cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14566278.v1
title: Supplementary Material for: RNA-seq analysis for exploring the pathogenesis of Retinitis pigmentosa in P23H knock-in mice

description: Medicine
DOI: 10.6084/m9.figshare.5122897.v1
title: Supplementary Material for: Mendelian Randomization Study of Interleukin-6 in Chronic Obstructive Pulmonary Disease

description: <i>Background:</i> Cross-sectional studies have demonstrated that increased levels of interleukin-6 (IL6) are present in the airways and blood samples of patients with chronic obstructive pulmonary disease (COPD). <i>Objectives:</i> To investigate the association between IL6 and the risk of COPD using a Mendelian randomization approach. <i>Methods:</i> Eight common single-nucleotide polymorphisms (SNPs) in the region of the <i>IL6 </i>gene were genotyped using both TaqMan and Illumina in the Rotterdam Study, a prospective population-based cohort study consisting of 7,983 participants aged 55 years or older, including 928 COPD patients. At baseline, blood was drawn in a random sample of 714 subjects to measure the IL6 plasma level. Analysis of variance, logistic regression, and Cox proportional hazard models – adjusted for age, gender, pack years, and BMI – were used for analyses. <i>Results:</i> High levels of IL6 (&gt;2.4 pg/ml, the highest tertile) were associated with a three-fold increased risk of developing COPD, in comparison to low levels (&lt;1.4 pg/ml, the lowest tertile). The rs2056576 SNP was associated with a 10% increase in the risk of COPD per additional T allele. However, the association was no longer significant after adjustment. No association was found with other common SNPs in the <i>IL6 </i>gene and COPD. <i>Conclusions:</i> Although increased IL6 plasma levels at baseline are associated with the risk of developing COPD during follow-up, there was no strong evidence for an association between common variation in the <i>IL6 </i>gene and the risk of COPD.
DOI: 10.6084/m9.figshare.25567845.v1
title: Dataset Szabo et al.

description: Dataset of the manuscript.
DOI: 10.6084/m9.figshare.13285778.v1
title: Lake Edward system stock assessment data

description: This data set is of length frequencies, catch per unit effort and catches for lakes Edward, George and kazinga channel in the :Lake Edward system, Uganda. The data is associated with a paper "Assessment of exploited fish species in the Lake Edward System, East Africa" under review in the Journal of Applied Ichthyology
DOI: 10.6084/m9.figshare.25386496.v1
title: Data for: The genome architecture of the copepod <i>Eurytemora carolleeae,</i> the highly invasive Atlantic clade of the <i>E. affinis</i> species complex

description: Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems.<b> </b>Among copepods, populations of the <i>Eurytemora affinis</i> species complex are numerically dominant in many coastal habitats and serve as the food source for major fisheries. Intriguingly, certain populations possess the unusual capacity to invade novel salinities on rapid time scales. Despite their ecological importance, high-quality genomic resources have been absent for calanoid copepods, limiting our ability to comprehensively dissect the genome architecture underlying the highly invasive and adaptive capacity of certain populations.<b> </b>Here, we present the first chromosome-level genome of a calanoid copepod, from the Atlantic clade (<i>Eurytemora carolleeae</i>) of the <i>E. affinis</i> species complex. This genome was assembled using high-coverage PacBio and Hi-C sequences of an inbred line, generated through 30 generations of full-sib mating. This genome, consisting of 529.3 Mb (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb), was anchored onto four chromosomes. Genome annotation predicted 20,262 protein-coding genes, of which ion transporter gene families were substantially expanded based on comparative analyses of 12 additional arthropod genomes. Also, we found genome-wide signatures of historical gene body methylation of the ion transporter genes and the significant clustering of these genes on each chromosome.<b> </b>This genome represents one of the most contiguous copepod genomes to date and among the highest quality marine invertebrate genomes. As such, this genome provides an invaluable resource that could help yield fundamental insights into the ability of this copepod to adapt to rapidly changing environments.
DOI: 10.6084/m9.figshare.26377171.v1
title: DevCCFv1

