cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10053143.v1
title: Covariates list for generating DTB100 of China

description: This is a list of environmental covariates for generating depth-to-bedrock map of China at a spatial resolution of 100 meters. covariates code, title, description, resolution, citation url and publication date are given in corresponding column. The 'RF', 'GBT', 'QRF' clunmns seperately represent whether the covariate is used by random forest model, gradient boosting tree model and quantitle regression forest model(1 stand for it is used, 0 is not).
DOI: 10.6084/m9.figshare.21968318.v1
title: Fewer pests and more ecosystem service arthropods in shady African cocoa farms: Insights from a data integration study

description: Datasets used for analyses. For detailed description, refer to readme file.
DOI: 10.6084/m9.figshare.24310153.v1
title: Melt flux and meltwater volume over polar ice sheets from satellite passive microwave observations

description: Greenland and Antarctic surface melt flux at an enhanced-resolution (3.125 km) from SSMI(S) during 1992-2022/23.<br>
DOI: 10.6084/m9.figshare.25942435.v2
title: Data.xls

description: The data of meta-analysis on photosynthetic and respiratory thermal acclimation.
DOI: 10.6084/m9.figshare.8235587.v2
title: Position Weight Matrices used for HbP2 sequence analysis in “Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity”

description: This file contains the position weight matrices used to analyze the sequence of the Hunchback P2 enhancer for transcription factor binding sites.<br>For SynHbP2, we used Position Weight Matrices to predict binding sites for other TFs to screen against the creation of those sites in our neutral backbone<br>
DOI: 10.17632/r4m88s8m8w
title: Alexandre and Santos 2020 Zm N uptake latitude and temperature

description: By combining latitudinal gradient analysis with laboratory responses to temperature manipulation, we showed that ocean warming will increase the nitrogen demand of the globally distributed seagrass Z. marina and this demand may be met by an increasing uptake of organic nitrogen forms, highlighting that Z. marina will be winner under global change conditions of increased temperature and CO2.
DOI: 10.6084/m9.figshare.10191890.v2
title: Uncertainties of a mixed-integer distribution system planning considering energy storage system degradation

description: This file covers data of PV output, WT output, load demand, LMP, regulation service signal and prices in the 33 bus distribution system under 4, 20, 40 and 100 scenarios. All these typical scenarios are generated via a Gaussian Mixture Model (GMM) method.
DOI: 10.6084/m9.figshare.12085623.v2
title: A comprehensive study on identifying the structural and functional SNPs of human neuronal membrane glycoprotein M6A (GPM6A)

description: Glycoprotein M6A, a stress related gene, plays an important role in synapse and filopodia formation. Filopodia formation is vital for development, immunity, angiogenesis, wound healing and metastasis. In this study, structural and functional analysis of high-risk SNPs associated with Glycoprotein M6-A were evaluated using six different bioinformatics tools. Results classified T210I, T134I, Y153H, I215T, F156L, T160I, I226T, R247W, R178C, W159R, N157S and P151L as deleterious mutants that are crucial for the structure and function of the protein causing malfunction of M6-a and ultimately leads to disease development. The three-dimensional structure of wild-type M6-a and mutant M6-a were also predicted. Furthermore, the effects of high risk substitutions were also analyzed with interaction with valproic acid. Based on structural models obtained, the binding pocket of ligand bound glycoprotein M6-A structure showed few core interacting residues which are different in the mutant models. Among all substitutions, F156L showed complete loss of binding pocket when interacting with valproic acid as compared to the wild type model. Up to the best of our knowledge this is the first comprehensive study where GPM6A mutations were analyzed. The mechanism of action of GPM6A is still not fully defined which limits the understanding of functional details encoding M6-A. Our results may help enlighten some molecular aspects underlying glycoprotein M6-A. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12639542.v1
title: Supplementary Material for: Dietary Restriction Suppresses Steatosis-Associated Hepatic Tumorigenesis in Hepatitis C Virus Core Gene Transgenic Mice

