National Neuroinformatics Framework for Canadian Consortium on Neurodegeneration in Aging (CCNA)

The Canadian Institutes for Health Research (CIHR) launched the “International Collaborative Research Strategy for Alzheimer's Disease” as a signature initiative, focusing on Alzheimer's Disease (AD) and related neurodegenerative disorders (NDDs). The Canadian Consortium for Neurodegeneration and Aging (CCNA) was subsequently established to coordinate and strengthen Canadian research on AD and NDDs. To facilitate this research, CCNA uses LORIS, a modular data management system that integrates acquisition, storage, curation, and dissemination across multiple modalities. Through an unprecedented national collaboration studying various groups of dementia-related diagnoses, CCNA aims to investigate and develop proactive treatment strategies to improve disease prognosis and quality of life of those affected. However, this constitutes a unique technical undertaking, as heterogeneous data collected from sites across Canada must be uniformly organized, stored, and processed in a consistent manner. Currently clinical, neuropsychological, imaging, genomic, and biospecimen data for 509 CCNA subjects have been uploaded to LORIS. In addition, data validation is handled through a number of quality control (QC) measures such as double data entry (DDE), conflict flagging and resolution, imaging protocol checks1, and visual imaging quality validation. Site coordinators are also notified of incidental findings found in MRI reads or biosample analyses. Data is then disseminated to CCNA researchers via a web-based Data-Querying Tool (DQT). This paper will detail the wide array of capabilities handled by LORIS for CCNA, aiming to provide the necessary neuroinformatic infrastructure for this nation-wide investigation of healthy and diseased aging

aces/Loris: LORIS Release v24.1.6

<h2>What's Changed</h2> <ul> <li>[issue_tracker] Do not display inactive users in issue form by @charlottesce in https://github.com/aces/Loris/pull/8841</li> <li>[LINST] skip metadatafields for surveys by @zaliqarosli in https://github.com/aces/Loris/pull/8961</li> <li>[tools] Fix efficiency of fix_candidate_age script by @CamilleBeau in https://github.com/aces/Loris/pull/8992</li> <li>[media] fixes issue when media module try to instantiate a non existing instrument. by @racostas in https://github.com/aces/Loris/pull/8903</li> <li>[LINST] fix survey and date issues by @ridz1208 in https://github.com/aces/Loris/pull/8858</li> <li>[JSX] Modal Width Prop by @skarya22 in https://github.com/aces/Loris/pull/8893</li> <li>[libraries] Get examiner sites by UserID by @CamilleBeau in https://github.com/aces/Loris/pull/8994</li> <li>[genomic_browser] Download button not showing up in the Files tab by @ridz1208 in https://github.com/aces/Loris/pull/8480</li> <li>[issue_tracker - raisinbread/tools] Fix issue tracker history wrong module ID by @zaliqarosli in https://github.com/aces/Loris/pull/8677</li> <li>[Issue Tracker] Issue Change Notifications by @skarya22 in https://github.com/aces/Loris/pull/8885</li> <li>[behavioural_qc] fixes visitLevel feedback not showing up. by @racostas in https://github.com/aces/Loris/pull/8900</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/aces/Loris/compare/v24.1.5...v24.1.6</p&gt

