cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25573/data.14701440.v1
title: (high-temp) No 3. Filtering: (16S rRNA/ITS) Output

description: <b>Output files from the No 3. Filtering Workflow</b> page of the SWELTR high-temp study. ASV filtering for 16S rRNA & ITS using <b>a</b>) Arbitrary filtering, <b>b</b>) PERFect (PERmutation Filtering test for microbiome data), and <b>c</b>) PIME (Prevalence Interval for Microbiome Evaluation) Workflow objects:<br><b>filtering_wf.rdata:</b> contains all variables and phyloseq objects from 16s rRNA and ITS ASV filtering. To see the <b>Objects</b>, in R run <i>load("</i><i>filtering_wf.rdata", verbose=TRUE)</i><br>Additional files:<br>For convenience, we also include individual phyloseq objects for each filtered data set.<br><b>Arbitrary: <br></b><b><b>ssu18_ps_filt.rds: </b></b>phyloseq object for Arbitrary filtered 16S rRNA ASVs.<b><b><br>its18_ps_filt.rds: </b></b>phyloseq object for Arbitrary filtered ITS ASVs.<b><b><br><br></b></b><b>PERfect:</b><br><b><b><b>ssu18_ps_perfect.rds</b>: </b></b>phyloseq object for PERfect filtered 16S rRNA ASVs.<b><b><br><b>its18_ps_perfect.rds</b>: </b></b>phyloseq object for PERfect filtered ITS ASVs.<b><b><br></b></b><br><b><b>PIME: </b> </b><br><b>ssu18_ps_pime.rds</b>: phyloseq object for PIME filtered 16S rRNA ASVs.<br><b>its18_ps_pime.rds</b>: phyloseq object for PIME filtered ITS ASVs.<br><b>Source code</b> for the workflow can be found here:https://github.com/sweltr/high-temp/blob/master/filtering.Rmd <br>
DOI: 10.6084/m9.figshare.27037915.v1
title: UR_Acoe_1.0_genomic_annotation.gff3.gz

description: Genome annotation for Florida Scrub-Jay long-read genome assembly
DOI: 10.6084/m9.figshare.28131200.v1
title: Meta-analysis data of sex differences in physiological and subjective thermal responses

description: Data collected from articles studying steady-state thermal conditions without any localised heating or cooling and for which all the environmental and personal conditions, i.e. the mean observed values of the air temperature (TA), mean radiant temperature (TMR), relative humidity (RH), air velocity (VA), participants' clothing insulation in clo and metabolic rate in met were reported. All the studies surveyed the thermal sensation vote on the classical ASHRAE seven-point scale: “Hot” (+3), “Warm” (+2), “Slightly Warm” (+1), “Neutral” (0), “Slightly Cool” (-1), “Cool” (-2), and “Cold” (-3), except for Yang and colleagues, that used an extended nine-point scale. We calculated the Fanger PMV index for each exposure, expressed on the ASHRAE seven-point thermal sensation scale. All the studies involved at-rest activities of an office-type (reading, typing, etc.), so the metabolic rate was always set equal to 1.1 met based on standard tabulated values. When the clothing insulation was not explicitly reported but a description of the clothing was provided, it was estimated using standard tabulated values as well. For each article, we extracted the sample size, mean, and standard deviation of thermal sensation, mean skin temperature, and core body temperature for female and male groups. Data were taken from the main text, tables, and figures. Mean and standard deviation data presented in the articles' figures were manually extracted using the freely available software program Plot Digitizer (http://plotdigitizer. sourceforge.net/). Data from seven studies were directly provided by the authors upon request by email. We used the raw mean differences between female and male thermal sensation, mean skin temperature, and core body temperature data as effect size metrics. In both cases, a difference of 0.0 represents no difference between the sexes. In the different studies, mean skin temperature was calculated using different weighting formulae from different skin locations and core body temperature was measured on various body parts (ear, oesophageal or rectal temperature). Many of the considered studies provide more than one effect size estimate, so their effect sizes are not independent.
DOI: 10.6084/m9.figshare.28904204.v1
title: gravity observations data.grd

