cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/m4jrt9snhv
title: Gender Differences in Functional Limitations of Frail Older People Ageing in Place Alone in Italy

description: The dataset includes data collected for the study "Inclusive ageing in place” (IN-AGE), funded by Fondazione Cariplo (Italy), Grant N. 2017-0941. This cross-sectional qualitative survey was carried out in 2019 in both urban and rural sites of three Italian regions (Lombardy, Marche, and Calabria). Semi-structured interviews were administered face-to-face to a purposive sample of 120 frail older people aged 65 years and over (males and females). Inclusion criteria were the following: living at home; alone or with a private personal care assistant (PCA); no cognitive impairment; intermediate mobility between limited/reduced within the home, and outside the home with help; and absence of help by close family members (living in the same urban block/rural building).
The dataset contains socio-demographic dimensions (e.g., age groups, gender, living situation, marital status, education), daily activities performed alone/in autonomy, with help, not performed (i.e., the senior is “not able”), and type of support. The dataset puts in relation the difficulties of older men and women in carrying out Basic and Instrumental Activities of Daily Living (ADLs-IADLs), in addition to two mobility limitations (going up/down the stairs and bending to pick up an object), and sensory limitations (hearing and eyesight). The level of physical limitations is further assessed with four grades: “mild” when older person is able to perform all the activities (no activity labelled “not able” is referred); “moderate” when older person is unable to perform one-two activities; “high” when older person is unable to perform three-four activities; “very high” when older person is unable to perform five or more activities. The following sources of support are addressed: relatives/children, friends, neighbours, operators from private services (e.g., Domestic Home Helper, DHH), from public services (e.g., Home Care Worker, HCW), and personal/private care assistant (PCA). 
Main results show that men are more limited than women, and cleaning the house, shopping, bathing/showering, and washing the laundry are overall the most difficult activities, but particularly for men. The family, especially children, represents the greater support for both genders, in addition to public/private services. However, older men are supported by HCWs and PCAs more than women, and the latter are supported by DHHs and friends/neighbours more than men. For both genders, some limitations, i.e., poor mobility, poor eyesight and hearing, and poor memory, affect transversally several activities of daily living. These results can offer insights for policymakers to develop adequate policies, taking in consideration the gender dimension.
The dataset is provided in open format (Microsoft Excel) and includes the following: a “numeric” dataset regarding the un-labelled dimensions used for statistics elaboration; a codebook with the complete variables list and variables labels we used.
DOI: 10.6084/m9.figshare.11342267.v3
title: Search Operators

description: Figshare supports a predefined set of operators and specific characters for advanced in field searches and these have been outlined in the table. <br><br>
DOI: 10.17632/9b264dw38s
title: Phylogeny_of_foetal_haematopoiesis_2020_LCM_images

description: These are the histological images to accompany the manuscript "Lineage tracing of human embryonic development and foetal haematopoiesis through somatic mutations" (bioRxiv 2020.05.29.088765; doi: https://doi.org/10.1101/2020.05.29.088765). The laser capture micro-dissection (LCM) images were taken from the camera on the laser-capture microdissection system (Leica LMD7) at 20-40x magnification. In most cases there are images from before and after LCM to illustrate the precise area cut and subjected to targeted or whole-genome sequencing. The slide scanner images (ending .ndpi) are high-resolution histology images taken with a Hamamatsu slide scanner, and should be viewed together with the corresponding annotation file (ending .ndpa) which highlights the areas undergoing LCM, and the corresponding unique identifier. They can be viewed using freely available software NDP.view (available at https://www.ndpserve.com/ndp/serve/home). The tissues are 5-10um thick and are from two human foetuses of 8- and 18-pcw weeks as described in manuscript. For the 8-pcw foetus there are images taken from epidermis, connective tissue of the limb, inter-vertebral discs, kidney, gut, heart, blood from inside the chambers of the heart and placenta. For the 18-pcw foetus there are images from the epidermis, hair follicles, peripheral nerves, heart and kidney.
DOI: 10.17632/bk6p72jnk5
title: LINF_160018000

