cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.942376.v1
title: Retrospective Risk-Taking Questionnaire

description: Retrospective questionnaire measures This questionnaire was created to retrospectively assess the sensation seeking, risk-taking, and impulsive behaviors in a longitudinal neuroimaging (MRI) cohort. As no behavioral markers of risk-taking were collected from participants concomitantly with the MRI data, we collected retrospective information of these behaviors using this written questionnaire. Participants were mailed this two-part questionnaire in 2013 to self-assess retrospectively their behaviors during adolescence. The first part of the questionnaire included three questions relating to the individual’s general recall of their own teenage behavior: i) How old were you when you engaged in the most risky behavior? ii) Compared to your peers, how much risky behavior did you engage in as a teenager? iii) Please describe the types of risky behaviors you engaged in as a teenager. Risky behavior was defined in the questionnaire as ‘behavior that is unsafe or might result in negative consequences.’ The second part of the questionnaire included adaptations of the following measures: Sensation-seeking Scale (SSS), Cognitive Appraisal of Risky Events (CARE) Questionnaire, Youth Risk Behavior Surveillance, Barratt Impulsiveness Scale (BIS), and Behavioral Inhibition System/Behavioral Approach System Scales.
DOI: 10.6084/m9.figshare.28540652.v1
title: Gräns_2025_Supp_Data.xlsx

description: Supporting data for 'From tradition to innovation: Effects of manual and automated ikejime on welfare and product quality of rainbow trout and hybrid striped bass' by Albin Gräns<sup>1</sup>, Linas Kenter<sup>2</sup>, Waiman Meinhold<sup>3</sup>, Andreas Saxer<sup>4</sup>, Thorsten Schwerte<sup>5</sup>, and Jeroen Brijs<sup>5</sup>
DOI: 10.6084/m9.figshare.23553813.v1
title: Data from: Convergent losses of arbuscular mycorrhizal symbiosis in carnivorous plants

description: Data for reproducible analysis
DOI: 10.6084/m9.figshare.19499540.v1
title: patches and local annotations, slide 057, 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.27245016.v1
title: Supporting data for Mendes et al 202X The urbanisation of seed dispersal networks

description: Urbanisation is rapidly expanding, affecting the composition of wild communities and creating novel ecosystems worldwide. Seed dispersal is key for ecosystem persistence, particularly in fragmented landscapes, however, generalisations regarding the impacts of urbanisation are still hindered by the lack of studies encompassing the urban matrix. We reconstructed the seed dispersal networks in natural forests and urbanized habitats in Tenerife Island to explore the effects of urbanisation on seed dispersal. For one year, we conducted frugivory observations and identified seeds in animal faeces in the thermophilous vegetation belt, where anthropogenic pressure is highest. The forest network comprised 150 interactions between 83 plant and 18 animal species, while the urban network presented 89 interactions between 41 plant and 9 animal species. The urban matrix supported a lower richness of fleshy-fruited plants and dispersers. We found that urbanisation simplified seed dispersal networks, reducing interaction diversity. Importantly, novel interactions dominated the urban seed dispersal network, with exotic plants deeply integrated by interacting with native frugivores, accounting for 61% of the interactions (vs. 15 % in the forest). Eight frugivores (42%) maintained the functional connectivity between these habitats; likely facilitating the spread and invasive species from the urban areas into the forests due to their generalist diets. Six dispersers (32%) completely avoided urbanized habitats for which the later represent a particular stringent form of habitat fragmentation, with likely consequences for long-term plant genetic diversity. These findings highlight the need for sustainable urban planning and active stakeholder engagement to conserve the seed dispersal service.
DOI: 10.6084/m9.figshare.21548658.v2
title: Viscosity-temperature data of MRFs and base oils

description: This data set is a summary of the data covered in the paper " Modeling of the Temperature Effects on Magnetorheological Fluids over a Wide Temperature Range based on Free Volume Theory".
DOI: 10.6084/m9.figshare.5129626.v1
title: Supplementary Material for: Relative Brain Size and Its Relation with the Associative Pallium in Birds

