cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23605833.v1
title: Assessing and mitigating batch effects in large-scale multiomics studies

description: <strong>Quartet RNA reference materials and multi-batch RNA-seq dataset</strong> The Quartet RNA reference materials were derived from the Epstein-Barr Virus (EBV) immortalized B-lymphoblastoid cell lines from four members of a Chinese family quartet including monozygotic twin daughters (D5 and D6), father (F7), and mother (M8). RNA-seq datasets from the Quartet RNA reference materials were then collected, consisting of 252 RNA-seq libraries from 21 batches generated in eight labs using two library construction protocols (PolyA selection and RiboZero) and two sequencing platforms (Illumina NovaSeq (ILM) and MGI DNBSEQ-T7 (BGI)). Here, a batch is defined as 12 libraries from a standard sample set, consisting of 12 vials with each representing one of the triplicates of the Quartet RNA reference sample groups, whose library construction and sequencing experiments were conducted simultaneously. To facilitate the adoption of reference materials, reference datasets, and quality metrics from the Quartet Project, we developed a Quartet Data Portal (http://chinese-quartet.org/) for access to the Quartet resources and enhancing quality consciousness of the community. Researchers can request the reference materials, datasets, and reference datasets from the data portal. <br> <strong>Dataset used in this study</strong> A subset of datasets from Quartet RNA reference materials for illustrating visualization tools in terms of diagnostics of batch effects. This example dataset includes 27 libraries from three RNA-seq batches. Different numbers of replicates (n=5~9) of reference materials are included in each batch to mimic a confounded scenario that replicates of reference materials are not equally distributed across batches. <br> <strong>Data analysis</strong> Expression matrix in log2-transformed Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were used as expression profiles before batch correction. Expression profiles based on detected genes were used for further analysis. A gene was considered detectable (expressed) in a biological group within a batch if ≥ 3 reads were mapped onto it in at least two of the three replicates. Ratio-based scaling was conducted for batch correction. Specifically, ratio-based scaling were calculated based on log2FPKM values. For each gene, the mean of expression profiles of replicates of reference sample(s) (e.g. D6) was first calculated, and then subtracted from the log2FPKM values of that gene in each study.
DOI: 10.6084/m9.figshare.23623104.v1
title: Supplementary Material for: Preservation of vision after early recognition of anterior ischemic optic neuropathy in a patient with sepsis

description: Non-arteritic ischemic optic neuropathy (NAION) can rarely occur in the setting of sudden vascular compromise, especially in patients with a “disk-at-risk” appearance. Anemia and hypotension are believed to be the main precipitators of shock induced NAION. Early recognition of this phenomena can prevent further visual loss and result in partial visual recovery. We here present a 56-year-old patient who developed NAION characterized by optic disc edema in both eyes and visual loss in the left eye secondary to hypotension in the setting of septic shock. He received aggressive blood pressure management which resulted in stabilization of vision in the right eye and likely prevented further visual loss in the left eye.
DOI: 10.6084/m9.figshare.7117178.v1
title: DataRepository.sav

description: Handwriting data of patients with psychosis, bipolar disorder and healthy controls.
DOI: 10.17632/jp3v9859cx
title: Survey data on livelihoods and inputs and outputs of crop production activities in Quzhou county on the North China Plain

description: Crop production faces a dilemma regarding sustainability in the North China Plain. On the one hand, productivity and profitability should be at least maintained to secure national food self-sufficiency. On the other hand, there is a need to mitigate the negative externalities of agriculture, such as groundwater depletion, eutrophication of surface water, greenhouse gas emissions due to high fertilizer use, and pesticide contamination of soil and water. The objective of collecting this data is to provide an overview of crop production activities and livelihoods on the North China Plain and to generate data-based evidence that can help design cropping systems and optimize management practices. The database provides quantitative data on the village, farm household, and crop scale in Quzhou county, which lies in the middle part of North China Plain, one of the Agricultural Green Development focus areas—the village data file source from the yearbook of 2017 and village cadres survey of 2018. The village dataset includes village structure, crop pattern within a village, and crop production-related resources of all the villages in Quzhou county. Those data are used to do the village typology analysis to allow us to target the effort of household survey across the main agricultural village types in Quzhou to ensure the representativeness of the sample and avoid important village types being underrepresented or time being spent on survey in villages with no or marginal agricultural activity. The result of village typology is also included in the village dataset. The data of the farm household dataset and crop dataset is from the household survey in 2020, which covers 525 questionnaires across 35 villages belonging to seven village types (five for each type). The farm household dataset provides farm-level data, including demographic data of farming decision-makers and their household members, land use and machinery resources, crop production management practices, and government subsidies. The crop dataset provides input-output inventories for each crop grown during one year on each field greater than 1/30th ha within a year.
DOI: 10.17632/pghzmkknm6
title: RAW DATA SPSS AND QUESTIONNAIRE (MALAY AND ENGLISH VERSION)

