cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25240684.v1
title: <b>Transcriptomic approach on </b><b><i>Villorita cyprinoides</i></b><b> (black clam)</b>

description: <i>Villorita cyprinoides</i> is an ecologically and aquaculturally significant endemic species. This project aims to create reference transcriptomes that will provide a baseline for advancing studies to address the species localized habitat, underlying response mechanisms to various environmental stressors, and to improve genetically enhanced stress and disease-resistant individuals.
DOI: 10.6084/m9.figshare.27436206.v1
title: Supplementary Material for: A territory wide follow-up of primary and secondary extramammary Paget disease of two decades – effects of local disease on survival

description: Introduction
Extramammary Paget disease (EMPD) is an uncommon malignant cutaneous neoplasm that are divided into primary and secondary forms. In this multicenter study, histologically proven cases of primary and secondary EMPD were reviewed for clinical outcomes with subgroup analysis for secondary EMPD.

Methodology
Cases of EMPD were identified from pathology report of the involved institutions over a period of over two decades. Cases of secondary EMPD were identified review of case notes, radiology, and pathology reports. Clinicopathological and outcome data were retrieved for statistical analysis.

Results
A total of 109 cases were retrieved, including 19 cases of secondary EMPD, most commonly associated with colorectal (n=6), anal (n=5) and prostatic carcinomas (n=3). A difference was observed between older age and secondary (versus primary) EMPD (p=0.016), but no differences were seen in other clinico-demographical parameters. Male sex (p=0.018), age over 60 years old (p=0.004) and involvement of margins (resectable) (p=0.018) were associated with shorter OS. For DSS, involvement of margins (p=0.009) was an adverse predictor. Secondary EMPD had a shorter DSS than primary EMPD (p=0.005). Multivariable analysis confirmed all above associations (p&lt;0.05). In subgroup analysis for secondary EMPD, margin involvement remained associated with shorter OS (p = 0.007) and DSS (p = 0.003). 

Conclusions
Secondary EMPD is associated with poorer outcomes. Margin involvement is strong and independent indicator of shorter OS and DSS, including secondary EMPD. Resectability is a strong predictor of favorable outcome and excision with clear margins should be attempted when surgically feasible.
DOI: 10.6084/m9.figshare.26053123.v1
title: IEEE123NMdata

description: This is the data of IEEE 123-bus test system for NMs.
DOI: 10.6084/m9.figshare.3563307.v1
title: Appendix A. Figures showing distribution of spider personality types among mesocosm treatments, relationship between individual variation in spider activity and spider body-size, and spider cannibalism compared across treatments.

description: Figures showing distribution of spider personality types among mesocosm treatments, relationship between individual variation in spider activity and spider body-size, and spider cannibalism compared across treatments.
DOI: 10.6084/m9.figshare.26060338.v2
title: Canadian Road Network File for 2021 (Shapefile)

description: This dataset provides the 2021 Census Road Network Profile as a Shapefile
DOI: 10.6084/m9.figshare.28577627.v1
title: 20241005_123618.mrc

description: 4D STEM dataset, MoS2 flake encapsulated with aBN
DOI: 10.6084/m9.figshare.25991257.v1
title: Supplementary Material for: Are newer drugs better? An analysis of neonatal pharmacological treatments across generations

description: Introduction: We evaluated the relative effects of newer versus older medications for neonatal conditions and trends in margin of superiority across generations. Materials and Methods: We assessed network meta-analyses (NMAs) on neonatal pharmacological interventions identified from Medline, Cochrane, and PROSPERO. Interventions were chronologically arranged based on the earliest study and compared for their effects against placebo or no treatment and their immediate predecessor. We assessed the time trend in effect sizes using the Mann-Kendall test. Results: From 8048 retrieved records, 10 neonatal NMAs covering 352 trials and 102,653 participants were included. Compared to placebo, 56/61 (91.8%) interventions showed superiority with 23 (37.7%) statistically significant. Compared to previous generation, 47/72 (65.3%) showed superiority with 3 (4.2%) statistically significant. No significant trends in effect sizes were observed across generations for most conditions (p = 0.09 to 1). Conclusions: We found no evidence that newer-generation medications in neonatal care are consistently more effective than older-generation medications.
DOI: 10.35092/yhjc.10250534.v1
title: H1N1 pdm PA::GFP intracellular movement in Nocodazole (16 µm) treated A549 cells during infection

