cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24128553.v1
title: Signal Classification in Large-Scale Multi-Sequence Integrative Analysis Under the HMM Dependence

description: The integrative analysis of multiple sequences of multiple tests has enjoyed increasing popularity in many applications, especially in large-scale genomics. In the context of large-scale multiple testing, the concept of signal classification has been developed recently for cases when the same features are involved in several independent studies, with the goal of classifying each feature into one of several classes. This article considers the problem of such signal classification in a generalized compound decision-making framework, where the observed data are assumed to be generated from an underlying four-state Cartesian hidden Markov model. Two oracle procedures are proposed for the total and set-specific control of misclassification rates, respectively, while the number of correct classifications is maximized. Optimal data-driven procedures are also proposed, with their asymptotic properties derived. It is shown that signal-classification could be improved significantly by taking into account the dependence structure among features, and the proposed procedures could have a better performance than their competitors that ignore the dependence structure. The proposed methods are applied to a psychiatric genetics study for detecting genetic variants that affect either or both of bipolar disorder and schizophrenia.
DOI: 10.6084/m9.figshare.3531092.v1
title: Data Paper. Data Paper

description: File List BROT_2008.11.txt -- ASCII text, records delimited by new lines, columns delimited by tabs, 11 columns and 8263 records (not including header row). No compression scheme was used. Description Plant trait information is essential for understanding plant evolution, vegetation dynamics, and vegetation responses to disturbance and management. Furthermore, in Mediterranean ecosystems, changes in fire regime may be more relevant than direct changes in climatic conditions, making the knowledge of fire-related traits especially relevant. Thus the purpose of this data set was to compile the most updated and comprehensive information on fire-related traits for vascular plant species of the Mediterranean Basin; that is, traits related to plant persistence and regeneration after fire. Data were collected from an extensive literature review and from field and experimental observations. The data source is documented for each value. Since life history traits may vary spatially or with environmental conditions, we did not aggregate them by species; i.e., traits and species are repeated in different records if they were observed by different researchers. Life history traits included in the data set are: life form, resprouting ability (after fire, after clipping, or after other disturbances that remove all the aboveground biomass), resprouting bud source, heat-stimulated germination, other germination cues, seed bank location and longevity, post-fire seedling emergence and survival, maturity age of resprouts and saplings, and seed mass. Several traits are unknown for many species; consequently, the data set reflects the state of the knowledge on the topic. However, since the ability to resprout is a trait of paramount relevance in fire-prone environments, it was considered a core trait in the data set, and thus species whose resprouting capacity was unknown were not included. Life form is also provided for all taxa. The structure of the database allows different levels of information (and accuracy) for each entry, and thus some traits may include different types of data (quantitative, semi-quantitative, or categorical) from different sources. The data set is structured in 8263 records and 11 columns, obtained from 301 published and unpublished sources of information. It includes 952 taxa determined at specific or infraspecific level, which comprise 859 species, 384 genera, and 79 families. Although this is the most comprehensive data sets of fire-relevant plant traits for Mediterranean species, there is still a considerable need for observations and experiments, especially in little-studied Mediterranean areas, such as northern Africa. <i>Key words: database; fire ecology; fire-stimulated germination; fire traits; functional traits; Mediterranean Basin; Mediterranean ecosystems; post-fire response; resprouters; resprouting ability; seeders; traitbase</i>.
DOI: 10.17632/2xjxsvctzr
title: dead_fish_dataset

description: dataset for YOLOv8 based dead fish UAV detection in aquaculture
DOI: 10.17632/574xng767z
title: Analysis of definitions of emergency medicine and terms from titles of research papers published in emergency medicine journals

description: This dataset presents the results of an analysis of definitions of emergency medicine and terms from the titles of research papers published in emergency medicine journals.
The dataset contains three files:
1) Dataset_Selection of Definitions.xlsx – the table contains a sample of definitions of emergency medicine found in peer-reviewed journal articles, free online dictionaries, free online encyclopaedias, websites of professional organisations specialised in emergency medicine, and books on emergency medicine.
2) Dataset_Automated analysis of definitions.xlsx – the table contains an output of the automated analysis of definitions. The analysis was carried out using Copilot (Microsoft Corporation, USA). The output is presented as it was generated by Copilot, without manual corrections.
3) Dataset_Automated analysis of terms.xlsx – the table contains an output of the automated analysis of terms collected from titles of research papers. The analysis was carried out using Copilot. The output is presented as it was generated by Copilot, without manual corrections.
DOI: 10.17632/mbcw4pkh57
title:  Peninsular Malaysia Datasets

