cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9704930.v1
title: Supplementary Material for: Possible Involvement of Nitric Oxide in the Antipruritic Effect of Metformin on Chloroquine-Induced Scratching in Mice

description: <b><i>Background:</i></b> Metformin ameliorates non-histamine-mediated itch. We have recently reported that the nitric oxide (NO) pathway is involved in chloroquine (CQ)-induced scratching behavior. Here we investigated the involvement of the NO pathway in the antipruritic effect of metformin on CQ-induced itch. <b><i>Methods:</i></b> Metformin (5–200 mg/kg, given intraperitoneally [i.p.]) was injected 4 h before CQ (400 µg/site, given intradermally [i.d.]) or compound 48/80 (100 µg/site, i.d.). A nonspecific nitric oxide synthase (NOS) inhibitor, NG-nitro-L-arginine methyl ester (L-NAME; 1 and 10 mg/kg, i.p.), or an NO precursor, L-arginine (10 and 100 mg/kg, i.p.) was administered 30 min before injection of CQ. A neural NOS (nNOS) inhibitor, 7-nitroindazole (7-NI; 1 and 10 nmol/site, i.d.) was concurrently administered with CQ. The scratching behavior was recorded for 30 min following the injection of CQ. We studied the changes in skin and spinal nitrite levels after treatments. <b><i>Results:</i></b> Our results showed that metformin (100 and 200 mg/kg) significantly reduced the CQ-induced scratching behavior but not the compound 48/80-induced scratching behavior. L-Arginine inhibited the antipruritic effect of metformin, while L-NAME and 7-NI significantly potentiated the inhibitory effects of a subeffective dose of metformin on the CQ-induced scratching behavior. The skin but not the spinal nitrite level was significantly increased after CQ administration. The elevated cutaneous nitrite level was reversed by effective doses of either metformin or 7-NI, but not by the subeffective doses of metformin + 7-NI. <b><i>Conclusion:</i></b> Acute injection of metformin significantly inhibits CQ-induced scratching behavior. This effect is mediated through inhibition of the NO pathway, especially by inhibiting the dermal nNOS enzyme.
DOI: 10.6084/m9.figshare.13567475.v1
title: EI and mental health problems among adolescents in Vietnam

description: Data set about mental health problems and emotional intelligence among adolescents in Vietnam
DOI: 10.6084/m9.figshare.14175611.v5
title: Data and codes for Visual and Semantic Co-Occurrence Analysis Based on the Improved Graph Convolutional Network for Urban Scene Classification

description: Data and codes for Visual and Semantic Co-Occurrence Analysis Based on the Improved Graph Convolutional Network for Urban Scene Classification
DOI: 10.6084/m9.figshare.14696763.v1
title: Occurrence records CHIKV 1996-2020

description: Occurrence records for chikungunya virus as described in Tjaden et al. 2021. Zip file containing 2 CSV files:<br>occurrence_records_chikungunya.csv contains the occurrence recordsoccurrence_records_chikungunya_sources.csv contains detailed source information<br>
DOI: 10.6084/m9.figshare.25055282.v1
title: Travel mode choice data for parents of pupils from CoMobility schools (COMOB-M)

description: Data on the features of available alternatives for transport mode choices derived from Open Trip Planner based on the information on travel diaries reported in wave 1 of Parental social surveys.
DOI: 10.6084/m9.figshare.25780953.v1
title: Subsistence yields for maize, soybean, wheat and rice used for analysis in the study "Geography and availability of natural habitat determine whether cropland intensification or expansion is more detrimental to biodiversity"

description: ISIMIP is an international network of climate-impact modellers who develop and provide datasets for cross-sectorally consistent climate impact modeling. This data is ISIMIP2a data from the EPIC-BOKU model & WFDEI.GPCC climate forcing (PM set, Penman-Monteith evapotranspiration calculation method), for the default setup and four crops (corn, soybean, rice and winter wheat) under subsistence management. The first string ("CRXXXYYY") of the first field is a unique gridcell identifier of a global half-degree grid. There might be more than 1 record per CR (could be averaged). The mapping between the 'CRXXXYYY' field and half-degree grid lat-lon coordinates is the following:lon = (as.numeric(XXX) - 1)*0.5 - 179.75lat = 89.75 + 0.5*(1 - as.numeric(YYY))YLDG: dry‐matter yield (t DM / ha, to be used as harvested crop yield for grain and tubers)<br>YLDF: raw dry‐matter yield (t DM / ha, to be used as harvested crop yield for cotton and sugar cane)BIOM: total biomass (t DM / ha)<br>YLN: N used by crop in biomass (kg/ha)<br>YLP: P used by crop in biomass (kg/ha)<br>FTN: N applied (kg/ha)<br>IRGA: irrigation volume applied (mm)<br>YLC: C in biomass
DOI: 10.6084/m9.figshare.5128714.v1
title: Supplementary Material for: Grade Increases in Gastroenteropancreatic Neuroendocrine Tumor Metastases Compared to the Primary Tumor

