cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28695986.v1
title: Data for article "The Role of Focused Laser Plasmonics in Shaping SERS Spectra of Molecules on Nanostructured Surfaces"

description: Reflectance spectrum of gold film over nanospheres (AuFoN).SERS spectra of aminobenzenethiol adsorbed on AuFoN, recorded for different Z-focusing positions.FDTD simulations of electric field spectrum near the AuFoN surface.
DOI: 10.6084/m9.figshare.27916602.v1
title: raw data for manuscript <b>Individuals Adjust Their Degree of Advice Taking to Impress Others</b>

description: all the raw data for manuscript <b>Individuals Adjust Their Degree of Advice Taking to Impress Others</b>
DOI: 10.6084/m9.figshare.28601408.v1
title: Scale and environmental data for the analysis of year class growth of coregonids from Lake Starnberg

description: Animal growth is shaped by a complex interplay of environmental conditions and intrinsic life-history trade-offs, yet long-term datasets allowing the reconstruction of individual growth histories in natural populations remain rare. Here, we use scale analysis to reconstruct age-specific growth histories of coregonid fish from Lake Starnberg, Germany, over a 22-year period, evaluating the roles of lake phosphorus concentrations and spring temperatures as potential drivers. Linear mixed-effects models revealed age-specific changes in scale growth over time: while growth remained stable or increased slightly in younger age classes (ages 1 and 2), growth significantly declined over time in mature fish (age 3). During the observed period, phosphorus concentrations decreased, indicating reduced nutrient availability, whereas spring temperatures showed no significant long-term trend. Our analyses further indicated significant interactions between temperature and age class, suggesting that temperature effects on growth may have varied by age, even though there was no overall change in temperature during the monitored time period. The observed decline in growth among mature individuals aligns with predictions from life-history theory, reflecting a potential allocation shift from somatic growth to reproductive investment following maturation. This study provides rare empirical evidence from a natural fish population that long-term environmental changes interact with intrinsic life-history strategies, resulting in clear age-specific patterns of growth variation.
DOI: 10.6084/m9.figshare.28741655.v1
title: The chromosome-level genome assembly and annotation of the Salvelinus malma

description: <i>Salvelinus malma</i>, belonging to the Salmonidae family, is an a critically endangered species in theChina. To support genetic research and strengthen the protection of wild fish resources, the first chromosome-level reference genome of <i>S. malma</i> generated through integrated technologies from PacBioand Hi-C sequencing platforms. The genome assembly has a total length of 2.52 Gb and a contig N50 of 1.29 Mb, with contigs further assigned to 42 chromosomes. A total of 45,385 protein-coding genes were predicted, showing 98.8% BUSCO completeness. The chromosome-level genome of <i>S. malma</i> will serve as a valuable resource for future functional genomics research, while greatly facilitating its exploration and conservation.
DOI: 10.6084/m9.figshare.5123647.v1
title: Supplementary Material for: Raising Doubts about the Pathogenicity of Mitochondrial DNA Mutation m.3308T&gt;C in Left Ventricular Hypertraveculation/Noncompaction

description: Medicine
DOI: 10.21233/0jm7-8s41
title: East Ujimqin Banner ostracode surface sample dataset

description: Raw data for the East Ujimqin Banner ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.6084/m9.figshare.11854371.v2
title: ChromSCape_scChIP_scATAC_compiled_datasets

