cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5726696
title: Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome

description: <br> Abbreviation of species names in each folder: Palb, P. alba; Pade, P. adenopoda; Pdav, P. davidiana; Ptra, P. tremula; Ptrs, P. tremuloides; Prot, P. rotundifolia; Pqio,P. qiongdaoensis. 1. FST<br> Relative divergence (FST) for pairwise species comparisons was calculated for all sites with 100 Kbp non-overlapping windows. 2. dxy<br> Absolute divergence (dxy) was calculated for all sites with 100 Kbp non-overlapping windows. 3. Nucleotide diversity<br> Nucleotide diversity (π) was calculated for all sites with 100 Kbp non-overlapping windows. 4. Derived allele frequency<br> The derived frequencies of 4 different functional categories. Each folder contains seven Populus resluts 5. Derived_allele_statistics<br> The statistics of homozygous and heterozygous derived alleles for loss of function, deleterious, tolerated and synonymous variants for each individual. The last two individuals in each file are outgroups 6. dsuite-dinvestigate<br> The outputs of 10 trios using program Dinvestigate from Dsuite. The sliding window is 50 SNPs, and the step is 20 SNPs. 7. Recombination rate<br> The result of population-scaled recombination rate was calculated by LDhat v2.2. 8. Volcanofinder<br> Genome-wide scans of introgression sweeps within each species was implemented using VolcanFinder v.1.0 with the Model over 10 Kbp non-overlapping windows. 9. ihh12<br> phased SNPs were used to computed ihh12 by selscan v1.3.0. 10 populus162.phased.recode.vcf.gz<br> SNPs were phased with Beagle v.4.1 for the 162 non-hybrid individuals. 11 populus227.snp.rm_indel.para_filter.biallelic.GQ30.max_miss20.bed.recode.vcf.gz <br> The vcf of 227 Populus samples.
DOI: 10.5281/zenodo.5726695
title: Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome

description: <br> Abbreviation of species names in each folder: Palb, P. alba; Pade, P. adenopoda; Pdav, P. davidiana; Ptra, P. tremula; Ptrs, P. tremuloides; Prot, P. rotundifolia; Pqio,P. qiongdaoensis. 1. FST<br> Relative divergence (FST) for pairwise species comparisons was calculated for all sites with 100 Kbp non-overlapping windows. 2. dxy<br> Absolute divergence (dxy) was calculated for all sites with 100 Kbp non-overlapping windows. 3. Nucleotide diversity<br> Nucleotide diversity (π) was calculated for all sites with 100 Kbp non-overlapping windows. 4. Derived allele frequency<br> The derived frequencies of 4 different functional categories. Each folder contains seven Populus resluts 5. Derived_allele_statistics<br> The statistics of homozygous and heterozygous derived alleles for loss of function, deleterious, tolerated and synonymous variants for each individual. The last two individuals in each file are outgroups 6. dsuite-dinvestigate<br> The outputs of 10 trios using program Dinvestigate from Dsuite. The sliding window is 50 SNPs, and the step is 20 SNPs. 7. Recombination rate<br> The result of population-scaled recombination rate was calculated by LDhat v2.2. 8. Volcanofinder<br> Genome-wide scans of introgression sweeps within each species was implemented using VolcanFinder v.1.0 with the Model over 10 Kbp non-overlapping windows. 9. ihh12<br> phased SNPs were used to computed ihh12 by selscan v1.3.0. 10 populus162.phased.recode.vcf.gz<br> SNPs were phased with Beagle v.4.1 for the 162 non-hybrid individuals. 11 populus227.snp.rm_indel.para_filter.biallelic.GQ30.max_miss20.bed.recode.vcf.gz <br> The vcf of 227 Populus samples.
DOI: 10.5281/zenodo.5713591
title: Molecular mapping of urinary complement peptides in kidney diseases