description: <b><i>Background/Aim:</i></b> The neuroendocrine tumor (NET) proliferation-based grading system (ENETS/WHO) for gastroenteropancreatic (GEP) tumors has proved reliable for prognostic stratification. To date, concerns exist regarding Ki-67 heterogeneity within the tumor and little is known on whether grade varies between primary and secondary sites. As tumor heterogeneity may have a significant impact on clinical management, our aim was to retrospectively evaluate Ki-67 on a series of GEP NETs in order to establish whether there is variability in different samples of the same lesion or between primary and metastatic disease (local/distant, synchronous/metachronous). <b><i>Methods:</i></b> Sixty patients with multiple samples of tumor were accrued from a total of 338 GEP NETs; 44 of them also had tissue from local/distant metastases and a further 5 had multiple metastatic foci from unknown primary tumors. Immunohistochemistry for Ki-67 was performed on all paraffin blocks from both primary and metastatic tumors. <b><i>Results:</i></b> Intratumor Ki-67 heterogeneity sufficient to change grade at first diagnosis was seen in 3/60 cases (5%). Out of 49 patients with primary NETs and/or multiple metastases, discrepancy in grade between sites was identified in 19 (39%) cases and in particular in 11/47 (23%) and in 10/12 (83%) patients with synchronous and metachronous metastases, respectively (p = 0.0002). Change in grade was more frequent in distant compared to locoregional metastases (p = 0.024) and in particular in distant sites other than the liver (p = 0.006). <b><i>Conclusions:</i></b> NETs show frequent differences in grade between primary sites and their synchronous/metachronous metastases; assessment of Ki-67 at all sites may prove to be significant for patient management.
DOI: 10.6084/m9.figshare.14822454.v1
title: Summary of gsea results

description: The file 'gsea_summary.txt' contains significantly enriched gene sets for U3065MG.<br>The file 'gsea_summary_30173071.txt' contains significantly enriched gene sets for U3017MG and U3071MG.<br><br>
DOI: 10.6084/m9.figshare.16695457.v2
title: Phodopus roborovskii assembly

description: De novo genome assembly of Phodopus roborovskii from ONT and Illumina data.
DOI: 10.6084/m9.figshare.22491340.v1
title: C. elegans embryogenesis

description: scRNA-seq time-series dataset of C. elegans embryogenesis assayed using 10x genomics v2 chemistry. Packer et al. (Science 2019) assigned cells to the known C. elegans lineage tree based on marker gene expression and assigned a time label to each cell by comparing it with a bulk reference time course. Following Forrow et al. (Nat. Comms 2021), this dataset represents a subset of the original data, containing all 46,151 cells with at least partial lineage information. This dataset contains raw counts. <br> Please cite the original publication: https://doi.org/10.1126/science.aax1971
DOI: 10.6084/m9.figshare.26405008.v2
title: <b><i>De novo </i></b><b>transcriptome assembly of </b><b><i>Acartia tonsa </i></b><b>adults</b><b><i> </i></b><b>using Nanopore long-read sequencing</b>

description: <i>Acartia tonsa </i>is a calanoid copepod with a cosmopolitan distribution. It generally reaches relatively high abundances and often becomes the dominant zooplankton species during summer, making it the most numerous taxon in several ecosystems. Its ecological relevance makes it a useful bioindicator organism for assessing the toxicity of various compounds. However, transcriptomic assemblies of <i>A. tonsa</i> using long-read technologies have not yet been described. The use of long-read sequencing technologies in transcriptomics allows the study of alternative splicing, structural variations and alternative polyadenylation sites. In this study, we present a <i>de novo </i>transcriptome of <i>A. tonsa </i>adult copepods exposed to different neonicotinoids obtained from Nanopore sequences. Our transcriptome exhibits higher completeness and longer sequences than the largest assemblies reported previously. We also provide a complete annotation by sequence homology (NR database), domain identification (InterProScan) and functional classification (Gene Ontology). Our transcriptome represents a solid baseline for further transcriptomic studies on this copepod and, specifically, its response to currently used pesticides.
DOI: 10.6084/m9.figshare.27236782.v2
title: On the Modeling and Prediction of High-Dimensional Functional Time Series

