cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/3011
title: Strategic use of (un)certainty expressions
title: Strategic Use of (Un)certainty expressions

description: Speakers have a number of options when introducing propositions which they take to be uncertain: for instance, they can use verbs such as 'know', 'believe' or 'think'. The production of uncertainty expressions is highly context dependent. One promising approach to capturing the semantic meaning of these expressions takes them to be available only when the speaker's confidence in the proposition exceeds some threshold. However, it is unclear whether this approach deals satisfactorily with the full range of usages of uncertainty expressions. For instance, speakers may use them to achieve social goals such as toning down the force of their assertion. In this case they pursue another communicative goal than just being cooperative, they also aim to be polite. The current study investigates the speakers' motivations in choosing between uncertainty expressions such as 'believe' or the factive 'know' in two controlled contexts. More specifically, we show that speakers' choice of expression is influenced by (i) how likely they estimate an event to be and (ii) strategic considerations relating to the communicative context in which they are working. Thus, speakers adjust their language as a manipulative process. We situate these results in the context of threshold semantics.
DOI: 10.7488/ds/3402
title: Demographic and COM-B data from project 'are we working (too) comfortably'

description: Dataset includes data related to paper submission to BJHP January 2022
description: 1 x Excel file of data relating to demographics, sedentary behaviour and COMB variables 1 X excel file of open ended responses to questions
DOI: 10.7488/ds/3012
title: Data pertaining to publication: Meta-GWAS Reveals Novel Genetic Variants Associated with Urinary Excretion of Uromodulin
title: Meta_Analysis of Urinary Uromodulin

description: Uromodulin, the most abundant protein excreted in normal urine, plays major roles in kidney physiology and disease. The mechanisms regulating the urinary excretion of uromodulin remain essentially unknown. We conducted a meta-analysis of genome-wide association studies for raw (uUMOD) and indexed to creatinine (uUCR) urinary levels of uromodulin in 29,512 individuals of European ancestry from 13 cohorts. We tested whether variants in disease-causing genes associate with uromodulin levels and investigated the effects of keratin-40 (KRT40) on uromodulin processing. Results: Two genome-wide significant signals were identified for uUMOD: A novel locus (P 1.24E-08) over the KRT40 gene coding for KRT40, a type1 keratin expressed in the kidney, and the UMOD-PDILT locus (P 2.17E-88), which included two independent sets of SNPs spread over UMOD and PDILT. The meta-GWAS for uUCR yielded two genome-wide significant signals on the UMOD-PDILT locus and at the novel WDR72 locus previously associated with kidney function, urine pH and risk of kidney stones.
description: Please see "Uromodulin Meta_Analysis_ReadMe file.txt". Please note the '.txt' files in this dataset contain millions of rows of tab-delimited data.
DOI: 10.7488/ds/3025
title: Quantitative fetal fibronectin to improve decision making in women with signs and symptoms of preterm birth (QUIDS): Spontaneous preterm birth within 7 days risk predictor
title: Development and validation of a risk prediction model of preterm birth for women with preterm labour symptoms (the QUIDS study): A prospective cohort study and individual participant data meta-analysis

description: This workbook contains anonymised data from the study Quantitative fetal fibronectin to improve decision making in women with signs and symptoms of preterm birth (QUIDS): Spontaneous preterm birth within 7 days risk predictor.
description: Readme: A Readme.txt file Datashare: An excel (.xlsx) work book with 3 worksheets 1. Information: information about the study, authors, funding, approval, registration and publication 2. Data Dictionary 3. QUIDS data
DOI: 10.7488/ds/3015
title: Supplementary files supporting the paper "Microarray profiling emphasizes transcriptomic differences between hippocampal in vivo tissue and in vitro cultures"
title: Microarray data

