cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7743026.v1
title: ALL_GENE_EXPR_DEG_ANALYSIS.xlsx

description: Information for each sample, including the expression abundance of each gene, testing statistics and DEGs<br> ---------------------------------<br>target_id gene ID test_stat sleuth DEG testing statistics pval p-value qval adjusted p-value ext_gene gene symbol description gene categories including protein_coding, lincRNA, antisense_RNA, NOVEL_lncRNA, sense_intronic and sense overlapping HCM269-sc6.LV expression abundance (TPM) for each gene in each sample HCM the mean of expression abundance of all HCM samples Normal the mean of expression abundance of all Normal samples Log2FC log2 fold change between HCM and Normal StatSig Statistically significant BioSig Biologically significant Sig Both statistically and biologically significant
DOI: 10.17632/wb7f2r7d7r
title: Airfoil Shape Optimization RL Environment

description: This file contains MATLAB RL environment code for the optimization of NACA airfoil. The agents need to be trained using the RL Designer App in MATLAB to facilitate simulation and obtain optimized airfoil geometries. The environment can be customized according to the user’s requirements.
DOI: 10.6084/m9.figshare.12398309.v2
title: Search query lists

description: Lists of search queries used in the analysis of the paper<br>
DOI: 10.17632/6rxj72n2sf
title: A program for calculating Regge trajectories in potential scattering

description: Title of program: REGGE TRAJECTORY Catalogue Id: AAGA_v1_0 Nature of problem This program solves the radial Schrodinger equation and finds the positions and residues of Regge poles for a Yukawa potential and follows these poles automatically as a function of energy. Alternatively, it will compute the S-matrix and phase shifts at a specified grid of points in the complex angular momentum plane and for a given set of energies. The program can be modified to calculate Regge trajectories for any potential which can be specified by an analytic formula. Versions of this program held in the CPC repository in Mendeley Data AAGA_v1_0; REGGE TRAJECTORY; 10.1016/0010-4655(69)90003-4 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)
DOI: 10.6084/m9.figshare.28439858.v1
title: <b>Cerv-D: A Dataset of Cervical Deviations During Shoulder Exercises Derived from 3D Kinematic Analysis</b>

description: <b>Cerv-D</b> measures cervical (neck) deviations during shoulder exercises using 3D kinematic data obtained from pose estimation and landmark tracking <i>(Shoulder-KX Dataset)</i>. The process begins by identifying key anatomical landmarks, including the nose and the left and right claws (located in the foot). The midpoint between the two claws is calculated and a line is drawn from the nose to this midpoint. The angle between this line and the vertical axis is then determined, representing the tilt of the head and neck. The neck deviation is calculated as the difference between this angle and the ideal upright posture of 90 degrees; this deviation quantifies how much the head is misaligned during the exercise.
DOI: 10.6084/m9.figshare.28899986.v1
title: Genesis of exceptionally scandium-rich clinopyroxene in magnetite ore at El Laco: Implications for the formation of iron oxide-apatite (IOA) deposits

description: Data for the manuscript entitled "Genesis of exceptionally scandium-rich clinopyroxene in magnetite ore at El Laco: Implications for the formation of iron oxide-apatite (IOA) deposits" by Qiuhong Xie et al.
DOI: 10.17632/sxz7kpw4vk
title: YTHDC1 cooperates with the THO complex to prevent RNA damage-induced DNA breaks

description: Original files (microscopy and gel/blot images) for the above named manuscript. Please see the manuscript (doi: https://doi.org/10.1101/2024.03.14.585107) for details.
DOI: 10.17632/wgd66f8n6h
title: Wheat Leaf Dataset

