cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20484808.v1
title: Additional file 7 of Identification of immune-related key genes in the peripheral blood of ischaemic stroke patients using a weighted gene coexpression network analysis and machine learning

description: Additional file 7. Table S6. The key genes identified by the LASSO regression and/or SVM-RFE algorithm.
DOI: 10.6084/m9.figshare.7378763.v1
title: Additional file 1: of The long noncoding RNA LINC00312 induces lung adenocarcinoma migration and vasculogenic mimicry through directly binding YBX1

description: Table S1. Correlation between LINC00312 expression, VM density and clinicopathological parameters. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.12096234.v1
title: Additional file 5 of Internal ammonium excess induces ROS-mediated reactions and causes carbon scarcity in rice

description: Additional file 5: Table S2. GO enrichment analysis of DEGsin rice roots and shoots following a 4 h rapid NH4+ accumulation treatment. (XLS 192 kb)
DOI: 10.6084/m9.figshare.12096237.v1
title: Additional file 6 of Internal ammonium excess induces ROS-mediated reactions and causes carbon scarcity in rice

description: Additional file 6: Table S3. KEGG Enrichment Analysis of DEGsin rice roots and shoots following a 4 h rapid NH4+ accumulation treatment. (XLS 56 kb)
DOI: 10.6084/m9.figshare.12096237
title: Additional file 6 of Internal ammonium excess induces ROS-mediated reactions and causes carbon scarcity in rice

description: Additional file 6: Table S3. KEGG Enrichment Analysis of DEGsin rice roots and shoots following a 4 h rapid NH4+ accumulation treatment. (XLS 56 kb)
DOI: 10.6084/m9.figshare.20485829
title: Additional file 5 of Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection

description: Additional file 5: Table S5. Differentially expressed miRNA.
DOI: 10.6084/m9.figshare.20485829.v1
title: Additional file 5 of Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection

description: Additional file 5: Table S5. Differentially expressed miRNA.
DOI: 10.6084/m9.figshare.20485835
title: Additional file 7 of Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection

description: Additional file 7: Table S7. Primers used in this study.
DOI: 10.6084/m9.figshare.20485832
title: Additional file 6 of Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection

description: Additional file 6: Table S6. Differentially expressed lncRNA.
DOI: 10.5281/zenodo.10474674
title: Replication package for Fine-grained, accurate and scalable source differencing

description: Replication package for the article Fine-grained, accurate and scalable source differencing accepted at the 46th International Conference on Software Engineering (ICSE 2024).

List of files:



dataset: the folder containing the four datasets used in the paper, including the file-pairs and the script to regenerate them.

qualitative_experiment_diffs: the folder containing the GUI used by the participants of the qualitative experiment on the 100 cases.

gumtree: the folder containing the code of GumTree used to run the experiments.

analysis: the folder containing the CSV files and notebooks for the analysis of the results.
DOI: 10.6084/m9.figshare.20485817
title: Additional file 1 of Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection

description: Additional file 1: Table S1. Overview of the RNA sequencing data.
DOI: 10.5281/zenodo.10624440
title: Relationship Between NM Data and Radiation Dose at Aviation Altitudes During GLE Events - Data

description: Computed data that was used within the "Relationship Between NM Data and Radiation Dose at Aviation Altitudes During GLE Events" paper.  Contains the atmospheric effective dose yield functions used for radiation computation, computed radiation doses over 21 gorund-level enhancement events at three different altitides, and asymptotic cones for several used neutron monitors.
DOI: 10.5281/zenodo.10624441
title: Relationship Between NM Data and Radiation Dose at Aviation Altitudes During GLE Events - Data

description: Computed data that was used within the "Relationship Between NM Data and Radiation Dose at Aviation Altitudes During GLE Events" paper.  Contains the atmospheric effective dose yield functions used for radiation computation, computed radiation doses over 21 gorund-level enhancement events at three different altitides, and asymptotic cones for several used neutron monitors.
DOI: 10.6084/m9.figshare.20485823.v1
title: Additional file 3 of Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection

