cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12666758
title: Contrasted gene decay in subterranean vertebrates

description: Data_Supp1. Summary of the number of genes retrieved from each species and for each gene set, along with the number of pseudogenes and the number of LoF mutations.<br><br><br>Data_Supp2. Sequences predicted with exonerate and ID of sequences retrieved from Ensembl.<br><br><br>Data_Supp3. Results obtained with different methods for dating relaxed selection on eye genes in Lucifuga dentata.<br><br><br>Description of Supplementary files content:<br>Divergence_values: Pairwise nucleotidic distances between species for each gene set.<br>Lucifuga_Supplementary_files_Genome: Original GFF3 file with functional annotations and scaffolds smaller than 200 bp not uploaded to NCBI.<br>MutPred2_Results: Raw output of MutPred2. Parsed results files to be used with the script provided in github (MutPred2_Script.R) are also provided.<br>Phylogenies: Gene phylogenies computed with iQTree and displayed with iTOL. The model used for each phylogeny can be found on the “Models” folder.<br>Concatenated_Alignments: Concatenated alignments for vision, circadian and pigmentation genes.
DOI: 10.6084/m9.figshare.12666758.v1
title: Contrasted gene decay in subterranean vertebrates

description: Data_Supp1. Summary of the number of genes retrieved from each species and for each gene set, along with the number of pseudogenes and the number of LoF mutations.<br><br><br>Data_Supp2. Sequences predicted with exonerate and ID of sequences retrieved from Ensembl.<br><br><br>Data_Supp3. Results obtained with different methods for dating relaxed selection on eye genes in Lucifuga dentata.<br><br><br>Description of Supplementary files content:<br>Divergence_values: Pairwise nucleotidic distances between species for each gene set.<br>Lucifuga_Supplementary_files_Genome: Original GFF3 file with functional annotations and scaffolds smaller than 200 bp not uploaded to NCBI.<br>MutPred2_Results: Raw output of MutPred2. Parsed results files to be used with the script provided in github (MutPred2_Script.R) are also provided.<br>Phylogenies: Gene phylogenies computed with iQTree and displayed with iTOL. The model used for each phylogeny can be found on the “Models” folder.<br>Concatenated_Alignments: Concatenated alignments for vision, circadian and pigmentation genes.
DOI: 10.6084/m9.figshare.12666575
title: Ayer C. Status of Nutritional Literacy in Adolescents in Turkey.sav

description: This study was carried out to determine the nutritional literacy status and the factors affecting them of 9th grade students in the semi-rural area. Data were collected with a two-part questionnaire, including sociodemographic characteristics and the Adolescent Nutrition Literacy Scale (ANLS).
DOI: 10.6084/m9.figshare.12666575.v1
title: Ayer C. Status of Nutritional Literacy in Adolescents in Turkey.sav

description: This study was carried out to determine the nutritional literacy status and the factors affecting them of 9th grade students in the semi-rural area. Data were collected with a two-part questionnaire, including sociodemographic characteristics and the Adolescent Nutrition Literacy Scale (ANLS).
DOI: 10.6084/m9.figshare.12666449
title: NEM 3398 Supplementary Table 1

description: The results of biomass calculations are presented in Tables 1-6 in the article. In the article data are separately shown for different life stages in each of 115 genera in all families of plant-parasitic nematodes. Data at species or population level are accessible here.
DOI: 10.6084/m9.figshare.12666449.v1
title: NEM 3398 Supplementary Table 1

description: The results of biomass calculations are presented in Tables 1-6 in the article. In the article data are separately shown for different life stages in each of 115 genera in all families of plant-parasitic nematodes. Data at species or population level are accessible here.
DOI: 10.6084/m9.figshare.12666359
title: Information for Effects of the current strike-slip faulting on the hydrological and geothermal structures beneath the northeastern part of the Gonghe Basin, northeastern Tibet

description: This dataset includes all figures, tables, and supporting information cited in the articles "Effects of the current strike-slip faulting on the hydrological and geothermal structures beneath the northeastern part of the Gonghe Basin, northeastern Tibet".
DOI: 10.6084/m9.figshare.12666359.v1
title: Information for Effects of the current strike-slip faulting on the hydrological and geothermal structures beneath the northeastern part of the Gonghe Basin, northeastern Tibet

