cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13139335
title: Serum anion gap at admission predicts all-cause mortality in critically ill patients with cerebral infarction: evidence from the MIMIC-III database

description: Recent studies reported that serum anion gap could be regarded as a prognostic biomarker for patients admitted to intensive care units. However, the association between AG and mortality in cerebral infarction patients remained largely unknown. Relevant clinical data were collected from Medical Information Mart for Intensive Care III. Patients were divided into three groups according to tertiles of AG. Kaplan–Meier curve and Cox proportional hazards models were used to evaluate the association between AG levels and all-cause mortality. Subgroup analyses were performed to verify the predictive role of AG on mortality. Kaplan–Meier analysis showed that patients with higher AG had shorter survival time. Cox regression model indicated high AG as an independent risk factor of 30-day, 60-day and 180-day all-cause mortality (30-day: HR = 2.45, 95% CI = 1.21–4.97, 60-day: HR = 2.04, 95% CI = 1.07–3.89, and 180-day: HR = 1.85, 95% CI = 1.02–3.36). However, no significance was observed between AG and 365-day all-cause mortality (HR = 1.56, 95% CI = 0.87–2.78). High AG was associated with increased risk of all-cause mortality, and AG could be an independent short-term prognostic factor for cerebral infarction.
DOI: 10.6084/m9.figshare.6847871.v1
title: Additional file 2: of Interleukin-15 facilitates muscle regeneration through modulation of fibro/adipogenic progenitors

description: Figure S1. Flow cytometric gating strategy for isolation FAPs using FACS. Figure S2. The number of FAPs dropped quickly after 3 dpi, IL-15 can promote the growth of FAPs. (a) Representative immunofluorescence images of TA sections after glycerol injection. (b) Quantification of number of FAPs in TA muscles after administration of IL-15. (c) The growth of FAPs can be stimulated by IL-15 in vitro. Figure S3. IL-15 enhances collagen deposition in muscle with CTX injection. (a) A shcematic showing the experiment in vivo: IL-15 was administered from 1dpi to 3 dpi after CTX injection and samples were sectioned on 10 dpi. (b) Immunofluorescence for collagen I after IL-15 injection in injured muscle 5 dpi. Scale bar, 20Îźm. (c) Quantification of collagen deposition area (shown in percentage). (ZIP 2164 kb)
DOI: 10.5281/zenodo.8358874
title: Dataset from: Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure

description: Genetic variation of the entire genome represents population structure, yet individual loci can show distinct patterns. Such deviations identified through genome scans have often been attributed to effects of selective factors instead of randomness, assuming that the genomic intervals are long enough to average out randomness in underlying genealogies. However, an alternative explanation to distinct patterns has not been fully addressed: too few genealogies to average out the effect of randomness. Specifically, distinct patterns of genetic variation may be due to reduced local recombination rate, since the number of genealogies in a genomic interval corresponds to the number of ancestral recombination events. Here, we associate distinct patterns of local genetic variation with reduced recombination rate in a songbird, the Eurasian blackcap, using genome sequences and recombination maps. We find that distinct patterns of local genetic variation represent haplotype structure at low-recombining regions present either in all populations or only in a few populations. At the former species-wide low-recombining regions, genetic variation depicts conspicuous haplotypes segregating in multiple populations. On the contrary, at the latter population-specific low-recombining regions, genetic variation primarily represents cryptic haplotype structure among individuals of the low-recombining populations. With simulations, we confirm that reduction in recombination rate alone can cause distinct patterns of genetic variation mirroring our empirical data. Our results highlight that distinct patterns of genetic variation can emerge through evolution of reduced local recombination rate. Recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.
DOI: 10.6084/m9.figshare.13139337.v2
title: Aminoglycoside riboswitch control of the expression of integron associated aminoglycoside resistance adenyltransferases