description: We propose a two-step procedure to model and predict high-dimensional functional time series, where the number of function-valued time series <i>p</i> is large in relation to the length of time series <i>n</i>. Our first step performs an eigenanalysis of a positive definite matrix, which leads to a one-to-one linear transformation for the original high-dimensional functional time series, and the transformed curve series can be segmented into several groups such that any two subseries from any two different groups are uncorrelated both contemporaneously and serially. Consequently in our second step those groups are handled separately without the information loss on the overall linear dynamic structure. The second step is devoted to establishing a finite-dimensional dynamical structure for all the transformed functional time series within each group. Furthermore the finite-dimensional structure is represented by that of a vector time series. Modeling and forecasting for the original high-dimensional functional time series are realized via those for the vector time series in all the groups. We investigate the theoretical properties of our proposed methods, and illustrate the finite-sample performance through both extensive simulation and two real datasets. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.3114655.v1
title: Job satisfaction

description: satisfaction
DOI: 10.17632/khm93dzhyz
title: Global Coral Reef Dataset

description: Global coral reef data from 2003-2016 used for Eason, T. and Garmestani, A. S.,  Assessing spatiotemporal change in  coral reef ecosystems. Under Review (IScience).

The data was culled from publicly accessible data gathered for a global bleaching study performed by Sully et al. 2019.  The full dataset is available at https://github.com/InstituteForGlobalEcology/Coral-bleaching-a-global-analysis-of-the-past-two-decades.

Reference:  Sully S, Burkepile DE, Donovan MK, Hodgson G, van Woesik R. A global analysis of coral bleaching over the past two decades. Nat Commun. 2019;10(1):1264
DOI: 10.6084/m9.figshare.12932794.v1
title: Supporting Data 4: Sanger sequencing files

description: Sanger sequencing datasets supporting the conclusions of Fig. S5.
DOI: 10.6084/m9.figshare.21671888.v1
title: Table

description: This is the original geochemical data.
DOI: 10.6084/m9.figshare.22794176.v1
title: Molinari, Gutiérrez, Lim. 2023. Systematics and biogeography of <em>Anoura </em>(Mammalia, Chiroptera)_Supplementary Information (data)

description: MS Excel spreadsheet containing the results of the data analyses.
DOI: 10.6084/m9.figshare.22959878.v1
title: PacBio Full-length 16S Sequencing data

description: This is the data from our study "<b>Associations Between Gut Microbiota Characteristics and Non-Motor Symptoms Following Pharmacological and Surgical Treatments in Parkinson's Disease Patients</b>".<br>DNA was amplified using dual-unique barcoded primers targeting 16S-ITS-23S, the so-called StrainID kit from Shoreline Biome using StrainID Set A, 96 Barcodes (Shoreline Biome, Shoreline Wave StrainID set A Kit, WAVESID-A). Briefly, this approach involves a single-step PCR, made up of primers that contain the barcode and target-specific primers, and generates amplicons ready for PacBioSMRTbell template prep and subsequent sequencing on the PacBio Sequel Systems. The whole protocol, from input DNA to amplicon purification and pooling, followed the Shoreline Wave for PacBio Technical Manual. The pooled amplicons (83-96 amplicons including controls) were quantified using fluorometry as described above, and their length was verified using an Advanced Analytical Fragment Analyzer System with the Fragment Analyzer NGS Fragment Kit (Agilent, DNF-473-1000). As well as the input DNA of interest, five controls were included: a no template control, ZymoBIOMICSMicrobial Community DNA Standard, ZymoBIOMICS Microbial Community DNA Standard II, ZymoBIOMICS Fecal Reference with TruMatrix™ Technology, and ZymoBIOMICS Gut Microbiome Standard (Zymo Research; D6305, D6311, D6323, and D6331, respectively).Thereafter, barcoded SMRTbell libraries were constructed using an Express TPK 2.0 (PacBio, 100-938-900) in conjunction with the Barcoded Overhang Adapter Kit 8A & 8B (PacBio, 101-628-400 & 101-628-500) and according to the Shoreline Protocol for High-Density Multiplexing on PacBio Sequel Systems. The quantity and size of each SMRTbell library were selected as detailed above using Qubit and a Fragment Analyzer. Two barcoded SMRTbell libraries were sequenced using the PacBio SMRT cell 8M. A PacBio Sequel II 2.1 binding kit (PacBio, 101-843-000) was used for polymerase binding, and a Sequel II 2.0 sequencing kit along with the Sequel II DNA Internal Control (PacBio 101-820-200), CCS sequencing mode and a 10h movie time for sequencing. After each run, reads were sorted into the original sample pools by demultiplexing theSMRTbell barcodes using PacBio SMRTLink v9.0 software. After SMRTbell demultiplexing and primer removal, the resulting pooled amplicon files were further demultiplexed into individual samples, and taxonomic identification was assigned to all reads using the Shoreline Biome SBanalyzer 3.1 (CentOS command line installation (https://shorelinebiome.com/resources) and Athena Microbial Reference Database (v2.2) by running the pipeline StrainID_OR_NanoID_Kit.txt with default settings. The Interfaculty Bioinformatics Unit at the University of Bern performed this step.
DOI: 10.17632/chk93csgsp
title: Collateral Competition: Evidence from Central Counterparties