description: This dataset includes all figures, tables, and supporting information cited in the articles "Effects of the current strike-slip faulting on the hydrological and geothermal structures beneath the northeastern part of the Gonghe Basin, northeastern Tibet".
DOI: 10.6084/m9.figshare.12666233
title: Chinese Financial News Data

description: Unprocessed Chinese text data for NLP.
DOI: 10.6084/m9.figshare.12666185
title: Annotation of Syngnathus typhle

description: GeneMark-ES v2.3e was run on the genome assembly and SNAP v20131129 on the genes found by CEGMA. MAKER v2.31 used the trained gene predictors, a Trinity transcriptome assembly, all repeats in RepBase as called by MAKER and proteins from UniProtKB/SwissProt r2014_9 for a first pass annotation of the genome assembly. The result of the first pass was used to retrain SNAP and train AUGUSTUS v3.0.2 and a second iteration was performed using the same set-up. The protein sequences from final output of MAKER were BLASTed against the UniProtKB/SwissProt proteins and InterProScan v5.4-47 was used to classify protein domains in the protein sequences. This information was transferred to all output of MAKER. This annotated 19,668 gene models. InterProScan was run on the predicted proteins of these and gene names were allocated based on match with proteins in UniProt/SwissProt.<br>The files starting with Syngnathus_typhle is a more recent annotation done with Funannotate. The files starting with syty is the MAKER annotation
DOI: 10.6084/m9.figshare.12666227
title: supplementary materials

description: The supplementary materials of manuscript <b>PECAM EMPs regulate the apoptosis of pulmonary microvascular endothelial cells in COPD by activating Akt signaling pathway.</b>
DOI: 10.6084/m9.figshare.12666227.v1
title: supplementary materials

description: The supplementary materials of manuscript <b>PECAM EMPs regulate the apoptosis of pulmonary microvascular endothelial cells in COPD by activating Akt signaling pathway.</b>
DOI: 10.6084/m9.figshare.12666122
title: Reducing delays to Multidrug-Resistant Tuberculosis case detection through a revised routine surveillance system-BMC

description: Background: Routine surveillance is required to monitor the performance of tuberculosis diagnostic programme and is essential for the rapid detection of drug resistance. The main objective of this study was to explore the effectiveness and stakeholder perception of the current routine surveillance system for previously treated tuberculosis cases in Tanzania with a view to identify interventions to improve and accelerate positive patient outcomes.<b></b>Methods:<b> </b>A study using quantitative and qualitative methods of data collection including in-depth interviews and focus group discussions with health care service providers was conducted in four regions. Quantitative data were extracted from the routine databases to assess performance.Results: Quantitative findings from 2011 to 2013 showed 2,750 specimens from previously treated TB cases were received at the reference laboratory. The number increased year on year, but even in the most recent year was only 61% of that expected. The median and interquartile range of turnaround time in days from specimen reception to results reported for smear microscopy, culture and drug susceptibility testing were 1(1, 1), 61(43, 71) and 129(72, 170) respectively. Contaminated specimens were reported in 3.6% of cases. The qualitative analysis showed the system of sending specimens using postal services was seen to be efficient by participants. However, there were many challenges and significant delays in specimens reaching the reference laboratory associated with lack of funds to transfer specimens, weak form completion, inadequate training and poor supervision. These all adversely affected the implementation of the routine surveillance system.Conclusions: Many issues limit the effectiveness of the routine surveillance system in Tanzania. Priority areas for strengthening are; specimen transportation, supervision and availability of commodities. A pilot study of a revised routine surveillance system that takes into account the observations from this study alongside improved access to drug susceptibility testing using Xpert MTB/RIF should be considered
DOI: 10.6084/m9.figshare.12666104
title: Table A1.xlsx

description: Supplementary tables for manuscript entitled: "Phylogeography of the marine pathogen, <i>Vibrio vulnificus</i>, revealed the ancestral scenarios of its evolution" .
DOI: 10.6084/m9.figshare.12666122.v2
title: Reducing delays to Multidrug-Resistant Tuberculosis case detection through a revised routine surveillance system-BMC

