cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29066708.v1
title: <b>Intratumoral microbiota-derived sphingolipids enhance the </b><b>combination therapy</b><b> of </b><b>Capecitabine and Nivolumab</b>

description: Intratumoral microbiota have exerted a profound impact on cancer treatments, however, its complex mechanistic underpinnings remain incompletely elucidated. Herein we sought to delineate the critical role of intratumoral microbiota in potentiating combination therapeutics against colorectal cancer (CRC). By conducting comparative analyses of germ-free (GF) and specific pathogen-free (SPF) mice models, we have screened out the intratumoral microbiota-augmented tumor regression and prolonged survival of SPF mice receiving Capecitabine-Nivolumab combination regimen. Its metagenomic and metabolomic profiling revealed an enrichment of <i>Bacteroides fragilis</i> by Capecitabine-Nivolumab combination therapy, concomitant with elevated microbial sphingosine-1-phosphate (S1P). Further mechanistic exploration demonstrated that intratumoral microbiota-derived S1P up-regulated PD-1 expression via epigenetic modulation—specifically, by enhancing histone deacetylation at the PDCD1 locus. Then we identified microbial sphingosine kinase 2 (SphK2) as a putative predictive biomarker for clinical benefit, underscoring the potential for intratumoral microbiota-targeted strategies to optimize CRC management. To conclude, these findings have advanced our understanding of the intricate interplay among intratumoral microbiota, sphingolipid metabolites and immunochemotherapeutic interventions, highlighting the promise of leveraging the intratumoral microbiome to enhance clinical outcomes in CRC.
DOI: 10.6084/m9.figshare.3547719.v1
title: Supplement 1. R source code for the statistical methods described in this paper, with a short tutorial describing their use.

description: File List plots.R -- R source code for making plots simpleeg.R -- R source code for the simple example described in the paper Phillips_and_Elith_online_tutorial.pdf -- A short tutorial describing how to use the R code PhillipsElith.zip -- Data for the New South Wales case study used in the tutorial, together with the above files. Description The R code in plots.R creates POC-plots, which are presence-only analogs of calibration plots. The plots are described in the original paper, and instructions for use of the R code are in Phillips_and_Elith_online_tutorial.pdf.
DOI: 10.6084/m9.figshare.648063.v1
title: CIL:39549

description: This is a time lapse image series of Saccharomyces cerevisiae expressing GFP tagged Bub2, a GTPase activator involves in mitotic cell cycle spindle orientation checkpoint and regulation of exit from mitosis. These phase and GFP z-series images are part of an image group containing CIL 39546-39550. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
DOI: 10.17632/dvkjsb6ysb
title: Educational Goals, Self-efficacy, Perceived Impact and Educational Attitudes in Response to Explosive Racist Remarks

description: The present study explored how teachers prioritize educational goals and their attitudes towards racist remarks made by students after the October 7th massacre in Israel in a hypothetical vignette.
DOI: 10.17632/m6pdjy4bx5
title: March 2024 update for DEMO "SAND - software for generation of packed beds"

description: The SAND code for packed bed generation has been uploaded to Mendeley Data and is available for free use by the scientific community. This Python-based open-source code, developed by the authors, aims to streamline the process of generating packed beds for various applications, particularly within computational fluid dynamics (CFD) simulations. Researchers and practitioners can access the code on Mendeley Data, where it is readily available for download and implementation in their studies and projects. The SAND code offers a user-friendly interface and efficient algorithms to facilitate the generation of packed beds, addressing the limitations of existing software tools. We encourage researchers to explore and utilize the SAND code to enhance their research endeavors in the field of packed bed simulations.
DOI: 10.17632/rbss2nk6r8
title: Assessment of outcomes of calciphylaxis lesions treated with intralesional sodium thiosulfate

description: Supplemental Table I and II
DOI: 10.6084/m9.figshare.14601411.v1
title: Open Data Package for article "Characterizing Technical Debt in Evolving Open-Source Software"

description: Replication Package consisting of SonarQube 9.0.1 databases, analysis scripts, analysis results in XLSX format for 112 target application versions (38 releases of FreeMind, 46 releases of jEdit and 28 releases of TuxGuitar).
DOI: 10.6084/m9.figshare.25117844.v1
title: Supplementary Material for: The incidence of necrotizing enterocolitis and late-onset sepsis during the COVID-19 pandemic in Sweden: A population-based cohort study

