cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25435894.v1
title: <b>Health Professionals Evaluations and Use of Phage Therapy</b>

description: NOTES: To accompany deposited data set. Data file includes only the variables reported in: Factors of Prescribing Phage Therapy among UK Healthcare Professionals: Evidence from Conjoint Experiment and Interviews. In the data file the variable SAMPLE designates which platform/sample respondents are from. Prolific Health Professional Sample (HEALTH) and PANELBASE sample of GPs (GP).<br>The data are a wide file format with the results of a discrete choice experiment.
DOI: 10.25345/c5154f089
title: MassIVE MSV000094359 - Molecular signatures of T cells targeting multiple myeloma
title: Wagner TR, Kehl N, Steiger S, Kilian M, Foster K, Boschert T, Hernandez GM, Abelin JG, Lindner K, Sester LS, Frenking JH, Schonfelder B, Schumacher S, Galas-Filipowicz D, Fitzsimons E, Green EW, Schmidt P, Uhrig S, Bunse L, Chain B, Muller-Tidow C, Goldschmidt H, Weinhold N, Frohling S, Muller-Tidow C, Carr SA, Yong K, Rippe K, Raab MS, Platten M, Eichmuller SB, and Friedrich MJ. 2024. T cell receptors (TCRs) play a crucial role in orchestrating cellular immunity in both health and disease and act as an essential component to detect infected or mutated cells. In cancer immunotherapy, microenvironmental cues and T cell repertoire composition are particularly important in mediating durable treatment responses. However, whether endogenous tumor reactive TCRs are commonly present in hematological cancers or mediate the effects of immunotherapy is currently unknown. Here, we employed a microfluidics-based forward screening approach of single T cells against autologous tumor cells to map T cell specificities and transcriptional phenotypes in bone marrow biopsies of treatment-naive patients with multiple myeloma. Together with MHC immunoprecipitation of autologous cancer cells, we established a comprehensive single-cell TCR atlas of the diseased human bone marrow, uncovering the cellular complexity and functional heterogeneity of naturally occurring tumor- and virus-specific TCRs. These analyses demonstrate clinically relevant endogenous anti-tumor reactivity in a rare subset of CD29 expressing bone marrow-resident T cells. In mouse tumor models, CD29 surface expression selectively indicated homing of tumor-specific, but not tumor-irrelevant TCRs. In patients with multiple myeloma, we found that tumor reactive T cells undergo selective clonal expansion in the bone marrow and in some cases recognize tumor antigens shared by multiple patients. Furthermore, the presence of tumor reactive T cells before treatment predicted clinical response to induction chemotherapy and bispecific antibody treatment in two patient cohorts. This antigen-agnostic dissection of the human bone marrow T cell repertoire enables the identification and monitoring of clinically relevant T cell responses targeting hematological cancers.
DOI: 10.5281/zenodo.10816799
title: Single-cell datasets for perturbation studies

description: This is a collection of datasets to experiment, benchmark and develop computational tools for perturbation modeling studies in single-cell technologies.

 

 
description: The following datasets are available through SeuratData package: 

adiposeref.SeuratData                                          Azimuth Reference: adipose      human
bmcite.SeuratData                                                   30k Bone Marrow Cells      human
bonemarrowref.SeuratData                                    Azimuth Reference: bonemarrow      human
cbmc.SeuratData                              scRNAseq and 13-antibody sequencing of CBMCs      human
celegans.embryo.SeuratData         6k C. elegans embryos from Packer and Zhu et al (2019) C. elegans
fetusref.SeuratData                                              Azimuth Reference: fetus      human
hcabm40k.SeuratData        40,000 Cells From the Human Cell Atlas ICA Bone Marrow Dataset      human
heartref.SeuratData                                              Azimuth Reference: heart      human
humancortexref.SeuratData                                  Azimuth Reference: humancortex      human
ifnb.SeuratData                                         IFNB-Stimulated and Control PBMCs      human
kidneyref.SeuratData                                            Azimuth Reference: kidney      human
lungref.SeuratData                                                Azimuth Reference: lung      human
mousecortexref.SeuratData                                  Azimuth Reference: mousecortex      mouse
panc8.SeuratData                         Eight Pancreas Datasets Across Five Technologies      human
pancreasref.SeuratData                                        Azimuth Reference: pancreas      human
pbmc3k.SeuratData                                              3k PBMCs from 10X Genomics      human
pbmcMultiome.SeuratData                                10X Genomics PBMC Multiome Dataset      human
pbmcref.SeuratData                                                Azimuth Reference: pbmc      human
pbmcsca.SeuratData                   Broad Institute PBMC Systematic Comparative Analysis      human
ssHippo.SeuratData                              Slide-seq v2 dataset of mouse hippocampus      mouse
stxBrain.SeuratData                               10X Genomics Visium Mouse Brain Dataset      mouse
stxKidney.SeuratData                             10X Genomics Visium Mouse Kidney Dataset      mouse
thp1.eccite.SeuratData                                                   ECCITE-seq THP-1      human
tonsilref.SeuratData                                            Azimuth Reference: tonsil      human
DOI: 10.5281/zenodo.10816800
title: Single-cell datasets for perturbation studies