description: <b>Ages included</b>:<br>Embryonic day (E)11.5, 13.5, 15.5, 18.5, Postnatal day (P)4, P14, P56<br>See <b>DevCCFv1_ReadMe.md</b> forData ElementsAbbreviationsContents DescriptionLicenseConditions for UseCitation InformationSupportRelated LinksRelease Notes.<b>Content Organization</b>Data folders are labeled by ageExample Data Folder Contents:MRI template from at least 4 contrasts (ADC, DWI, FA, T2w)LSFM template registered to MRI morphologyMasks designating Brain from background (and head if relevant)DevCCF Annotation filesExtras Folder containing additional files (e.g. additional MRI contrast template, epDevCCF templates aligned to MRI)Data files within each 'Age' folder are labeled by Age, Template, Modality, and Isotropic Resolution and can be overlayed in the same physical morphology.Additional information in ReadMe file<b>Conditions for Use</b>The DevCCF is a Brain Initiative Cell Census Network (BICCN) resource.BICCN data, tools, and resources, including the DevCCF are generally released under the Creative Commons Attribution 4.0 International Public License (CC BY 4.0, https://creativecommons.org/licenses/by/4.0/legalcode) (“CC BY 4.0 License”). Under the CC BY 4.0 License external data users may freely download, analyze and publish results based on any BICCN open-access data and tools as soon as they are released, provided they give appropriate credit, a link to the license, and indicate if changes were made. The CC BY 4.0 License applies to all open-access datasets generated by individual members of the Network, regardless of type or size.Researchers using unpublished BICCN data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. The Network will continue to publish the results of its own analysis efforts in independent publications.<b>Citation Information</b>Please cite both the DevCCF Manuscript in Nature Communications and this dataset if using the DevCCF in your work.We require that researchers who use BICCN datasets (published or unpublished) in any tools, web applications, presentations, and publications cite and acknowledge the BICCN and BICCN production laboratory(s) for referenced dataset(s).<b>Release Notes</b>DevCCFv1 (current release):This update is paired with the Kronman et al (2024) DevCCF Nature Communications ManuscriptDevCCF_OntologyStructure_v4 has columns for each age denoting included ROIs.Addition of P56, P14, and P04 stereotaxic coordinates filesITK-SNAP Labels for DevCCF, CCFv3 updated to include segmentation abbreviation and full nameAddition of MolecularAtlas Annotations in DevCCF spaceDevCCF Ontology minor cell formatting updatesWhole brain DevCCF Annotations (from hemisphere)Annotation voxel resolution corrected from MRI resolution to 20umCCFv3 Annotations updated to 16bit labels from Kim LabE11.5 Templates & Labels centeredAdded Symmetric Version of Annotations<br>
DOI: 10.6084/m9.figshare.27960981.v3
title: unnamed

description: A full-factorial field experiment
DOI: 10.6084/m9.figshare.7768352.v1
title: Lock-in amplifier data collected using Python instrument control suite of Bluesky and instrbuilder

description: The archived data 'data_figshare.zip' produces figures 3-9 of the paper under review. Data includes .sqlite databases for each run, .json files that describe run starts, run stops, and events. An archive of numpy archives ('numpy_arrays.zip') that store captured time sequences (arrays) is also included, but is a much larger file and is only needed if modified post processing is to be applied on the ADA2200 data. <br>See acquisition and analysis code for more details including information on how to configure databroker to run the analysis code. The attached local_file.yml should be placed into ~/.config/databroker/ and the placeholder 'your_directory' must be modified to point to the data_figshare directory.<br>https://github.com/lucask07/instrbuilder/tree/master/instrbuilder/bluesky_demo/lockin_analysis<br><br>(no legal or ethical requirements)
DOI: 10.6084/m9.figshare.23596476.v1
title: Seric biochemical parameters

description: Seric biochemical parameters (means ± SD) obtained with Wistar rats (<em>Rattus norvegicus </em>Berkenhout, 1769).
DOI: 10.6084/m9.figshare.26965921.v1
title: Supporting Table S3

description: List of <i>Spiroplasma</i> strains used for a local Blastn search
DOI: 10.6084/m9.figshare.26060464.v1
title: LeafData.zip