description: Background: Routine surveillance is required to monitor the performance of tuberculosis diagnostic programme and is essential for the rapid detection of drug resistance. The main objective of this study was to explore the effectiveness and stakeholder perception of the current routine surveillance system for previously treated tuberculosis cases in Tanzania with a view to identify interventions to improve and accelerate positive patient outcomes.<b></b>Methods:<b> </b>A study using quantitative and qualitative methods of data collection including in-depth interviews and focus group discussions with health care service providers was conducted in four regions. Quantitative data were extracted from the routine databases to assess performance.Results: Quantitative findings from 2011 to 2013 showed 2,750 specimens from previously treated TB cases were received at the reference laboratory. The number increased year on year, but even in the most recent year was only 61% of that expected. The median and interquartile range of turnaround time in days from specimen reception to results reported for smear microscopy, culture and drug susceptibility testing were 1(1, 1), 61(43, 71) and 129(72, 170) respectively. Contaminated specimens were reported in 3.6% of cases. The qualitative analysis showed the system of sending specimens using postal services was seen to be efficient by participants. However, there were many challenges and significant delays in specimens reaching the reference laboratory associated with lack of funds to transfer specimens, weak form completion, inadequate training and poor supervision. These all adversely affected the implementation of the routine surveillance system.Conclusions: Many issues limit the effectiveness of the routine surveillance system in Tanzania. Priority areas for strengthening are; specimen transportation, supervision and availability of commodities. A pilot study of a revised routine surveillance system that takes into account the observations from this study alongside improved access to drug susceptibility testing using Xpert MTB/RIF should be considered
DOI: 10.6084/m9.figshare.12665681
title: JVASP-41269 to JVASP-41911

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12666122.v1
title: Reducing delays to Multidrug-Resistant Tuberculosis case detection through a revised routine surveillance system-BMC

description: Background: Routine surveillance is required to monitor the performance of tuberculosis diagnostic programme and is essential for the rapid detection of drug resistance. The main objective of this study was to explore the effectiveness and stakeholder perception of the current routine surveillance system for previously treated tuberculosis cases in Tanzania with a view to identify interventions to improve and accelerate positive patient outcomes.<b></b>Methods:<b> </b>A study using quantitative and qualitative methods of data collection including in-depth interviews and focus group discussions with health care service providers was conducted in four regions. Quantitative data were extracted from the routine databases to assess performance.Results: Quantitative findings from 2011 to 2013 showed 2,750 specimens from previously treated TB cases were received at the reference laboratory. The number increased year on year, but even in the most recent year was only 61% of that expected. The median and interquartile range of turnaround time in days from specimen reception to results reported for smear microscopy, culture and drug susceptibility testing were 1(1, 1), 61(43, 71) and 129(72, 170) respectively. Contaminated specimens were reported in 3.6% of cases. The qualitative analysis showed the system of sending specimens using postal services was seen to be efficient by participants. However, there were many challenges and significant delays in specimens reaching the reference laboratory associated with lack of funds to transfer specimens, weak form completion, inadequate training and poor supervision. These all adversely affected the implementation of the routine surveillance system.Conclusions: Many issues limit the effectiveness of the routine surveillance system in Tanzania. Priority areas for strengthening are; specimen transportation, supervision and availability of commodities. A pilot study of a revised routine surveillance system that takes into account the observations from this study alongside improved access to drug susceptibility testing using Xpert MTB/RIF should be considered
DOI: 10.6084/m9.figshare.12665681.v1
title: JVASP-41269 to JVASP-41911

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12665618
title: Data

description: supporting information
DOI: 10.6084/m9.figshare.12665636
title: ela-data.rar

description: the ela of TP
DOI: 10.6084/m9.figshare.12665618.v1
title: Data

description: supporting information
DOI: 10.6084/m9.figshare.12665579
title: JVASP-40592 to JVASP-41268

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12665636.v1
title: ela-data.rar

description: the ela of TP
DOI: 10.6084/m9.figshare.12665576
title: JVASP-39906 to JVASP-40591

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12665579.v1
title: JVASP-40592 to JVASP-41268

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12665573
title: JVASP-39155 to JVASP-39905

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12665576.v1
title: JVASP-39906 to JVASP-40591

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12665573.v1
title: JVASP-39155 to JVASP-39905

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12665441
title: JVASP-37155 to JVASP-37726

