cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24228852.v1
title: Integrated analysis of transcriptomic and proteomic alterations in mouse models of ALS/FTD identify early metabolic adaptions with similarities to mitochondrial dysfunction disorders

description: Sporadic and familial amyotrophic lateral sclerosis (ALS) is a fatal progressive neurodegenerative disease that results in loss of motor neurons and, in some patients, associates with frontotemporal dementia (FTD). Apart from the accumulation of proteinaceous deposits, emerging literature indicates that aberrant mitochondrial bioenergetics may contribute to the onset and progression of ALS/FTD. Here we sought to investigate the pathophysiological signatures of mitochondrial dysfunction associated with ALS/FTD. By means of label-free mass spectrometry (MS) and mRNA sequencing (mRNA-seq), we report pre-symptomatic changes in the cortices of TDP-43 and FUS mutant mouse models. Using tissues from transgenic mouse models of mitochondrial diseases as a reference, we performed comparative analyses and extracted unique and common mitochondrial signatures that revealed neuroprotective compensatory mechanisms in response to early damage. In this regard, upregulation of both Acyl-CoA Synthetase Long-Chain Family Member 3 (ACSL3) and mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) were the most representative change in pre-symptomatic ALS/FTD tissues, suggesting that fatty acid beta-oxidation and mitochondrial protein translation are mechanisms of adaptation in response to ALS/FTD pathology. Together, our unbiased integrative analyses unveil novel molecular components that may influence mitochondrial homeostasis in the earliest phase of ALS.
DOI: 10.5281/zenodo.10460738
title: Are Prompt Engineering and TODO Comments Friends or Foes? An Evaluation on GitHub Copilot

description: Replication Package for "Are Prompt Engineering and TODO Comments Friends or Foes? An Evaluation on GitHub Copilot"
DOI: 10.5281/zenodo.10557120
title: Are Prompt Engineering and TODO Comments Friends or Foes? An Evaluation on GitHub Copilot

description: Replication Package for "Are Prompt Engineering and TODO Comments Friends or Foes? An Evaluation on GitHub Copilot"
DOI: 10.5281/zenodo.8206865
title: Are Prompt Engineering and TODO Comments Friends or Foes? An Evaluation on GitHub Copilot

description: Replication Package for "Are Prompt Engineering and TODO Comments Friends or Foes? An Evaluation on GitHub Copilot"
DOI: 10.5281/zenodo.8206866
title: Are Prompt Engineering and TODO Comments Friends or Foes? An Evaluation on GitHub Copilot

description: Replication Package for "Are Prompt Engineering and TODO Comments Friends or Foes? An Evaluation on GitHub Copilot"
DOI: 10.5281/zenodo.10557077
title: Phyclops - Sample Data - ConiferC 2023

description: Plant Electrophysiology Sample Data - ConiferC - Collected 2023
DOI: 10.5281/zenodo.10557078
title: Phyclops - Sample Data - ConiferC 2023

description: Plant Electrophysiology Sample Data - ConiferC - Collected 2023
DOI: 10.26071/ogsl-6360fffd-4f83
title: Drifter Trial in St. John Harbour for (2020-2022)
title: Lancement de bouées dérivantes dans le port de St. John (2020-2022)

description: Drifter release was initiated at the boundary of the Canaport Exclusion Zone in St. John Harbour and finished when all drifters were collected from their final destinations. Two types of drifters were deployed to track the course of surface currents from Saint John Harbour; long and disk drifters were used to capture the relative influences of wind and current. Shapefiles are also available. This project was funded by DFO Coastal Environmental Baseline Program under Canada’s Oceans Protection Plan (OPP).
description: La libération des bouées dérivantes a été amorcée à la limite de la zone d'exclusion de Canaport dans le port de St. John et terminées lorsque tous les bouées dérivantes ont été récupérées à partir de leurs destinations finales. Deux types de bouées dérivantes ont été déployées pour suivre le cours des courants de surface à partir du port de Saint John ; les dérivateurs longs et à disque ont été utilisés pour capter les influences relatives du vent et du courant. Des shapefiles sont aussi disponibles.

