cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/pkk4vtc57r.1
title: Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis

description: There is growing evidence that gastrointestinal (GI) parasitic worms can alter human gut microbiota during infection and it is thought that this is part of the mechanisms via which these parasites suppress immune responses. However, the diseases that have been studied to date involve the GI tract and have clear links with pre-existing dysbiosis, making it challenging to disentangle causality. Multiple sclerosis is a Th1-mediated disease of the nervous system whose pathogenesis has been recently linked to alterations in gut microbiome. Therefore, in the present study we investigated, for the first time, the changes in gut microbial profiles of human volunteers with relapsing-remitting multiple sclerosis (RRMS) prior to and following experimental infection with 25 hookworm stage 3 larvae (Necator americanus; N+), and following administration of anthelmintic treatment, then compared the findings with data obtained from a cohort of RRMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly increased microbial alpha diversity in the gut microbiota of N+ compared to PBO subjects over the course of infection, which is indicative of a healthier gut environment. Furthermore, significant differences in the abundance of several bacterial taxa, such as the immune-modulatory bacterial taxon Tenericutes/Mollicutes, were observed between samples from N+ and PBO subjects. Overall, these data demonstrate a significant impact of N. americanus infection on the human gut microbiota and lend support to the hypothesis of a contributory role of parasite-associated changes in gut microbial composition to the therapeutic properties of hookworm parasites. Amongst others the data set includes: 1. Compressed raw paired end read files - 2 per sample (demultiplexed): e.g. 463_MS_L001_R2_001.fastq.gz 2. OTU table created using Qiime: feature-table.biom and as text file feauture-table.txt 3. Taxonomy file including all of the taxonomic information of the samples: taxonomy.tsv 4. Metadata file containing the relevant contextual information for each sample: Metadata.xlsx 5. Weighted unifrac distance file to explore beta diversity: Weighted-unifrac.tsv
DOI: 10.17632/fgb2xt323b.1
title: LINF_090014000

description: Protein with domain of unknown function (DUF4464); Leishmania infantum
DOI: 10.17632/pzfs68rs76.1
title: LINF_090013600

description: ubiquitin ligase; Leishmania infantum
DOI: 10.17632/x496b5j6ft.1
title: LINF_090013400

description: CPSF30 | cleavage and polyadenylation specificity factor 30 kDa subunit; Leishmania infantum
DOI: 10.17632/8rs9sv6r2j.1
title: LINF_090011800

description: ATP-dependent DNA helicase; Leishmania infantum
DOI: 10.17632/dkpbzvtz3b.1
title: X-ray spectrometer simulation code with a detailed support of mosaic crystals

description: We present a newly developed ray tracing code called mmpxrt, dedicated to study and design X-ray crystal optics, with a special focus on mosaic crystal spectrometers. Its main advantage over other currently available ray tracing codes is that it includes a detailed and benchmarked algorithm to treat mosaic crystals, especially HOPG and HAPG (Highly Oriented/Annealed Pyrolitic Graphite). The code is primarily designed to study crystal spectrometers, therefore their implementation is very straightforward and includes the automated evaluation of their performance. It can, however, be used universally to study other Bragg crystal based instruments, such as monochromators, mirrors, and analyzers. The code is publicly available, written in Python3 and is distributed as a Python library with test cases and user manual included.
DOI: 10.17632/htv4rbysjr.1
title: LINF_340044000

description: 60S ribosomal protein L21; Leishmania infantum
DOI: 10.17632/j2hmvk3byz.1
title: LINF_160009700

description: 60S ribosomal protein L21; Leishmania infantum
DOI: 10.17632/t3vpkrnsrg.1
title: new-Excel Data Self-control and Hope 2020

description: The data comprised of responses to the questionnaire Self-Control Scale and Herth Hope Scale from 244 respondents. Self-Control Scale has 24 items and measured six dimensions which are impulsivity, simple task, risk-seeking, physical activities, self-centeredness and temper. Herth Hope Scale has 30 items measuring three dimensions which are cognitive-temporal, affiliative-contextual and affective-behavioral.
DOI: 10.17632/rdm29gyd4c.1
title: NN_Barnett Experiment 2_Zif268 images

description: The following folders contain the Zif268 images for each rat in the retrosplenial cortex (RSC), hippocampus (HPC) and prefrontal cortex (PFC), as well as the auditory cortex (AUD) which acted as a control region. The images contained in the blue folder show the Zif268 expression under blue light regular theta burst stimulation, and the orange folder contains the images showing Zif268 expression under control orange light stimulation.
DOI: 10.17632/krh5fyng35.1
title: NN_Barnett_Scripts used for NeuroExplorer