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12665438
title: Nostoc metagenome 25 ice-binding proteins

description: The Nostoc metagenome includes many epiphytic bacteria, many of which have their own ice-binding proteins
DOI: 10.6084/m9.figshare.12665444
title: JVASP-38434 to JVASP-39154

description: JARVIS-DFT<br>
DOI: 10.6084/m9.figshare.12665438.v1
title: Nostoc metagenome 25 ice-binding proteins

description: The Nostoc metagenome includes many epiphytic bacteria, many of which have their own ice-binding proteins
DOI: 10.6084/m9.figshare.12665441.v1
title: JVASP-37155 to JVASP-37726

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12665366
title: Angelman_Cluster_2020

description: The dataset includes seven children with Angelman syndrome and severe to profound developmental disabilities exposed to a microswitch-cluster technology to promote object manipulation and reduce tongue protrusion. A long term follow-up (i.e., 24 months) was conducted. Intervals with indices of positive participation as an outcome measure of constructive engagement were additionally recorded.
DOI: 10.6084/m9.figshare.12665444.v1
title: JVASP-38434 to JVASP-39154

description: JARVIS-DFT<br>
DOI: 10.6084/m9.figshare.12665393
title: Social Validation_Angelman_2020

description: The dataset includes social validation scores of 4 groups of external raters (i.e., caregivers, physiotherapists, psychologists, and teachers) who assessed the videos of 7 children exposed to a Microswitch-cluster technology-based regabilitative program
DOI: 10.6084/m9.figshare.12665366.v1
title: Angelman_Cluster_2020

description: The dataset includes seven children with Angelman syndrome and severe to profound developmental disabilities exposed to a microswitch-cluster technology to promote object manipulation and reduce tongue protrusion. A long term follow-up (i.e., 24 months) was conducted. Intervals with indices of positive participation as an outcome measure of constructive engagement were additionally recorded.
DOI: 10.6084/m9.figshare.12665108
title: Table 2 - MIC

description: RAW Data from the paper "<b>Cell death and biomass reduction in biofilms of multidrug resistant extended spectrum β-lactamase-producing uropathogenic <i>Escherichia coli</i> isolates by 1,8-cineole</b>" from Plos One.
DOI: 10.6084/m9.figshare.12665108.v2
title: Table 2 - MIC

description: RAW Data from the paper "<b>Cell death and biomass reduction in biofilms of multidrug resistant extended spectrum β-lactamase-producing uropathogenic <i>Escherichia coli</i> isolates by 1,8-cineole</b>" from Plos One.
DOI: 10.6084/m9.figshare.12665108.v1
title: Table 2 - MIC

description: RAW Data from the paper "<b>Cell death and biomass reduction in biofilms of multidrug resistant extended spectrum β-lactamase-producing uropathogenic <i>Escherichia coli</i> isolates by 1,8-cineole</b>" from Plos One.
DOI: 10.6084/m9.figshare.12664970
title: Figure 2 images

description: Dataset for FiguresDataset for figures<br>
DOI: 10.6084/m9.figshare.12664997
title: Figure 4 data

description: Dataset for Figure4
DOI: 10.6084/m9.figshare.12664970.v1
title: Figure 2 images

description: Dataset for FiguresDataset for figures<br>
DOI: 10.6084/m9.figshare.12664982
title: Figure 4 images

description: Dataset for FiguresDataset for figures<br>
DOI: 10.6084/m9.figshare.12664988
title: Figure 3 data

description: Dataset for FiguresDataset for figures<br>
DOI: 10.6084/m9.figshare.12664997.v1
title: Figure 4 data

description: Dataset for Figure4
DOI: 10.6084/m9.figshare.12664967
title: Figure 1 images

description: Dataset for FiguresDataset for figures<br>
DOI: 10.6084/m9.figshare.12664982.v1
title: Figure 4 images

description: Dataset for FiguresDataset for figures<br>
DOI: 10.6084/m9.figshare.12664967.v1
title: Figure 1 images

description: Dataset for FiguresDataset for figures<br>
DOI: 10.6084/m9.figshare.12664988.v1
title: Figure 3 data

description: Dataset for FiguresDataset for figures<br>
DOI: 10.6084/m9.figshare.12664949
title: Severe SARS-CoV-2 infection in humans is defined by a shift in the serum lipidome resulting in dysregulation of eicosanoid immune mediators

