cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7689161.v1
title: Evolution of hybridogenetic lineages in Cataglyphis ants -Variant file in VCF format.

description: Several species of Cataglyphis desert ants have evolved a peculiar breeding system called social hybridogenesis. Under this system, two divergent genetic lineages coexist within a species. Workers develop from hybrid crosses between lineages, whereas queens and males are produced by parthenogenesis and carry only the maternal genome. To gain a better understanding of the evolutionary history of social hybridogenesis in Cataglyphis, we studied its phylogeographic distribution in the Iberian Peninsula using both SNP nuclear markers.
DOI: 10.6084/m9.figshare.12793472.v1
title: Supplementary Material for: Psychological Resilience as an Emergent Characteristic for Well-Being: A Pragmatic View

description: Currently, there is no clear agreement on the definition and conceptualization for psychological resilience (PR) in old age. Adopting a pragmatic view, this article elucidates the definition and conceptualization of PR by (1) extracting existing PR concepts that are relevant to aging, and (2) elucidating the contributing and delimiting factors for developing and sustaining PR as guided by the biopsychosocial framework. In addition, a comprehensive review of the tools used to measure PR was conducted to examine how scholars have conceptualized PR. Consequently, the renewed understanding defines PR as an emergent construct which is malleable, enduring, and can be developed and sustained by a dynamic interplay of biological, psychological, spiritual, and social factors. Correlates in terms of physical and mental well-being in the context of aging are identified.
DOI: 10.6084/m9.figshare.24549829.v1
title: Transport and food data

description: The file includes data of rural transportation infrastructure and food insecurity of Pakistan's district-wise
DOI: 10.15468/dl.r6ry7w
title: Occurrence Download

description: A dataset containing 121786 species occurrences available in GBIF matching the query:
{
 "PublishingOrg" : [
 "is c461e0ec-aaa8-4601-bae9-4b08d6e804f1"
 ]
}

 The dataset includes 121786 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009458-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.24720453.v1
title: reactivity_dataset

description: RMechDB profiles
DOI: 10.6084/m9.figshare.3568701.v1
title: Supplement 1. Data and code for implementing model selection approaches for occupancy model.

description: File List occ.aux.mcmc.R (MD5: 9d685abe2f0c8f99f7070f9b77b95fe2) section.3.script.R (MD5: 12312816b70fb311b311fe193f705c96) section.4.c.script.R (MD5: 9fc45f466660b8223d7d157b23b86740) section.4.g.script.R (MD5: 9d8448444db1e44336e4b0f9ed999b55) section.5.script.R (MD5: 61ecda7858117325985da1da24261cf9) wt.csv (MD5: fcef00421bb21150fe3b4b9ae15e8333) USGS_Disclaimers.txt (MD5: f9465db5e3077500926435799380311f) Description occ.aux.mcmc.R: Main MCMC algorithm written in R. section.3.script.R: R script for performing analyses in section 3. section.4.c.script.R: R script for performing analyses in section 4c. section.4.g.script.R: R script for performing analyses in section 4g. section.5.script.R: R script for performing analyses in section 5. wt.csv: Willow tit data file. Column definitions y.1, binary variable indicating detection (1) on occasion 1. y.2, binary variable indicating detection (1) on occasion 2. y.3, binary variable indicating detection (1) on occasion 3. elev, continuous variable indicating elevation in meters. forest, continuous variable indicating percent forest cover. Missing values are denoted by NA. USGS_Disclaimers: Required disclaimers from the USGS.
DOI: 10.6084/m9.figshare.749728.v9
title: Crassostrea gigas high-throughput bisulfite sequencing (gill tissue)

description: This fileset contains two files in generic feature format (GFF) of methylation-enriched high-throughput bisulfite sequencing data for Pacific oyster (Crassostrea gigas), gill tissue. The first GFF includes the location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage Cgigas_gill_HTbisulfiteSeq_CG_AllData.gff. The second GFF is limited to those CpG loci where the proportion of methylation is ≥ 0.5 (Cgigas_gill_HTbisulfiteSeq_CG_methylated.gff) In addition, this fileset includes the SQL queries used to derive each of the GFF files from the original <em>methratio</em> output. A link to the public <em>methratio</em> dataset, which includes the unfiltered methylation data for all cytosines covered, can be found below.
DOI: 10.6084/m9.figshare.23722350.v1
title: Additional file 2 of L-GIREMI uncovers RNA editing sites in long-read RNA-seq