description: Code and pseudo-data for our paper, "Collateral Competition: Evidence from Central Counterparties." The actual administrative micro-data used in the paper cannot be shared.

We analyze competition and risk management at central counterparties (CCPs) using a granular transaction-level dataset, and find that CCPs decrease collateral in response to lower collateral at their competitors, an effect that becomes stronger as the correlation between positions increases. To interpret our findings, we derive a model in which collateral is driven by risk and CCP competition. Our results are consistent with the model and suggest that a single monopolistic CCP would require more collateral. We also show that amid the substantial increase in collateral during the Covid-19 pandemic, the probability of a margin breach did not significantly change.
DOI: 10.17632/tbrngpxjfw
title: Spatio-temporal Dynamics of Urban Sprawl in a Rapidly Urbanizing City: Analysis Using Machine Learning Classification

description: Supplimentaary data
DOI: 10.6084/m9.figshare.14256434.v1
title: PACMEDY Coral&Bivalve database_v1

description: Synthesis of Coral and Bivalve geochemical records of the Holocene and late glacial period. <br>Includes d18O, d13C, Sr/Ca, U/Ca, Mg/Ca, Ba/Ca, B/Ca data.Made available in csv, matlab and R formats. <br>See the Methods & Structure file for details<br><br>
DOI: 10.6084/m9.figshare.20192180.v1
title: Supplementary Material for: Formin like 2 is a potential biomarker of poor prognosis in nasopharyngeal carcinoma

description: Introduction: Nasopharyngeal carcinoma (NPC) is the most common malignant tumor in southern China and Southeast Asia. Although substantial research on NPC has been conducted, the resulting improvement in clinical outcomes remains very disappointing. NPC treatment typically involves radiation therapy and chemotherapy, but the high incidence of metastasis and recurrence in NPC patients result in poor survival. Therefore, identifying potential biomarkers and discovering therapeutic targets are necessary to design tailored treatments based on the genetic profiles of NPC patients. Methods: Correlations of protein immunostaining with clinicopathological features were analyzed by Pearson’s chi-square test. The Kaplan–Meier method with a log-rank test was used to generate survival curves. Multivariate analysis was performed using the Cox proportional hazards model. Results: In this study, we comparatively analyzed cytoskeletal organization and biogenesis (GO:0007010) and tumorigenesis in the NPC transcriptome (GSE12452) and found that formin like 2 (FMNL2) expression was significantly upregulated in NPC tumor tissues. Moreover, high FMNL2 expression was significantly correlated with primary tumor stage (p value=0.001), lymph node status (p value=0.004), cancer stage (p value=0.006), and histological grade (p value=0.040). More importantly, high FMNL2 expression was significantly correlated with poor survival in NPC patients according to univariate analysis and multivariate analysis. Conclusion: This study reveals that FMNL2 may be an important potential biomarker for evaluating the prognosis of NPC patients.
DOI: 10.6084/m9.figshare.21405225.v1
title: iPSC_PeakTMM_matrix

description: The file contains the TMM counts for all narrow peaks in iPSCs.
DOI: 10.6084/m9.figshare.21679035.v3
title: EEG datasets of stroke patients

