cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4539824
title: Sexual deception of a beetle pollinator through floral mimicry

description: Details of voucher specimens for the phylogenetic analysis for the paper "Sexual deception of a beetle pollinator through floral mimicry" published in Current Biology.
DOI: 10.5281/zenodo.4539823
title: Sexual deception of a beetle pollinator through floral mimicry

description: Details of voucher specimens for the phylogenetic analysis for the paper "Sexual deception of a beetle pollinator through floral mimicry" published in Current Biology.
DOI: 10.6084/m9.figshare.13828514.v1
title: Online Supplement-Code and Data for NP-ODE: Neural Process Aided Ordinary Differential Equations for Uncertainty Quantification of Finite Element Analysis

description: This supplementary file includes data, code, and appendices for the paper "NP-ODE: Neural Process Aided Ordinary Differential Equations for Uncertainty Quantification of Finite Element Analysis", published in IISE Transactions.
DOI: 10.6084/m9.figshare.13818989
title: Supplementary material - Impact of Na+ permeation on collective migration of pulmonary arterial endothelial cells (Xu et al)

description: Collective migration of endothelial cells is Endothelial migration is important for wound healing and angiogenesis. During such migration, each constituent endothelial cell coordinates its magnitude and direction of migration with its neighbors while retaining intercellular adhesion. Ensuring coordination and cohesion involves a variety of intra- and inter-cellular signaling processes. However, the role of permeation of extracellular Na<sup>+</sup> in collective cell migration remains unclear. Here, we examined the effect of Na<sup>+</sup> permeation in collective migration of pulmonary artery endothelial cell (PAEC) monolayers triggered by a scratch injury or barrier removal over 24 hours. In the scratch assay, PAEC monolayers migrated in two approximately linear phases. The first phase started with fast closure speed which then rapidly reduced within 5 hours after scratching. The second phase maintained at slow and stable speed from 6 to 24 hours. In the absence of extracellular Na<sup>+</sup>, we found that wound closure distance reduced more than 50%, fewer cells at the leading edge protruded prominent lamellipodia, and some sustained interendothelial gaps progressively increased in size over time and fused with adjacent gaps. When scratch-associated cellular injury was also missing, PAEC monolayer migrated much more slowly, and interendothelial gaps increased in size obviously towards the end. Pharmacological inhibition of the epithelial Na<sup>+</sup> channel (ENaC) using amiloride reduced wound closure distance by 30%. Inhibition of both the ENaC and the Na<sup>+</sup>/Ca<sup>2+</sup> exchanger (NCX) using benzamil further reduced wound closure distance in the second phase and caused accumulation of floating particles in the media. Surprisingly, pharmacological inhibition of the Ca<sup>2+</sup> release-activated Ca<sup>2+</sup> (CRAC) channel protein 1 (Orai1) using GSK-7975A, the transient receptor potential channel protein 1 and 4 (TRPC1/4) using Pico145, or both Orai1 and TRPC1/4 using combined GSK-7975A and Pico145 treatment did not affect wound closure distance dramatically. GSK-7975A also inhibits smaller inward Ca<sup>2+</sup> currents via Orai2 and Orai3 channels, whereas Pico145 also blocks TRPC4, TRPC5, and TRPC1/5 channels. Nevertheless, the combined treatment appeared to also cause accumulation of floating particles. Orai1 gene silencing using shRNAs led to a 25% reduction of wound closure in the first 6 hours but had no effect afterwards. However, in the absence of extracellular Na<sup>+</sup> or cellular injury, Orai1 did not affect PAEC collective migration. Overall, the data revealed that Na<sup>+</sup> permeation into cells contributed to PAEC monolayer collective migration by increasing lamellipodial formation, causing accumulation of floating particles, and impairing intercellular adhesion.
DOI: 10.6084/m9.figshare.13818989.v1
title: Supplementary material - Impact of Na+ permeation on collective migration of pulmonary arterial endothelial cells (Xu et al)

