cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/knhnhf8v4p
title: Dataset: Geochemical and Meteorological Data from the Salar de Llamara

description: Datasets accompanying manuscript titled "Lake morphology and meteorological conditions impact stratification of saline lakes in the Atacama Desert". Attached spreadsheets include datasets from the meteorological station, as well as in situ and laboratory based geochemical measurements of lake chemistry from Puquio 1 and Puquio 4 in the Salar de Llamara, Atacama Desert, Northern Chile.
DOI: 10.6084/m9.figshare.13818518.v1
title: Ant Eye Measurements and Statistics

description: Automatic (output from the ommatidia detecting algorithm, ODA) and manual measurements of ommatidia count and diameter of replicas of five ant species taken previously: Notoncus ectatommoides and Camponotus aeneopilosus (from Palavalli-Nettimi and Narendra (2018)), Myrmecia nigrocincta, M. tarsata, and Rhytidoponera inornata (from Palavalli-Nettimi et al. (2019)).<br>References:<br><br>Palavalli-Nettimi, Ravindra, and Ajay Narendra. 2018. “Miniaturisation Decreases Visual Navigational Competence in Ants.” Journal of Experimental Biology 221(7):jeb177238.<br>Palavalli-Nettimi, Ravindra, Yuri Ogawa, Laura A. Ryan, Nathan S. Hart, and Ajay Narendra. 2019. “Miniaturisation Reduces Contrast Sensitivity and Spatial Resolving Power in Ants.” Journal of Experimental Biology 222(12). doi: 10.1242/jeb.203018.
DOI: 10.6084/m9.figshare.22032575.v1
title: Effects of aging on word position coding in Chinese reading

description: This is the data for the manuscript entitled "Effects of aging on word position coding in Chinese reading".
DOI: 10.6084/m9.figshare.22721032.v1
title: Superior ferroelectricity and nonlinear optical response in a hybrid germanium iodide hexagonal perovskite

description: Data for figures in the manuscript and supplement
DOI: 10.6084/m9.figshare.112.v1
title: India Africa Asia HGDP HapMap frappe K10

description: These are the results of a structure analysis performed by FRAPPE, with default settings and K=10, on a combined dataset consisting in 3146 autosomal SNPs for 4025 individuals from 167 populations. Each line corresponds to an individual. The first column is the population identifier, the second column is the individual identifier, the last columns are the proportions of the different ancestry classes determined by FRAPP for the individual. The analyzed data consists in genome-wide SNPs that were obtained from 5 different sources, keeping the SNPs common to all 5 sources.
DOI: 10.6084/m9.figshare.13048730.v1
title: Integrated 3D model of South China in 2020

description: We present an integrated 3D model of velocity, temperature, density and bulk compositional structure of the upper mantle beneath the South China based on the joint inversion of Rayleigh wave phase and group dispersions, topography, geoid height, and surface heat flow data. "Xiaoyu_Yang_3D_integrated_model.xlsx" is the final 3D model, which includes the 3D distributions of temperature, density, Vs, Vp and 2D distributions of lithosphere-asthenosphere boundary (LAB) and magnesium number in the upper mantle. <br>
DOI: 10.6084/m9.figshare.20223093.v1
title: Genome assembly of the medicinal plant Voacanga thouarsii

description: <em>Voacanga thouarsii</em> transcript sequences (Voacanga_thouarsii_transcripts.fasta) and protein sequences (Voacanga_thouarsii_proteins.fasta)
DOI: 10.6084/m9.figshare.3363433.v1
title: Vertes2016_PhilTransB_data.mat

description: This dataset contains all fMRI (and related) data needed to replicate analyses in the referenced paper.<br>The file is in MATLAB .mat format and contains the following variables:<br>
<b>ROI_mni:</b> the x, y, z coordinates in MNI space for all 308 initial regions of interest – these are the coordinates used for matching to the Allen Institute for Brain Science gene expression data.
 	
<b>names:</b> the anatomical labels for all 308 initial regions of interest
 
<b>vonEconomo: </b>a vector containing the cytoarchitectonic class assigned to each of the 308 cortical regions of interest. Classes are numbered 1 to 7, in the same order as defined in Figure 1 of the main text.
<br>
<b>excluded_ROI_fmri:</b> a binary vector containing one entry per region of interest (308x1).  The 21 regions which were excluded from further analysis due to fMRI dropout have value =1, all other regions have value = 0.
 
