cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23748927.v2
title: Supplementary Data for "<strong>Fast and Accurate Variant Identification Tool for Sequencing-Based Studies</strong>"

description: Benchmark datasets used in this study to evaluate the performance of VCFer and bcftools.Gut_microbiome_benchmark.tar.gz contains gut microbiome reference genomes with <i>in silico</i> SNPs and indels, including SRX5976902 <i>Akkermansia muciniphila</i> (<i>A. muciniphila</i>), SRX5977424 <i>Bacteroides </i>faecis (<i>BaFa</i>), SRX5976649 <i>Bacteroides fragilis</i> (<i>B. fragilis</i>), SRX5976729 <i>Bacteroides ovatus</i> (<i>B. ovatus</i>), SRX6045315 <i>Bacteroides vulgatus</i> (<i>BaVu</i>), SRX6044844 <i>Bacteroides xylanisolvens </i>(<i>BaXy</i>), SRX6044813 <i>Bifidobacterium adolescentis</i> (<i>BiAd</i>), SRX5991169 <i>Escherichia coli </i>(<i>EsCo</i>), and SRX5992782 <i>Parabacteroides distasonis</i> (<i>PaDi</i>).COVID_benchmark.tar.gz contains SARS-Cov-2 (NC_045512.2) reference genomes with <i>in silico</i> SNPs and indels.ExampleDataFig4-6.zip contains sam and vcf output files that support the examples shown in Fig 4-6.
DOI: 10.6084/m9.figshare.23748927.v1
title: Supplementary Data for "<strong>Fast and Accurate Variant Identification Tool for Sequencing-Based Studies</strong>"

description: Benchmark datasets used in this study to evaluate the performance of VCFer and bcftools. Gut_microbiome_benchmark.tar.gz contains gut microbiome reference genomes with <em>in silico</em> SNPs and indels, including SRX5976902 <em>Akkermansia muciniphila</em> (<em>A. muciniphila</em>), SRX5977424 <em>Bacteroides </em>faecis (<em>BaFa</em>), SRX5976649 <em>Bacteroides fragilis</em> (<em>B. fragilis</em>), SRX5976729 <em>Bacteroides ovatus</em> (<em>B. ovatus</em>), SRX6045315 <em>Bacteroides vulgatus</em> (<em>BaVu</em>), SRX6044844 <em>Bacteroides xylanisolvens </em>(<em>BaXy</em>), SRX6044813 <em>Bifidobacterium adolescentis</em> (<em>BiAd</em>), SRX5991169 <em>Escherichia coli </em>(<em>EsCo</em>), and SRX5992782 <em>Parabacteroides distasonis</em> (<em>PaDi</em>). COVID_benchmark.tar.gz contains SARS-Cov-2 (NC_045512.2) reference genomes with <em>in silico</em> SNPs and indels.
DOI: 10.5063/f1qv3k0r
title: Climate data, host plants, length of leafhopper in typical karst areas of Guizhou, China

description: The climate and host plant data of Typhlocybinae species in Guizhou, China were investigated, and their representative species were photographed and measured by scanning electron microscopy.Table S1: Climate data in each plot. Table S2: Leaf characteristics of host plants in each plot. Table S3: Community structure of typhlocybine leafhoppers in the study areas. Table S4: Sample selection of scanning electron micro-scope photography. Table S5: Length (μm) data measured by scanning electron microscope (mean ± SE) (N=3). Table S6: Statistics on the sensilla of Typhlocybinae. Table S7: Number of focal leafhopper species of different host plants in different Study sites.
DOI: 10.5281/zenodo.5574357
title: Public perceptions of an avian reintroduction aiming to connect people with nature

description: Full raw dataset (quantitative and qualitative) and R code for quantitative analyses, associated with the publication "Public perceptions of an avian reintroduction aiming to connect people with nature" <em>People and Nature</em>. Survey responses are presented here anonymised. Please note that where the term 'Proactive' sample is used this is referred to as the 'Self selecting' sample in the associated journal article.
DOI: 10.5281/zenodo.5574356
title: Public perceptions of an avian reintroduction aiming to connect people with nature