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 cells infected with H1N1 pdm PA::GFP and treated with nocodazole (16 µm). Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. These data correspond to Supplementary Movie 7 and analysis of these movies provided data presented in Figure 4 and Supplementary Figure 8.<br>Supplementary Movie 7: A549 cells infected with H1N1 pandemic influenza expressing GFP-tagged PA protein and treated with nocodazole (16 µm). <br>Figure 4: Effect of cytoskeleton depolymerization on motion dynamics of influenza vRNP in A549 cells. <br>Supplementary Figure 8: Impact of cytoskeletal depolymerizing drugs on the transport of PA::GFP.
DOI: 10.6084/m9.figshare.12325904.v1
title: Supplementary Material for: Concomitant Use of Gabapentinoids with Opioids Is Associated with Increased Mortality and Morbidity among Dialysis Patients

description: <b><i>Background:</i></b> The opioid epidemic is a public health emergency and appropriate medication prescription for pain remains challenging. Physicians have increasingly prescribed gabapentinoids for pain despite limited evidence supporting their use. We determined the prevalence of concomitant gabapentinoid and opioid prescriptions and evaluated their associations with outcomes among dialysis patients. <b><i>Methods:</i></b> We used the United States Renal Data System to identify patients treated with dialysis with Part A, B, and D coverage for all of 2010. Patients were grouped into 4 categories of drugs exposure status in 2010: (1) no prescriptions of either an opioid or gabapentinoid, (2) ≥1 prescription of an opioid and no prescriptions of gabapentinoids, (3) no prescriptions of an opioid and ≥1 prescription of gabapenbtinoids, (4) ≥1 prescription of both an opioid and gabapentinoid. Outcomes included 2-year all-cause death, dialysis discontinuation, and hospitalizations assessed in 2011 and 2012. <b><i>Results:</i></b> The study population included 153,758 dialysis patients. Concomitant prescription of an opioid and gabapentin (15%) was more common than concomitant prescription of an opioid and pregabalin (4%). In adjusted analyses, concomitant prescription of an opioid and gabapentin compared to no prescription of either was associated with increased risk of death (hazard ratio [HR] 1.16, 95% CI 1.12–1.19), dialysis discontinuation (HR 1.14, 95% CI 1.03–1.27), and hospitalization (HR 1.33, 95% CI 1.31–1.36). Concomitant prescription of an opioid and pregabalin compared to no prescription of either was associated with increased mortality (HR 1.22, 95% CI 1.16–1.28) and hospitalization (HR 1.37, 95% CI 1.33–1.41), but not dialysis discontinuation (HR 1.13, 95% CI 0.95–1.35). Prescription of opioids and gabepentinoids compared to only being prescribed opioids was associated with higher risk of hospitalizations, but not mortality, or dialysis discontinuation. <b><i>Conclusions:</i></b> Concomitant prescription of opioids and gabapentinoids among US dialysis patients is common, and both drugs have independent effects on outcomes. Future research should prospectively investigate the potential harms of such drugs and identify safer alternatives for treatment of pain in end-stage renal disease patients.
DOI: 10.6084/m9.figshare.19127285.v1
title: S2 File

description: MEG raw data obtained from two subjects speaking in turns with a sampling rate of 600 Hz. Anony_SiteA_(number).fif files contains the MEG of site A (the Hokkaido University Medical and Dental Research Building; customized, Elekta Neuromag; 101 ch.) and the voice signal of the subject at site A (EEG 03) and that of the subject at site B (EEG 04). The voice signals were used to identify voice onset of the subject at the opposite site. Anony_SiteB_(number).fif files contains the MEG of site B (Hokkaido University Hospital; VectorView, Elekta Neuromag, 306 ch.). The TTL signals (STI 014 of both files) can be used for time adjustment between the MEG of site A and site B. Other TTL signals are irrelevant for this analysis. Anony_Site(A/B)_e.fif files are the environmental magnetic fields without subjects to monitor noise levels. Note: The MEG device of site A was a customized one. Sensors with following number were used only for reference; [5,8,13,20,24,26,31,37,46,51,55,60,63,70,77,80,84,90,93,96,97,98,99,100,101]. The names of the subjects have been removed to anonymize the data.
DOI: 10.6084/m9.figshare.23549526.v1
title: Human and Mouse UTRomes

