cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25493/sz0m-ee6
title: Investigating cellular diversity in a novel Alzheimer’s disease mouse model using the optimized QUINT workflow (v1)

description: This study includes 40 mice (20 at 6 months(m), 20 at 14 months(m); 2 males and 38 females). Of the mice, 29 are from 14 AD-BXD strains, 2 are the C57B1/6J founder strain, 6 are the F1 B6/DBA/2J (D2) 5XFAD founder strain, and 3 are nontransgenic (Ntg)-BXD. Hemibrains were sent to Neuroscience Associates (NSA Inc., Knoxville, TN, USA) to be embedded, processed, and stained simultaneously in blocks of 40. The brains were freeze sectioned coronally at 40 μm intervals (not including the hypothalamus and cerebellum). Hemibrains were serially stained for thionine, NeuN, Iba1, GFAP, and AB1-42. Images were taken with 20x objective. Cropped and down-sampled images from NSA were processed using the QUINT workflow. Ilastik pixel classification was used to establish cell detection parameters for each stain. Brain sections were registered to the Allen Mouse Brain Atlas CCFv3 (2015) using the QuickNII software and refined using VisuAlign. Post-registration quality control assessment was performed using the novel QCAlign tool. Segmentation and registration steps were combined using Nutil Quantifier to output regional percent stain-positive coverage per region area, hereafter referred to as stain load. Regional changes in cell composition were assessed between animals.
DOI: 10.25493/7bwk-rm5
title: ACRALL – The Nicotinic Acetylcholine Receptor Allosteric Ligand Library (v1)

description: The nicotinic acetylcholine receptor allosteric ligand library ([ACRALL](https://ifm.chimie.unistra.fr/acrall)) is a public searchable database of allosteric ligands of the nicotinic acetylcholine receptor, a very relevant pharmacological target in the brain and the nervous system. Using automatic approaches, we have collected about 5000 small molecules from the literature with documented modulatory activity at the three most abundant receptor subtypes: the neuronal homomeric α7; the neuronal heteromeric α4β2; and the muscle-type receptor in both fetal (α1β1δγ) and adult (α1β1δε) form. The data was retrieved by searching for protein-ligand interactions in three popular drug banks (i.e., [ChEMBL](https://www.ebi.ac.uk/chembl/), [PubChem](https://pubchem.ncbi.nlm.nih.gov/), and [BindingDB](https://www.bindingdb.org/)) and applying filtering and mapping procedures to produce a self-consistent, curated database. The database provides quantitative information on the pharmacological attributes of the modulatory ligands in terms of potency, efficacy, and selectivity along with links to the relevant publications. In addition, an original structural annotation is given based on the topographical location of the ligand-binding site on the receptor to distinguish between orthosteric and allosteric ligands.
DOI: 10.6073/pasta/dc63123cb2338d24eaf23871e37128a8
title: The Jefferson Project 2020 weather data from seven surface weather stations on Lake George, NY, USA.

description: The Jefferson Project at Lake George – a partnership between Rensselaer Polytechnic Institute, IBM Research, and Lake George Association – combines Internet of Things technology and powerful analytics with science to create a new model for environmental monitoring and prediction. The project is building a computing platform that captures and analyzes data from a network of sensors tracking water quality and movement. These sensor data are combined with other monitoring and experimental data to create a thorough understanding of the factors that drive the lake's food web, hydrology, and water quality. More information about The Jefferson Project is available at https://jeffersonproject.rpi.edu/ In 2020, The Jefferson Project had seven weather monitoring stations around the lake collecting data on precipitation, temperature, wind speed, wind direction, barometric pressure, and relative humidiity. These stations are WX_CedarLane, WX_DFWI, WX_GullRock, WX_MossyPoint, WX_WhaleRock, WX_PilotKnob, and WX_Glenburnie. The stations have a sensor payload that include some combination of the following sensors: Rotronic HC2-S3 sensor, Campbell Scientific CS616 soil moisture sensor, Li-Cor LI-200R pyranometers, RM Young 85006 anemometer, Vaisala Weather Transmitter WXT series (520 & 530 models), HyQuest TB3 tipping bucket rain gauge, and N-Con wet deposition sampler. The sensors collect data at high-frequency (~1 sample per minute) and the data are transferred in near real-time to off-site databases for monitoring and review by Jefferson Project researchers. The data provided here are level 4 data which has undergone data correction and downsampling to an hourly frequency.
DOI: 10.5281/zenodo.7700747
title: TFold data

description: Data for the pipeline TFold for modeling peptide-MHC complexes. Includes cleaned PDB files, MHC and TCR sequences with IMGT numbering, weights and parameters for the neural network seqnn.
DOI: 10.5281/zenodo.7700748
title: TFold data