description: Additional file 2: Table S1. Performance of L-GIREMI in different types of regions of the Alzheimer's Disease Brain dataset. Table S2. Performance of L-GIREMI in different types of regions of the GM12878 dataset. Table S3. Primer sequences of validated sites.
DOI: 10.6084/m9.figshare.26489884.v1
title: Gen AI data

description: This was a study about the use of Artificial intelligence tools among medical faculty in Uganda.
DOI: 10.6084/m9.figshare.19499345.v1
title: patches and local annotations, slide 189, zoom 248x248 um2

description: patches and local annotations: data for slide with ID of the last 3 characters of the file name: local annotations in csv format and a folder with patches at zoom level indicated at the 6th character of the file name
DOI: 10.6084/m9.figshare.5121280.v1
title: Supplementary Material for: Rapid Neutrophil Destruction following Phagocytosis of Staphylococcus aureus

description: Mechanisms underlying the enhanced virulence phenotype of community-associated methicillin-resistant <i>Staphylococcus aureus</i> (CA-MRSA) are incompletely defined, but presumably include evasion of killing by human polymorphonuclear leukocytes (PMNs or neutrophils). To better understand this phenomenon, we investigated the basis of rapid PMN lysis after phagocytosis of USA300, a prominent CA-MRSA strain. Survival of USA300 clinical isolates after phagocytosis ultimately resulted in neutrophil lysis. PMNs containing ingested USA300 underwent morphological changes consistent with apoptosis, but lysed rapidly thereafter (within 6 h), whereas cells undergoing FAS-mediated apoptosis or phagocytosis-induced cell death remained intact. Phagosome membranes remained intact until the point of PMN destruction, suggesting lysis was not caused by escape of <i>S. aureus</i> from phagosomes or the cytolytic action of pore-forming toxins. Microarray analysis of the PMN transcriptome after phagocytosis of representative community-associated <i>S. aureus</i> and healthcare-associated MRSA strains revealed changes unique to community-associated <i>S. aureus</i> strains, such as upregulation of transcripts involved in regulation of calcium homeostasis. Collectively, the data suggest that neutrophil destruction after phagocytosis of USA300 is in part a form of programmed necrosis rather than direct lysis by <i>S. aureus</i> pore-forming toxins. We propose that the ability of CA-MRSA strains to induce programmed necrosis of neutrophils is a component of enhanced virulence.
DOI: 10.6084/m9.figshare.28732370.v1
title: CARE checklist for Radical Urethrectomy with Partial Cystectomy and Bladder Outlet Reconstruction in Giant Female Urethral Adenocarcinoma Infiltrating the Bladder: A Rare Case Report

description: CARE Checklist for Radical Urethrectomy with Partial Cystectomy and Bladder Outlet Reconstruction in Giant Female Urethral Adenocarcinoma Infiltrating the Bladder: A Rare Case Report
DOI: 10.6084/m9.figshare.22698181.v3
title: Datasets for "Continental fragments in the South China Block – constraints from crustal radial anisotropy"

description: This project contains the datasets needed to produce the radially anisotropic crustal shear-wave velocity model in a manuscript submited for publicaiton with Journal of Geophysicsl Research - Solid Earth. <br> The tar.gz file has the following files: <br> T-T.CCFs: Love wave cross-correlation functions (CCFs) Z-Z.CCFs: Rayleigh wave CCFs readme readme stns.txt station coordinates <br> Each of the T-T.CCFs and Z-Z.CCFs folders contains the final stacked CCFs in SAC format between all available station pairs, e.g., COR_S003_S005.SAC COR_S003_S007.SAC ... ... <br> The CCF file name show the names of station pairs (e.g., S003, S005, S007). <br> With these cross-functions, following a standard ambient noise inversion procedure, i.e., measuring surface wave dispersion for both Rayleigh and Love waves, developing dispersion models for both waves, and appying a joint inverting, the radial anisotropic crustal shear wave model presented in our study can be reproduced. For details of the method, readers are referred to the following papers: Bodin, T., and M. Sambridge (2009), Seismic tomography with the reversible jump algorithm, <em>Geophysical Journal International</em>, <em>178</em>(3), 1411-1436, doi:10.1111/j.1365-246X.2009.04226.x. <br> Yuan, H., and T. Bodin (2018), A probabilistic shear wave velocity model of the crust in the central West Australian Craton constrained by transdimensional inversion of ambient noise dispersion, <em>Tectonics</em>, <em>37</em>(7), 1994-2012. <br> <br> <br> The two datasets are the only data needed to produce the model in our study.
DOI: 10.6084/m9.figshare.25288510.v1
title: Supplementary Material for: Personalized Paths: Unlocking Alzheimer's via the Gut-Brain Axis