description: <strong>Abstract: </strong>Defective complement activation has been associated with various types of kidney disease. This led to the hypothesis that specific urine complement fragments may be associated with kidney disease etiologies, and disease progression may be reflected by changes in these complement fragments. We investigated the occurrence of complement fragments in urine, their association with kidney function and disease etiology in 16,027 subjects, using mass spectrometry based peptidomics data from the Human Urinary Proteome/Peptidome Database. Twenty-three different urinary peptides originating from complement proteins C3, C4 and factor B (CFB) could be identified. Most C3-derived peptides showed inverse association with estimated glomerular filtration rate (eGFR), while the majority of peptides derived from CFB demonstrated positive association with eGFR. Several peptides derived from the complement proteins C3, C4 and CFB were found significantly associated with specific kidney disease etiologies. These peptides may depict disease-specific complement activation and could serve as non-invasive biomarkers to support development of complement interventions through assessing complement activity for patients’ stratification and monitoring of drug impact. Further investigation of these complement peptides may provide additional insight into disease pathophysiology and could possibly guide therapeutic decisions, especially when targeting complement factors.
DOI: 10.5281/zenodo.5713590
title: Molecular mapping of urinary complement peptides in kidney diseases

description: <strong>Abstract: </strong>Defective complement activation has been associated with various types of kidney disease. This led to the hypothesis that specific urine complement fragments may be associated with kidney disease etiologies, and disease progression may be reflected by changes in these complement fragments. We investigated the occurrence of complement fragments in urine, their association with kidney function and disease etiology in 16,027 subjects, using mass spectrometry based peptidomics data from the Human Urinary Proteome/Peptidome Database. Twenty-three different urinary peptides originating from complement proteins C3, C4 and factor B (CFB) could be identified. Most C3-derived peptides showed inverse association with estimated glomerular filtration rate (eGFR), while the majority of peptides derived from CFB demonstrated positive association with eGFR. Several peptides derived from the complement proteins C3, C4 and CFB were found significantly associated with specific kidney disease etiologies. These peptides may depict disease-specific complement activation and could serve as non-invasive biomarkers to support development of complement interventions through assessing complement activity for patients’ stratification and monitoring of drug impact. Further investigation of these complement peptides may provide additional insight into disease pathophysiology and could possibly guide therapeutic decisions, especially when targeting complement factors.
DOI: 10.6084/m9.figshare.17039935
title: Appendix S1.csv from Annual precipitation predicts the phylogenetic signal in bat-fruit interaction networks across the Neotropics

description: Closely related species tend to be more similar than randomly selected species from the same phylogenetic tree. This pattern, known as a phylogenetic signal, has been extensively studied for intrinsic (e.g. morphology), as well as extrinsic (e.g. climatic preferences), properties but less so for ecological interactions. Phylogenetic signals of species interactions (i.e. resource use) can vary across time and space, but the causes behind such variations across broader spatial extents remain elusive. Here, we evaluated how current and historical climates influence phylogenetic signals of bat–fruit interaction networks across the Neotropics. We performed a model selection relating the phylogenetic signals of each trophic level (bats and plants) with a set of current and historical climatic factors deemed ecologically important in shaping biotic interactions. Bat and plant phylogenetic signals in bat–fruit interaction networks varied little with climatic factors, although bat phylogenetic signals positively covaried with annual precipitation. These findings indicated that water availability could increase resource availability, favouring higher niche partitioning of trophic resources among bat species and hence bat phylogenetic signals across bat–fruit interaction networks. Overall, our study advances our understanding of the spatial dynamics of bat–fruit interactions by highlighting the association of current climatic factors with phylogenetic patterns of biotic interactions.
DOI: 10.6084/m9.figshare.17039935.v3
title: Appendix S1.csv from Annual precipitation predicts the phylogenetic signal in bat-fruit interaction networks across the Neotropics

