cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.5kayjz
title: Occurrence Download

description: A dataset containing 5471 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phasianus colchicus Linnaeus, 1758",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Machine Observation, Observation, Occurrence evidence)",
 "Year is 2023",
 "Country is United States of America",
 "StateProvince is Montana"
 ]
}

 The dataset includes 5471 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072193-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.23617767
title: A Critical Evaluation of Deep-Learning Based Phylogenetic Inference Programs Using Simulated Data Sets

description: This repository contains 7 optimized machine learning models (7 on CNN and 6 on PhyDL), their training data and data sets simulated for PhtDL and Tree_learning (CNN) evaluation.Each folder corresponds to each topic in our study:Folder "Simulated data for PhyDL inference" contains test data sets used to evaluate PhyDL models under LBA (simuLBA.LGFG, simuLBA.C20F.1050sites and simuLBA.C60F.1098sites) and LBR (simuLBR.LGFG, simuLBR.C20F.1050sites and simuLBR.C60F.1098sites) conditions. Moreover, the trees employed for simulating these datasets are documented in simuLBA.fourtaxa and simuLBR.fourtaxa, with each tree corresponding to 100 alignments. For instance, simuLBA.1050sites.2.3.16 indicates that this alignment is the 16th one simulated from tree LBA.tre.2.3. Note that aignments simulated under LG+C20+F+Γ and LG+C60+F+Γ are in PHYLIP format, alignments simulated under LG+F+Γ are in fasta format.Folder "Simulated data for CNN inference" contains test data sets used in general evaluation of CNN (BL.INDEL.1000.tar.bz2 and BL.INDEL.1000.tar.bz2) and data sets under 13 regions in branch-length space(REGIONS.INDEL.1000.tar.bz2 and REGIONS.NOGAP.1000.tar.bz2).Folder “CNN_Training_data” contains data sets used to train CNN_NOGAP.Ori, CNN_FA and CNN_FE. For CNN_NOGAP.Extragaps and CNN_INDEL.Extragap, training data was generated by randomly replace 10% of characters with gaps in original data (i.e., the training data of CNN_NOGAP.Ori and CNN_INDEL.Ori).Note that CNN50K (Suvorov et al., 2020) is named as CNN_INDEL.Ori here.Folder “PhyDL_Training_data” contains training and validation data sets used to train DNN_LBA10K, DNN_LBA40K, DNN_LBR10K, DNN_LBR40K, DNN_60K and DNN_160K. Alignments are attached with reference tree using ".link_to_alignment" function in ete3 package and pickled.Folder “CNN_models” and “PhyDL_models” contains newly trained models.<br>Please let me know if you have any question about them.Email: xingxingshen@zju.edu.cn<br>
DOI: 10.15468/dl.2kccvv
title: Occurrence Download

description: A dataset containing 5471 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phasianus colchicus Linnaeus, 1758",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Machine Observation, Observation, Occurrence evidence)",
 "Year is 2023",
 "Country is United States of America",
 "StateProvince is Montana"
 ]
}

 The dataset includes 5471 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072194-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/qe7q6x
title: NIEK_NES_2024

description: This is the data from the National Environment Survey(2021-2022) conducted by the National Institute of Ecology.
DOI: 10.34740/kaggle/dsv/10483220
title: Egypt Gold Prices | Daily Updated
DOI: 10.17909/5149-1615
title: TESS Data for TOI-402 used in JWST COMPASS Paper

description: TESS Data for TOI-402 used in JWST COMPASS Paper
DOI: 10.15468/dl.k2huvu
title: Occurrence Download

description: A dataset containing 5471 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phasianus colchicus Linnaeus, 1758",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Machine Observation, Observation, Occurrence evidence)",
 "Year is 2023",
 "Country is United States of America",
 "StateProvince is Montana"
 ]
}

