434</td>\n",
" <td>PMC10568416</td>\n",
" <td>10.1016/j.nicl.2023.103519</td>\n",
" <td>Subregional analysis of striatum iron in Parki...</td>\n",
" <td>[Alushaj E, Hemachandra D, Kuurstra A, Menon R...</td>\n",
" <td>2023</td>\n",
" <td>9</td>\n",
" <td>28</td>\n",
" <td>Neuroimage Clin</td>\n",
" <td>40</td>\n",
" <td></td>\n",
" <td>109513</td>\n",
" <td>103519</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" pmid pmcid doi \\\n",
"0 37663773 PMC10474320 10.1016/j.dib.2023.109513 \n",
" pmid pmcid doi \\\n",
"0 37864501 10.1111/jnc.15990 \n",
"1 37797434 PMC10568416 10.1016/j.nicl.2023.103519 \n",
"\n",
" title \\\n",
"0 A population-averaged structural connectomic b... \n",
"0 Focal acetylcholinergic modulation of the huma... \n",
"1 Subregional analysis of striatum iron in Parki... \n",
"\n",
" authors year month day \\\n",
"0 [Xiao Y, Gilmore G, Kai J, Lau JC, Peters T, K... 2023 10 1 \n",
"0 [Chakraborty S, Lee SK, Arnold SM, Haast RAM, ... 2023 10 21 \n",
"1 [Alushaj E, Hemachandra D, Kuurstra A, Menon R... 2023 9 28 \n",
"\n",
" journal volume issue pages \n",
"0 Data Brief 50 109513 "
" journal volume issue pages \n",
"0 J Neurochem \n",
"1 Neuroimage Clin 40 103519 "
]
},
"execution_count": 6,
Expand Down Expand Up @@ -443,14 +466,14 @@
},
"papermill": {
"default_parameters": {},
"duration": 4.093607,
"end_time": "2023-10-01T05:10:31.994912",
"duration": 3.447548,
"end_time": "2023-11-01T05:11:07.282276",
"environment_variables": {},
"exception": null,
"input_path": "/home/runner/work/khanlab.github.io/khanlab.github.io/get_publications.ipynb",
"output_path": "/home/runner/work/khanlab.github.io/khanlab.github.io/get_publications.ipynb",
"parameters": {},
"start_time": "2023-10-01T05:10:27.901305",
"start_time": "2023-11-01T05:11:03.834728",
"version": "2.3.3"
},
"vscode": {
Expand Down

0 comments on commit 18254b7

Please sign in to comment.