description: Collective migration of endothelial cells is Endothelial migration is important for wound healing and angiogenesis. During such migration, each constituent endothelial cell coordinates its magnitude and direction of migration with its neighbors while retaining intercellular adhesion. Ensuring coordination and cohesion involves a variety of intra- and inter-cellular signaling processes. However, the role of permeation of extracellular Na<sup>+</sup> in collective cell migration remains unclear. Here, we examined the effect of Na<sup>+</sup> permeation in collective migration of pulmonary artery endothelial cell (PAEC) monolayers triggered by a scratch injury or barrier removal over 24 hours. In the scratch assay, PAEC monolayers migrated in two approximately linear phases. The first phase started with fast closure speed which then rapidly reduced within 5 hours after scratching. The second phase maintained at slow and stable speed from 6 to 24 hours. In the absence of extracellular Na<sup>+</sup>, we found that wound closure distance reduced more than 50%, fewer cells at the leading edge protruded prominent lamellipodia, and some sustained interendothelial gaps progressively increased in size over time and fused with adjacent gaps. When scratch-associated cellular injury was also missing, PAEC monolayer migrated much more slowly, and interendothelial gaps increased in size obviously towards the end. Pharmacological inhibition of the epithelial Na<sup>+</sup> channel (ENaC) using amiloride reduced wound closure distance by 30%. Inhibition of both the ENaC and the Na<sup>+</sup>/Ca<sup>2+</sup> exchanger (NCX) using benzamil further reduced wound closure distance in the second phase and caused accumulation of floating particles in the media. Surprisingly, pharmacological inhibition of the Ca<sup>2+</sup> release-activated Ca<sup>2+</sup> (CRAC) channel protein 1 (Orai1) using GSK-7975A, the transient receptor potential channel protein 1 and 4 (TRPC1/4) using Pico145, or both Orai1 and TRPC1/4 using combined GSK-7975A and Pico145 treatment did not affect wound closure distance dramatically. GSK-7975A also inhibits smaller inward Ca<sup>2+</sup> currents via Orai2 and Orai3 channels, whereas Pico145 also blocks TRPC4, TRPC5, and TRPC1/5 channels. Nevertheless, the combined treatment appeared to also cause accumulation of floating particles. Orai1 gene silencing using shRNAs led to a 25% reduction of wound closure in the first 6 hours but had no effect afterwards. However, in the absence of extracellular Na<sup>+</sup> or cellular injury, Orai1 did not affect PAEC collective migration. Overall, the data revealed that Na<sup>+</sup> permeation into cells contributed to PAEC monolayer collective migration by increasing lamellipodial formation, causing accumulation of floating particles, and impairing intercellular adhesion.
DOI: 10.5281/zenodo.4539873
title: Morphological features associated with Dapi and Nissl images from seqFISH and seqFISH+ datasets

description: To go with the convnet.morpho package from: https://bitbucket.org/qzhudfci/convnet.morpho/src/master/
DOI: 10.25919/xstd-fs30
title: Parkes observations for project PX600 semester 2020APRS_33

description: The Galactic Center (GC) is a key target for the radio component of Breakthrough Listen (BL) program. Offering the largest amount of stars in any given direction in the sky, the GC is widely cited as a location believed to harbour advanced civilizations, and it is also the most energetic region in the Milky Way. We aim to conduct BL-GC Survey with Parkes radio telescope for around 350 hours. We will cover the frequency range from 700 MHz to 4 GHz, utilizing the newly installed ultra-wideband receiver. Our team has already leveraged both standard and bespoke tools to construct a flexible software stack to search data for signals of interest. We will look for signals from extraterrestrial intelligence (ETI) by searching for both simple narrow-band signals and complex modulated signals. Along with that, as an ancillary science, we will also search for accelerated pulsars — likely orbiting a supermassive black hole at the centre of the Milky Way Galaxy. Data products produced during this program will also be publically available to engage larger pulsar community
DOI: 10.6084/m9.figshare.13984436
title: Distributed Generation Landscape in Pakistan: An Overview

description: Pakistan issued net-metering regulations in 2015. These regulations allowed for on-site renewable systems installations (three-phase connections) by domestic, commercial and industrial end-users with capacities ranging between 1 kW to 1 MW. The concept of on-grid citizen energy generation however is still at its infancy in Pakistan. As of 30th December 2019, cumulative distributed generation installed capacity reached 47.6 MW. This brief has been organized to provide major insights on the growth of Distributed Generation in Pakistan (across the 11 distribution companies). The analysis is based on a complete database covering all installations from the year 2016- 2019. It breaks down the distributed generation growth from standpoint of several dimensions including year-wise distribution of net-metering based installed capacity; distribution company wise progression of net-metering installation; as well as category-wise spread of these installations among different sectors.
DOI: 10.6084/m9.figshare.13984436.v2
title: Distributed Generation Landscape in Pakistan: An Overview

description: Pakistan issued net-metering regulations in 2015. These regulations allowed for on-site renewable systems installations (three-phase connections) by domestic, commercial and industrial end-users with capacities ranging between 1 kW to 1 MW. The concept of on-grid citizen energy generation however is still at its infancy in Pakistan. As of 30th December 2019, cumulative distributed generation installed capacity reached 47.6 MW. This brief has been organized to provide major insights on the growth of Distributed Generation in Pakistan (across the 11 distribution companies). The analysis is based on a complete database covering all installations from the year 2016- 2019. It breaks down the distributed generation growth from standpoint of several dimensions including year-wise distribution of net-metering based installed capacity; distribution company wise progression of net-metering installation; as well as category-wise spread of these installations among different sectors.
DOI: 10.6084/m9.figshare.13984436.v1
title: Distributed Generation Landscape in Pakistan: An Overview

