cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12180027.v1
title: Supplementary tables for: Natural selection outweighs genetic drift at Toll-like receptor (TLR) genes in the populations of Galápagos mockingbirds

description: The files contain supporting data for a manuscript about Toll-like receptor diversity in Galapagos mockingbirds. In this project we sequenced three Toll-like receptors (TLR1B, TLR4 and TLR15) by pair-end Illumina amplicon sequencing and the files presented here contain information about the sequence quality, genotyping and refined genotypes of individual mockingbirds. More details about methods can be found in the manuscript that will be published soon.<br>Description of the files:Supporting information 2 - amplicon statistics.tsv<br>This file contains various statistics of sequencing data presented per each amplicon (PCR_ID). The columns contain: number of raw sequencing reads (Raw_read_pairs), number of read pairs that survived trimmomatic filtering (both_survived), percentage of those reads from total (bs_perc), number of forward only reads that survived trimmomatic filtering (F_survived), their percentage (Fs_perc), number of reverse only reads that survived trimmomatic filtering (R_survived), their percentage (Rs_perc), number of reads that did not pass quality filtering (dropped), percentage of dropped reads( drop_perc), average sequence length (avg_sequence_length) and its range (Length_range), total number of refined sequences (Total Sequences), GC content (%GC).<br>Supporting information 3 - amplicon frequency.tsvThe file presents number of unique haplotypes per each TLR amplicon (AMPLICON_ID). The frequency of the five most frequent haplotypes shown (Frequency_{1..5}). If the ratio of frequencies of second to first haplotype (ratio_second_first) was higher then 1/3 we considered the locus heterozygous. <br>Supporting information 4 - genebank accession numbers.tsvThe file contains link between accession number in Genebank database and haplotype name (Allele name) used in genotype table (next file). <br>Supporting information 5 - individuals and their genotypes.tsvThis file contains TLR genotypes for each individual (sample name) belonging to particular island (population). Information about genotype (TLR1Ballele-1, TLR1Ballele-2, etc.) together with haplotype sequences stored in Genebank data can be used for recovery of the population level dataset.<br><br>Supporting information 6 multiqc_report.html<br>Multiqc report of amplicon dataset after trimmomatic filtering.
DOI: 10.6084/m9.figshare.12179925
title: LinkPhinder benchmarking splits

description: Benchmarking splits used to evaluate the LinkPhinder and other protein phosphorylation prediction models. <br>The XY numbers in the benchmark folder names reflect the train-test data ratio (e.g. 'benchmark9010' means the training and testing data are 90% and 10%, respectively, of the benchmark dataset). The nZ number then means the number of negatives per each positive (e.g. 'benchmark7030n10' means a 70/30 train/test split with ten negatives per each positive). PhosphoSitePlus (https://doi.org/10.1093/nar/gku1267) was used as the benchmark dataset in most cases, with the exception of folders tagged with 'cutillas20' (this is based on the kinase-substrate interaction dataset published in https://doi.org/10.1038/s41587-019-0391-9). The columns in the training and testing split files correspond to the kinase, site, and substrate respectively. The columns in the scores files correspond to the kinase uniprot accession id, the site, the substrate uniprot accession id and the LinkPhinder score respectively.
DOI: 10.6084/m9.figshare.12179880
title: Network structure of vertebrate scavenger assemblages at the global scale: drivers and ecosystem functioning implications

description: Dataset used in the study: Sebastián-González et al. 2020. Network structure of vertebrate scavenger assemblages at the global scale: drivers and ecosystem functioning implications. Ecography, 43:1-14. doi: 10.1111/ecog.05083 Data on vertebrate scavenger assemblages from worldwide. We include information on the characteristics of the study sites, the scavenger assemblages, network metrics and related references
DOI: 10.6084/m9.figshare.12179406
title: Unrecognized diversity of <i>Trocheta</i> species (Hirudinea: Erpobdellidae): resolving a century-old taxonomic problem in Crimean leeches