description: The proliferation of antibiotic resistance has its origins in horizontal gene transfer. The class 1 integrons mediate gene transfer by assimilating antibiotic-resistance genes through site-specific recombination. For the class 1 integrons the first assimilated gene normally encodes an aminoglycoside antibiotic resistance protein which is either an aminoglycoside acetyltransferase (AAC), nucleotidyltransferase – (ANT), or adenyl transferase (AAD). An aminoglycoside-sensing riboswitch RNA in the leader RNA of AAC/AAD that controls the expression of aminoglycoside resistance genes has been previously described. Here we explore the relationship between the recombinant products of integron recombination and a series of candidate riboswitch RNAs in the 5ʹ UTR of <i>aad</i> (aminoglycoside adenyltransferases) genes. The RNA sequences from the 5ʹ UTR of the <i>aad</i> genes from pathogenic strains that are the products of site-specific DNA recombination by class 1 integrons were investigated. Reporter assays, MicroScale Thermophoresis (MST) and covariance analysis revealed that a functional aminoglycoside-sensing riboswitch was selected at the DNA level through integron-mediated site-specific recombination. This study explains the close association between integron recombination and the aminoglycoside-sensing riboswitch RNA.
DOI: 10.6084/m9.figshare.24151235.v1
title: Additional file 3 of Comparative transcriptomic analysis of wheat cultivars differing in their resistance to Fusarium head blight infection during grain-filling stages reveals unique defense mechanisms at play

description: Additional file 3: Table S2. Transcriptome reads and reference genome comparison rate statistics results.
DOI: 10.5281/zenodo.10623362
title: Dataset from: Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure

description: Genetic variation of the entire genome represents population structure, yet individual loci can show distinct patterns. Such deviations identified through genome scans have often been attributed to effects of selection instead of randomness. This interpretation assumes that long enough genomic intervals average out randomness in underlying genealogies, which represent local genetic ancestries. However, an alternative explanation to distinct patterns has not been fully addressed: too few genealogies to average out the effect of randomness. Specifically, distinct patterns of genetic variation may be due to reduced local recombination rate, whichreduces the number of genealogies in a genomic window. Here, we associate distinct patterns of local genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using genome sequences and recombination maps. We find that distinct patterns of local genetic variation reflect haplotype structure at low-recombining regions either shared in most populations or found only in a few populations. At the former species-wide low-recombining regions, genetic variation depicts conspicuous haplotypes segregating in multiple populations. At the latter population-specific low-recombining regions, genetic variation represents variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns of haplotype structure evolve dueto reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolution of reduced local recombination rate. Recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.
DOI: 10.5281/zenodo.8358873
title: Dataset from: Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure

description: Genetic variation of the entire genome represents population structure, yet individual loci can show distinct patterns. Such deviations identified through genome scans have often been attributed to effects of selection instead of randomness. This interpretation assumes that long enough genomic intervals average out randomness in underlying genealogies, which represent local genetic ancestries. However, an alternative explanation to distinct patterns has not been fully addressed: too few genealogies to average out the effect of randomness. Specifically, distinct patterns of genetic variation may be due to reduced local recombination rate, whichreduces the number of genealogies in a genomic window. Here, we associate distinct patterns of local genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using genome sequences and recombination maps. We find that distinct patterns of local genetic variation reflect haplotype structure at low-recombining regions either shared in most populations or found only in a few populations. At the former species-wide low-recombining regions, genetic variation depicts conspicuous haplotypes segregating in multiple populations. At the latter population-specific low-recombining regions, genetic variation represents variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns of haplotype structure evolve dueto reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolution of reduced local recombination rate. Recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.
DOI: 10.6084/m9.figshare.24151238
title: Additional file 4 of Comparative transcriptomic analysis of wheat cultivars differing in their resistance to Fusarium head blight infection during grain-filling stages reveals unique defense mechanisms at play

description: Additional file 4: Table S3-1. Statistical analyses identifying differentially expressed genes A1589_T2_vs_T1.
DOI: 10.6084/m9.figshare.24151238.v1
title: Additional file 4 of Comparative transcriptomic analysis of wheat cultivars differing in their resistance to Fusarium head blight infection during grain-filling stages reveals unique defense mechanisms at play

description: Additional file 4: Table S3-1. Statistical analyses identifying differentially expressed genes A1589_T2_vs_T1.
DOI: 10.6084/m9.figshare.20479680.v1
title: Additional file 3 of Molecular basis of high temperature-induced bolting in lettuce revealed by multi-omics analysis