description: This folder contains three analysis of one scChIP-seq and one scATAC-seq datasets for the purpose of being visualised by ChromSCape (https://github.com/vallotlab/ChromSCape). <b><br></b><b>Datasets</b><br><b><br></b><b>H3K27me3 scChIP-seq datasets:</b>The samples correspond to mouse cells from patient-derived xenograft (PDX) originating from two different human donors (Grosselin et al., 2019). Raw FASTQ reads were processed using the latest version of our scChIP-seq data engineering pipeline that allowed a more precise removal of PCR and RT duplicates (code available at https://github.com/vallotlab/scChIPseq_DataEngineering) to produce 50kbp binned count matrices given as input to ChromSCape (matrices available at https://figshare.com/projects/Single-Cell_ChIP-seq_of_Mouse_Stromal_Cells_in_PDX_tumour_models_of_resistance/66419).<br><b>scATAC-seq datasets:</b> The single-cell ATAC-seq dataset is composed of two cell types derived from two acute myeloid leukaemia (AML) patient (blastocytes (blast) and leukemic stem cells (LSC) produced in (Corces et al., 2016)) as well as multiple cell lines : GM12878, TF1, BJ, H1, HL60, K562 (3 replicates) produced in (Buenrostro et al., 2015), K562 (3 replicates) produced in (Schep et al., 2017); monocytes (Mono) and lymphoid primed multipotent progenitor (LMPP) produced in (Corces et al., 2016)). The count matrix of reads in peaks was downloaded from GEO accession number GSE99172, split into distinct matrices for each sample and formatted to be accepted as input by ChromSCape. Code availability Source code, guidelines for installation and use of the application are provided at https://github.com/vallotlab/ChromSCape. A Docker environment containing all libraries required to launch the application is also available on DockerHub at https://hub.docker.com/repository/docker/pacomito/chromscape, with all set-up steps clearly described on the GitHub repository.
DOI: 10.6084/m9.figshare.14730441.v1
title: Supplementary Material for: Polypharmacy and the Progression of Chronic Kidney Disease: Korean Cohort Study for Outcome in Patients with Chronic Kidney Disease

description: <b><i>Introduction:</i></b> The renal hazard of polypharmacy has never been evaluated in predialysis chronic kidney disease (CKD) patients. <b><i>Objective:</i></b> We aimed to analyze the renal hazard of polypharmacy in predialysis CKD patients with stage 1–5. <b><i>Method:</i></b> The data of 2,238 patients from a large-scale multicenter prospective Korean study (2011–2016), excluding 325 patients with various missing data, were reviewed. Polypharmacy was defined as taking 6 or more medications at the time of enrollment; renal events were defined as a ≥50% decrease in kidney function from baseline values, doubling of the serum creatinine levels, or initiation of renal replacement treatment. Hazard ratio (HR) and 95% confidence interval (CI) were calculated using Cox proportional-hazard regression analysis. <b><i>Results:</i></b> Of the 1,913 patients, the mean estimated glomerular filtration rate was 53.6 mL/min/1.73 m<sup>2</sup>. The mean medication count was 4.1, and the prevalence of polypharmacy was 27.1%. During the average period of 3.6 years, 520 patients developed renal events (27.2%). Although increased medication counts were associated with increased renal hazard with HR (95% CI) of 1.056 (1.007–1.107, <i>p</i> = 0.025), even after adjusting for various confounders, adding comorbidity score and kidney function nullified the statistical significance. In mediation analysis, 55.6% (<i>p</i> = 0.016) of renal hazard in increased medication counts was mediated by the kidney function, and there was no direct effect of medication counts on renal event development. In subgroup analysis, the renal hazard of the medication counts was evident only in stage 1–3 of CKD patients (<i>p</i> for interaction = 0.014). <b><i>Conclusions:</i></b> We cannot identify the direct renal hazard of multiple medications, and most of the potential renal hazard was derived from intimate relationship with disease burden and kidney function.
DOI: 10.6084/m9.figshare.14899845.v4
title: GEO Mountains Inventory of In Situ Observational Infrastructure v2.0

description: This inventory is a compilation of information on in situ observatories and other long term monitoring infrastructure in the world's mountains that can be viewed as an interactive web map, with the corresponding dataset also available for download.The dataset itself is accessible from GEO Mountains website following simple registration process.For further details, see "READ_ME.txt"
DOI: 10.6084/m9.figshare.24790872.v1
title: Monitoring and dynamically controlling glucose uptake rate and central metabolism

description: Datasets
DOI: 10.6084/m9.figshare.22124219.v11
title: The Urbanity Global Network Dataset