description: Data about the socioeconomic demographic of 200 families living in high-risk drug environments located in East Coast states of Peninsular Malaysia – survey questionnaire through face-to-face interviews in April 2021
DOI: 10.6084/m9.figshare.27192711.v1
title: Score based ratio of gene expression between control condition and various stress conditions (SR score) in RNA-Seq dataset

description: This is csv file including score based on the ratio of gene expression between control condition and various stress conditions (SR score) in RNA-Seq dataset.
DOI: 10.6084/m9.figshare.5129584.v1
title: Supplementary Material for: Isobolographic Analysis of Interaction for Three-Drug Combination of Carbamazepine, Phenobarbital and Topiramate in the Mouse Maximal Electroshock-Induced Seizure Model

description: <b><i>Background/Aims:</i></b> To characterize the anticonvulsant effects of a combination of 3 antiepileptic drugs (AEDs; i.e. carbamazepine (CBZ), phenobarbital (PB) and topiramate (TPM)) at the fixed-ratio of 1:1:1 in the mouse maximal electroshock (MES)-induced seizure model. <b><i>Methods:</i></b> Tonic hind limb extension (seizure activity) was evoked in adult male albino Swiss mice by a current (sine-wave, 25 mA, 500 V, 50 Hz, 0.2 s stimulus duration) delivered via auricular electrodes. Type I isobolographic analysis for parallel dose-response relationship curves (DRRCs) was used to analyze the 3-drug combination. <b><i>Results:</i></b> In the mouse MES model, all the studied AEDs (i.e. CBZ, PB and TPM) administered singly had their DRRCs parallel to each other. With type I isobolography for parallel DRRCs, a combination of CBZ, PB and TPM at the fixed-ratio of 1:1:1 exerted supra-additive (synergistic) interaction in the mouse MES model. <b><i>Conclusions:</i></b> Synergistic interaction among CBZ, PB and TPM at the fixed-ratio of 1:1:1 against MES-induced seizures is worthy of consideration in further clinical settings. All detailed calculations required to perform type I isobolographic analysis for the 3-drug combination were presented.
DOI: 10.17632/58mfpfxksk
title: FOOD PRODUCTS INGREDIENT DATASET

description: Ingredients are the building blocks of packaged food product that enables a product to have texture, flavor, and nutritional information as well. The companies dealing with these products add some ingredients in the form of artificial flavor enhancers, color, and sweeteners to enhance the flavor and appearance of a product. Artificial additives may have health implications as the consumers are not very much aware of the products that are being used therefore it is a complex task for a common person to figure out manually that the product based on its ingredients is good for health. Complex tasks are very efficiently performed in the field of artificial intelligence and machine learning as they are trained for solving complex mathematical problems. With the availability of an appropriate dataset, machine learning can easily solve complex tasks using statistical techniques by model built on available dataset. To achieve the objective, the ingredients dataset has generated by extracting text from images containing ingredient lists of different ready-to-eat food products. In the dataset, several images of different lines of food products have been acquired to create a harmonized dataset. The dataset contains the list of ingredients named with 7 categories and corresponding attributes with appropriate labeling. The dataset will be very useful for training and testing machine learning models for food product classification through their ingredients.
DOI: 10.17632/86mxp9c9bf
title: A compact reformulation of the two-stage robust resource-constrained project scheduling problem: Complete results