Ce projet a été financé par le Programme sur les données environnementales côtières de référence dans le cadre du Plan de protection des océans (PPO)
DOI: 10.5281/zenodo.10557145
title: Observation of the 2D-1D Dimensional Crossover in Strongly Interacting Ultracold Bosons

description: All data for the preprint "Experimental Observation of the 2D-1D Dimensional Crossover in Strongly Interacting Ultracold Bosons" 

The Innsbruck team acknowledges funding by a Wittgenstein prize grant under project number Z336-N36 and by the European Research Coun-cil (ERC) under project number 789017. MH thanks the doctoral school ALM for hospitality. This work is also supported by the Swiss National Science Foundation under grant number 200020-188687. Numerical calculations make use of the ALPS scheduler library and statistical analysis tools.
DOI: 10.5281/zenodo.8167238
title: Observation of the 2D-1D Dimensional Crossover in Strongly Interacting Ultracold Bosons

description: All data for the preprint "Experimental Observation of the 2D-1D Dimensional Crossover in Strongly Interacting Ultracold Bosons" 

The Innsbruck team acknowledges funding by a Wittgenstein prize grant under project number Z336-N36 and by the European Research Coun-cil (ERC) under project number 789017. MH thanks the doctoral school ALM for hospitality. This work is also supported by the Swiss National Science Foundation under grant number 200020-188687. Numerical calculations make use of the ALPS scheduler library and statistical analysis tools.
DOI: 10.5281/zenodo.8167239
title: Experimental Observation of the 2D-1D Dimensional Crossover in Strongly Interacting Ultracold Bosons

description: All data for the preprint "Experimental Observation of the 2D-1D Dimensional Crossover in Strongly Interacting Ultracold Bosons" 

The Innsbruck team acknowledges funding by a Wittgenstein prize grant under project number Z336-N36 and by the European Research Coun-cil (ERC) under project number 789017. MH thanks the doctoral school ALM for hospitality. This work is also supported by the Swiss National Science Foundation under grant number 200020-188687. Numerical calculations make use of the ALPS scheduler library and statistical analysis tools.
DOI: 10.5281/zenodo.10552038
title: Synergistic CloudSat-CALIPSO-MODIS retrievals of Cloud-Aerosol-Precipitation (CCM-CAP)

description: The dataset contains cloud and microphysical data retrievals based on observations from the A-train of satellites. Combined observations from CloudSat, CALIOP, and MODIS are used together with data from ECMWF and the liDAR-raDAR (DARDAR) cloud classification to simultaneously retrieve cloud, precipitation and aerosol properties. The dataset includes Particle Size Distribution (PSD) parameters for ice, rain and liquid, further microphysical parameters derived from these PSDs, and aerosol properties.

The dataset contains data from 2007 and 2008. Files each include a single granule of retrievals and observations together with errors and metadata of retrieval quality.
DOI: 10.5281/zenodo.10552039
title: Synergistic CloudSat-CALIPSO-MODIS retrievals of Cloud-Aerosol-Precipitation (CCM-CAP)

description: The dataset contains cloud and microphysical data retrievals based on observations from the A-train of satellites. Combined observations from CloudSat, CALIOP, and MODIS are used together with data from ECMWF and the liDAR-raDAR (DARDAR) cloud classification to simultaneously retrieve cloud, precipitation and aerosol properties. The dataset includes Particle Size Distribution (PSD) parameters for ice, rain and liquid, further microphysical parameters derived from these PSDs, and aerosol properties.

The dataset contains data from 2007 and 2008. Files each include a single granule of retrievals and observations together with errors and metadata of retrieval quality.
DOI: 10.5281/zenodo.10557144
title: Replication package - Potential Effectiveness and Efficiency Issues in Usability Evaluation within Digital Health: A Systematic Literature Review

description: 1. File: Maqbool_SLR_2023_JSS_Inclusion_610.xlsm.

There are two sheets in file. A. Final_Selected_papers, (sheet) aims to provide a comprehensive list of articles (n=610) selected for our SLR, whose process and data items specified and detailed in the article. 

B. Rejected_After_Full_Review, (sheet) aims to provide a comprehensive list of articles (n=153) rejected for our SLR based on inclusion or exclusion criteria after full article review process, whose process and data items specified and detailed in the article. 