description: Additional file 3: Table S3. Characteristics of the reads from small RNAsequencing libraries.
DOI: 10.6084/m9.figshare.20485823
title: Additional file 3 of Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection

description: Additional file 3: Table S3. Characteristics of the reads from small RNAsequencing libraries.
DOI: 10.6084/m9.figshare.20485835.v1
title: Additional file 7 of Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection

description: Additional file 7: Table S7. Primers used in this study.
DOI: 10.5281/zenodo.10624657
title: atherinosoma_microstoma_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.10624658
title: atherinosoma_microstoma_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.20485817.v1
title: Additional file 1 of Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection

description: Additional file 1: Table S1. Overview of the RNA sequencing data.
DOI: 10.6084/m9.figshare.16815933
title: Additional file 5 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 5. Download path of FASTA sequences for the lncRNAs from 25 plants.
DOI: 10.6084/m9.figshare.16815936
title: Additional file 6 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 6. The collected transcriptome analysis data.
DOI: 10.6084/m9.figshare.16815936.v1
title: Additional file 6 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 6. The collected transcriptome analysis data.
DOI: 10.6084/m9.figshare.16815921
title: Additional file 1 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 1. Genomic sequences and their corresponding annotations of 25 flowering plants.
DOI: 10.6084/m9.figshare.16815921.v1
title: Additional file 1 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 1. Genomic sequences and their corresponding annotations of 25 flowering plants.
DOI: 10.6084/m9.figshare.21534610
title: Severe community-acquired pneumonia caused by <i>Chlamydia psittaci</i> genotype E/B strain circulating among geese in Lishui city, Zhejiang province, China

description: Between November 2021 and January 2022, four patients of community-acquired pneumonia were admitted to the hospitals in Lishui city, Zhejiang province, China. Their main clinical manifestations were fever and dry cough as well as radiographic infiltrate, but the empiric antimicrobial therapy or traditional Chinese medicine was not effective for their illness. Clinical specimens from the patients as well as environmental and poultry specimens were collected for the determination of the causative pathogen. The <i>ompA</i> gene and seven housekeeping genes of <i>Chlamydia psittaci</i> were successfully amplified from all the patients, and the sequences of each gene were identical to one another, suggesting that they were infected by the same strain of <i>C. psittaci</i>. A novel strain of <i>C. psittaci</i> (LS strain) was isolated from the bronchoalveolar lavage fluid of patient 2 and its whole genome was obtained. Phylogenetic analyses based on the whole-genome sequences showed that the isolate is most closely related to the strain (WS/RT/E30) identified as genotype E/B. In addition, The <i>ompA</i> gene and four housekeeping genes of <i>C. psittaci</i> were also amplified from two of four faeces samples of geese at the home of patient 2, and the sequences from geese were 100% identical to those from the patients. Accordingly, these cases could be attributed to a circulating <i>C. psittaci</i> strain of genotype E/B in the local geese. Therefore, there is an urgent need to strengthen the regional surveillance on <i>C. psittaci</i> among poultry and humans for prevention and control of the outbreak of psittacosis in the city.
DOI: 10.6084/m9.figshare.16815927
title: Additional file 3 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 3. GO annotations of 196 conserved lncRNAs.
DOI: 10.5281/zenodo.10624654
title: Jurassic Raw data
DOI: 10.6084/m9.figshare.16815930
title: Additional file 4 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 4 Significant enrichment functions (n = 39) of conserved lncRNA set (n = 196).
DOI: 10.5281/zenodo.10438819
title: Jurassic Raw data
DOI: 10.5281/zenodo.10438820
title: Raw data
DOI: 10.6084/m9.figshare.16815933.v1
title: Additional file 5 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 5. Download path of FASTA sequences for the lncRNAs from 25 plants.
DOI: 10.6084/m9.figshare.16815924
title: Additional file 2 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 2. Conserved lncRNAs ratios for each species.
DOI: 10.6084/m9.figshare.16815930.v1
title: Additional file 4 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 4 Significant enrichment functions (n = 39) of conserved lncRNA set (n = 196).
DOI: 10.6084/m9.figshare.16815924.v1
title: Additional file 2 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 2. Conserved lncRNAs ratios for each species.
DOI: 10.6084/m9.figshare.16815927.v1
title: Additional file 3 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

