cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/fsghbfmj4w.1
title: Data for: Phase stability of the tin monochalcogenides SnS and SnSe: a quasi-harmonic lattice-dynamics study

description: This repository provides additional data to accompany the paper:

"Phase stability of the tin monochalcogenides SnS and SnSe: a quasi-harmonic lattice-dynamics study"

I. Pallikara and J. M. Skelton
Physical Chemistry Chemical Physics 23, 19219 (2021), DOI: 10.1039/D1CP02597J

This article examines the relative stability of the Pnma, Cmcm, rocksalt and pi-Cubic phases of the tin chalcogenides SnS and SnSe with respect to pressure and temperature. This repository makes available raw data from these calculations, including:

* Quasi-harmonic phonon calculations and derived finite-temperature properties;
* Transition-state searches between the rocksalt and pi-Cubic phases using the nudged elastic-band (NEB) method; and
* Electronic density of states (DoS) and band structures.

For details of how this data was generated, users are referred to the published article and supporting information. Brief details of file formats and links to further documentation are given in the included README file.
DOI: 10.17632/25tmhkss42.1
title: Dataset for Fishing Productivity Gap and Marine Plastic Pollution: A Decomposition Analysis for Coastal Artisanal Fishers in Ecuador and Peru

description: The data contain information of artisanal fishing producers in Ecuador and Peru. Official plastic waste data are integrated in this dataset. Attached is a dofile that helps to calculate two key variables in our econometric models: fishing productivity and standardized plastic waste.
DOI: 10.17632/25tmhkss42.2
title: Dataset for: Fishing Productivity Gap and Marine Plastic Pollution: A Decomposition Analysis for Coastal Artisanal Fishers in Ecuador and Peru

description: The data contain information of artisanal fishing producers in Ecuador and Peru. Administrative plastic waste data are appended in this dataset.

Given the key global role of the fishing sector, there is a need for further understanding of the heterogeneous impact of marine plastic pollution on social and economic outcomes. Focusing on the artisanal fishing sector in Ecuador and Peru, we explore whether fishers are more exposed to productivity losses due to plastic pollution. We use primary data on artisanal fishers from the Ecuadorian and Peruvian coastal zones and find that Peruvian fishers are 37.8% more productive than Ecuadorian respondents. Moreover, Oaxaca–Blinder decomposition analysis indicates that plastic debris affects Ecuadorian producers the most as the productivity gap in favor of Peruvian producers increases with higher plastic pollution exposure. Robustness check strategies support our results and that the endowment and structural effects are drivers of this gap. We also find that association membership, and age reduce the productivity differential, whereas training in plastic waste management widens it.
DOI: 10.17632/25tmhkss42.3
title: Dataset for: Fishing Productivity Gap and Marine Plastic Pollution: A Decomposition Analysis for Coastal Artisanal Fishers in Ecuador and Peru

description: The data contain information of artisanal fishing producers in Ecuador and Peru. Administrative plastic waste data are appended in this dataset.

Given the key global role of the fishing sector, there is a need for further understanding of the heterogeneous impact of marine plastic pollution on social and economic outcomes. Focusing on the artisanal fishing sector in Ecuador and Peru, we explore whether fishers are more exposed to productivity losses due to plastic pollution. We use primary data on artisanal fishers from the Ecuadorian and Peruvian coastal zones and find that Peruvian fishers are 37.8% more productive than Ecuadorian respondents. Moreover, Oaxaca–Blinder decomposition analysis indicates that plastic debris affects Ecuadorian producers the most as the productivity gap in favor of Peruvian producers increases with higher plastic pollution exposure. Robustness check strategies support our results and that the endowment and structural effects are drivers of this gap. We also find that association membership, and age reduce the productivity differential, whereas training in plastic waste management widens it.
DOI: 10.17632/25tmhkss42.4
title: Dataset for: The Heterogenous Effects of Marine Plastic Pollution on Fishing Productivity: A Decomposition Analysis for Coastal Artisanal Fishers in Ecuador and Peru

description: The data contain information of artisanal fishing producers in Ecuador and Peru. Administrative plastic waste data are appended in this dataset.