description: Complete results corresponding to the research presented in the paper entitled 'A compact reformulation of the two-stage robust resource-constrained project scheduling problem', submitted to 'Computers and Operations Research' in April 2020 (Bold and Goerigk, 2020). The uncertain resource-constrained project scheduling problem (RCPSP) test instances on which these results are obtained are derived from deterministic instances in the PSPLIB (http://www.om-db.wi.tum.de/psplib/) involving 30 activities (j30). 3 robust counterparts corresponding to the delaying of (Gamma=) 3, 5 and 7 activities respectively have been generated for each of the 480 deterministic PSPLIB instances. Hence, a total of 1440 test instances have been generated. This data set contains four data files corresponding to the results of four variants of the model proposed in Bold and Goerigk (2020). These are a 'basic' model (basic_results_full.txt), and three extended models: including transitivity constraints (trans_results_full.txt), warm-start (warmstart_results_full.txt), transitivity constraints plus warm-start (warmstarttrans_results_full.txt). See Bold and Goerigk (2020) for details of these methods. Each data set reports for each instance the instance number (corresponding to the deterministic PSPLIB instance), the number of activities delayed (Gamma), the Gurobi solution status code, the best lower and upper-bound found by the solver, the gap between these two values, and the CPU run-time for that instance. Results show that the proposed model out-performs the current state-of-the-art algorithms for solving the two-stage robust resource-constrained project scheduling problem, being much quicker to solve, and reaching optimality for 50% more instances on the same benchmark set.
DOI: 10.6084/m9.figshare.24107604.v1
title: CARE CHECKLIST

description: CARE CHECKLIST for case report on Thanatophoric dysplasia.
DOI: 10.6084/m9.figshare.27084091.v3
title: Raw Data

description: The raw data, including the research data, is available as part of the dataset availability
DOI: 10.6084/m9.figshare.27135192.v1
title: Coupled oxygenation, manganese carbonate mineralization, and Mo cycling during the Neoproterozoic ocean

description: We studied iron speciation, molybdenum and nitrogen isotopes from black shales and associated manganese carbonates in the upper Ediacaran Doushantuo Formation, South China, to elucidate the coupled relationship between oceanic oxygenation, manganese mineralization, and molybdenum geochemical cycling.
DOI: 10.6084/m9.figshare.28761455.v1
title: Supplementary material <b>Phosphorus buffer capacity </b>article

description: <b>Article supplementary material: </b>Phosphorus buffer capacity of soils with medium clay and high organic matter content
DOI: 10.6084/m9.figshare.28768157.v2
title: An underlying mechanism of bovine mastitis: PGE<sub>2</sub> regulates <i>Staphylococcus aureus</i>-induced inflammatory response through TLR2, TLR4, and NLRP3 in macrophages

description: <i>Staphylococcus aureus</i> (<i>S. aureus</i>) evades the immune system by altering macrophage functions, including immune regulation and phagocytosis, leading to the development of bovine mastitis. Therefore, this study analyzed bovine mastitis's internal pathogenic mechanism from both the host and pathogen perspectives, using prostaglandin E<sub>2</sub> (PGE<sub>2</sub>) as a bridge. The results showed that during bovine mastitis, the macrophages are recruited into the mammary gland, accompanied by a significant upregulation of inflammatory mediators in the mammary tissue. Furthermore, S. aureus lipoproteins could increase the inflammatory response by mediating MAPKs and NF-κB signaling pathway activation through TLR2, TLR4, and NLRP3, leading to the secretion of inflammatory mediators, including PGE<sub>2</sub>, in bovine bone marrow-derived macrophages (bBMMs). The bBMMs were treated with TLR2, TLR4, and NLRP3 inhibitors, which can decrease the expression of COX-2 and mPGES-1, further regulating PGE<sub>2 </sub>synthesis and secretion in <i>S. aureus </i>infection. In addition to TLR2, TLR4, and NLRP3 affecting PGE<sub>2</sub> synthesis and secretion, inhibitors of COX-2 and mPGES-1 can regulate the expression of TLR2 and NLRP3 and the activation of MAPKs and NF-κB signaling pathways in <i>S. aureus</i>-infected bBMMs. Moreover, excess PGE<sub>2</sub> treatment can regulate TLR2-, TLR4-, and NLRP3-mediated inflammatory responses and the phagocytosis of macrophages in <i>S. aureus</i>-infected bBMMs. Altogether, during <i>S. aureus</i> infection, TLR2, TLR4, NLRP3, and <i>S. aureus</i> lipoproteins play essential roles in PGE<sub>2 </sub>synthesis and secretion. Meanwhile, there is cross-talk between TLR2, TLR4, NLRP3, and PGE<sub>2</sub> during <i>S. aureus</i> infection. Moreover, PGE<sub>2</sub> can regulate macrophage phagocytosis, notably involving <i>S. aureus</i> lipoproteins in this process.
DOI: 10.6084/m9.figshare.5566843.v1
title: RAD-seq and tGBS SNP data for pearl millet breeding population

