cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28070090.v1
title: Comparison of highly sensitive, multiplex immunoassay platforms for streamlined clinical cytokine quantification

description: Selecting the optimal platforms to quantitate cytokines is challenging due to varying performance and the plethora of options available. To compare performance of three highly sensitive, multiplex assays on three different platforms – MSD S-plex, Olink Target 48, and Quanterix SP-X – to MSD V-plex which is widely used for quantitative cytokine assay. Serum and stimulated plasma samples were analyzed across each platform. The proportion of quantifiable samples was compared for each analyte and correlation analyses were performed to relate the data. For MSD S-plex, parallelism and antibody pair knockdown experiments gauged specificity of the kit. MSD S-plex was the most sensitive multiplex platform followed by Olink Target 48, Quanterix SP-X, and MSD V-plex. Concentrations across platforms differed greatly for some cytokines, but all platforms showed strong correlation. Results for MSD S-plex were confirmed by parallelism and knockdown. MSD S-plex should be a priority platform for ultra-sensitive assay. Olink Target 48 offers an enticing combination of sensitivity and multiplex capability that warrants consideration when many cytokines require quantitation. MSD V-plex, MSD S-plex and Olink quantitative assays offer high utility across drug development programs, but fit-for-purpose performance should be assessed on a per-analyte basis.
DOI: 10.17044/scilifelab.12901388
title: Genotype data from: "Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling."

description: This data contains genotype data from the GlobalScreeningArray and imputed genotypes from 303 healthy blood donors, generated within a project to investigate pQTLs regulating interferon receptor responses.<br>Results are published in Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling (https://doi.org/10.1371/journal.pgen.1009199)<br><br>Abstract:Interferons (IFNs) are cytokines that are central to the host defence 
against viruses and other microorganisms. If not properly regulated, 
IFNs may contribute to the pathogenesis of inflammatory autoimmune, or 
infectious diseases. To identify genetic polymorphisms regulating the 
IFN system we performed an unbiased genome-wide protein-quantitative 
trait loci (pQTL) mapping of cell-type specific type I and type II IFN 
receptor levels and their responses in immune cells from 303 healthy 
individuals. Seven genome-wide significant (p &lt; 5.0E-8) pQTLs were 
identified. Two independent SNPs that tagged the multiple sclerosis 
(MS)-protective HLA class I alleles A*02/A*68 and B*44, respectively, 
were associated with increased levels of IFNAR2 in B and T cells, with 
the most prominent effect in IgD<sup>–</sup>CD27<sup>+</sup> memory B 
cells. The increased IFNAR2 levels in B cells were replicated in cells 
from an independent set of healthy individuals and in MS patients. 
Despite increased IFNAR2 levels, B and T cells carrying the 
MS-protective alleles displayed a reduced response to type I IFN 
stimulation. Expression and methylation-QTL analysis demonstrated 
increased mRNA expression of the pseudogene <em>HLA-J</em> in B cells 
carrying the MS-protective class I alleles, possibly driven via 
methylation-dependent transcriptional regulation. Together these data 
suggest that the MS-protective effects of HLA class I alleles are 
unrelated to their antigen-presenting function, and propose a previously
 unappreciated function of type I IFN signalling in B and T cells in MS 
immune-pathogenesis.
DOI: 10.17044/scilifelab.12901388.v1
title: Genotype data from: "Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling."