<b>Co:</b> contains the 38 fully weighted 287x287 connectivity matrices for all 38 usable subjects and all 287 usable regions of interest.
<br>
<b>Com:</b> the modular assignment of all 287 usable regions based on consensus modular partition of the group average correlation matrix at 10% connection density.
<br>
<b>meas: </b>a structure containing nodal network metrics for all 287 usable MRI regions of interest. The measures included are: degree (meas.k), inter-modular degree (meas.Inter_k), intra-modular degree (meas.Intra_k), participation coefficient (meas.PC) and average nodal distance (meas.d).
 
<b>excluded_ROI_genes: </b>a binary vector containing one entry per region of interest (308x1).  The 2 regions which were excluded from PLS analyses due to outlier gene data have value =1, all other regions have value = 0.<br>
DOI: 10.6084/m9.figshare.4560862.v3
title: Transcriptome - Nutomonas longa CCAP 1958/5

description: <i>Nutomonas longa</i>'s transcriptome<i> </i>(formerly known as <i>Planomonas carolina)</i><br><br>Reads are deposited in NCBI: https://www.ncbi.nlm.nih.gov/sra/SRX736986<br><br>- Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br>- clean.fasta: Assembly cleaned from cross-contamination of other species multiplexed (Corallochytrium limacisporum India, Ichthyophonus hoferi and Sphaerothecum destruens) after applying CroCo V0.1.1 (Simion et al. in prep). It may contain bacterial contamination.<br><br><br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015)<br><em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em><br><strong><em>Current Biology </em></strong>25(18):2404-10.<br><br>www.multicellgenome.com
DOI: 10.6084/m9.figshare.6265367.v1
title: Patient04

description: Female Patient with 197 slice of pulmonary embolism CT-Angiography.
DOI: 10.6084/m9.figshare.24802788.v2
title: PDBbind v.2013 core set prepared

description: PDBbind v.2013 core set manually curated to optimize the hydrogen bond network considering protein and ligand protonation states.The description of this dataset preparation is published in the following reference:Guedes, I. A.; Barreto, A. M. S.; Marinho, D.; Krempser, E.; Kuenemann, M. A.; Sperandio, O.; Dardenne, L. E.; Miteva, M. A. New Machine Learning and Physics-Based Scoring Functions for Drug Discovery. <i>Sci Rep</i> <b>2021</b>, <i>11</i> (1), 3198. https://doi.org/10.1038/s41598-021-82410-1.
DOI: 10.6084/m9.figshare.5043136.v3
title: Introduction to Thinking About Data I

description: An introductory lecture (slide set and video) on how to identify patterns in data and use them to generate and test hypotheses.
DOI: 10.6084/m9.figshare.7869293.v2
title: An optimization method tracking EMG, ground reactions forces and marker trajectories for musculo-tendon forces estimation in equinus gait

description: A dataset of emulated equinus gait (toe walking) measured on a healthy adult participant (lower limbs kinematics, kinetics, EMG).<br>
DOI: 10.6084/m9.figshare.21640027.v1
title: Factors associated with alcohol abuse in nursing professionals in São Paulo State, Brazil

description: Abstract Objective: to identify factors associated with alcohol abuse in nursing professionals in São Paulo State. Methods: this is a case-control nested in a cross-sectional study. We collected data on demographic characteristics, lifestyle, work ability, occupational features, physical and psychosocial work environment, and alcohol abuse (CAGE Questionnaire). Multiple logistic regression analyses were performed. Results: the study involved 119 participants in the case group and 356 in the control group. After age adjustment, alcohol abuse was associated with male sex (OR: 3.39; 95%CI: 1.96;5.85), current or former smoking (OR: 2.11; 95%CI: 1.32;3.38), and poor sleep quality (OR: 1.91; 95%CI: 1.12;3.25); and negatively associated with ≥50 weekly working hours (OR: 0.54;95%CI: 0.32;0.92) and a monthly family income ≥6.1 minimum wages(OR: 0.37; 95%CI: 0.20;0.67). Conclusions: working hours and individual characteristics were associated with alcohol abuse. Workplaces should implement programs to prevent and treat alcohol abuse in nursing professionals to reduce workers’ and patients’ alcohol-related harms.
DOI: 10.6084/m9.figshare.26166640.v1
title: 332 Yeasts Annotations