description: This data set consists of electroencephalography (EEG) data from 50 (Subject1 – Subject50) participants with acute ischemic stroke aged between 30 and 77 years. The participants included 39 male and 11 female. The time after stroke ranged from 1 days to 30 days. 22 participants had right hemisphere hemiplegia and 28 participants had left hemisphere hemiplegia. All participants were originally right-handed. Each of the participants sat in front of a computer screen with an arm resting on a pillow on their lap or on a table and they carried out the instructions given on the computer screen. At the trial start, a picture with text description which was circulated with left right hand, were presented for 2s. We asked the participants to focus their mind on the hand motor imagery which was instructed, at the same time, the video of ipsilateral hand movement is displayed on the computer screen and lasts for 4s. Next, take a 2s break.
DOI: 10.6084/m9.figshare.23605977.v1
title: Use of smartphone in Medical Students

description: This is a systematic review
DOI: 10.6084/m9.figshare.23787303.v1
title: A megaraptorid (Dinosauria: Theropoda) frontal from the upper Strzelecki Group (Lower Cretaceous) of Victoria, Australia Supplementary Information

description: The data contained within is supplementary information relating to the article entitled "A megaraptorid (Dinosauria: Theropoda) frontal from the upper Strzelecki Group (Lower Cretaceous) of Victoria, Australia
DOI: 10.6084/m9.figshare.27366351.v1
title: Source Data for paper "Extremely depleted radiocarbon impact on estimation of Glacial North Pacific Intermediate Water ventilation"

description: Stable oxygen and carbon isotope data of benthic foraminifera from core LV55-36-1 for paper "Extremely depleted radiocarbon impact on estimation of Glacial North Pacific Intermediate Water ventilation"<br>
DOI: 10.6084/m9.figshare.28755017.v3
title: U-Net GIS Data

description: The GIS database used in this project serves as a centralized repository for all spatial datasets required for wildfire threat analysis and model training. It includes CAL FIRE’s Wildland Fire Threat layer, which provides pixel-based classifications of wildfire potential across California, as well as transportation infrastructure layers, including primary and secondary roads and railways.<br>To support impact analysis, 1,000-foot buffer zones were generated around each infrastructure feature to define zones of interest for wildfire segmentation. The database is structured for integration into both machine learning workflows and GIS environments, enabling seamless overlay, visualization, and spatial querying within platforms such as ArcGIS Pro or QGIS.
DOI: 10.6084/m9.figshare.3568413.v1
title: Appendix E. Extrapolation formulas for Hill numbers of q = 1 and q ≥ 2 based on abundance data.

description: Extrapolation formulas for Hill numbers of q = 1 and q ≥ 2 based on abundance data.
DOI: 10.6084/m9.figshare.4789045.v2
title: Medaka Fish Tracker and Fish 3D Polygon Models

description: Release.zip:<br>Medaka_Fish_Tracker_3.7 Executable files for windows.<br>Medaka_tracking_newGUI.zip:<br>Medaka_Fish_Tracker_3.7 Source Code (Visual Studio 2013).<br>killfish_models.zip:<br>Medaka_Fish_3D_Polygon_Models (3dsMax).<br>
DOI: 10.6084/m9.figshare.7576712.v1
title: Additional file 6: of Sirt6 regulates efficiency of mouse somatic reprogramming and maintenance of pluripotency

description: Table S2. Gene ontology analysis from downregulated gene sets in Sirt6-null iPS-like cells. (XLSX 41 kb)
DOI: 10.17632/6jkc53sb29
title: Circular RNAs trigger nonsense-mediated mRNA decay. Boo et al.

description: Circular RNAs (circRNAs) are covalently closed single-stranded RNAs produced predominantly through a back-splicing process. They play regulatory roles in various biological and physiological processes; however, the molecular mechanisms by which circRNAs operate remain unclear. Herein, we demonstrate that circRNAs facilitate rapid mRNA degradation through RNA-RNA interactions between circRNAs and the 3′-untranslated regions (3′UTRs) of mRNAs. This interaction positions the exon-junction complexes (EJCs), deposited onto circRNAs by back-splicing, near the 3′UTRs of the mRNAs, thereby leading to EJC-dependent nonsense-mediated mRNA decay (NMD), a process we describe as circRNA-induced NMD (circNMD). Our transcriptomic analysis reveals hundreds of potential circNMD candidates, and the biological importance of circNMD in cellular apoptosis is validated. We also demonstrate that exogenously expressed circRNAs designed to interact with the 3′UTRs of endogenous mRNAs significantly downregulate the mRNA levels. Collectively, our observations provide compelling molecular evidence for circNMD and its potential therapeutic application in selective mRNA downregulation.