description: Cullin-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.6084/m9.figshare.28458278.v1
title: Supplementary Material for: Hyaluronic Acid Binding Peptide Regulates Extracellular Matrix Deposition And Diminishes Fibroblast Contractility

description: Fibroblasts are central to variety of homeostatic events such as wound healing and tissue regeneration. However, their pathologic activation is thought to play roles in a variety of diseases not only limited to fibrosis, foreign body reaction, scleroderma but also cancer metastasis. Biophysical properties of the extracellular matrix (ECM) deposited by an activated fibroblast determine whether there is a pro-regenerative or scarring response. Compared to aged fibroblasts, embryonic fibroblasts were shown to deposit a pro-regenerative ECM characterized by early hyaluronic acid (HA) deposition and increased levels of pro-regenerative collagens such as type III collagen. Since HA is also a regulator of collagen organization, we propose that early accumulation of HA by fibroblasts can facilitate a pro-regenerative matrix formation. Given that the molecular weights of HA present in pro-regenerative matrix are higher than synthetic HA, we strategize attracting HA synthesized by fibroblasts. In this study, we used a synthetic peptide sequence known to have affinity to HA as a strategy to instruct fibroblasts to retain HA on the surface. We hypothesized that hyaluronic acid binding peptide (HABP) may instruct fibroblast endogenous HA deposition onto functionalized surfaces. We functionalized silica glass surfaces with HABP using aminoorganosilane mediated chemisorption and screened primary human dermal fibroblasts (hDF) for cell morphology, cytoskeletal arrangement, and alpha-smooth muscle actin (α-SMA) expression. Our results show HABP treated surfaces retain higher levels of HA on silica glass compared to control surfaces on fibroblast derived matrices. Analysis of α-SMA shows increased α-SMA expression on hDFs and increased stress fiber formation. HABP treated surfaces were found to have reduced α-SMA expression. The physical features of collagen fibers deposited by fibroblasts were also organized differently in the presence of HABP. We propose that HABPs are a potentially viable strategy to instruct pro-regenerative fibroblasts and can be used therapeutically to treat fibrotic diseases.
DOI: 10.6084/m9.figshare.14553081.v1
title: Supplementary Material for: Explaining the Differences in Opioid Overdose Deaths between Scotland and England/Wales: Implications for European Opioid Policies

description: <b><i>Backgrounds:</i></b> Between 2009 and 2018, the number of opioid-related deaths (ORDs) in Scotland showed a dramatic increase, whereas in England and Wales, a much lower increase in ORD was seen. This regional difference is remarkable, and the situation in Scotland is worrisome. Therefore, it is important to identify the drivers of ORD in Scotland. <b><i>Methods:</i></b> A systematic literature review according to PRISMA guidelines was conducted to identify peer-reviewed studies about key drivers for the observed differences in ORDs between Scotland and England/Wales. In addition, non-peer-reviewed reports on nationwide statistical data were retrieved via Google and Google Scholar and analysed to quantify differences in ORD drivers between Scotland and England/Wales. <b><i>Results:</i></b> The systematic review identified some important drivers of ORD, but none of these studies provided direct or indirect comparisons of ORD drivers in Scotland and England/Wales. However, the reports with nationwide statistical data showed important differences in ORD drivers between Scotland and England/Wales, including a higher prevalence of people using opioids in a problematic way (PUOP), more polydrug use in people using drugs in a problematic way (PUDP), a higher age of PUDP, and lower treatment coverage and efficacy of PUDP in Scotland compared to England/Wales, but no regional differences in injecting drug use, incarceration/prison release without treatment, and social deprivation in PUDP. <b><i>Conclusion:</i></b> It is concluded that the opioid crisis in Scotland is best explained by a combination of drivers, consisting of a higher population involvement in (problematic) opioid use (notably methadone), relatively more polydrug use (notably benzodiazepines and gabapentinoids), a steeper ageing of the PUOP population in the past 2 decades, and lower treatment coverage and efficacy in Scotland compared to England/Wales. The findings have important consequences for strategies to handle the opioid crisis in Scotland.
DOI: 10.6084/m9.figshare.26143207.v4
title: Chromosome-level genome assembly and annotation of Tibetan argali