description: Despite growing interest in the evolution of enlarged brains, the biological significance of brain size variation remains controversial. Much of the controversy is over the extent to which brain structures have evolved independently of each other (mosaic evolution) or in a coordinated way (concerted evolution). If larger brains have evolved by the increase of different brain regions in different species, it follows that comparisons of the whole brain might be biologically meaningless. Such an argument has been used to criticize comparative attempts to explain the existing variation in whole-brain size among species. Here, we show that pallium areas associated with domain-general cognition represent a large fraction of the entire brain, are disproportionally larger in large-brained birds and accurately predict variation in the whole brain when allometric effects are appropriately accounted for. While this does not question the importance of mosaic evolution, it suggests that examining specialized, small areas of the brain is not very helpful for understanding why some birds have evolved such large brains. Instead, the size of the whole brain reflects consistent variation in associative pallium areas and hence is functionally meaningful for comparative analyses.
DOI: 10.6084/m9.figshare.24411913.v3
title: Allele‐aware chromosome‐scale assembly of theallopolyploid genome of hexaploid Ma bamboo(Dendrocalamus latiflorus Munro)

description: Dendrocalamus latiflorus Munro is a woodyclumping bamboo with rapid shoot growth. Bothgenetic transformation and clustered regularly in terspaced short palindromic repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9) gene editingtechniques are available for D. latiflorus, enablingreverse genetic approaches. Thus, D. latiflorushas the potential to be a model bamboo species.However, the genome sequence of D. latiflorushas remained unreported due to its polyploidyand large genome size. Here, we sequenced theD. latiflorus genome and assembled it into threeallele‐aware subgenomes (AABBCC), representingthe largest genome of a major bamboo species.We assembled 70 allelic chromosomes (2, 737 Mb)for hexaploid D. latiflorus using both single‐molecule sequencing from the Pacific Biosciences(PacBio) Sequel platform and chromosome conformation capture sequencing (Hi‐C). Repetitivesequences comprised 52.65% of the D. latiflorusgenome. We annotated 135 231 protein‐codinggenes in the genome based on transcriptomesfrom eight different tissues. Transcriptome sequencing using RNA‐Seq and PacBio single‐molecule real‐time long‐read isoform sequencingrevealed highly differential alternative splicing (AS)between non‐abortive and abortive shoots, suggesting that AS regulates the abortion rate ofb amboo shoots. This high‐quality hexaploid genome and comprehensive strand‐specific transcriptome datasets for this Poaceae familymember will pave the way for bamboo researchusing D. latiflorus as a model species.. Please cite following reference if you use this dataset in your study:Zheng, Y., Yang, D., Rong, J., Chen, L., Zhu, Q., He, T., ... & Gu, L. (2022). Allele‐aware chromosome‐scale assembly of the allopolyploid genome of hexaploid Ma Bamboo (Dendrocalamus latiflorus Munro). <i>Journal of Integrative Plant Biology</i>, <i>64</i>(3), 649-670.All suggestions are welcome to lfgu@fafu.edu.cn
DOI: 10.6084/m9.figshare.20115731.v1
title: Secondary metabolites of Saposhnikovia divaricata regulate adaptation to drought stress

description: The data is the raw data of <em>Saposhnikovia divaricata </em>based on UPLC-MS.
DOI: 10.6084/m9.figshare.24129558.v1
title: Sequencing data for pilot run

description: Cost-Effective Complete Genome Sequencing Using the MinION Platform for Identification of Recombinant Enteroviruses
DOI: 10.6084/m9.figshare.3563217.v1
title: Appendix A. References used for data collection.

description: References used for data collection.
DOI: 10.6084/m9.figshare.25919473.v1
title: Supplementary Material for: Consumption of sugar-sweetened beverages before 2 years of age and attention-deficit/hyperactivity disorder

description: Introduction: This study examined the association between sugar-sweetened beverage consumption before the first 24 months of life and attention-deficit/hyperactivity disorder (ADHD).
Methods: A population administrative cohort study was conducted in Korea (2008–2019) using linked national insurance data and a health screening survey. The cohort included 25,305 children in the exposed group with high sugar-sweetened beverage drinks (≥200 ml) and 339,931 in the reference groups (&lt;200 ml) at 24 months of age. The primary outcome was the development of ADHD based on the International Classification of Disease (ICD) codes. Cox proportional model was used to identify the association between sugar-sweetened beverage consumption during early childhood and the later development of ADHD while controlling for multiple risk factors. 
Results: Over a mean follow-up period of 9.2 years, the incidence rates of ADHD were 29.6 and 23.8 per 10,000 person-years (PY) in the exposed and reference groups, respectively. Compared with the reference group, children consuming high-sugar drinks were at an increased risk of ADHD (adjusted hazard ratio [aHR] 1.17, 95% confidence interval [CI] 1.08–1.27). These associations remained significant even after applying alternative ADHD definitions or adjusting for confounding variables. 
Conclusion: Children who consume sweetened beverages during early childhood are at increased risk of developing ADHD later in life.
DOI: 10.6084/m9.figshare.1393269.v1
title: Public data archiving in ecology and evolution: how well are we doing?