description: Introduction: The effect of the pandemic restrictions in the NICUs is not well studied. Necrotizing enterocolitis (NEC) is characterized by intestinal inflammation and bacterial invasion. This study aimed to investigate whether the incidence of NEC has changed during the COVID-19 pandemic in Sweden and whether it was associated with a change in the frequency of extremely preterm births.
Methods: Data were retrieved from the Swedish Neonatal Quality Register (SNQ) for infants registered between January 2017 and December 2021 born below a gestational age of 35 weeks. The registry completeness is 98-99%. The diagnosis of NEC was the primary outcome. Generalized linear model analysis was used to calculate the risk ratio for NEC.
Results: Totally 13239 infants were included. 235 (1.8%) infants developed NEC, out of which 91 required surgical treatment. 8967 infants were born before COVID-19 pandemic and 4272 during. Median gestational age at birth was 32.8 weeks in both periods. The incidence of NEC was significantly lower during COVID-19 pandemic compared to the prior period (1.43% vs 1.94% p 0.037), but not the incidence of surgical NEC. The crude Risk ratio of developing NEC during COVID-19 pandemic was 0.74 (95% CI(0.55-0.98)). The incidence of Late onset sepsis with positive culture was also declined during COVID-19 (3.21% vs 4.15%, p value 0.008).
Conclusion: While we found significant reduction in the incidence of NEC and culture-positive late-onset sepsis during the COVID-19 pandemic, the number of extremely preterm births was unchanged.
DOI: 10.6084/m9.figshare.28846766.v1
title: State of the Culinary Tourism Industry [2024]

description: Comprehensive 2024 report analyzing global trends in food and beverage tourism, with expert insights from the World Food Travel Association.
DOI: 10.17632/tyjntw9pp2
title: Cases of Pesticide Exposure

description: Set of samples resulting from an evaluative, population-based cross-sectional study, approved by the Research Ethics Committee of Federal University of Alfenas, protocol: 415856. These samples pertain to 1,027 rural workers from the southern region of Minas Gerais, Brazil, where comprehensive data on socioeconomic factors, history of pesticide intoxication and hospitalization, and usage of personal protective equipment were collected. Blood samples were obtained to measure biomarkers of pesticide exposure as well as indicators of renal and hepatic sequelae. Each sample encompasses 79 condition attributes and 1 decision attribute pertaining to the Diagnosis. All volunteers provided their informed consent by signing the Free and Informed Consent Form after receiving the necessary information.
DOI: 10.6084/m9.figshare.12998822.v2
title: Project Portfolio Dataset

description: This dataset comprises a portfolio of six projects each having a PMB consisting of a budget derived from a standardised first-principles, bottom-up estimation technique utilising a homogeneous set of resources, both consumable and non-consumable, which are inter-related in a highly complex, multi-dimensional manner with appropriate correlation between quantity, productivity rates and cost rates. The data set also includes detailed time-phased actual costs and progress over the life of each project as well as the time-phased values of revenue claimed for each project. The collection and attribution of 12,139 actual costs and the measurement of progress over a period of just under 109 consecutive weeks is consistent and standardised across all six projects providing a unique differentiator to other datasets. The data was collected over a continuous 109 week period, and is valid for research in portfolio, program or project management or control of multiple resource-constrained projects, where projects are managed collectively, generally in a standardised manner to support a strategic business aim.
DOI: 10.6084/m9.figshare.25111781.v1
title: Data: Pilfering personalities: effects of small mammal personality on cache pilferage

description: These data and code accompany the paper: "Humphreys & Mortelliti, 2024. Pilfering personalities: effects of small mammal personality on cache pilferage." These data can be used to replicate all main analyses in the paper. These data are not intended for use in other publications. Please contact the authors if you would like to collaborate on a project using these data or if additional comments or questions arise: Brigit Humphreys (brigit.humphreys@maine.edu)Alessio Mortelliti (alessio.mortelliti@maine.edu)
DOI: 10.6084/m9.figshare.27763944.v1
title: Orogastric Exposure of Macaques to Bovine H5N1 Causes Subclinical Infection

description: Routes of infection were tested using a bovine isolate (HPAIV H5N1 clade 2.3.4.4b, Ohio) in cynolmolgus macaques. Intranasal or intratracheal inoculation of macaques caused systemic infection resulting in mild and severe respiratory disease, respectively. In contrast, infection by the orogastric route resulted in limited infection and seroconversion of macaques which remained subclinical.
DOI: 10.6084/m9.figshare.3561723.v1
title: Appendix A. Characteristics of the study plant species and model parameterization.