description: This data contains genotype data from the GlobalScreeningArray and imputed genotypes from 303 healthy blood donors, generated within a project to investigate pQTLs regulating interferon receptor responses.<br>Results are published in Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling (https://doi.org/10.1371/journal.pgen.1009199)<br><br>Abstract:Interferons (IFNs) are cytokines that are central to the host defence 
against viruses and other microorganisms. If not properly regulated, 
IFNs may contribute to the pathogenesis of inflammatory autoimmune, or 
infectious diseases. To identify genetic polymorphisms regulating the 
IFN system we performed an unbiased genome-wide protein-quantitative 
trait loci (pQTL) mapping of cell-type specific type I and type II IFN 
receptor levels and their responses in immune cells from 303 healthy 
individuals. Seven genome-wide significant (p &lt; 5.0E-8) pQTLs were 
identified. Two independent SNPs that tagged the multiple sclerosis 
(MS)-protective HLA class I alleles A*02/A*68 and B*44, respectively, 
were associated with increased levels of IFNAR2 in B and T cells, with 
the most prominent effect in IgD<sup>–</sup>CD27<sup>+</sup> memory B 
cells. The increased IFNAR2 levels in B cells were replicated in cells 
from an independent set of healthy individuals and in MS patients. 
Despite increased IFNAR2 levels, B and T cells carrying the 
MS-protective alleles displayed a reduced response to type I IFN 
stimulation. Expression and methylation-QTL analysis demonstrated 
increased mRNA expression of the pseudogene <em>HLA-J</em> in B cells 
carrying the MS-protective class I alleles, possibly driven via 
methylation-dependent transcriptional regulation. Together these data 
suggest that the MS-protective effects of HLA class I alleles are 
unrelated to their antigen-presenting function, and propose a previously
 unappreciated function of type I IFN signalling in B and T cells in MS 
immune-pathogenesis.
DOI: 10.17632/bv8s42y5n2.1
title: LINF_360047000

description: glycine cleavage complex (GCC) T-protein | GCVT-2 | Aminomethyltransferase
Leishmania infantum (strain JPCM5)
DOI: 10.6084/m9.figshare.28228496
title: Code to Reproduce Analysis

description: This repository contains the R code used to produce the figures featured in the manuscript. The scripts include data processing, statistical analyses, and visualization workflows, ensuring full reproducibility of the graphical outputs presented in the publication.Survey Data is embargoed by DAFM and will be shareable upon request - the R script generates the necessary data to reproduce the analysis. If you require the raw survey data please contact me directly to be provided with a data state agreement by DAFM. Each script is annotated for clarity, detailing the steps required to generate each figure from the raw or processed data. Users can adapt the code for their own analyses or use it as a reference for similar research.For more information, please refer to the manuscript: If you have questions or require additional details, feel free to contact me.
DOI: 10.6084/m9.figshare.28228496.v1
title: Code to Reproduce Analysis

description: This repository contains the R code used to produce the figures featured in the manuscript. The scripts include data processing, statistical analyses, and visualization workflows, ensuring full reproducibility of the graphical outputs presented in the publication.Survey Data is embargoed by DAFM and will be shareable upon request - the R script generates the necessary data to reproduce the analysis. If you require the raw survey data please contact me directly to be provided with a data state agreement by DAFM. Each script is annotated for clarity, detailing the steps required to generate each figure from the raw or processed data. Users can adapt the code for their own analyses or use it as a reference for similar research.For more information, please refer to the manuscript: If you have questions or require additional details, feel free to contact me.
DOI: 10.15468/dl.5utamn
title: Occurrence Download

description: A dataset containing 5830 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Colombia",
 "TaxonKey is Cerambycidae"
 ]
}

 The dataset includes 5830 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000119-250117103327516/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n747uu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Salmo salaroides Güldenstädt, 1814"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000120-250117103327516/datasets/export for details.
DOI: 10.15468/dl.jmrp9x
title: Occurrence Download

description: A dataset containing 30556 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gunnera L."
 ]
}

 The dataset includes 30556 records from 398 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000121-250117103327516/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8qua9d
title: Occurrence Download

description: A dataset containing 1177 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Données complémentaires de spécimens d'herbiers de IBAAN, Côte d'Ivoire"
 ]
}

 The dataset includes 1177 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000123-250117103327516/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pvzu8y
title: Occurrence Download

description: A dataset containing 7053 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Occurrences des échantillons de plantes de l'Herbier de l'Institut Botanique Aké-Assi d'Andokoi (IBAAN), Côte d'Ivoire"
 ]
}