description: Below are the two custom scripts used in experiment 1 and 2 prior to passing the data into NeuroExplorer's "Power Spectral Density for Continuous" and "Coherence for Continuous" analyses. In experiment 1 the data was bandpass and notch filtered, in experiment 2 the data was decimated by a factor of 128 before being notch and bandpass filtered.
DOI: 10.17632/pjy522xydk.1
title: NN_Barnett_ Raw data for figures in main text

description: Each folder contains the raw data used to generate each of the key figures, as well as their SPSS or statistica input and associated output
DOI: 10.17632/ptptjcnznv.1
title: Primary School Cultural Elements and Indicators

description: Elementary school cultural elements and indicators for Bangkok school teachers and administrators under the supervision of Thailand’s Office of the Basic Education Commission (OBEC)
DOI: 10.17632/jj2kjz2wsp.1
title: Replication Files for “Assessing the Impact of China Shocks on the Trade Creation Effect in ASEAN”

description: Replication Files for “Assessing the Impact of China Shocks on the Trade Creation Effect in ASEAN”
DOI: 10.17632/msxrz7fgmd.2
title: Flexion synergy-muscle spasticity correlation in chronic stroke

description: This is the data set for the paper titled "Perturbation induced electromyographic activity during the expression of the flexion synergy is a sensitive measure of post-stroke motor impairment" submitted to the European Journal of Neurology.
DOI: 10.17632/psjc3yytvk.1
title: TOTAL PREDICTED MHC-I EPITOPE LOAD IS INVERSELY ASSOCIATED WITH POPULATION MORTALITY FROM SARS-COV-2. Wilson et al

description: Supplemental table S1 and S3. Code to replicate results can be found at: https://github.com/eawilson-CompBio/EnsembleMHC-Covid.git
DOI: 10.17632/njh724xgtg.1
title: CmdStan-RUS Bilayer Demonstration Files and Code

description: This repository contains all of necessary input files for the CmdStan-RUS Bilayer code to reproduce the dual-likelihood, optimization plus Laplace approximation fits, of virtual bilayer "VB-4" and experimental bilayer "EB-1" published in: B.R. Goodlet, B. Bales and T.M. Pollock, "A New Elastic Characterization Method for Anisotropic Bilayer Specimens via Bayesian Resonant Ultrasound Spectroscopy", Ultrasonics (2021). The .stan buildfile is highly annotated with: - block and function descriptions - input data for 2 experiments (exp_1 = bare substrate, exp_2 = bilayer specimen) - parameter definitions, bounds, and units - transformed parameters (coordinates) - prior distributions - code for both a "normal" and "log-normal" noise model Datafile-vb4.dat and Datafile-eb1.dat each give the input data for exp_1 and exp_2 - Note: the computational precision for these models, particularly the bilayer model, are set to compute "publish quality" fits that may require 32+ GB of RAM and a runtime in excess of 24 hours. - To test the code on a computer with less RAM, try a low-precision fit using: P_exp1 = 10, and PX_exp2 = 12, PY_exp2 = 12, PZ_sub_exp2 = 1, PZ_coat_exp2 = 0 (and if the fit completes, expect some biased parameter estimates due to insufficient P) - If the code crashes before a single iteration is written to the output.csv file, you may be (i) exceeding the RAM of your computer, or (ii) if you increased the computational precision of the fit, you may be exceeding the computational limits of the code Runfile-vb4.txt and Runfile-eb1.txt each give 3 sets of commands: the first two conduct a optimization (using the LBFGS algorithm) followed by a Laplace approximation, the third conducts a full HMC inference (using the NUTS algorithm) - The first set of commands does not specify initial conditions, so random initial conditions are generated, followed by 1000 optimization iterations and 1000 laplace draws - The second set of commands specifies that "init-vb4.dat" be used for initial conditions, followed by 1000 optimization iterations and 1000 laplace draws - The third set of commands sample the posterior with HMC, using 250 warm-up samples (a bare minimum for successful HMC auto-tuning) followed by 500 sampling samples (from which posterior distributions are computed) - Be advised: HMC sampling of the posterior (as opposed to Laplace approximations of the posterior) can require 10 to 100 times as many forward model evaluations, with "publish quality" fits taking 30+ days of continuous compute time. init-vb4.dat details how initial conditions are specified - Any or all of the parameters (defined in the .stan buildfile) can be specified with initial conditions - Initial conditions for transformed parameters are ignored
DOI: 10.17632/x949kwgzf3.1
title: Libro de códigos y matriz de análisis de contenido sistemático y estructural de la campaña electoral a las elecciones de la Alcaldía en Bogotá, Colombia (2019)