description: Deep tectonics is an important factor controlling the stability of the crust, including gravity anomalies, deep faults, and crustal structures. The regional Bouguer gravity anomaly is caused by the difference in underground rock density, geological structure properties, and morphological changes, and it is the response to the comprehensive factors of underground materials.
DOI: 10.6084/m9.figshare.20279733.v1
title: reactionSmilesFigShare.txt

description: A reaction SMILES dataset (234K), each line in the file represents a valid reaction SMILES. Source material US patents <sub>collection</sub> by Daniel Lowe with data enhancement. Source material also includes reaction SMILES drawn from the general literature. All SMILES are valid by RDKit. Also see https://kmt.vander-lingen.nl
DOI: 10.6084/m9.figshare.21408288.v2
title: CIED-Activity data, 2015-2018

description: The Chinese Industrial Emissions Database (CIED) provides inventory of particulate matter (PM), SO2 and NOX from Chinese industries from 2015 to 2018, based on direct measurements from China’s continuous emission monitoring systems (CEMS) network. This document provides activity data for China’s different industrial emission sources.
DOI: 10.6084/m9.figshare.26511229.v1
title: Dataset for Paper 'An Empirical Study of Kubernetes Configuration Bugs'

description: Dataset and source code used for the paper titled 'Configuration Defects in Kubernetes'
DOI: 10.6084/m9.figshare.28586249.v1
title: Code to reproduce figures for Information Predictive Control

description: MATLAB code to reproduce figures for Information Predictive Control. Contains data from one dyad using wrist movements to track a randomly moving target.
DOI: 10.6084/m9.figshare.11283224.v1
title: Rattlesnake Recombination Maps

description: Recombination maps inferred using LDhelmet from whole genome resequencing data of the prairie rattlesnake (<i>Crotalus viridis</i>) and northern Pacific rattlesnake (<i>Crotalus oreganus</i>).
DOI: 10.6084/m9.figshare.11710290.v1
title: Dataset from Calcified gill filaments increase respiratory function in fishes

description: All data analyzed in the manuscript.
DOI: 10.6084/m9.figshare.23685147.v1
title: Biogeographic context mediates multifaceted diversity-productivity relationships in island and mainland forests

description: 1. Biotic and abiotic conditions have been found to strongly influence how biodiversity affects ecosystem functioning in forests. This context dependency of biodiversity-productivity relationships in real-world ecosystems may be shaped by the biogeographic context <i>via</i> deep-time processes acting on the size and composition of the species pool such as dispersal limitation, environmental filtering, speciation, and invasibility.<i> </i>However, the role of the biogeographic context in shaping multifaceted biodiversity and forest productivity relationships remains uncertain.2. Using data from the Spanish National Forest Inventory in climatically similar forests on the Canary Islands (637 plots) and mainland Spain (1,434 plots), we investigate the extent to which aboveground productivity is determined by ecological and evolutionary processes associated with the biogeographic context. We used structural equation models to test the drivers of aboveground productivity in both contexts, that operate <i>via</i> multifaceted tree diversity (taxonomic, phylogenetic, and functional diversity) or alternative mechanisms, i.e., environmental conditions, non-native species, and the number of trees.3. Our results show that mainland and island forests exhibit similar levels of productivity, yet island forests display overall lower multifaceted diversity. We found that the number of trees increased multifaceted diversity and also increased productivity directly and <i>via</i> their effects on phylogenetic diversity in both mainland and island forests. Further, non-native species increased productivity in island forests.<i>Synthesis.</i><b> </b>Our results suggest that multifaceted diversity, by capturing the diversity of evolutionary history, contributes to elucidating diversity-productivity relationships in mainland and island forests that could not be detected by taxonomic diversity alone. By filling empty niches in island forests, we find that non-native species are fundamentally altering ecosystem functioning on islands and thus, reveal how biogeographic context can shape biodiversity-productivity relationships.
DOI: 10.6084/m9.figshare.27148524.v1
title: Source hic files for Hi-C contact maps of P. fissidentatus, P. mayeri and P. entomophagus.