description: Erpobdellid leeches of the genus <i>Trocheta</i> are among the biggest and most charismatic members of their class. The studies of the group have a long and complicated history due to the lack of reliable distinguishing features, which impedes the taxonomy of the genus. A number of <i>Trocheta</i> species have been misclassified for years if not centuries. Our present research demonstrates that the genus <i>Trocheta</i> is characterized by high cryptic diversity since some populations that have been viewed as the same species should be, in fact, assigned to different species. <i>Trocheta</i> leeches from the Dniester basin and the Crimean Peninsula have been both confused with each other and erroneously assigned to species that do not occur in southern Ukraine. Here, a new species from the Crimean Peninsula, <i>Trocheta blanchardi</i> sp. nov., is described based on a phylogenetic analysis of <i>cox1</i> gene sequences and a reassessment of morphological characters such as colouration, annulation, size and arrangement of papillae, and genital anatomy. The analysis suggests close relationships of <i>T. blanchardi</i> sp. nov. to Anatolian species. Given its fragile habitats and restricted range, the species needs serious protection and further surveys. Obviously, more species await description as is evident from the significant genetic differences between leech populations. http://zoobank.org/urn:lsid:zoobank.org:pub:8610460D-862B-4F28-8520-5C8D11AEB015
DOI: 10.6084/m9.figshare.12179406.v1
title: Unrecognized diversity of <i>Trocheta</i> species (Hirudinea: Erpobdellidae): resolving a century-old taxonomic problem in Crimean leeches

description: Erpobdellid leeches of the genus <i>Trocheta</i> are among the biggest and most charismatic members of their class. The studies of the group have a long and complicated history due to the lack of reliable distinguishing features, which impedes the taxonomy of the genus. A number of <i>Trocheta</i> species have been misclassified for years if not centuries. Our present research demonstrates that the genus <i>Trocheta</i> is characterized by high cryptic diversity since some populations that have been viewed as the same species should be, in fact, assigned to different species. <i>Trocheta</i> leeches from the Dniester basin and the Crimean Peninsula have been both confused with each other and erroneously assigned to species that do not occur in southern Ukraine. Here, a new species from the Crimean Peninsula, <i>Trocheta blanchardi</i> sp. nov., is described based on a phylogenetic analysis of <i>cox1</i> gene sequences and a reassessment of morphological characters such as colouration, annulation, size and arrangement of papillae, and genital anatomy. The analysis suggests close relationships of <i>T. blanchardi</i> sp. nov. to Anatolian species. Given its fragile habitats and restricted range, the species needs serious protection and further surveys. Obviously, more species await description as is evident from the significant genetic differences between leech populations. http://zoobank.org/urn:lsid:zoobank.org:pub:8610460D-862B-4F28-8520-5C8D11AEB015
DOI: 10.15468/zgdtpj
title: Tanaidacea (Crustacea: Peracarida) of the northeast Atlantic: Chauliopleona Dojiri and Sieg, 1997 and Saurotipleona n. gen. from the ‘ Atlantic Margin’

description: This dataset contains the digitized treatments in Plazi based on the original journal article Bird, Graham John (2015): Tanaidacea (Crustacea: Peracarida) of the northeast Atlantic: Chauliopleona Dojiri and Sieg, 1997 and Saurotipleona n. gen. from the ‘ Atlantic Margin’. Journal of Natural History 49 (25): 1507-1547, DOI: 10.1080/00222933.2015.1005715
DOI: 10.6084/m9.figshare.12179190
title: LMS values: reference levels for anogenital distance in healthy children.xlsx

description: The International AGD consortium (IAC) was created in 2015 and consists of data from four clinical centers. Reference ranges for “short” and “long” AGD, TIDES- and Cambridge method were generated using the Lambda-Mu-Sigma (LMS) method.All data were from population-based studies, recruiting from maternity or obstetric units from four research centers (1:USA, 2:Cambridge, 3:Odense, 4:Copenhagen) associated with a university hospital.<br>This study included a total of 7295 AGD examinations performed on 3705 healthy, mainly Caucasian children aged 0-24 months. <br>
DOI: 10.6084/m9.figshare.12179184
title: Raw dataset for figures 3b-6 from Allocation of gene products to daughter cells is determined by the age of the mother in single <i>Escherichia coli</i> cells

description: Fluorescence and elongation rate of new and old daughters
DOI: 10.6084/m9.figshare.12179190.v2
title: LMS values: reference levels for anogenital distance in healthy children.xlsx

description: The International AGD consortium (IAC) was created in 2015 and consists of data from four clinical centers. Reference ranges for “short” and “long” AGD, TIDES- and Cambridge method were generated using the Lambda-Mu-Sigma (LMS) method.All data were from population-based studies, recruiting from maternity or obstetric units from four research centers (1:USA, 2:Cambridge, 3:Odense, 4:Copenhagen) associated with a university hospital.<br>This study included a total of 7295 AGD examinations performed on 3705 healthy, mainly Caucasian children aged 0-24 months. <br>
DOI: 10.6084/m9.figshare.12179178
title: Raw dataset for figure 3a from Allocation of gene products to daughter cells is determined by the age of the mother in single <i>Escherichia coli</i> cells