 The dataset includes 5471 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072195-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28217330
title: Raw data about trofinetide

description: Raw data about trofinetide
DOI: 10.6084/m9.figshare.28217351
title: Supplementary Material for: Mendelian Randomization Analysis Reveals a Causal Relationship Between Membranous Nephropathy and the Gut Microbiome

description: Background: With the increasing prevalence of membranous nephropathy (MN), the gut microbiome (GM) is increasingly implicated in its cause, yet the intricate mechanisms remain unclear. Whether changes in the diversity and richness of gut microbial populations among MN patients contribute to disease prevalence is still unanswered, necessitating further exploration into the potential causative link between the GM and MN.
Methods: We conducted a comprehensive bidirectional Mendelian randomization (MR) study. We selected 211 bacterial taxa using Genome-wide association study (GWAS) data provided by the MiBioGen consortium, while GWAS data relevant to MN were obtained from ebi-a-GCST010005. The inverse-variance weighted (IVW) method was the primary technique used to delineate the causal relationship between exposures and outcomes. To confirm the robustness of our results, we used additional methods, including MR-Egger, weighted median, simple mode, and weighted mode. Sensitivity analyses included tests for pleiotropy, heterogeneity, and leave-one-out sensitivity to ensure the integrity of our conclusions. Finally, reverse MR analyses were conducted to assess the likelihood of reverse causality.
Results: Using various analytical methods, including the IVW approach, MR-Egger, weighted median, simple mode, and weighted mode, our study identified six microbial taxa with a statistically significant causal link to MN, as indicated by p-values less than 0.05. The implicated taxa are Butyrivibrio (OR= 1.25, 95 % CI: 1.001-1.565, P = 0.048), Butyricicoccus (OR = 2.15, 95 % CI: 1.005-4.621, P = 0.048), Catenibacterium (OR = 1.49, 95 % CI: 1.043-2.134, P = 0.028), Ruminiclostridium5 (OR = 1.78, 95 % CI: 1.140-2.763, P = 0.03), RuminococcaceaeUCG003 (OR = 1.78, 95 % CI: 1.140-2.763, P = 0.011) and Bacillales (OR = 1.52, 95 % CI: 1.135-2.025, P = 0.005). Each of these taxa has been established as a risk factor for MN. Notably, Ruminococcaceae UCG-003 and Bacillales were identified as having a bidirectional causal relationship with the disease.
Conclusion: Our MR study has revealed a causal link between six microbial taxa and MN, highlighting their potential involvement in the disease's development. These findings represent an initial step into this complex field and underscore the need for more in-depth research.
DOI: 10.6084/m9.figshare.28217351.v1
title: Supplementary Material for: Mendelian Randomization Analysis Reveals a Causal Relationship Between Membranous Nephropathy and the Gut Microbiome

description: Background: With the increasing prevalence of membranous nephropathy (MN), the gut microbiome (GM) is increasingly implicated in its cause, yet the intricate mechanisms remain unclear. Whether changes in the diversity and richness of gut microbial populations among MN patients contribute to disease prevalence is still unanswered, necessitating further exploration into the potential causative link between the GM and MN.
Methods: We conducted a comprehensive bidirectional Mendelian randomization (MR) study. We selected 211 bacterial taxa using Genome-wide association study (GWAS) data provided by the MiBioGen consortium, while GWAS data relevant to MN were obtained from ebi-a-GCST010005. The inverse-variance weighted (IVW) method was the primary technique used to delineate the causal relationship between exposures and outcomes. To confirm the robustness of our results, we used additional methods, including MR-Egger, weighted median, simple mode, and weighted mode. Sensitivity analyses included tests for pleiotropy, heterogeneity, and leave-one-out sensitivity to ensure the integrity of our conclusions. Finally, reverse MR analyses were conducted to assess the likelihood of reverse causality.
Results: Using various analytical methods, including the IVW approach, MR-Egger, weighted median, simple mode, and weighted mode, our study identified six microbial taxa with a statistically significant causal link to MN, as indicated by p-values less than 0.05. The implicated taxa are Butyrivibrio (OR= 1.25, 95 % CI: 1.001-1.565, P = 0.048), Butyricicoccus (OR = 2.15, 95 % CI: 1.005-4.621, P = 0.048), Catenibacterium (OR = 1.49, 95 % CI: 1.043-2.134, P = 0.028), Ruminiclostridium5 (OR = 1.78, 95 % CI: 1.140-2.763, P = 0.03), RuminococcaceaeUCG003 (OR = 1.78, 95 % CI: 1.140-2.763, P = 0.011) and Bacillales (OR = 1.52, 95 % CI: 1.135-2.025, P = 0.005). Each of these taxa has been established as a risk factor for MN. Notably, Ruminococcaceae UCG-003 and Bacillales were identified as having a bidirectional causal relationship with the disease.
Conclusion: Our MR study has revealed a causal link between six microbial taxa and MN, highlighting their potential involvement in the disease's development. These findings represent an initial step into this complex field and underscore the need for more in-depth research.
DOI: 10.6084/m9.figshare.28217327
title: Final Code and Data for Election Paper