description: Plant diseases pose a significant threat to agricultural sustainability by reducing crop productivity. The rapid and accurate diagnosis and management of these diseases are crucial. Recent advancements in artificial intelligence have facilitated the development of automated systems for disease detection. This study aims to enhance the classification and severity estimation of diseases on coffee leaf images. The proposed method utilizes Enhanced Multivariance Product Representation (EMPR) to decompose the image into its components prior to classification. A new image is generated from selected components, and its contrast is enhanced using High-Dimensional Model Representation (HDMR) to emphasize the diseased areas of the leaves. The performance of popular convolutional neural network (CNN) architectures, including AlexNet, VGG16, and ResNet50, is tested. The results indicate that VGG16 achieves the highest classification accuracy, approximately 96%, while all models exhibit strong performance in estimating disease severity levels with accuracies exceeding 85%. Notably, the ResNet50 model attains accuracy levels surpassing 90%.
DOI: 10.6084/m9.figshare.25770132.v1
title: Dataset

description: This is the anonymized dataset associated with the study: <b>Quality Of Life in HIV Patients Treated at a Primary Care Clinic: A Cross Sectional Study in Tobago</b>
DOI: 10.6084/m9.figshare.24680751.v1
title: ET modality

description: Folder including the ET (eye-tracking) modality of I DARE, IULM Dataset of Affective REsponses.
DOI: 10.6084/m9.figshare.24903246.v1
title: Realization of an Extremely Anisotropic Heisenberg Magnet in Rydberg Atom Arrays

description: Strong mutual interaction which correlates elementary excitations of quantum matter plays a key role in a range of emergent phenomena, from binding and condensation to quantum thermalization and many-body localization. Here, we employ a Rydberg quantum simulator to experimentally demonstrate strongly correlated spin transport in anisotropic Heisenberg magnets, where the magnon-magnon interaction can be tuned two orders of magnitude larger than the magnon hopping strength. In our approach, the motion of magnons is controlled by an induced spin-exchange interaction through far off-resonant driving, which enables coherent transport of a single Rydberg excitation across a chain of ground-state atoms. As the most prominent signature of a giant anisotropy, we show that nearby Rydberg excitations form distinct types of magnon bound states, where a tightly bound pair exhibits frozen dynamics in a fragmented Hilbert space, while a loosely bound pair propagates and establishes correlations beyond a single lattice site. Our scheme complements studies using resonant dipole-dipole interactions between Rydberg states, and opens the door to exploring quantum thermodynamics with ultrastrong interactions and kinetic constraints.
DOI: 10.6084/m9.figshare.27899610.v1
title: <b>Em</b><b>powering ChatGPT</b><b>with </b><b>a guidance-based approach</b><b>in MTPE learning: effect on student translators</b><b>’</b><b>cognitive process, final translation quality, and learning motivation</b>

description: ChatGPT shows significant potential in machine translation and post-editing (MTPE), prompting discussions on its integration into translator education. However, concerns exist about students’ over-reliance, which can hinder their independent thinking, genuine learning, and overall translation quality. To address this, the study introduces a guidance-based ChatGPT MTPE learning approach inspired by Lee et al. (2024). This model encourages students to articulate their initial thoughts on translation and MTPE tasks before consulting ChatGPT and to use its feedback interactively to refine their strategies. A quasi-experimental study involving 30 first-year translation postgraduates was conducted to examine the effects of the guidance-based approach on student translators’ cognitive processes, final translation quality, and learning motivation, compared to traditional ChatGPT MTPE methods, over a seven-week ChatGPT practicum. Data were collected using eye-tracking, translation quality assessments, and the questionnaire.
DOI: 10.6084/m9.figshare.12477251.v1
title: Interview data

description: This file included the data related to our interviews<br>
DOI: 10.6084/m9.figshare.9702947.v3
title: Supplemental Material- JCEM-AMINO ACID POLYMORPHISMS IN HLA CLASS II DIFFERENTIATE BETWEEN THYROID AND POLYGLANDULAR AUTOIMMUNITY