description: Data for the pipeline TFold for modeling peptide-MHC complexes. Includes cleaned PDB files, MHC and TCR sequences with IMGT numbering, weights and parameters for the neural network seqnn.
DOI: 10.5281/zenodo.7803946
title: TFold data

description: Data for the pipeline TFold for modeling peptide-MHC complexes. Includes cleaned PDB files, MHC and TCR sequences with IMGT numbering, weights and parameters for the neural network seqnn.
DOI: 10.6084/m9.figshare.22564942
title: McLeod2022_SM3.xlsx

description: Excel workbook with all primary collected field data and statistical analyses.
DOI: 10.6084/m9.figshare.22564945
title: McLeod_2022_SM2.kmz

description: Google Earth .kmz with field localities
DOI: 10.6084/m9.figshare.22564945.v1
title: McLeod_2022_SM2.kmz

description: Google Earth .kmz with field localities
DOI: 10.6084/m9.figshare.21636710.v4
title: Deciphering the causal relationship between blood pressure and regional white matter integrity: a two-sample Mendelian randomization study

description: Table S1. A list of 39 regional white matter (WM) integrity measured by fractional antitropy (FA). Table S2. Self-report neurological characteristics of UK Biobank's participants from two independent association sample sets for the two-sample Mendelian randomization (MR) analysis. Table S3. Numbers of candidate instrumental variables (IVs) determined at each step of our statistical method by separately using UK Biobank (UKB) GWAS and existing meta-analyzed GWAS. Table S4. Gene annotations for determined valid instrumental variables (IVs) carried into the two-sample Mendelian Randomization (MR) analysis by separately using UK Biobank (UKB) GWAS and existing meta-analyzed GWAS. Table S5. Results of association analysis and Mendelian Randomization analysis (implemented with generalized version of inverse-variance weighted (gen-IVW) approach) in the study samples. Table S6. Results of alternative Mendelian randomization (MR) approach and sensitivity analyses by using data from UK Biobank (UKB) cohort. Table S7. Results of adaptively weighted (AW) Fisher's method and mendelian randomization analysis implemented with a generalized version of inverse-variance weights method (gen-IVW) Table S8. Results and numbers of candidate instrumental variables (IVs) in each step of our two reverse two-sample Mendelian Randomization (MR) analyses using UK Biobank (UKB) cohort. Supplmentary File. Results of leave-one-out analyses STROBE-MR checklist. STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME) checklist
DOI: 10.6084/m9.figshare.22564981
title: MongoDB database

description: MongoDB database and collections for the GO-BP annotation of species
DOI: 10.6084/m9.figshare.22564981.v1
title: MongoDB database

description: MongoDB database and collections for the GO-BP annotation of species
DOI: 10.6084/m9.figshare.12252896
title: Legumes baits filtration info

description: Filtration criteria for creating baits for the 507 nuclear loci for Fabaceae<br>
DOI: 10.6084/m9.figshare.12252896.v1
title: Legumes baits filtration info

description: Filtration criteria for creating baits for the 507 nuclear loci for Fabaceae<br>
DOI: 10.6084/m9.figshare.12252890
title: Legumes baits

description: Baits targeted based on 30 transcriptomes across Fabaceae and mapped against Medicago and Phaseolous genomes, then chosen the Phaseolus version with the stringent criteria. This set targets 507 nuclear genes.<br>
DOI: 10.6084/m9.figshare.12252890.v2
title: Legumes baits

description: Baits targeted based on 30 transcriptomes across Fabaceae and mapped against Medicago and Phaseolous genomes, then chosen the Phaseolus version with the stringent criteria. This set targets 507 nuclear genes.<br>
DOI: 10.6084/m9.figshare.12252890.v1
title: Legumes baits

description: Baits targeted based on 30 transcriptomes across Fabaceae and mapped against Medicago and Phaseolous genomes, then chosen the Phaseolus version with the stringent criteria. This set targets 507 nuclear genes.<br>
DOI: 10.6084/m9.figshare.22565011
title: Digital Voting

description: Utilization of digital voting by each country
DOI: 10.17608/k6.auckland.22564996
title: Adult brain cortex GRN

description: Gene regulatory network for adult brain cortex.
DOI: 10.17608/k6.auckland.22564996.v1
title: Adult brain cortex GRN

description: Gene regulatory network for adult brain cortex.
DOI: 10.6084/m9.figshare.22565020
title: eukaryotes.zip

description: This folder contains all the derived raw and processed data for the phylogenetic analysis of Eukaryotes based on ribosomal sequences, heat shock protein families and proteostasis semantic profiles.
DOI: 10.6084/m9.figshare.22565020.v1
title: eukaryotes.zip