description: Data for: Roche DG, Kruuk LEB, Lanfear R, Binning SA (2015) Public data archiving in ecology and evolution: how well are we doing? <em>PLOS Biology</em> e1002295 doi:10.1371/journal.pbio.1002295 Data collected by DGR and SAB. Please refer to the manuscript for data collection methods and statistical analyses. For questions or to notify the authors if any errors are identified in the data, please contact Dominique Roche (dominique.roche@mail.mcgill.ca), Loeske Kruuk (loeske.kruuk@anu.edu.au), Rob Lanfear (rob.lanfear@gmail.com), or Sandra Binning (sandra.binning@mail.mcgill.ca).
DOI: 10.6084/m9.figshare.23050862.v1
title: KIR3DL3 data for figures

description: Data organized by figure panel for Palmer et al 2023
DOI: 10.15468/dl.cp2a3w
title: Occurrence Download

description: A dataset containing 107 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Galeruca laticollis Sahlberg, 1838"
 ]
}

 The dataset includes 107 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009579-250426092105405/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.28409135.v1
title: poleward flux

description: <b>Modeling studies of the mechanism of spindle stability and poleward flux regulating spindle length during metaphas</b>
DOI: 10.6084/m9.figshare.5311120.v1
title: Supplementary Material for: Antibiotic Susceptibility and Molecular Characterization of Escherichia coli O157 Isolates from Urinary Tract Infections

description: <b><i>Background:</i></b><i>Escherichia coli O157</i> is an important food-borne pathogen that can cause diarrhoea, hemorrhagic colitis, and hemolytic uraemic syndrome. Enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) and multilocus sequence typing (MLST) are good methods for molecular typing and the extensive use of antibiotics is a contributing factor to the increasing incidence of antimicrobial-resistant for these strains. <b><i>Objectives:</i></b> The aim of this study was to determine the prevalence, antimicrobial resistance, and genetic diversity of <i>E. coli O157</i> based on the prevalence of urinary tract infection (UTI) in Hubei, China. <b><i>Results:</i></b> We obtained 23 (8.07%) <i>E. coli O157</i> isolates from 285 UTI patients in Hubei, China. All isolates were subjected to antibiotic susceptibility analysis, and molecular typing was performed using ERIC-PCR and MLST. Antimicrobial susceptibility results indicated that most strains were resistant to penicillin (95.65%), chloramphenicol (73.91%), and ampicillin (69.57%). All isolates were discovered to be multiresistant (resistance to more than 3 antibiotics). Genetic variability analysis showed that all of the isolates were grouped into 4 clusters both by ERIC-PCR and MLST. <b><i>Conclusion:</i></b> Our findings demonstrated the presence of <i>E. coli O157</i> in UTIs, provided insights into the dissemination of antibiotic-resistant strains, and improved our knowledge of <i>E. coli O157</i> risk assessment in UTIs.
DOI: 10.6084/m9.figshare.28788107.v1
title: Supplementary Material for: Comparing Stroke Profiles and Outcomes between Urban and Rural India: A Secondary Analysis of the SPRINT INDIA Trial