description: Ethiopia has a huge resource for planting several crops, thus wheat is one of the major crops which feed the population, but the crop has been infected by viruses, Bacteria, and Fungi. In this study, the two major diseases namely Stripe Rust and Septoria wheat leaf image were used for experimentation. Currently, the wheat disease mentioned above is a major headache not only for farmers but also for plant pathologists. Furthermore, the pathologist uses the naked eye observation for the detection of wheat disease, sometimes it is challenging to detect without using the laboratory material. Several types of research conducted disease identification and detection using the traditional machine learning algorithms. Thus algorithms have drawbacks since the feature extraction is expert-based and the amount of data processing required is high relative to the machine learning. Because of this, the deep learning methodology was used to detect wheat disease. The approach has three main phases. The first phase is to collect the dataset from the wheat farm, and the image has three categories i.e. ‘Healthy Wheat Leaf’, ‘Strip Rust’, and ‘Septoria Disease’. Then the dataset is partitioned using the 80%-10%-10% approach which is used for training, validation, and testing respectively. The second phase is to design a neural network by experimenting with the best hyperparameter. Finally, the best model was selected and tested with unseen image data. The dataset contains 208 stripe rust affected leaf, 102 healthy leaf and 97 septoria affected leaf disease-infected image pictures. From this, 80% of the images were used for training, l0% were used for validation, and the remaining 10% were used for testing. During training, the data augmentation technique is used to generate more images to fit the proposed model. The experimental result demonstrates that the proposed model is effective for the detection of wheat leaf disease (Strip Rust and Septoria). The pretrained model used for experimentation are VGG19, InceptionV3, MobileNet, and EfficientNet. Among mentioned pretrained models MobileNet has achieved the best result and the model can successfully classify the given image with a testing accuracy of 90% with images captured in the real wheat farm with a heterogeneous environment.
DOI: 10.17632/xk9bzb6kbc
title: Pacific spiny dogfish (Squalus suckleyi) thermal tolerance

description: Datasets are presented for analyses in Bouyoucos et al. (In Prep). See the 'metadata' text file for descriptions of individual .csv files and descriptions of column headings. Experiments on male Pacific spiny dogfish (Squalus suckleyi) were approved by the Bamfield Marine Sciences Centre (BMSC) Animal Care Committee (animal user protocol RS-22-10). Male dogfish were collected using rod-and-reel and demersal longline in Barkley Sound (British Columbia, Canada) under the approval of Fisheries and Oceans Canada permit XR-199 2022. This dataset supported a study that tested the hypothesis that behavioural responses to acute temperature increase are associated with cardiorespiratory thermal tolerance and thermal cellular stress. Dogfish were first tested for cardiorespiratory and behavioural thermal limits to test for associations between thermal performance and tolerance. Then, biochemical markers of secondary stress, aerobic and anaerobic enzyme activities, and molecular markers of cellular stress were determined for various tissues at the agitation temperature, and secondary stress markers were determined at the critical thermal maximum. These data provide new information on putative physiological mechanisms underpinning the agitation temperature and expand knowledge on thermal tolerance in elasmobranchs.
DOI: 10.6084/m9.figshare.21843330.v3
title: Promotion

description: This repository hosts data for reproducing results in the paper "The Gender Gap in Scholarly Self-Promotion on Social Media".
DOI: 10.6084/m9.figshare.24207942.v1
title: <b>S1 Dataset.</b>

description: <b>Raw data set of test 1 with information regarding answers of each participant, optical determination done by the principal investigator and MALDI-TOF results.</b>
DOI: 10.6084/m9.figshare.27315477.v1
title: Facial Drug Abuse Synthetic Dataset Generated with Face Fusion and Genetic Algorithms

description: Facial Drug Abuse Synthetic Dataset Generated with Face Fusion and Genetic Algorithms
DOI: 10.17632/ccrv9p4jbt
title: The Looming Threat of Material Price Surges to Decarbonization in Developing Economies

description: This folder contains supplementary data used to generate figures and results for "The Looming Threat of Material Price Surges to Decarbonization in Developing Economies" by Pengfei Yuan et al
all_metal_scenario_means contains data in Fig. 1.
DOI: 10.6084/m9.figshare.16754965.v1
title: Consensus protein localization encodings for all OpenCell targets

description: This dataset consists of the raw consensus encodings (or latent-space representations) of the protein localization patterns for all targets in the OpenCell library. These encodings are generated by a self-supervised machine learning model called cytoself trained on the OpenCell imaging dataset. Briefly, these encodings correspond to the flattened VQ2 layer of the VQ-VAE2-like component of the cytoself model, and are provided here as a mean over all images of each target. The resulting matrix of encodings has dimensions of 1294x9216, corresponding to the library of 1294 OpenCell targets and the 9216 dimensions of the flattened VQ2 layer of the cytoself model. This matrix is provided along with target metadata in the form of an `anndata` object. Please refer to our GitHub repo (2021-opencell-figures) for usage examples.
DOI: 10.6084/m9.figshare.2066907.v2
title: Conference Datasets

description: Each file contains information about scientists conference attendance for particular conference series. Data are fully anonymized.
DOI: 10.6084/m9.figshare.28587083.v1
title: Additional file 2 of Health-related quality of life in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Post COVID-19 Condition: a systematic review

description: Additional file 2
DOI: 10.17632/2rth9mzk8m
title: Data for: A Bi-level Programming Approach for Global Investment Strategies with Financial Intermediation

description: Stock returns from USA listed enterprises within the period 2003-2014. Each compressed folder contain 12 CSV files, corresponding to the stock returns of each listed enterprise along the analyzed year (for 12 years). The first folder contains daily stock returns, while the second folder contains monthly stock returns. A graphical visualization of this data set is available in Figure 2, Section 5.1 of the article.
DOI: 10.17632/sr7t6xfh8w
title: Research Data-Dataset of usage pattern and energy analysis of an Internet of Things-enabled ceiling fan.

