cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25386/genetics.15053076
title: Supplemental Material for Razzaq, et al., 2021

description: Supplemental figures, tables, and files for Genetics manuscript "The SAGA and NuA4 component Tra1 regulates Candida albicans drug resistance and pathogenesis - Supplemental files"<br><b>Figure S1. Regulatory associations of Sfp1 with the <i>tra1<sub>Q3</sub></i> differentially expressed genes in <i>S. cerevisiae</i>. </b>Sfp1<b> </b>associations with differentially expressed genes in the <i>tra1<sub>Q3</sub></i> strain assessed using YEASTRACT+. The experimental evidence underlying each regulatory association (solid lines for DNA-binding evidence; dashed lines for expression evidence), as well as the sign of the interaction—positive (green), negative (red), positive and negative (brown), or undefined (black) are displayed. <b>Figure S2. Characterization of <i>TRA1</i> mutant strains. (a) </b><i>tra1∆/∆</i> mutants were validated by PCR. Two PCRs (left panel) confirmed the absence of the <i>TRA1</i> open reading frame (ORF) via primers located inside the ORF, and up- or down-stream of the ORF. Two additional PCRs (right panel) confirmed the integration of the knockout cassette at the <i>TRA1</i> locus (left side), as well as integration of the CRISPR-Cas9 plasmid in the <i>C. albicans</i> genome (right side). For all PCRs, control strains were added that contain the <i>TRA1</i> ORF, which include fRS1 (SC5314 wild-type <i>C. albicans</i>), and fRS302 (fRS1 containing a non-targeting Cas9 plasmid integrated in the genome), as well as a no DNA template control. <i>tra1∆/∆</i> mutant strains ‘1’ and ‘2’ were selected for further phenotypic characterization.<i> </i><b>(b) </b>The <i>TRA1</i> deletion strain is severely impaired in growth. Deletion strains and corresponding wild-type strains were grown up overnight in liquid YPD media for 15.5 hours at 37˚C.<b> (c) </b><i>TRA1</i> deletion results in severely impaired growth on solid medium. <i>C. albicans</i> strains were serially diluted (1:10 dilutions) and spotted onto solid YPD agar media.<b> (d) </b><i>tra1<sub>Q3</sub></i> mutant strains are not defective in overall growth rate. Kinetic growth curves between <i>C. albicans</i> wild-type strain and <i>tra1<sub>Q3</sub></i> mutant strains indicate no differences in overall growth dynamics over time. <b> </b> <b>Figure S3. Limited overlap between the Tra1- and Gcn5-regulated genes in <i>C. albicans</i>. (a)</b> Volcano plot showing the distribution of the previously identified 336 differentially expressed genes in <i>gcn5Δ </i>(from (Shivarathri <i>et al.</i> 2019))<i> </i>within the <i>tra1<sub>Q3</sub></i> dataset. Genes significantly (log<sub>2</sub> fold change <i>tra1<sub>Q3</sub></i>/<i>TRA1</i> &gt; 1 and <i>P </i>&lt; 0.05) altered in expression are highlighted in blue (downregulated) and red (upregulated). <b>(b) </b>Differentially regulated Gcn5 targets in <i>tra1<sub>Q3</sub></i> dataset are listed in the table with both the log<sub>2</sub> fold change within the original <i>gcn5Δ<b> </b></i>and the <i>tra1<sub>Q3<b> </b></sub></i>datasets.<br> <b></b><br>
DOI: 10.15468/c98264
title: Anthribidae Of Guam

description: This dataset contains the digitized treatments in Plazi based on the original book chapter Zimmerman, Elwood C. (1942): Anthribidae Of Guam. In: Insects of Guam I. Honolulu, Hawaii: Bernice P. Bishop Museum: 65-72, DOI: http://doi.org/10.5281/zenodo.5159835
DOI: 10.5281/zenodo.5159915
title: Risk of bias assessments for the Cochrane review 'SARS-CoV-2-neutralising monoclonal antibodies for treatment of COVID-19'

description: Risk of bias assessments and support for judgement with ROB 2 tool for the Cochrane Review: SARS-CoV-2-neutralising monoclonal antibodies for treatment of COVID-19.
description: funded by the Federal Ministry of Education and Research, Germany (NaFoUniMedCovid19, funding number: 01KX2021; part of the project "COVIM")
DOI: 10.5281/zenodo.4739959
title: Risk of bias assessments for the Cochrane review 'SARS-CoV-2-neutralising monoclonal antibodies for treatment of COVID-19'