description: Tibetan argali genome assembly and annotation
DOI: 10.17632/m88sdrg64t
title: data in brief content validity table

description: The dataset comprises meticulously curated information extracted from a total of 101 primary studies obtained through systematic searches across reputable digital databases. These studies were meticulously selected based on stringent inclusion and exclusion criteria, ensuring their relevance and adherence to methodological standards. The dataset includes key details such as the title, author(s), year of publication, source title, and pertinent information regarding content validity methods employed in each study. Additionally, the dataset provides insights into the data extraction process, research questions addressed, and the methodology utilized for data interpretation. Organized in Excel format, this dataset serves as a comprehensive resource for researchers and practitioners seeking to explore and analyze the utilization of content validity methods across various fields of study.
DOI: 10.17632/r47847kcb6
title: Oversampling techniques for diabetes classification: A comparative study

description: Supplementary Material: In this study, several tests were conducted to evaluate the occurrence of overfitting when applying different oversampling variants and machine learning algorithms. Therefore, we have compared the results obtained in the test dataset with the results obtained in the training dataset.
Table S[1 - 3] show the F1-Score results obtained for each oversampling variant. The results concerning the application of different machine learning algorithms to training data are presented for each fold (K=10) dataset, as well as the mean of these values.
DOI: 10.17632/bx98gcrzbg
title: Molecular electrostatics and pKa shifts calculations with the Generalized Born model. A tutorial through examples with Bluues2

description: Biomolecular electrostatics is of key importance for biological function and recognition. The continuum electrostatic model based on the Poisson-Boltzmann (PB) equation has been widely used to study biomolecular electrostatics. The solution of the PB equation gives the electrostatic potential over the space enclosing the molecule(s) of interest, typically obtained at points of a suitable grid.

The Generalized Born (GB) model has been used to provide a useful approximation to the solution obtained by solving numerically the PB equation. The main advantage of the GB approach is to express the electrostatic energy of the system as the sum of pairwise interactions. The latter depend on geometric parameters (the GB radii) which depend on all atoms, and their radii, of the system. In this work we present a tutorial through examples for a more efficient and general version of the program Bluues which is able to compute:

1) the generalized Born radius of each atom;

2) the electrostatic potential at the surface of the molecule mapped to solvent accessible atoms;

3) the solvent accessible surface in a PDB formatted file;

4) the electrostatic potential in the volume surrounding the molecule;

5) the electrostatic free energy and different contributions to it;

6) the pH-dependent properties of proteins (total charge and pH-dependent free energy of folding) in the pH range −4 to 18;

7) the pKa shifts due to molecular structure of all ionizable groups.
DOI: 10.17632/fbm46jt4zb
title: Asian seabass, KU, Thailand

description: The repository contains two files: 1) growth data file of 390 days old Asian seabass including average daily growth (ADG), fillet weight (FW), total length, standard length, head length, body depth, body size measurements (M12 - M78), condition factor, body area measurements (FA, HA, CFA and TBA), and 2) SNP genotype file.
DOI: 10.17632/3vbmz58ch8
title: The topography and flow raw data of the ten tests used

description: the file contains 2 types of files: topography and flow field.
1- dune topography temporal evolution (every 15 minutes)
2- flow field above migrating subaqueous dune 2h after the beginning of an experiment
DOI: 10.6084/m9.figshare.14098685.v1
title: Lampe et al 2021 - Table S1 - Reference transcriptome statistics

description: Reference transcriptome sequencing statistics for each Illumina run on both isolates.
DOI: 10.15468/dl.8w64he
title: Occurrence Download

description: A dataset containing 2408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Rhingia campestris Meigen, 1822"
 ]
}