description: The data consists of timestamp, temperature, humidity, and speed of a BLDC ceiling fan. The dataset is comprised of the usage pattern from the fans of bedroom, living room, and lounge obtained with the resident’s consent. This data is useful for data scientists, environmentalists, fan manufacturers, architects, social scientists, and several other field enthusiasts.
DOI: 10.6084/m9.figshare.1153921.v1
title: Human TCRs and CDR3s sequenced from healthy volunteers and HIV-infected patients, before and after 14 weeks of therapy

description: We have employed an error-correcting, high-throughput transcript sequencing protocol to profile impact of HIV infection upon the T-cell receptor repertoire. We have sequences both alpha and beta chain TCR repertoires from 2.5ml of peripheral blood for 16 antiretroviral (ART)-naive HIV patients (de-identified reference numbers prefixed 'P0'). Two samples per patient were processed: one immediately before starting therapy ('v1') and another shortly after starting ('v2', after an average 14 weeks). We additionally sequenced the repertoires of ten healthy volunteers ('HV'), taking two blood samples three months apart for four of those donors (HV01 to HV04) in order to compare TCR dynamics over a comparable time frame. One of these healthy donors (HV01) and a further healthy donor (HVD1) also gave a larger blood sample, which was separated into CD4+ and CD8+ T-cell populations by FACS, and their TCR repertoires were seqeunced. Having amplified and sequenced the TCR repertoires of these 100 samples, we identified their VJ recombinations using a modified version of Decombinator (called vDCR), TCR analysis software designed in our lab. We then made use of random barcode sequences introduced before amplification to error- and frequency-correct our Decombinator assignations (DCRs), before translating them and extracting their complementarity determining region 3 (CDR3) sequences. Here we present the results of these analyses. The .dcrcdr3 files in this fileset consist of a unique DCR assignation per line, the CDR3 sequence it encodes, and the frequency with which that TCR appeared in the data following error-correction. Each line follows the format: 'V, J, Vdel, Jdel, insert: CDR3, freq' (V = V gene, J = J gene, Vdel = number of deletions from V, Jdel = number of deletions from J, insert = string of nucleotides from the end of the deleted V to the start of the deleted J, CDR3 = translation CDR3 sequence, from the second conserved cysteine residue in the V to the conserved phenylalanine of the FGXG motif of the J, freq = error-corrected frequency of that assignation.) The raw sequence data fastq files from which these TCRs were extracted is available in the Sequence Read Archive (SRA) under the Study accession number SRP045430. The AccessionKey.xls spreadsheet cross-references all filenames with their appropriate SRA individual accession numbers. The Python scripts which were used to generate this data from that raw fastq data are also available on figshare (see links below).
DOI: 10.6084/m9.figshare.1209620.v1
title: Gossip-Based Solutions for Discrete Rendezvous in Populations of Communicating Agents

description: Data supporting the results of the PLoS ONE journal paper "Gossip-Based Solutions for Discrete Rendezvous in Populations of Communicating Agents"
DOI: 10.6084/m9.figshare.26122543.v1
title: Synthetic Design-Related Data Generated by LLMs

description: To produce a domain-specific dataset, GPT-4 is assigned the role of an engineering design expert. Furthermore, the ontology, which signifies the design process and design entities, is integrated into the prompts to label the synthetic dataset and enhance the GPT model's grasp of the conceptual design process and domain-specific knowledge. Additionally, the CoT prompting technique compels the GPT models to clarify their reasoning process, thereby fostering a deeper understanding of the tasks.
DOI: 10.6084/m9.figshare.28697042.v2
title: Black Spruce Phenology using PhenoCam and Satellite Data