description: RAD-seq and tGBS genotyped data without imputation and imputation by Beagle for pearl millet breeding populationPearl_millet_cGBS.vcf: RAD-seq without imputationPearl_millet_cGBS_Beagle.vcf: RAD-seq with imputation by BeaglePearl_millet_tGBS.vcf: tGBS without imputationPearl_millet_tGBS_Beagle.vcf: tGBS with imputation by Beagle
DOI: 10.6084/m9.figshare.5877033.v1
title: Data File 4: qPCR data for Polysome Gradients

description: These are the numerical data that were generated by polysome gradient fractionation and analysis of translational changes in response to Fhit loss. Briefly, most cancer-linked mRNAs see translation decreases when Fhit is lost. They are the numerical values exported from a Biorad CFX Connect qPCR machine. The data are normalized to an added spike control RNA (Luciferase) and relative values (vs total gradient input) are calculated for both E1 and D1 cell lines.
DOI: 10.6084/m9.figshare.1122789.v1
title: Prodeco Emprende

description: Presentación del programa Prodeco Emprende. Realizado en la Empresa Almida en colaboración con profesorado de la Universidad Nacional de Educación a Distancia. El programa pretende mejorar el emprendimiento y la insercción laboral de población con necesiades educativas diferentes en la Comunidad de Castilla La Mancha. En esta comunicación se muestran los objetivos del proyecto, así como las herramientas utilizadas para llevarlo a cabo.
DOI: 10.6084/m9.figshare.24517123.v2
title: State of Open Data Survey 2023 additional resources

description: Anonymised raw data and questionnaire for the 2023 State of Open Data survey developed between Springer Nature, figshare and Digital Science. The annual survey looks to understand attitudes and behaviours of research authors to the sharing, reuse and redistribution of openly available data.
DOI: 10.6084/m9.figshare.25210049.v1
title: FARM: A fully automated rice mapping framework combining Sentinel-1 SAR and Sentinel-2 multi-temporal imagery

description: Rice farming exemplifies intensive agriculture, demanding significant inputs to achieve optimal yields. Thus, accurate and precise mapping of rice cultivation is vital for effective agricultural management and food security. However, such studies have been limited by the challenges of obtaining optical cloud-free data and dealing with radar data’s speckle noise. Identifying crops using a single data source poses many difficulties. Additionally, acquiring sufficient representative training samples that accurately reflect diverse phenological patterns is challenging for large-scale monitoring and rice cultivation classification. To address these challenges, this study proposed a fully automated rice-mapping framework (FARM) that combines the strengths of time-series synthetic aperture radar (SAR) and optical satellite imagery for large-scale rice mapping without manual sample collection. First, an object-based, fully automatic training sample generation strategy is introduced. The phenology constraint rule, based on time-series SAR satellite images and specific rice-flooding features, is used to extract rice sample objects. Second, the extracted rice sample objects, adhering to phenological rules, serve as training samples for paddy rice extraction by integrating multiple random forest (RF) classifiers, referred to as the multiRF method, where each RF is individually built using images acquired during each phenological phase of the growing season. Furthermore, the study explored the availability of the method in early-season rice identification by transferring the training samples acquired by the FARM to a new year. This dataset is the final classification maps of the proposed FARM framework.
DOI: 10.6084/m9.figshare.28029863.v2
title: Observation data

description: DWL observations of Typhoon IN-FA, including wind speed data, temperature, pressure, humidity data
DOI: 10.6084/m9.figshare.28046606.v1
title: METADATA__rAmIT_Cartografia_20241217

