cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1316468.v1
title: Supporting dataset

description: Positive and negative phosphorylation site sequence data corresponding to four kinases PKA, PKC, MAPK and CK2 divided into training and test dataset.
DOI: 10.6084/m9.figshare.20551302.v1
title: FUZZY CONTROLLER APPLIED TO TEMPERATURE ADJUSTMENT IN INCUBATION OF FREE-RANGE EGGS

description: ABSTRACT Temperature variation in egg incubation can negatively affect the hatching time and weight gain of chicks, hence improving the incubator temperature accuracy can improve hatching rates. Controllers based on the fuzzy methodology have shown great potential for use in controlling incubator temperature variations. Therefore, the objective of this study is to develop and evaluate a fuzzy logic-based controller for egg incubation. Four identical incubators were configured: two with a fuzzy controller and two with a conventional controller. After evaluation and validation, a case study of the incubating eggs of free-range chickens was conducted on where 12 incubation cycles consisting of 20 eggs per incubator. The variables obtained include hatchability and electricity consumption. The results showed that the fuzzy logic-based controller maintained uniform internal temperature and a 10.68% saving on electricity usage when compared with the conventional controller. Thus, the fuzzy methodology has great potential for use in the incubation of free-range eggs.
DOI: 10.6084/m9.figshare.24635439.v5
title: Main dataset from Saeedi et al. 2024 Nature communications

description: <b>Main dataset from Saeedi et al. 2024.</b>Companion code located at: https://github.com/alirezasaeedi1988/Saeedi-et-al-2024<br>Detailed information about the provided files can be found in the GitHub repository as well.<br><br>Supplementary videos are located at: https://doi.org/10.6084/m9.figshare.20365056.v2<br>Please always check the latest version of these repositories for more extended data.
DOI: 10.6084/m9.figshare.25930579.v1
title: UTUC.h5ad

description: Processed human upper tract urothelial carcinoma (UTUC) IMC dataset from Ohara et al. (<i>Nat Commun</i>, 2024), containing 16 images with manually annotated topological domain labels.
DOI: 10.6084/m9.figshare.28191122.v1
title: Supplementary data

description: <b>Supplementary data</b> Supplementary data consisting of genotyping data (<i>Pan</i> I, <i>hb</i> b <i>1</i><i> </i>and inversion scoring) as well as metadata for the paper:<b> </b><b>A century of anthropogenic perturbations impact genomic signatures of the iconic </b><b>migratory Atlantic cod</b> by Cecilia Helmerson, Joël M. Durant, Siv Nam Khang Hoff, Marine Servane Ono Brieuc, Paul Ragnar Berg, Per Erik Jorde, Marius Filomeno Maurstad, Ian Bradbury, Olav Sigurd Kjesbu, Jane Aanestad Godiksen, Nils Chr. Stenseth, Bastiaan Star, Kjetill S. Jakobsen, Sissel Jentoft<br><br>
DOI: 10.6084/m9.figshare.23736702.v1
title: STAMPS 2023 example data

description: example files for the STAMPS 2023 GToTree tutorial: https://hackmd.io/@AstrobioMike/STAMPS2023-GToTree
DOI: 10.6084/m9.figshare.25013798.v1
title: Representative phylogenetic tree

description:  <b>To extend the iFrame repository, there is a phylogenetic tree file on the github platform with all representative genomes, where third-user could add new genomes. This could be possible with the use of pplacer. In the iFrame github we provide a step-by-step instruction on how to update the representative phylogenetic tree.</b>
DOI: 10.6084/m9.figshare.27891141.v1
title: Original data for Modulation of the Plasma Lipidomic Profile in Piglets FedPolar Lipid-Rich Diets

description: Original data for paper Modulation of the Plasma Lipidomic Profile in Piglets Fed Polar Lipid-Rich Diets
DOI: 10.6084/m9.figshare.28068359.v1
title: Supplementary Material for: Association between metabolic disorders and impaired kidney function thereafter in the Japanese general population