Given the key global role of the fishing sector, there is a need for further understanding of the heterogeneous impact of marine plastic pollution on social and economic outcomes. Focusing on the artisanal fishing sector in Ecuador and Peru, we explore whether fishers are more exposed to productivity losses due to plastic pollution. We use primary data on artisanal fishers from the Ecuadorian and Peruvian coastal zones and find that Peruvian fishers are 37.8% more productive than Ecuadorian respondents. Moreover, Oaxaca–Blinder decomposition analysis indicates that plastic debris affects Ecuadorian producers the most as the productivity gap in favor of Peruvian producers increases with higher plastic pollution exposure. Robustness check strategies support our results and that the endowment and structural effects are drivers of this gap. We also find that association membership, and age reduce the productivity differential, whereas training in plastic waste management widens it.
DOI: 10.17632/6rx2k6xhjg.2
title: Screening and molecular mechanism research on bile microRNAs associated with chemotherapy efficacy in perihilar cholangiocarcinoma

description: This dataset includes high-throughput sequencing data of bile microRNAs (miRNAs) and mRNAs from patients with advanced perihilar cholangiocarcinoma (pCCA) treated with hepatic arterial infusion chemotherapy (HAIC) using oxaliplatin (OXA) and 5-fluorouracil (5-Fu). The study aimed to identify miRNAs associated with chemotherapy resistance in pCCA patients. Bile samples were collected from patients with varying survival outcomes, and sequencing data were used to identify differentially expressed miRNAs and mRNAs. Key miRNAs, such as miR-532-3p, miR-1250-5p, and miR-4772-5p, were found to correlate with patient survival, and miR-532-3p was shown to promote chemotherapy resistance through negative regulation of SPARC. This dataset may help in further understanding the molecular mechanisms of chemotherapy resistance and identifying potential biomarkers or therapeutic targets for pCCA.
DOI: 10.17632/g36zrks68z.1
title: Data Related to the Rwanda Quality Basic Education for Human Capital Development Project Impact Assessment: Upper primary and lower secondary Teachers’ performance and Pedagogical Beliefs in Mathematics and Science Cohort II

description: The Rwanda Quality Basic Education for Human Capital Development (RQBEHCD) is a World Bank Group financed project through the government of Rwanda to support Mathematics and Science teachers from upper primary and lower secondary schools. The project was confirmed in 2019 and initiated in 2020. The dataset deposited here comprises two types of data; (1) teacher performance scores per subject taught [Math (for both primary and secondary school teachers), Physics, Chemistry, Biology taught in secondary, and Science and Elementary Technology (SET) taught in upper primary school], (2) teacher belief scores. The data were collected before and after a continuous profession development (CPD) training program of five months starting from March to July 2023. The training program comprised four channels that are ICT integration in teaching math and science, content knowledge (SCK), Math and Science laboratory activities, and innovative pedagogy. The data are collected from seven districts of Rwanda that were involved in the second cohort of training (2022-2023).
DOI: 10.17632/3vwgpnw979.1
title: Datasets for YaliFunTome database

description: All the data and the metadata are also presented in the form of a searchable database YaliFunTome, to be found via the link: https://sparrow.up.poznan.pl/tsdatabase/
General:
The aim of this project was to examine the potential implications of transcription factors (TFs) identified in Yarrowia lipolytica genome in stress resistance and/or in the synthesis of heterologous proteins (recombinant proteins: r-Prots). The amount and potential of the data we gathered from completing experimental design inspired us to present them in the form of a searchable catalog.
This database can be used to characterize functional behavior of a specific TF across an array of conditions or to screen for TFs that were responsive to a specific combination of environmental factors in our studies.

Experimental setup:
In short: A collection of 125 Y. lipolytica strains over-expressing (OE) individually TFs was subjected to extensive phenotype screening under different environmental conditions, and the data processing was assisted by mathematical modeling. It was presumed that apart from genetic engineering of the TFs-encoding genes by their OE, implementation of the environmental perturbations will further manipulate the activation status of the TFs.