description: Risk of bias assessments and support for judgement with ROB 2 tool for the Cochrane Review: SARS-CoV-2-neutralising monoclonal antibodies for treatment of COVID-19.
description: funded by the Federal Ministry of Education and Research, Germany (NaFoUniMedCovid19, funding number: 01KX2021; part of the project "COVIM")
DOI: 10.25386/genetics.15053076.v1
title: Supplemental Material for Razzaq, et al., 2021

description: Supplemental figures, tables, and files for Genetics manuscript "The SAGA and NuA4 component Tra1 regulates Candida albicans drug resistance and pathogenesis - Supplemental files"<br><b>Figure S1. Regulatory associations of Sfp1 with the <i>tra1<sub>Q3</sub></i> differentially expressed genes in <i>S. cerevisiae</i>. </b>Sfp1<b> </b>associations with differentially expressed genes in the <i>tra1<sub>Q3</sub></i> strain assessed using YEASTRACT+. The experimental evidence underlying each regulatory association (solid lines for DNA-binding evidence; dashed lines for expression evidence), as well as the sign of the interaction—positive (green), negative (red), positive and negative (brown), or undefined (black) are displayed. <b>Figure S2. Characterization of <i>TRA1</i> mutant strains. (a) </b><i>tra1∆/∆</i> mutants were validated by PCR. Two PCRs (left panel) confirmed the absence of the <i>TRA1</i> open reading frame (ORF) via primers located inside the ORF, and up- or down-stream of the ORF. Two additional PCRs (right panel) confirmed the integration of the knockout cassette at the <i>TRA1</i> locus (left side), as well as integration of the CRISPR-Cas9 plasmid in the <i>C. albicans</i> genome (right side). For all PCRs, control strains were added that contain the <i>TRA1</i> ORF, which include fRS1 (SC5314 wild-type <i>C. albicans</i>), and fRS302 (fRS1 containing a non-targeting Cas9 plasmid integrated in the genome), as well as a no DNA template control. <i>tra1∆/∆</i> mutant strains ‘1’ and ‘2’ were selected for further phenotypic characterization.<i> </i><b>(b) </b>The <i>TRA1</i> deletion strain is severely impaired in growth. Deletion strains and corresponding wild-type strains were grown up overnight in liquid YPD media for 15.5 hours at 37˚C.<b> (c) </b><i>TRA1</i> deletion results in severely impaired growth on solid medium. <i>C. albicans</i> strains were serially diluted (1:10 dilutions) and spotted onto solid YPD agar media.<b> (d) </b><i>tra1<sub>Q3</sub></i> mutant strains are not defective in overall growth rate. Kinetic growth curves between <i>C. albicans</i> wild-type strain and <i>tra1<sub>Q3</sub></i> mutant strains indicate no differences in overall growth dynamics over time. <b> </b> <b>Figure S3. Limited overlap between the Tra1- and Gcn5-regulated genes in <i>C. albicans</i>. (a)</b> Volcano plot showing the distribution of the previously identified 336 differentially expressed genes in <i>gcn5Δ </i>(from (Shivarathri <i>et al.</i> 2019))<i> </i>within the <i>tra1<sub>Q3</sub></i> dataset. Genes significantly (log<sub>2</sub> fold change <i>tra1<sub>Q3</sub></i>/<i>TRA1</i> &gt; 1 and <i>P </i>&lt; 0.05) altered in expression are highlighted in blue (downregulated) and red (upregulated). <b>(b) </b>Differentially regulated Gcn5 targets in <i>tra1<sub>Q3</sub></i> dataset are listed in the table with both the log<sub>2</sub> fold change within the original <i>gcn5Δ<b> </b></i>and the <i>tra1<sub>Q3<b> </b></sub></i>datasets.<br> <b></b><br>
DOI: 10.6084/m9.figshare.15105846
title: a Model of Fish Consumption Among Indonesian Youth with the Moderation on Their Perception of Fish Quality Assurance.xlsx