description: hic files of Hi-C contact map of P. fissidentatus (RS5133), P. mayeri (RS5460B) and P. entomophagus (RS0144B).
DOI: 10.6084/m9.figshare.28034225.v1
title: Data and Code for DI-ALH Analysis Using FAERS

description: This dataset and code are part of a pharmacovigilance study analyzing drug-induced autoimmune-like hepatitis (DI-ALH) reports from the FAERS database (2004–2024). It includes raw data and scripts used for signal detection analyses.
DOI: 10.6084/m9.figshare.7803626.v1
title: M. polymorpha assembly

description: #File descriptions<br>Directory Barcodes<br>run1barcodes.txt: this file contains the barcodes used for the ENA run accessions ERR3184756,ERR3184777-ERR3184779<br>run2barcodes.txt: this file contains the barcodes used for the ENA run accessions ERR3184780-ERR3184783<br><br><br>Directory Assembly_Nogapsestimated (Gaps between scaffolds/contigs of the v3.1 assembly are padded out with 100 N characters regardless of the estimated size of the gap)<br>Mpolylinkagemap_Nogapsestimated.chr.fasta:Fasta file containing sequences of the eight linkage groups (denoted as Chr1-Chr8) presented in the manuscript.Gaps between scaffolds/contigs of the v3.1 assembly was filled in with 100 N characters regardless of the estimated size of the gap.<br>Mpolylinkagemap_Nogapsestimated.fasta:Fasta file containing sequences of the eight linkage groups (denoted as Chr1-Chr8) and all the unassigned scaffolds/contigs of the v3.1 assembly.Headers of unassigned scaffolds/contigs are identical to those used in the v3.1 assembly.Gaps between scaffolds/contigs of the v3.1 assembly was filled in with 100 N characters regardless of the estimated size of the gap.<br>Mpolylinkagemap_Nogapsestimated.gff3:Annotation file (gff3 format) of the linkage map including annotation of the eight linkage groups and all unassigned contigs/scaffolds of the v3.1 assembly.<br>Mpolylinkagemap_Nogapsestimated.chain:The chain file describing the assignment of scaffolds/contigs of the v3.1 assembly along the eight linkage groups of the assembly.This file can be used to lift over annotations to from the v3.1 assembly to the eight linkage groups. <br><br><br>Directory Assembly_gapsestimated (Gaps between scaffolds/contigs of the v3.1 assembly correspond to the estimated size of the gap. They are padded put with N characters)<br>Mpolylinkagemap_gapsestimated.chr.fasta:Fasta file containing sequences of the eight linkage groups (denoted as Chr1-Chr8) presented in the manuscript.Gaps between scaffolds/contigs of the v3.1 assembly was filled in with 100 N characters regardless of the estimated size of the gap.<br>Mpolylinkagemap_gapsestimated.fasta:Fasta file containing sequences of the eight linkage groups (denoted as Chr1-Chr8) and all the unassigned scaffolds/contigs of the v3.1 assembly.Headers of unassigned scaffolds/contigs are identical to those used in the v3.1 assembly.Gaps between scaffolds/contigs of the v3.1 assembly was filled in with 100 N characters regardless of the estimated size of the gap.<br>Mpolylinkagemap_gapsestimated.gff3:Annotation file (gff3 format) of the linkage map including annotation of the eight linkage groups and all unassigned contigs/scaffolds of the v3.1 assembly.<br>Mpolylinkagemap_gapsestimated.chain:The chain file describing the assignment of scaffolds/contigs of the v3.1 assembly along the eight linkage groups of the assembly.This file can be used to lift over annotations to from the v3.1 assembly to the eight linkage groups.
DOI: 10.6084/m9.figshare.9638525.v1
title: Table 1

description: Outcrop data for each formation of the Arroyo Atravesado locality of 103 specimens and its anisotropy of magnetic susceptibility parameters. B. Plane: bedding strike (0º-360º) and dip (90° clockwise, from given strike, 0º-90º). Cleavage: direction (0º-360º) and dip (90° clockwise, from given strike, 0º-90º). S<sub>0</sub> and S<sub>1</sub> foliations measured in thin sections (0°-360°). K<i><sub>max</sub></i>: average orientation of the maximum axe of AMS; K<sub>m</sub> = (K<sub>max</sub>+K<sub>int</sub>+K<sub>min</sub>)/3: average susceptibility volume in SI units; P<sub>j</sub> av: average anisotropy degree (P = K<sub>max</sub>/K<sub>min</sub>: anisotropy degree according to <i>Nagata</i>, 1961); T: average shape parameter of Jelinek (<i>Jelinek</i>, 1981); L = K<sub>max</sub>/K<sub>int</sub>: Average lineation; F = K<sub>int</sub>/K<sub>min</sub>: Average foliation (<i>Flinn</i>, 1962).
DOI: 10.17632/97fk6csmxk
title: Data for: Evaluation of community pharmacists questioning and diagnostic skills and recommendation for a mystery shoppers minor illness