description: Characteristics of the study plant species and model parameterization.
DOI: 10.6084/m9.figshare.3569085.v1
title: Appendix C. Simulation methods for evaluating the degree to which tree regeneration depends on fire under historical and contemporary fire regimes.

description: Simulation methods for evaluating the degree to which tree regeneration depends on fire under historical and contemporary fire regimes.
DOI: 10.6084/m9.figshare.5124613.v1
title: Supplementary Material for: A Comparison of Traditional and Novel Definitions (RIFLE, AKIN, and KDIGO) of Acute Kidney Injury for the Prediction of Outcomes in Acute Decompensated Heart Failure

description: <b><i>Aims:</i></b> To determine if newer criteria for diagnosing and staging acute kidney injury (AKI) during heart failure (HF) admission are more predictive of clinical outcomes at 30 days and 1 year than the traditional worsening renal function (WRF) definition. <b><i>Methods:</i></b> We analyzed prospectively collected clinical data on 637 HF admissions with 30-day and 1-year follow-up. The incidence, stages, and outcomes of AKI were determined using the following four definitions: KDIGO, RIFLE, AKIN, and WRF (serum creatinine rise ≥0.3 mg/dl). Receiver operating curves were used to compare the predictive ability of each AKI definition for the occurrence of adverse outcomes (death, rehospitalization, dialysis). <b><i>Results:</i></b> AKI by any definition occurred in 38.3% (244/637) of cases and was associated with an increased incidence of 30-day (32.3 vs. 6.9%, χ<sup>2</sup> = 70.1; p &lt; 0.001) and 1-year adverse outcomes (67.5 vs. 31.0%, χ<sup>2</sup> = 81.4; p &lt; 0.001). Most importantly, there was a stepwise increase in primary outcome with increasing stages of AKI severity using RIFLE, KDIGO, or AKIN (p &lt; 0.001). In direct comparison, there were only small differences in predictive abilities between RIFLE and KDIGO and WRF concerning clinical outcomes at 30 days (AUC 0.76 and 0.74 vs. 0.72, χ<sup>2</sup> = 5.6; p = 0.02) as well as for KDIGO and WRF at 1 year (AUC 0.67 vs. 0.65, χ<sup>2</sup> = 4.8; p = 0.03). <b><i>Conclusion:</i></b> During admission for HF, the benefits of using newer AKI classification systems (RIFLE, AKIN, KDIGO) lie with the ability to identify those patients with more severe degrees of AKI who will go on to experience adverse events at 30 days and 1 year. The differences in terms of predictive abilities were only marginal.
DOI: 10.17632/gcsgc2byps
title: Linkages between East China Sea Deep-sea Oxygenation and the Variability of the East Asian Summer Monsoon and Kuroshio Current over last 400,000 years

description: This dataset contains the percentage abundance of dominant benthic foraminifera, Biofacies abundance, and percentage abundance of dominant oxic, suboxic, dysoxic species of benthic foraminifera at Integrated Ocean Drilling Program Site U1429 in the East China Sea over the last 400 ka. An additional datasheet contains Shannon Index (H) and abundance of Quinqueloculina, Globobulimina, and Bulimina genus for the same period from the same site.
DOI: 10.6084/m9.figshare.22006271.v1
title: Supplementary Material for: Cross-species convergence of brain transcriptomic and epigenomic findings in posttraumatic stress disorder: A systematic review