description: Additional file 3. GO annotations of 196 conserved lncRNAs.
DOI: 10.23645/epacomptox.22587706
title: Evaluating the utility of a high throughput thiol-containing fluorescent probe to screen for reactivity: A case study with the Tox21 library (ORD-050365)

description: Dataset for the manuscript "Evaluating the utility of a high throughput thiol-containing fluorescent probe to screen for reactivity: A case study with the Tox21 library"
<br>
Science Inventory, CCTE products: https://cfpub.epa.gov/si/si_public_search_results.cfm?advSearch=true&showCriteria=2&keyword=CCTE&TIMSType=&TIMSSubTypeID=&epaNumber=&ombCat=Any&dateBeginPublishedPresented=07/01/2017&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&DEID=&personName=&personID=&role=Any&journalName=&journalID=&publisherName=&publisherID=&sortBy=pubDate&count=25
DOI: 10.6084/m9.figshare.7378763
title: Additional file 1: of The long noncoding RNA LINC00312 induces lung adenocarcinoma migration and vasculogenic mimicry through directly binding YBX1

description: Table S1. Correlation between LINC00312 expression, VM density and clinicopathological parameters. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.25152498
title: Evaluating Dynamic Conditional Quantile Treatment Effects with Applications in Ridesharing

description: Many modern tech companies, such as Google, Uber, and Didi, utilize online experiments (also known as A/B testing) to evaluate new policies against existing ones. While most studies concentrate on average treatment effects, situations with skewed and heavy-tailed outcome distributions may benefit from alternative criteria, such as quantiles. However, assessing dynamic quantile treatment effects (QTE) remains a challenge, particularly when dealing with data from ride-sourcing platforms that involve sequential decision-making across time and space. In this paper, we establish a formal framework to calculate QTE conditional on characteristics independent of the treatment. Under specific model assumptions, we demonstrate that the dynamic conditional QTE (CQTE) equals the sum of individual CQTEs across time, even though the conditional quantile of cumulative rewards may not necessarily equate to the sum of conditional quantiles of individual rewards. This crucial insight significantly streamlines the estimation and inference processes for our target causal estimand. We then introduce two varying coefficient decision process (VCDP) models and devise an innovative method to test the dynamic CQTE. Moreover, we expand our approach to accommodate data from spatiotemporal dependent experiments and examine both conditional quantile direct and indirect effects. To showcase the practical utility of our method, we apply it to three real-world datasets from a ride-sourcing platform. Theoretical findings and comprehensive simulation studies further substantiate our proposal.
DOI: 10.6084/m9.figshare.25152498.v1
title: Evaluating Dynamic Conditional Quantile Treatment Effects with Applications in Ridesharing

description: Many modern tech companies, such as Google, Uber, and Didi, utilize online experiments (also known as A/B testing) to evaluate new policies against existing ones. While most studies concentrate on average treatment effects, situations with skewed and heavy-tailed outcome distributions may benefit from alternative criteria, such as quantiles. However, assessing dynamic quantile treatment effects (QTE) remains a challenge, particularly when dealing with data from ride-sourcing platforms that involve sequential decision-making across time and space. In this paper, we establish a formal framework to calculate QTE conditional on characteristics independent of the treatment. Under specific model assumptions, we demonstrate that the dynamic conditional QTE (CQTE) equals the sum of individual CQTEs across time, even though the conditional quantile of cumulative rewards may not necessarily equate to the sum of conditional quantiles of individual rewards. This crucial insight significantly streamlines the estimation and inference processes for our target causal estimand. We then introduce two varying coefficient decision process (VCDP) models and devise an innovative method to test the dynamic CQTE. Moreover, we expand our approach to accommodate data from spatiotemporal dependent experiments and examine both conditional quantile direct and indirect effects. To showcase the practical utility of our method, we apply it to three real-world datasets from a ride-sourcing platform. Theoretical findings and comprehensive simulation studies further substantiate our proposal.
DOI: 10.6084/m9.figshare.7378790
title: Additional file 3: of The long noncoding RNA LINC00312 induces lung adenocarcinoma migration and vasculogenic mimicry through directly binding YBX1