description: This data was collected by a female mystery shopper who visited 131 community pharmacies and spoke with pharmacists requesting for medication for stomach ache. The conversation between the mystery patient and the pharmacists. The pharmaceutical consultations were recorded and transcribed verbatim. The questioning skill of the pharmacists was evaluated using the WWHAM mnemonic and relevant questions deloped and approved by a six-member panel of experts comprising two general practice physician and four clinical pharmacy lecturers with community pharmacy practice experience. Demographic characteristic of the participants, number, and type of WWHAM questions/EPRQs asked, WWHAM and EPRQs scores, diagnoses of the mystery patients minor illness, the reason for diagnoses etc can be obtained from the data set.
DOI: 10.6084/m9.figshare.20773552.v1
title: Optical emissivity dataset of multi-material heterogeneous designs generated with automated figure extraction

description: Archive with a set of JSON files containing emissivity records and supporting information on device and method of measurement.
DOI: 10.6084/m9.figshare.21379209.v1
title: Additional file 7. Flow cytometry of primary cells

description: <strong>Flow cytometry of primary cells.</strong> The eGFP and mCherry fluorescence is detected by flow cytometry for each of the four constructs transfected into Small Airway Epithelial Cells and Renal Epithelial Cells.
DOI: 10.6084/m9.figshare.23256080.v1
title: Supplementary Material for: The top 100 most cited articles on Acupuncture in the last 20 years: a Bibliometric Analysis

description: Background: Acupuncture has gained increasing international attention in recent decades. The act of incorporating acupuncture treatment into the routine treatment of COVID-19 in China drove us to review the 100 most influential articles of the last 20 years to learn about the current status and trends of acupuncture. Method: Articles related to acupuncture from January 1, 2001 to July 4, 2022 were searched in the Clarivate Analytics Web of Science Core Collection database. The top 100 most cited publications were selected and information were extracted. Software VOSviewer, GraphPad Prism, Scimago Graphica and CiteSpace were used to visualize and analyze the extracted data. Result: The 100 most cited articles were identified, with an average of 218 citations (range: 131-625). The majority of the top 100 articles were from the United States (n = 53). The institution that published the most highly cited papers was Harvard University (n = 16). The most influential team was Klaus Linde's group. Pain was the top ranked journal in terms of number of publications. The largest clusters for co-occurrence keyword analysis focused on acupuncture and electroacupuncture analgesia and brain imaging responses to acupuncture stimulation via functional MRI. The two highest strength burst keywords were "randomized controlled trials" and "osteoarthritis", with "randomized controlled trials" being a consistent burst keyword from 2011 to the present. Conclusion: This study provides insight into articles of historical significance in the field of acupuncture through bibliometric analysis. These data should provide clinicians and researchers with insight into future directions related to acupuncture.
DOI: 10.6084/m9.figshare.26965252.v1
title: S1 Data. Analytical data set for the Housing_price and Machine learning study

description: The Hedonic Price Model, used in existing house price modeling, may not address the relationship between house prices and streetscapes perceived at the human eye level. Therefore, in this study, we analyzed the relationship between streetscapes perceived at eye level and single-family home prices in Seoul, Korea, using computer vision technology and machine learning algorithms. We used transaction data for 13,776 single-family housing sales between 2017 and 2019. To measure visually perceived streetscapes, this study used the Deeplab V3+ deep-learning model with 233,106 Google Street View panoramic images. Then, the best machine-learning model was selected by comparing the explanatory powers of the hedonic price model and all alternative machine-learning models. According to the results, the Gradient Boost model, a representative ensemble machine learning model, performed better than XGBoost, Random Forest, and Linear Regression models in predicting single-family house prices. In addition, this study used an interpretable machine learning model of the SHAP method to identify key features that affect single-family home price prediction. This solves the "black box" problem of machine learning models. Finally, by analyzing the nonlinear relationship and interaction effects between perceived streetscape characteristics and house prices, we easily and quickly identified the relationship between variables the hedonic price model partially considers.
DOI: 10.17632/95xt9sngzc
title: Open access scientific documents from eLIBRARY.RU