description: This repository contains annotations of predicted protein-coding genes in the genome assemblies of 332 yeast species belonging to the subphylum Saccaromycotina, underlying analyses in the publication: Crandall, J.G., Zhou, X. Rokas, A., and Hittinger, C.T. "Specialization restricts the evolutionary paths available to yeast sugar transporters." In press, https://doi.org/10.1093/molbev/msae228
DOI: 10.6084/m9.figshare.13289342.v1
title: Dataset for 'A soft and transparent contact lens for the wireless quantitative monitoring of intraocular pressure'

description: Dataset for 'A soft and transparent contact lens for the wireless quantitative monitoring of intraocular pressure'
DOI: 10.6084/m9.figshare.13718065.v3
title: Earthquake event sequence age PDFs for lakes Kaniere, Mapourika, Paringa and Ellery

description: Earth event sequence age PDFs for lakes Kaniere, Mapourika, Paringa and Ellery.
DOI: 10.6084/m9.figshare.19692028.v1
title: BGE data

description: Data used for analysis in "<strong>Plastic pollution fosters more microbial growth in lakes than natural organic matter"</strong>
DOI: 10.6084/m9.figshare.27054835.v2
title: Hippocampus_trimaculatus_assembly_gene_annotation

description: Hippocampus trimaculatus assembly and gene annotation
DOI: 10.6084/m9.figshare.24195579.v1
title: annot_COCO

description: The labeling of intussusception data is stored in JSON format,JSON file includes training, validation, and test sets.<br>
DOI: 10.6084/m9.figshare.25585452.v1
title: Analysis of COVID-19 Patients' Symptoms and Vaccine Impact Using Deep Learning Approach, and Development Machine Learning Based Risk Calculator: A Multicentric Collaborative Study

description: Background: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global pandemic that has affected millions of people worldwide. This study aims to bridge the knowledge gap between acute and chronic symptoms, vaccination impact, and associated factors in patients across different low-income countries.Methods: The study included 2,445 participants aged 18 years and older, testing positive for COVID-19. Data collection involved screening for medical histories, testing records, symptomatology, and persistent symptoms. Validated instruments, including the DePaul Symptom Questionnaire (DSQ-2) and Patient Health Questionnaire-9 (PHQ-9), were used. We applied a self-supervised and unsupervised deep neural network to extract features from the questionnaire. Gradient boosted machines (GMB) model was used to build a risk calculator for chronic fatigue, depression, and prolonged COVID-19 symptoms. The best-performing models were implemented in a shiny app and deployed online at: [https//ahmedshaheen.shinyapps.io/shaheen-covid-19/]. Also, there is an offline version of the application that can be downloaded: [link].Findings: Out of the study cohort, 69.5% of the patients had symptoms lasting longer than 2 weeks. The most frequent symptoms were loss of smell 46.8%, dry cough (40.1%), loss of taste (37.8%), headaches (37.2%), and sore throat (28.9%). The patients also reported high rates of depression (47.7%), chronic fatigue (6.5%), and infection after vaccination (24.2%). Factors associated with chronic fatigue syndrome included sex, age, and smoking. Vaccinated individuals demonstrated lower odds of experiencing prolonged COVID-19 symptoms, chronic fatigue syndrome, and depression. The predictive models achieved a high area under the receiver operating characteristic curve (AUC) scores of 0.87, 0.82, and 0.74, respectively.Interpretation: The results provide insights into the consequences of COVID-19 and a predictive tool to understand factors influencing depression, chronic fatigue syndrome, and prolonged COVID-19 symptoms. The study reveals variables affecting these outcomes and the interplay between pre-existing conditions, treatments, and the duration of symptoms post-recovery.
DOI: 10.6084/m9.figshare.13017545.v1
title: R0160_20170505a_videos

description: Rat 0160, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.20052149.v1
title: Lozano_et_al_2022