 The dataset includes 2408 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009145-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/shw6684cfh
title: A Multicenter Descriptive Analysis of 270 Men with Frontal Fibrosing Alopecia and Lichen Planopilaris in the United States

description: Supplemental methods and data for "A Multicenter Descriptive Analysis of 270 Men with Frontal Fibrosing Alopecia and Lichen Planopilaris in the United States"
DOI: 10.6084/m9.figshare.25481020.v2
title: Data and code for McCaffrey et al. "<i>Testing the effects of drought, parasite infection, and their interaction on freshwater snails</i>"

description: These data and code accompany McCaffrey et al. "Testing the effects of drought, parasite infection, and their interaction on freshwater snails". All analyses and figures therein can be recreated with these materials.
DOI: 10.17632/78tbfhwkdf
title: Exploration of the mutational landscape of cutaneous leiomyoma confirms FH as a driver gene and identifies targeting purine metabolism as potential therapeutic strategy

description: Supplementary files to accompany the manuscript entitled "Exploration of the mutational landscape of cutaneous leiomyoma confirms FH as a driver gene and identifies targeting purine metabolism as potential therapeutic strategy"
DOI: 10.17632/6wnfvkz6gb
title: Genomic data of food waste and wheat straw co-digestion

description: Impact of trace element addition relative to wheat straw co-digestion on anaerobic digestion of food waste
DOI: 10.17632/4vnndy59fp
title: CODEX, a neural network approach to explore signaling dynamics landscapes

description: Supplementary data and R/Python code required to reproduce the figures from the accompanying publication: Jacques et al. "CODEX, a neural network approach to explore signaling dynamics landscapes". The pre-print available here: https://doi.org/10.1101/2020.08.05.237842 Included datasets: * Single-cell ERK/Akt activity dynamics in responses to GF treatment. Acquired in-house by Paolo Gagliardi. * p53 responses to ionizing radiation. Data kindly provided by Galit Lahav and Jacob Ornstein-Stewart. * SMAD2 response to TGFb. Data kindly provided by Alexander Loewer. * Drosophila speed movement. Data obtained from https://github.com/benfulcher/hctsa_phenotypingFly * Synthetic data
DOI: 10.17632/2z5cbjmnbx
title: Data for: Nonnegative matrix factorization-based blind source separation for full-field and high-resolution modal identification from video

description: Videos related to the recently submitted MSSP paper: "Nonnegative matrix factorization-based blind source separation for full-field and high-resolution modal identification from video", 2019.
DOI: 10.6084/m9.figshare.28758929.v1
title: Fasta files of alignments Nerillidae South China Sea phylogeny (18S, 28S, COI and H3)

description: Nerillidae is the most species-rich, meiofaunal, annelid family, but little is known about its diversity and distribution in the Northwest Pacific. Four sampling campaigns to Jeju Island, South Korea and the Ryukyu Islands, Japan retrieved an unexpectedly high diversity of about 167 nerillid species in subtidal and submarine cave localities of the East China Sea. Bayesian inference and maximum likelihood methods were performed on datasets of concatenated gene sequences (18S rRNA, 28S rRNA, COI, and H3) comprising a total of 55 terminals from 11 different genera of Nerillidae. Integrating detailed morphological assessments (light-, scanning electron-, and confocal laser scanning microscopy) with molecular analyses, we here describe seven new species and a new genus,<i> Cirrinerilla</i> gen. nov. None of the species show geographical overlap between South Korea and the Ryukyu Islands, possibly due to oceanographic and anchialine dispersal barriers and poor dispersal capabilities of Nerillidae. However, two congeneric terminals of <i>Meganerilla</i> and two of <i>Leptonerilla</i> from different islands of the Ryukyus show relatively high molecular similarity, suggesting recent vicariance of these populations (or species). The anchialine caves hold a remarkably high diversity of nerillids compared to coastal subtidal localities, supporting a preadaptation of Nerillidae to these isolated habitats under freshwater influence. This study underlines the need for further exploration of the unique anchialine habitats as well as additional subtidal meiofauna surveys in the East China Sea, for shedding further light on benthic diversification and colonization processes in this region.
DOI: 10.17632/c4zptxvw8z
title: Moderate crowding affects immune cell number and longevity in sex specific manner in Drosophila melanogaster