description: Background: Alzheimer's disease is characterised by abnormal protein aggregates in the brain that lead to cognitive decline. While current therapies only treat symptoms, disease-modifying treatments are urgently needed. Studies suggest that the composition of the microbiota is altered in people with Alzheimer's disease (AD), suggesting a link between gut bacteria and AD-related brain changes. 
Summary: In our narrative review, we explore various microbial interventions, such as faecal microbiota transplantation (FMT), probiotics and diet, as powerful potential treatments. Studies suggest changes in microbiota composition following these interventions, with some beneficial effects on cognitive function. However, the mechanism of action of these microbial interventions is still unknown.
Key message: Our aim here is to highlight the importance of personalised approaches, taking into account individual metabolic and microbiome profiles. We try to address gaps in current research and emphasise the need for microbiota analysis at different stages of the disease and its integration with clinical parameters and lifestyle information for a comprehensive understanding of AD progression (summarised in Figure 1).
DOI: 10.6084/m9.figshare.20322423.v1
title: Adjacent forest moderates insect pollination of oil palm

description: Natural habitat plays a role in many agroecosystems as a source of pollination services and other ecological spillover, but these effects are largely unquantified in oil palm (<em>Elaeis guineensis</em>), a globally important crop linked to deforestation. In a field experiment in Sumatra, Indonesia, we manipulated floral visitor access to female oil palm inflorescences over a 100 m distance gradient from forest into oil palm and sampled insects with sticky traps placed above male and female inflorescences. Full exclusion of floral visitors decreased mean oil palm fruit set to 12%, demonstrating that insect pollination was necessary to maintain favorable fruit set and yield. Treatment group means of fruit set under open pollination (62%) and when excluding large (&gt;1.4 mm diameter) organisms (72%), did not differ significantly from open pollination augmented with hand pollination (61%), suggesting no difference in pollen limitation. In contrast, when we examined change in fruit set with distance from forest, we found a significant trend of higher fruit set in oil palms closer to the forest when large organisms were excluded, which increased estimated fruit set at the forest edge to 87%, compared to open-pollinated palms (70%). This trend with distance from forest was absent when we fully excluded floral visitors, showing that the effect of forest was not likely due to an abiotic gradient (e.g., changing soil nutrients). Of the arthropod taxa collected from sticky traps, Drosophilidae (Diptera) and Gelechiidae (Lepidoptera) decreased and increased with distance from forest, respectively. The taxa <em>Elaeidobius kamerunicus</em> (Coleoptera: Curculionidae), Gelechiidae, and the families Thripidae and Phlaeothripidae (Thysanoptera) were abundant on both male and female inflorescence sticky traps. <em>Elaeidobius kamerunicus</em>, an introduced oil palm pollinator, had the only significant relationship with fruit set. Our results confirm pollination by insects as a key ecosystem service for oil palm production. Although further work is needed to clarify the relationship between fruit set, biodiversity, and distance from forest, we speculate that excluding large organisms could have increased fruit set closer to forest by mediating interactions between pollinators, forest predators, and farm mesopredators. Understanding the relationships between nearby forest and pollination services could better connect oil palm production to its landscape context and associated biodiversity. This would be important for landscape-scale conservation planning that considers both the ecosystem service needs and ecological impacts of oil palm agriculture.
DOI: 10.6084/m9.figshare.25679568.v1
title: 膝骨关节炎的患病率和危险因素。 XLSX系列

description: 中国南京市1045名居民的膝骨关节炎患病率信息及相关危险因素的测量结果。
DOI: 10.6084/m9.figshare.28648262.v1
title: Alignments and trees

description: <b>Multi-locus molecular study of </b><b><i>Colletotrichum humuli </i></b><b>from an ancient herbarium specimen of </b><b><i>Humulus lupulus</i></b><b> and </b><b><i>C. humulicola</i></b><b> sp. nov. from </b><b><i>H. scandens</i></b>
DOI: 10.6084/m9.figshare.6958877.v1
title: Figure 16.xlsx

description: Figure 16
DOI: 10.6084/m9.figshare.7928474.v1
title: gVCF_HG03850

description: 1000 Genomes gVCF mapped to hs37d5 for HG03850. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.12649691.v1
title: Processed EVAL Dataset (30 secs window - bfill)