description: This is a collection of datasets to experiment, benchmark and develop computational tools for perturbation modeling studies in single-cell technologies.

 

 
description: The following datasets are available through SeuratData package: 

adiposeref.SeuratData                                          Azimuth Reference: adipose      human
bmcite.SeuratData                                                   30k Bone Marrow Cells      human
bonemarrowref.SeuratData                                    Azimuth Reference: bonemarrow      human
cbmc.SeuratData                              scRNAseq and 13-antibody sequencing of CBMCs      human
celegans.embryo.SeuratData         6k C. elegans embryos from Packer and Zhu et al (2019) C. elegans
fetusref.SeuratData                                              Azimuth Reference: fetus      human
hcabm40k.SeuratData        40,000 Cells From the Human Cell Atlas ICA Bone Marrow Dataset      human
heartref.SeuratData                                              Azimuth Reference: heart      human
humancortexref.SeuratData                                  Azimuth Reference: humancortex      human
ifnb.SeuratData                                         IFNB-Stimulated and Control PBMCs      human
kidneyref.SeuratData                                            Azimuth Reference: kidney      human
lungref.SeuratData                                                Azimuth Reference: lung      human
mousecortexref.SeuratData                                  Azimuth Reference: mousecortex      mouse
panc8.SeuratData                         Eight Pancreas Datasets Across Five Technologies      human
pancreasref.SeuratData                                        Azimuth Reference: pancreas      human
pbmc3k.SeuratData                                              3k PBMCs from 10X Genomics      human
pbmcMultiome.SeuratData                                10X Genomics PBMC Multiome Dataset      human
pbmcref.SeuratData                                                Azimuth Reference: pbmc      human
pbmcsca.SeuratData                   Broad Institute PBMC Systematic Comparative Analysis      human
ssHippo.SeuratData                              Slide-seq v2 dataset of mouse hippocampus      mouse
stxBrain.SeuratData                               10X Genomics Visium Mouse Brain Dataset      mouse
stxKidney.SeuratData                             10X Genomics Visium Mouse Kidney Dataset      mouse
thp1.eccite.SeuratData                                                   ECCITE-seq THP-1      human
tonsilref.SeuratData                                            Azimuth Reference: tonsil      human
DOI: 10.5519/qd.m1efuz5e
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (687 records)
DOI: 10.6084/m9.figshare.25435948
title: Figshare: HIV64148 Results

description: Contain genome assembly in FASTA, BLAST result in CSV, and HIV64148 report in HTML.- Result_2M_Assembly.zip :: Results from assembling 2M dataset by 7 tools on Server machine- Result_2C_Assembly.zip :: Results from assembling 2C dataset by 7 tools on Server machine- Result_1M1C_Assembly.zip :: Results from assembling 1M1C dataset by 7 tools on Server machine- Result_2M1C_Assembly.zip :: Results from assembling 2M1C dataset by 7 tools on Server machine- Result_CSV_Resource_Usage_Performance_Benchmark.zip Contains resource usage overtime (CPU, Memory) measured on 3 computational platforms over 7 tools in CSV format.
DOI: 10.6084/m9.figshare.25435948.v1
title: Figshare: HIV64148 Results