description: Full raw dataset (quantitative and qualitative) and R code for quantitative analyses, associated with the publication "Public perceptions of an avian reintroduction aiming to connect people with nature" <em>People and Nature</em>. Survey responses are presented here anonymised. Please note that where the term 'Proactive' sample is used this is referred to as the 'Self selecting' sample in the associated journal article.
DOI: 10.5281/zenodo.8267100
title: trichilia_minutiflora_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267099
title: trichilia_minutiflora_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8266711
title: SYSTEMS LEVEL IDENTIFICATION OF A MATRISOME-ASSOCIATED MACROPHAGE POLARIZATION STATE IN MULTI-ORGAN FIBROSIS

description: This Zenodo repository contains the processed Seurat objects for "SYSTEMS LEVEL IDENTIFICATION OF A MATRISOME-ASSOCIATED MACROPHAGE POLARIZATION STATE IN MULTI-ORGAN FIBROSIS". The Seurat objects include: Tissue-specific monocytes / macrophages (used in Figure 1,3,4) endo.rds: Endometrium monocytes / macrophages heart.rds: Heart monocytes / macrophages kidney.rds: Kidney monocytes / macrophages liver.rds: Liver monocytes / macrophages lung.rds: Lung monocytes / macrophages skin.rds: Skin monocytes / macrophages SPP1 macrophages across all six tissues (used in Figure 2,3,4,5) SPP1seu.rds Code for generating these objects can be found at: https://github.com/the-ouyang-lab/mam-reproducibility
DOI: 10.5281/zenodo.8266710
title: SYSTEMS LEVEL IDENTIFICATION OF A MATRISOME-ASSOCIATED MACROPHAGE POLARIZATION STATE IN MULTI-ORGAN FIBROSIS

description: This Zenodo repository contains the processed Seurat objects for "SYSTEMS LEVEL IDENTIFICATION OF A MATRISOME-ASSOCIATED MACROPHAGE POLARIZATION STATE IN MULTI-ORGAN FIBROSIS". The Seurat objects include: Tissue-specific monocytes / macrophages (used in Figure 1,3,4) endo.rds: Endometrium monocytes / macrophages heart.rds: Heart monocytes / macrophages kidney.rds: Kidney monocytes / macrophages liver.rds: Liver monocytes / macrophages lung.rds: Lung monocytes / macrophages skin.rds: Skin monocytes / macrophages SPP1 macrophages across all six tissues (used in Figure 2,3,4,5) SPP1seu.rds Code for generating these objects can be found at: https://github.com/the-ouyang-lab/mam-reproducibility
DOI: 10.5281/zenodo.8267106
title: spatula_rhynchotis_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267105
title: spatula_rhynchotis_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267112
title: trichilia_hirta_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267111
title: trichilia_hirta_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267019
title: Nutrient availability and stoichiometry mediate microbial effects on soil carbon sequestration in tropical forests

description: A one-year <em>in situ</em> soil incubation experiment using mesh bags (mesh size of 38 µm, allowing colonization of bacteria and penetration of fungal hyphal but precluding root penetration) with fertile sugarcane soil and infertile sand along an elevational gradient characterized by varied climatic and biotic conditions in a tropical forest. Biomarkers, including phospholipid fatty acids, carbon-nitrogen-phosphorus acquiring hydrolases, glomalin-related proteins and amino sugars were measured to characterize the production and accumulation of microbial living biomass, exo-enzymes, extracellular glycoprotein and microbial necromass, and to elucidate their contributions to SOC sequestration.
DOI: 10.5281/zenodo.8267018
title: Nutrient availability and stoichiometry mediate microbial effects on soil carbon sequestration in tropical forests