description: The files include code and data to reproduce the results from the paper. The rds fils include data and R codes are provided separately. The codes are self-explanatory.
DOI: 10.6084/m9.figshare.28217327.v1
title: Final Code and Data for Election Paper

description: The files include code and data to reproduce the results from the paper. The rds fils include data and R codes are provided separately. The codes are self-explanatory.
DOI: 10.26036/cnp0006791
title: Exploring the therapeutic effect of stem cell-derived small extracellular vesicles on myocardial ischemia-reperfusion injury

description: hUMSC derived small extracellular vesicles suppress cardiomyocyte apoptosis through miR-490-3p/RN7SL1 axis via RN7SL1 with complete structure
DOI: 10.15468/dl.uq6c2h
title: Occurrence Download

description: A dataset containing 691 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (Snow Entomological Museum Collection, Frost Entomological Museum, The Purdue Entomological Research Collection, University of Texas, Biodiversity Center, Entomology Collection (UTIC), Catálogo de insectos de la colección del Centro de Entomología, Stuart M. Fullerton Collection of Arthropods (UCFC), University of Central Florida, Illinois Natural History Survey Insect Collection, Vermont Bark and Ambrosia Beetle Records - Vermont Department of Forest, Parks and Recreation, The Albert J. Cook Arthropod Research Collection, iNaturalist Research-grade Observations)",
 "Geometry POLYGON((-134.46437 5.37229,-46.3043 5.37229,-46.3043 58.36415,-134.46437 58.36415,-134.46437 5.37229))",
 "TaxonKey is Ips pini (Say & T., 1826)"
 ]
}

 The dataset includes 691 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072196-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5xjrxd
title: Occurrence Download

description: A dataset containing 113 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nepenthes ampullaria Jack",
 "Year 2021-2024"
 ]
}

 The dataset includes 113 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072197-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/tc6tq-7hz47
title: Noise Level PSD and Teleseismic Earthquake Data of DAS Arrays in California

description: This dataset contains DAS waveforms of five high signal-to-noise ratio teleseismic earthquakes, DAS and station locations, DAS noise level PSD results, and 1D velocity models.
DOI: 10.5281/zenodo.14666556
title: LBP-1

description: Dataset for LBP dentists project in Jakarta.
DOI: 10.5281/zenodo.14666557
title: LBP-1

description: Dataset for LBP dentists project in Jakarta.
DOI: 10.6084/m9.figshare.28216991
title: Agrometeorological Hazard Warning Dataset

description: The meteorological disaster warning signal, which is triggered and graded using a predefined threshold, provides information close to the time of disaster occurrence. The associated Agrometeorological Hazard Warning Dataset is compiled by extracting key information, i.e., the date and time, affected county, disaster type, warning level, and the timeliness and details of the information from the text description of the publically issued warning signal associated with agriculture. It is quality controlled and structured. The dataset covers the black soil area of northeast China from 2021–2023.<br>
DOI: 10.15468/dl.p8f6gz
title: Occurrence Download

description: A dataset containing 659 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "TaxonKey is Quercus canariensis Willd."
 ]
}

 The dataset includes 659 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072199-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28217128.v1
title: Additional file 2 of Differential use of multiple food sources at a bathyal benthic ecosystem in the central Sagami Bay revealed by amino acid nitrogen isotopic compositions

description: Additional file 2.
DOI: 10.15468/dl.3u93q5
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-135.68402 22.5676,-55.11452 22.5676,-55.11452 58.40881,-135.68402 58.40881,-135.68402 22.5676))",
 "TaxonKey is Ips avulsus Wood & Bright, 1992"
 ]
}