description: Here are the data that have been analyzed in Lozano et al. 2012. The maize data were originally published in Lipka et al. (2013) (https://doi.org/10.1534/g3.113.006148), and the sorghum data were orginally publisehd in Morris et al. (2013) (https://doi.org/10.1073/pnas.121598511)
DOI: 10.6084/m9.figshare.25632762.v1
title: ecology letters data

description: The data for ecology letters.
DOI: 10.6084/m9.figshare.1405612.v5
title: fatty liver disease

description: fatty liver disease
DOI: 10.6084/m9.figshare.24993519.v1
title: Global Soil Respiration Raster Data Generated From "Increases in Global Soil Respiration Following the Köppen Climate Zones Driven by Moisture and Temperature"

description: Global soil respiration raster data generated from "<b>Increases in Global Soil Respiration Following the Köppen Climate Zones Driven by Moisture and Temperature</b>". The data is generated by a random forest model trained on SRDB.
DOI: 10.6084/m9.figshare.26180446.v2
title: q2-metnet package

description: <b>QIIME2 package to analyze 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota.</b>Ensure that the file <b>setup.py</b> is inside the <b>q2-metnet</b> folder prior installation.
DOI: 10.6084/m9.figshare.90818.v1
title: SciFund Success and Social Media

description: SciFund results and data were discussed partly by Zen Faulkes, who also led a succesfully funded project, at http://neurodojo.blogspot.com/2011/12/sayonara-scifund.html and in social media such as in this comment, "Funding was correlated to likes on Facebook" in https://twitter.com/#!/DoctorZen/status/169213149759807488. Data were shared via a Google Document at the link below and had been compiled from public sources. <strong>About SciFund: The #SciFund Challenge raised over <strong>$75,000</strong> for science, from 1440 contributors! </strong> <strong></strong><strong>What?</strong> Can scientists raise money for their research by convincing the general public to open their wallets for small-amount donations? The process is called crowdfunding. <strong>Who?</strong> Forty-nine scientists from a wide variety of disciplines (ecology to computer science to applied math) in five countries signed on to crowdfund their research. <strong>When?</strong> November 1-December 15, 2011. <strong>Where?</strong> The #SciFund Challenge was run through RocketHub, http://www.rockethub.com/projects/scifund a major crowdfunding platform on the Internet. A blog was the community hub for the Challenge, http://scifund.wordpress.com/.
DOI: 10.17632/ssjfpsxxws
title: S6 _SEM BSE and EDS images for calcite, dolomite and magnetite in CM chondrites

description: SEM BSE and EDS images for calcite, dolomite and magnetite in CM chondrites ALH 83100, ALH 84034, and MET 01070
DOI: 10.6084/m9.figshare.4816807.v1
title: Raw Data

description: This folder contains the raw data from the experiment days as well as the matlab script for analyzing the data.
DOI: 10.6084/m9.figshare.9108341.v1
title: Umbilical artery resistance

description: Data from resistance index of umbilical artery in dog foetuses<br>
DOI: 10.17632/yky4rzy4dd
title: Joint Inversion of Geophysical Data for Geologic Carbon Sequestration Monitoring: A Differentiable Physics-Informed Neural Network Model

description: Data and codes for the paper "Joint Inversion of Geophysical Data for Geologic Carbon Sequestration Monitoring: A Differentiable Physics-Informed Neural Network Model"
DOI: 10.6084/m9.figshare.25892869.v1
title: Gold Open Access 2024

description: Gold Open Access 2024 covers serious OA publishing (articles in DOAJ-listed journals) for 2019-2023, including more than 19,000 journals that published more than 1.4 million articles in 2023.
DOI: 10.6084/m9.figshare.28407980.v2
title: BLASTP vs SwissProt

description: BLASTP vs SwissProt
DOI: 10.6084/m9.figshare.3839586.v3
title: Plasmodium sequences and alignments from the genomes of six Plasmodium species.