description: Source data and additional method details for analysis from:Schwarz, Benjamin, et al. "Severe SAR-CoV-2 infection in humans is defined by a shift in the serum lipidome resulting in dysregulation of eicosanoid immune mediators." <i>medRxiv</i> (2020).<br>
DOI: 10.6084/m9.figshare.12664910
title: List of TE types and frequencies in the yellow drum

description: This table gives a list of TE types and frequencies in the Yellow drum genome.
DOI: 10.6084/m9.figshare.12664910.v1
title: List of TE types and frequencies in the yellow drum

description: This table gives a list of TE types and frequencies in the Yellow drum genome.
DOI: 10.6084/m9.figshare.12664949.v1
title: Severe SARS-CoV-2 infection in humans is defined by a shift in the serum lipidome resulting in dysregulation of eicosanoid immune mediators

description: Source data and additional method details for analysis from:Schwarz, Benjamin, et al. "Severe SAR-CoV-2 infection in humans is defined by a shift in the serum lipidome resulting in dysregulation of eicosanoid immune mediators." <i>medRxiv</i> (2020).<br>
DOI: 10.6084/m9.figshare.12664885
title: Table S1 species list.xlsx from Introduced bees (<i>Osmia cornifrons</i>) collect pollen from both coevolved and novel host-plant species within their family-level phylogenetic preferences

description: Studying the pollen preferences of introduced bees allows us to investigate how species use host-plants when establishing in new environments. <i>Osmia cornifrons</i> is a solitary bee introduced into North America from East-Asia for pollination of Rosaceae crops such as apples and cherries. We investigated whether <i>O. cornifrons</i> (i) more frequently collected pollen from host-plant species they coevolved with from their geographic origin or (ii) prefer hosts-plant species of specific plant taxa independent of origin. To address this question, using pollen metabarcoding, we examined the identity and relative abundance of pollen in larval provisions from nests located in different landscapes with varying abundance of East-Asian and non-Asian plant species. Our results show that <i>O. cornifrons</i> disproportionately, yet not exclusively, collected pollen from their native range. Plants in the family Rosaceae were their most preferred pollen hosts, where they differentially collected species native to East-Asia, Europe, or North America depending on the landscape. Our results suggest that while <i>O. cornifrons</i> more frequently collect pollen of East-Asian origin, the collection of pollen from novel species within their phylogenetic familial affinities can facilitate pollinator establishment. This phylogenetic preference highlights the effectiveness of <i>O. cornifrons</i> as crop pollinators of a variety of Rosaceae crops from different geographic origins. Our results imply that globalization of non-native plant species may ease the naturalization of their coevolved pollinators outside of their native range.
DOI: 10.6084/m9.figshare.12664885.v1
title: Table S1 species list.xlsx from Introduced bees (<i>Osmia cornifrons</i>) collect pollen from both coevolved and novel host-plant species within their family-level phylogenetic preferences

description: Studying the pollen preferences of introduced bees allows us to investigate how species use host-plants when establishing in new environments. <i>Osmia cornifrons</i> is a solitary bee introduced into North America from East-Asia for pollination of Rosaceae crops such as apples and cherries. We investigated whether <i>O. cornifrons</i> (i) more frequently collected pollen from host-plant species they coevolved with from their geographic origin or (ii) prefer hosts-plant species of specific plant taxa independent of origin. To address this question, using pollen metabarcoding, we examined the identity and relative abundance of pollen in larval provisions from nests located in different landscapes with varying abundance of East-Asian and non-Asian plant species. Our results show that <i>O. cornifrons</i> disproportionately, yet not exclusively, collected pollen from their native range. Plants in the family Rosaceae were their most preferred pollen hosts, where they differentially collected species native to East-Asia, Europe, or North America depending on the landscape. Our results suggest that while <i>O. cornifrons</i> more frequently collect pollen of East-Asian origin, the collection of pollen from novel species within their phylogenetic familial affinities can facilitate pollinator establishment. This phylogenetic preference highlights the effectiveness of <i>O. cornifrons</i> as crop pollinators of a variety of Rosaceae crops from different geographic origins. Our results imply that globalization of non-native plant species may ease the naturalization of their coevolved pollinators outside of their native range.