cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1613343.v1
title: Genetic relatedness provides support for a species complex of myxosporeans infecting the Indian major carp, Labeo rohita

description: Myxozoans are an economically important group of microscopic metazoan parasites of fish. The myxozoan species <em>Thelohanellus filli</em> infects commercially important freshwater fish both in wild and in cultured habitat. This parasite causes gill hemorrhagic disease and significant damage to the respiratory surface of the infected fish. In the present study, the 18S rDNA gene sequence of morphologically identified <em>T. filli</em> infecting the gill lamellae of the Indian major carp, <em>Labeo rohita</em>, was characterized. This revealed that we are actually dealing with a species complex containing <em>T. bifurcata</em>, <em>T. jiroveci</em> and <em>T. seni</em>. Phylogenetically, <em>T. filli</em> clustered with other myxozoan parasites, with the species most closely related to <em>T. filli</em> having 96 to 97% sequence similarity. The intraspecific variation demonstrated in this study points towards the importance of newer approaches to facilitate reassessment of taxa and detecting species complexes and cryptic species.
DOI: 10.6084/m9.figshare.4272392.v3
title: International Journal of Systematic and Evolutionary Microbiology (IJSEM) phenotypic database

description: The International Journal of Systematic and Evolutionary Microbiology (IJSEM) is the official publication of the International Committee on Systematics of Prokaryotes and the Bacteriology and Applied Microbiology Division of the International Union of Microbiological Societies, and the official journal of record for novel bacterial and archaeal taxa (http://ijs.microbiologyresearch.org/content/journal/ijsem). We manually searched IJSEM articles to extract phenotypic, metabolic and environmental tolerance data of bacterial strains from 2004 to 2014.<br><br> We focused on the most recent entries as they presumably used standardized and state-of-the-art methods, up-to-date taxonomic nomenclature, most strains had easily retrievable 16S rRNA gene sequence data, and many strains also had publicly available genome sequence data available. Data was manually collected using Google Forms as variable structure of the articles and inconsistent reporting of relevant information precluded the use of automatic text parsing algorithms. <br>
DOI: 10.6084/m9.figshare.5241184.v1
title: Erratum: Why Do the Clients of Georgian Needle Exchange Programmes Inject Buprenorphine?

description: <i>Aim:</i> The aim of the study was to understand the prevalence and patterns of the non-medical injecting use of buprenorphine among drug injectors in Georgia. <i>Method:</i> A self-administered questionnaire was distributed among injecting drug users enrolled in Georgian needle exchange programmes. The questions covered topics related to drug use career, patterns (frequency, history, dosage) and reasons for the use of buprenorphine. <i>Results:</i> Pharmaceutical buprenorphine in the form of Subutex® was the most commonly injected drug in terms of lifetime (95.5%) and last-month (75%) prevalence of use. 48% of those study participants who had injected Subutex at some point reported having used it to cope with withdrawal or to give up other opioids. 90.5% of Subutex injectors used 1–2 mg as a single dose, and the mean frequency of its injection was 6 times per month. 75% of Subutex injectors had used 3 or more types of illegal drugs during the last 30 days. <i>Conclusion:</i> While widely misused by Georgian drug injectors, Subutex is neither the principal nor the favourite drug, and it is rather used as self-treatment. The authors consider the introduction of buprenorphine maintenance treatment to be a promising effective measure to decrease its non-medical and illegal use.
DOI: 10.17632/p3ntt2z294
title: Sperm chromatin dispersion bright field images

description: This dataset is constructed with 130 images and annotations for bright field microscopic images (20x objective) from results of sperm chromatin dispersion test.

Sperm chromatin dispersion test (SCD) is a microscopic method for determining sperm DNA fragmentation, sperm DNA is dispersed into the gel on the slide by the lysing buffer. Sperms with higher DNA fragmentation produces more single-stranded DNA in the nucleus, and preventing the dispersion process. Wright-Giemsa staining is performed to visualize the DNA on the slide, thus sperms with DNA damage is revealed by the relatively smaller halos.