description: Introduction: 
Stroke causes significant death and disability, with urban-rural disparities in healthcare, and limited studies in India, despite its rural majority of 70%. The post-hoc study aimed to explore differences in stroke profiles, risk factors, and outcomes between urban and rural participants using data from the SPRINT INDIA trial.
Methods: 
The SPRINT INDIA trial was a multi-centre Randomised clinical trial RCT across 31 Indian sites. Data was collected between April 28, 2018, and Nov 30, 2021. Index stroke patients, aged 18 and older, presenting within two days to three months of symptom onset, were randomized using a centralized web-based system into intervention or control groups. The intervention included SMS, videos, and an interactive educational workbook for secondary stroke prevention in 11 Indian languages. Baseline data captured in Case report form (CRF) included participants' urban or rural location. Primary outcome was a composite endpoint that included recurrent stroke, high-risk transient ischemic attack (TIA), acute coronary syndrome (ACS), and all-cause mortality within one year after randomization. The trial is registered by Clinicaltrials.gov, NCT03228979 and Clinical Trials Registry-India CTRI/2017/09/009600).
Results: 
The trial enrolled 4,298 sub-acute stroke patients, out of which 3038 (70.68%) were followed-up of which 1620 (53.32%) were urban and 1418 (46.68%) were rural. Primary composite outcome (recurrent stroke, high-risk TIA, ACS, and mortality) was higher in urban areas compared to rural areas 61 (3.8%) vs 34 (2.4%); p=0.018 at one year follow-up. All cases of high-risk TIA occurred in urban participants (p&lt;0.001). 
Urban participants were more educated 795 (49.1%) vs rural 394 (27.8%); p&lt;0.001), with higher rates of dyslipidemia 335 (20.7%) vs 247 (17.4%); p=0.023, and higher BMI 25.17±4.31 vs. 24.76±4.23; p=0.008. Behavioural risk factors of alcohol intake and smoking tobacco were higher in rural patients compared to urban patients 65 (4.6%) vs. 73 (4.5%); p&lt;0.001 and 59 (4.2%) vs. 65 (4.0%); p&lt;0.001 respectively.
Conclusion:
Urban patients show higher stroke recurrence and lifestyle-related conditions, while rural patients face more behavioural risks like smoking and alcohol use. To address these disparities, requires targeted interventions; urban patients would benefit from lifestyle-focused programs, such as dietary improvements and stress management. For rural patients, programs should focus on reducing behavioural risks like smoking and alcohol use through community-based education and accessible cessation support services.
DOI: 10.6084/m9.figshare.6553697.v1
title: ctd data

description: Environmental Data
DOI: 10.6084/m9.figshare.7867760.v1
title: Supporting data Heinz et al 2019

description: Supporting data for Heinz et al 2019 Caribbean multi-centre study of Klebsiella pneumoniae: whole genome sequencing, antimicrobial resistance and virulence factors.
DOI: 10.6084/m9.figshare.14493708.v1
title: Supplementary Material for: Pembrolizumab as Second-Line Therapy for Advanced Hepatocellular Carcinoma: A Subgroup Analysis of Asian Patients in the Phase 3 KEYNOTE-240 Trial

description: <b><i>Introduction:</i></b> KEYNOTE-240 investigated the efficacy and safety of pembrolizumab plus best supportive care (BSC) in sorafenib-treated patients with advanced hepatocellular carcinoma (HCC). Results for the subgroup of patients from Asia are described. <b><i>Methods:</i></b> Adults with advanced HCC previously treated with sorafenib were randomized 2:1 to pembrolizumab or placebo plus BSC. Here, the Asian subgroup comprised patients enrolled in Hong Kong, Japan, Korea, the Philippines, Taiwan, and Thailand. Primary endpoints were progression-free survival (PFS) per blinded central imaging review and overall survival (OS). Secondary endpoints included objective response rate (ORR) per blinded central imaging review, duration of response (DOR), and safety. <b><i>Results:</i></b> The Asian subgroup included 157 patients. As of January 2, 2019, the median follow-up in this subgroup was 13.8 months for pembrolizumab and 8.3 months for placebo. The median PFS was 2.8 months for pembrolizumab (95% confidence interval [CI] 2.6–4.1) versus 1.4 months (95% CI 1.4–2.4) for placebo (hazard ratio [HR] 0.48; 95% CI 0.32–0.70). The median OS was 13.8 months (95% CI 10.1–16.9) for pembrolizumab versus 8.3 months (95% CI 6.3–11.8) for placebo (HR 0.55; 95% CI 0.37–0.80). ORR was 20.6% (95% CI 13.4–29.5) for pembrolizumab versus 2.0% (95% CI 0.1–10.6) for placebo (difference: 18.5%; 95% CI 8.3–27.6). The median DOR was 8.6 and 2.8 months for pembrolizumab and placebo, respectively. Any grade treatment-related adverse events (TRAEs) occurred in 63 patients (58.9%) receiving pembrolizumab and 24 patients (48.0%) receiving placebo; 14 (13.1%) and 2 (4.0%) patients experienced grade 3–5 TRAEs, respectively. No treatment-related deaths occurred. <b><i>Conclusion:</i></b> Pembrolizumab demonstrated antitumor activity and was well tolerated in the Asian subgroup of KEYNOTE-240. A trend toward greater benefit with pembrolizumab in the Asian subgroup was observed compared with the overall cohort, supporting further evaluation of pembrolizumab treatment in this population.
DOI: 10.6084/m9.figshare.11799780.v2
title: Trends of syphilis in Brazil: a growth portrait of the treponemic epidemic