description: This dataset contains unfiltered PhenoCam images from the year 2017 to 2020, Time-series indices, Anova model results and Google Earth Engine (GEE) codes for indices extraction.<br>This dataset contains PhenoCam raw data, analysis of time-series indices, ANOVA model results and Google Earth Engine (GEE) codes for satellite-derived vegetation indices in the boreal forest of Quebec, Canada, from 2017 to 2020.<br>Dataset posted on 2025-03-31, 10:27 authored by <b>Akash Kumar, Ganesh Sai Sivani Noolu, Siddhartha Khare and Sergio Rossi.</b><br><br><i>All communications are forwarded to </i><b><i>akash_k@ce.iitr.ac.in</i></b>
DOI: 10.6084/m9.figshare.8293319.v1
title: vTemperature.m from Nectar, humidity, honey bees (<i>Apis mellifera</i>) and varroa in summer: a theoretical thermofluid analysis of the fate of water vapour from honey ripening and its implications on the control of <i>Varroa destructor</i>

description: This theoretical thermofluid analysis investigates the relationships between honey production rate, nectar concentration and the parameters of entrance size, nest thermal conductance, brood nest humidity and the temperatures needed for nectar to honey conversion. It quantifies and shows that nest humidity is positively related to the amount, and water content of the nectar being desiccated into honey and negatively with respect to nest thermal conductance and entrance size. It is highly likely that honeybees, in temperate climates and in their natural home, with much smaller thermal conductance and entrance, can achieve higher humidities more easily and more frequently than in man-made hives. As a consequence, it is possible that <i>Varroa destructor</i>, a parasite implicated in the spread of pathogenic viruses and colony collapse, which loses fecundity at absolute humidities of 4.3 kPa (approx. 30 gm<sup>−3</sup>) and above, is impacted by the more frequent occurrence of higher humidities in these low conductance, small entrance nests. This study provides the theoretical basis for new avenues of research into the control of varroa, via the modification of beekeeping practices to help maintain higher hive humidities.
DOI: 10.17632/nrm732hd83
title: Lake-water-temperature regulation under diurnal and seasonal scales of environmental forcing, Agamon Hula, Israel

description: Measured enviromental forcing and lake-water temperature regulation for 20 m from Agamon Hula, Isreal.
DOI: 10.6084/m9.figshare.27914634.v1
title: Classification of the reports and publications related.xlsx

description: Antimicrobial resistance (AMR) is a global issue impacting environmental, animal, and human health. The presence of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARG) has been increasingly reported in humans, the environment, and wild animals. This study aimed to analyze and compare AMR occurrence in bacterial isolates from wild animals in South American environments with low and high anthropogenic impact through a systematic review. While several studies were identified, half of the included countries had no reports. Most studies focused on the Aves and Mammalia classes, particularly the Chiroptera and Rodentia orders, and <i>Escherichia coli</i> and <i>Salmonella enterica</i> bacterial species. Subgroup meta-analyses revealed that, for most antimicrobials, a higher proportion of AMR was found in environments with high anthropogenic impact or no significant difference. Surprisingly, some beta-lactams showed a higher proportion of AMR in environments with low anthropogenic impact. This finding raises questions about the origin and spread of AMR in wild animals and highlights the need for further studies to understand the dynamics of AMR in environments with different levels of human intervention.
DOI: 10.6084/m9.figshare.3563772.v1
title: Supplement 1. Matlab source code for performing TVARSS(p), TVVARSS(1), and SETARSS(p) model fitting.

description: File List TVARSS.m -- Matlab source code to run TVARSS(p) model fitting -- (MD5: a84eab62b227b7e74cd28f42ec144e45) <br> TVVAR1SS.m -- Matlab source code to run TVVARSS(1) model fitting -- (MD5: 7395757e2c19dfe261a3a3422231af6f) <br> SETARSS.m -- Matlab source code to run SETARSS(p) model fitting -- (MD5: a39cf09301a343a622a8cc2834493236) <br> timevaryingfunct_24Apr12.m -- Matlab source code called by TVARSS -- (MD5: aa488ed19ac261db895e1565487b1816) <br> VAR1funct_24Apr12.m -- Matlab source code called by TVVARSS -- (MD5: 9070310f4eb934f3f4f5c0b7090c02b1) <br> twopointfunct_25Nov11.m -- Matlab source code called by SETARSS -- (MD5: 66becb86164b59403b3152b5868d3a18) <br> anneal.m -- Matlab source code for simulated annealing (from Joachim Vandekerckhove) -- (MD5: 70672ad1d98fcf004cea433bbcbc214d)<br> IvesDakos_Fig2.m -- Matlab source code to produce Fig. 2 -- (MD5: 946a820ebea42355170aebdb3b759c04) <br> IvesDakos_Fig4.m -- Matlab source code to produce Fig. 4 -- (MD5: 0864b27fcdd01571340dc7fbf61a2161) <br> IvesDakos_Fig5.m -- Matlab source code to produce Fig. 5 -- (MD5: fae8fc7fb7e9cde13f36b6291b46a9ca) <br> IvesDakos_Fig6.m -- Matlab source code to produce Fig. 6 -- (MD5: 63b775992103040060c44389337ec70c) <br> ASS_May_tomin.m -- Matlab source code generating the May harvesting model -- (MD5: 0f2941acf30fe7f84a08d20926e007a9) <br> ASS_NB_tomin.m -- Matlab source code generating the Nicholson-Bailey model -- (MD5: 67dbcc602da7d02b947f4bb11cb80270) Description The functions TVARSS.m, TVVAR1SS.m, and SETARSS.m perform statistical analyses for TVARSS, TVVARSS, and SETARSS models. The code IvesDakos_FigX.m produces Fig. <i>X</i> in the manuscript. The remaining code is called by the other programs.
DOI: 10.17632/6hp9ck4r3w
title: Replication data for "Geography, Trade, and Internal Migration in China"