description: a Model of Fish Consumption Among Indonesian Youth with the Moderation on Their Perception of Fish Quality Assurance This study conducted at end of February until March 2021 in Indonesia. The target population was Indonesian youth between 17 and 26 years old. According to Indonesia Statistics in 2019, the population is 270.2 million and around 8.63% among them are around the age of 17 to 26 years old ([BPS] Badan Pusat Statistik, 2019). Data were collected based on representative’s population among 3 parts of the region in Indonesia based in Indonesian Food Culture Mapping (Wijaya, 2019); Western part of Indonesia consist of 4 main islands (Sumatera, Java, Bali, West Nusa Tenggara, and those nearest islands), Central part of Indonesia consists of 2 main islands (Sulawesi, Kalimantan, and surrounding islands), and East part of Indonesian consist of 3 main islands (East Nusa Tenggara, Maluku, Papua, and surrounding islands). From those 3 parts, based on Indonesian Statistics, 81.8% population are in the western part of Indonesia, 13.4 % of the population are in the central part of Indonesia, and 4.8% are in the eastern part of Indonesia. Five point of Likert Scale questionnaire was distributed online to more than 1500 university students between 17 and 26 years old. As a result, a total of 1,163 answers were analyzed.
DOI: 10.6084/m9.figshare.15105846.v1
title: a Model of Fish Consumption Among Indonesian Youth with the Moderation on Their Perception of Fish Quality Assurance.xlsx

description: a Model of Fish Consumption Among Indonesian Youth with the Moderation on Their Perception of Fish Quality Assurance This study conducted at end of February until March 2021 in Indonesia. The target population was Indonesian youth between 17 and 26 years old. According to Indonesia Statistics in 2019, the population is 270.2 million and around 8.63% among them are around the age of 17 to 26 years old ([BPS] Badan Pusat Statistik, 2019). Data were collected based on representative’s population among 3 parts of the region in Indonesia based in Indonesian Food Culture Mapping (Wijaya, 2019); Western part of Indonesia consist of 4 main islands (Sumatera, Java, Bali, West Nusa Tenggara, and those nearest islands), Central part of Indonesia consists of 2 main islands (Sulawesi, Kalimantan, and surrounding islands), and East part of Indonesian consist of 3 main islands (East Nusa Tenggara, Maluku, Papua, and surrounding islands). From those 3 parts, based on Indonesian Statistics, 81.8% population are in the western part of Indonesia, 13.4 % of the population are in the central part of Indonesia, and 4.8% are in the eastern part of Indonesia. Five point of Likert Scale questionnaire was distributed online to more than 1500 university students between 17 and 26 years old. As a result, a total of 1,163 answers were analyzed.
DOI: 10.18112/openneuro.ds003758.v1.0.0
title: Dynamic representation of the subjective value of information
DOI: 10.5281/zenodo.3518685
title: API Database of Python frameworks & Labeled Issues

description: PyLibAPIs.7z : contains public API data (MongoDB dump) for these frameworks: TensorFlow Keras Scikit-learn Pandas Flask Django Label.xlsx: contains issues and their labels Breaking Changes for All Frameworks.pdf: contains the breaking change distributions of all six frameworks
description: Our code for python framework API extraction and deprecated API usage detection tool is available here: https://github.com/sqlab-sustech/PyCompat.
DOI: 10.5281/zenodo.2756358
title: API Database of Python frameworks & Labeled Issues

description: PyLibAPIs.7z : contains public API data (MongoDB dump) for these frameworks: TensorFlow Keras Scikit-learn Pandas Flask Django Label.xlsx: contains issues and their labels Breaking Changes for All Frameworks.pdf: contains the breaking change distributions of all six frameworks
description: Our code for python framework API extraction and deprecated API usage detection tool is available here: https://github.com/sqlab-sustech/PyCompat.
DOI: 10.3886/e145661v1
title: Associations Between Online Instruction in Lateral Reading Strategies and Fact-checking COVID-19 News Among College Students