description: <b>Context</b>: The structure of the human leucocyte antigen (HLA) peptide-binding clefts within the major histocompatibility complex strongly contributes to monoglandular and polyglandular autoimmunity (AP). <b>Objective</b>: To investigate the impact of amino acid polymorphisms on the peptide binding interactions within HLA class II and its association with AP <b>Design: </b>immunogenetic study <b>Setting</b>: Tertiary referral center for autoimmune endocrine diseases <b>Subjects</b>: 587 subjects with AP, autoimmune thyroid disease (AITD), type 1 diabetes (T1D) and healthy controls were typed for HLA class II. <b>Methods: </b>Positions within HLA class II exon 2 where codons translate into different amino acids were detected in all subjects. Amino acids were listed for all codon positions and overall comparisons between disease and control groups with respect to allele distribution at a given locus were performed by assembling rare alleles applying an exact Freeman Halton contingency table test with Monte-Carlo p values based on 150000 samples. <b>Results</b>: The Montecarlo Exact Fisher Test demonstrated marked differences in all three Loci, DQA1, DQB1, DRB1 (p&lt;0.0001) between AP versus both AITD and controls as well as between AP type II (Addison’s disease as major component) and type III (T1D+AITD). Differences were also noted between AP and T1D pertaining to the DRB1 allele (p&lt;0.041). The following seven positions DRB1-13, DRB1-26, DRB1-71, DRB1-74, DQA1-47, DQA1-56, and DQB1-57 significantly contributed to AP <b>Conclusion</b>: Amino acid polymorphisms in codon positions within HLA class II exon 2 confer risk to AP and differentiate between thyroid and polyglandular autoimmunity.
DOI: 10.6084/m9.figshare.7670690.v1
title: RGB Image data of grasses collected for 4 months

description: Gif of grasses imaged for 4 months, capturing its entire life cycle.Plant imaged at the University of Nebraska-Lincoln Innovation Greenhouse from 11 October 2017 through 05 February 2018.<br><br>List of species and PI numbers (Species | Common name | PI number | Variety):Echinochloa esculenta | Japanese millet | PI315699 | BN-14698-63Eleusine coracana | Finger millet | PI462738 | I. E. 595Eragrostis tef | Teff | PI494311 | R286Eragrostis tef | Teff | PI557457 | Red DABIPanicum miliaceum | Proso millet | PI578073 | EarlybirdPennisetum glaucum | Pearl millet | PI537070 | C042Pennisetum glaucum | Pearl millet | PI613116 | NM-6R1Setaria italica | Foxtail millet | N/A | Yugu1Setaria italica subsp. Italica | Foxtail millet | PI614815 | N-Si-2Sorghum bicolor | Sorghum | PI564163 | Tx623bSorghum bicolor | Sorghum | PI533948 | CM052Sorghum bicolor | Sorghum | PI656005 | CM291Zea mays | Maize | PI550558 | DE811Zea mays | Maize | Am24989 | Va99Zea mays | Maize | PI 550473 | B73<br><br>
DOI: 10.6084/m9.figshare.21929466.v1
title: Supplementary Material for: IMPACT OF THE COVID-19 PANDEMIC ON CERVICAL CANCER SCREENING IN SÃO PAULO STATE, BRAZIL

description: INTRODUCTION: The early identification of precursor lesions followed by appropriate treatment prevents development of cervical cancer and its consequences OBJECTIVE: The present study evaluated the influence of the Covid-19 pandemic on cervical cancer screening by comparing the quantity of tests to detect cervical cellular changes performed in Sao Paulo state in 2019, prior to the detection of SARS-CoV-2 in Brazil, to the first (2020) and second (2021) years following its appearance. MATERIALS AND METHODS: Data from Fundação Oncocentro de São Paulo (FOSP), the agency that analyses approximately 220,000 Pap tests annually, was reviewed. RESULTS: A median of 1835 Papanicolaou (Pap) tests were performed in 55 municipalities in 2019. This was reduced to 815 tests in 2020, a 56% decrease (p = 0.0026). In 2021, the median number was 1745, a 53% increase over 2020 levels (p = 0.0233). The 26 municipalities with &gt;1000 tests in 2020 had a median reduction from 4433 in 2019 to 2580 in 2020 (p = 0. 0046). The 29 municipalities with &lt;1000 tests had a median reduction from 951 in 2019 to 554 in 2020 (p &lt; 0.0001). There was a 44% reduction in the number of follow-up cytological evaluations from 2019 to 2020, followed by a 30% increase the following year. However, the percentage of women with a normal finding or with any abnormality remained unchanged. The findings from a histological evaluation of women in Sao Paulo city indicated that the percent of cases positive for CIN-1 (p&lt;0.0410) and CIN-3 (p&lt;0.0012) increased in 2020 and 2021 as compared to 2019 levels. CONCLUSION: A reduction in testing for cervical cancer in the first year of the Covid-19 pandemic, accompanied by an elevated incidence of precancerous lesions in each of the first two years following its initiation, may portend a subsequent increased occurrence of cervical cancer in Brazil.
DOI: 10.6084/m9.figshare.28524467.v1
title: Tables S1 S2 S3_collection 100225.xlsx