description: Sequences of all cDNAs and proteins and alignments.<br>From six Plasmodium species P. berghei: PB, P. chabaudi: PC, P. yoelii: PY, P. falciparum: PF, P. vivax: PV and P. knowlesii: PK.<br>As described in:A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome. Methods Mol. Biol. 2015:1201:65-90.<br>See also the worked example pdf.
DOI: 10.6084/m9.figshare.13311737.v1
title: Supplementary Material for: Impact of Lung Biopsy on Lung Function in Idiopathic Pulmonary Fibrosis

description: <b><i>Background:</i></b> Video-assisted surgical lung biopsy (SLB) is performed in 10–30% of cases to establish the diagnosis of idiopathic pulmonary fibrosis (IPF). <b><i>Objectives:</i></b> The aim of the study was to analyze the impact of SLB on lung function in patients eventually diagnosed with IPF. <b><i>Methods:</i></b> This is an observational, retrospective, monocentric study of all consecutive patients eventually diagnosed with IPF in multidisciplinary discussion who underwent SLB over 10 years in a specialized center. The primary end point was the variation in forced vital capacity (FVC) before and after the SLB. The secondary end points were the variations in forced expiratory volume in one second (FEV1), total lung capacity (TLC), carbon monoxide diffusion capacity (DLCO), and morbidity and mortality associated with the SLB. <b><i>Results:</i></b> In 118 patients who underwent SLB and were diagnosed with IPF, a relative decrease in FVC of 4.8% (<i>p</i> &lt; 0.001) was found between measurements performed before and after the procedure. The mean FVC decrease was 156 ± 386 mL in an average period of 185 days, representing an annualized decline of 363 ± 764 mL/year. A significant decrease was also observed after SLB in FEV1, TLC, and DLCO. Complications within 30 days of SLB occurred in 14.4% of patients. Two patients (1.7%) died within 30 days, where one of them had poor lung function. Survival at 1 year was significantly poorer in patients with FVC &lt;50% at baseline. <b><i>Conclusion:</i></b> In this uncontrolled study in patients ultimately diagnosed with IPF, SLB was followed by a significant decline in FVC, which appears to be numerically greater than the average decline in the absence of treatment in the literature. <b><i>Summary at a Glance:</i></b> This study evaluated the change in lung function in 118 consecutive patients diagnosed with idiopathic pulmonary fibrosis by surgical lung biopsy. Forced vital capacity decreased by 156 ± 386 mL in a mean of 185 days between the last measurement before and first measurement after biopsy, representing an annualized decline of 363 ± 764 mL/year.
DOI: 10.6084/m9.figshare.13713172.v1
title: Determinants of preterm birth in Public Hospitals in central Ethiopia: An unmatched case-control study

description: About 15 million babies are born prematurely in the world every year. The most common cause of neonatal death in Ethiopia is premature birth. To reduce the rate of preterm delivery by correcting modifiable or preventable causes, the availability of local data is important. Hence, this study aimed to identify the determinants of preterm birth among women who gave birth in public hospitals in central Ethiopia.
DOI: 10.6084/m9.figshare.29119322.v1
title: Data from "Abrupt, but not gradual, warming reduces temporal stability of grassland productivity through dual mechanisms"

description: The spreadsheet contains the raw data. All the methodological details can be found in the article.
DOI: 10.17632/79fk29dvk6
title: Data for: Urinary Essential Elements of Young Children with Autism Spectrum Disorder and their Mothers

description: Inductively coupled plasma mass spectrometry for 18 essential and 20 toxic elements by Doctor’s Data
DOI: 10.6084/m9.figshare.27063610.v2
title: The impact of epistasis on the genomic prediction of non-assessed and non-overlapping single crosses in multienvironment trials

description: The SNP files are identified as sample and the phenotype files are identified as values.
DOI: 10.17632/ytstmynn4m
title: R codes for longitudinal healthspan data analysis

description: R codes for assessing longitudinal health span data ( frailty Index). These codes are for 0. Preparation steps for calculating Total Scores (mean scores) and converting measurement dates to measurement IDs 1. Repeated Measures Correlation: To assess the correlation between life-expectancy (Remaining Lifespan) and total score ( considering the Intra-dependency of the data set). 2. Mixed Model (mouse as Random effect, treatment and time as fixed effects): Now, to assess the statistical difference between the slopes of regression lines, we applied a mixed model to the combined data set of AKG and control and compared the slopes ( considering the Intra-dependency of the data set collected throughout the study). 3. Mann-Kendall Trend Test : To assess the possible monotonic trend for each frailty phenotype with aging (time).