description: Fluorescence of polar halves of new and old daughters
DOI: 10.6084/m9.figshare.12179184.v1
title: Raw dataset for figures 3b-6 from Allocation of gene products to daughter cells is determined by the age of the mother in single <i>Escherichia coli</i> cells

description: Fluorescence and elongation rate of new and old daughters
DOI: 10.6084/m9.figshare.12179190.v1
title: LMS values: reference levels for anogenital distance in healthy children.xlsx

description: The International AGD consortium (IAC) was created in 2015 and consists of data from four clinical centers. Reference ranges for “short” and “long” AGD, TIDES- and Cambridge method were generated using the Lambda-Mu-Sigma (LMS) method.All data were from population-based studies, recruiting from maternity or obstetric units from four research centers (1:USA, 2:Cambridge, 3:Odense, 4:Copenhagen) associated with a university hospital.<br>This study included a total of 7295 AGD examinations performed on 3705 healthy, mainly Caucasian children aged 0-24 months. <br>
DOI: 10.6084/m9.figshare.12179175
title: Raw dataset for figures 2b from Allocation of gene products to daughter cells is determined by the age of the mother in single <i>Escherichia coli</i> cells

description: Fluorescent measurements of cellular polar halves
DOI: 10.6084/m9.figshare.12179178.v1
title: Raw dataset for figure 3a from Allocation of gene products to daughter cells is determined by the age of the mother in single <i>Escherichia coli</i> cells

description: Fluorescence of polar halves of new and old daughters
DOI: 10.6084/m9.figshare.12179085
title: Assessing and addressing the social determinants of noncommunicable diseases in primary care: a systematic review - Supplementary web appendix

description: PRISMA checklist, risk of bias assessment, and Medline search strategy for 'Assessing and addressing the social determinants of noncommunicable diseases in primary care: a systematic review', WHO Bulletin special issue on Primary Health Care, by Allen LA, Smith RW, Simmons-Jones F, Roberts N, Honney R, Currie J.
DOI: 10.6084/m9.figshare.12179067
title: Water content calculations

description: water content calculations
DOI: 10.6084/m9.figshare.12179085.v1
title: PRISMA checklist

description: PRISMA checklist for Allen et al. Assessing and addressing the social determinants of noncommunicable diseases in primary care: a systematic review. WHO Bulletin special issue on Primary Health Care
DOI: 10.6084/m9.figshare.12179085.v2
title: Assessing and addressing the social determinants of noncommunicable diseases in primary care: a systematic review - Supplementary web appendix

description: PRISMA checklist, risk of bias assessment, and Medline search strategy for 'Assessing and addressing the social determinants of noncommunicable diseases in primary care: a systematic review', WHO Bulletin special issue on Primary Health Care, by Allen LA, Smith RW, Simmons-Jones F, Roberts N, Honney R, Currie J.
DOI: 10.6084/m9.figshare.12179046
title: Experimental data.xlsx

description: raw data
DOI: 10.6084/m9.figshare.12179046.v1
title: Experimental data.xlsx

description: raw data
DOI: 10.6084/m9.figshare.12178929
title: entsoe-hourly-prices.csv

description: Hourly prices for bidding zones retrieved from the ENTSO-E Transparency Platform<br>
DOI: 10.6084/m9.figshare.12178869
title: example

description: insecticide resistance mornitoring
DOI: 10.6084/m9.figshare.12178695
title: Supplementary Material for: Genetic Variants in the Activation of the Brown-Like Adipocyte Pathway and the Risk for Severe Obesity

description: <b><i>Background:</i></b> Regular physical activity has an important role in energy expenditure and combats the development of obesity. During exercise, <i>PPARGC1A</i> is overexpressed, stimulating an increase of the expression of <i>FNDC5</i>. This protein is cleaved to release the hormone irisin, which activates a browning process in white adipose tissue through an increase in <i>UCP1</i> expression. As a result, irisin leads to mitochondrial heat production and energy expenditure. <b><i>Objectives:</i></b><i></i>The aim of this study was to investigate whether genetic variants in genes related to browning are associated with severe obesity and obesity-related features. This case-control study comprised 210 individuals with severe obesity (median body mass index [BMI] 45.6 [range 40.5–52.2]) and 191 normal-weight subjects (BMI 22.8 [21.1–23.9]). <b><i>Methods:</i></b> Genomic DNA was extracted from peripheral blood and the genotypes of the <i>PPARGC1A</i>(rs8192678, rs3736265, rs2970847, and rs3755863) and <i>UCP1</i> (rs6536991 and rs12502572) genes were obtained using Taqman® assay. For the <i>FNDC5</i> gene, screening of exons 3–5 as well as their intron-exon boundaries was performed using automatic sequencing. <b><i>Results:</i></b> Our results demonstrated that <i>PPARGC1A</i>rs2970847 and <i>UCP1</i>rs12502572 are associated with severe obesity. Furthermore, these polymorphisms influence anthropometric traits, such as BMI, body weight, and body adiposity index. Our findings also showed a dose-effect relationship between <i>PPARGC1A</i> rs8192678 and fasting plasma glucose. Finally, 5 rare mutations were identified in <i>FNDC5</i>, and 1 of these is a novel missense mutation. <b><i>Conclusion:</i></b> This study shows that genetic variants in the activation of brown-like adipocyte pathway play an important role in the susceptibility to severe obesity.
DOI: 10.6084/m9.figshare.12178701
title: Online Data Supplement

