cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25957564.v1
title: Supplementary Material for: Identification of early events in serrated pathway colorectal tumorigenesis by using digital spatial profiling

description: Introduction: The colorectal serrated pathway involves precursor lesions known as sessile serrated lesions (SSL) and traditional serrated adenomas (TSA). Mutations in BRAF or KRAS are crucial early events in this pathway. Additional genetic and epigenetic changes contribute to the progression of these lesions into high-grade lesions and, eventually, invasive carcinoma. Methods: We employed digital spatial profiling to investigate the transcriptional changes associated with SSL and TSA. The genes identified are confirmed by immunohistochemical (IHC) staining. Colorectal (CRC) cell lines with CEACAM6 overexpression and knockdown were established to study the roles of CEACAM6 on tumorigenesis of CRC. Results: Ten genes were upregulated in SSL and TSA, and seven were upregulated in both types of lesions. IHC staining confirmed overexpression of CEACAM6, LCN2, KRT19, and lysozyme in SSL and TSA. CEACAM6 expression is an early event in the serrated pathway but a late event in the conventional pathway. Using cell line models, we confirmed that CEACAM6 promotes CRC cells' proliferation, migration, and invasion abilities. Conclusion: These results highlight that the transcriptional changes in the early stages of tumorigenesis exhibit relative uniformity. Identifying these early events may hold significant promise in elucidating the mechanisms behind tumor initiation.
DOI: 10.6084/m9.figshare.7775720.v1
title: Supplementary Data 3: Length–width measurements of Cycadopites sp. pollen grains at surface or adjacent the body.

description: This specimen is CNU-MEC-MA2017012.
DOI: 10.6084/m9.figshare.28722251.v1
title: 论文补充材料 ”<b>酵母多样性高</b><b>神农架原始森林</b><b>，包括 23 个新物种，以形态学、系统发育和基因组分析为特征</b>"

description: 补充图 – 基于 D1/D2 或 ITS 序列的邻接树补充表 1 – 本研究收集的 624 个样本的信息补充表 2 – 本研究中 4,451 种酵母分离物的数据集补充表 3 – 本研究中用于系统发育分析的菌株和 GenBank 登录号补充表 4 – 本研究中分离的每种菌株的数量补充表 5 – 本研究中新物种和密切相关物种之间的序列差异补充表 6 – 本研究中新物种和密切相关物种之间的生理和生化差异补充表 7 – 本研究中对其基因组进行了测序的所有菌株的信息补充表 8 – 本研究中使用的所有组装基因组的信息补充表 9 – 本研究中计算的 ANI 值
DOI: 10.6084/m9.figshare.12284249.v1
title: Data from:Mortality, population and community dynamics of the glass sponge dominated community "The Forest of the Weird" from the Ridge Seamount, Johnston Atoll, Pacific Ocean.

description: Data for the above paper. The 2D projection of the abundant specimens from the Forest of the Weird
DOI: 10.6084/m9.figshare.16695457.v5
title: Phodopus roborovskii assembly

description: De novo genome assembly of Phodopus roborovskii from ONT and Illumina data. <br> Annotations in version 5 correspond to version submitted to ENA. <br> Please refer to the genome report for details: <br> Andreotti, S., Altmüller, J., Quedenau, C., Borodina, T., Nouailles, G., Teixeira Alves, L. G., Landthaler, M., Bieniara, M., Trimpert, J., & Wyler, E. (2022). De Novo Whole Genome Assembly of the Roborovski Dwarf Hamster (Phodopus roborovskii) Genome, an Animal Model for Severe/Critical COVID-19. <em>Genome biology and evolution</em>, evac100. https://doi.org/10.1093/gbe/evac100
DOI: 10.6084/m9.figshare.24304438.v1
title: Supplementary Material for: Is the pentagon-copying task more than a cognitive feature? Associations with handgrip strength, gait speed and frailty in older adults

description: Background: The pentagon copy is a sensitive item to the prediction of cognitive decline and dementia. Cognitive and physical/motor decline are able to accelerate the evolution of each other, by representing a common pathway towards frailty. Objectives: To investigate the association of the pentagon-copying task with physical and motor performances and with frailty, in a sample of older adults. Method: This observational, cross-sectional and single-center study was conducted in a Geriatric Outpatients Clinic. Subjects aged ≥ 65 years were consecutively recruited, on a voluntary basis. Subjects with positive psychiatric history, with a severe neurocognitive disorder, with severe limitations on the upper limbs and/or reporting sensory deficits were excluded. The pentagon-copying task was scored from the Mini Mental State Examination; the Qualitative Scoring Pentagon Test (QSPT) was also used. Handgrip strength was measured; a 46-item Frailty Index was calculated; in subjects with autonomous walking, a 4-meter gait speed was also measured. Results: The study included 253 subjects (mean age 80.59 ± 6.89 years). Subjects making a wrong pentagon copy showed greater odds of exhibiting a strength deficit (OR = 3.57; p=0.001) and of being frail (OR= 4.80; p&lt;0.001), and exhibited a slower gait. The QSTP score was significantly correlated with handgrip strength (r= 0.388) and gait speed (r= 0.188), and inversely correlated with frailty (r= -0.428); the QSTP score was significantly different between the quartiles of handgrip strength and frailty. Conclusions: The pentagon copying-task might also be confirmed as a quick screening tool of aging trajectories towards frailty, by jointly evaluating cognitive and physical performances.
DOI: 10.6084/m9.figshare.8849036.v1
title: Phyloseq object