description: This repository contains instructional materials, de-identified data, analysis code and output, and supplemental analyses and tables for our paper examining the effects of online instruction in lateral reading on college students' fact-checking strategies and their fact-checking of online news about the COVID-19 pandemic.<br><br>The abstract for our paper, entitled "Associations Between Online Instruction in Lateral Reading Strategies and Fact-checking COVID-19 News Among College Students" may be found below: <br><br>College students, and adults in general, may find it hard to identify trustworthy information amidst the proliferation of false news and misinformation about the COVID-19 pandemic. In Fall 2020, college students (N = 221) in an online general education civics course were taught through asynchronous assignments how to use lateral reading strategies to fact-check online information. Students improved from pretest to posttest in use of lateral reading to fact-check information; lateral reading was predicted by the number of assignments completed and students’ reading comprehension test scores. Students reported greater use, endorsement, and knowledge of Wikipedia at posttest, aligning with the curriculum’s emphasis on using Wikipedia to investigate information sources. Students also reported increased confidence in their ability to fact-check COVID-19 news. While confidence was related to perceived helpfulness of the assignments, it was only weakly associated with lateral reading. Findings support the effectiveness of the online curriculum for improving fact-checking.
DOI: 10.5281/zenodo.4597074
title: Practical Bigraphs via Subgraph Isomorphism - Benchmark Instances

description: A set of 11176 test instances for comparing the existing SAT solver found in BigraphER with the new Subgraph based solver using the Glasgow subgraph solver. See README for details. Also included in results.tar.xz are those presented in the paper.
DOI: 10.5281/zenodo.4597073
title: Practical Bigraphs via Subgraph Isomorphism - Benchmark Instances

description: A set of 11176 test instances for comparing the existing SAT solver found in BigraphER with the new Subgraph based solver using the Glasgow subgraph solver. See README for details. Also included in results.tar.xz are those presented in the paper.
DOI: 10.6073/pasta/7c4295695344f4a85845a7a1d7238375
title: Vegetation Response in Simulated Hurricane Experiment at Harvard Forest since 1990

description: Wind disturbance profoundly shapes temperate forests but few studies have evaluated patterns and mechanisms of long-term forest dynamics following major windthrows. In 1990, we initiated a large hurricane simulation experiment in a 0.8 ha manipulation (pulldown) and 0.6 ha control area of a maturing Quercus rubra-Acer rubrum forest in New England. We toppled 276 trees in the pulldown, using a winch and cable, in the northwesterly direction of natural treefall from major hurricanes. Eighty percent of canopy trees and two-thirds of all trees greater than 5 cm dbh suffered direct and indirect damage. We used twenty years of measurements to evaluate the trajectory and mechanisms of forest response after intense disturbance. Based on the patch size and disturbance magnitude, we expected pioneer tree and understory species to drive succession. The first decade of analyses emphasized tree seedling establishment and sprouting by damaged trees as the dominant mechanisms of forest recovery in this extensive damaged area. However, despite 80% canopy damage and 8000 m2 patch size, surviving overstory and advance regeneration controlled longer-term forest development. Residual oaks make up 42% of stand basal area after 20 years. The new cohort of trees, dominated by black birch advance regeneration, contributes 30% of stand basal area. There were shifts in understory vegetation composition and cover, but few species were gained or lost after 20 years. Stand productivity rebounded quickly (litterfall recovered to pre-disturbance levels in six years), but we predict that basal area in the pulldown will lag behind the control (which gained 6 m2/ha over 20 years) for decades to come. This controlled experiment showed that although the scale and intensity of damage were great, abundant advance regeneration, understory vegetation, and damaged trees remained, allowing the forest to resist changes in ecosystem processes and invasion by new species.
DOI: 10.15468/c7e3ms
title: Neuropteroid Insects from Guam

description: This dataset contains the digitized treatments in Plazi based on the original book chapter Banks, Nathan (1942): Neuropteroid Insects from Guam. In: Insects of Guam I. Honolulu, Hawaii: Bernice P. Bishop Museum: 25-30, DOI: http://doi.org/10.5281/zenodo.5159923
DOI: 10.5517/ccdc.csd.cc2189m8
title: CCDC 1884819: Experimental Crystal Structure Determination

description: Related Article: Yanhong Liu, Chen Lin, Bowen Li, Jian Wang, Man Wang, Na Zhang, Yue Feng, Pengyan Wu|2020|Inorg.Chem.Front.|7|3541|doi:10.1039/D0QI00590H
DOI: 10.5517/ccdc.csd.cc21yq2t
title: CCDC 1905386: Experimental Crystal Structure Determination

description: Related Article: Jingquan Sha, Jingwen Sun, Zhibo Tong, Xiao Li, Mengting Li, Mingqi Xu, Qian Li, Chang Liu|2020|Inorg.Chem.|59|9244|doi:10.1021/acs.inorgchem.0c01150
DOI: 10.5281/zenodo.5159903
title: GPUSAT3 Benchmark Data and Source Code