description: <b><i>Background and Aims:</i></b> Dietary restriction (DR) is a preventive strategy for obesity, metabolic syndrome, cardiovascular disease, and diabetes. Although an interconnection between obesity, metabolic syndrome, fatty liver, and hepatocellular carcinoma has been documented, the mechanism and impact of DR on steatosis-derived hepatocarcinogenesis are not fully understood. This study aimed to evaluate whether DR can prevent hepatic tumorigenesis. <b><i>Methods:</i></b> Male hepatitis C virus core gene transgenic (HCVcpTg) mice that develop spontaneous age-dependent insulin resistance, hepatic steatosis, and ensuing liver tumor development without apparent hepatic fibrosis, were fed with either a control diet ad libitum (control group) or 70% of the same control diet (DR group) for 15 months, and liver phenotypes were investigated. <b><i>Results:</i></b> DR significantly reduced the number and volume of liver tumors. DR attenuated hepatic oxidative and endoplasmic reticulum stress and markedly suppressed nuclear factor-κB, signal transducer and activator of transcription 3 (STAT3) and STAT5, and phosphorylation of extracellular signal-regulated kinase, leading to downregulation of several pro-oncogenic mediators, such as cyclin D1. Serum insulin and insulin-like growth factor 1 levels, as well as hepatic expression of insulin receptor substrate 1/2, phosphatidylinositol-3 kinase, and serine/threonine-protein kinase AKT, were downregulated by DR. A transcriptome analysis revealed that STAT3 signaling and lipogenesis were the most suppressed hepatocarcinogenic pathways affected by DR. Additionally, DR stimulated autophagy and p62/sequestosome 1 degradation, enhanced phosphorylation of AMP-activated protein kinase α, increased fibroblast growth factor 21 expression, and attenuated expression of senescence-associated secretory phenotypes. <b><i>Conclusion:</i></b> DR suppressed steatosis-associated hepatic tumorigenesis in HCVcpTg mice, mainly due to attenuation of pathways involved in inflammation, cellular stress, cell proliferation, insulin signaling, and senescence. These findings support the notion that persistent 30% reduction of daily food intake is beneficial for preventing steatosis-associated hepatocarcinogenesis caused by HCV core protein.
DOI: 10.6084/m9.figshare.16609054.v3
title: Klebsiella genome-scale metabolic models isolated from Grey-headed flying foxes

description: This data is associated with the manuscript entitled: <i>Transmission of Klebsiella strains and plasmids within and between Grey-headed flying fox colonies</i><br>This 7zip file contains:1) Scripts used to construct figures and perform analysis2) Genbank files with annotations matching:3) Genome-scale metabolic models of corresponding genomes in .json format. 4) MEMOTE reports of model files
DOI: 10.6084/m9.figshare.24745482.v2
title: Raindrop Dataset

description: This Dataset contains raindrop data: hyd_diameter (mm), hyd_fall_speed (m s<sup>-1</sup>), hyd_axis_ratio_3d, hyd_azimuth_angle (deg), hyd_zenith_angle (deg), rain_rate (mm h<sup>-1</sup>) , hyd_U_speed (m s<sup>-1</sup>) and turbulence_dissipation_rate (m<sup>2</sup> s<sup>-3</sup>). <i>The data is in Python numpy ('.npy') format and can be read with the following Python code:</i><i>import numpy as np</i><i>hyd_diameter_read = np.load(path_data_save + '</i><i>hyd_diameter</i><i>.npy')</i><br>
DOI: 10.6084/m9.figshare.27014713.v1
title: Genome assembly and annotation of <i>Cyperus iria</i>

description: Genome assembly and annotation of <i>Cyperus iria</i>
DOI: 10.6084/m9.figshare.29117393.v1
title: <b>FROM-GLC Plus 3.0: Multi-modal Land Change Mapping with SAM and Dense Surface Observations</b>