For steps to utilize this dataset, see the descriptions below.
DOI: 10.17632/z9b6vn6x2x
title: code and data for the paper "In-sample and out-of-sample Sharpe ratios of multi-factor asset pricing models"

description: This replication package contains the data and code for the paper "In-sample and out-of-sample Sharpe ratios of multi-factor asset pricing models."
The file README.pdf provides detailed information of the data and the programs used to generate the tables and figures in the paper.
The folder "Data" contains the external data that are used to generate the tables. 
The folder "Tables" contains the Matlab datasets, programs, and functions to generate the tables in the paper. 
The folder "Figures" contains the Matlab programs and functions to generate the figures in the paper.
DOI: 10.17632/bxhmvjmck7
title: A proof-of-concept study utilising 2D NMR Spectrometry for in situ characterisation and quantitation of key biomarkers and actives in tape stripped ex vivo human skin data

description: Data sets for Tape Strip paper
DOI: 10.17632/r6d79tgg4t
title: Long-run Effects of Super Low Fertility on Housing Markets

description: Title: MATLAB Codes for "Long-run Effects of Super Low Fertility on Housing Markets"

Description:
This repository contains MATLAB code used in the paper "Long-run Effects of Super Low Fertility on Housing Markets." The project features an overlapping generations (OLG) general equilibrium model incorporating housing markets and demographic transitions specific to South Korea.

The included MATLAB scripts simulate the model and generate the results and figures reported in the main text of the paper.

Requirements:
The code is written in MATLAB, a high-level language developed by MathWorks. While MATLAB is a commercial product, the included code can be run using MATLAB Online, MATLAB Runtime, or through an institutional license—most economics departments will have one. No separate license purchase is necessary to run this code if you use these alternatives.

Folder Structure:

Code_Baseline/
Contains the core MATLAB scripts used to produce the main results of the paper.

Code_OpenEconomy/
Includes MATLAB scripts for a robustness check based on a small open economy variation of the model.

How to Run:
To reproduce all key tables and figures from the main text:

Navigate to the root directory in MATLAB.

Run KOR_runme_2024.m

This will execute the baseline model and generate all relevant outputs.

Contact:
For questions or comments, please contact the authors of the paper (jylee22@inu.ac.kr or hsuh@inha.ac.kr).
DOI: 10.17632/fkf4nwvgxg
title: Data on Teachers in Higher Educational Institutions

description: Data were collected from teachers in higher education in Meghalaya, India. The researchers used the third-person technique under the projective methods to collect the data. The respondents were provided with the story and asked to respond to statements on a 14-point Likert scale based on their level of agreement. The ideal values were calculated through Delphi method where the experts were provided with information. In this process, the experts were given the questionnaires in 2 or more rounds. In the end, all the responses were compiled and reported, and an ideal response was generated.
DOI: 10.6084/m9.figshare.21500454.v1
title: Chromosome-level assemblies of wild water chestnut (Trapa incisa)

description: The genome and its protein-coding gene annotaion file of wild water chestnut (<em>Trapa incisa</em>).
DOI: 10.17632/9h5cf9wkrk
title: PRJEB44932 SARS-CoV-2 Wastewater Sequences Processed

description: The data come from NCBI BioProject PRJEB44932, as analyzed in Jahn et. al (2022).
These data are short read sequences from wastewater in 6 locations in a tourist-heavy area of Switzerland from 2021-02-01 to 2021-11-30, with daily sampling for most sampling sites.
There are 303 unique dates in these data, but only 227 of these dates were common to all WasteWater Treatment Plants (WWTPs).
For our analysis, we are treating each date as if they are one "unit" away, even though there are many cases of 2 and 3 days between time points (up to a maximum of 8 days).
See Jahn et. al (2022) for a detailed description of the genomic sequencing process.

Data processing involved alignment of the short reads to the Wuhan-1 reference sequence (NC_045512) with `minimap2` v2.28, identifying the mutations relative to the reference, and recording the number of times a mutation was observed (counts) and the depth of coverage.
The frequency is calculated as the counts divided by the coverage.
The mutation pre-processing pipeline is available at \url{https://github.com/DASL-Lab/data-treatment-plant}, and heavily relies on the GromStole pipeline (\url{https://github.com/PoonLab/gromstole}).

After being processed into counts and coverage, the data were filtered to only include mutations that are relevant to analysis. There were many mutations with either consistently low counts (possibly due to sequencing errors) or low coverage.
After filtering the data for sampling dates that were common to all locations, there are 1,061 unique mutations at each location on each sampling date.

We found all mutations that had both a frequency of at least 0.1 and a frequency below 0.9 (with a coverage at least 40) at at least two time points during the study in any location. This ensures that we have all of the mutations that were potentially part of a circulating lineage without relying on lineage definitions.