description: A one-year <em>in situ</em> soil incubation experiment using mesh bags (mesh size of 38 µm, allowing colonization of bacteria and penetration of fungal hyphal but precluding root penetration) with fertile sugarcane soil and infertile sand along an elevational gradient characterized by varied climatic and biotic conditions in a tropical forest. Biomarkers, including phospholipid fatty acids, carbon-nitrogen-phosphorus acquiring hydrolases, glomalin-related proteins and amino sugars were measured to characterize the production and accumulation of microbial living biomass, exo-enzymes, extracellular glycoprotein and microbial necromass, and to elucidate their contributions to SOC sequestration.
DOI: 10.26302/sshade/bandlist_raman_gaspeite
title: Raman bandlist of natural Gaspeite

description: MIR-FIR Raman bandlist of natural Gaspeite at 295K
DOI: 10.26302/sshade/bandlist_raman_mg-gaspeite
title: Raman bandlist of natural magnesian Gaspeite

description: MIR-FIR Raman bandlist of natural magnesian Gaspeite at 295K
DOI: 10.6084/m9.figshare.23995101
title: Pathogenesis-adaptive polydopamine nanosystem for sequential therapy of ischemic stroke

description: This is the raw data of the figures in the manuscript and supplementary materials of "Pathogenesis-adaptive polydopamine nanosystem for sequential therapy of ischemic stroke".
DOI: 10.6084/m9.figshare.23995101.v1
title: Pathogenesis-adaptive polydopamine nanosystem for sequential therapy of ischemic stroke

description: This is the raw data of the figures in the manuscript and supplementary materials of "Pathogenesis-adaptive polydopamine nanosystem for sequential therapy of ischemic stroke".
DOI: 10.25345/c50r9mf18
title: MassIVE MSV000092700 - Parallel host and microbial pathways regulate lipid desaturation
title: 4 datasets, each in their own subfolder. 1) acdh-11 comparative metabolomics. 4 genotypes (N2, fcmt-1, WT FAT-7::GFP, and acdh-11;FAT-7::GFP) grown at 3 temperatures (15, 20, 25). Conditioned media (exo-metabolome) and worm pellet (endo-metabolome) isolated and extracted separately. 2) acdh-11 comparative metabolomics re: diet. 2 genotypes (WT FAT-7::GFP, and acdh-11;FAT-7::GFP) and 2 diets (WT E. coli, BW25113, and cyclopropane-deficient E. Coli, JW1653-1). The cyclopropane-deficient strain was additionally supplemented with cyclopropane fatty acids lactobacillic acid (LBA) or dihydrosterculic acid (DHSA) at 20 uM. 3) fcmt-1 comparative metabolomics. 4 genotypes (N2, fcmt-1(gk155709), fcmt-1(tm2382), hacl-1(tm6725)) grown at 20C. Conditioned media (exo-metabolome) and worm pellet (endo-metabolome) isolated and extracted separately. 4) vaccenic acid isotope labeling. 2 genotypes (N2 and hacl-1(tm6725)) grown at 20C. Each genotype was supplemented with vehicle, cis-vaccenic acid (cis-VA), stable isotope labeled D13-cis-VA, trans-vaccenic acid (trans-VA), and stable isotope labeled D13-trans-VA. Conditioned media (exo-metabolome) and worm pellet (endo-metabolome) isolated and extracted separately.
DOI: 10.21227/ag98-hc11
title: Dark Web Links - A Comprehensive VAPT procedure for Dark Websites

description: This dataset corresponds to the research paper - "A Comprehensive Vulnerability Assessment and Penetration Testing Procedure for Dark Websites". This dataset contains the dark web onion links on which the VAPT procedure was performed. The dataset includes links related to dark web cybercrime websites, namely fake Bitcoins, drugs, weapons, terrorism, malware, hacking, andmiscellaneous (a mixture of a few random cyber crimes) websites. A total of 163 websites are listed, out of which 147 dark websites are vulnerable to exploitation related to JavaScript libraries, WordPress, and the deprecationof critical security headers like X-Frame-Options, X-Content-Type-Options, and X-XSS-Protection. As part of penetrationtesting, 102 websites are exploited with Cookie Stealing, SessionHijacking, Password Reset Poisoning, Denial of Service (DoS), and Clickjacking attacks.
DOI: 10.6084/m9.figshare.23995083
title: Untitled Item