description: Land cover mapping plays a critical role in monitoring land system changes. Despite advancements in remote sensing technologies, traditional satellite-based approaches are often constrained by cloud cover, coarse temporal resolution, and limitations in capturing fine-scale landscape dynamics, leading to gaps in continuous and real-time monitoring. Near surface cameras offer a solution by providing high-frequency, ground-level observations that bridge temporal gaps and enhance spatial detail. Therefore, this study makes significant contributions by pioneering the integration of near surface camera observations with satellite imagery, addressing key challenges in imaging perspective differences and limited coverage of ground-based observations for enhanced land cover monitoring at a 30-m/10-m scale. A key innovation lies in leveraging near surface cameras to reconstruct dense satellite data time series and capture daily land cover dynamics, addressing critical temporal gaps in traditional satellite-based approaches. The research further advances the field by implementing state-of-the-art deep learning techniques, particularly the Segment Anything Model (SAM), to achieve precise parcel-level delineation and reduce classification noise at a high-resolution (meter- and sub-meter level) scale. Furthermore, the framework's ability to synthesize multi-modal data sources (near surface cameras, Sentinel-1/2, and high-resolution imagery) represents a methodological breakthrough in space and surface sensor integration for real-time land cover change detection, enabling time-sensitive applications and early warning systems for land system changes.
DOI: 10.60893/figshare.sss.28183688.v1
title: 01993-08

description: Ag 3d 100 Pa
DOI: 10.17632/zryyk4dgxv
title: Cement Production Life Cycle Inventory Dataset for China

description: The dataset aims to address the data challenges faced in Life Cycle Assessment (LCA) of cement production in China. Cement production is a significant contributor to greenhouse gas emissions and is crucial for China's efforts to reduce emissions and achieve carbon neutrality. The dataset comprises 148 processes collected from peer-reviewed publications, following strict rules to ensure data traceability and transparency. It offers more accurate and reliable information for LCA studies on China's cement industry, facilitating informed decision-making for sustainable development and downstream supply chain management.
DOI: 10.6084/m9.figshare.27682515.v1
title: Trophic downgrading in China-protected areas struggle to preserve food web complexity.zip

description: We compiled a dataset on terrestrial wildlife of PAs in China from camera trap studies.
DOI: 10.17632/ffyh87pkpc
title: Test dataset for BBQ methods

description: The provided dataset contains images of fixed infected RAW264.7 cells infected with Mycobacterium tuberculosis and imaged by fluorescence confocal microscopy. These images are provided to test the proposed Bacterial Burden Quantification (BBQ) workflows that can be found on GitHub here : https://github.com/jaugenst/BBQ
DOI: 10.6084/m9.figshare.21334896.v2
title: Data from: A survey of researchers' methods sharing practices and priorities

description: Research data associated with the preprint "A survey of researchers' methods sharing practices and priorities." This dataset has three files: A pdf of the survey instrument, as presented to respondents An Excel spreadsheet containing completed responses to the survey's fixed response questions. Country-level data were replaced by region-level data. An Excel spreadsheet containing completed responses to the survey's open response questions. Open response data have been delinked from demographic data.
DOI: 10.6084/m9.figshare.24218766.v1
title: Knee-bend test score

description: Comparing CFA (complete freund adjuvant) and MIA (monosodium iodoacetate) to induce different kinds of arthritis
DOI: 10.6084/m9.figshare.11709657.v1
title: 10-L2146-Triketide-18p

description: triketide docked in L2146A mutant ER model
DOI: 10.6084/m9.figshare.21444870.v1
title: Soil type

description: Soil type in China with 1-km resolution was obtained from the Resource and Environment Science and Data Center (RESDC) (https://www.resdc.cn/data.aspx?DATAID=145), which is a Chinese website, and we re-uploaded it here.
DOI: 10.6084/m9.figshare.25483339.v2
title: Source data and custom script for Miao <i>et al. </i><i>Nature Neuroscience, </i>2024

description: <b>This is the data deposit for Miao et al., </b><b><i>Nature Neuroscience</i></b><b>, 2024. Files include statistical source data for all the main figures and extended figures. This also includes a custom MATLAB script that quantifies sleep in the model animal. Details of the data and the script can be found in the publication.</b>
DOI: 10.6084/m9.figshare.20380185.v1
title: Supplementary data for O'Grady et al. TBC

description: Supplementary Data File for Publication (details TBC)
DOI: 10.6084/m9.figshare.25479805.v2
title: Supplemental data - Understanding changes in echocardiographic parameters at different ages following fetal growth restriction: a systematic review and meta-analysis

description: Our meta-analysis revealed echocardiographic differences between fetal growth restricted and control offspring in humans during the neonatal period: a reduced left ventricular mass and interventricular septum thickness, reduced mitral annular peak velocity and mitral lateral early diastolic velocity. We were unable to pool echocardiographic parameters in animal studies and human adults due to an insufficient number of studies per individual outcome. The few studies on myocardial strain analysis showed small preclinical changes in FGR offspring.
DOI: 10.6084/m9.figshare.7627145.v1
title: splitGAL4_pIP10