description: Differential expression was performed using the R package "limma" (R package version 3.44.3) (Supplementary files 1-4; 1_diff_expr_WT_cell_vs_tissue, 2_diff_expr_101LL_cell_vs_tissue, 3_diff_expr_cell_WT_ vs_101LL, 4_diff_expr_tissue_WT_ vs_101LL) and gene ontology analysis was performed using the R package "topGO" (R package version 2.40.0) (Supplementary files 5-6; 5_go_all_bp_WT_cell_vs_tissue, 6_go_all_bp_101LL_cell_vs_tissue). Primary hippocampal cell cultures are routinely used as an experimentally accessible model platform for the hippocampus and brain tissue in general. Containing multiple cell types including neurons, astrocytes and microglia in a state that can be readily analysed optically, biochemically and electrophysiologically, such cultures have been used in many in vitro studies. To what extent the in vivo environment is recapitulated in primary cultures in an on-going question. Here we compare the transcriptomic profiles of primary hippocampal cell cultures and intact hippocampal tissue. In addition, by comparing profiles from wild type and the PrP 101LL transgenic model of prion disease, we also demonstrate that gene conservation is predominantly conserved across genetically altered lines.
DOI: 10.7488/ds/3014
title: ATEC manuscript 4 - supporting data: "The Effect of Antecedence on Empirical Model Forecasts of Crop Yield from Observations of Canopy Properties"

description: Identification of yield deficits early in the growing season for cereal crops (e.g., Triticum aestivum) could help to identify more precise agronomic strategies for intervention to manage production. We investigated how effective crop canopy properties, including leaf area index (LAI), leaf chlorophyll content, and canopy height, are as predictors of winter wheat yield over various lead times. Models were calibrated and validated on fertiliser trials over two years in fields in the UK. Correlations of LAI and plant height with yield were stronger than for yield and chlorophyll content. Yield prediction models calibrated in one year and tested on another suggested that LAI and height provided the most robust outcomes. Linear models had equal or smaller validation errors than machine learning. The information content of data for yield prediction degraded strongly with time before harvest, and in application to years not included in the calibration. Thus, impact of soil and weather variation between years on crop phenotypes was critical in changing the interactions between crop variables and yield (i.e., slopes and intercepts of regression models) and was a key contributor to predictive error. These results show that canopy property data provide valuable information on crop status for yield assessment, but with important limitations.
DOI: 10.7488/ds/3018
title: Rules of formation of H–C–N–O compounds at high pressure and the fates of planetary ices

description: The solar system’s outer planets, and many of their moons, are dominated by matter from the H–C–N–O chemical space, based on solar system abundances of hydrogen and the planetary ices H2O, CH4 , and NH3 . In the planetary interiors, these ices will experience extreme pressure conditions, around 5 Mbar at the Neptune mantle–core boundary, and it is expected that they undergo phase transitions, decompose, and form entirely new compounds. While temperature will dictate the formation of compounds, ground-state density functional theory allows us to probe the chemical effects resulting from pressure alone. These structural developments in turn determine the planets’ interior structures, thermal evolution, and magnetic field generation, among others. Despite its importance, the H–C–N–O system has not been surveyed systematically to explore which compounds emerge at high-pressure conditions, and what governs their stability. Here, we report on and analyze an unbiased crystal structure search among H–C– N–O compounds between 1 and 5 Mbar. We demonstrate that simple chemical rules drive stability in this composition space, which explains why the simplest possible quaternary mixture HCNO—isoelectronic to diamond—emerges as a stable compound and discuss dominant decomposition products of planetary ice mixtures.
description: See README.txt
DOI: 10.7488/ds/3019
title: Raw DFT data for "High-temperature phase transitions in dense germanium"

description: Through a series of high-pressure x-ray diffraction experiments combined with in situ laser heating, we explore the pressure–temperature phase diagram of germanium (Ge) at pressures up to 110 GPa and temperatures exceeding 3000 K. In the pressure range of 64–90 GPa, we observe orthorhombic Ge-IV transforming above 1500 K to a previously unobserved high-temperature phase, which we denote as Ge-VIII. This high-temperature phase is characterized by a tetragonal crystal structure, space group I4/mmm. Density functional theory simulations confirm that Ge-IV becomes unstable at high temperatures and that Ge-VIII is highly competitive and dynamically stable at these conditions. The existence of Ge-VIII has profound implications for the pressure–temperature phase diagram, with melting conditions increasing to much higher temperatures than previous extrapolations would imply.
description: See README.txt. The tarballs in this repository contain the following raw DFT data relevant to "High-temperature phase transitions in dense germanium", as published in J. Chem. Phys.: * PBE & PBEsol enthalpies * Seeds for structure search * Phonons (computed with QE) * MD trajectories * All necessary pseudopotentials
DOI: 10.7488/ds/3013
title: High and asymmetric somato-dendritic coupling of V1 layer 5 neurons independent of visual stimulation and locomotion
title: Ex vivo calibration of GCaMP6s and GCaMP6f signals in soma and apical tuft dendrites