description: Libro de códigos y matriz de análisis de contenido que caracteriza los debates más destacados en Twitter Colombia sobre la campaña por la Alcaldía de Bogotá, 2019. La muestra recogida comprende 51 Trending Topics (TT) y 503 tweets. Como resultado se destaca el protagonismo de Claudia López, ganadora de la elección. Asimismo, la preponderancia de los medios masivos de información posicionando temas en la agenda mediática de Twitter y su vínculo estrecho con líderes de opinión.
DOI: 10.17632/674mz2htb2.2
title: Complete Marginal Assessment versus Sectional Assessment in Surgically Excised High-Risk and Recurrent Keratinocyte Carcinomas: A Systematic Review

description: Supplemental Figure 1. Study selection flow chart adapted from the PRISMA statement Supplemental Figure 2. Forest plot comparing recurrence between CMA vs SA in aggressive BCC 12 studies were included in this analysis. The point estimate is the proportion of tumors that had a recurrence, the size of the square is proportional to the weight of the study, and the bars show the corresponding 95% CIs. The blue diamonds are centered on the summary of the proportions of the included studies, and the width indicates the corresponding 95% CI Supplemental Table 1. Recurrence outcomes of high-risk keratinocyte carcinomas treated with CMA or SA
DOI: 10.17632/z63ncvdgxj.1
title: The Effect of Child Neglect and Abuse Information Studies on Parents' Awareness Levels during the COVID-19 Pandemic

description: Dataset of The Effect of Child Neglect and Abuse Information Studies on Parents' Awareness Levels during the COVID-19 Pandemic
DOI: 10.17632/6xs7pzpmz6.1
title: Scaled-model vehicle - Paris-Saclay University (2020-06-04-00-22-50)

description: Indoor LiDAR data collected onboard a scaled-model vehicle for SLAM experiments.
DOI: 10.5281/zenodo.4537231
title: Dataset related to article "Intrahepatic Cholangiocellular Carcinoma With Radiological Enhancement Patterns Mimicking Hepatocellular Carcinoma"

description: This record contains raw data related to article “Intrahepatic Cholangiocellular Carcinoma With Radiological Enhancement Patterns Mimicking Hepatocellular Carcinoma" Abstract Non-invasive diagnosis of hepatocellular carcinoma (HCC) in cirrhotic patients requires demonstration of wash-in and wash-out on contrast-enhanced imaging. Recent studies have reported misclassification of mass-forming intrahepatic cholangiocarcinoma (MFCCC) as HCC. We aimed to analyze the contrast enhancement patterns of MFCCC, focusing especially on lesions mimicking HCC. We retrospectively evaluated all consecutive patients with MFCCC who underwent surgery between 2007 and 2017. Patients with mixed HCC-MFCCC were excluded. Two expert radiologists reviewed preoperative CT and MRI. Full-nodule hyperenhancement in the arterial phase in conjunction with hypoenhancement in the portal/late phase was classified as an "HCC-like pattern". Imaging of MFCCCs with an HCC-like pattern was reviewed by an additional radiologist blinded to clinical data. Ninety-two patients were analyzed. All patients were investigated with multiphase CT and 85 with MRI. Twelve tumors (13%) showed full-nodule arterial hyperenhancement. Of these, four were hypoenhancing in the portal/late phase. Overall, 4/92 (4%) MFCCCs (4/45 in patients with cirrhosis/hepatitis, 9%) showed an HCC-like pattern accounting for misclassification as HCC on imaging review. HCC-like MFCCCs accounted for 9% of single tumors ≤ 50 mm. All HCC-like MFCCCs occurred in patients with cirrhosis or hepatitis, whereas only 47% of non-HCC-like MFCCCs did so (p = 0.053). After a median follow-up of 29 months, all patients with HCC-like MFCCCs are alive and disease free (median 64 months). In conclusion, MFCCC was misdiagnosed as typical HCC in 4% of all cases and in 9% of patients with single tumors ≤ 50 mm or with cirrhosis/hepatitis. The risk of misdiagnosis should be considered prior to treatment planning.
DOI: 10.5281/zenodo.4537230
title: Dataset related to article "Intrahepatic Cholangiocellular Carcinoma With Radiological Enhancement Patterns Mimicking Hepatocellular Carcinoma"