description: Table S2. Proteins associated with biotinylated LINC00312 in RNA pull-down assay. (XLS 425 kb)
DOI: 10.6084/m9.figshare.25150445
title: Supplementary Data required by article entiled "A c-di-GMP signing module controls responses to iron in Pseudomonas aeruginosa"

description: Supplementary Data required by article entiled "A c-di-GMP signing module controls responses to iron in Pseudomonas aeruginosa"<br><br>1) "AF-Q9I243-F1-model_v4.pdb" and "AF-Q9I2P4-F1-model_v4.pdb" are the starting point for IsmP-ImcA complex mdoelling;<br>2) IsmP-ImcA_Hetero-Tetramer_candidate_model.pdb: IsmP-ImcA complex candidate model;<br>3) IsmP_predicted_FE_binding_pocket: predicted Fe binding pocket for IsmP.<br>4）test_86405_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb: predicted apo dimeric model by ColabFOLD
DOI: 10.6084/m9.figshare.25150445.v1
title: Supplementary Data required by article entiled "A c-di-GMP signing module controls responses to iron in Pseudomonas aeruginosa"

description: Supplementary Data required by article entiled "A c-di-GMP signing module controls responses to iron in Pseudomonas aeruginosa"<br><br>1) "AF-Q9I243-F1-model_v4.pdb" and "AF-Q9I2P4-F1-model_v4.pdb" are the starting point for IsmP-ImcA complex mdoelling;<br>2) IsmP-ImcA_Hetero-Tetramer_candidate_model.pdb: IsmP-ImcA complex candidate model;<br>3) IsmP_predicted_FE_binding_pocket: predicted Fe binding pocket for IsmP.<br>4）test_86405_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb: predicted apo dimeric model by ColabFOLD
DOI: 10.6084/m9.figshare.21534610.v1
title: Severe community-acquired pneumonia caused by <i>Chlamydia psittaci</i> genotype E/B strain circulating among geese in Lishui city, Zhejiang province, China

description: Between November 2021 and January 2022, four patients of community-acquired pneumonia were admitted to the hospitals in Lishui city, Zhejiang province, China. Their main clinical manifestations were fever and dry cough as well as radiographic infiltrate, but the empiric antimicrobial therapy or traditional Chinese medicine was not effective for their illness. Clinical specimens from the patients as well as environmental and poultry specimens were collected for the determination of the causative pathogen. The <i>ompA</i> gene and seven housekeeping genes of <i>Chlamydia psittaci</i> were successfully amplified from all the patients, and the sequences of each gene were identical to one another, suggesting that they were infected by the same strain of <i>C. psittaci</i>. A novel strain of <i>C. psittaci</i> (LS strain) was isolated from the bronchoalveolar lavage fluid of patient 2 and its whole genome was obtained. Phylogenetic analyses based on the whole-genome sequences showed that the isolate is most closely related to the strain (WS/RT/E30) identified as genotype E/B. In addition, The <i>ompA</i> gene and four housekeeping genes of <i>C. psittaci</i> were also amplified from two of four faeces samples of geese at the home of patient 2, and the sequences from geese were 100% identical to those from the patients. Accordingly, these cases could be attributed to a circulating <i>C. psittaci</i> strain of genotype E/B in the local geese. Therefore, there is an urgent need to strengthen the regional surveillance on <i>C. psittaci</i> among poultry and humans for prevention and control of the outbreak of psittacosis in the city.
DOI: 10.6084/m9.figshare.20484975
title: Additional file 3 of Construction of a predictive model for immunotherapy efficacy in lung squamous cell carcinoma based on the degree of tumor-infiltrating immune cells and molecular typing

description: Additional file 3: Table S2. The main clinical information of TCGA-LUSC, GSE126044, GSE135222 and our independent LUSC cohort.
DOI: 10.6084/m9.figshare.23926029
title: Water Quality Index Calculations