description: Contain genome assembly in FASTA, BLAST result in CSV, and HIV64148 report in HTML.- Result_2M_Assembly.zip :: Results from assembling 2M dataset by 7 tools on Server machine- Result_2C_Assembly.zip :: Results from assembling 2C dataset by 7 tools on Server machine- Result_1M1C_Assembly.zip :: Results from assembling 1M1C dataset by 7 tools on Server machine- Result_2M1C_Assembly.zip :: Results from assembling 2M1C dataset by 7 tools on Server machine- Result_CSV_Resource_Usage_Performance_Benchmark.zip Contains resource usage overtime (CPU, Memory) measured on 3 computational platforms over 7 tools in CSV format.
DOI: 10.5281/zenodo.10030949
title: Data for the study titled "Productivity suppression by manganese recycling in suboxic hypolimnion of a eutrophic lake."

description: Data for the study titled "Productivity suppression by manganese recycling in suboxic hypolimnion of a eutrophic lake."
DOI: 10.5281/zenodo.10838673
title: Data for the study titled "Productivity suppression by manganese recycling in suboxic hypolimnion of a eutrophic lake."

description: Data for the study titled "Productivity suppression by manganese recycling in suboxic hypolimnion of a eutrophic lake."
DOI: 10.5281/zenodo.8254293
title: Data for the study titled "Productivity suppression by manganese recycling in suboxic hypolimnion of a eutrophic lake."

description: Data for the study titled "Productivity suppression by manganese recycling in suboxic hypolimnion of a eutrophic lake."
DOI: 10.5281/zenodo.8254294
title: Data for the study titled "Eutrophication induced productivity suppression by manganese recycling in suboxic hypolimnions."

description: Data for the study titled “Eutrophication induced productivity suppression by manganese recycling in suboxic hypolimnions.”
DOI: 10.18112/openneuro.ds004091.v1.3.0
title: GAZE PRF
DOI: 10.21227/a3k1-vh71
title: Predicting Antibody and ACE2 Affinity for SARS-CoV-2 BA.2.86 with In Silico Protein Modeling and Docking

description: The emergence of the Omicron sublineage of SARS-CoV-2 virusBA.2.86 (nicknamed “Pirola”) has raised concerns about its potentialimpact on public health and personal health as it hasmany mutations with respect to previous variants. We conductedan in silico analysis of neutralizing antibody binding toBA.2.86. Selected antibodies came from patients who were vaccinatedand/or infected. We predicted binding affinity betweenBA.2.86 and antibodies. We also predicted the binding affinitybetween the same antibodies and several previous SARS-CoV-2 variants (Wuhan and Omicron descendants BA.1, BA.2, andXBB.1.5). Additionally, we examined binding affinity betweenBA.2.86 and human angiotensin converting enzyme 2 (ACE2)receptor, a cell surface protein crucial for viral entry. We foundno statistically significant difference in binding affinity betweenBA.2.86 and other variants, indicating a similar immune response.These findings contradict media reports of BA.2.86’shigh immune evasion potential based on its mutations. We discussthe implications of our findings and highlight the need formodeling and docking studies to go above and beyond mutationand basic serological neutralization analysis. Future researchin this area will benefit from increased structural analyses ofmemory B-cell derived antibodies and should emphasize the importanceof choosing appropriate samples for in silico studies toassess protection provided by vaccination and infection. Thisresearch contributes to understanding the BA.2.86 variant’s potentialimpact on public health. Moreover, we introduce newmethodologies for predictive medicine in ongoing efforts to combatthe evolving SARS-CoV-2 pandemic and prepare for otherhazards.
DOI: 10.5281/zenodo.10836297
title: Data for: Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but  well-resolved phylogeny

description: Sequence alignments and gene trees for: Braun et al. "Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny." See README file for detailed description of all files.
DOI: 10.5281/zenodo.10836298
title: Data for: Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but  well-resolved phylogeny

description: Sequence alignments and gene trees for: Braun et al. "Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny." See README file for detailed description of all files.
DOI: 10.18112/openneuro.ds004091.v1.3.1
title: GAZE PRF
DOI: 10.18112/openneuro.ds004091.v2.0.0
title: GAZE PRF
DOI: 10.5281/zenodo.10838474
title: GIS web application for sustainable dike reinforcement solutions using nearby floodplains