The search of the TFs within the Y. lipolytica genome and construction of the strains co-over-expressing (co-OE) individually one of 125 identified TFs and a reporter protein (RedStar2) was done previously, by our Colleagues: doi:10.1093/femsyr/foy037. Both genes were cloned under a constitutive promoter pTEF (more details can be found here: doi:10.1093/femsyr/fov052).
The TF co-OE strains were cultured under a combination of enviromental conditions. The experimental setup was designed using DoE (Design of Experiments; DesignExpert software; StatSoft)

Data presentation 
Each strain overexpressing an individual TF (TF-OE strain) was tested under an array of conditions, and so was the reference strain. Raw data for:
optical density at 600 nm wavelength as a proxy of growth,
fluorescence intensity from a reporter protein as a proxy of r-Prot synthesis,
are presented in a form of heat-maps of fold change (FC) of a given measure response in the TF-OE strain over the control strain (file RAW DATA YaliFunTome.xlsx).
The data were also processed according to the Response Surface Methodology to acquire models describing a behavior of a given read parameter within the range of investigated variables (Model Factor's Contributions.xlsx). The adopted data processing strategy enabled the evaluation of each specific variable's contribution to the response's variability (growth, amount of r-Prot) elicited by a given TF-OE strain. This evaluation is presented in Factor's Contribution tables indicating the dominant level of a variable (color-coded and as +1 or -1, according to the adopted coding system) and a percentage contribution of the variable to the response.
DOI: 10.17632/czvdjmscj8.1
title: Evaluation of SARS-CoV-2 identification methods through surveillance of companion animals in SARS-CoV-2-positive homes in North Carolina, March to December 2020

description: Population and sample data for SARS-CoV-2-exposed housepets evaluated for SARS-CoV-2 by PCR and serology. Oral and/or rectal swabs were collected from dogs and/or cats at the time of owner illness and for up to 28 days after initial illness onset. Swabs were tested for viral RNA. Positives were confirmed on a second PCR platform. Serology was collected from days 14-180. Questionnaires were given to owners about their relationship with their pets, and results were analyzed against positive results to measure for associations. ELISA results were compared to negative pre-2019 controls to determine positive cut-offs for IgG and IgM.
DOI: 10.17632/9bs9j9nbk4.1
title: Tables - Impacto da violência sofrida pela mulher no vínculo mãe-filho e no comportamento da criança em idade pré-escolar - Coorte IVAPSA

description: Tabelas do artigo - Impacto da violência sofrida pela mulher no vínculo mãe-filho e no comportamento da criança em idade pré-escolar - Coorte IVAPSA
DOI: 10.17632/stwjg4ddym.1
title: Short Communication: Timber harvesting impacts small mammal foraging behavior and tick infestation

description: Small mammals are important blood-meal hosts for the blacklegged tick, Ixodes scapularis, and reservoirs for the pathogens it transmits. Timber harvesting, a widespread forest management practice within I. scapularis’s endemic range, may impact tick densities and infection prevalence via effects on rodent communities. We compared rodent population size, activity patterns, tick burdens, and tick-borne pathogen infection rates in forests under different timber harvesting regimes. We found that harvest intensity correlates negatively with rodent foraging intensity and positively with tick burdens. Thus, host behavior may mechanistically link forest structure to tick densities in managed forests.
DOI: 10.17632/7mshy2kcf3.3
title: Respiratory pressure and split flow data collection device with rapid expiratory shuttering

description: The venturi-based flow meter utilises split inspiratory and expiratory flow pathways, for greater configurability with additional respiratory monitoring or simulation devices, as well for ease of data processing. The venturi is designed to be integrated in series with respiratory circuitry, using standard 22mm male and female connections. In its current application the inspiratory input port (22mm male connection) is connected to a CPAP device using its accompanying circuitry (or is unconnected when CPAP is not required), the expiratory output port vents to atmosphere (22mm female connection), and the subject port (22mm male connection) is connected to a mouthpiece, filter, or mask. Differential Pressure Sensors were also upgraded (SSCDRRN001PD2A5) to capture larger flow ranges (seen in maximal breaths and panting).

Additionally, a modular expiratory shutter attachment is outlined for identification of passive respiratory mechanics. Specifically, the rapid expiratory shuttering allows for breath-wise identification of elastance and resistance during shutter instances. Thus, eliminating the issue of trade-off associated with the simultaneous fitting of elastance and resistance to expiratory profiles.

Ultimately, the device provides researchers with:

- Rapid expiratory occlusion for identification of passive lung mechanics 
- A low-cost alternative to commercial sensor systems 
- Individual inspiratory and expiratory flow pathways 
- Non-invasive data collection 
- A modular design with high customisability
DOI: 10.17632/9dp48p3hwy.1
title: Single-cell multiome sequencing clarifies enteric glial diversity and identifies an intraganglionic population poised for neurogenesis

description: H5 files for gene expression, output by the 10X Cell Ranger pipeline. Raw FASTQ files, which can be used as input for the Cell Ranger pipeline, are deposited with the NCBI Gene Expression Omnibus with accession GSE184981 (link below). This repository also contains fully processed Seurat objects in RDS format for each dataset.