description: Water Quality Index Scores for 21 stormwater ponds in Brampton, Ontario. Scores calculated using teh CCME WQI score calculator. Guidelines obtained from CCME resources.
DOI: 10.6084/m9.figshare.23907993
title: Stormwater pond site features

description: Features of 21 stormwater ponds surveyed in Brampton, Ontario. Impervious cover and area calculated by Daniel McIsaac.
DOI: 10.6084/m9.figshare.23907993.v1
title: Stormwater pond site features

description: Features of 21 stormwater ponds surveyed in Brampton, Ontario. Impervious cover and area calculated by Daniel McIsaac.
DOI: 10.6084/m9.figshare.23908059
title: Pesticide detections and concentrations in stormwater samples

description: Pesticide analysis results from stormwater samples collected from 21 stormwater ponds in Brampton, Ontario. Analyses completed by AFL in Guelph, Ontario.
DOI: 10.6084/m9.figshare.23908059.v1
title: Pesticide detections and concentrations in stormwater samples

description: Pesticide analysis results from stormwater samples collected from 21 stormwater ponds in Brampton, Ontario. Analyses completed by AFL in Guelph, Ontario.
DOI: 10.6084/m9.figshare.23908074
title: List of pesticide analytes

description: List of pesticides included in the analysis conducted by AFL in Guelph, Ontario, on stormwater and biofilm samples collected from 21 stormwater sites in Brampton, Ontario.
DOI: 10.6084/m9.figshare.23907840
title: E.coli and Coli analysis in stormwater samples

description: Stormwater samples from 21 stormwater ponds in Brampton, Ontario, were collected following a rain event. Samples were submitted to the Agriculture and Food Lab in Guelph, Ontario, for plate-count analysis of E.coli and coliform bacteria.
DOI: 10.6084/m9.figshare.23907840.v1
title: E.coli and Coli analysis in stormwater samples

description: Stormwater samples from 21 stormwater ponds in Brampton, Ontario, were collected following a rain event. Samples were submitted to the Agriculture and Food Lab in Guelph, Ontario, for plate-count analysis of E.coli and coliform bacteria.
DOI: 10.6084/m9.figshare.23908077
title: Detection and quantification limits for pesticides analysis

description: Method detection and quantification limits for pesticide analysis on stormwater and biofilm samples conducted by AFL in Guelph, Ontario.
DOI: 10.6084/m9.figshare.23908077.v1
title: Detection and quantification limits for pesticides analysis

description: Method detection and quantification limits for pesticide analysis on stormwater and biofilm samples conducted by AFL in Guelph, Ontario.
DOI: 10.6084/m9.figshare.23907939
title: Nutrient analysis in stormwater samples

description: Stormwater samples were collected from 21 ponds in Brampton, Ontario, for analysis of nutrient concentrations by ALS in Waterloo, Ontario. Analytes included NO2, NO3, NH4, and P.
DOI: 10.6084/m9.figshare.23907939.v1
title: Nutrient analysis in stormwater samples

description: Stormwater samples were collected from 21 ponds in Brampton, Ontario, for analysis of nutrient concentrations by ALS in Waterloo, Ontario. Analytes included NO2, NO3, NH4, and P.
DOI: 10.6084/m9.figshare.24192528
title: Biofilm analysis results (AFDW and Chlorophyll-a)

description: Results of analysis on biofilm samples collected from 21 stormwater pond sites in Brampton, Ontario. Ash-free dry weight (AFDW; mg per cm2) was measured gravimetrically and chlorophyll-a content (ug per cm2) was measured fluorometrically.
DOI: 10.6084/m9.figshare.24192528.v1
title: Biofilm analysis results (AFDW and Chlorophyll-a)

description: Results of analysis on biofilm samples collected from 21 stormwater pond sites in Brampton, Ontario. Ash-free dry weight (AFDW; mg per cm2) was measured gravimetrically and chlorophyll-a content (ug per cm2) was measured fluorometrically.