description: This is the dataset and instructions used for the GIS web application developed for the Dutch RAAKpubliek project Rivierwerken (Project nr.: RAAK.PUB09.018).
DOI: 10.5281/zenodo.10838475
title: GIS web application for sustainable dike reinforcement solutions using nearby floodplains

description: This is the dataset and instructions used for the GIS web application developed for the Dutch RAAKpubliek project Rivierwerken (Project nr.: RAAK.PUB09.018).
DOI: 10.6084/m9.figshare.25436023
title: HIV64148 Supplementary data

description: Figure S1. The MetaQUAST assessment evaluated contigs from the assemblers processing four median read-length FASTQ inputs: (A) 1,000-nt, (B) 2,000-nt, (C) 3,000-nt, and (D) 4,000-nt (Table 3). The x-axis displays the percentage sequence similarity obtained from a BLAST alignment with the corresponding reference genomes, while the y-axis represents the aligned length, indicating the longest continuous alignment between each contig and its reference genome. Dot sizes indicate the genome fraction (%Ref Aligned), calculated as the ratio of continuous aligned bases to the total reference genome length. Subplots above and beside each figure display histograms of the contig counts. Additionally, (E) shows the averaged genome fraction (%) of contigs from different long-read assembler pipelines. The complete data are available in Table S9.Figure S2. The average completeness of major HIV-1 open reading frames (ORFs) of the contigs generated from the assemblers analyzing FASTQ inputs of 4 median read lengths: (A) 1,000-nt, (B) 2,000-nt, (C) 3,000-nt, or (D) 4,000-nt.Figure S3. Contig size distribution of all assemblers processing the simulated FASTQ inputs of the 4 HIV-1 mixtures.Table S1. A list of experimental data and additional information. N/A: not applicable.Table S2. A statistical summary of runtime measurements taken from an assembly phase of the pipelines.Table S3. The memory usage and maximum CPU utilization of each assembler on three computational systems. The benchmark utilized 100 samples of two HIV-1 group M mixture with 2,000x coverage and 8,000-nt median read length.Table S4. The genome statistics of contigs generated from (A) Full genome laboratory isolate NL4-3, (B) Mpox propagated in a CV-1 cell line and (C) Mpox from pustular lesion, and (D) SARS-CoV-2 data by the selected assemblers.Table S5. The genome statistics of contigs generated from (A) Polio virus, (B) Hepatitis C virus (HCV), and (C) ZIKA Virus (ZIKV) data by the selected assemblers.Table S6. HIV Combinations for Data Simulation (Excel)Table S7. Characteristics of Simulated Samples Readlength Experiment (Excel)Table S8. Characteristics of Simulated Samples HIV mixture Experiment (Excel)Table S9. An Assembly Evaluation of HIV-1 Read Length Experiment (Excel)Table S10. An Assembly Evaluation of HIV-1 Subtype Mixtures Experiment (Excel)Table S11. Subtypes Recall Rates (Excel)Table S12. REGA Subtyping (Excel)Table S13. 5’ Half Genomes of NL4-3 Alignment Statistics (Excel)Table S14. Other Viruses Alignment Statistics (Excel)
DOI: 10.6084/m9.figshare.25435681
title: Training Dataset for FeatureLTE: Binary Classification

description: Training datasets for the binary classification task of FeatureLTE.
DOI: 10.35078/7yqvnm/0xjaaf
title: Dicionário dos dados da pesquisa_VJ.docx

description: :unav
DOI: 10.35078/7yqvnm/ox3zcf
title: IniciativasCOVID_Pósdoc.csv

description: :unav
DOI: 10.14473/csda/wuwlic/ndaizx
title: D_CSDA00192_jihomoravsky.pdf

description: Dotazník_CSDA00192_jihomoravsky
DOI: 10.14473/csda/wuwlic/3otb0e
title: TI_CSDA00181-CSDA00194.pdf