Jahn, Katharina, David Dreifuss, Ivan Topolsky, Anina Kull, Pravin Ganesanandamoorthy, Xavier
Fernandez-Cassi, Carola Bänziger, et al. 2022. “Early Detection and Surveillance of SARS-
CoV-2 Genomic Variants in Wastewater Using COJAC.” Nature Microbiology 7 (8): 1151–60.
https://doi.org/10.1038/s41564-022-01185-x.
DOI: 10.17632/jbdmgsjvt7
title: Carbon Taxes and the Geography of Fossil Lending

description: This is the data and codes necessary to replicate the analysis in the paper "Carbon Taxes and the Geography of Fossil Lending" by Luc Laeven and Alexander Popov in the Journal of International Economics.
DOI: 10.17632/rtytpmt7w8
title: Supplemental Material: An Alternative Method for Postoperative Scalpel Blade Removal

description: Our video shows an alternative method for postoperative scalpel blade removal that can be used in a surgical setting
DOI: 10.5522/04/12159366.v1
title: Lithium-ion Battery INR18650 MJ1 3D X-ray CT Data: NMC811 Cathode (EIL-014)

description: <b>3D data on an 18650 Li-ion Battery Nickel-Rich NMC811 Cathode</b><br> <br>Collected using an 810 Ultra X-ray-CT instrument (Zeiss Xradia 810 Ultra, Carl Zeiss., CA, USA).<br>Accelerating tube voltage of 35 kVp that employs a rotating chromium anode. <br><br>Quasi-monochromatic beam with a characteristic emission peak of 5.4 keV (Cr-Kα).<br> A capillary condenser produces focused X-rays for a full-field illumination of the sample, projected onto the scintillator detector using a Fresnel zone plate. <br><br>In order to capture the full electrode thicknesses, two CT scans were conducted of the sample.<br> The two Zernike phase-contrast nano-CT scans of the cathode required 1200 X-ray radiograph projections per scan, with a 30 second exposure time per projection. <br><br>The raw radiographs can be made available upon request - please state 'EIL-011.tif' and 'EIL-012.tif'.<br> The two nano-CT datasets were then reconstructed using commercial software employing parallel-beam filtered back-projection algorithms (‘Reconstructor Scout-and-Scan’, Carl Zeiss., CA, U.S.A.),producing an isotropic voxel length of 63.1 nm.<br> The reconstructed volumes were then stitched using Avizo Fire software (Avizo, Thermo Fisher Scientific, Waltham, Massachusetts, U.S.A.) producing one nano-CT tomogram (EIL-014.tif).<br><br><br>
DOI: 10.6084/m9.figshare.19448384.v1
title: Callable sites

description: These files are to show how many sites were mapped and where SNPs could be called. These files <strong>DO NOT </strong>have the final filtered set of SNPs or indels. They can be used to see the depth of coverage or to obtain the number of utilizable sites (as a denominator). <br> These files were used to perform analyses in the manuscript - "<strong>A population-genetic lens into the process of gene loss following whole-genome duplication"</strong>.
DOI: 10.6084/m9.figshare.26942266.v1
title: Reaction rate constants

description: This is a PDF file containing 166 reaction rate constants of 166 organic compounds with hydroxyl radical.
DOI: 10.6084/m9.figshare.28938134.v1
title: HORs annotated by centroAnno on chromosome 1 of R. pubera

description: HORs annotated by centroAnno on chromosome 1 of R. pubera
DOI: 10.17632/96xg3wmppf
title: Data on SiC-based bundle lifetime variability: the insufficiency of external phenomena affecting the flaw size

description: The data presented here correspond to a comprehensive analysis on lifetime variability for SiC-based bundle. These data are associated to the supplementary communication to https://doi.org/10.1016/j.ijfatigue.2020.106072
DOI: 10.17632/ypkr6r726j
title: Python-based code for automation of repeating calculations in Ansys Fluent

description: Here is the compiled Python-based code for automation calculations in Ansys Fluent for the fluid flow tasks.
DOI: 10.6084/m9.figshare.19131416.v3
title: A thermodynamic database of membrane protein-protein complexes and mutants for understanding their binding affinity

description: We developed a database, MPAD (Membrane Protein complex binding Affinity Database), which includes 5436 experimental data from 950 proteins on the binding affinities of membrane protein complexes and their mutants along with sequence, structure, and functional information, membrane specific features, experimental conditions, as well as literature information. The database can be freely accessed at https://web.iitm.ac.in/bioinfo2/mpad.
DOI: 10.6084/m9.figshare.6265589.v1
title: Patient24