description: This is an SPSS data set to see the effect of DM on COVID-19 outcome from Eka Kotebe Hospital, Addis Ababa, Ethiopia
DOI: 10.6084/m9.figshare.23995083.v1
title: Untitled Item

description: This is an SPSS data set to see the effect of DM on COVID-19 outcome from Eka Kotebe Hospital, Addis Ababa, Ethiopia
DOI: 10.5281/zenodo.8267125
title: mareca_sibilatrix_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267124
title: mareca_sibilatrix_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267130
title: agave_potatorum_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267129
title: agave_potatorum_spades_01.fasta.gz

description: .
DOI: 10.34740/kaggle/ds/3638509
title: MMLU Dataset
DOI: 10.3886/e148361v2-141003
title: Data and code for: North-South Displacement Effects of Environmental Regulation: The Case of Battery Recycling

description: This study examines the effect of a tightening of the U.S. air-quality standard for lead in 2009 on the relocation of battery recycling to Mexico and on infant health in Mexico. In the U.S., airborne lead dropped sharply near affected plants, most of which were battery-recycling plants. Exports of used batteries to Mexico rose markedly. In Mexico, production increased at battery-recycling plants, relative to comparable industries, and birth outcomes deteriorated within two miles of those plants, relative to areas slightly farther away. The case provides a salient example of a pollution-haven effect between a developed and a developing country.
DOI: 10.5281/zenodo.7796840
title: Using neural networks to model Main Belt Asteroid albedos as a function of their proper orbital elements

description: This repository contains a copy of the following repository https://github.com/r-zachary-murray/Asteroid-Albedos. It contains weights for an ensemble of neural nets trained on the Asteroid Family Portal proper elements and NEOWISE albedos. These weights can be used to predict albedos of asteroids based of their proper elements. Example.ipynb contains an ipython notebook that shows how these predictions can be made.
DOI: 10.5281/zenodo.7796841
title: Using neural networks to model Main Belt Asteroid albedos as a function of their proper orbital elements

description: This repository contains a copy of the following repository https://github.com/r-zachary-murray/Asteroid-Albedos. It contains weights for an ensemble of neural nets trained on the Asteroid Family Portal proper elements and NEOWISE albedos. These weights can be used to predict albedos of asteroids based of their proper elements. Example.ipynb contains an ipython notebook that shows how these predictions can be made.
DOI: 10.5281/zenodo.8267138
title: pouteria_glomerata_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267137
title: pouteria_glomerata_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267147
title: millerichthys_robustus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267146
title: millerichthys_robustus_spades_01.fasta.gz

description: .
DOI: 10.26302/sshade/bandlist_raman_nitratine
title: Raman bandlist of natural Nitratine

description: MIR-FIR Raman bandlist of natural Nitratine at 295K
DOI: 10.5281/zenodo.8267152
title: micropsitta_finschii_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267151
title: micropsitta_finschii_spades_01.fasta.gz

description: .
DOI: 10.26302/sshade/bandlist_raman_smithsonite
title: Raman bandlist of natural Smithsonite

description: MIR-FIR Raman bandlist of natural Smithsonite at 295K
DOI: 10.5281/zenodo.8267173
title: stereochilus_marginatus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267172
title: stereochilus_marginatus_spades_01.fasta.gz

description: .
DOI: 10.26302/sshade/bandlist_raman_spherocobaltite
title: Raman bandlist of natural Spherocobaltite