description: OverviewThis dataset contains BED and GTF files representing the cleavage sites and 3'UTR isoform annotations derived from reprocessing Microwell-seq data. These objects are part of the minimum dataset required for verifying the analysis reported in Fansler et al., bioRxiv, 2023.DescriptionThe <b>BED files</b> contain candidate cleavage sites from the Mouse Cell Atlas and Human Cell Landscape datasets. In brief, paired-end reads were merged with PEAR when overlapping, cell barcodes extracted with <code>umi_tools</code>, poly-A tails removed with <code>cutadapt</code>, and then remaining reads mapped to the <code>hg38</code> or <code>mm10</code> genomes using HISAT2. Reads were partitioned into cell types according to annotations from the original publications. Per cell type, the 5' end of alignments were summarized, counts were merged to the mode with 30 nts, and finally filtered to a minimum threshold of 5 TPM. The resulting BED files identify the cell type cluster in the <code>name</code> column and the number of observed reads in the <code>score</code> column.The <b>GTF files</b> are augmentations of GENCODE vM25 and v39, using novel cleavage sites, and then truncated to 500 nt. In brief, the sites provided in the BED files were harmonized across cell types by merging to the mode within 30 nts. The candidate sites were then serially classified as (1) "validated" if already in GENCODE (2) "supported" if found in PolyASite2.0 at 3 TPM or higher (3) "likely" if <code>cleanUpdTSeq</code> scored the posterior probability of being an internal priming site below 0.0001% (4) "unlikely", otherwise. The "supported" and "likely" candidates were then used to augment GENCODE annotations of protein coding transcripts, and each transcript was truncated to the 500 nts at the 3' end. The final annotations identify the regions where the scUTRquant pipeline will quantify scRNA-seq data.Data GenerationAll code required to generate these files is available at:https://github.com/Mayrlab/mca-utrome (https://doi.org/10.5281/zenodo.8118416)https://github.com/Mayrlab/hcl-utrome (https://doi.org/10.5281/zenodo.8118411)
DOI: 10.6084/m9.figshare.22713770.v1
title: Clear cell carcinoma of the ovary and venous thromboembolism: a systematic review and meta-analysis

description: As the second most common subtype of Epithelial ovarian cancers (EOCs), ovarian clear cell carcinoma (OCCC) is associated with a high rate of cancer-associated thrombosis. Previous studies revealed the wide range prevalence (6–42%) of venous thromboembolism (VTE) among OCCC patients. This study aimed to determine the prevalence of VTE among OCCC patients as well as factors affecting it. PubMed, Scopus, Embase, and Cochrane Library databases were searched up to December 12<sup>th</sup>, 2022. Studies reporting venous thromboembolic events in women with clear cell carcinoma of the ovary were included. Demographic data, clinical, and paraclinical features of the patients were independently extracted by two reviewers. Out of the 2254 records, 43 studies were processed for final review. The qualified studies involved 573 VTE cases among 2965 patients with OCCC. The pooled prevalence of VTE among OCCC patients was 21.32% (95%CI=(17.38–25.87)). Most VTE events were reported in Japanese women (26.15%), followed by Americans (24.41%) and UK (21.57%), and Chinese (13.61%) women. VTE was more common in patients with advanced stages (37.79%) compared to those with early stages of the disease (16.54%). Ovarian clear cell carcinoma is associated with a high rate of cancer-associated thrombosis. VTE events in OCCC patients were higher in advanced stages and Japanese women.
DOI: 10.6084/m9.figshare.24233629.v13
title: <b>Unlocking Optimal ORM Designs: Accelerated Tradeoff </b><b>Analysis with Transformers</b>

description: Optimizing object-relational database mapping (ORM) design is essential for software system performance. However, current ORM design tools widely used in practice offer limited support for evaluating performance implications. State-of-the-art relying on systematic tradeoff analysis provides greater assistance but becomes impractical for large-scale, real-world systems. In this paper, we introduce an innovative solution grounded in machine learning to efficiently and scalably identify optimal ORM database tradeoffs.Our approach involves training a transformer model using a dataset of formally analyzed object-relational database designs to identify Pareto-optimal design tradeoffs, significantly reducing the number of design candidates. The extensive experiments across various software database systems demonstrate the high effectiveness of the approach in identifying optimal design alternatives overlooked by leading ORM tools. Additionally, our results show a remarkable 98.21 % improvement in analysis efficiency compared to the current state-of-the-art, reducing tradeoff analysis time from over 15 days to around 18 minutes on average.<br><br>
DOI: 10.23645/epacomptox.7660976.v2
title: Archived Distributed Structure-Searchable Toxicity (DSSTox) Data