description: See the readme file inside for replication steps
DOI: 10.17632/hdgpwpjbh9
title: Ambroggi. Etude géologique du versant méridional du Haut Atlas Occidental et de la plaine du Sous. Faculté des sciences , 1963.

description: Maestrichtian consulted on pages 203-207;
Eocene consulted on pages 209-214;
Probable Upper Oligocene consulted on pages 215-219;
Miocene consulted on pages 219-220;
Pliocene and Quaternary consulted on pages 212-256.
DOI: 10.17632/sd97vh79v8
title: Pervasive Warming Bias in CMIP6 Tropospheric Layers

description: CMIP6 and observational data for trend comparisons in the lower- and mid-troposphere
DOI: 10.6084/m9.figshare.29095823.v1
title: Data for Yu et al., 2025 “Predicting Avian Roadkill Risks in Shanghai: Insights from Ensemble Modelling of Small, Opportunistic Data”

description: Data for Yu et al., 2025 "Predicting Avian Roadkill Risks in Shanghai: Insights from Ensemble Modelling of Small, Opportunistic Data". For the zipped files, "Env.zip" contained all pre-processed candidate explanatory variables listed in this study (original sources are listed in the publication); "Predictions.zip" contained the output raster files of the ensemble model (i.e. the predicted avian roadkill risks in Shanghai). Two .csv files are the pre-processed avian roadkill samples used to develop the ensemble model (i.e. "Preprocessed_avian_roadkill_occurrence_sample.csv") and independent validation sample data digitalised from the interactive map in a citizen science mobile app, known in translation as “Road-killed Animal Survey Records”, developed by the Lab of Animal Behavior & Conservation from Nanjing University.
DOI: 10.6084/m9.figshare.5128399.v1
title: Supplementary Material for: Improving Research Practice in Rat Orthotopic and Partial Orthotopic Liver Transplantation: A Review, Recommendation, and Publication Guide

description: <b><i>Background:</i></b> Due to a worldwide shortage of donor organs for liver transplantation, alternative approaches, such as split and living donor liver transplantations, were introduced to increase the donor pool and reduce mortality on liver transplant waiting lists. Numerous details concerning the mechanisms and pathophysiology of liver regeneration, small-for-size syndrome, rejection, and tolerance in partial liver transplantation facilitated the development of various animal models. The high number of preclinical animal studies contributed enormously to our understanding of many clinical aspects of living donor and partial liver transplantations. <b><i>Summary:</i></b> Microsurgical rat models of partial orthotopic liver transplantation are well established and widely used. Nevertheless, several issues regarding this procedure are controversial, not clarified, or not yet properly standardized (graft rearterialization, size reduction techniques, etc.). The major aim of this literature review is to give the reader a current overview of rat orthotopic liver transplantation models with a special focus on partial liver transplantation. The aspects of model evolution, microsurgical training, and different technical problems are analyzed and discussed in detail. Our further aim in this paper is to elaborate a detailed publication guide in order to improve the quality of reporting in the field of rat liver transplantation according to the ARRIVE guidelines and the 3R principle. <b><i>Key Messages:</i></b> Partial orthotopic liver transplantation in rats is an indispensable, reliable, and cost-efficient model for transplantation research. A certain consensus on different technical issues and a significant improvement in scientific reporting are essential to improve transparency and comparability in this field as well as to foster refinement.