description: Introduction: Metabolic syndrome (MetS) and chronic kidney disease are both important risk factors for cardiovascular disease and are closely related to each other. We retrospectively investigated whether MetS or its components increase the risk of development of impaired kidney function in the Japanese general population. 
Methods: This is a retrospective cohort study　which enrolled 14917 participants who visited our hospital for physical checkups from 2008 to 2018 and had normal estimated glomerular filtration rate (eGFR≥60 mL/min/1.73 m2) during the baseline examination. Participants were followed up for the median of 1847 days until 2019 with the development of impaired kidney function (eGFR&lt;60 mL/min/1.73 m2) as the endpoint. The definition of MetS was based on Japanese diagnostic criteria (2005).
Results: Throughout the study, 2150 participants (25.9 per 1000 person-year) developed impaired kidney function after their baseline checkup. The incidence of impaired kidney function was more frequent in participants with MetS (39.3 per 1000 person-year) than without (24.2 per 1000 person-year, p&lt;0.001). Moreover, each metabolic syndrome component was positively associated with the incidence of impaired kidney function, where the incidence of impaired kidney function increased with the number of MetS components at baseline (0, 1, 2 and ≥3 component(s); 17.3, 26.9, 32.9 and 39.7 per 1000 person-year, respectively). Multivariate Cox hazard analysis revealed that MetS was an independent risk factor for impaired kidney function after adjusting for known risk factors (hazard ratio, 1.29; 95% confidence interval, 1.15–1.45). 
Conclusions: Testing for MetS and its components can help evaluate the risk of developing impaired kidney function in the general population.
DOI: 10.6084/m9.figshare.3554727.v1
title: Appendix E. Coverage-based extrapolation.

description: Coverage-based extrapolation.
DOI: 10.6084/m9.figshare.7764065.v1
title: 91 ancient brown bear .bam files

description: 91 ancient brown bear samples mapped to the UrsMar1.0 reference and subsampled down to ~20000 reads per sample.<br>
DOI: 10.6084/m9.figshare.13725901.v1
title: The gff file, cds file and pep file of the African lungfish genome

description: The gene set was predicted according to the methods described in the manuscript "https://doi.org/10.1016/j.cell.2021.01.047".
DOI: 10.6084/m9.figshare.17061728.v1
title: 10x Neutrophil sequencing data.7z

description: 10x seq data from control, mild and severe COVID-19 patients
DOI: 10.6084/m9.figshare.17284823.v3
title: Supporting data of "Pleiotropic actions of phenothiazine drugs are detrimental to bacterial persister cells" article

description: This data support the paper "Pleiotropic actions of phenothiazine drugs are detrimental to bacterial persister cells"<b></b>
DOI: 10.6084/m9.figshare.19786234.v1
title: MAGs and cultured isolate genomes

description: High and medium quality MAGs (136) alongside cultured isolate genomes (22)
DOI: 10.6084/m9.figshare.25335436.v2
title: scDiffusion data

description: Here are the data used in the work <b><i>scDiffusion: conditional generation of high-quality single-cell data </i></b><b><i>using diffusion model</i></b>. ScDiffusion is a model developed for the generation of scRNA-seq data. This model combines the power of latent diffusion model and pre-trained model, and can generated scRNA-seq data with given conditions.<br>
DOI: 10.6084/m9.figshare.13335542.v1
title: chromInfo.hg19.tsv

description: hg19 chromosome sizes<br>
DOI: 10.6084/m9.figshare.15134328.v4
title: Edlinger_etal_database.xlsx

description: The dataset analysed during the study incl. metadata, AMF OTU & taxonomy table.Updated April 2022
DOI: 10.6084/m9.figshare.15181143.v1
title: Study area shapefiles

description: Shapefiles related to study area. Jharia coalfield and Colliery boundary within Jharia coalfield<br>
DOI: 10.6084/m9.figshare.27240027.v1
title: Research on energy optimization control strategy for parallel hybrid tractor based on AIPSO

description: Research on energy optimization control strategy for parallel hybrid tractor based on AIPSO
DOI: 10.6084/m9.figshare.27851817.v4
title: <b>Intestinal permeability of N-acetylcysteine is driven by gut microbiota-dependent cysteine palmitoylation</b>