 The dataset includes 7053 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000122-250117103327516/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7g4tk2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oncorhynchus mykiss x Salmo salar"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000124-250117103327516/datasets/export for details.
DOI: 10.17632/35xtyptswp.2
title: Temporal evolution of the intensity of light scattered by evaporating microdroplets of SiO2 and polystyrene nanoparticle suspensions in DMSO and diethylene glycol, respectively.

description: The dataset comprises the results of measuring the temporal evolution of light intensity scattered by evaporating microdroplets of a SiO2 nanoparticle suspension with a diameter of 450 nm in DMSO, (SiO2 concentration was ~2 wt%) and a polystyrene nanoparticle(PSn) suspension with a diameter of 200 nm (3200A, Thermo Scientific) in diethylene glycol (DEG). These microdroplets were levitated in a quadrupole trap and illuminated by counter-propagating laser beams: a red (658 nm) vertically polarized (V) beam and a green (532 nm) horizontally polarized (H) beam, both with respect to the scattering plane. A comprehensive description of the experimental geometry is available in (M. Kolwas et al., Phys. Chem. Chem. Phys., 2015, 17, 6881--6888).

The SiO2_450_DMSO_*.csv file includes the following data:
Column 1: Time
Column 2: Intensity of scattered light integrated over the field of view, with the laser and detection channel both vertically polarized (V)
Column 3: Intensity of scattered light integrated over the field of view, with the laser vertically polarized (V) and the detection channel horizontally polarized (H) in cross-polarization
Column 4: Intensity of scattered light integrated over the field of view, with the laser and detection channel both horizontally polarized (H)
Column 5: Intensity of scattered light integrated over the field of view, with the laser horizontally polarized (H) and the detection channel vertically polarized (V) in cross-polarization
Column 6: DC voltage applied to the upper and lower electrodes of the electrodynamic balance required to counteract the gravitational force
Column 7: Operating frequency of the trapping AC electric field
Column 8: Time evolution of the radius of the evaporating droplet obtained using the library method described in (D. Jakubczyk et al., JQSRT 126 (2013) 99–104).
The SiO2_450_DMSO_*.avi files serve as examples of experimental measurements.

The Ps_200_in_DEG_*.csv file includes the following data:
Column 1: Time
Column 2: Intensity of scattered light integrated over the field of view, with the laser and detection channel both vertically polarized (V)
Column 3: Intensity of scattered light integrated over the field of view, with the laser and detection channel both horizontally polarized (H)
Column 4: DC voltage applied to the upper and lower electrodes of the electrodynamic balance required to counteract the gravitational force
Column 5: Operating frequency of the trapping AC electric field
Column 6: Time evolution of the radius of the evaporating droplet obtained using the library method. 

The structure of the Ps_200_in_DEG_v3_Iv.csv and Ps_200_in_DEG_v3_Ih.csv files is as follows: the first column contains the observation angles, and the following columns contain the values of light intensity scattered by the droplet at corresponding angles. Each column corresponds to a specific moment in time. The time step between columns is equal to 0.029 seconds.
DOI: 10.17632/3d9sgmghm5.2
title: Clinical and Kinematic Data of the ENHANCE trial in patients with stroke

description: Clinical and kinematic data from a clinical trial involving a novel training approach motivated by motor control theory where reaching training was done within a spasticity-free elbow extension ranges determined individually or in a non-specific range. Patients with subacute stroke (≤6mo; n=46) and elbow flexor spasticity were randomly allocated to a 10-day upper limb training protocol, either personalized by restricting reaching to the spasticity-free range defined by the tonic stretch reflex threshold (TSRT) of elbow flexors or non-personalized (non-restricted). Outcomes assessed before, after, and one-month post-intervention were elbow flexor TSRT angle and reach-to-grasp arm kinematics (primary), and stretch reflex velocity sensitivity, clinical measures of impairment, and activity levels (secondary).