description: Syphilis is a chronic infectious disease with its prevalence being described since the 15<sup>th</sup> century. Although its etiological agent and also the treatment measures are widely known, syphilis is still a great public health problem worldwide, mainly in countries with limited resources associated to low investments in health primary care. The aim of the present study was to analyze the trend and regional distribution of syphilis in Brazil between 2007 and 2017. This is an ecological study using secondary data from the Brazilian notification system. The Ministry of Health selected 100 municipalities which presented the worse outcomes related to syphilis from the 5,570 Brazilian municipalities as a target for a comprehensive project in order to tackle the prevalence of syphilis, called the “No Syphilis Project”. These priority municipalities represent 57.7% of syphilis cases and about one third of the Brazilian population. They were compared with other 189 non-priority municipalities with more than 100 thousand inhabitants among the Brazilian regions (North, Northeast, Southeast, South and Center-West). Polynomial regression methods and Joinpoint analyses were used to analyze the trend, from which the Annual Average Percent Change (AACP) for each time period was calculated. There was a significant growth trend in all regions for the main three forms of syphilis (in pregnancy, congenital and acquired), especially in the South. The ratio between syphilis in pregnancy and congenital syphilis increased in both priority (AAPC: 8.54%; <i>p</i>&lt;0.001) and non-priority municipalities (AAPC: 2.61%; <i>p</i>=0.005), as well as in the regions, except the Center-West. High growth trends in syphilis prevalence were found in all municipalities, as well as all five regions between 2007 and 2017, showing that the challenge to reduce or even eliminate syphilis in Brazil is still difficult.
DOI: 10.6084/m9.figshare.27959733.v1
title: Supplementary Material for: Hypothyroidism promotes microglia M1 polarization by inhibiting BDNF-promoted PI3K-Akt signaling pathway

description: Hypothyroidism greatly affects the health­related quality of patients’ life, and microglia in brain have essential functions on neurodegeneration, but the underlying link between hypothyroidism and microglia function is largely ambiguous. 
Methods: Methimazole-induced mice was used to construct hypothyroidism model and explore the polarization of microglia. Lipopolysaccharide (LPS)-treated BV2 cells were used to investigate the effecting factors on microglia M1 polarization. Finally, global transcriptome sequencing (RNA-seq) was utilized to identify the underlying regulatory mechanisms. 
Results: The biomarkers of microglia M1 polarization and pro-inflammatory cytokines were significantly increased in hypothyroidism mice brain; hypothyroidism could also repress the expression of BDNF and TrkB, and the anti-inflammatory cytokine such as IL-10. In BV2 cells, LPS treatment decreased expression of BDNF, IL-10, and Arg1, while BDNF overexpression (BDNF-OE) significantly reversed the inflammation-induced by LPS by repressing iNOS and TNF-α, while increasing IL-10 and Arg1. RNA-seq analysis demonstrated that in LPS-treated BV2 cells, BDNF-OE significantly altered expression pattern of genes involved in PI3K-Akt signaling pathway, including the upregulated Thbs3, Myc, Gdnf, Thbs1, and Ccnd1, and the downregulated Gnb4, Fgf22, Pik3r3, Pgf, Cdkn1a, and Pdgfra. Myc, Gdnf, Thbs1, and Ccnd1 showed much higher expression levels than other genes in PI3K-Akt signaling pathway. 
Conclusions: Our study demonstrated a sound conclusion that hypothyroidism promotes microglia M1 polarization by inhibiting BDNF-activated PI3K-Akt signaling pathway in brain, which could serve as a promising therapeutic target for microglia-induced neurodegenerative or emotional disorders in future.
DOI: 10.6084/m9.figshare.28156466.v1
title: stomatal_size.csv

description: Stomatal size traits for three species of leafy greens grown in aquaponics or soil for several weeks. Variables for calculating stomatal size include guard cell dimensions.
DOI: 10.6084/m9.figshare.14224505.v1
title: Bibliography ecological stability

description: To generate this bibliographic collection, we searched for the terms (ecolog* AND stability) or (ecolog* AND resilience) in Clarivate Analytics Web of Science in the period from 1955 to 16<sup>th</sup> of October 2019. We selected the ecological journals Ecology, American Naturalist, Oikos, Ecology Letters, Journal of Ecology, Trends in Ecology & Evolution, Frontiers in Ecology and the Environment, Ecology and Society and Journal of Animal Ecology, complemented with the multidisciplinary journals Nature, Science and Proceedings of the National Academy of Sciences of the United States of America (PNAS). In total, we retrieved title, author lists, journal, year of publishing, keywords, text and references of 2028 unique articles