description: Additional file 3. Table S2. Overlap between DEGs and DE miRNA targets during high temperature treatment at 2 day
DOI: 10.6084/m9.figshare.20479689.v1
title: Additional file 6 of Molecular basis of high temperature-induced bolting in lettuce revealed by multi-omics analysis

description: Additional file 6. Differentially methylated loci.
DOI: 10.5061/dryad.39272/8
title: European_American_Airway_Inspiration

description: CFD [computational fluid dynamics data] for European_American_Airway_inspiration [csv format]
DOI: 10.5061/dryad.39272/9
title: Neanderthal_Airway_Expiration

description: CFD [computational fluid dynamics data] for Neanderthal_Airway_Expiration [csv format]
DOI: 10.5061/dryad.6373nd6/1
title: AIS_spatial_data_files

description: Spatial data layers describing: (1) mean annual vessel intensity, occupancy and pressure for (A) bulk carrier and cargo vessels, (B) offshore service vessels, (C) passenger vessels, and (D) tankers in the Republic of Congo (Congo-Brazzaville) derived from Automatic Identification System (AIS) data from 2012 - 2014 obtained under commercial licence from © 2018 exactEarth Ltd; and (2) distribution of (A) broad-scale seabed habitats, (B) marine boundaries, (C) marine ecosystems and (D) legally defined zones within the Republic of Congo's waters. This file also includes all figures presented in the paper and supporting information.
DOI: 10.5061/dryad.6jc55mn/2
title: Environmental Data_Plot_Years

description: This file contains environmental attributes data for each of the study reaches. It contains attributes that do not change between years (geology, elevation, etc.) and also attributes that change between years (Cattle Exclosure and Annual Precipitation). Columns are the environmental criteria, rows are the individual plot_years.
DOI: 10.5061/dryad.6jc55mn/3
title: Environmental Data_for ESD

description: This file contains the environmental attributes of each plot that did not change between the years of sampling. It was used in the Ecological Site cluster analysis to create the Ecological Site classification.
DOI: 10.5061/dryad.6jc55mn/4
title: R Code for Riparian ESD:STM paper

description: This is the R code used to produce all the analyses in the paper (cluster analyses, indicator species analysis, CART analysis, and summary statistics). It requires that you install the packages loaded at the beginning of the script. If you don't want to run the code in R, but you do want to see the code and output, you can also look at the accompanying html file of the same name.
DOI: 10.5061/dryad.6jc55mn/5
title: Supporting Information

description: This supporting information document links all the plant species codes used in the analysis with the full species names. It also includes attribute information for each of the species in the analysis (family, wetland status, etc.).
DOI: 10.5061/dryad.6jc55mn/6
title: R Code for Riparian ESD:STM paper.nb

description: This is the html output of the R script. It shows the code and the outputs from each step of the analysis.
DOI: 10.5061/dryad.8m5v4/1
title: Experiment 1 (NET3) Raw read counts (with duplicates)

description: Experiment 1 (NET3) Raw read counts (with duplicates), mapped to the oyster genome v9 coding regions.
DOI: 10.5061/dryad.8m5v4/2
title: Experiment 2 (NET1) Raw read counts (with duplicates)

description: Experiment 2 (NET1) Raw read counts (with duplicates), mapped against the oyster genome v9 coding regions.
DOI: 10.5061/dryad.8m5v4/3
title: Experiment 1 (NET3) Raw read counts (duplicates removed)

description: Experiment 1 (NET3) Raw read counts (duplicates removed), mapped against the oyster genome v9 coding regions
DOI: 10.5061/dryad.8m5v4/4
title: Experiment 2 (NET1) Raw read counts (duplicates removed)

description: Experiment 2 (NET1) Raw read counts (duplicates removed), mapped against the oyster genome v9 coding regions
DOI: 10.5061/dryad.8p6m07g/1
title: Candidate regions of parallel selection on admixture variation

description: The 41 shared highly divergent regions (SHDRs) that group the species by male nuptial coloration and are thus candidates of parallel selection. The genes in the vicinity of the regions are shown above. The Fst values between the older species at Makobe Island and between the younger species at Python Island are shown in windows of 15 SNPs. Windows that the HMM approach assigned to the high differentiation state are shown with red or orange color. The next row shows excess allele sharing (fd) in windows of 20 kb. Windows that have a TWISST weight of the color topology &gt;0.66 are indicated in black. The next rows show the mean nucleotide diversity, dxy, difference in nucleotide diversity, extended haplotype length (EHL) statistics, Tajima's D and the recombination rate.
DOI: 10.5061/dryad.9k4h503/1
title: Supplementary dataset 1