description: The objective of this paper is to derive the thermal and crustal thickness models beneath the entire Peninsular Malaysia and environs using the potential field data. The estimated depths to bottom of magnetic layer were used to infer the geothermal gradient as well as the heat flow for the study area. We then compare our curie depth estimates with crustal thickness estimates based on gravity inversion.
DOI: 10.6084/m9.figshare.3444899.v2
title: From Manhatten to Manikarnika: A Study of the ‘Aghori’ Cult and Its Influence on the Life of Allen Ginsberg

description: My Paper entitled ‘From Manhatten to Manikarnika’ traces down the history of Allen Ginsberg’s stay in India. It aims to draw parallels between the Beat writers of the apocalyptic 60’s in America and the revered ‘Aghori’ sadhus in India. For an average American in the 60’s, the East, especially India was a queer nation, it was this queerness that fascinated the Beats writers of the 1960's in America. The reverence and reception of nudity, the celebration of the body, the adoration of death, the consumption of hallucinatory drugs for spiritual connection; approval of everything bizarre and gory lured the west to turn to the ‘heathen’ east for spiritual liberation from its constrained, materialistic society. The ‘aghoris’ managed to impress the Beat writers of the west to such an extent that Ginsberg ended up himself being a ‘yogi’ after his visit to India. Apart from Hinduism in general the one aspect that I wish to talk about and study in detail is the influence of the aghor philosophy on the mindset of Allen Ginsberg.
DOI: 10.17632/bn7ch8tvyp
title: Digital images of defective and good condition tyres

description: The dataset contains 1854 digital tyres images, categorized into two classes: defective and good condition. Each image is in a digital format and represents a single tyre. The images are labelled based on their condition, i.e., whether the tyre is defective or in good condition.

This dataset can be used for various machine learning and computer vision applications, such as image classification and object detection. Researchers and practitioners in transportation, the automotive industry, and quality control can use this dataset to train and test their models to identify the condition of tyres from digital images. The dataset provides a valuable resource to develop and evaluate the performance of algorithms for the automatic detection of defective tyres.

The dataset may also help improve the tyre industry's quality control process and reduce the chances of accidents due to faulty tyres. The availability of this dataset can facilitate the development of more accurate and efficient inspection systems for tyre production.
DOI: 10.6084/m9.figshare.10279733.v1
title: Knowledge and Practice of Tacrolimus Usage among Sudanese Renal Transplant Recipients: A cross-Sectional Survey

description: A questionnaire designed by the researcher to test the Sudanese knowledge and practice of Kidney Transplant Recipients about tacrolimus usage
DOI: 10.6084/m9.figshare.26213900.v2
title: Data for "Religion on CGG"

description: This dataset and Stata do file are created for the replication of paper 'The power of Informal Institutions: Evidence from the Impact of Religious Culture on Corporate Green Governance in China' by L.Yang, Y.WANG and H.Geng.Beyond formal environmental regulations, we specifically investigate the role of religious culture in informal regulations influencing corporate green governance (CGG) practices. By employing a unique instrumental variable, namely the number of religious sites per city during Qing dynasty, we delve into the causal impact of religious culture on CGG, focusing on pollutant discharge fees (PDF) and environmental information disclosure (EID). Our dataset applies 848 Chinese A-share listed firms across 14 polluting industries from 2009 to 2018.Stata Dataset: A 2009-2018year data.dtaStata do-file: AAAcode.do<br>
DOI: 10.6084/m9.figshare.29109623.v1
title: Interview Henry.docx

description: In-depth interview transcription
DOI: 10.17632/gczynnjzcp
title: Shape Dynamic Time Warping for Seismic Waveform Inversion

description: We illustrate shape dynamic time warping (ShapeDTW) for 1D structure waveform inversion with examples from Tanzania, East Africa, and Northeastern Oklahoma. Seismograms of the Mw 5.9 Lake Rukwa, Tanzania earthquake (18 August, 1994) were recorded by 14 regional broadband seismographic stations. Seismograms of the Mw5.7 Prague, Oklahoma earthquake (6 November, 2011) were recorded by 8 regional broadband seismographic stations. 