 The dataset includes 96 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072200-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28217137
title: Additional file 2 of Immune responses of cattle vaccinated by various routes with Mycobacterium bovis Bacillus Calmette-Guérin (BCG)

description: Supplementary Material 2. Supplemental Figure 1 (.pdf). Gating strategy for flow cytometry analysis. FSC = forward scatter; SSC = side scatter. Supplemental Figure 2 (.pdf). USDA approved scatterplot used for interpretation of CCT tuberculin skin test results.
DOI: 10.6084/m9.figshare.28217134
title: Additional file 1 of Immune responses of cattle vaccinated by various routes with Mycobacterium bovis Bacillus Calmette-Guérin (BCG)

description: Supplementary Material 1. Supplemental Table 1. (.docx) Routes of administration and dosages of M. bovis BCG in colony-forming units/ml. Supplemental Table 2. (.docx) Comparative cervical tuberculin skin test results of cattle vaccinated by various routes with M. bovis BCG Danish. Supplemental Table 3. (.docx) Survivability of BCG Danish pre-lyophilization and various times post-lyophilization while stored at 33.8°C. Supplemental Table 4. (.docx) Survivability of BCG Danish pre-lyophilization and various times post-lyophilization while stored at -20 °C, -4 °C, or 25 °C.
DOI: 10.6084/m9.figshare.28217000
title: The Workplace Exploitation Scale (Wex-5) original data

description: This is the original dataset associated with the workplace exploitation scale (Wex-5) that has been published under the Creative Commons licence and can be found here along with the scoring: 10.6084/m9.figshare.28216910<br>For more information, contact the author, Dr. S. Rama Gokula Krishnan. Email: ramagokulakrishnan@gmail.com
DOI: 10.15468/dl.xv4bry
title: Occurrence Download

description: A dataset containing 7080 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((-109.71321 38.60317,-109.47772 38.60317,-109.47772 38.84694,-109.71321 38.84694,-109.71321 38.60317))"
 ]
}

 The dataset includes 7080 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072201-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w9hepx
title: Occurrence Download

description: A dataset containing 2687 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "GadmGid is COL.25_2",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 2687 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072202-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2atzae
title: Occurrence Download

description: A dataset listing the 458 species recorded in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((29.59592 -29.94138,29.92246 -29.93431,29.92347 -29.62496,29.59693 -29.629,29.59592 -29.94138))",
 "IucnRedListCategory is one of (EN, VU, NT, LC, DD, NE)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 458 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072198-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6qzwpt
title: Occurrence Download

description: A dataset containing 52030 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nothofagus Blume)",
 "Country is one of (New Zealand, Chile, Argentina, Australia, New Caledonia, Papua New Guinea)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 52030 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072203-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xx9e62
title: Occurrence Download

description: A dataset containing 2032 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erysiphe necator Schwein."
 ]
}

 The dataset includes 2032 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072205-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vrmc97
title: Occurrence Download

description: A dataset containing 659 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "TaxonKey is Quercus canariensis Willd."
 ]
}

 The dataset includes 659 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072206-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jfrm7r
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((29.51104 -24.83162,30.21979 -24.80436,30.15553 -24.26696,29.23652 -24.18289,29.51104 -24.83162))",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 36 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072207-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.frpyrc
title: Occurrence Download

description: A dataset containing 2032 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erysiphe necator Schwein."
 ]
}

 The dataset includes 2032 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072208-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ddzmtz
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "TaxonKey is Arundo donax L."
 ]
}

 The dataset includes 12 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0262037-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pzghse
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lycalopex sechurae (Thomas, 1900)"
 ]
}

 The dataset includes 91 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0205650-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pysvdk
title: Occurrence Download

description: A dataset containing 408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neotiara nodulosa (Gmelin, 1791)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is MANAGED"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is not null"
 ]
 }
 }
 ]
 },
 {
 "or" : [
 "OccurrenceStatus is Present",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is not null"
 ]
 }
 }
 ]
 }
 ]
}

 The dataset includes 408 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061879-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdsbsq
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 {
 "or" : [
 "TaxonKey is Lytoneuron columbinum (Hook.) Smith-Braga & Schwartsburd",
 "TaxonKey is Pellaea columbina (Hook.) Hook.",
 "TaxonKey is Lytoneuron columbinum var. columbinum",
 "TaxonKey is Lytoneuron columbinum var. caparaoense Brade ex Smith-Braga & Schwartsburd"
 ]
 }
 ]
}

 The dataset includes 13 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0258198-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.