description: MIR-FIR Raman bandlist of natural Spherocobaltite at 295K
DOI: 10.34740/kaggle/dsv/6334480
title: MoviesDatasets
DOI: 10.5281/zenodo.8267188
title: agapornis_swindernianus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267187
title: agapornis_swindernianus_spades_01.fasta.gz

description: .
DOI: 10.26302/sshade/bandlist_raman_otavite
title: Raman bandlist of natural Otavite

description: MIR-FIR Raman bandlist of natural Otavite at 295K
DOI: 10.26302/sshade/bandlist_raman_rhodochrosite
title: Raman bandlist of natural Rhodochrosite

description: MIR-FIR Raman bandlist of natural Rhodochrosite at 295K
DOI: 10.5281/zenodo.8267198
title: eurycea_quadridigitata_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267197
title: eurycea_quadridigitata_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23995140
title: Search strategy and sources

description: The electronic databases search strategy, the sources used, and the consulted websites are listed in the extended data.
DOI: 10.6084/m9.figshare.23995140.v1
title: Search strategy and sources

description: The electronic databases search strategy, the sources used, and the consulted websites are listed in the extended data.
DOI: 10.5281/zenodo.8267210
title: siren_sphagnicola_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267209
title: siren_sphagnicola_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23587482.v1
title: <strong>Molecular Dynamics Simulation of Polyacrylamide Adsorption on Calcite</strong>

description: Supplementary material for " <strong>Molecular Dynamics Simulation of Polyacrylamide Adsorption on Calcite"</strong>
DOI: 10.5281/zenodo.8267226
title: plethodon_glutinosus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267225
title: plethodon_glutinosus_spades_01.fasta.gz

description: .
DOI: 10.25345/c5w08ws6k
title: MassIVE MSV000092701 - GNPS-Mechanisms of myocarditis and progressive cardiac fibrosis in chronic Trypanosoma cruzi infection; - detection of metabolites during the drug administration in the mice model
title: Chagas disease is caused by Trypanosoma cruzi which affects approximately 6.5 million people worldwide. Chronic infection with the parasite results in persistent low-grade myocarditis and progressive fibrosis, which results in significant cardiac dysfunction called Chronic Chagasic Cardiomyopathy (CCC). The victims suffering from CCC have higher cardiac inflammation, fibrosis, and circulating inflammatory and fibrotic markers that correlate with disease severity. The study aims to detect metabolites in association with the different treatment options offered during the state of the infection in the mice model, using uninfected stages as quality checks. By using HILIC and C8 columns on LCMS, the metabolites were detected. The portions of heart and liver harvested from the T. cruzi infected mice were lysed and extracted at both aqueous and organic phases. The extracts were seeded in 96 well plates, dried, dissolved in re-suspension diluent and LCMS run using the above-mentioned columns.
DOI: 10.5281/zenodo.8267240
title: eurycea_bislineata_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267239
title: eurycea_bislineata_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23995413
title: Ground-dwelling ant species adapt their body traits and food resources to specific microhabitats along an elevation gradient

description: Understanding the responses of species to changing climates is becoming increasingly urgent with global change impacts. Of particular importance is the impact of global environmental change on species fundamental to the functioning of ecosystems. Using elevation gradients as a proxy for climate change, we investigated the intraspecific responses of ant traits across elevations from 100-700m in a subtropical evergreen broadleaf forest. Specifically, we quantified the relationships between environmental factors, trait variation, and trophic level in two ground-dwelling ant species (<i>Ectomomyrmex javanus</i>,<i> Odontoponera transversa</i>). Morphological traits (dry mass, head length, body size and leg length) generally increased with elevation. Ant<i> δ</i><sup>13</sup>C increased significantly with elevation, whereas δ<sup>15</sup>N did not. Ant <i>δ</i><sup>13</sup>C values of <i>E. javanus</i> correlated negatively with mean annual temperature (MAT), and the <i>δ</i><sup>13</sup>C values of both species correlated positively with soil C:N ratio. Our study reveals that changing temperatures along elevations are associated with changes in the individual traits and <i>δ</i><sup>13</sup>C signatures of ground-dwelling ants, revealing that ants are able to adapt their body traits and food resources to specific microhabitats.
DOI: 10.6084/m9.figshare.23995413.v1
title: Ground-dwelling ant species adapt their body traits and food resources to specific microhabitats along an elevation gradient