This dataset includes seismograms and solved velocity models.
In two examples, observed and synthetic seismograms are saved as SAC files in 'SAC_FILES' folders. The station numbers are listed in 'stationlist.txt' files. The 1D velocity models are saved as 'model.txt'.
DOI: 10.6084/m9.figshare.22736609.v1
title: Image datasets for training, validating and testing deep learning models to detect microfossil fish teeth and denticles called ichthyolith using YOLOv7

description: This repository contains datasets to train, validate and test deep learning models to detect microfossil fish teeth and denticles called "ichthyoliths". All the dataset contains images of glass slides prepared from deep-sea sediment obtained from Pacific Ocean, and annotation label files formatted to YOLO. 01_original_all The dataset contains 12219 images and 6945 label files. 6945 images include at least one ichthyolith and 5274 images include no ichthyolith. These images and label files were randomly split into three subset, "train" that contains 9740 images and 5551 label files, "val" that contains 1235 images and 695 label files and "test" that contains 1244 images and 699 label files. All the images were selected manually. 02_original_selected This dataset is generated from 01_original_all by removing images without ichthyoliths. The dataset contains 6945 images that include at least one ichthyolith and 6945 label files. The dataset contains three subset, "train" that contains 5551 images and label files, "val" that contains 695 images and label files and "test" that contains 699 images and label files. 03_extended_all This dataset is generated from 01_original_all by adding 4463 images detected by deep learning models. The dataset contains 16682 images and 9473 label files. 9473 images include at least one ichthyolith and 7209 images include no ichthyolith. These images and label files were split into three subset, "train" that contains 13332 images and 7594 label files, "val" that contains 1690 images and 947 label files and "test" that contains 1660 images and 932 label files. Label files were checked manually. 04_extended_selected This dataset is generated from 03_extended_all by removing images without ichthyoliths. The dataset contains 9473 images that include at least one ichthyolith and 9473 label files. The dataset contains three subset, "train" that contains 7594 images and label files, "val" that contains 947 images and label files and "test" that contains 932 images and label files.
DOI: 10.6084/m9.figshare.28856687.v1
title: Multivocal proccess data - SBES

description: This dataset supports the multivocal literature review titled <i>“Socio-Technical Entanglements of Code and Community Smells in Open-Source Code Samples”</i>. It includes the full corpus of selected studies and practitioner documents analyzed during the review. The dataset contains:<br>A table of 18 peer-reviewed studies (Systematic Literature Review), each mapped to the research questions based on thematic relevance.A table of 17 documents from grey literature sources (e.g., blogs, industry reports, technical articles), similarly analyzed and categorized.Visual figures illustrating the article selection and mapping processes.Metadata for each source, including title, URL or DOI, access date, and mapping to RQs.<br><br>All artifacts were used to analyze the socio-technical conditions under which Code Smells and Community Smells emerge, evolve, and reinforce each other in open-source ecosystems. The dataset is provided in xlsx and image formats to ensure transparency and facilitate reuse in future research.
DOI: 10.6084/m9.figshare.7672121.v1
title: Additional file 7 of Understanding the evolutionary trend of intrinsically structural disorders in cancer relevant proteins as probed by Shannon entropy scoring and structure network analysis

description: Shannon entropy score of proteins under Calpain-type cysteine protease DEK1 protein family responsible for acute lymphoblastic leukemia. (XLSX 15 kb)
DOI: 10.17608/k6.auckland.8009921.v4
title: Examining STEM employability prospects through the lens of self-efficacy

description: Raw data and analysis, Questionnaire, Codes, Examples
DOI: 10.17632/5cpbmrtzbr
title: PolyPal: A parallel microscale virtual specimen generator