aces/Loris: LORIS Release v24.1.2

This releases fixes bugs that were discovered since the v24.1.1 release. Most notably: [SQL] Reorder release patches for 24.0 release #8390 [Performance] Do not load module logger from constructor #8200 Download NIfTI file from imaging browser when a NIfTI file is available in addition to a MINC file #8206 [behavioural_qc] Fix critical error #8245 [issue tracker] Email watchers when issue is updated or created #8248 [core] return error message on invalid dob (rebase 24.1) #8279 [core] Fix incorrect message/error for instrument access #8284 [tools] Fix path in recreate_conflict #8292 [issue tracker] Fix emailing bug found in HBCD #8300 [issue_tracker] make assignee drop down not required #8301 [issue tracker] Fix issue description #8351 [imaging browser] Fix download of JSON, Bval and Bvec files when they are on s3 #8354 [imaging browser] Fix Human dangling out of nowhere #8363 [NDB_BVL_Instrument] Add get function to access protected selectMultipleElements #8381 [CSS/instruments] Fix control panel position when scrolling #8383 [MRI Violations] Fixes links to BrainBrowser from the MRI violations module #8392 Update CONTRIBUTING.md #8421 Full Changelog: https://github.com/aces/Loris/compare/v24.1.1...v24.1.2 Upgrade Process from version 23.X.Y to 24.1.2 (amendments) Note: The instructions below REPLACE the instructions in the release notes of released versions 24.0.0 AND 24.1.0. The instructions in those releases should be disregarded. 23.x.y to 24.0.0 Get the 24.1.2 source code Source the SQL/Release_patches/23.0_To_24.0_upgrade_A.sql SQL file into your database. Run the following scripts: php tools/configuration_check.php This script is used to validate the configuration of LORIS. It checks configuration settings and server paths to make sure that the application and underlying architecture are set up to allow LORIS to run properly. php tools/single_use/SaveUserIDToInstrumentData.php confirm This script is intended for a one-time use only to restore the value of the UserID column of instrument tables and the UserID key of the instrument JSON Data in the flag table. php tools/single_use/remove_publication_users_edit_perm_rel_duplicates.php _This script deletes duplicate rows in publication_users_edit_perm_rel to make sure the patch '2020-01-07-publication_users_edit_perm_relpk.sql' will execute successfully php tools/single_use/Cleanup_Special_Chars_Document_Repository.php This script is written to clean up the files with special characters from the document repository data table as well as clean up the quotes appearing as %22 in the file names in the file system php tools/single_use/Cleanup_Special_Chars_Media.php This script is written to clean up the files with special characters from the media data table as well as clean up the quotes appearing as %22 in the file names in the file system php tools/single_use/Remove_duplicate_examiners.php This script is written to clean up duplicate userIDs in the examiners table Make sure the RegistrationProjectID column in the candidate table of the dataabse does not contain any NULL values. If it does, either assign an existing project to the candidate/scanner or create a new project for these entries before running the release patch (see "Notes for existing projects" for more details). Source the SQL/Release_patches/23.0_To_24.0_upgrade_B.sql SQL file into your database. Run the following scripts: php tools/single_use/populate_visits.php _This script populates the visits table based on the config.xml, session table and Visit_Windows table._ php tools/single_use/Set_Required_elements_completed_flag.php confirm _This script is written to migrate the Data_entry_completion_status field from the instrument table (or Data column of the flag table) to it's own column in the flag table called Required_elements_completed. Note that this script can take a long time to complete on large projects._ Run make all on the LORIS root directory OPTIONAL: Source SQL patches from the SQL/Archive/24.0/Cleanup directory at your discretion to remove superfluous or deprecated entries in the database. OPTIONAL: Run the tools/single_use/Remove_Data_entry_completion_status_instr_column.php PHP script to generate an SQL patch containing all DROP COLUMN statements for the now unused Data_entry_completion_status field in instruments. This script will generate the SQL patch and store it in the SQL/Archive/autogenerated/single_use/ directory under the name Remove_Data_entry_completion_status.sql. OPTIONAL: Remove the &lt;visitLabel subprojectID="X"&gt; tags in the Config.xml file *NOTE: The tools/single_use/SaveUserIDToInstrumentData.php can take several hours up to a day to run depending on the size and age of the databse and number of instruments used* 24.0.0 to 24.1.2 Source the SQL/Release_patches/24.0_To_24.1_upgrade.sql SQL file into your database. If you have LORIS-MRI installed, make sure to upgrade LORIS-MRI to 24.1.0 since the SQL changes will affect the MRI insertion scripts. </ol

aces/Loris: LORIS Release v24.1.3

This releases fixes bugs that were discovered since the v24.1.2 release. Most notably: [issue_tracker] Make Comments and History easier to read #8370 [document_repository] Fix download path to correct user #8378 [media] add feedback to dropdown field when is empty #8402 [imaging_browser] Fix control panel positioning #8424 [examiner] Remove link to edit examiner if certification is not enabled #8425 [SQL] Fix 23 Cleanup patches #8430 [Build] apt deps issue #8431 [dqt] Fix loading saved query #8436 [SQL] 24.0.0 release patch fix truncation error #8438 [Genomic Browser] UserSiteMatch fix #8468 [SQL] Fix hardcoded parent ID for IssueTrackerDataPath in patches #8475 </ul

LORIS (Longitudinal Online Research and Imaging System)

&lt;h2&gt;What's Changed&lt;/h2&gt; &lt;ul&gt; &lt;li&gt;[media] React Warning on Upload Tab by @skarya22 in https://github.com/aces/Loris/pull/8721&lt;/li&gt; &lt;li&gt;[issue_tracker] Do not display inactive users in issue form by @charlottesce in https://github.com/aces/Loris/pull/8841&lt;/li&gt; &lt;li&gt;[LINST] skip metadatafields for surveys by @zaliqarosli in https://github.com/aces/Loris/pull/8961&lt;/li&gt; &lt;li&gt;[dictionary] Fixes for correct displaying &quot;Data Type&quot; column for the enumeration type in the &quot;Data Dictionary (Beta)&quot; table by @yagurdmitriy in https://github.com/aces/Loris/pull/8976&lt;/li&gt; &lt;li&gt;[tools] Fix efficiency of fix_candidate_age script by @CamilleBeau in https://github.com/aces/Loris/pull/8992&lt;/li&gt; &lt;li&gt;[media] fixes issue when media module try to instantiate a non existing instrument. by @racostas in https://github.com/aces/Loris/pull/8903&lt;/li&gt; &lt;li&gt;[instrument_list] Fix deprecation warning by @driusan in https://github.com/aces/Loris/pull/8867&lt;/li&gt; &lt;li&gt;[LINST] fix survey and date issues by @ridz1208 in https://github.com/aces/Loris/pull/8858&lt;/li&gt; &lt;li&gt;[JSX] Modal Width Prop by @skarya22 in https://github.com/aces/Loris/pull/8893&lt;/li&gt; &lt;li&gt;[libraries] Get examiner sites by UserID by @CamilleBeau in https://github.com/aces/Loris/pull/8994&lt;/li&gt; &lt;li&gt;[genomic_browser] Download button not showing up in the Files tab by @ridz1208 in https://github.com/aces/Loris/pull/8480&lt;/li&gt; &lt;li&gt;[issue_tracker - raisinbread/tools] Fix issue tracker history wrong module ID by @zaliqarosli in https://github.com/aces/Loris/pull/8677&lt;/li&gt; &lt;li&gt;[Issue Tracker] Issue Change Notifications by @skarya22 in https://github.com/aces/Loris/pull/8885&lt;/li&gt; &lt;li&gt;[behavioural_qc] fixes visitLevel feedback not showing up. by @racostas in https://github.com/aces/Loris/pull/8900&lt;/li&gt; &lt;li&gt;[battery_manager] Update Test Plan by @skarya22 in https://github.com/aces/Loris/pull/8782&lt;/li&gt; &lt;/ul&gt; &lt;h2&gt;New Contributors&lt;/h2&gt; &lt;ul&gt; &lt;li&gt;@yagurdmitriy made their first contribution in https://github.com/aces/Loris/pull/8976&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;&lt;strong&gt;Full Changelog&lt;/strong&gt;: https://github.com/aces/Loris/compare/v25.0.1...v25.0.2&lt;/p&gt;If you use this software, please cite it using these metadata