description: This record contains raw data related to article “Intrahepatic Cholangiocellular Carcinoma With Radiological Enhancement Patterns Mimicking Hepatocellular Carcinoma" Abstract Non-invasive diagnosis of hepatocellular carcinoma (HCC) in cirrhotic patients requires demonstration of wash-in and wash-out on contrast-enhanced imaging. Recent studies have reported misclassification of mass-forming intrahepatic cholangiocarcinoma (MFCCC) as HCC. We aimed to analyze the contrast enhancement patterns of MFCCC, focusing especially on lesions mimicking HCC. We retrospectively evaluated all consecutive patients with MFCCC who underwent surgery between 2007 and 2017. Patients with mixed HCC-MFCCC were excluded. Two expert radiologists reviewed preoperative CT and MRI. Full-nodule hyperenhancement in the arterial phase in conjunction with hypoenhancement in the portal/late phase was classified as an "HCC-like pattern". Imaging of MFCCCs with an HCC-like pattern was reviewed by an additional radiologist blinded to clinical data. Ninety-two patients were analyzed. All patients were investigated with multiphase CT and 85 with MRI. Twelve tumors (13%) showed full-nodule arterial hyperenhancement. Of these, four were hypoenhancing in the portal/late phase. Overall, 4/92 (4%) MFCCCs (4/45 in patients with cirrhosis/hepatitis, 9%) showed an HCC-like pattern accounting for misclassification as HCC on imaging review. HCC-like MFCCCs accounted for 9% of single tumors ≤ 50 mm. All HCC-like MFCCCs occurred in patients with cirrhosis or hepatitis, whereas only 47% of non-HCC-like MFCCCs did so (p = 0.053). After a median follow-up of 29 months, all patients with HCC-like MFCCCs are alive and disease free (median 64 months). In conclusion, MFCCC was misdiagnosed as typical HCC in 4% of all cases and in 9% of patients with single tumors ≤ 50 mm or with cirrhosis/hepatitis. The risk of misdiagnosis should be considered prior to treatment planning.
DOI: 10.5281/zenodo.4537700
title: The Weierbach Experimental Catchment (WEC) hydrological and isotopic database

description: The Weierbach experimental catchment (0.45 km<sup>2</sup>) is the most instrumented and studied sub-catchment in the Alzette River basin in Luxembourg. Within the last decade, it has matured towards an interdisciplinary critical zone observatory focusing on a better understanding of hydrological and hydro-geochemical processes. Since 2009, the Weierbach has been extensively equipped for continuously monitoring water fluxes and physico-chemical parameters within different compartments of the critical zone. Additionally, these compartments are sampled fortnightly at several locations to analyze d<sup>18</sup>O and d<sup>2</sup>H isotopic composition of water including rainfall, throughfall, soil water, groundwater and streamwater. This link provide the entire database acquired from 2009 to 2019 for hydro-climatological parameters and water isotopic composition. This repository contains a summary table containing site and monitoring meta data (<strong>Weierbach_site-description_2009-2019.xls</strong>). Hydro-climatological data: Rainfall (2009-2019, 10- and 15-min interval, 1 site). Throughfall (2012-2019, fortnightly, 3 sites). Air temperature and air humidity (2012-2019, 15-min interval, 2 sites) Water discharge (2009-2019, 15-min interval, 4 sites). Groundwater depths (2009-2019, 15-min interval, 5 sites) Soil water content at 10, 20, 40 and 60 cm depths (2012-2019, 30-min interval, 7 sites). Soil temperature at 10, 20, 40 and 60 cm depths (2012-2019, 30-min interval, 7 sites). d<sup>18</sup>O and d<sup>2</sup>H isotopic composition of water: Rain water (2009-2019, accumulated fortnightly). Throughfall (2009-2019, accumulated fortnightly). Stream water (2009-2019, fortnightly). Groundwater (2009-2019, fortnightly). Soil solutions at 20, 40, 60 and 100 cm depth (2009-2014, accumulated fortnightly). Riparian water at 10 cm depth (2010-2019, accumulated fortnightly). Tritium measurements in water: Stream water (2011-2017, sporadically).
description: The authors acknowledge funding from the Luxembourg National Research Fund (FNR) for sampling and analysis through the projects: BIGSTREAM (CORE/C09/SR/14), SOWAT (CORE/C10/SR/799842), ECSTREAM (CORE/C12/SR/40/8854), CAOS (INTER/DFG/11/01), CAOS2 (INTER/DFG/14/02), AFR Cristina Moragues (AFR/9188481), STORE‐AGE project (CORE/C14/SR/8353440), HYDRO-CSI (PRIDE15/10623093), PATHFINDER (AFR/10189601) and EFFECT (CORE/C17/SR/11702136).
DOI: 10.5281/zenodo.4061553
title: The Weierbach Experimental Catchment (WEC) hydrological and isotopic database