description: The Global Urban Network (GUN) dataset provides pre-computed node and edge attribute features for various cities. Each layer is available in .geojson format and can easily be converted into NetworkX, igraph, PyG, and DGL graph formats.
<br>
For node attributes, we adopt a uniform Euclidean approach, as it provides a consistent, straightforward, and extensible basis for integrating heterogeneous data sources across different network locations. Accordingly, we construct 100 metres euclidean buffers for each network node and compute the spatial intersection with spatial targets (e.g., street view imagery points, points of interest, and building footprints). To ensure spatial consistency and accurate distance computation, we project spatial entities into local coordinate reference systems (CRS). Users can employ the Urbanity package to generate Euclidean buffers of arbitrary distance. 
<br>
For edge attributes, we adopt a two-step approach: 1) compute the distance between each spatial point of interest and its proximate edges in the network, and 2) assign entities to the corresponding edge with lowest distance. To account for remote edges (e.g., peripheral routes that are not located close to any amenities), we specify a distance threshold of 50 metres. For buildings, we compute the distance between building centroids and their respective network edge.  Accordingly, we compute spatial indicators based on the set of elements assigned to each network edge.
<br>
We also release aggregated subzone statistics for each city. Similarly, users can employ the Urbanity package to generate aggregate statistics for any arbitrary geographic boundary. 
<br>
Urbanity Python package: https://github.com/winstonyym/urbanity.
<br>
<br>
<br>
<br>
<br>
DOI: 10.6084/m9.figshare.24863016.v3
title: Data for Yilan crater

description: Seimic_data_Yilan is the resampled data for Yilan crater, including one local event and two teleseismic events.HVSR results are also available in HVSR_Yilan.Columns: Label, Longitude, Latitude, frequency, amplitude, standard deviation of amplitude.new_YL_final_vs2 includes the velocity from tomography. Columns: Longitude, Latitude, depth, velocity, standard deviation of velocity with one reference model, standard deviation of velocity with multi-reference models.
DOI: 10.17632/tjw29ph975
title: Mode I fracture and fatigue behavior of thick adhesive joints with and without crack-arresting features

description: This dataset contains the results of mode-I fracture and fatigue experiments conducted on thick glass fiber-reinforced polymer composite-epoxy adhesive joints commonly used in wind turbine rotor blades. These joints comprise additively manufactured design elements specifically engineered to arrest cracks under quasi-static fracture and fatigue loading conditions. The dataset also includes the quasi-static tensile experimental data of composite materials and the crack-arresting features.
DOI: 10.6084/m9.figshare.1276105.v5
title: A new method to analyze species abundances in space: R Source and model output

description: R and R markdown source code, and model output files for the manuscript: Saravia, L.A. (2015). A new method to analyse species abundances in space using generalized dimensions. <i>Methods Ecol. Evol.</i>, 6, 1298–1310Available as a pre-print: https://dx.doi.org/10.7287/peerj.preprints.745v5 Other code used in the manuscript is - The neutral/hierarchical model: https://github.com/lsaravia/neutral - The generalized dimension estimation software: https://github.com/lsaravia/mfsba
DOI: 10.17632/djm2cg27vx
title: Espécies Daninhas na Campina Experimental do Cerrado

description: A Campina Experimental do Cerrado é um jardim experimental com espécies herbáceas e arbustivas nativas do cerrado paulista, bem como de outras plantas cultivadas ou naturalizadas no território brasileiro. A Campina está situada no Câmpus de Bauru da Universidade Estadual Paulista (UNESP), especificamente no pátio da Central de Laboratórios da Faculdade de Arquitetura, Artes, Comunicação e Design (FAAC), em uma área de 222,40 m², na região centro-oeste do estado de São Paulo, no sudeste do Brasil. Começou a ser semeado em novembro de 2022 e, com o decorrer do tempo, diversas espécies espontâneas passaram a emergir no local em razão do banco de sementes presente no solo e do fluxo de animais e pessoas que circulam pela área. Algumas dessas espécies foram incorporadas ao jardim devido ao seu valor estético — seja por suas flores, folhagens ou pela harmonia com a composição paisagística —, além de não apresentarem, em geral, comportamento competitivo em relação às espécies cultivadas. 
 Entretanto, outras passaram a se proliferar de forma excessiva nos canteiros, ocupando espaço e comprometendo o desenvolvimento das espécies intencionalmente cultivadas. As espécies apresentadas e classificadas neste documento têm como objetivo a identificação e classificação de espécies daninhas na Campina Experimental do Cerrado, buscando proporcionar orientação em ações de controle e remoção. Para a identificação precisa, os exemplares foram catalogados após emergência no solo, após coleta para evidenciar suas estruturas, no ambiente natural e no ambiente controlado.
DOI: 10.6084/m9.figshare.16634914.v1
title: Supplementary Material for: Oligogenic causes of human differences of sex development: Facing the challenge of genetic complexity