description: confocal stack images of pIP10 splitGAL4
DOI: 10.6084/m9.figshare.11346875.v1
title: arabidopsis_2029_Maf001_filter95

description: arabidopsis_2029_Maf001_filter95 <br>
DOI: 10.6084/m9.figshare.13060556.v1
title: Supplementary Material for: High Expression of MMP-9 in Primary Tumors and High Preoperative MPO in Serum Predict Improved Prognosis in Colorectal Cancer with Operable Liver Metastases

description: <b><i>Introduction:</i></b> The liver metastases of colorectal cancer (CRC) can be surgically treated in selected cases, with continuously improving results. Matrix metalloproteinases (MMPs) contribute to cancer invasion by degrading the extracellular matrix, and elevated levels of MMP-2, MMP-8, and MMP-9 have been detected in several malignancies. Myeloperoxidase (MPO) is a mediator of tissue damage that can oxidatively activate latent MMPs. We evaluated the prognostic value of MMP-2, MMP-8, and MMP-9 in tissue samples of primary tumors and liver metastases and the pre- and postoperative serum levels of MMP-8, MMP-9, and MPO in CRC patients undergoing liver resection. <b><i>Methods:</i></b> Tissue and serum samples were obtained from 111 patients who had primary colorectal tumors and their liver metastases surgically treated at the Helsinki University Hospital between 1988 and 2007. Tissue expression of MMP-2, MMP-8, and MMP-9 in primary tumors and liver metastases was evaluated by immunohistochemistry. Pre- and postoperative serum concentrations of MMP-8, MMP-9, and MPO were determined using a time-resolved immunofluorometric assay or commercially available enzyme-linked immunosorbent assay kits. Clinical data were retrieved from patient records and the Central Statistical Office of Finland. Associations with disease-free survival (DFS) and overall survival (OS) were estimated using Cox regression analysis and the Kaplan-Meier method. <b><i>Results:</i></b> High expression of MMP-9 in colorectal tumor tissue was associated with better DFS (<i>p</i> = 0.010), and high preoperative MPO in serum with improved DFS and OS (<i>p</i> &lt; 0.001 and <i>p</i> = 0.014, respectively). The prognostic significance varied according to gender, age, and the synchronicity of liver metastases. <b><i>Conclusion:</i></b> Low preoperative MPO in serum might identify patients at high risk of recurrence and death after resection of colorectal liver metastases. Elevated preoperative MPO and high expression of MMP-9 in colorectal tumor tissue indicate an improved prognosis. The use of these biomarkers should be adjusted according to clinical characteristics.
DOI: 10.6084/m9.figshare.14925222.v1
title: Can Program Analysis Tools Find More Code Review Defects?

description: Program analysis tools find defects in code, checking code against rules to reveal potential defects. Many studies have evaluated these tools by measuring their ability to detect known defects in code. But these studies measure the current state of tools rather than their future potential to find more defects. To investigate the prospects for tools to find more defects, we conducted a study where we examined the potential to create rules, which might be checked by tools, which would prevent defects found in code review. We first gathered a corpus of 1323 defects found through code review. Through a qualitative analysis process, for each defect we identified a violated rule and the type of program analysis tool (PAT) which might check this rule.We found that PATs might, in principle, be used to detect as many as 76% of code review defects, considerably more than current tools have been demonstrated to successfully detect. Among a variety of types of program analysis tools, Style Checkers and AST Pattern Checkers had the broadest coverage of defects, each with the potential to detect 25% of all code review defects. To detectable defects, existing tools require features like supporting custom and more complex rules. Defects not detectable by PATs require human judgement and are violations of rules lacking formalism.
DOI: 10.6084/m9.figshare.20439894.v1
title: Supplemental excel file

description: FPKM dataset
DOI: 10.6084/m9.figshare.21802096.v1
title: Nitrogen increases soil organic carbon accrual and alters its functionality