description: The Weierbach experimental catchment (0.45 km<sup>2</sup>) is the most instrumented and studied sub-catchment in the Alzette River basin in Luxembourg. Within the last decade, it has matured towards an interdisciplinary critical zone observatory focusing on a better understanding of hydrological and hydro-geochemical processes. Since 2009, the Weierbach has been extensively equipped for continuously monitoring water fluxes and physico-chemical parameters within different compartments of the critical zone. Additionally, these compartments are sampled fortnightly at several locations to analyze d<sup>18</sup>O and d<sup>2</sup>H isotopic composition of water including rainfall, throughfall, soil water, groundwater and streamwater. This link provide the entire database acquired from 2009 to 2019 for hydro-climatological parameters and water isotopic composition. This repository contains a summary table containing site and monitoring meta data (<strong>Weierbach_site-description_2009-2019.xls</strong>). Hydro-climatological data: Rainfall (2009-2019, 10- and 15-min interval, 1 site). Throughfall (2012-2019, fortnightly, 3 sites). Air temperature and air humidity (2012-2019, 15-min interval, 2 sites) Water discharge (2009-2019, 15-min interval, 4 sites). Groundwater depths (2009-2019, 15-min interval, 5 sites) Soil water content at 10, 20, 40 and 60 cm depths (2012-2019, 30-min interval, 7 sites). Soil temperature at 10, 20, 40 and 60 cm depths (2012-2019, 30-min interval, 7 sites). d<sup>18</sup>O and d<sup>2</sup>H isotopic composition of water: Rain water (2009-2019, accumulated fortnightly). Throughfall (2009-2019, accumulated fortnightly). Stream water (2009-2019, fortnightly). Groundwater (2009-2019, fortnightly). Soil solutions at 20, 40, 60 and 100 cm depth (2009-2014, accumulated fortnightly). Riparian water at 10 cm depth (2010-2019, accumulated fortnightly). Tritium measurements in water: Stream water (2011-2017, sporadically).
description: The authors acknowledge funding from the Luxembourg National Research Fund (FNR) for sampling and analysis through the projects: BIGSTREAM (CORE/C09/SR/14), SOWAT (CORE/C10/SR/799842), ECSTREAM (CORE/C12/SR/40/8854), CAOS (INTER/DFG/11/01), CAOS2 (INTER/DFG/14/02), AFR Cristina Moragues (AFR/9188481), STORE‐AGE project (CORE/C14/SR/8353440), HYDRO-CSI (PRIDE15/10623093), PATHFINDER (AFR/10189601) and EFFECT (CORE/C17/SR/11702136).
DOI: 10.15468/dpvd9p
title: Redescription of Nogueirapis Moure, 1953 with two new species from the Amazon forest (Hymenoptera: Apidae: Meliponini)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Nogueira, David Silva, Ribeiro, Cristiano Feitosa, Oliveira, Marcio Luiz De (2020): Redescription of Nogueirapis Moure, 1953 with two new species from the Amazon forest (Hymenoptera: Apidae: Meliponini). Zootaxa 4859 (1): 138-150, DOI: https://doi.org/10.11646/zootaxa.4859.1.6
DOI: 10.6084/m9.figshare.13952975
title: lefsedata-niches.txt

description: The table supplied to LEfSe analysis
DOI: 10.6084/m9.figshare.13952993
title: Master_Metadata.txt

description: Master Metadata file for all samples included in this study
DOI: 10.6084/m9.figshare.13953005
title: merged-taxtable.w_smd.biom

description: BIOM file used for samples in this study. Includes taxonomic annotation.
DOI: 10.5519/qd.3t6i635i
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.18112/openneuro.ds003515.v1.0.0
title: Attended speaker paradigm (own name in ignored)