description: Medicine
DOI: 10.6084/m9.figshare.8097488.v1
title: Life history stage explains social behavior

description: This file contains the data and R markdown file to complete the analysis and re-create the figures in the PeerJ manuscript "Life history stage explains behavior in a social network before and during the early breeding season in a cooperatively breeding bird."<br>The data file contains group-by-individual matrices for the 2017 and 2018 pre and early breeding season of Florida scrub-jays at Archbold Biological Station. Individual attributes, including sex and life history stage for each individual are included as well as resident territory and the territory on which each observation was recorded.<br>Individual identities of the birds have been obscured and the identity of a bird in this data set does not relate to the identification number of the same bird in any other published data set on this population. If you wish to use longitudinal data from this population please contact the Avian Ecology Program at Archbold Biological Station.<br>
DOI: 10.25442/hku.27193857.v1
title: Supporting data for "MAMERR Interacts with HSF2BP and BRCA2 to Regulate the Ubiquitination of Mouse Pachytene Spermatocytes"

description: This study is associated with the meiosis process, especially the pachytene stage of meiosis prophase I. In this study, we found a new function of MAMERR in mouse pachytene spermatocytes. Despite of function as a recombination regulator, MAMERR also plays a role in the transcription regulation and ubiquitination process of mouse pachytene spermatocytes. Deletion of MAMERR causes transcription dysregulation and enhanced ubiquitination, and MSCI suffers defects, eventually resulting in spermatogenesis defects.The dataset associated with this study is put in the main folder. The main folder contains 6 sub-folders and the sub-read-me file is prepared for each sub-folder. 6 sub-folders match the 6 parts in the thesis. The results mainly contain immunoblotting, IHC, IF, HE staining, IP assays, etc. All results can be found in the figure files. For RNA sequencing and ubiquitination-mediated mass spectrometry, the Excel files are also prepared in the matching sub-folders. The figure files contain the legend details for easy reading.Dataset 3.1 mainly focuses on the expression pattern of MAMERR. Generation and verification of the MAMERR KO mice model. The exact stage of cell apoptosis.Dataset 3.2 mainly illustrates the flowchart of pachytene spermatocyte isolation and RNA sequencing of isolated pachytene cells.Dataset 3.3 contains the immunoblotting analysis of isolated pachytene cells' ubiquitination. Generation and verification of MAMERR Overexpression mice model.Dataset 3.4 almost illustrates the ubiquitination-mediated mass spectrometry data from testes and isolated pachytene cells.Dataset 3.5 mainly focuses on HEK293T transfection experiments, IP assays, and DUBs assays.Dataset 3.6 includes a scheme of the potential mechanism of MAMERR's function in pachytene spermatocytes.
DOI: 10.6084/m9.figshare.13070285.v2
title: Dry season data for the Amazon Basin

description: Maps of the Amazon basin dry season (start, length and peak), based on data from the Climate Hazards Group InfraRed Precipitation with Station (CHIRPS). <br><br><br>
DOI: 10.15468/dl.gz2xap
title: Occurrence Download

description: A dataset containing 722464 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aphididae"
 ]
}

 The dataset includes 722464 records from 660 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009347-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/fkjv82s5r4
title: Preprocessed Corpus Articles

description: It is somewhat helpful to use well-understood and commonly used standard datasets so that the findings can be quickly evaluated. Nevertheless, most of the corpora datasets are prepared for NLP tasks. Wikipedia is a good source of well-organised written text corpora with a wide range of expertise. These articles are available online freely and conveniently. Based on the number of English articles that exist in Wikipedia, we have randomly chosen several articles to be used as corpus datasets in this experiment. The sample size is determined from the confidence level, margin of error, population proportion, and population size. That means 385 articles are needed to achieve a 95 percent confidence level that the actual value is within ± 5% of the calculated value.
DOI: 10.6084/m9.figshare.6233660.v1
title: Supplementary Dataset Associated with "Genome-centric view of carbon processing in thawing permafrost"