description: We present an open source program, PolyPal, that can generate a polycrystalline virtual specimen in the micrometer scale for atomistic calculations and visualization. Unlike regular meshes or perfect lattices, atomic positions in polycrystalline materials need to be defined before calculations, and the capability of an atom-generation code is evaluated by the maximum size of the virtual specimen it can generate as well as by the efficiency of the necessary input-output process. Present atom-generation codes are implemented in a serial fashion, and the maximum size of the virtual specimen is limited by the on-board memory. Furthermore, it is difficult to handle a single position file with billions of atoms not only because it takes a long time to read in a row but also full domain decomposition takes hours. PolyPal addresses these challenges with a fully parallelized MPI input-output scheme that supports multiple export options on a Linux cluster. It has no limit in the system size with virtually perfect scalability. Additionally by controlling the size distribution and homogeneity of grains, the program can simulate different microstructures, as typically found in the bulk system or in thin-film samples, prepared with different fabrication processes. PolyPal will harness molecular dynamics codes in the coming age of the exascale computing.
DOI: 10.6084/m9.figshare.24419938.v8
title: The South China Sea metagenome dataset

description: MAGs and other files generated using <b>the </b><b>South China Sea</b> microbial dataset.
DOI: 10.6084/m9.figshare.24464380.v1
title: Temperature calibration

description: Function to convert a luminous intensity image into a temperature visualization image
DOI: 10.6084/m9.figshare.26324239.v2
title: <b>A chromosome-level genome assembly of tropical purple sea urchin </b><b><i>Heliocidaris crassispina</i></b>

description: This study employed a combination of PacBio HiFi and Hi-C sequencing data to present a high-quality, chromosome-level assembly of <i>H. crassispina</i> genome.
DOI: 10.6084/m9.figshare.27184389.v1
title: Supplemental File 5: CDS file of the <i>P. eatonii</i> genome assembly

description: CDS file of the genome assembly of a <i>Penstemon eatonii</i> specimen collected in American Fork Canyon in Utah in 2023.
DOI: 10.6084/m9.figshare.3513908.v1
title: Appendix C. Model-averaged estimates of age-specific mortality, survivorship, net reproductive rate, life expectancy, population age distribution (live animals), and death distribution.

description: Model-averaged estimates of age-specific mortality, survivorship, net reproductive rate, life expectancy, population age distribution (live animals), and death distribution.
DOI: 10.6084/m9.figshare.c.3894727_d12.v1
title: Additional file 6 of MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics

description: Table S5. The input metabolite APM data of human fecal metabolomic samples from healthy control people and NAFLD patients. (XLS 41kb)
DOI: 10.17632/3wc6t92rrg
title: Adult Inpatient Patient Portal Dataset

description: Data for 826,843 diagnostic test reports on 40,640 unique patients. Specific data fields include: unique patient identification number (deidentified), number of inpatient admissions in 2018, whether test report was during the initial admission in 2018 or a subsequent admission, specific diagnostic test ordered, diagnostic test category, sex (as officially noted in the electronic health record), patient portal status (active or inactive), whether diagnostic test report was viewed in the patient portal, the most common self-declared race categories, simplified race category (White or non-White), age at time of testing, age category, primary/preferred language (as recorded in electronic health record), primary/preferred language (English on non-English), whether there was a legal proxy that had access to the patient’s portal account, and insurance category (private/commercial or public/uninsured).
DOI: 10.17632/9zjnzd9325
title: Base de dados de artigos sobre Hortas e Educação