description: Comparison of Immune cell number, fecundity and longevity in Drosophila melanogaster outbred population reared in crowded (300eggs/6ml media) and uncrowded condition (60 eggs/6ml media). Crowded condition further grouped into early, mid and late developing individuals for comparison.
DOI: 10.17632/gsgtzzfwh4
title: Data for: Diminished brain responses to second-language words are linked with native-language literacy skills in dyslexia

description: Mismatch negativity (MMN) mean amplitudes for English word forms (shy, she, shoy*) and Finnish word forms (sai, sii*, soi) in Finnish 9-11-year-old children with dyslexia (DYS) and their controls (CON). Nine fronto-central channels (10-20-system).
DOI: 10.17632/mk2f7vs7c6
title: Amplicon sequencing data of riverine metagenomic samples obtained from Takamigawa River in Nara Prefecture, Japan

description: The amplicon sequencing data of the partial coding regions of mitochondrial cox1, nuclear histone H3 and 18S rRNA genes were obtained from the bulk community samples. 
1. Sampling sites and dates
Aridoshi (ARD) on 17-March-2017, 34°23′23″N 135°59′17″E, Shisetsu at Kozugawa (SST) on 29-June-2017, 34°23′53″N 135°59′34″E. 
Sampling was performed in the run environment (slow riffle) of ARD and SST (SST-run), and in the rapid environment of SST (SST-rapid). The samples ARD1~ARD6 listed in Table 1 were obtained from ARD. The samples SST1~3, SST7~9, and SST13~15 were obtained from SST-rapid. The samples SST4~6, SST10~12, and SST16~18 were obtained from SST-run.
2. Amplicon sequencing
High-throughput parallel sequencing was performed by Miseq (Illumina, San Diego, CA, USA) capable of generating 2 × 300 base paired-end reads. Primer sequences of PCR amplification, accession numbers of DNA sequence data are summarized in Table 1. 
3. Operational taxonomic units (OTUs)
Amplicon sequence reads of histone H3 (DRR131047~DRR131054) were classified into a total of 563 OTUs (file name: Takamigawa-H3.fasta) based on the criteria described previously by Wakimura et al. (doi: 10.1016/j.dib.2022.108599). Amplicon sequence reads of 18S rRNA (DRR131055~DRR131062) were classified into a total of 3001 OTUs (file name: Takamigawa-18S.fasta) by QIIME. The OTUs of cox1 are available in Mendeley Data (doi: 10.17632/pfhf4kt37s.1). OTUs are named and numbered arbitrarily.
4. GMYC analyses
Phylogenetic trees of the OTUs were reconstructed using Markov chain Monte Carlo (MCMC) methods by MrBayes 3.2.7a with the GTR+I+G molecular clock model. Species boundaries were estimated using SPLITS package in R. The analyses delimited 369 species for cox1 data (figures 1a and 1b of Wakimura et al., doi: 10.1016/j.dib.2022.108599) and 141 species for histone H3 data (file name: H3_tree.pdf), respectively. In the cladograms of cox1 and histone H3, each vertical bar indicates a cluster of OTUs or singleton assigned to a single GMYC species. Numbers in parentheses after the OTU name indicate the number of reads of the OTU. Numbers with dotted lines refer to the GYMC species IDs.
5. Frequency of sequence reads
Numbers of sequence reads within the GMYC-delimited species (cox1 and histone H3) or of each operational taxonomic unit (18S rRNA) are summarized in the Table 2 (cox1), Table 3 (histone H3) and Table 4 (18S rRNA), respectively.