description: Chemical metadata from the CompTox Chemicals Dashboard are linked through the unique DSSTox chemical identifier (DTXCID) enabling integration to predicted mass spectral data. Chemical metadata includes CASRN, molecular formula, SMILES, presence in lists, and data source occurrences.Science Inventory, CCTE products: https://cfpub.epa.gov/si/si_public_search_results.cfm?advSearch=true&showCriteria=2&keyword=CCTE&TIMSType=&TIMSSubTypeID=&epaNumber=&ombCat=Any&dateBeginPublishedPresented=07/01/2017&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&DEID=&personName=&personID=&role=Any&journalName=&journalID=&publisherName=&publisherID=&sortBy=pubDate&count=25
DOI: 10.6084/m9.figshare.13235537.v1
title: Sartor_L.guttulus_x_L.geoffroyi.xlsx

description: Microsatellite data from 135 individuals of Leopardus guttulus, 140 individuals of L. geoffroyi and their hybrids. The samples were genotyped for 13 loci.
DOI: 10.6084/m9.figshare.28878782.v1
title: BD_RSL_RV-Fobia

description: Base de datos completa de la investigación Realidad Virtual para el tratamiento terapeutico de Fobias Frecuentes
DOI: 10.6084/m9.figshare.19407125.v2
title: Behavioral data

description: Behavioral data for Benoit et al. "Adolescent thalamic inhibition leads to long-lasting impairments in prefrontal cortex function" (NN-A76458A).<br>Rescue behavior shows ASST data with and without adolescent thalamic inhibition, and with and without acute thalamic activation.NMS dev and adult show acquisition of NMS task behavioral data for developmental and adult cohorts.ASST dev and adult show ASST data for developmental and adult cohorts.<br><br>
DOI: 10.15468/dl.kzupyj
title: Occurrence Download

description: A dataset containing 30816 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Megathyrsus maximus (Jacq.) B.K.Simon & S.W.L.Jacobs"
 ]
}

 The dataset includes 30816 records from 668 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009477-250426092105405/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.22581151.v5
title: Full-length transcriptome assembly annotation

description: The production of semen in boars involves multiple reproductive glands, including the testis (Tes), epididymis (Epi), vesicular gland (VG), prostate gland (PG), and bulbourethral gland (BG). However, previous studies on boar reproduction primarily focused on the testis, with little attention paid to the other glands. Here, we integrated single-molecule long-read sequencing with short-read sequencing to characterize the RNA landscape from five glands of Banna mini-pig inbred line (BMI) and Diannan small-ear pigs (DSE). We identified 110,996 full-length isoforms from 22,298 genes, and further classified the alternative splicing (AS) events in these five glands. Transcriptome-wide variation analysis indicated that the number of single nucleotide polymorphisms (SNPs) in five tissues of BMI was significantly lower than that in the non-inbred pig, DSE, revealing the effect of inbreeding on BMI. Additionally, we performed small-RNA sequencing and identified 299 novel miRNAs across all glands. Overall, our findings provide a comprehensive overview of the RNA landscape within these five glands, paving the path for future investigations on reproductive biology and the impact of inbreeding on pig transcriptome.
DOI: 10.6084/m9.figshare.23936217.v1
title: Concentrations of trace metals in sediments from Hangzhou Bay

description: Concentrations of trace metals in sediments from Hangzhou Bay.
DOI: 10.6084/m9.figshare.28489571.v1
title: Data and scripts supporting Elkouk et al. (2024) "towards understanding parametric controls on runoff sensitivity to climate in the community land model: A Case study over the Colorado River Headwaters"