description: Introduction: Posttraumatic stress disorder (PTSD) is a complex multifactorial disorder influenced by the interaction of genetic and environmental factors. Analyses of epigenomic and transcriptomic modifications may help to dissect the biological factors underlying the gene-environment interplay in PTSD. To date, most human PTSD epigenetics studies have used peripheral tissue, and these findings have complex and poorly-understood relationships to brain alterations. Studies examining brain tissue may help characterize the brain-specific transcriptomic and epigenomic profiles of PTSD. In this review, we compiled and integrate brain-specific molecular findings of PTSD from humans and animals. Methods: A systematic literature search according to the PRISMA criteria was performed to identify transcriptomic and epigenomic studies of PTSD, focusing on brain tissue from human postmortem samples or animal-stress paradigms. Results: Gene- and pathway-level convergence analyses revealed PTSD-dysregulated genes and biological pathways across brain regions and species. A total of 243 genes converged across species, 17 of them significantly enriched for PTSD. Chemical-synaptic transmission and signaling by G-protein-coupled receptors (GPCRs) were consistently enriched in across -omics and species. Discussion: Our findings point out dysregulated genes highly replicated across PTSD studies in humans and animal models and suggest a potential role for the corticotropin-releasing hormone/orexin pathway in PTSD’s pathophysiology. Further, we highlight current knowledge gaps and limitations and recommend future directions to address them.
DOI: 10.17632/5nv63tjbvs
title: Soft landings for tough times: the impact of ground cover traits on the overwintering survival of Anisota stigma (Notodontidae) and Manduca sexta (Sphingidae) in urban ecosystems.

description: Subsurface pupation among arboreal Lepidoptera is widespread and species are vulnerable to microhabitat conditions during this life stage. We investigated how ground cover type influences soil health, subsurface temperature, and fitness in Manduca sexta (Sphingidae) and Anisota stigma (Saturniidae). Overwintering survival decreased in the field compared to controls in growth chambers, with M. sexta experiencing particularly high mortality. Canopy density had a positive relationship with survival in A. stigma. Substrate type also significantly influenced emergence rates, with A. stigma showing the highest success, 36.84%, in forest cover, followed by mulch (29.63%), mature turf (27.50%), layered urban understories (9.80%), recently established turf (5.88%), and bare soil (5.40%). Female overwinter water retention in A. stigma was positively correlated with average daily maximum soil temperature, suggesting the use of discontinuous gas exchange for water conservation under stress. Finally, observed surface-related pupal deaths accounted for a minimum of 16.19% and 8.72% of total overwintering mortality in A. stigma and M. sexta, respectively. Soil compaction, which was negatively correlated with organic matter, and the proportion of bare soil cover was positively correlated with surface pupation in our focal species. The findings reveal that current landscaping practices likely contribute to urban declines in lepidopteran diversity and abundance. These results emphasize the importance of “soft landings” beneath moth host plants, which protect the soil with foliage cover. We recommend soil remediation strategies especially following disturbance, such as mulching or incorporating organic soil amendments, to enhance habitat productivity. Within these pupation sanctuaries, managers should also minimize foot and mower traffic to reduce soil compaction and lower risk of injury to pupae. 

These data include: Adult moth emergence information, environmental and caterpillar variables for each site, pupae observed on the surface during the fall and winter that did not successfully burrow into soil, and temperature data from subsurface data loggers.
DOI: 10.17632/dzkh6kynbr
title: Replication package for "The Real Effects of Brexit on Labor Demand: Evidence from Firm-level Data"

description: Replication package for "The Real Effects of Brexit on Labor Demand: Evidence from Firm-level Data".
DOI: 10.6084/m9.figshare.14387126.v1
title: ASM130575v2

description: modifined DNA Zoo donkey genome (ASM130575v2)ASM130575v2.gtf
DOI: 10.6084/m9.figshare.20411424.v1
title: Crop classification maps for Northeast China

description: This dataset maps the distribution of crop types in Northeast China with the 30-m resolution with reliable accuracies. We believe our dataset can be helpful for relevant studies on regional agricultural production management.
DOI: 10.6084/m9.figshare.5668114.v1
title: Wheat yield in the Cerrado as affected by nitrogen fertilization and inoculation with Azospirillum brasilense

description: Abstract: The objective of this work was to evaluate the effect of inoculation with Azospirillum brasilense, associated with N rates and sources, in soil of the Cerrado (Brazilian savanna), on the grain yield of irrigated wheat (Triticum aestivum). The experiment was carried out under a no-tillage system in a Typic Haplustox. The experimental design was randomized complete blocks with four replicates, in a 2x5x2 factorial arrangement: two N sources (urea and urea with NBPT urease inhibitor); five N rates applied as topdressing (0, 50, 100, 150, and 200 kg ha-1); and with or without seed inoculation with A.brasilense. The increase in the N rates positively affected spike length, number of spikelets and of grains per spike, number of spikes per meter, N accumulation in the straw, leaf chlorophyll content, and grain yield of irrigated wheat, regardless of the use of NBPT urease inhibitor with conventional urea. Singly, inoculation with A.brasilense does not affect production components and grain yield, despite the increase in N content in wheat straw. The inoculation with A.brasilense, associated with the application of 140 kg ha-1 N, provides the highest grain yield of irrigated wheat cropped after corn in low-altitude Cerrado.
DOI: 10.6084/m9.figshare.97169.v1
title: Gaussian Job Archive for C6H3MnO5