Ethical approval was obtained from the appropriate ethics committees before the beginning of the study. The Centre de Recherche Interdisciplinaire en Réadaptation du Montréal Métropolitain (Montréal, Canada) approved the study for the Jewish Rehabilitation Hospital and the Institut de Réadaptation Gingras-Lindsay de Montréal (CRIR1112-1115). The Institutional Ethics Review Board of Loewenstein Rehabilitation Hospital (Ra’anana, Israel) approved the study for the Loewenstein Rehabilitation Hospital (000-11-15-LOE) and the Institutional Ethics Committee of Tel Aviv University (Tel Aviv, Israel). The Institutional Ethics Committee of Kasturba Hospital (Manipal, India) approved the study for the Kasturba Medical Hospital (IEC-32/2016). 

The database includes 2 files: 
ENHANCE_RawData.xlsx - data file
ENHANCE-Clinical and Kinematic Raw Data Definitions.doc - data definitions file
DOI: 10.17632/b69dj53t8g.1
title: LINF_260008400

description: Nucleoside hydrolase; Leishmania infantum (strain JPCM5)
DOI: 10.17632/xk4sdppkwy.2
title: Field study on the effects of microbial substrate application on rice straw degradation

description: The data describes the raw data collected from a field study conducted to analyse the effects of microbial substrate application on rice straw degradation. Soil analysis was conducted from pre-season and continued throughout the rice planting season.
DOI: 10.17632/nch6wf3s5h.1
title: LINF_260011800

description: Protein of unknown function (DUF2012); Leishmania infantum (strain JPCM5)
DOI: 10.17632/sycx9ppmvx.1
title: LINF_260012600

description: RNA-binding protein | RBP19; Leishmania infantum (strain JPCM5)
DOI: 10.17632/n2cyh3pk4h.1
title: Attenuated replication and damaging effects of SARS-CoV-2 Omicron variants in an intestinal epithelial barrier model

description: Many COVID-19 patients suffer from gastrointestinal symptoms and impaired intestinal barrier function may play a key role in harmful inflammatory responses and Long COVID. Despite its importance, the impact of SARS-CoV-2 on intestinal epithelia is poorly understood. To address this, we established an intestinal barrier model integrating epithelial Caco-2 cells and mucus-secreting HT29 cells in the presence or absence of human Raji cells. We show that this gut epithelial model allows efficient differentiation of Caco-2 cells into M (microfold) cell-like cells and faithfully mimics intestinal barrier function. It is highly permissive to SARS-CoV-2 infection due to high expression of the viral entry factors ACE2 and TMPRSS2. Early strains of SARS-CoV-2 and the Delta variant replicated with high efficiency, severely disrupted barrier function and depleted tight junction proteins, such as claudin-1, occludin and ZO-1. In comparison, Omicron subvariants also depleted ZO-1 from tight junctions but had less damaging effects on mucosal integrity and barrier function. Remdesivir and the TMPRSS2 inhibitor Camostat prevented SARS-CoV-2 replication and thus epithelial barrier damage, while the Cathepsin inhibitor E64d was ineffective. Our results support that SARS-CoV-2 disrupts intestinal barrier function but further suggest that circulating Omicron variants are less damaging than earlier viral strains.
DOI: 10.17632/z66t2vx3sh.1
title: LDHU3_16.1550

description: Mitoribosomal protein mS48; Leishmania donovani (HU3 strain)
DOI: 10.17632/jkrxc667bw.1
title: Plano de Gestão de Dados - Projeto de Auxílio à Pesquisa (2019/24950-4)

description: Este arquivo do word contém os links para ter acesso aos dados utilizados e disponibilizados pelos autores dos papers que foram publicados durante a vigência do Projeto de Auxílio à Pesquisa (2019/24950-4), Título: "Dinâmica temporal da resposta inflamatória em anfíbios".