description: Open access scientific documents from website eLIBRARY.RU. The dataset consists of a zip-archive with raw text documents and a csv file with documents metadata. It contains information about publication year, topic according to State Rubricator of Scientific and Technical Information (SR STI), language and ID of the document in the www.elibrary.ru database.

Acknowledgments
The authors are grateful to the Scientific Electronic Library eLIBRARY.RU and personally Gennady Eremenko and Viktor Glukhov for the data provided.
DOI: 10.6084/m9.figshare.12105510.v1
title: Supplement

description: <b>Supplement 1 and Supplement 2.</b> Impedance-pH monitoring in the diagnosis of gastroesophageal reflux disease in cystic fibrosis
DOI: 10.6084/m9.figshare.12966323.v2
title: Pesticide mixtures in soil: a global outlook

description: This data set includes four global maps of aggregated pesticides: (1) the total pesticide content in the topsoil of global croplands expressed in the unit of mg/kg-soil; (2) the number of pesticides detected in the topsoil; (3) the pesticide leaching rate to below the root zone expressed in the unit of mg/m<sup>2</sup>/year; and (4) the number of pesticides that exceeded a leaching rate of 1 mg/m<sup>2</sup>/year. This data set also includes two zip folders containing the topsoil residue and leaching rate of individual pesticide substances in nine different cropping systems. The surface area of the nine cropping systems can be obtained from the PEST-CHEMGRIDS dataset (Maggi et al., 2019). <br> A zip folder containing an example of input files required to run the model is attached together with this data set. Details of the methods used to produce these maps and the tabulated data can be found in Tang F.H.M and Maggi F. (2021). Pesticide mixtures in soil: a global outlook, Environmental Research Letters.<br>
DOI: 10.6084/m9.figshare.13244504.v1
title: MOT_data.mat

description: Data form the Multiple object tracking task (MOT). In the file there is the preprocessed pupilometry data, Bold, and average Time varying functional connectivity for each load condition (2-5).
DOI: 10.6084/m9.figshare.16419618.v1
title: Simulated FORC measurements of randomly oriented single-stranded chains of prismatic magnetosomes

description: Simulated FORC measurements of ~10<sup>5</sup> isolated, randomly oriented single-stranded chains of prismatic magnetosomes, in VARIFORC format.<br>
DOI: 10.6084/m9.figshare.23501034.v1
title: des8/XRCC2 50K data

description: 50K iselect marker F3 recombination data neccecary to run analysis and plotting scripts here: https://github.com/BioJNO/des8
DOI: 10.6084/m9.figshare.28827632.v1
title: Supplementary data for "Algorithm-level data-guided correction for class imbalance in biological machine learning predictions: Protein interactions as a case"

description: In real-world biomedical applications of data mining, machine learning and artificial intelligence, there are situations where the widespread problem of class imbalance cannot be addressed by data-level methods such as over- or under-sampling. Correct and efficient use of algorithm-level methods, on the other hand, needs paying heed to data structure and content. This study aims to devise and examine simple methods for addressing the imbalanced class distribution issue in predicting the protein-protein interaction (PPI) sites in membrane proteins as a biomedical case experiment. Using an adopted dataset of membrane protein complexes and a retrieved validation set, a class-weighted random forests (CWRF) classifier model was built for predicting interfacial residues from positional frequencies and an evolutionary index. Among several class weighting methods, a data imbalance-emulating weighting method for the CWRF model achieved an area under the receiver operating characteristics curve (AUC) of 0.815 (95% CI: 0.805-0.823) in the independent test prediction and 0.802 (95% CI: 0.794-0.809) in the prediction for the external validation set, which outperformed previous similar studies. A case prediction confirmed the practical utility of this method. The proposed approach implies potential applications in other fields of biomedicine and beyond. It also highlights the role of algorithm-data interplay in addressing the class imbalance.