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.28638116.v1
title: Interview Transcript (Mental Health Disorders and Privacy).docx

description: Interview data on mental health
DOI: 10.17632/bvrzf2s9j7
title: Depression among Pet owners and Non-pet owners: A comparative cross-sectional study in Dhaka, Bangladesh

description: Depression is one of the leading causes of Disability Adjusted Life Years (DALY) calculated for all ages that often begins during teens and continues to affect later years. It is shown that pets can influence a human being psychologically and emotionally, including preventing depression. This study determined the association between keeping household pets and depression. A comparative cross-sectional methodology was followed, and data were drawn using both online and offline approaches. Independent sample t-test and chi-square test were used to compare continuous variables and categorical variables between pet-owners and nonowners. Logistic regression was used to identify an association between pet ownership and depression.  Pet owners were found to be 41% less depressed than nonowners (AOR-0.59 (95% CI: 0.31-1.14). Among other variables, male gender [AOR-3.38 (95% CI: 3.38: 1.50-7.62)], unmarried status [AOR-2.10 (95% CI: 1.05-4.16)], tobacco consumption [AOR-5.27 (95% CI: 1.50-18.53)], physical disability [AOR-5.27 (95% CI: 1.50-18.53)] were significantly and positively associated with depression.
DOI: 10.6084/m9.figshare.12115773.v1
title: EEG raw data - Economical Assessment of Working Memory and Response Inhibition in ADHD

description: This study aims to validate a combined <i>n</i>-back/nogo paradigm by comparing it to single task versions and to demonstrate its applicability for ADHD research. Twenty-five healthy individuals and 34 ADHD patients between 9 and 16 years participated in this ERP study. Healthy controls underwent single task versions of a 2-back working memory task and a go/nogo response inhibition task as well as the introduced combined 2-back/nogo task.<br>This file contains the raw EEG data of this study.<br>
DOI: 10.6084/m9.figshare.24465700.v1
title: Chicken_heart_spatialRNAseq_highres_images

description: High-resolution H&E images (TIFF files) and Loupe Browser-derived image alignment files (JSON files) for spatial transcriptomics datasets of developing chicken hearts.
DOI: 10.17632/7zg2n94bvc
title: Microplate approach to resin screening and parameter estimation applied to chromatography column modeling of gradient elution operation

description: # Microplate data used for materials screening and estimation of equilibrium parameters

The experimental data whit 4 microplates containing 96 wells, white already discounted. Each plate had a different amount of resin into the wells. The buffer solutions with different concentrations of ethanol: ϕ1, ϕ2, ϕ3 in different columns. Different amounts of resins were added into the wells of the other plates, named P1, P2, P3 and P4, each with: 10, 15, 25 and 50 mg into the plates named P1, P2, P3 and P4, respectively. Each of the 8 total rows per plate corresponded to a different type of resin.
Spreadsheet P1- P4: supernatant concentration data
Spreadsheet Config: experiment setup

# Column chromatography estimation

The experimental concentration chromatographic peak of NP40 was used to estimate the parameters. These data already take into account the corrections for the dead volume of 5.8 mL and the permanence volume of 10.94 mL.
DOI: 10.6084/m9.figshare.23600328.v1
title: Data and code for European hedgehog entanglement paper

description: The original data obtained from the entanglement questionnaire sent to the rescue centres. The code is for the population dynamic mortality model.
DOI: 10.6084/m9.figshare.3564156.v1
title: Appendix H. Model documentation of carbon sequestration in aboveground woody biomass without climate and flooding parameters.

description: Model documentation of carbon sequestration in aboveground woody biomass without climate and flooding parameters.
DOI: 10.6084/m9.figshare.22257871.v1
title: ENCODE_K562_eCLIP_peak.annotation

description: ENCODE K562 peaks annotation using HOMER
DOI: 10.6084/m9.figshare.27037207.v1
title: Corporate biodiversity governance index of listed firms in China 2001-2021

description: This is the dataset on Corporate Biodiversity Governance Index (CBGI), of listed firms in China 2001-2021.