description: Trillions of intestinal microbiota are essential to the permeability of orally administered drugs. However, identifying microbial-drug interactions remains challenging due to the highly variable composition of intestinal flora among individuals. Using single-pass intestinal perfusion (SPIP) platform, we established the microbiota-based permeability screening framework involving germ-free (GF) and specific-pathogen-free (SPF) rats to compare<i> </i><i>in-situ</i> <i>P</i><sub>eff</sub>-values and metabolomic profiles of 32 orally administered drugs with disputable classifications of permeability. In contrast with SPF controls, N-Acetylcysteine (NAC) exhibited significantly increased permeability in GF rats, which was inversely related to reduced cysteine-3-ketosphinganine by <i>Bacteroides</i>. To further validate these microbiome features, we integrated clinical descriptors from a prospective cohort of 319 participants to optimize a 15-feature eXtreme Gradient Boosting (XGB) model. This machine learning (ML) model of clinical prediction revealed that cysteine palmitoylation by intestinal microbiota has significantly affected NAC permeability, thus leading to discordant biopharmaceutics classification.
DOI: 10.6084/m9.figshare.11911272.v1
title: WN18RR

description: WN18RR is derived from WN18, with data removed to eliminate test-set leakage due to inverse relations. WN18RR contains 93003 triples, connecting 40943 entities via 11 relations.<br><br>Info about WN18: This WORDNET TENSOR DATA consists of a collection of triplets (synset, relation_type, triplet) extracted from WordNet 3.0 (http://wordnet.princeton.edu). This data set can be seen as a 3-mode tensor depicting ternary relationships between synsets.<br>All *.txt files contain one triplet per line, with 2 synset_ids and relation type identifier in a tab separated format. The first element is the synset_id of the left hand side of the relation triple, the third one is the synset_id of the right hand side and the second element is the name of the type of relations between them.<br>The WN18RR.zip file contains the other files, with more compression than the default "download all".<br>
DOI: 10.6084/m9.figshare.14550870.v2
title: User Experience in Social Robots

description: Social robots are increasingly penetrating our daily lives. They are used in various domains, such as healthcare, education, home use and manufacturing. However, introducing this technology for use into conventional environments is not trivial. For users to accept social robots, a positive user experience is vital and it should be considered as a critical part of the robots development process. This may potentially lead to excessive use of social robots and strengthen their diffusion in society<b>. </b>The goal of this study is to summarize the extant literature that is focused on user experience in social robots, and to identify the challenges and benefits of UX evaluation in social robots. To achieve this goal, the authors carried out a systematic literature review that relies on the guidelines for secondary studies in software engineering.<b> </b>Our findings revealed that the most common methods to evaluate UX in social robots are interviews and surveys. UX evaluations were found out to be beneficial in providing early feedback and consequently in handling errors at an early stage. However, despite the importance of UX in social robots, robot developers often neglect to set UX goals due to lack of knowledge or lack of time. This study emphasizes the need for robot developers to acquire the required theoretical and practical knowledge on how to perform a successful UX evaluation.<br>
DOI: 10.6084/m9.figshare.23736036.v1
title: Supplementary Material for: Sex differences in the neural song circuit and its relationship to song acoustic complexity in house wrens (Troglodytes aedon)

description: The song circuit in passerine birds is an outstanding model system for understanding the relationship between brain morphology and behavior, in part due to varying degrees of sex differences in structure and function across species. House wrens (Troglodytes aedon) offer a unique opportunity to advance our understanding of this relationship. Intermediate sex differences in song rate and complexity exist in this species compared to other passerines, and, among individual females, song complexity varies dramatically. Acoustic complexity in wild house wrens was quantified using a new machine learning approach. Volume, cell number, cell density, and neuron soma size were then measured for three song circuit regions, Area X, HVC (used as a proper name), and the robust nucleus of the arcopallium (RA), and one control region, the nucleus rotundus (Rt). For each song control area, males had a larger volume with more cells, larger somas, and lower cell density. Male songs had greater acoustic complexity than female songs, but these distributions overlapped. In females, increased acoustic complexity was correlated with larger volumes of and more cells in Area X and RA as well as larger soma size in RA. In males, song complexity was unrelated to morphology, although our methods may underestimate male song complexity. This is the first study to identify song control regions in house wrens and one of few examining individual variation in both sexes. Parallels between morphology and the striking variability in female song in this species provide a new model for understanding relationships between neural structure and function.
DOI: 10.6084/m9.figshare.28143683.v1
title: FeS XRD Data