ATAC fragment files associated with this project are available at doi 10.17632/jzn8cg3hx5.2. (link below)

These data are described in Guyer at al (2023), doi: 10.1016/j.celrep.2023.112194. (link below)
DOI: 10.17632/5rmrxkybbz.1
title: Saved RStudio Workspaces

description: Saved RStudio workspaces containing raw simulation results.
DOI: 10.17632/ztjvhx4587.1
title: Inthawong et al 2024 Scrub typhus NHP model intradermal inoculation dose evaluation

description: Scrub typhus, endemic to the Asia-Pacific region is caused by Orientia tsutsugamushi and transmitted to humans through bites of infected larval Leptotrombidium mites (chiggers). Currently, no protective vaccines exist. Animal models have substantially advanced our understanding of immune response dynamics, pathophysiology and pathogenesis of scrub typhus. Our group previously validated a non-human primate (NHP) model using an intradermal (ID) challenge approach. To further refine this model, we evaluated the effects of progressively increasing doses of human pathogenic O. tsutsugamushi on disease progression, clinical outcomes, bacterial kinetics and immune responses in rhesus macaques (Macaca mulatta). Macaques were inoculated ID with O. tsutsugamushi strain Karp at doses of 106, 107 and 107.8 based on murine median Lethal Dose (muLD50). All NHPs demonstrated characteristic signs of human scrub typhus, including eschar formation, regional lymphadenopathy, elevated body temperature, and bacteremia. Dose-dependent responses were observed, with higher doses (107 and 107.8 muLD50), showing more severe clinical signs and pronounced adaptive immune responses. Increased production of Th1 and Th2 cytokines, with a significant rise surrogate markers, were observed in the 107 muLD50 group. This study demonstrates the critical role of differential serum IFN- levels in shaping immunity, and suggests that the 107 muLD50 dose is optimal for reliably inducing surrogate markers and immune responses resembling human infection dynamics. Our study highlights the importance of thorough inoculum dose characterisation in animal models to ensure accurate and reproducible outcome measures. The fundamental findings will serve emerging research on scrub typhus, particularly in establishing experimental studies.
DOI: 10.17632/8srzx429ms.1
title: Mass Spec data associated with Proteomics analysis of the polyomavirus DNA replication initiation complex reveals a novel functional phosphorylated residue- IJMS 2024

description: Polyomavirus Large T-antigen (LT) is the major viral regulatory protein that targets numerous cellular factors/pathways for cellular transformation and viral replication. LT directly recruits the cellular replication factors involved in recognition of the viral origin, origin unwinding, and primer synthesis carried out by mutual interactions between LT, DNA polymerase alpha-primase (Polprim), and single-stranded DNA binding complex, (RPA). The activities as well as protein-protein interactions of these complexes, are known to be modulated by post-translational modifications; however, modern high-sensitivity proteomic analyses of the PTMs as well as proteins associated with the three have been lacking. Using high resolution liquid chromatography tandem mass spectrometry (LC-MS/MS) of the immunoprecipitated factors (IPMS) we identified 602 PAARs for the 8 polypeptides of LT, Polprim and RPA, of which 479 had not previously been identified: 82 PAARs on SV40 LT, 305 on the Polprim heterotetrametric complex and 92 on the RPA heterotrimeric complex. Using phosphomimetic mutation of one of the novel phosphorylated aa residues, Threonine 518 detected on LT in this study, we have demonstrated a dramatic decrease in DNA replication functions of SV40 Large T- antigen both in vitro and in cell culture. The expansion of our understanding of PAAR sites provides new avenues to investigate regulation of important viral-host interactions with implications for devising targeted therapeutic strategies.
The MS data includes raw data as excel files from the UB Mass Spec Facility with Sequence maps in paper. 
Excel documents: SV40 LT (Cont and Etoposide treated: ETO), POLA (Cont and ETO) and RPA (Cont and ETO). 