description: Female Patient with 139 slice of pulmonary embolism CT-Angiography.
DOI: 10.17632/s27zfxgbpj
title: Study dataset: Real-time ultrasound demonstration of uterine isthmus contractions during pregnancy

description: This dataset includes transvaginal ultrasound recordings of the uterine cervix in the form of extended video clips (over 15 minutes) from 30 individuals in their second trimester of pregnancy. Each individual also has a fast-motion video clip (at 40x speed) available. The accompanying .csv file provides demographic information about the cohort. 
The full analysis of this dataset is published in the American Journal of Obstetrics and Gynecology as an original research paper: https://doi.org/10.1016/j.ajog.2023.07.025

The .csv file consists of the following columns: 
- Individual (number) 
- SG_eco: completed weeks of pregnancy 
- Dies_eco: completed days of the current week of pregnancy 
- Paritat: number of previous pregnancies ≥23.0wk 
- Cesaries: number of previous cesarean sections 
- Edat: maternal age at the time of ultrasound examination (in years) 
- Pes: maternal weight at the start of the pregnancy (in kg) 
- Talla: maternal height (in cm) 
- Contraccio: 0=no, 1=yes (presence of isthmic contraction during the examination, subjectively assessed) 
- Orina: volume of urine collected before the ultrasound examination (in ml)
DOI: 10.6084/m9.figshare.21391155.v1
title: Sequence_alignment_sealice_viruses

description: The sequence alignments from "Sea lice harbor and are infected by divergent RNA viruses".
DOI: 10.6084/m9.figshare.26885734.v1
title: Database for layered intercalation compounds and host layered materials

description: Here, we provide a database of electronic band structures for layered intercalation compounds and layered hosts. Each ".tar.gz" file contains input files for VASP ("POSCAR", "KPOINTS", "KPOINTS-mesh") and an output file ("vasprun.xml") generated by VASP. The "POSCAR" file is the input structure file, the "KPOINTS" file is the line-mode KPOINTS file used for band structure calculations, and the "KPOINTS-mesh" file is the KPOINTS file used for electronic structure calculations before the band structure calculation. The potential files used for each element are listed in "Potentials.xlsx".
We also provide a python script "plot_bands.py" to describe the band structure. See readme_for_python_scripts.txt for instructions.
DOI: 10.6084/m9.figshare.28827971.v1
title: Data for modeling American chestnut distribution circa 1940 in Monroe County, New York State, US

description: Contained in this item are data to perform species distribution modeling or related analysis of American chestnut distribution in the mid-20th century in Monroe County, New York State, US. Modeling in the associated study was original performed using MaxEnt 3.4.4 software, but the data in this item could be used for training a species distribution model using any presence-only modeling technique. This item contains two files:<br><b>"castanea_dentata_1940.csv"</b> is a CSV file containing the estimated locations of woodlots 1938-1940 where American chestnut was observed. It contains latitude and longitude columns, with coordinates stored in the State Plane New York West coordinate reference system (NAD 1983, meters, WKID 32117). Data are based on maps from the following publication:Shanks, R.E., 1966. An ecological survey of the vegetation of Monroe County, New York. Proceedings of the Rochester Academy of Science 11, 105–255.<br><b>"predictors_ascii_10m.zip" </b>contains zipped ASCII gridded data layers for 11 environmental variables. Data are provided at 10 m resolution, and are stored in the State Plane New York West coordinate reference system (NAD 1983, meters, WKID 32117). Sources for the data, and software to create the data layers, are as follows:NRCS, 2014. Description of SSURGO database [WWW Document]. URL http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/survey/?cid=nrcs142p2_053627 (accessed 12.1.23).USGS, 2023. 3D Elevation Program 1/3 Arc-Second Resolution Digital Elevation Model [WWW Document]. The National Map Download. URL https://www.sciencebase.gov/catalog/item/63fd9914d34e70052b9b6738 (accessed 3.31.25).Esri, 2023. ArcGIS Pro 3.1. Redlands, CA USA.
DOI: 10.6084/m9.figshare.8956481.v1
title: Microbial responses to warming enhance soil carbon loss following translocation across a tropical forest elevation gradient

description: sequence and meta-data for article 'Microbial responses to warming enhance soil carbon loss following translocation across a tropical forest elevation gradient'
DOI: 10.6084/m9.figshare.19033130.v2
title: Plio-Pleistocene climate record on the Tibetan plateau