2. File: Maqbool_SLR_2023_JSS_Data_Extraction_Form.pdf

This file aims to provide a comprehensive data extraction form, whose process and data items specified and detailed in the article. The form was used to elicit data relevant to answer the postulated research questions. This form served as the foundation for the additional information presented in the final paper.

3. File: Bilal_SLR_JSS_Primary_Studies_References.pdf

This file contains the primary selected studies (n=610) for the systematic literature review. The systematic review aims to explore and analyse research literature related to usability evaluation methods and their effectiveness and efficiency in the context of digital health applications. This file will help to identity reference of the primary selected study that is cited in the paper using a prefix (S, e.g. S137). This file can be used for peer review, ensuring the reliability and correctness of findings.

4. File: SLR_Analysis_updated_2023.nvp

The data extracted from each article was recorded in a worksheet (Excel) and then coded in NVivo 12/14 to categorise (classify) and compare extracted facets. Each data item's category and related paper id are coded in the given Excel file. Papers were not included in the NVivo project due to copyright concerns. Relevant papers can be tracked using the provided spreadsheet file (see Paper ID cell).The file(s) are cleaned as much as reasonable and other raw data is removed. This file does not include the matrix tables or codes, which were produced and analysed run-time during the analysis phase. Although the given package allows for re-generation.

-------- UPDATE: --------

5. File: SLR_Analysis_updated_2023_for_MAC.nvpx

This is an extra copy of NVivo project, created for the MAC user.

 

This replication package is produced and published here. Research conducted by Karlstad University researchers. We publish data sets to improve coverage and accessibility. For more info or concerns, contact us.

 

Linked paper published at: Maqbool, Bilal, and Sebastian Herold. "Potential effectiveness and efficiency issues in usability evaluation within digital health: A systematic literature review." Journal of Systems and Software (2023): 111881.

DOI: https://doi.org/10.1016/j.jss.2023.111881 

This work was funded, in parts, by Region Värmland through the DHINO project, Sweden (Grant: RUN/220266) and Vinnova through the DigitalWell Arena (DWA) project, Sweden (Grant: 2018-03025).
DOI: 10.5281/zenodo.8217565
title: Replication package - Potential Effectiveness and Efficiency Issues in Usability Evaluation within Digital Health: A Systematic Literature Review

description: 1. File: Maqbool_SLR_2023_JSS_Inclusion_610.xlsm.

There are two sheets in file. A. Final_Selected_papers, (sheet) aims to provide a comprehensive list of articles (n=610) selected for our SLR, whose process and data items specified and detailed in the article. 

B. Rejected_After_Full_Review, (sheet) aims to provide a comprehensive list of articles (n=153) rejected for our SLR based on inclusion or exclusion criteria after full article review process, whose process and data items specified and detailed in the article. 

2. File: Maqbool_SLR_2023_JSS_Data_Extraction_Form.pdf

This file aims to provide a comprehensive data extraction form, whose process and data items specified and detailed in the article. The form was used to elicit data relevant to answer the postulated research questions. This form served as the foundation for the additional information presented in the final paper.

3. File: Bilal_SLR_JSS_Primary_Studies_References.pdf

This file contains the primary selected studies (n=610) for the systematic literature review. The systematic review aims to explore and analyse research literature related to usability evaluation methods and their effectiveness and efficiency in the context of digital health applications. This file will help to identity reference of the primary selected study that is cited in the paper using a prefix (S, e.g. S137). This file can be used for peer review, ensuring the reliability and correctness of findings.

4. File: SLR_Analysis_updated_2023.nvp

The data extracted from each article was recorded in a worksheet (Excel) and then coded in NVivo 12/14 to categorise (classify) and compare extracted facets. Each data item's category and related paper id are coded in the given Excel file. Papers were not included in the NVivo project due to copyright concerns. Relevant papers can be tracked using the provided spreadsheet file (see Paper ID cell).The file(s) are cleaned as much as reasonable and other raw data is removed. This file does not include the matrix tables or codes, which were produced and analysed run-time during the analysis phase. Although the given package allows for re-generation.

-------- UPDATE: --------

5. File: SLR_Analysis_updated_2023_for_MAC.nvpx

This is an extra copy of NVivo project, created for the MAC user.

 

This replication package is produced and published here. Research conducted by Karlstad University researchers. We publish data sets to improve coverage and accessibility. For more info or concerns, contact us.