description: Supplementary Table 1. The genes involved in OSASupplementary Table 2. miRNA in OSASupplementary Table 3. lncRNA in OSASupplementary Table 4. DNA methylation in OSASupplementary Table 5. The chemical compounds involved in OSASupplementary Table 6. Patient and animal models for OSA
DOI: 10.6084/m9.figshare.12178869.v1
title: example

description: insecticide resistance mornitoring
DOI: 10.6084/m9.figshare.12178695.v1
title: Supplementary Material for: Genetic Variants in the Activation of the Brown-Like Adipocyte Pathway and the Risk for Severe Obesity

description: <b><i>Background:</i></b> Regular physical activity has an important role in energy expenditure and combats the development of obesity. During exercise, <i>PPARGC1A</i> is overexpressed, stimulating an increase of the expression of <i>FNDC5</i>. This protein is cleaved to release the hormone irisin, which activates a browning process in white adipose tissue through an increase in <i>UCP1</i> expression. As a result, irisin leads to mitochondrial heat production and energy expenditure. <b><i>Objectives:</i></b><i></i>The aim of this study was to investigate whether genetic variants in genes related to browning are associated with severe obesity and obesity-related features. This case-control study comprised 210 individuals with severe obesity (median body mass index [BMI] 45.6 [range 40.5–52.2]) and 191 normal-weight subjects (BMI 22.8 [21.1–23.9]). <b><i>Methods:</i></b> Genomic DNA was extracted from peripheral blood and the genotypes of the <i>PPARGC1A</i>(rs8192678, rs3736265, rs2970847, and rs3755863) and <i>UCP1</i> (rs6536991 and rs12502572) genes were obtained using Taqman® assay. For the <i>FNDC5</i> gene, screening of exons 3–5 as well as their intron-exon boundaries was performed using automatic sequencing. <b><i>Results:</i></b> Our results demonstrated that <i>PPARGC1A</i>rs2970847 and <i>UCP1</i>rs12502572 are associated with severe obesity. Furthermore, these polymorphisms influence anthropometric traits, such as BMI, body weight, and body adiposity index. Our findings also showed a dose-effect relationship between <i>PPARGC1A</i> rs8192678 and fasting plasma glucose. Finally, 5 rare mutations were identified in <i>FNDC5</i>, and 1 of these is a novel missense mutation. <b><i>Conclusion:</i></b> This study shows that genetic variants in the activation of brown-like adipocyte pathway play an important role in the susceptibility to severe obesity.
DOI: 10.6084/m9.figshare.12178701.v1
title: Untitled Item

description: Supplementary Table 1. The genes involved in OSASupplementary Table 2. miRNA in OSASupplementary Table 3. lncRNA in OSASupplementary Table 4. DNA methylation in OSASupplementary Table 5. The chemical compounds involved in OSASupplementary Table 6. Patient and animal models for OSA
DOI: 10.6084/m9.figshare.12178869.v2
title: example

description: insecticide resistance mornitoring
DOI: 10.6084/m9.figshare.12178869.v4
title: example

description: insecticide resistance mornitoring
DOI: 10.6084/m9.figshare.12178869.v3
title: example

description: insecticide resistance mornitoring
DOI: 10.6084/m9.figshare.12178701.v3
title: Online Data Supplement

description: Supplementary Table 1. The genes involved in OSASupplementary Table 2. miRNA in OSASupplementary Table 3. lncRNA in OSASupplementary Table 4. DNA methylation in OSASupplementary Table 5. The chemical compounds involved in OSASupplementary Table 6. Patient and animal models for OSA
DOI: 10.6084/m9.figshare.12178701.v2
title: Untitled Item

description: Supplementary Table 1. The genes involved in OSASupplementary Table 2. miRNA in OSASupplementary Table 3. lncRNA in OSASupplementary Table 4. DNA methylation in OSASupplementary Table 5. The chemical compounds involved in OSASupplementary Table 6. Patient and animal models for OSA
DOI: 10.6084/m9.figshare.12178659
title: Increased risk and early onset of ALS in professional players from Italian Soccer Teams