description: Ex vivo calibration of GCaMP6s and GCaMP6f signals in soma and apical tuft dendrites of layer 5 pyramidal neurons from the mouse primary visual cortex (V1). We examined the relationship between neuronal spiking and calcium event amplitudes in proximal and distal neuronal compartments, ex vivo, by combining calcium imaging and whole-cell recordings in acute cortical slices from mouse V1. We imaged the soma and distal apical dendrite (nexus) of GCaMP6s- and GCaMP6f- expressing layer 5 neurons whilst driving neuronal spiking either by somatic current injections (somatic stimulation) or L1 electrical stimulation (dendritic stimulation). Dataset corresponding to Figure 4 and Figure 4 supplementary 1.
DOI: 10.7488/ds/3021
title: scRNA transcription profile of adult zebrafish podocytes
title: zebrafish podocyte fluorescent reporters and transcription profile

description: Background/Aims: The role of podocytes is well conserved across species from drosophila to teleosts, and mammals. Identifying the molecular markers that actively maintain the integrity of the podocyte will enable a greater understanding of the changes that lead to damage. Methods: We generated transgenic zebrafish, expressing fluorescent reporters driven by the podocin promoter, for the visualization and isolation of podocytes. We have conducted single cell RNA sequencing (scRNA-seq) on isolated podocytes from a zebrafish reporter line. Results: We demonstrated that the LifeAct-TagRFP-T fluorescent reporter faithfully replicated podocin expression in vivo. We were also able to show spontaneous GCaMP6s fluorescence using light sheet (single plane illumination) microscopy. We identified many podocyte transcripts, encoding proteins related to calcium-binding and actin filament assembly, in common with those expressed in human and mouse mature podocytes. Conclusion: We describe the establishment of novel transgenic zebrafish and their use to identify and isolate podocyte cells for the preparation of a scRNA-seq library from normal podocytes. The scRNA-seq data identifies distinct populations of cells and potential gene switching between clusters. These data provide a foundation for future comparative studies and for exploiting the zebrafish as a model for kidney development, disease, injury and repair.
description: FASTQ files: Pod_RFP_S2_L001_l1_001.fastq.gz; Pod_RFP_S2_L001_R1_001.fastq.gz; Pod_RFP_S2_L001_R2_001.fastq.gz; Pod_RFP_S2_L002_l1_001.fastq.gz; Pod_RFP_S2_L002_R1_001.fastq.gz; Pod_RFP_S2_L002_R2_001.fastq.gz; Pod_RFP_S2_L003_l1_001.fastq.gz; Pod_RFP_S2_L003_R1_001.fastq.gz; Pod_RFP_S2_L003_R2_001.fastq.gz; Pod_RFP_S2_L004_l1_001.fastq.gz; Pod_RFP_S2_L004_R1_001.fastq.gz; Pod_RFP_S2_L004_R2_001.fastq.gz; Processed file: Pod_RFP_expression_matrix.csv
DOI: 10.7488/ds/3016
title: Microarray data CEL files supporting the paper "Microarray profiling emphasizes transcriptomic differences between hippocampal in vivo tissue and in vitro cultures"
title: Microarray data
title: Microarray data CEL files

description: Affymetrix microarray processing produced 16 (4 WT cell, 4 101LL cell, 4 WT tissue, 4 101LL tissue) probe cell intensity data (CEL) files. Primary hippocampal cell cultures are routinely used as an experimentally accessible model platform for the hippocampus and brain tissue in general. Containing multiple cell types including neurons, astrocytes and microglia in a state that can be readily analysed optically, biochemically and electrophysiologically, such cultures have been used in many in vitro studies. To what extent the in vivo environment is recapitulated in primary cultures in an on-going question. Here we compare the transcriptomic profiles of primary hippocampal cell cultures and intact hippocampal tissue. In addition, by comparing profiles from wild type and the PrP 101LL transgenic model of prion disease, we also demonstrate that gene conservation is predominantly conserved across genetically altered lines.
DOI: 10.7488/ds/3147
title: Whole slide images of armadillo liver from M.leprae dataset