description: Closely related species tend to be more similar than randomly selected species from the same phylogenetic tree. This pattern, known as a phylogenetic signal, has been extensively studied for intrinsic (e.g. morphology), as well as extrinsic (e.g. climatic preferences), properties but less so for ecological interactions. Phylogenetic signals of species interactions (i.e. resource use) can vary across time and space, but the causes behind such variations across broader spatial extents remain elusive. Here, we evaluated how current and historical climates influence phylogenetic signals of bat–fruit interaction networks across the Neotropics. We performed a model selection relating the phylogenetic signals of each trophic level (bats and plants) with a set of current and historical climatic factors deemed ecologically important in shaping biotic interactions. Bat and plant phylogenetic signals in bat–fruit interaction networks varied little with climatic factors, although bat phylogenetic signals positively covaried with annual precipitation. These findings indicated that water availability could increase resource availability, favouring higher niche partitioning of trophic resources among bat species and hence bat phylogenetic signals across bat–fruit interaction networks. Overall, our study advances our understanding of the spatial dynamics of bat–fruit interactions by highlighting the association of current climatic factors with phylogenetic patterns of biotic interactions.
DOI: 10.6084/m9.figshare.17039935.v2
title: Appendix S1.csv from Annual precipitation predicts the phylogenetic signal in bat–fruit interaction networks across the Neotropics

description: Closely related species tend to be more similar than randomly selected species from the same phylogenetic tree. This pattern, known as a phylogenetic signal, has been extensively studied for intrinsic (e.g. morphology), as well as extrinsic (e.g. climatic preferences), properties but less so for ecological interactions. Phylogenetic signals of species interactions (i.e. resource use) can vary across time and space, but the causes behind such variations across broader spatial extents remain elusive. Here, we evaluated how current and historical climates influence phylogenetic signals of bat–fruit interaction networks across the Neotropics. We performed a model selection relating the phylogenetic signals of each trophic level (bats and plants) with a set of current and historical climatic factors deemed ecologically important in shaping biotic interactions. Bat and plant phylogenetic signals in bat–fruit interaction networks varied little with climatic factors, although bat phylogenetic signals positively covaried with annual precipitation. These findings indicated that water availability could increase resource availability, favouring higher niche partitioning of trophic resources among bat species and hence bat phylogenetic signals across bat–fruit interaction networks. Overall, our study advances our understanding of the spatial dynamics of bat–fruit interactions by highlighting the association of current climatic factors with phylogenetic patterns of biotic interactions.
DOI: 10.5281/zenodo.5727490
title: SUPPLEMENTARY DATA_HODEL et al_Southwest Pacific Eocene-Oligocene paleoceanography

description: Supplementary data set for <strong>Eocene-Oligocene Southwest Pacific Ocean paleoceanography</strong> New insights from foraminifera chemistry (DSDP Site 277, Campbell Plateau) By F. Hodel et al.
DOI: 10.5281/zenodo.5727489
title: SUPPLEMENTARY DATA_HODEL et al_Southwest Pacific Eocene-Oligocene paleoceanography

description: Supplementary data set for <strong>Eocene-Oligocene Southwest Pacific Ocean paleoceanography</strong> New insights from foraminifera chemistry (DSDP Site 277, Campbell Plateau) By F. Hodel et al.
DOI: 10.5281/zenodo.5727449
title: Example datasets from 16S rRNA amplicon Illumina paired end sequencing

description: Six example datasets from 16S rRNA amplicon Illumina paired-end sequencing.
DOI: 10.5281/zenodo.5727394
title: Example datasets from 16S rRNA amplicon Illumina paired end sequencing

description: Six example datasets from 16S rRNA amplicon Illumina paired-end sequencing.
DOI: 10.6084/m9.figshare.13395470.v3
title: An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes

description: This is the data supplement for the manuscript "An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes"<br><br>Authors: Edmund R. R. Moody1, Tara A. Mahendrarajah2, Nina Dombrowski2, James W. Clark1, Celine Petitjean1, Pierre Offre2, Gergely J. Szöllősi3,4,5, Anja Spang2,6*, Tom A. Williams1*<br>1. School of Biological Sciences, University of Bristol, Bristol BS8 1TH, UK.2. NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry; AB Den Burg, The Netherlands3. Dept. of Biological Physics, Eötvös Loránd University, 1117 Budapest, Hungary 4. MTA-ELTE “Lendület” Evolutionary Genomics Research Group, 1117 Budapest, Hungary; 5. Institute of Evolution, Centre for Ecological Research, 1121 Budapest, Hungary6. Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden<br>*Co-corresponding authors: tom.a.williams@bristol.ac.uk, anja.spang@nioz.nl<br>This data supplement contains sequence alignments, trees, and python scripts used for analysis as well as tables of results.
DOI: 10.6084/m9.figshare.17081960
title: DATA_LST_MIRA.rar