 

Linked paper published at: Maqbool, Bilal, and Sebastian Herold. "Potential effectiveness and efficiency issues in usability evaluation within digital health: A systematic literature review." Journal of Systems and Software (2023): 111881.

DOI: https://doi.org/10.1016/j.jss.2023.111881 

This work was funded, in parts, by Region Värmland through the DHINO project, Sweden (Grant: RUN/220266) and Vinnova through the DigitalWell Arena (DWA) project, Sweden (Grant: 2018-03025).
DOI: 10.5281/zenodo.8217566
title: Replication package - Potential Effectiveness and Efficiency Issues in usability evaluation within Digital Health: A Systematic Literature Review

description: 1. File: <strong>Maqbool_SLR_2023_JSS_Inclusion_610.xlsm.</strong> There are two sheets in file. A. <strong>Final_Selected_papers</strong>, (sheet) aims to provide a comprehensive list of articles (n=610) selected for our SLR, whose process and data items specified and detailed in the article. B. <strong>Rejected_After_Full_Review</strong>, (sheet) aims to provide a comprehensive list of articles (n=153) rejected for our SLR based on inclusion or exclusion criteria after full article review process, whose process and data items specified and detailed in the article. 2. File: <strong>Maqbool_SLR_2023_JSS_Data_Extraction_Form.pdf</strong> This file aims to provide a comprehensive data extraction form, whose process and data items specified and detailed in the article. The form was used to elicit data relevant to answer the postulated research questions. This form served as the foundation for the additional information presented in the final paper. 3. File: <strong>Bilal_SLR_JSS_Primary_Studies_References.pdf</strong> This file contains the primary selected studies (n=610) for the systematic literature review. The systematic review aims to explore and analyse research literature related to usability evaluation methods and their effectiveness and efficiency in the context of digital health applications. This file will help to identity reference of the primary selected study that is cited in the paper using a prefix (S, e.g. S137). This file can be used for peer review, ensuring the reliability and correctness of findings. 4. File: <strong>SLR_Analysis_updated_2023.nvp</strong> The data extracted from each article was recorded in a worksheet (Excel) and then coded in NVivo 12/14 to categorise (classify) and compare extracted facets. Each data item's category and related paper id are coded in the given Excel file. Papers were not included in the NVivo project due to copyright concerns. Relevant papers can be tracked using the provided spreadsheet file (see Paper ID cell).<br> The file(s) are cleaned as much as reasonable and other raw data is removed. This file does not include the matrix tables or codes, which were produced and analysed run-time during the analysis phase. Although the given package allows for re-generation. This replication package is produced and published here. Research conducted by Karlstad University researchers. We publish data sets to improve coverage and accessibility. For more info or concerns, contact us.<br> This work was funded, in parts, by Region Värmland via the DigitalWell Arena project (Dnr RV2018-678).
DOI: 10.5281/zenodo.8218076
title: Replication package - Potential Effectiveness and Efficiency Issues in Usability Evaluation within Digital Health: A Systematic Literature Review

description: 1. File: Maqbool_SLR_2023_JSS_Inclusion_610.xlsm.
There are two sheets in file. A. Final_Selected_papers, (sheet) aims to provide a comprehensive list of articles (n=610) selected for our SLR, whose process and data items specified and detailed in the article. 
B. Rejected_After_Full_Review, (sheet) aims to provide a comprehensive list of articles (n=153) rejected for our SLR based on inclusion or exclusion criteria after full article review process, whose process and data items specified and detailed in the article. 
2. File: Maqbool_SLR_2023_JSS_Data_Extraction_Form.pdf
This file aims to provide a comprehensive data extraction form, whose process and data items specified and detailed in the article. The form was used to elicit data relevant to answer the postulated research questions. This form served as the foundation for the additional information presented in the final paper.
3. File: Bilal_SLR_JSS_Primary_Studies_References.pdf
This file contains the primary selected studies (n=610) for the systematic literature review. The systematic review aims to explore and analyse research literature related to usability evaluation methods and their effectiveness and efficiency in the context of digital health applications. This file will help to identity reference of the primary selected study that is cited in the paper using a prefix (S, e.g. S137). This file can be used for peer review, ensuring the reliability and correctness of findings.
4. File: SLR_Analysis_updated_2023.nvp
The data extracted from each article was recorded in a worksheet (Excel) and then coded in NVivo 12/14 to categorise (classify) and compare extracted facets. Each data item's category and related paper id are coded in the given Excel file. Papers were not included in the NVivo project due to copyright concerns. Relevant papers can be tracked using the provided spreadsheet file (see Paper ID cell).The file(s) are cleaned as much as reasonable and other raw data is removed. This file does not include the matrix tables or codes, which were produced and analysed run-time during the analysis phase. Although the given package allows for re-generation.
This replication package is produced and published here. Research conducted by Karlstad University researchers. We publish data sets to improve coverage and accessibility. For more info or concerns, contact us.
 