description: Whole slide images of H&E stained sections of liver from nine-banded armadillos chronically systemically infected by Mycobacterium leprae, resistant to systemic infection by Mycobacterium leprae, or uninfected. Images acquired on a Hamamatsu NanoZoomer in .ndpi format.
description: Provided in Readme.txt.
DOI: 10.7488/ds/3022
title: Loss of Adam10 disrupts ion transport in immortalised kidney collecting duct cells

description: The kidney cortical collecting duct (CCD) comprises of principal cells (PC), intercalated cells (IC) and the recently discovered intermediate cell type. Kidney pathology in a mouse model of the syndrome of apparent aldosterone excess (SAME) revealed plasticity of the cortical collecting duct (CCD), with altered principal cell (PC): intermediate cell: intercalated cell (IC) ratio. The self-immortalized mouse CCD cell line, mCCDcl1, shows functional characteristics of PCs but displays a range of cell types, including intermediate cells, making it ideal to study plasticity. We knocked out Adam10, a key component of the Notch pathway, in mCCDcl1 cells, using CRISPR-Cas9 technology, and isolated independent clones, which exhibited severely affected sodium transport capacity and loss of aldosterone response. Single-cell RNA sequencing revealed significantly reduced expression of major PC-specific markers, such as Scnn1g (gamma-ENaC) and Hsd11b2 (11ßHSD2), but no significant changes in transcription of components of the Notch pathway were observed. Immunostaining in the knockout clone confirmed the decrease in expression of gamma-ENaC and importantly, showed an altered, diffuse distribution of PC and IC markers, suggesting altered trafficking in the Adam10 knockout clone as an explanation for the loss of polarisation.
description: FASTQ files: 11630MJ0002TXP-N__Library_2_S2_L002_l1_001.fastq.gz; 11630MJ0002TXP-N__Library_2_S2_L002_R1_001.fastq.gz; 11630MJ0002TXP-N_Library__2_S2_L002_R2_001.fastq.gz; 11924MJ0001TXP-N__A1_S1_L002_l1_001.fastq.gz; 11924MJ0001TXP-N__A1_S1_L002_R1_001.fastq.gz; 11924MJ0001TXP-N__A1_S1_L002_R2_001.fastq.gz; Processed file: mCCDA1_expression_matrix.csv
DOI: 10.7488/ds/3020
title: Dataset for "Time-resolved spectral-domain optical coherence tomography with CMOS SPAD sensors"

description: Scripts and raw data used for the manuscript "Time-resolved spectral-domain optical coherence tomography with CMOS SPAD sensors"
description: Description of the dataset can be found in readme.txt
DOI: 10.7488/ds/3031
title: Systematic Review and Meta-Analysis on the Impact of Polycyclic Aromatic Hydrocarbons Exposure in Cognitive Function and Neurodegeneration in Humans
title: Polycyclic Aromatic Hydrocarbons Impact in Cognitive Function and Neurodegeneration in Humans - A systematic review data

description: Exposure to air pollution is now recognized globally by governments, leading research scientists, and civil society as one of the greatest public health hazards of the 21st century. Polycyclic aromatic hydrocarbons (PAH) are a group of air pollutants discharged mainly from incomplete combustion and pyrolysis of hydrocarbons, predominantly found in: coal, oil, wood and petrol. PAH exist in the atmosphere in a gaseous state or adsorbed to particulate matter, mainly of 2.5mm diameter or less (PM2.5). Given the anthropogenic nature of PAH sources and their small size, they are difficult to regulate and account for, but their exposure has been associated with worsening asthma, coronary heart disease, various types of cancers, decreased immune function and organ damage. However, their implications on cognitive functions and neuronal health in humans has not been systematically recorded/analysed up to date as only sporadic studies have been conducted in few countries. This submission contains the results of the systematic search, data extraction and meta-analyses from systematically reviewing the existent literature on the impact of PAH exposure in cognitive function and neurodegeneration in humans. The data is contained in two excel spreadsheets. One spreadsheet contains details of the search (i.e., search strategy, keywords, databases, search results, included references, excluded references with reasons for exclusion, and duplicates). The other spreadsheet contains the data extracted from analysing the papers reviewed (i.e., included), and the meta-analyses (multi-variable graphs and forest plots with their sources). Worksheets not containing meta-analyses are also provided in csv (comma delimited) format.
DOI: 10.7488/ds/3041
title: Red-shifted environmental fluorophores and their use for the detection of Gram-negative bacteria_raw spectral data