description: In situ Laser Heating Diamond Anvil Cell dataset for FeS phase diagram
DOI: 10.17632/dbj9n55pks
title: DVR3D: a program suite for the calculation of rotation–vibration spectra of triatomic molecules

description: Abstract The DVR3D program suite calculates energy levels, wavefunctions, and where appropriate dipole transition moments, for rotating and vibrating triatomic molecules. Potential energy and, where necessary, dipole surfaces must be provided. Expectation values of geometrically defined functions can be calculated, a feature which is particularly useful for fitting potential energy surfaces. The programs use an exact (within the Born–Oppenheimer approximation) Hamiltonian and offer a choice of Jacobi ... Title of program: DVR3DRJZ Catalogue Id: ACNE_v3_0 [ADTB] Nature of problem DVR3DRJZ calculates the bound vibrational or Coriolis decoupled ro-vibrational states of a triatomic system in body-fixed Jacobi (scattering) or Radau coordinates [1,2]. Versions of this program held in the CPC repository in Mendeley Data acne_v1_0; DVR3D; 10.1016/0010-4655(93)90050-M acne_v2_0; DVR3DRJ; 10.1016/0010-4655(94)00139-S acne_v3_0; DVR3DRJZ; 10.1016/j.cpc.2003.10.003 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)
DOI: 10.17632/vjyh3g8w2r
title: A dataset of dynamical social map in ancient China: 618-1644

description: The data set of this article is related to the paper "Dynamical structure of social map in ancient China"  (2022, Physica A, https://doi.org/10.1016/j.physa.2022.128209) . This article demonstrates the data of social relations between cities in ancient China, ranging from 618 AD to 1644 AD. The raw data of social associations between elites used to build social maps are extracted from the China Biographical Database. The raw data contain 14610 elites and 29673 social associations, which cover 366 cities in China. The dataset of this article is relevant both for social and natural scientists interested in the social and economic history of ancient China. The data can be used for further insights/analyses on the evolutionary pattern of geo-social architecture, and the geo-history from the viewpoint of social network.

The dataset contains $3$ files: "Networks.xlsx", "Coordinates.xlsx", and "SocialMap.html". The "Networks.xlsx" has 3 columns, representing the source node (city), target node (city), and weight of a link between two nodes, respectively. The "Networks.xlsx" contains $9$ sheets, which are the data for different dynasties named by Early Tang, Late Tang, Early Northern-Song, Late Northern-Song, Early Southern-Song, Late Southern-Song, Yuan, Early Ming, and Late Ming. Noticeably, the "Networks.xlsx" can be visualized by the network software of Gephi directly. The "Coordinates.xlsx" has 4 columns storing longitude and latitude for all cities that appeared in 9 networks. The first and second columns are English names and Chinese names of cities; the third and fourth columns are longitudes and latitudes of cities. The "SocialMap.html" provides a visualization platform, in which users could select and illustrate the evolution of social maps intuitively.
DOI: 10.17632/w7k5bvr6tv
title: Silk fibroin / DegraPol DP30 - a hybrid biomaterial for biodegradable electrospun heart valve substitutes

description: Processed measurement data for experiments within publication.
DOI: 10.6084/m9.figshare.12245366.v1
title: Dataset for C57BL/6 mice related to "Rapid decay in fast delta following prolonged wakefulness marks a phase of wake-inertia in NREM sleep"

description: This dataset includes 38 binary files for C57BL/6 mice containing sleep/wake scores, power spectra, EEG/EMG variance, and in a subset, cortical temperature. Also included are raw EEG traces for 37 of these mice. Matlab scripts to read both file formats, a data descriptor of the programs included, as well as an algorithm for detecting slow-waves, is included. Data represents 48h of baseline recordings, followed by a 6h sleep deprivation, and 42h of recovery, for a total of 96h. See data_descriptor.pdf for more information.<br><br>
DOI: 10.6084/m9.figshare.22138781.v1
title: hand-dataset

description: 8000 different hand datasets
DOI: 10.6084/m9.figshare.23567292.v1
title: Sequence-based drug design as a concept in computational drug design

description: This is the source data of the manuscript titled 'Sequence-based drug design as a concept in computational drug design'.
DOI: 10.6084/m9.figshare.24271966.v1
title: Low Physical activity