description: File to be used in the: https://github.com/arianesasso/aime-2020, notebook: processing_predictions/extract_blfeatures_and_predict_bp_from_ppg_eval.ipynb
DOI: 10.6084/m9.figshare.12280547.v4
title: BeeWalk dataset 2008-23

description: DESCRIPTIONFocussed on bees in the genus Bombus (bumblebees) and Apis (honeybees), with occasional records of other bee species. No particular intentional bias in habitats surveyed.GEOGRAPHIC DESCRIPTIONThe BeeWalk survey covers Great Britain (but not Northern Ireland). Recording effort is biased towards Somerset, South Wales and the Scottish central belt as a result of publicity pushes, but East Anglia, Cornwall, north/mid Wales and north-west Scotland are somewhat under-represented in the dataset. Records within this dataset are generally collected at 100m resolution.PURPOSERecords were collected with the aim of better understanding the abundance and distribution of British bumblebee species, and creating an index of abundance in the same way as has been done for butterflies with the UKBMS dataset.DATA QUALITYData are collected by volunteers whose identification abilities will vary. Frequent bumblebee ID training courses are provided for volunteers, identification resources are provided on the project website, and the category 'indeterminate bumblebee' is provided as a catch-all for bees where the identification is uncertain. Trials carried out as part of the NPPMF project have found that volunteer's error rate using the BeeWalk methodology is not significantly different to that of an expert. Photographs and/or specimens are not required for each sighting, but unusual sightings (rare or difficult-to-identify species) are checked by referral to the recorder unless they are known to be experts. The dataset has been validated and verified using the NBN Record Cleaner, and as a consequence some erroneous grid references have been corrected and records outside their range have been checked and confirmed by an expert after referral to the original recorder, or downgraded to 'indeterminate bumblebee' where no evidence could be provided. The cryptic Bombus lucorum complex are treated as B. lucorum sensu lato, and only queens and males of B. terrestris & B. lucorum (sl) are recorded to species (indistinguishable workers are treated as the aggregate species terrestris/lucorum).METHODSVolunteers walk a set transect on a monthly basis between March and October (inclusive), recording all bumblebees seen within a 4m x 4m 2m 'recording box' in front of the recorder (see www.beewalk.org.uk for full details). Photographs are not submitted in support of all records, but netting and photographing bumblebees to help ID is encouraged. BBCT also run a series of ID training events aimed at BeeWalkers to upskill volunteers. Records submitted are validated and their distribution verified using the NBN Record Cleaner with verification rules from the Bees, Wasps and Ants Recording Society. Records which fail verification or validation checks are referred back to recorders for further evidence.
DOI: 10.6084/m9.figshare.14113037.v1
title: Supplementary Material for: Effects of Diet after Early Breast Cancer Treatment: A Systematic Review and Meta-Analysis of Clinical Trials

description: <b><i>Purpose:</i></b> Randomized clinical trials (RCT) are inconclusive regarding the role of dietary interventions in anthropometric measurements and survival in breast cancer patients. Our aim was to conduct a systematic review and meta-analysis to assess the effects of diet on these outcomes in women treated for early-stage breast cancer. <b><i>Methods:</i></b> Embase, MEDLINE, the Cochrane Database of Systematic Reviews, and the Cochrane Central Register of Controlled Trials were searched for RCT comparing dietary interventions (individualized dietary counseling, prescription of a specific diet, or others) with usual care in women that were treated for early breast cancer. Primary outcomes were overall survival (OS) and disease-free survival (DFS); secondary outcome was a change in body mass index (BMI). <b><i>Results:</i></b> We found 12 RCT eligible for analysis, 7 of which were included in the quantitative analysis. Two studies reported OS and DFS and 6 reported BMI data. The hazard ratio (HR) for OS and DFS was 0.91 (95% confidence interval [CI] 0.77–1.07, <i>p</i> = 0.25) and 0.92 (95% CI 0.79–1.08, <i>p</i> = 0.31) for the intervention and control groups, respectively. Intervention was associated with BMI reduction in subjects who received a specific diet instead of counseling or other types of intervention (–0.67; 95% CI –1.14 to –0.21). <b><i>Conclusions:</i></b> Despite increasing survival among breast cancer patients due to better oncological treatments, there is still a lack of prospective data regarding the effects of dietary interventions in this population. We found positive association between prescription of specific diets in terms of anthropometric measures; there were no differences in OS or DFS.
DOI: 10.6084/m9.figshare.20400717.v1
title: China_POP_0.1deg_2018.rar