description: Understanding the responses of species to changing climates is becoming increasingly urgent with global change impacts. Of particular importance is the impact of global environmental change on species fundamental to the functioning of ecosystems. Using elevation gradients as a proxy for climate change, we investigated the intraspecific responses of ant traits across elevations from 100-700m in a subtropical evergreen broadleaf forest. Specifically, we quantified the relationships between environmental factors, trait variation, and trophic level in two ground-dwelling ant species (<i>Ectomomyrmex javanus</i>,<i> Odontoponera transversa</i>). Morphological traits (dry mass, head length, body size and leg length) generally increased with elevation. Ant<i> δ</i><sup>13</sup>C increased significantly with elevation, whereas δ<sup>15</sup>N did not. Ant <i>δ</i><sup>13</sup>C values of <i>E. javanus</i> correlated negatively with mean annual temperature (MAT), and the <i>δ</i><sup>13</sup>C values of both species correlated positively with soil C:N ratio. Our study reveals that changing temperatures along elevations are associated with changes in the individual traits and <i>δ</i><sup>13</sup>C signatures of ground-dwelling ants, revealing that ants are able to adapt their body traits and food resources to specific microhabitats.
DOI: 10.5281/zenodo.8267250
title: loricariichthys_derbyi_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267249
title: loricariichthys_derbyi_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23995419
title: NNI Dataset updated

description: This dataset is an update of the dataset published by Ciampitti et al., 2022 (A global dataset to parametrize critical nitrogen dilution curves for major crop species). This dataset contains the result of extracting data of plant biomass, plant N concentration and harvest yield.
DOI: 10.6084/m9.figshare.23995404
title: Test

description: Test
DOI: 10.6084/m9.figshare.23995404.v1
title: Test

description: Test
DOI: 10.5281/zenodo.8267258
title: parotocinclus_spilosoma_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8267257
title: parotocinclus_spilosoma_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23814470.v1
title: Neurotrophic tropomyosin receptor kinase (NTRK) fusion positive tumors: a historical cohort analysis

description: NTRK gene fusions have been identified in various tumors; some requiring aggressive therapy and sometimes new TRK inhibitors (TRKi). We aimed to describe a national, unselected, retrospective, multicenter cohort. Patients were identified through the French sarcoma diagnostic laboratory at Institut Curie through samples analyzed by RT-qPCR or whole-transcriptome sequencing. From 2001 to 2019, 65 NTRK fusion tumors were identified within 2120 analyses (3.1%): 58 by RNA sequencing (including 20 after RT-qPCR analysis) and 7 exclusively by RT-qPCR. Of the 61 patients identified, 37 patients had infantile soft tissue or kidney fibrosarcomas (IFS), 15 other mesenchymal (Other-MT) and nine central nervous system (CNS) tumors. They encompassed 14 different tumor types with variable behaviors. Overall, 53 patients had surgery (3 mutilating), 38 chemotherapy (20 alkylating agents/anthracycline), 11 radiotherapy, two ‘observation strategy’ and 13 received TRKi. After a median follow-up of 61.0 months [range, 2.5–226.0], 10 patients died. Five-year overall survival is, respectively, 91.9% [95%CI, 83.5–100.0], 61.1% [95%CI, 34.2–100.0] and 64.8% [95%CI, 39.3–100.0] for IFS, Other-MT, and CNS groups. NTRK-fusion positive tumors are rare but detection is improved through RNA sequencing. TRKi could be considered at diagnosis for CNS NTRK-fusion positive tumors, some IFS, and Other-MT. Not adapted.