description: The zip file consists of climate datasets obtained from Worldclim and all intermediate data for calculating the Land Surface Temperature (LST) for the Tiruchchirappalli region, Tamil Nadu, India.
DOI: 10.6084/m9.figshare.17081960.v1
title: DATA_LST_MIRA.rar

description: The zip file consists of climate datasets obtained from Worldclim and all intermediate data for calculating the Land Surface Temperature (LST) for the Tiruchchirappalli region, Tamil Nadu, India.
DOI: 10.48320/f5509d39-b2d4-409d-ad37-9e72570206ad
title: Maidan Oral History Archive
DOI: 10.20375/0000-000e-75c4-1
title: DocuDataCollection.pdf
DOI: 10.20375/0000-000e-75c5-0
title: Lists_of_pol_prisoners_Russia.zip
DOI: 10.48320/decaaca8-fb9a-4fcf-9153-da09332cc02a
title: List of Political Prisoners of the Russian Federation, 2014-2016
DOI: 10.15129/352f9a13-69bb-4531-a792-1776a30e1973
title: Data for: "Electrochemical Strategies for the Screening of Synthetic Cannabinoid BB-22 (QUCHIC) within a Toxicological Specimen"

description: Data for "Electrochemical Strategies for the Screening of Synthetic Cannabinoid BB-22 (QUCHIC) within a Toxicological Specimen" This includes all cyclic voltammetry and differential pulsed voltammograms for the screening of BB-22 in biological matrices and the supplementary data for this publication Data embargo until 25/11/2022
DOI: 10.21227/m21d-9e37
title: Differential ad-hoc detector of XOR H-MAP for 2 BPSK sources in H-MAC.

description: We present detailed derivation of probability functions of differential ad-hoc detector and coherent detectors of XOR H-map for 2 (differentially encoded) BPSK source in H-MAC channel. Matlab script-files for (analytical) H-BER computation are provided.
DOI: 10.15468/87fvuz
title: Darwin wasps of the subfamily Pimplinae (Hymenoptera: Ichneumonidae) of Mexico: genera Apechthis Förster, Itoplectis Förster and Pimpla Fabricius

description: This dataset contains the digitized treatments in Plazi based on the original journal article Khalaim, Andrey I., Ruíz-Cancino, Enrique (2021): Darwin wasps of the subfamily Pimplinae (Hymenoptera: Ichneumonidae) of Mexico: genera Apechthis Förster, Itoplectis Förster and Pimpla Fabricius. Zootaxa 5071 (4): 451-491, DOI: https://doi.org/10.11646/zootaxa.5071.4.1
DOI: 10.15468/qd8fbq
title: New records for associations between peritrich protozoan ciliates (Ciliophora, Sessilida) and polychaete worms (Annelida) from off the southeastern coast of India

description: This dataset contains the digitized treatments in Plazi based on the original journal article Bharathidasan, Veeraiyan, Sarathy, Palanivel Partha, Murugesan, Perumal, Nogueira, João Miguel De Matos (2021): New records for associations between peritrich protozoan ciliates (Ciliophora, Sessilida) and polychaete worms (Annelida) from off the southeastern coast of India. Zootaxa 5071 (4): 492-504, DOI: https://doi.org/10.11646/zootaxa.5071.4.2
DOI: 10.21227/sawp-ax73
title: AI-based Automated Extraction of Entities, Entity Categories and Sentiments on COVID-19 Situation