description: This folder contains all the derived raw and processed data for the phylogenetic analysis of Eukaryotes based on ribosomal sequences, heat shock protein families and proteostasis semantic profiles.
DOI: 10.6084/m9.figshare.22565023
title: prokaryotes.zip

description: This folder contains all the derived raw and processed data for the phylogenetic analysis of Prokaryotes based on ribosomal sequences, heat shock protein families and proteostasis semantic profiles.
DOI: 10.6084/m9.figshare.22565023.v1
title: prokaryotes.zip

description: This folder contains all the derived raw and processed data for the phylogenetic analysis of Prokaryotes based on ribosomal sequences, heat shock protein families and proteostasis semantic profiles.
DOI: 10.6084/m9.figshare.22565086
title: main_analysis.zip

description: This folder contains all the results and figures from the main part of the analysis:<br> 1. Construction of phylogenetic clustergrapms for rRNA sequences, heat shock proteins and proteostasis semantic networks<br> 2. Comparison of the four evolutionary criteria<br> 3. Deconvolution of proteostasis semantic profile<br> 4. Validation of proteostasis network contribution to other evolutionary conserved mechanisms
DOI: 10.6084/m9.figshare.22565086.v1
title: main_analysis.zip

description: This folder contains all the results and figures from the main part of the analysis:<br> 1. Construction of phylogenetic clustergrapms for rRNA sequences, heat shock proteins and proteostasis semantic networks<br> 2. Comparison of the four evolutionary criteria<br> 3. Deconvolution of proteostasis semantic profile<br> 4. Validation of proteostasis network contribution to other evolutionary conserved mechanisms
DOI: 10.6084/m9.figshare.22565116
title: 11728896 - Malek Alaouie - Mould Data - DEP1.xlsx

description: This data reflects indoor mould concentrations in syrian Refugee shelters in Lebanon.
DOI: 10.6084/m9.figshare.22565116.v1
title: 11728896 - Malek Alaouie - Mould Data - DEP1.xlsx

description: This data reflects indoor mould concentrations in syrian Refugee shelters in Lebanon.
DOI: 10.5281/zenodo.6641115
title: MineDojo Internet Knowledge Base (Reddit)

description: MineDojo Internet Knowledge Base (Reddit)
DOI: 10.5281/zenodo.6640449
title: MineDojo Internet Knowledge Base (Wiki)

description: MineDojo Internet Knowledge Base (Wiki)
DOI: 10.5281/zenodo.6641143
title: MineDojo Internet Knowledge Base (YouTube)

description: MineDojo Internet Knowledge Base (YouTube)
DOI: 10.34740/kaggle/dsv/3803175
title: EPRI Distribution Inspection Imagery
DOI: 10.5281/zenodo.6629972
title: Annotated Genome Pseudomonas Species MWU 12.2311

description: Annotated genome Pseudomonas species MWU 12.2311 isolated from cultivated bogs in southeastern Massachusetts.
DOI: 10.5281/zenodo.6629971
title: Annotated Genome Pseudomonas Species MWU 12.2311

description: Annotated genome Pseudomonas species MWU 12.2311 isolated from cultivated bogs in southeastern Massachusetts.
DOI: 10.6084/m9.figshare.20066198
title: ATACseq

description: ATACseqData
DOI: 10.6084/m9.figshare.20066198.v2
title: ATACseq

description: ATACseqData
DOI: 10.6084/m9.figshare.20066198.v1
title: A_07_EKDL210009141-1a_HT7NNDSX2_L3_coverage_norm_dedup.bw

description: ATACseqData
DOI: 10.5281/zenodo.6047869
title: Data set: Infrared spectra of HCN and HCN:H2O from 40-140 K

description: IR spectra of pure HCN and mixed H2O:HCN (~15:1) ice in temperature intervals of 10K from 40-140 K. Spectra are saved as individual files, where the first column is wavenumber (cm^-1) and the second column is IR absorbance. No baseline subtraction has been performed.
DOI: 10.5281/zenodo.6047868
title: Data set: Infrared spectra of HCN and HCN:H2O from 40-140 K

description: IR spectra of pure HCN and mixed H2O:HCN (~15:1) ice in temperature intervals of 10K from 40-140 K. Spectra are saved as individual files, where the first column is wavenumber (cm^-1) and the second column is IR absorbance. No baseline subtraction has been performed.
DOI: 10.6084/m9.figshare.14727231.v6
title: A multi-sensor human gait dataset captured through an optical system and inertial measurement units