description: TABLE S1. Soil properties of the sampling sites.TABLE S2. List of isolates obtained. In the taxonomy columns, the number in parenthesis (%) indicates the level of confidence of taxonomy assignment.TABLE S3. Number of root segments giving fungal isolates and numbers of isolates sequences.
DOI: 10.6084/m9.figshare.19314488.v2
title: Abundance of Zelandopsyche ingens, 2002-4, after experimental manipulation

description: We conducted a replicated density perturbation experiment to manipulate late instar larvae of nine populations of a stream caddisfly, Zelandopsyche ingens, and measured the resulting abundance of the next generation over two years covering the complete lifecycle of one cohort to evaluate influences on their population dynamics. Two datasets are included that cover Z. ingens abundance at (a) the manipulation and (b) patterns of the generation after the manipulation. The locations of the streams used around the University of Canterbury's Cass Mountain Research Field Station in the upper Waimakariri River catchment, New Zealand are described in a map and table in the associated publication.<br>
DOI: 10.6084/m9.figshare.25156559.v1
title: Chromosome-level genome assembly of <i>Platycarya strobilacea</i>

description: <i>Platycarya strobilacea</i> belongs to the walnut family (Juglandaceae), is commonly known as species endemic to East Asia, and is an ecologically important, wind pollinated, woody deciduous tree<i>.</i> To facilitate this ancient tree for the ecological value and conservation of this ancient tree, we report a new high-quality genome assembly of <i>P. strobilacea</i>. The genome size was 677.30 Mb, with a scaffold N50 size of 45,791,698 bp, and 98.43% of the assembly was anchored to 16 chromosomes. We annotated 32,246 protein-coding genes in the genome, of which 96.30% were functionally annotated in six databases.
DOI: 10.6084/m9.figshare.28192085.v1
title: <b>Mystery of Deep Soil Organic Carbon Dynamics Uncovered through Long-term Conservation Tillage Experiments</b>

description: The boreal ecosystem in China serving as a crucial store of soil organic carbon (SOC). However, agricultural soil degradation threatens this carbon reservoir. Conservation tillage has been shown to enhance soil fertility and biodiversity, with the potential to increase SOC stocks. Yet, the composition and origins of SOC in boreal regions—particular in deep soil profiles (i.e., 20–100 cm) —remain unclear. Here, we present findings from a 15-year field trial in a typical boreal agroecosystem, comparing no-till with straw mulching (NT) and conventional tillage (CT) under a maize-soybean crop rotation. We found that NT significantly increased active SOC fractions in deep soil, including microbial biomass carbon (MBC, by 104%), particulate organic carbon (POC, by 112%), light fraction organic carbon (LFOC, by 42%) and dissolved organic carbon (DOC, by 22%). NT increased the stability of microbial necromass carbon (MNC) in the deep soil by increasing the ratio of fungal necromass C to bacterial necromass C (by 55% compared to topsoil). Plant-derived carbon showed increased stability in the deep soil, as evidenced by decreased (Ac/Al)s values (-58%) and (Ac/Al)v values (-28%) and a 84% rise in V-type phenols under NT. In the 20-100 cm layer, FNC and MBC emerged as key factors influencing SOC contents. Our findings suggest that long-term NT in boreal agroecosystems affects SOC dynamics in both topsoil and deep soil, providing new insights into carbon sequestration under long-term conservation tillage. These results contribute to a more comprehensive understanding of the carbon cycle in sustainable agriculture.
DOI: 10.6084/m9.figshare.4765150.v1
title: Extroverts tweet differently from introverts in Weibo

description: Specification of the Dataset<br>1. The data set comes from our paper titled “Extroverts tweet differently from introverts in Weibo”. <br>2. psychological-score.txt contains genders, ages, and scores of Big-Five personality traits of the 293 valid participants (anonymized and permit the publication) from self-reports.<br>3. user-data contains the Weibo data of the 293 participants (1.txt ~ 293.txt) and the 7249 users (294.txt ~ 7542.txt) identified by our SVM classifiers. For each user, a json format of its completely anonymized online profiles (a tweet in each line) is given.<br>4. Any issues please contact jichang@buaa.edu.cn.