description: The coronavirus disease (COVID-19) pandemic has affected the lives of social media users in an unprecedented manner. They are constantly posting their satisfaction or dissatisfaction over the COVID-19 situation at their location of interest. For example, many international travelers who are unable to return to their residential locations owing to measures such as lockdowns, curfews, and the suspension of flights are posting their dissatisfaction over government efficiency in dealing with this situation. Therefore, understanding location-oriented sentiments about this situation is of prime importance for diplomats, political leaders, and strategic decision-makers. To this end, we present a new fully automated algorithm based on artificial intelligence (AI), for extraction of location-oriented public sentiments on the COVID-19 situation. We designed the proposed system to obtain exhaustive knowledge and insights on social media feeds related to COVID-19 in 110 languages through AI-based translation, sentiment analysis, location entity detection, and decomposition tree analysis. We deployed and tested this algorithm on live Twitter feeds from July 15, 2021 to August 10, 2021. Out of 1866 tweet messages analyzed, 990 Tweets contained one or more location entities. In total 1,322 location entities were detected falling under city, contitinent, country region, language and state entity categories.
DOI: 10.6084/m9.figshare.17082071
title: Data for the Paper - "On the Path to Thermo-stable Collagen: Culturing the Versatile Sponge Chondrosia reniformis" Orel et al.

description: Data for the paper: "On the Path to Thermo-stable Collagen: Culturing the Versatile Sponge <i>Chondrosia reniformis" Orel et al.</i>
DOI: 10.6084/m9.figshare.17082071.v1
title: Data for the Paper - "On the Path to Thermo-stable Collagen: Culturing the Versatile Sponge Chondrosia reniformis" Orel et al.

description: Data for the paper: "On the Path to Thermo-stable Collagen: Culturing the Versatile Sponge <i>Chondrosia reniformis" Orel et al.</i>
DOI: 10.6084/m9.figshare.14717676
title: Data from: Multiple anthropogenic pressures lead to seed dispersal collapse of the southernmost palm Jubaea chilensis

description: Original data from:Cordero, S., F. Gálvez & F.E. Fontúrbel. 2021. Multiple anthropogenic pressures lead to seed dispersal collapse of the southernmost palm Jubaea chilensis. Frontiers in Ecology and Evolution. doi: 10.3389/fevo.2021.719566<br>This repository contains two files:(1) dispersal_data.txt - results from our camera-trap survey.(2) demography.xlsx - detailed calculations of palm demography
DOI: 10.6084/m9.figshare.14717676.v1
title: Data from: Multiple anthropogenic pressures lead to seed dispersal collapse of the southernmost palm Jubaea chilensis

description: Original data from:Cordero, S., F. Gálvez & F.E. Fontúrbel. 2021. Multiple anthropogenic pressures lead to seed dispersal collapse of the southernmost palm Jubaea chilensis. Frontiers in Ecology and Evolution. doi: 10.3389/fevo.2021.719566<br>This repository contains two files:(1) dispersal_data.txt - results from our camera-trap survey.(2) demography.xlsx - detailed calculations of palm demography
DOI: 10.6084/m9.figshare.13395470.v4
title: An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes

description: This is the data supplement for the manuscript "An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes"<br><br>Authors: Edmund R. R. Moody1, Tara A. Mahendrarajah2, Nina Dombrowski2, James W. Clark1, Celine Petitjean1, Pierre Offre2, Gergely J. Szöllősi3,4,5, Anja Spang2,6*, Tom A. Williams1*<br>1. School of Biological Sciences, University of Bristol, Bristol BS8 1TH, UK.2. NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry; AB Den Burg, The Netherlands3. Dept. of Biological Physics, Eötvös Loránd University, 1117 Budapest, Hungary 4. MTA-ELTE “Lendület” Evolutionary Genomics Research Group, 1117 Budapest, Hungary; 5. Institute of Evolution, Centre for Ecological Research, 1121 Budapest, Hungary6. Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden<br>*Co-corresponding authors: tom.a.williams@bristol.ac.uk, anja.spang@nioz.nl<br>This data supplement contains sequence alignments, trees, and python scripts used for analysis as well as tables of results.
DOI: 10.6084/m9.figshare.16822978.v2
title: deepMTJ test-set data

description: This dataset comprises 1344 images of muscle-tendon junctions recorded with 3 ultrasound imaging systems (Aixplorer V6, Esaote MyLab60, Telemed ArtUs), on 2 muscles (Lateral Gastrocnemius, Medial Gastrocnemius), and 2 movements (isometric maximum voluntary contractions, passive torque movements).<br>