description: Raw Mexican Bison antiquus mesowear data, including shape and relief of cusps, mesowear 0-3 univariate scale, and both individual and averaged mesowear III scores for each mexican specimen employed in the paper.
DOI: 10.5061/dryad.9k4h503/2
title: Supplementary dataset 2

description: Mesowear data employed in the Discriminant function analysis of the paper. With data from Danowitz et al. (2016).
DOI: 10.5061/dryad.b32jm/1
title: manuscript PONE-D-16-44696R1 PLOS ONE data

description: Sociodemographic and health-related variables used in the analyses.
DOI: 10.5061/dryad.cs80878/1
title: BB bacteria

description: R scripts and associated data files for statistical analysis of bee bread bacterial composition.
DOI: 10.5061/dryad.dt378/1
title: LeroseyAubril&Peel_SupplementaryTableS1

description: Taxonomic distribution of frontal auxiliary impressions (non-exhaustive)
DOI: 10.5061/dryad.f3n5ts4/1
title: cleaned original morphological and HTS files used
DOI: 10.5061/dryad.f3n5ts4/2
title: file used for statistical analyses
DOI: 10.5061/dryad.f3n5ts4/3
title: all morphological and qpcr raw data
DOI: 10.5061/dryad.h14r5/2
title: deJong&Saastaminen_Cold Tolerance_Column explanations_data_2018

description: This file describes the column names used in data file 'deJong & Saastamoinen_ColdTolerance_data_2018-file'
DOI: 10.5061/dryad.ht529/1
title: Figuresnew
DOI: 10.5061/dryad.k55hh8f/7
title: Input data files and R code to examine overfitting by Random Forest for 1,000 loci and 10,000 loci data sets
DOI: 10.5061/dryad.m8k99/1
title: Data on the occurrences of predators and prey in the semi-arid Big Desert region of SE Australia.

description: This data includes information on the fire history of landscapes (RECENTLY BURNED, LONG UNBURNED), the extent of mallee vegetation (MALLEE) and the occurrences of dingoes (Canis, dingo), foxes (Vulpes vulpes), Mitchell’s hopping mouse (Notomys mitchelli), and silky mouse (Pseudomys apodemoides)
DOI: 10.5061/dryad.mb79n/1
title: isakbaeva_2005_cruise_norovirus_outbreak_data

description: Norovirus outbreak data, taken from Isakbaeva, Elmira T., et al. "Norovirus transmission on cruise ship." Emerging infectious diseases 11.1 (2005): 154.
DOI: 10.5061/dryad.n0b8m/10
title: Infotaxis database

description: Base database for running infotaxis simulations. To see how to prepare and populate this database with simulated trajectory data, see the file _paper_auxiliary_code in the GitHub repository http://github.com/rkp8000/wind_tunnel.
DOI: 10.5061/dryad.n0b8m/3
title: Part 3
DOI: 10.5061/dryad.n0b8m/4
title: Part 4
DOI: 10.5061/dryad.n0b8m/5
title: Part 5
DOI: 10.5061/dryad.n0b8m/6
title: Part 6
DOI: 10.5061/dryad.n0b8m/7
title: Part 7
DOI: 10.5061/dryad.n0b8m/8
title: Part 8
DOI: 10.5061/dryad.n0b8m/9
title: Part 9
DOI: 10.5061/dryad.r7m1n/1
title: Data Master file Sialendoscopy 6 Months Dryad

description: SPSS data file containing clinical outcome measures such as salivary flow, CODS, Xerostomia Inventory and ESSPRI data for 3 groups of patients participating in this study. Treatment groups: 1 = control group, 2 = saline group, 3 = saline/TA group. Data is measured at baseline (T0), 1 week (T1), 8 weeks (T8), 16 weeks (T16) and 24 week (T24) after intervention. The data file is created with Statistical Package for the Social Sciences software (SPSS; .sav file). Abbrevations: SS Sjögren's Syndrome, UWS = Unstimulated Salivary Flow, SWS = Stimulated Salivary Flow, SPF = Stimulated Parotid Flow, CODS = Clinical Oral Dryness Score, XI = Xerostomia Inventory, ESSPRI = EULAR Sjögren's Syndrome Patient Reported Index. Total ESSPRI and the seperate ESSPRI dryness domain is reported.
DOI: 10.5061/dryad.rt83q/1
title: Davidson et al Repeatable aversion across threat types Raw Data