Following are brief explanations of all columns in the tables: 
Sequence - the peptide sequence identified 
# PSMs - how many times a spectrum has been matched to this peptide sequence ( a crude quantitative value) 
# Proteins - how many protein(s) this peptide can be inferred to 
# Protein groups - similar with above but several proteins can be grouped to one protein group if no unique peptides can be identified to discriminated one from the other 
Protein group accessions - Uniprot (or other protein database) accession number 
Modifications - PTMs identified on the peptide 
deltaCn - the difference of XCorr (search engine score) between the best match and the second best match (which is a match to another peptide, usually only the best match is considered as the "correct" match) 
phosphoRS site probabilities - Predicted probabilities of PTM localization 
XCorr - search engine score from Sequest HT, the higher XCorr the more confident the identification 
Charge, MH+, RT - basic probabilities of the peptide ion 
deltaM - mass difference between the theoretical and detected peptide ion 
# Missed cleavages - how many K/Rs left in the peptide sequence, which should be cleaved by trypsin but are not
DOI: 10.17632/mxvwntb5wy.2
title: Data for: Linear-Scaling Density Functional Theory (DFT) Simulations of Point, Frenkel and Schottky Defects in CeO2

description: This repository hosts computational data supporting the findings in the open-access paper: Linear-Scaling Density Functional Theory (DFT) Simulations of Point, Frenkel and Schottky Defects in CeO2, Nabeel Anwar, Robert M. Harker, Mark T. Storr, Marco Molinari and Chris-Kriton Skylaris, Comp. Mater. Sci., 2023, 229, 112396. Available from https://doi.org/10.1016/j.commatsci.2023.112396.

UK Ministry of Defence © Crown owned copyright 2023/AWE
DOI: 10.17632/sfnymk5mr8.1
title: A multi-taxa approach reveals contrasting responses of arthropod communities and related ecosystem services to field margin proximity and crop type

description: Here can be found the raw data from arthropod and ecosystem services sampled during the study´and the species list sampled with their red list status.
DOI: 10.17632/y6mbd6tg54.1
title: LDHU3_11.0210

description: Cytoplasmic translation machinery associated protein; Leishmania donovani (HU3 strain)
DOI: 10.17632/j6725v7265.1
title: LDHU3_11.0150

description: NGG1 interacting factor 3-like protein; Leishmania donovani (HU3 strain)
DOI: 10.17632/dksvmygxnv.3
title: Computational NMR Structural Revision of Marinoaziridines A and B

description: Mnova file with GMMX conformational searches
webcocon (https://cocon.nmr.de/) input file and sdf generated structures
DFT Orca computations
StereoFitter input (.txt ) and output (.json) files
Chiroptical Gaussian16 computations
DOI: 10.17632/z9w23xvhbt.1
title: MaRoReS (Machining, Roughness and Residual Stresses generated in turning of 42CrMo4+QT steel)

description: This repository is part of the MaRoReS (Machining, Roughness and Residual Stress) project, with which the authors aim to determine the influence of the main turning parameters (here feed rate (mm/rev), cutting speed (m/min), depth of cut (mm), and insert radius(mm)) on the roughness and residual surface stress of a 42CrMo4+QT steel. 

For this purpose, a large experimental campaign was designed using a CCD-type design of experiments in which 68 different specimens were machined under different cutting conditions. The turning process was fully monitored regarding forces, accelerations, sound, and current consumed by the lathe. Once the specimens were machined, surface roughness and longitudinal residual stress were measured.

The repository is organized as follows. Initially, the user will find two folders: "Raw Data" and "Processed Data". On the one hand, the first folder is subdivided into 3 subfolders containing respectively the raw data obtained from the roughness measurement, the surface residual stresses, and the data obtained from monitoring the turning process. On the other hand, the second folder is dedicated to entering the post-processed data. A more detailed explanation of each folder can be found by double-clicking on them. In addition, in the section "Steps to reproduce", the reader will find an exhaustive explanation of the acquisition methods and the post-processing analysis implemented in each case.
DOI: 10.17632/jv32cvpn3r.1
title: CAD5 Brie Library Quality Control

description: Whole-genome mouse CRISPR-KO Brie library in CAD5 cells - quality control run.
DOI: 10.17632/pxw323z9xp.1
title: Pseudophilothrips ichini flexible feeding

description: This data repository contains the data presented in the manuscript "The Brazilian peppertree biological control agent Pseudophilothrips ichini (Thysanoptera: Phlaeothripidae) displays a flexible feeding strategy between foliage and reproductive tissues."