description: This multi-sensor gait dataset comprises inertial and optical motion data from 25 subjects free of lower-limb injury, aged between 18 and 47 years. A smartphone and an IMU were attached to one of the subject's legs to capture accelerometer data, and 42 reflexive markers were taped over the whole body to record three-dimensional trajectories. The participants were instructed to walk on a straight-level walkway at their normal pace. Ten trials for each participant were recorded and preprocessed in each of two sessions, performed on different days. This amounts to 500 trials of three-dimensional trajectories, 500 trials of accelerations from the IMU, and 500 trials of accelerations from the smartphone.
DOI: 10.25452/figshare.plus.20029387
title: "Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq" Replogle et al. 2022 processed Perturb-seq datasets

description: This dataset includes data from three Perturb-seq experiments described in Replogle et al. 2022 (https://doi.org/10.1016/j.cell.2022.05.013): K562 genome-scale perturb-seq sampled at day 8 post-transduction (K562_gwps) K562 essential-scale perturb-seq sampled at day 6 post-transduction (K562_essential) RPE1 essential-scale perturb-seq sampled at day 7 post-transduction (rpe1) For each dataset, there are four processed Perturb-seq files in AnnData format (<sub>https://anndata.readthedocs.io/en/latest/</sub>). Raw, single-cell expression data for genes expressed at &gt;0.01 UMI per cell (named $pop_raw_singlecell_01.h5ad) Raw, pseudo-bulk expression data for genes expressed at &gt;0.01 UMI per cell (named $pop_raw_bulk_01.h5ad) gemgroup Z-normalized single-cell expression data for genes expressed at &gt;0.01 UMI per cell (named $pop_normalized_singlecell_01.h5ad) gemgroup Z-normalized pseudo-bulk expression data for genes expressed at &gt;0.01 UMI per cell (named $pop_normalized_bulk_01.h5ad) In the anndata format, the .var annotation details genes while the .obs annotation details single-cells/pseudobulk populations.
DOI: 10.5281/zenodo.6643621
title: Simulated X-ray Photon Fluctuation Spectroscopy Dataset

description: Dataset for simulated X-ray Photon Fluctuation Spectroscopy (XPFS) detector images and photon maps. XPFS is a X-ray speckle imaging technique used at SLAC National Accelerator Laboratory to study ultrafast materials dynamics.
description: {"references": ["Burdet, Nicolas Georges, et al. \"Absolute contrast estimation for soft X-ray photon fluctuation spectroscopy using a variational droplet model.\" Scientific Reports 11.1 (2021): 1-9."]}
DOI: 10.5281/zenodo.6643838
title: MineDojo Internet Knowledge Base (YouTube)

description: MineDojo Internet Knowledge Base (YouTube)
DOI: 10.5281/zenodo.6643843
title: MineDojo Internet Knowledge Base (Reddit)

description: MineDojo Internet Knowledge Base (Reddit)
DOI: 10.15468/dl.3g7t5a
title: Occurrence Download

description: A dataset containing 166370 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 2020-2020"
 ]
}

 The dataset includes 166370 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074342-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k4y2dw
title: Occurrence Download

description: A dataset containing 1616 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Asplenium theciferum (Kunth) Mett."
 ]
}

 The dataset includes 1616 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0297592-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.74uk38
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-92.83859 44.57946,-92.83859 44.57225,-92.8331 44.57176,-92.8331 44.56883,-92.83825 44.56858,-92.83825 44.56528,-92.83327 44.56479,-92.82864 44.56308,-92.82778 44.56198,-92.82761 44.55794,-92.8228 44.55782,-92.8228 44.55941,-92.81799 44.55953,-92.81593 44.55598,-92.8161 44.55121,-92.82314 44.55097,-92.82314 44.54693,-92.81336 44.54669,-92.81301 44.54363,-92.80958 44.54289,-92.8101 44.54094,-92.8101 44.53824,-92.80821 44.53678,-92.80151 44.54326,-92.79825 44.54351,-92.79722 44.55072,-92.79293 44.5506,-92.79259 44.5539,-92.79808 44.55757,-92.79757 44.56039,-92.79774 44.56479,-92.80443 44.56516,-92.80443 44.57164,-92.81507 44.57176,-92.81765 44.57029,-92.81679 44.56821,-92.81851 44.5665,-92.82022 44.56736,-92.82297 44.56748,-92.82297 44.57555,-92.8331 44.5758,-92.83344 44.57934,-92.83859 44.57946))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "TaxonKey is Hesperiidae",
 "TaxonKey is Nymphalidae",
 "TaxonKey is Lycaenidae",
 "TaxonKey is Pieridae",
 "TaxonKey is Papilionidae"
 ]
 }
 ]
}

 The dataset includes 16 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0293470-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ur43at
title: Occurrence Download

description: A dataset containing 5037739 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5037739 records from 2398 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059865-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh2634696.08fu
title: SH2634696.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2634697.08fu
title: SH2634697.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2062219.08fu
title: SH2062219.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.