description: The 0.01° grid population data of China mainland in 2018 can be accessed freely at the figshare repository. <br> GCS：GCS_WGS_1984 Cell: 0.01 degree datum: D_WGS_1984 <br> The data collection contains one .rar file, labelled China_POP_0.01deg_2018.rar, which contains the annually average Tencent LBS data in 2018 (TN_hSum2018.tif), the 0.01° grid population data of China mainland in 2018 (POP2018.tif), and the county-level boundary polygon feature joining with statistical population in 2018 (statisitcal_pop_polygon_features.rar).
DOI: 10.6084/m9.figshare.21541650.v1
title: A corpus of machine-annotated incident reports of medication errors

description: Our dataset contains 478,175 named entities related to medication errors and also differentiates between incident types by recognising discrepancies between what was intended and what actually occurred. <br> To use this dataset, one should also cite this original data source: Medical Adverse Event Information Collection Project [Iryō jiko jōhō shūshū-tō jigyō] Japan Council for Quality Health Care; 2022 [Available from: https://www.med-safe.jp/index.html.
DOI: 10.6084/m9.figshare.21213896.v1
title: Data for: Estimating heritability of song considering within-individual variance in a wild songbird: the collared flycatcher

description: Data for: Heritability of song in the collared flycatcher <br> The table "songheritability_data.csv" contains all data used in the animal models investigating variance components five song traits: song length, mean frequency, frequency bandwidth, tempo and complexity. The other variables are date and year of the measurements, age and identity of the birds, order of the songs in the recording, recording ID and song ID. Continuous variables were z-transformed. <br> The table "geneticsimilaritymatrix.csv" contains the genetic similarity matrix of the individuals with song data, used in the animal models. <br> The R script file "songheritability_code.R" contains R code necessary for reproducing the results reported in the manuscript. <br> Song recording was collected from collared flycatchers (<em>Ficedula albicollis</em>) from 2008-18. We catched these birds and collected blood samples from them and recorded their age (one-year old or older). Five song traits, which were extracted from the song recordings with the help of Ficedula toolbox, were used in the analyses: song length, mean frequency, frequency bandwidth, tempo and complexity. All continuous variables included into the models were z-transformed. Genetic similarity matrix was calculated based on more than 50 000 single nucleotide polymorphism.
DOI: 10.6084/m9.figshare.26533825.v1
title: salivary microbiome

description: Periodontally healthy middle-aged humans and monkeys display different levels of alveolar bone resorption, gingival inflammatory infiltrate, and salivary microbiota profile
DOI: 10.6084/m9.figshare.26732956.v1
title: Additional file 5 of Assessing transcriptomic heterogeneity of single-cell RNASeq data by bulk-level gene expression data

description: Supplementary Material 5. Table S2: (A) The confusion table of the clustering outcomes on the breast cancer sc-RNASeq dataset GSE161529. Rows indicate clusters of cells, and three columns indicate the PAM50 subtypes of the samples encompassing the cells, (B) The confusion table of the virtual data simulated by M1, rows and columns correspond to cell types (π) and sample subtypes (s) respectively, (C) The confusion table of the virtual data simulated by M1.
DOI: 10.6084/m9.figshare.3568212.v1
title: Appendix A. Frequency of occurrence (number of plots) of understory taxa in WS1 and WS3, H. J. Andrews Experimental Forest, Oregon, over the study period (1979–2008).

description: Frequency of occurrence (number of plots) of understory taxa in WS1 and WS3, H. J. Andrews Experimental Forest, Oregon, over the study period (1979–2008).
DOI: 10.6084/m9.figshare.10646693.v2
title: Downregulation of miR-193a-3p is involved in the pathogenesis of hepatocellular carcinoma by targeting CCND1 Peer J #40214

description: 1.The detail results of dual luciferase reporter experiments.txt2.The details of KEGG and GO analyses.xlsx3. Expression levels of miR-193a-3p and CCND1 in TCGA database and qRT-PCR in house
DOI: 10.6084/m9.figshare.7527764.v1
title: Porous hypercrosslinked polymer-TiO2-graphene composite photocatalysts for visible-light-driven CO2 conversion

description: <b>The data supporting the plots within this paper and other findings of this study are available from the corresponding author on request. The source data underlying Figs 3a-f and 4a–e and Supplementary Figs 7-12, 14,16, 18-23, 25-30 and 32-40 are provided as a Source Data file.</b><i></i><sub></sub><sup></sup><br>