description: <i>Objective</i>: Since the observation of several deaths from amyotrophic lateral sclerosis (ALS) among Italian professional soccer players, an association between ALS and soccer has been postulated. The objective of the study is to investigate the association between professional soccer and the risk of ALS in a large cohort of former professional soccer players with prolonged follow-up. <i>Methods</i>: All professional soccer players practicing in the period 1959–2000 were identified through the archives of an Italian soccer cards publisher. For each player, date and place of birth, playing role, and team history were recorded. Each player was followed since 15 years of age. Incident ALS cases were all soccer players first diagnosed during the period 1959–2018. The expected incidence rate was the number of ALS cases/100,000 person-years expected in the cohort. SIR was the ratio between observed and expected incidence rate. <i>Results</i>: 34 ALS cases were detected. The number of expected cases was 17.8. The SIR was 1.91 (95% CI 1.32–2.67) in the entire sample and 4.66 (95% CI 2.66–7.57) in subjects aged less than 45 years. The mean age at diagnosis was 45.0 years. Compared to the mean age of onset of ALS in the general population (65.2 years), the disease in former soccer players occurred 20.2 years earlier. <i>Conclusions</i>: Professional soccer players are at higher risk of developing ALS than the general population. Soccer players with ALS develop the disease at a younger than expected age.
DOI: 10.6084/m9.figshare.12178659.v1
title: Increased risk and early onset of ALS in professional players from Italian Soccer Teams

description: <i>Objective</i>: Since the observation of several deaths from amyotrophic lateral sclerosis (ALS) among Italian professional soccer players, an association between ALS and soccer has been postulated. The objective of the study is to investigate the association between professional soccer and the risk of ALS in a large cohort of former professional soccer players with prolonged follow-up. <i>Methods</i>: All professional soccer players practicing in the period 1959–2000 were identified through the archives of an Italian soccer cards publisher. For each player, date and place of birth, playing role, and team history were recorded. Each player was followed since 15 years of age. Incident ALS cases were all soccer players first diagnosed during the period 1959–2018. The expected incidence rate was the number of ALS cases/100,000 person-years expected in the cohort. SIR was the ratio between observed and expected incidence rate. <i>Results</i>: 34 ALS cases were detected. The number of expected cases was 17.8. The SIR was 1.91 (95% CI 1.32–2.67) in the entire sample and 4.66 (95% CI 2.66–7.57) in subjects aged less than 45 years. The mean age at diagnosis was 45.0 years. Compared to the mean age of onset of ALS in the general population (65.2 years), the disease in former soccer players occurred 20.2 years earlier. <i>Conclusions</i>: Professional soccer players are at higher risk of developing ALS than the general population. Soccer players with ALS develop the disease at a younger than expected age.
DOI: 10.6084/m9.figshare.12178170
title: Additional file 7 of Interactions between sucrose and jasmonate signalling in the response to cold stress

description: Additional file 7 Hormone, anthocyanin and sugar contents in Col-0, jar1–1, Col-gl and coi1–16 plants grown at cold (4 °C) or warm (20 °C) temperature.
DOI: 10.6084/m9.figshare.12178164
title: Additional file 6 of Interactions between sucrose and jasmonate signalling in the response to cold stress

description: Additional file 6. Correlation between hormones, anthocyanins and sugars.
DOI: 10.6084/m9.figshare.12178170.v1
title: Additional file 7 of Interactions between sucrose and jasmonate signalling in the response to cold stress

description: Additional file 7 Hormone, anthocyanin and sugar contents in Col-0, jar1–1, Col-gl and coi1–16 plants grown at cold (4 °C) or warm (20 °C) temperature.
DOI: 10.6084/m9.figshare.12178164.v1
title: Additional file 6 of Interactions between sucrose and jasmonate signalling in the response to cold stress

description: Additional file 6. Correlation between hormones, anthocyanins and sugars.
DOI: 10.6084/m9.figshare.12178152
title: Additional file 4 of Interactions between sucrose and jasmonate signalling in the response to cold stress

description: Additional file 4. Two-way ANOVA testing for sucrose effects, genotype effects and interactions between sucrose treatment and genotype.
DOI: 10.6084/m9.figshare.12178152.v1
title: Additional file 4 of Interactions between sucrose and jasmonate signalling in the response to cold stress

description: Additional file 4. Two-way ANOVA testing for sucrose effects, genotype effects and interactions between sucrose treatment and genotype.