description: Crucial to the assessment of future water security is how the land model component of Earth System Models partition precipitation into evapotranspiration and runoff, and the sensitivity of this partitioning to climate. This sensitivity is not explicitly constrained in land models nor the model parameters important for this sensitivity identified. Here, we seek to understand parametric controls on runoff sensitivity to precipitation and temperature in a state-of-the-science land model, the Community Land Model version 5 (CLM5). Process-parameter interactions underlying these two climate sensitivities are investigated using the sophisticated variance-based sensitivity analysis. This analysis focuses on three snow-dominated basins in the Colorado River headwaters region, a prominent exemplar where land models display a wide disparity in runoff sensitivities. Runoff sensitivities are dominated by indirect or interaction effects between a few parameters of subsurface, snow, and plant processes. A focus on only one kind of parameters would therefore limit the ability to constrain the others. Surface runoff exhibits strong sensitivity to parameters of snow and subsurface processes. Constraining snow simulations would require explicit representation of the spatial variability across large elevation gradients. Subsurface runoff and soil evaporation exhibit very similar sensitivities. Model calibration against the subsurface runoff flux would therefore constrain soil evaporation. The push toward a mechanistic treatment of processes in CLM5 have dampened the sensitivity of parameters compared to earlier model versions. A focus on the sensitive parameters and processes identified here can help characterize and reduce uncertainty in water resource sensitivity to climate change. (https://doi.org/10.1029/2024WR037718)
DOI: 10.6084/m9.figshare.26308075.v1
title: Data for "Persistent interactive effects of developmental salinity and temperature in Atlantic killifish (<i>Fundulus heteroclitus</i>)"

description: Climate change alters multiple abiotic environmental factors in aquatic environments but relatively little is known about their interacting impacts, particularly in developing organisms where these exposures have the potential to cause long-lasting effects. To explore these issues, we exposed developing killifish embryos (<i>Fundulus heteroclitus</i>) to 26°C or 20°C and 20ppt or 3ppt salinity in a fully-factorial design. After hatching, fish were transferred to common conditions of 20°C and 20ppt to assess the potential for persistent developmental plasticity. Warm temperature increased hatching success and decreased hatch time, whereas low salinity negatively affected hatching success, but this was only significant in fish developed at 20°C. Temperature, salinity, or their interaction affected mRNA levels of genes typically associated with thermal and hypoxia tolerance (<i>hif1a, hsp90b, hsp90a, hsc70, </i>and<i> hsp70.2</i>) across multiple developmental timepoints. These differences were persistent into the juvenile stage, where the fish that developed at 26°C had higher expression of <i>hif1a, hsp90b, hsp90a, </i>and <i>hsp70.2 </i>than fish developed at 20°C, and this was particularly evident for the group developed at both high temperature and salinity. There were also long-lasting effects of developmental treatments on body size after four months of rearing under common conditions. Fish developed at low salinity or temperature were larger than fish developed at high temperature or salinity, but there was no interaction between the two factors. These data highlight the complex nature of the developmental effects of interacting stressors which has important implications for predicting the resilience of fishes in the context of climate change.
DOI: 10.6084/m9.figshare.5525404.v1
title: MicroCT of mouse tibiae-oim2

description: MicroCT of mouse tibiae-oim2
DOI: 10.25442/hku.20349192.v1
title: Dataset and supplementary movies for geophysical mass flows against a flexible ring net barrier

description: The supplementary movies S1, S2, and S3 (presented in Figures 1 and 3) show typical debris flow, debris avalanche, and rock avalanche impacting a flexible ring net barrier with vint = 6 m/s, respectively. <br> These data are generated by desk computers in the lab and are about geophysical flows against a flexible ring net barrier. Tables 4, 5, 6, 7 and E1 provide original data for Figures 4, 5, 6, 7 and E1 in the paper, respectively. <br> The experimental data used for comparison in Figure 4b from the large-scale flume test V6-B1 with a flexible ring net barrier was published open access in the below article (Vicari <em>et al.,</em> 2021). <br> Vicari, H., Ng, C. W., Nordal, S., Thakur, V., De Silva, W. R. K., Liu, H., & Choi, C. E. (2021). The Effects of Upstream Flexible Barrier on the Debris Flow Entrainment and Impact Dynamics on a Terminal Barrier. Canadian Geotechnical Journal, 59(6), 1007-1019. https://doi.org/10.1139/cgj-2021-0119
DOI: 10.6084/m9.figshare.1136081_d80
title: Ex3R43C2 Arc-3 from Synaptic molecular imaging in spared and deprived columns of mouse barrel cortex with array tomography.

description: This data represents repeated immunohistochemical staining and stripping (elution) cycles of an array tomography tissue ribbon from mouse barrel cortex following chessboard deprivation. Included are images from consecutive 70 nm serial sections aligned to produce a high-resolution volumetric reconstruction of a given antibody stain.
DOI: 10.6084/m9.figshare.25366453.v1
title: HenanRainstorm

description: This is a text data downloaded from Sina Weibo related to flood disasters.