description: Technická informace_CSDA00181-CSDA00194
DOI: 10.14473/csda/wuwlic/rax0s1
title: D_CSDA00181-CSDA00194.pdf

description: Dotazník_CSDA00181-CSDA00194
DOI: 10.14473/csda/wuwlic/rhlu5l
title: OM_CSDA00181-CSDA00194.pdf

description: Ostatní materiály_CSDA00181-CSDA00194
DOI: 10.14473/csda/wuwlic/wxwc1e
title: 12_JM kraj - volby do PS 2013_data_opr.tab

description: CSDA_00192
DOI: 10.14473/csda/wuwlic
title: Předvolební výzkumy pro volby do PS 2013 – Jihomoravský kraj

description: Předvolební výzkumy před volbami do PS 2013 ve všech krajích ČR pro Českou televizi realizovaly společnosti Median a Stem/Mark. Hlavním výstupem byl tzv. volební potenciál v kraji, jehož výsledky sloužily k nominaci hostů do předvolebních debat ČT. Součástí dotazníku bylo i několik krajsky specifických tematických otázek.
DOI: 10.5281/zenodo.10809109
title: Data Repository: LRRK2 G2019S mutation affects human iPSC-derived endothelial cells (line H1)

description: Data repository for publication: LRRK2 G2019S mutation affects human iPSC-derived endothelial cells (healthy line 1)
description: The blood-brain barrier (BBB) serves as an interface between the periphery and central nervous system. It limits the movement of molecules and immune cells, regulates the entry of nutrients, and removes waste products from the brain. The dysfunction of the BBB has been identified in Parkinson´s disease (PD) but the role of the BBB and endothelial cells (ECs) has not been well studied. LRRK2 G2019S mutation is the most common PD causing mutation with similar pathophysiology than in sporadic cases. How the mutation affects EC function has not been investigated previously in patient’s cells. In the study, we used iPSC-derived ECs from PD patients with the LRRK2 mutation as well as cells from healthy individuals. We report that PD ECs have higher levels of α-synuclein, altered mitochondrial respiration and response to inflammatory exposure, especially to TNFα. In addition, transcriptomic analysis showed upregulation of fatty acid synthesis related pathways in PD ECs and downregulation of lncRNA MEG3, both of which have been associated with PD. Altogether, PD ECs manifest some of the PD related hallmarks and are likely to contribute to the pathogenesis of PD.
description: RNA sequencing of human induced pluripotent stem cell (hiPSC) derived endothelial cells (ECs).

raw data files (.fastq.gz), processed data files (.txt), MD5 files for raw data (.md5)

line 1: (TS1_R1_001.fastq.gz, TS1_R2_001.fastq.gz, TS1_R1_001.fastq.gz.md5, TS1_R2_001.fastq.gz.md5, TS1.counts.txt)

line 1 TNFalpha+IL-1beta (TS7_R1_001.fastq.gz, TS7_R2_001.fastq.gz, TS7_R1_001.fastq.gz.md5, TS7_R2_001.fastq.gz.md5, TS7.counts.txt)

line 1 TNFalpha (TS13_R1_001.fastq.gz, TS13_R2_001.fastq.gz, TS13_R1_001.fastq.gz.md5, TS13_R2_001.fastq.gz.md5, TS13.counts.txt)
description: Line information



Genotype: normal

Reference: TakaraBio


Cell culturing: hiPSCs were cultured in matrigel (Corning) coated dishes in E8 (Gibco) media. EC were differentiated according to previously published protocol (Harding et al. 2017).

Treatments



Nonexposed (TS1)

4 h TNFalpha+IL-1beta exposed (TS7)

4 h TNFalpha exposed (TS13)


RNA sequencing: Cells were lysed on ice (Buffer RLT + β-mercaptoethanol 10 µl/ml), and RNA was extracted directly after lysis with the Qiagen RNeasy Mini Kit (Qiagen) with DNase I digestion (Qiagen). 1-4 µg of RNA were sent for library preparation and sequencing (performed by Azenta). Quality was evaluated with FastQC, and sequencing was done with Illumina NovaSeq, PE 2x150. Sequence reads were trimmed by using Trimmomatic v.0.36 to remove possible adaptor sequences and nucleotides of poor quality. Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.