Linked paper published at: Maqbool, Bilal, and Sebastian Herold. "Potential effectiveness and efficiency issues in usability evaluation within digital health: A systematic literature review." Journal of Systems and Software (2023): 111881.
DOI: https://doi.org/10.1016/j.jss.2023.111881 
This work was funded, in parts, by Region Värmland through the DHINO project, Sweden (Grant: RUN/220266) and Vinnova through the DigitalWell Arena (DWA) project, Sweden (Grant: 2018-03025).
DOI: 10.5281/zenodo.10209855
title: Indexing and searching petabase-scale nucleotide resources

description: Searching vast and rapidly growing nucleotide content in resources, such as runs in Sequence Read Archive and assemblies for whole genome shotgun sequencing projects in GenBank, is currently impractical for most researchers. We present Pebblescout, a tool that navigates such content by providing indexing and search capabilities. Indexing uses dense sampling of the sequences in the resource. Search finds subjects (runs or assemblies) that have short sequence matches to a user query, with well-defined guarantees, and ranks them using informativeness of the matches. Eight databases that index over 3.7 petabases were created to illustrate the functionality of Pebblescout. They can be interactively searched at https://pebblescout.ncbi.nlm.nih.gov. Here we show that for a wide range of query lengths, Pebblescout provides a data-driven way for finding relevant subsets of large nucleotide resources; reducing the resources needed for downstream analysis significantly. We compare Pebblescout to MetaGraph and Sourmash and show that both methods do not report some results correctly reported by Pebblescout.
DOI: 10.5281/zenodo.10209856
title: Indexing and searching petabyte-scale nucleotide resources

description: Searching vast and rapidly growing nucleotide content in resources, such as runs in Sequence Read Archive and assemblies for whole genome shotgun sequencing projects in GenBank, is currently impractical for most researchers. We present Pebblescout, a tool that navigates such content by providing indexing and search capabilities. Indexing uses dense sampling of the sequences in the resource. Search finds subjects (runs or assemblies) that have short sequence matches to a user query, with well-defined guarantees, and ranks them using informativeness of the matches. Seven databases that index over 3.5 petabases were created to illustrate the functionality of Pebblescout. They can be interactively searched at https://pebblescout.ncbi.nlm.nih.gov. Here we show that for a wide range of query lengths, Pebblescout provides a data-driven way for finding relevant subsets of large nucleotide resources. We compare Pebblescout to MetaGraph and Sourmash and show that both methods do not report some results correctly reported by Pebblescout.
DOI: 10.5281/zenodo.10553679
title: Indexing and searching petabase-scale nucleotide resources

description: Searching vast and rapidly growing nucleotide content in resources, such as runs in Sequence Read Archive and assemblies for whole genome shotgun sequencing projects in GenBank, is currently impractical for most researchers. We present Pebblescout, a tool that navigates such content by providing indexing and search capabilities. Indexing uses dense sampling of the sequences in the resource. Search finds subjects (runs or assemblies) that have short sequence matches to a user query, with well-defined guarantees, and ranks them using informativeness of the matches. Eight databases that index over 3.7 petabases were created to illustrate the functionality of Pebblescout. They can be interactively searched at https://pebblescout.ncbi.nlm.nih.gov. Here we show that for a wide range of query lengths, Pebblescout provides a data-driven way for finding relevant subsets of large nucleotide resources; reducing the resources needed for downstream analysis significantly. We compare Pebblescout to MetaGraph and Sourmash and show that both methods do not report some results correctly reported by Pebblescout.