Effects of pre-operative isolation on postoperative pulmonary complications after elective surgery: an international prospective cohort study an international prospective cohort study

We aimed to determine the impact of pre-operative isolation on postoperative pulmonary complications after elective surgery during the global SARS-CoV-2 pandemic. We performed an international prospective cohort study including patients undergoing elective surgery in October 2020. Isolation was defined as the period before surgery during which patients did not leave their house or receive visitors from outside their household. The primary outcome was postoperative pulmonary complications, adjusted in multivariable models for measured confounders. Pre-defined sub-group analyses were performed for the primary outcome. A total of 96,454 patients from 114 countries were included and overall, 26,948 (27.9%) patients isolated before surgery. Postoperative pulmonary complications were recorded in 1947 (2.0%) patients of which 227 (11.7%) were associated with SARS-CoV-2 infection. Patients who isolated pre-operatively were older, had more respiratory comorbidities and were more commonly from areas of high SARS-CoV-2 incidence and high-income countries. Although the overall rates of postoperative pulmonary complications were similar in those that isolated and those that did not (2.1% vs 2.0%, respectively), isolation was associated with higher rates of postoperative pulmonary complications after adjustment (adjusted OR 1.20, 95%CI 1.05–1.36, p = 0.005). Sensitivity analyses revealed no further differences when patients were categorised by: pre-operative testing; use of COVID-19-free pathways; or community SARS-CoV-2 prevalence. The rate of postoperative pulmonary complications increased with periods of isolation longer than 3 days, with an OR (95%CI) at 4–7 days or ≥ 8 days of 1.25 (1.04–1.48), p = 0.015 and 1.31 (1.11–1.55), p = 0.001, respectively. Isolation before elective surgery might be associated with a small but clinically important increased risk of postoperative pulmonary complications. Longer periods of isolation showed no reduction in the risk of postoperative pulmonary complications. These findings have significant implications for global provision of elective surgical care. We aimed to determine the impact of pre-operative isolation on postoperative pulmonary complications after elective surgery during the global SARS-CoV-2 pandemic. We performed an international prospective cohort study including patients undergoing elective surgery in October 2020. Isolation was defined as the period before surgery during which patients did not leave their house or receive visitors from outside their household. The primary outcome was postoperative pulmonary complications, adjusted in multivariable models for measured confounders. Pre-defined sub-group analyses were performed for the primary outcome. A total of 96,454 patients from 114 countries were included and overall, 26,948 (27.9%) patients isolated before surgery. Postoperative pulmonary complications were recorded in 1947 (2.0%) patients of which 227 (11.7%) were associated with SARS-CoV-2 infection. Patients who isolated pre-operatively were older, had more respiratory comorbidities and were more commonly from areas of high SARS-CoV-2 incidence and high-income countries. Although the overall rates of postoperative pulmonary complications were similar in those that isolated and those that did not (2.1% vs 2.0%, respectively), isolation was associated with higher rates of postoperative pulmonary complications after adjustment (adjusted OR 1.20, 95%CI 1.05–1.36, p = 0.005). Sensitivity analyses revealed no further differences when patients were categorised by: pre-operative testing; use of COVID-19-free pathways; or community SARS-CoV-2 prevalence. The rate of postoperative pulmonary complications increased with periods of isolation longer than 3 days, with an OR (95%CI) at 4–7 days or ≥ 8 days of 1.25 (1.04–1.48), p = 0.015 and 1.31 (1.11–1.55), p = 0.001, respectively. Isolation before elective surgery might be associated with a small but clinically important increased risk of postoperative pulmonary complications. Longer periods of isolation showed no reduction in the risk of postoperative pulmonary complications. These findings have significant implications for global provision of elective surgical care