description: Plio-Pleistocene climate record on the Tibetan plateau (4.3 Ma to 0.8 Ma). <br><b>Supplementary Data 1</b>. Results of carbonate (CaCO<sub>3</sub>) content and carbonate stable isotopes including oxygen (δ<sup>18</sup>O<sub>c</sub>), carbon (δ<sup>13</sup>C<sub>c</sub>), and clumped isotopes (Δ<sub>47</sub>), as well as grain size and a suite of organic proxies including total nitrogen (TN), total organic carbon (TOC), carbon to nitrogen ratios (C/N), and carbon isotope ratios in organic matter (δ<sup>13</sup>C<sub>org</sub>). Clumped isotopes raw data, cross plots of δ<sup>18</sup>O<sub>c </sub>and<sub> </sub>∆<sub>47-</sub>based temperature, calculations related to mean annual air temperature calculation (MAAT), and surface uplift estimate are also included.<b>Supplementary Data 2</b>. Estimate of mean annual air temperature (MAAT) using a different temperature-∆<sub>47</sub> calibration for comparison.<b>Supplementary Data 3</b>. Calculation of permafrost thawing area and carbon release.<br>Supplement to <b>Cheng F. et al.</b>, Alpine permafrost could account for a quarter of thawed carbon based on Plio-Pleistocene paleoclimate analogue, <i>Nature Communications.</i><b></b>
DOI: 10.17632/x98zr48x5n
title: Competition and financial institutions and markets development: A dynamic panel data analysis

description: Panel data from 140 countries over 2000-2014 period, allow to investigate the relationship between market competition and financial development, using the new IMF- FD index covering financial institutions and markets access, depth and efficiency. Three competition indicators are employed, i.e. Boone, Lerner and banks concertation, in addition to control of corruption and others control variables. Dummies are added to assess the relationship over 2008 financial crisis. Data are gathered from IMF-FD, World Bank -WDI, GFD and WGI. A dynamic panel GMM model is employed. Strong evidence of the positive impact of market competition, as measured by Boone index, on financial institutions and markets development is found, while banks concentration has a damaging effect on FD. Interestingly, none of our competition indexes affects financial institutions returns, which hold even over 2008 financial crisis, likely at the expense of depth and access in developing countries. Institutions, as proxied by control of corruption, have broader positive impact on FD particularly on financial markets. These findings have important implications for developing countries keen to foster the development of their financial system.
DOI: 10.6084/m9.figshare.24592551.v1
title: Annotation file of Opsariichthys bidens from Zhejiang, China

description: Annotation file of Opsariichthys bidens from Zhejiang, China
DOI: 10.6084/m9.figshare.91309.v1
title: Computational Prediction and Validation of Protein Structure and Function in Protein Engineering and Rational Drug Design

description: Skou Fellowship. Danish research foundation
DOI: 10.6084/m9.figshare.92419.v3
title: 3 figures summarising field data on ocean-atmosphere gas transfer velocity

description: Plots (and code and data to generate plots) demonstrating our current understanding and field data on air-sea gas transfer velocity. If you want to re-plot then download all the files in this fileset into a directory and 'source' kw_plots.R (you'll need R installed). Note, code released under CC_BY-SA licence (share-alike). Plots CC-BY (just attribution required) Readme file and further details to follow.
DOI: 10.6084/m9.figshare.9976556.v5
title: Database published in Multiple elements of soil biodiversity drive ecosystem functions across biomes | Nature Ecology & Evolution

description: Database published in Multiple elements of soil biodiversity drive ecosystem functions across biomes | Nature Ecology & Evolution
DOI: 10.60893/figshare.jcp.28121528.v1
title: Supplement 1

description: Geometries
DOI: 10.17632/ydrf8vp9sn
title: Ahmed F, et al. Rosacea Diagnosis and Prescription Patterns in Underrepresented Groups: An All of Us Database Analysis. JAAD. 2023.

description: Supplemental methods and results.
DOI: 10.6084/m9.figshare.3464360.v1
title: Dog Part dataset + annotation software

description: Files used for computing dog body parts and their annotation file.In every folder the original .oni video files the annotation file .ann and segmentation parameters .sp<br>the redme file describes the annotation file format<br>Annotation software is also included to possibly annotate new sequences<br>
DOI: 10.6084/m9.figshare.8850686.v2
title: Table S9 from Light pollution increases West Nile virus competence of a ubiquitous passerine reservoir species.

description: Excel worksheet of DEseq2 results for each contrast.