O Pesquisador responsável foi o Prof. Dr. Fernando Ribeiro Gomes (Departamento de Fisiologia, Instituto de Biociências/USP), e contou com a colaboração da Dra. Vania Regina de Assis (Departamento de Fisiologia, Instituto de Biociências/USP; College of Public Health/USF), Dra. Stefanny Christie Monteiro Titon (Departamento de Fisiologia, Instituto de Biociências/USP) e Dra. Sandra Marcia Muxel (Instituto de Ciências Biomédicas/USP).
DOI: 10.17632/wpbm5sbsxk.1
title: LDHU3_16.1520

description: Cyclophilin 13 | CyP13; Leishmania donovani (HU3 strain)
DOI: 10.17632/v2tgdcf7yp.1
title: LDHU3_16.1600

description: Hypothetical protein - conserved; Leishmania donovani (HU3 strain)
DOI: 10.17632/3rkj9n6gnn.1
title: LINF_160014700

description: EF-hand domain pair/EF-hand domain containing protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/jmgg2zgj2r.1
title: LINF_360047400

description: Snf7
Leishmania infantum (strain JPCM5)
DOI: 10.17632/7vm9s9s496.2
title: LINF_250022000

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/ry5dkty7t7.3
title: TiTuSS Transport Database

description: The excel file provides a longitudinal database which integrates information for the road networks with demographic, administrative and socioeconomic data for the municipalities of mainland Portugal over the 50-year period from 1971 to 2020. Although the database refers to the road network and road-based accessibility, it also includes simple measures of the railway network, namely the number of active railway stations in each municipality and the road-based distance and travel time to the nearest active railway station. The database can be used to study the effects of improved road accessibility on multiple socioeconomic outcomes in Portugal (e.g., population growth/decline, employment growth/decline, regional cohesion, urbanization patterns, etc.) over a considerable long period of 50 years. The database was constructed as part of the project TiTuSS-Transport Infrastructure & Urban Spatial Structure: Economic, Social & Environmental Effects (PTDC/EGE-PTDC/EGE-ECO/28805/2017).
DOI: 10.17632/tbwrd8wd26.1
title: LINF_160011600

description: Meiotic recombination protein SPO11; Leishmania infantum (strain JPCM5)
DOI: 10.17632/y9ty7ty72f.1
title: Supplementary material from "Experimental verification of biomechanical model of bipedal walking to simulate vertical loads induced by humans"

description: 1-"Bipedal walking model" folder: Matlab code to estimate the ground reaction forces and center-of-mass movement of a walking pedestrian on rigid ground with a bipedal walking model.

2-"Parameters estimation" folder: Matlab code for Monte-Carlo simulations within ranges of input parameters to achieve the best correlations possible between the model’s predictions and measured GRF data.
DOI: 10.17632/7hkv383sxj.1
title: LINF_160016700

description: Coenzyme Q-binding protein COQ10-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.15468/dl.54xaty
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Echantillon extrait des collections IBAAN"
 ]
}

 The dataset includes 39 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000126-250117103327516/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/kfwvpxf9bp.1
title: LINF_160016600

description: Hypothetical protein - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.15468/dl.xvtqev
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Salmo truttasalar Lacépède, 1803"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000125-250117103327516/datasets/export for details.
DOI: 10.17632/837wftgxzv.1
title: Mag&ElecCalibration

description: This dataset corresponds the experiments mentioned in the article "Magnetic and Electric Antennas Calibration for Partial Discharge Charge Estimation in Gas-Insulated Substations". In the head of each column it can be found the corresponding Figure, subplot and the variable measured. The description of how the data was gathered can be found in the same paper. 
The data corresponding to Fig. 14 and 16, is the raw pulse measurements (in the time domain) for each estimated charge shown in these figures.
DOI: 10.17632/837wftgxzv.2
title: Mag&ElecCalibration

description: This dataset corresponds the experiments mentioned in the article "Magnetic and Electric Antennas Calibration for Partial Discharge Charge Estimation in Gas-Insulated Substations". In the head of each column it can be found the corresponding Figure, subplot and the variable measured. The description of how the data was gathered can be found in the same paper. 
The data corresponding to Fig. 14 and 16, is the raw pulse measurements (in the time domain) for each estimated charge shown in these figures.
DOI: 10.17632/wn52z3bzn7.1
title: LINF_360049300

description: Qb-SNARE protein
Leishmania infantum (strain JPCM5)