description: Nitrogen (N) availability has been considered as a critical factor for the cycling and storage of soil organic carbon (SOC), but effects of N enrichment on the SOC pool appear highly variable. Given the complex nature of the SOC pool, recent frameworks suggest that separating this pool into different functional components, e.g. particulate organic carbon (POC) and mineral‐associated organic carbon (MAOC), is of great importance for understanding and predicting SOC dynamics. Importantly, little is known about how these N-induced changes in SOC components (e.g. changes in the ratios among these fractions) would affect the functionality of the SOC pool, given the differences in nutrient density, resistance to disturbance and turnover time between POC and MAOC pool. Here, we conducted a global meta-analysis of 803 paired observations from 98 published studies to assess the effect of N addition on theses SOC components, and the ratios among these fractions. We found that N addition, on average, significantly increased POC and MAOC pools by 16.4% and 3.7%, respectively. In contrast, both the ratios of MAOC to SOC and MAOC to POC were remarkably decreased by N enrichment (4.1 % and 10.1 %, respectively). Increases in the POC pool were positively correlated with changes in aboveground plant biomass and with hydrolytic enzymes. However, the positive responses of MAOC to N enrichment were correlated with increases in microbial biomass. Our results suggest that although reactive N deposition could facilitate soil C sequestration to some extent, it might decrease the nutrient density, turnover time, and resistance to disturbance of the SOC pool. Our study provides mechanistic insights into the effects of N enrichment on the SOC pool and its functionality at global scale, which is pivotal for understanding soil C dynamics especially in future scenarios with more frequent and severe perturbations.
DOI: 10.6084/m9.figshare.25037645.v6
title: Occurrence Records of Tropical Asian Butterflies: 1970 - 2024

description: Occurrence records of tropical Asia's butterflies collated from online databases and published literature. This dataset consists of 730,190 occurrence records for 3,752 species.Methods:We collected occurrence records for tropical Asian Papilionoidea (Lepidoptera: Nymphalidae, Papilionidae, Lycaenidae, Pieridae, Hesperiidae, Riodinidae)(-11.426 – 35.64 N, 67.588 – 174.990 E) for the years 1970-present. Records were extracted from the Global Biodiversity Information Facility on 15 April 2024. We included only presence records derived from human observation, preserved specimens, material samples, or literature, provided they had associated coordinates. We omitted all records with &gt;100,000 m coordinate uncertainty, so-called “fuzzy” taxon matches, and records for which the scientific name was missing or incomplete, unless nomenclature could be extracted using a BOLD identifier (boldsystems.org/). This resulted in a final number of GBIF records = 651,285.We also extracted data from the B2D2 Database of Butterflies for Borneo provided by JKH/the Darwin Initiative (n = 19,417) and a dataset for Bangladesh provided by SC (Chowdhury et al. 2021) (n = 18,278), and unpublished datasets from coauthors AN, DJL, LVV, TK, and YB (n = 13,993). To fill geographic gaps when all of these records were plotted, we conducted targeted searches of the published literature on Google Scholar (details below), resulting in an additional 27,217 records. Pre-1970 data were omitted where possible from all sources. Final binomial synonym harmonization, validation, and authority assignment were conducted by DJL using a taxonomic reference prepared by Gerardo Lamas (Lamas, 2015. Catalogue of the butterflies (Papilionidae). Available from the author.).For geographic regions with relatively few GBIF records (e.g., China, Myanmar, Thailand) and for species with &lt; 10 records, we conducted targeted literature searches using Google Scholar in English, simplified Chinese, and traditional Chinese (genus OR genus + species + country name). For all species records in published sources, we extracted coordinates, locality name, locality type (e.g., exact coordinates, city, national park, island, or province), country, and year of record (where available). If exact coordinates were not provided by the source, we used Google Earth Pro (v7.3.6.9345) to estimate the locality centroid for any record provided at the province level or below (e.g., national park or city). For records from islands ≤ 100 km in length or diameter (e.g, localities within the Philippines and Indonesia), we estimated the island or archipelago centroid. If a range of coordinates was provided (e.g., records from The Butterflies of Vietnam), coordinates within the range were chosen haphazardly by selecting a point within the range provided on Google Earth Pro. Data sources for all records are provided in the reference column (C) in Occurrence Records of Tropical Asian Butterflies: 1970-2024 and alphabetically in Data Sources for: Occurrence Records of Tropical Asian Butterflies: 1970-2024.