description: Raw data associated with the paper by Davidson et al "Repeatable aversion across threat types is linked with life history traits but is dependent on how aversion is measured".
DOI: 10.5061/dryad.tr69js8/1
title: Phenotypic data

description: Data from offspring of within-population, between-population and between-region crosses of Lythrum salicaria plants originating from North America or Western Europe, grown under  'dry' and 'wet' experimental greenhouse conditions. Data are from individual plants. Information is included on cross type (including parental plant identity) and experimental design (realblock refers to spatial greenhouse blocking and timeblock refers to time-separated replications).
DOI: 10.5061/dryad.tr69js8/2
title: SAS_analysis_script

description: Statistical analysis script used for the statistical analyses presented in the manuscript. The script takes the phenotypic data file as input and was written in SAS version 9.4 for Windows.
DOI: 10.5061/dryad.v9m50r8/1
title: BEHECO-2017-0505 Dryad submission file

description: In the data file are three sheets: The first sheet contains song data for the analyses of individual song-type analyses. Sheet two contains data for the analyses repertoire variation. Sheet three contains data for the population-level analyses of song variation
DOI: 10.5061/dryad.vk245pd/1
title: Data from study recovering conotoxins from genomic DNA

description: I have included: (1) The target sequences the baits were designed from (2) the bait sequences themselves (3) the final phylogenetic alignment and (4) the final venom sequences.
DOI: 10.12751/g-node.d919d4
title: Multimodal Integration and Stimulus Categorization in Mushroom Body Output Neurons of the Honeybee

description: The dataset includes recordings of mushroom body extrinsic/output neurons (MBON) during stimulation with green light (stimG), blue light (stimB), Farnesol (stimFar), Citronellol (StimCit) and two olfactory visual compounds (stimCitG and stimFarB).
description: Related Reference: Strube-Bloss M, Roessler W: Multimodal Integration in Mushroom Body Output Neurons of the Honeybee. Submitted to proceedings of the royal society open science.
DOI: 10.5061/dryad.02dq2/2
title: Data for Weighing Trees with Lasers

description: Data used in publication, including lidar point clouds, resulting matlab quantitative structural models (QSMs) and Jupyter notebook and associated python code for reading and plotting these data, with worked examples.
DOI: 10.5061/dryad.0vm37/13
title: TrEMBL.result

description: Functional annotation(TrEMBL)
DOI: 10.5061/dryad.0vm37/14
title: README

description: readme
DOI: 10.5061/dryad.156j4/2
title: Waselkov Data SysBot 2018

description: Data (sequence alignments, tree files, and supplementary information) associated with Waselkov et al. 2018, Systematic Botany.
DOI: 10.5061/dryad.1989g0t/1
title: The dataset for statistical analyses
DOI: 10.5061/dryad.1qq7050/1
title: AK_CK_speech_tracking_2018
DOI: 10.5061/dryad.21fm7/1
title: Supporting Information Holmstrup et al Appendix 2

description: Abundance of Collembola species, groups, and species richness. Community-weighted traits.
DOI: 10.5061/dryad.2hj343f/1
title: Differential Coexpression Script

description: This script contains the use of previously normalized data to execute the DiffCoEx computational pipeline on an experiment with four treatment groups.
DOI: 10.5061/dryad.3qp36g8/1
title: Dataset_When is the best time to flower and disperse

description: Data used in "When is the best time to flower and disperse? A comparative analysis of plant reproductive phenology in the Mediterranean". It combines estimated means and standard errors of onset of flowering, onset of seed dispersal and seed maturation period for 138 plant species growing in the Mediterranean region of southern France.
DOI: 10.5061/dryad.54cd3.1
title: Data from: Configurational landscape heterogeneity shapes functional community composition of grassland butterflies