description: We designed a cross-sectional study during the year 2019 to identify the factors associated with LPA in workers of a clinic in Peru
DOI: 10.6084/m9.figshare.25131955.v1
title: All supplementary data used in each figure from Exposure to female olfactory cues hastens reproductive ageing and increases mortality when mating in male mice

description: Theories of ageing predict that investment in reproduction will trade-off against survival and later-life reproduction. Recent evidence from invertebrates suggests that just perceiving cues of a potential mate's presence can reduce lifespan, particularly in males, and that activation of neuroendocrine reward pathways associated with mating can alleviate these effects. Whether similar effects occur in vertebrates remains untested. We tested whether exposure to olfactory cues from the opposite sex would influence mortality and reproductive senescence in male mice. We observed that males exposed to female olfactory cues from middle- to old age (from 10–24 months of age) showed reduced late-life fertility, irrespective of whether they had also been allowed to mate with females earlier in life. Males that were exposed to female odours in conjunction with mating also showed an increased mortality rate across the exposure period, indicating that olfactory cues from females can increase male mortality in some environments. Our results show that exposure to female odours can influence reproductive ageing and mortality in male mice, highlighting that sensory perception of mates may be an important driver of life-history trade-offs in mammals.
DOI: 10.6084/m9.figshare.28737917.v1
title: Original and modified diploid Valencia sweet orange genomes for transposon element insertion detection

description: <pre>The compressed DVS_reference.zip contains two fasta files: "DVS.fasta" and "DVS.masked.34TE.fasta", which needs to be decompressed and put directly in the REF dir before running the pipeline. <br><br>DVS.fasta is the published unmodified diploid Valencia sweet orange genome. It contains both DVS_A1.0 (GCA_022201045.1) and DVS_B1.0 (GCA_022201065.1).<br>DVS.masked.34TE.fasta is the modified version of DVS.fasta, whose 34 TE families members have been masked and standalone TE family members have been added.<br><br># Sequence ID coversion between DVS.fasta and those in GCA_022201045.1 and GCA_022201065.1 <br>DVS_Sequence_ID Chromosome_name GenBank_accession RefSeq_accession Seq_length(bp) SequenceID<br>DVS1A 1 CM039161.1 NC_068556.1 24849987 1A<br>DVS2A 2 CM039162.1 NC_068557.1 32942340 2A<br>DVS3A 3 CM039163.1 NC_068558.1 52308633 3A<br>DVS4A 4 CM039164.1 NC_068559.1 29627743 4A<br>DVS5A 5 CM039165.1 NC_068560.1 38998145 5A<br>DVS6A 6 CM039166.1 NC_068561.1 26176707 6A<br>DVS7A 7 CM039167.1 NC_068562.1 29493366 7A<br>DVS8A 8 CM039168.1 NC_068563.1 30582302 8A<br>DVS9A 9 CM039169.1 NC_068564.1 33998288 9A<br>DVS1B 1 CM039170.1 - 29969561 1B<br>DVS2B 2 CM039171.1 - 32723412 2B<br>DVS3B 3 CM039172.1 - 50541887 3B<br>DVS4B 4 CM039173.1 - 28307159 4B<br>DVS5B 5 CM039174.1 - 37094048 5B<br>DVS6B 6 CM039175.1 - 25332903 6B<br>DVS7B 7 CM039176.1 - 31234485 7B<br>DVS8B 8 CM039177.1 - 32342904 8B<br>DVS9B 9 CM039178.1 - 32056483 9B</pre>
DOI: 10.6084/m9.figshare.13065986.v15
title: Gastric cancer lymph node data set

description: This is a dataset of pathological lymph nodes for gastric cancer. It can be used to test a gastric cancer lymph node metastasis detection model proposed in "Predicting gastric cancer outcome from resected lymph node histopathology images using deep learning".<br>
DOI: 10.6084/m9.figshare.28921397.v1
title: Pancreas dataset with supporting dimension reduction and preprocessing models

description: The AnnData object holds the CytoTRACE time-annotated pancreas dataset. Included are the <code>StandardScaler</code>, <code>PCA</code>, and <code>UMAP</code> models for preprocessing and dimensionality reduction.
DOI: 10.6084/m9.figshare.28924532.v1
title: Wendt & Nandke et al. 2025 Weender analysis.xlsx

description: chemical analysis of flower-rich fengrasland