description: Projeto “Experiências de Horta Escolar e de Estudo do Meio como estratégias educativas: um estudo de caso na Escola de Aplicação da FEUSP”. Coordenação: Martha Marandino; Pesquisador: Fausto Oliveira; Bolsistas: Camila Moreira Viana e Letícia Campos Graciani
Resumo: Não é de hoje que se discute a importância da utilização de hortas para o processo de ensino e aprendizagem, sendo que esta estratégia estimula a formação do aluno, não apenas no âmbito da educação ambiental e do desenvolvimento sustentável, mas também o trabalho coletivo e a articulação do conteúdo com a prática, mostrando diretamente a relação entre o ser humano e o meio ambiente em diversas áreas de conhecimentos e de forma interdisciplinar. Desta forma, o projeto de pesquisa “Experiências de Horta Escolar e de Estudo do Meio como estratégias educativas: um estudo de caso na Escola de Aplicação da FEUSP”, ligado ao Programa Unificado de Bolsas/PUB da USP, buscou, entre outros objetivos, realizar um mapeamento das iniciativas de hortas dentro do campus da capital da USP e nas escolas públicas da cidade.
Foi também objetivo realizar o levantamento bibliográfico sobre hortas e educação, nas seguintes bases de dados: Scielo, Periódico Capes, Jstor, Google Acadêmico e Eric. As palavras chaves escolhidas foram horta; horta escolar/na escola; jardim escolar/na escola; agroecologia e/na escola/educação; garden learning; garden based learning. Considerando o recorte temporal estabelecido, com início na década de 1990 até 2023, foram identificados oitenta e oito artigos nas cinco bases escolhidas. Com a finalidade de disponibilizar esses dados, disponibilizamos nesta base de o levantamento bibliográfico sobre Hortas e Educação com a lista de referências completas.
DOI: 10.6084/m9.figshare.23652387.v1
title: Supplementary Material

description: Supplementary Material
DOI: 10.6084/m9.figshare.23691819.v2
title: Chengdu's main 6 districts

description: Shape file of the boundaries of the six main districts of Chengdu, including Jinjiang, Qingyang, Jinniu, Wuhou, Chenghua, and Chengdu Hi-tech Industrial Development Zone (Gaoxin district).
DOI: 10.6084/m9.figshare.3559887.v1
title: Data Paper. Data Paper

description: File List BirdFuncDat.txt (MD5: d6197b2cd90ca3ece0a7393abbf8b7fc) MamFuncDat.txt (MD5: 59c3eee29d3ed0a33a002975a5a8cc75) BirdFuncDatSources.txt (MD5: e4793ab8baa813bba7d168a3d2d6b6a7) MamFuncDatSources.txt (MD5: 0c67fa8bf6b6ccb7a38fc5229f84508b) Description Species are characterized by physiological, behavioral, and ecological attributes that are all subject to varying evolutionary and ecological constraints and jointly determine their role and function in ecosystems. Attributes such as diet, foraging strata, foraging time, and body size, in particular, determine a large portion of the “Eltonian” niches of species. Here we present a global species-level compilation of these key attributes for all 9993 and 5400 extant bird and mammal species derived from key literature sources. Global handbooks and monographs allowed the consistent sourcing of attributes for most species. For diet and foraging stratum we followed a defined protocol to translate the verbal descriptions into standardized, semiquantitative information about relative importance of different categories. Together with body size (continuous) and activity time (categorical) this enables a much finer distinction of species’ foraging ecology than typical categorical guild assignments allow. Attributes lacking information for specific species were flagged, and interpolated values based on taxonomy were provided instead. The presented data set is limited by, among others, these select cases missing observed data, by errors and uncertainty in the expert assessment as presented in the literature, and by the lack of intraspecific information. However, the standardized and transparent nature and complete global coverage of the data set should support an array of potential studies in biogeography, community ecology, macroevolution, global change biology, and conservation. Potential uses include comparative work involving these traits as focal or secondary variables, ecological research on the trait or trophic structure of communities, or conservation science concerned with the loss of function among species or in ecosystems in a changing world. We hope that this publication will spur the sharing, collaborative curation, and extension of data to the benefit of a more integrative, rigorous, and global biodiversity science. <i>Key words</i>: <i>bird; body size; diet; eco-informatics; foraging; function; mammal; mass; niche; stratum; traits; vertebrate.</i>
DOI: 10.17632/c7n6sm95g9
title: Raw data for Cecilia Arriagada Dev Cell Paper 2024

description: Uncropped Western blots and Genotyping Information with Band Sizes
DOI: 10.17632/hbmmzjn3xn
title: Data for: Global-scale mapping and prediction of mine areas

description: Mine Production and GIS Data associated with the paper "Global-scale remote sensing of mines and analysis of factors explaining their extent"