description: La metadata describe una base de datos geoespacial que integra información relacionada con las presiones ambientales derivadas de las actividades humanas y el cambio climático, así como variables económicas, uso del suelo, y la presencia de instituciones de educación superior, ONG, centros de investigación, pesquerías y acuicultura. Esta base de datos organiza y cruza dichos datos con las microcuencas que conforman la gran cuenca amazónica, permitiendo un análisis detallado de los factores que influyen en cada microcuenca. Adicionalmente, la base de datos incluye índices calculados a partir de esta información, los cuales facilitan la priorización de microcuencas estratégicas. Estos índices constituyen una herramienta clave para la selección de sitios óptimos donde se podría establecer el Centro de Aguas Amazónicas (CAAm), garantizando que la ubicación responda a criterios ecológicos, económicos y sociales fundamentales para la gestión sostenible de los recursos acuáticos amazónicos.
DOI: 10.6084/m9.figshare.7768103.v2
title: MODIS based peak NDVI image Year 2009 Tile H25V05

description: MODIS based peak NDVI image Year 2009 Tile H25V05
DOI: 10.6084/m9.figshare.8845580.v1
title: RumourEval 2019 data

description: Manual stance and veracity judgments over a large set of English social media conversations. Judgments are expertsourced and crowdsourced with extensive quality control as detailed in the referenced paper. Conversations are around a central claim; claims are grouped into news themes, each theme centering on a current event. Social media platforms include Twitter and Reddit. This is the dataset for the SemEval-2019 task, RumourEval.
DOI: 10.17632/84jw497rwp
title: Network analysis dataset of System Dynamics models

description: A tool has been developed for the analysis of networks extracted from system dynamics models. The models developed in Vensim, Stella, and InsightMaker are converted into networks of state-variables, flows, and parameters by the developed Python program that also performs model reduction, modularity analysis and calculates the structural properties of the models and its main variables. The dataset covers the results of the analysis of nine models in sustainability science used for policy testing, prediction and simulation.
DOI: 10.17632/hck3d5cj6p
title: Datasets: Traffic Counts in Prague

description: This data was provided by the mobile measuring laboratory MobiLab from the Czech Technical University in Prague (https://mobilab.fd.cvut.cz). It presents four data sets with traffic counts measured every minute over a 24-hour period at the following four selected areas in Prague: Stodůlky (September 2021), Barrandov (June 2022), Radlice (September 2022), and Velká Chuchle (October 2022).

At each location, 3 to 6 points were chosen where traffic counts were collected in all possible directions along the corresponding road section or intersection. Directions are denoted by numbers 1-4 in the columns of each measured point. A detailed description of the data can be found in the following paper: 

Evženie Uglickich, Ivan Nagy, Poisson-based framework for predicting count data: Application to traffic counts in Prague areas, Journal of Computational Science, Volume 85, 2025, 102534, https://doi.org/10.1016/j.jocs.2025.102534. 

Please cite this paper when using the data.
DOI: 10.17632/tn2pv7dc4b
title: SLEEP QUALITY

description: Sleep disorders are a frequent complaint among peri and postmenopausal women. Hormonal changes and vasomotor symptoms related to these periods contributes to poor sleep quality, which is associated with increased metabolic and cardiovascular risk, depression and global impairment of health status Objective: To assess sleep quality identifying the different sleep disorders (insomnia, hypersomnia, and breathing disturbances) observed in postmenopausal women and to assess the related factors Subjects & Methods: 195 postmenopausal women were included in a cross-sectional study that was carried out in a tertiary hospital in Buenos Aires (Argentina). Sociodemographic, gynecological and clinical characteristics of the subjects were recorded and data related to sleep were assessed with the Pittsburgh Sleep Quality Index (PSQI), the Epworth Sleepiness Scale (ESS), and the Oviedo Sleep Quality Questionnaire (COSS). Conclusion: Dissatisfaction with sleep is a common complaint during postmenopausal years and almost one in two women referred impaired sleep quality requiring in most cases medical attention.
DOI: 10.4121/16832254.v1
title: LiDAR Dataset for Hypogenic Morro Vermelho Cave in Bahia, Brazil (2018)

description: LiDAR dataset collected in a 2018 fieldwork expedition to hypogenic (and epigenic) cave(s) in the State of Bahia, Brazil. The data consists of a dense point clouds (resolution of around 3-10 cm), and the size of the cave is around 50-100 meter in length. The data is collected with the mobile LiDAR device (GeoSLAM ZEB REVO).