description: Benchmark data and source code for GPUSAT3. This dataset contains: * decompositions_mccext.zip: Tree decompositions by htd, flowcutter and tamaki for the GPUSAT3 extended benchmark set. * track12.zip: Benchmark instances for the GPUSAT3 extended benchmark. * mccuda-source.zip: GPUSAT3 source code at the time of submission. * experiments.zip: Benchmark results for GPUSAT3 and compared solvers. *
DOI: 10.5281/zenodo.5159902
title: GPUSAT3 Benchmark Data and Source Code

description: Benchmark data and source code for GPUSAT3. This dataset contains: * decompositions_mccext.zip: Tree decompositions by htd, flowcutter and tamaki for the GPUSAT3 extended benchmark set. * track12.zip: Benchmark instances for the GPUSAT3 extended benchmark. * mccuda-source.zip: GPUSAT3 source code at the time of submission. * experiments.zip: Benchmark results for GPUSAT3 and compared solvers. *
DOI: 10.5519/qd.7y9gozab
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (775740 records)
DOI: 10.34943/9fc2d777-7a12-426c-940d-aa05264ff294
title: Endeavour North Current Meter Deployed 2012-06-19

description: The Nortek Aquadopp Current Meter A2L2557 was deployed on 2012-06-19 at Endeavour North. This north section of the Endeavour Hydrothermal Vents includes two moorings to monitor the regional circulation. This device is a Current Meter. Acoustic Current Meters (ACM) measure current speed and direction, using the Doppler Effect. Aquadopp current metres have a sensor head that contains 3 acoustic transducers, a tilt sensor, a temperature sensor and a pressure sensor. The instrument transmits a short pulse of sound, and then listens to its echo to measure the change in pitch or frequency. The change in pitch can determine the velocity of the current. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 2.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.5066/p9nwz15l
title: Wild and Scenic Rivers 2018 Linked to the NHDPlusV2.1

description: These data depict the National Hydrography Dataset Plus Version 2.1, NHDPlusV2.1, flowline representation of the National Wild and Scenic Rivers System throughout the conterminous United States as of 2018. U.S. Forest Service geospatial data on National Wild and Scenic River segments, USFS WSR Segment, from 3/1/2016 were joined to the NHDPlusV2.1. To ensure these data were up to date, spatial information from the National Wild and Scenic Rivers System (WSR) website was used to compare and improve these data. Additional information regarding river descriptions, history, and outstanding remarkable values (ORVs) were added to these data from the WSR website. This Information was collected in order to track specific details concerning river designations and justify the representation of each designated river in these data.
DOI: 10.34943/eef35dfd-5769-4914-86df-1717c1a6b70b
title: Endeavour North Current Meter Deployed 2011-09-13

description: The Nortek Aquadopp Current Meter A2L2499 was deployed on 2011-09-13 at Endeavour North. This north section of the Endeavour Hydrothermal Vents includes two moorings to monitor the regional circulation. This device is a Current Meter. Acoustic Current Meters (ACM) measure current speed and direction, using the Doppler Effect. Aquadopp current metres have a sensor head that contains 3 acoustic transducers, a tilt sensor, a temperature sensor and a pressure sensor. The instrument transmits a short pulse of sound, and then listens to its echo to measure the change in pitch or frequency. The change in pitch can determine the velocity of the current. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 2.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.6084/m9.figshare.15106224
title: Long-term small mammal trapping data

description: Site level moon data: Nine years of small mammal trapping at a restored tallgrass prairie (Nachusa Grasslands, Franklin Grove IL). Each row represents one night of trapping at each of 20 sites, with data describing the number of captures per species and presence/absence that night.<br>Entry times: Two years of small mamml trapping at a restored tallgrass prairie (Nachusa Grasslands, Franklin Grove IL). Each row represents one individual capture event. Trap-entry time was estimated using iButtons (Orrock and Connolly 2016 PLoS ONE).
DOI: 10.6084/m9.figshare.15106227
title: Metagenome-assembled genomes from Monte Cristo Cave, Diamantina, Brazil

description: Metagenome-assembled genomes from Monte Cristo Cave, Diamantina, Brazil