description: Pakistan issued net-metering regulations in 2015. These regulations allowed for on-site renewable systems installations (three-phase connections) by domestic, commercial and industrial end-users with capacities ranging between 1 kW to 1 MW. The concept of on-grid citizen energy generation however is still at its infancy in Pakistan. As of 30th December 2019, cumulative distributed generation installed capacity reached 47.6 MW. This brief has been organized to provide major insights on the growth of Distributed Generation in Pakistan (across the 11 distribution companies). The analysis is based on a complete database covering all installations from the year 2016- 2019. It breaks down the distributed generation growth from standpoint of several dimensions including year-wise distribution of net-metering based installed capacity; distribution company wise progression of net-metering installation; as well as category-wise spread of these installations among different sectors.
DOI: 10.5281/zenodo.4539891
title: A dataset of Vulnerable Code Changes of the Chormium OS project

description: This dataset is associated with the paper ""<em>Why Security Defects Go Unnoticed during Code Reviews? A Case-Control Study of the Chromium OS Project</em>" To cite this dataset please use following: <pre>@inproceedings{paul-2021-ICSE, author = {Paul, Rajshakhar and Turzo, Asif K. and Bosu, Amiangshu}, title = {Why Security Defects Go Unnoticed during Code Reviews? A Case-Control Study of the Chromium OS Project}, booktitle = {Proceedings of the 43th International Conference on Software Engineering}, series = {ICSE'21}, year = {2021}, location = {Madrid, Spain}, pages = {TBD}, note={Acceptance rate = 138/602 (22%)}, }</pre> ---------------------------------------------------------------------------------------------------------------- We conducted a case-control study of Chromium OS project to identify the factors that differentiate code reviews that successfully identified security defects from those that missed such defects. We identified the cases and the controls based on our outcome of interest, namely whether a security defect was identified or escaped during the code review of a vulnerability contributing commit (VCC). Using a keyword-based mining approach followed by manual validations on a dataset of 404,878 Chromium OS code reviews, we identified 516 code reviews that successfully identified security defects. In addition, from the Chromium OS bug repository, we identified 239 security defects that escaped code reviews. Using a modified version of the SZZ algorithm followed by manual validations, we identified 374 VCCs and corresponding code reviews that approved those changes. For each of the 890 identified VCCs, we computed 25 different attributes that may influence the identification of a vulnerability during code reviews. Our artifact includes locations of these 890 VCCs as well as the 25 attributes for each VCC. Among those 25 attributes, we considered 18 attributes to build our model. To analyze our data, we developed a Logistic Regression model following the guidelines suggested by Harrell Jr. using the 18 attributes. The model, which achieved an AUC of 0.91, found nine code review metrics that distinguish code reviews that missed a vulnerability from the ones that did not. We have also made the R script to reproduce our results in the Github repository. Our dataset includes 890 real world vulnerable files. Each of those vulnerabilities is classified using the CWE specification. We envision several ways researchers may benefit from this artefact such as evaluating static analysis tools, training machine learning models, and replicating this study under a different context.
DOI: 10.5281/zenodo.4458904
title: A dataset of Vulnerable Code Changes of the Chormium OS project

description: This dataset is associated with the paper ""<em>Why Security Defects Go Unnoticed during Code Reviews? A Case-Control Study of the Chromium OS Project</em>" To cite this dataset please use following: <pre>@inproceedings{paul-2021-ICSE, author = {Paul, Rajshakhar and Turzo, Asif K. and Bosu, Amiangshu}, title = {Why Security Defects Go Unnoticed during Code Reviews? A Case-Control Study of the Chromium OS Project}, booktitle = {Proceedings of the 43th International Conference on Software Engineering}, series = {ICSE'21}, year = {2021}, location = {Madrid, Spain}, pages = {TBD}, note={Acceptance rate = 138/602 (22%)}, }</pre> ---------------------------------------------------------------------------------------------------------------- We conducted a case-control study of Chromium OS project to identify the factors that differentiate code reviews that successfully identified security defects from those that missed such defects. We identified the cases and the controls based on our outcome of interest, namely whether a security defect was identified or escaped during the code review of a vulnerability contributing commit (VCC). Using a keyword-based mining approach followed by manual validations on a dataset of 404,878 Chromium OS code reviews, we identified 516 code reviews that successfully identified security defects. In addition, from the Chromium OS bug repository, we identified 239 security defects that escaped code reviews. Using a modified version of the SZZ algorithm followed by manual validations, we identified 374 VCCs and corresponding code reviews that approved those changes. For each of the 890 identified VCCs, we computed 25 different attributes that may influence the identification of a vulnerability during code reviews. Our artifact includes locations of these 890 VCCs as well as the 25 attributes for each VCC. Among those 25 attributes, we considered 18 attributes to build our model. To analyze our data, we developed a Logistic Regression model following the guidelines suggested by Harrell Jr. using the 18 attributes. The model, which achieved an AUC of 0.91, found nine code review metrics that distinguish code reviews that missed a vulnerability from the ones that did not. We have also made the R script to reproduce our results in the Github repository. Our dataset includes 890 real world vulnerable files. Each of those vulnerabilities is classified using the CWE specification. We envision several ways researchers may benefit from this artefact such as evaluating static analysis tools, training machine learning models, and replicating this study under a different context.
DOI: 10.6084/m9.figshare.13985021
title: Raw data for "Detection of CLas from roots recovered from cuttings" shown in Table 1