description: Spectral data (absorption, fluorescence, lifetime) of merocyanine derivatives described in the research article entitled "Red-shifted environmental fluorophores and their use for the detection of Gram-negative bacteria" published in Chemosensors (2021); The dataset contains absorption, fluorescence, and lifetime raw data on compounds numbered 1, 2, 12 and 13 in the article.
DOI: 10.7488/ds/3028
title: Raw data for Barium Polyhydride

description: Dataset relating to "Synthesis of Weaire-Phelan Barium Polyhydride". By combining pressures up to 50 GPa and temperatures of 1200 K, we synthesize the novel barium hydride, Ba8H46, stable down to 27 GPa. We use Raman spectroscopy, X-ray diffraction, and first-principles calculations to determine that this compound adopts a highly symmetric 𝑃𝑚3¯𝑛 structure with an unusual 534:1 hydrogen-to-barium ratio. This singular stoichiometry corresponds to the well-defined type-I clathrate geometry. This clathrate consists of a Weaire–Phelan hydrogen structure with the barium atoms forming a topologically close-packed phase. In particular, the structure is formed by H20 and H24 clathrate cages showing substantially weakened H–H interactions. Density functional theory (DFT) demonstrates that cubic 𝑃𝑚3¯𝑛 Ba8H46 requires dynamical effects to stabilize the H20 and H24 clathrate cages.
DOI: 10.7488/ds/3032
title: Ice-shelf basal melt channels stabilized by secondary flow: ELMER/Ice files and results
title: Program files and results for ELMER/Ice full-Stokes ice-flow modelling of ice-shelf flow in the vicinity of basal melt channels

description: Program files and results for ELMER/Ice full-Stokes ice-flow modelling of ice-shelf flow in the vicinity of basal melt channels. Program files and results correspond to Figure 1 from "Ice-shelf basal melt channels stabilized by secondary flow", Wearing et al.. Program files include: mesh file "mesh500.grd" and solver input file "basal_channel_MP8_xm25.sif". These files are input files to the multi-physics open-source finite-element-method suite ELMER. Files ending with '.grd' define the mesh on which the problem is defined. They are plain text and can be read or edited by any text editor. Results are compiled into a netcdf file: "Elmer_output_basal_channel.nc" with fields: time (yr), horizontal position (x (m)), vertical position (y (m)), horizontal velocity (u (m/yr)), vertical velocity (v (m/yr)). Model simulation results created using the open-source ice-flow model: ELMER/Ice: https://elmerice.elmerfem.org/ Details of ELMER's general model can be found here: https://www.csc.fi/web/elmer The sub-package used to generate these results may be found here: https://elmerice.elmerfem.org/3-3-dimensional .
description: Model simulation results created using the open-source ice-flow model: ELMER/Ice: https://elmerice.elmerfem.org/
DOI: 10.7488/ds/3042
title: Isotope quantum effects in the metallization transition in liquid hydrogen

description: Quantum effects in condensed matter normally only occur at low temperatures. Here we show a large quantum effect in high-pressure liquid hydrogen at thousands of Kelvins. We show that the metallization transition in hydrogen is subject to a very large isotope effect, occurring hundreds of degrees lower than the equivalent transition in deuterium. We examined this using path integral molecular dynamics simulations which identify a liquid-liquid transition involving atomization, metallization, and changes in viscosity, specific heat and compressibility. The difference between H2 and D2 is a quantum mechanical effect which can be associated with the larger zero-point energy in H2 weakening the covalent bond. Our results mean that experimental results on deuterium must be corrected before they are relevant to understanding hydrogen at planetary conditions.
DOI: 10.7488/ds/3043
title: CAD files for the Swing to measure the Centre of Gravity and Moment of Inertia

description: The dataset provides the CAD files describing the swing, which is available in FloWave Ocean Energy Research Facility. The described experimental setup can be used to measure the centre of gravity and the moment of inertia with one degree of freedom. The swing is supported by two movable frames. Two different pivot axes are available and the measurement process as well as the analysis is presented in a separate paper. The provided files allow to check how a potential model can be placed on the swing and supports the usage of this device. Four different types of files are available: IGES (igs), ACIS (sat), STL Stereolithography (stl) and Rhinoceros (3dm). The geometry was constructed in mm.