description: These data are associated with the manuscript "Genome-centric view of carbon processing in thawing permafrost". This includes the phylogenetic trees and alignments used to create the bacterial and archaeal trees, and the protein database.
DOI: 10.6084/m9.figshare.4748035.v1
title: Supplementary Material for: The Global Epidemiology of Hereditary Ataxia and Spastic Paraplegia: A Systematic Review of Prevalence Studies

description: <strong><em>Background:</em></strong> Hereditary cerebellar ataxias (HCA) and hereditary spastic paraplegias (HSP) are two groups of neurodegenerative disorders that usually present with progressive gait impairment, often leading to permanent disability. Advances in genetic research in the last decades have improved their diagnosis and brought new possibilities for prevention and future treatments. Still, there is great uncertainty regarding their global epidemiology. <b><i>Summary:</i></b> Our objective was to assess the global distribution and prevalence of HCA and HSP by a systematic review and meta-analysis of prevalence studies. The MEDLINE, ISI Web of Science and Scopus databases were searched (1983-2013) for studies performed in well-defined populations and geographical regions. Two independent reviewers assessed the studies and extracted data and predefined methodological parameters. Overall, 22 studies were included, reporting on 14,539 patients from 16 countries. Multisource population-based studies yielded higher prevalence values than studies based primarily on hospitals or genetic centres. The prevalence range of dominant HCA was 0.0-5.6/10<sup>5</sup>, with an average of 2.7/10<sup>5</sup> (1.5-4.0/10<sup>5</sup>). Spinocerebellar ataxia type 3 (SCA3)/Machado-Joseph disease was the most common dominant ataxia, followed by SCA2 and SCA6. The autosomal recessive (AR) HCA (AR-HCA) prevalence range was 0.0-7.2/10<sup>5</sup>, the average being 3.3/10<sup>5</sup> (1.8-4.9/10<sup>5</sup>). Friedreich ataxia was the most frequent AR-HCA, followed by ataxia with oculomotor apraxia or ataxia-telangiectasia. The prevalence of autosomal dominant (AD) HSP (AD-HSP) ranged from 0.5 to 5.5/10<sup>5</sup> and that of AR-HSP from 0.0 to 5.3/10<sup>5</sup>, with pooled averages of 1.8/10<sup>5</sup> (95% CI: 1.0-2.7/10<sup>5</sup>) and 1.8/10<sup>5</sup> (95% CI: 1.0-2.6/10<sup>5</sup>), respectively. The most common AD-HSP form in every population was spastic paraplegia, autosomal dominant, type 4 (SPG4), followed by SPG3A, while SPG11 was the most frequent AR-HSP, followed by SPG15. In population-based studies, the number of families without genetic diagnosis after systematic testing ranged from 33 to 92% in the AD-HCA group, and was 40-46% in the AR-HCA, 45-67% in the AD-HSP and 71-82% in the AR-HSP groups. <b><i>Key Messages:</i></b> Highly variable prevalence values for HCA and HSP are reported across the world. This variation reflects the different genetic make-up of the populations, but also methodological heterogeneity. Large areas of the world remain without prevalence studies. From the available data, we estimated that around 1:10,000 people are affected by HCA or HSP. In spite of advances in genetic research, most families in population-based series remain without identified genetic mutation after extensive testing.
DOI: 10.6084/m9.figshare.12550967.v3
title: supporting.docx

description: Supplementary data for "MicroRNA Profiles in Calcified and Healthy Aorta Differ: Therapeutic Impact of miR-145 and miR-378a".
DOI: 10.17632/y4pdxgjjry
title: Cross-Correlation Functions of Sichuan Basin and Southeastern Tibetan Plateau

description: Stations and its distribution used in seismic tomography in the Sichuan Basin and the southeastern Tibetan Plateau, as well as the cross-correlation functions of the vertical components used. Raw seismic waveform data are available from temporary and fixed stations at the International Earthquake Science Data Center (Doi:10.11998/ISDC).