description: Raw data for Table 1<br>
DOI: 10.6084/m9.figshare.13985021.v1
title: Raw data for "Detection of CLas from roots recovered from cuttings" shown in Table 1

description: Raw data for Table 1<br>
DOI: 10.6084/m9.figshare.13985198
title: Raw data for "a subsequent cultivation in different soil types using CLas-negative cuttings" shown in Supplementary Figures 2-6

description: Raw data for Supplementary Figures 2-6 <br>
DOI: 10.6084/m9.figshare.13985198.v1
title: Raw data for "a subsequent cultivation in different soil types using CLas-negative cuttings" shown in Supplementary Figures 2-6

description: Raw data for Supplementary Figures 2-6 <br>
DOI: 10.6084/m9.figshare.13651502.v1
title: Feature Enriched Dataset to Develop and Test Author Name Ambiguity Solutions

description: Author name ambiguity problem stems from the fact that many individuals share identical names in the real world. It is a non-trivial problem, commonly faced by digital libraries who index and retrieve scholarly articles written by distinct authors, on demand. The problem occurs when multiple authors share a common name or when multiple name variations of an author appear in the publication records, as, digital libraries do not provide an efficient way to accurately identify publications of an author. Furthermore, lack of complete meta data information of an author and publication hinders the development of a generic algorithm that can solve the under discussing problem. Many data collections exists which are used to develop and test author name ambiguity problem, however, majority of them lack basic author as well as publication related meta data, are incomplete, inconsistent and often biased as they are curated keeping view certain scenario or feature. To the best of our knowledge, there exists no free data collection which is enriched with useful features and holds the potential to comprehensively develop and evaluate author name ambiguity resolving techniques. Considering this, we have prepared a dataset (CustAND) which is based on 14 ambiguous author name blocks/groups, where each block is composed of distinct authors sharing common name or multiple name variations. The data set covers more than eleven authors as well as publication related features, containing 7886 publication records in total, belonging to 137 distinct authors. Raw data set is extracted automatically using web scrappers from authors scholarly profiles maintained on Google Scholar and ResearchGate . After pre-processing the raw data, we have employed a user study-based evaluation method wherein a group of graduate students manually annotated, and cross checked the publications and authors meta data. We believe that this dataset can provide the research community an opportunity to work with a diverse and unbiased, useful feature enriched dataset to develop and test author name disambiguation related techniques, which can be generic with better performance when employed in real world scenarios.
DOI: 10.6084/m9.figshare.13651502
title: Feature Enriched Dataset

description: Author name ambiguity problem stems from the fact that many individuals share identical names in the real world. It is a non-trivial problem, commonly faced by digital libraries who index and retrieve scholarly articles written by distinct authors, on demand. The problem occurs when multiple authors share a common name or when multiple name variations of an author appear in the publication records, as, digital libraries do not provide an efficient way to accurately identify publications of an author. Furthermore, lack of complete meta data information of an author and publication hinders the development of a generic algorithm that can solve the under discussing problem. Many data collections exists which are used to develop and test author name ambiguity problem, however, majority of them lack basic author as well as publication related meta data, are incomplete, inconsistent and often biased as they are curated keeping view certain scenario or feature. To the best of our knowledge, there exists no free data collection which is enriched with useful features and holds the potential to comprehensively develop and evaluate author name ambiguity resolving techniques. Considering this, we have prepared a dataset which is based on 14 ambiguous author name blocks/groups, where each block is composed of distinct authors sharing common name or multiple name variations. The data set covers more than eleven authors as well as publication related features, containing 7886 publication records in total, belonging to 137 distinct authors. Raw data set is extracted from multiple web sources, which is annotated and confirmed manually. After pre-processing the raw data, we have employed a user study-based evaluation method along with Cohen's Kappa Coefficient with 100 % agreement. We believe that this dataset can provide the research community an opportunity to work with a diverse and unbiased, useful feature enriched dataset to develop and test author name disambiguation related techniques, which can be generic with better performance when employed in real world scenarios.