description: Phyloseq RDS object for R import with the data of gonad, tresta and surface of red sea urchin microbiota. Negative control reads were cleaned from each sample.<br>
DOI: 10.6084/m9.figshare.4535618.v1
title: Supplementary Material for: Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges

description: Technological advances have led to an explosive growth of high-throughput functional genomic data. Exploiting the correlation among different data types, it is possible to predict one functional genomic data type from other data types. Prediction tools are valuable in understanding the relationship among different functional genomic signals. They also provide a cost-efficient solution to inferring the unknown functional genomic profiles when experimental data are unavailable due to resource or technological constraints. The predicted data may be used for generating hypotheses, prioritizing targets, interpreting disease variants, facilitating data integration, quality control, and many other purposes. This article reviews various applications of prediction methods in functional genomics, discusses analytical challenges, and highlights some common and effective strategies used to develop prediction methods for functional genomic data.
DOI: 10.6084/m9.figshare.27611421.v1
title: <b>An Empirical Study on Energy Usage Patterns of </b><b>Different Variants of Data Processing Libraries</b>

description: As computing power grows, so does the need for data processing, which uses a lot of energy in steps like cleaning and analyzing data. This study looks at the energy and time efficiency of four common Python libraries—<b>Pandas</b>, <b>Vaex</b>, <b>Scikit-learn</b>, and <b>NumPy</b>—tested on <b>five </b>datasets across <b>21 </b>tasks. We compared the energy use of the newest and older versions of each library. Our findings show that no single library always saves the most energy. Instead, energy use varies by task type, how often tasks are done, and the library version. In some cases, newer versions use less energy, pointing to the need for more research on making data processing more energy-efficient.<br><br>A zip file accompanying this study contains the scripts, datasets, and a README file for guidance. This setup allows for easy replication and testing of the experiments described, helping to further analyze energy efficiency across different libraries and tasks.
DOI: 10.6084/m9.figshare.26356276.v1
title: RoF SIA data

description: Data and code from Jackson et al: <b>Warming reduces trophic diversity in high-latitude freshwater food webs</b>
DOI: 10.6084/m9.figshare.5326870.v1
title: GCMP Australia OTU tables and metadata

description: Raw OTU tables and associated files from the Global Coral Microbiome Project Australia analysis.
DOI: 10.6084/m9.figshare.14199035.v3
title: CMRO2 in Rodents

description: Mean/standard deviation images of the fitted parameters under the two anaesthetics.<br>Extracted ROI data in .csv format. ** Corrected in latest version.<br>Jupyter Notebook with stats analysis.
DOI: 10.6084/m9.figshare.26981521.v1
title: Supporting Dataset S22

description: Files used to identify genomes encoding (pseudo)gene for “1-acyl-sn-glycerol-3-phosphate acyltransferase” (Clades: Mirum, Chrysopicola, Citri, and Poulsonii). Files used to identify genomes encoding (pseudo)gene for “lysophosphatase” of “alpha/beta hydrolase” homologues (Clades: Citri and Poulsoni).
DOI: 10.6084/m9.figshare.3397732.v1
title: A generic webcam image acquisition plugin for ImageJ

description: A new ImageJ acquisition plugin that allows to capture images or videos as series of images from any webcam compliant device in a platform-independent manner, using the Webcam Capture library.
DOI: 10.6084/m9.figshare.19679352.v1
title: Seed positioning in extruded pellets

description: Count data of emergence / survival of Jacksonia furcellata (Grey stinkwood), a native Banksia woodland shrub. Seeds were either positioned precisely at 2 mm (top), 6 mm (middle) and 12 mm (bottom) within pellets (+/- AC) or left untreated (non-enhanced) and sown under the soil surface in the equivalent positions. In two controlled trials; 1) extruded pellets sown above the soil surface and 2) extruded pellets sown below the soil surface and trays were either treated with a pre-emergent herbicide (Simazine), or left unsprayed
DOI: 10.6084/m9.figshare.5350678.v1
title: COMP 330: Software Engineering at Loyola University Chicago

description: In this course, students learn real-world theory and techniques organizations use to create high-quality software on time. Students work on a large programming team to create plans, review progress, measure quality, and make written and oral analyses of their project.
DOI: 10.6084/m9.figshare.13498524.v1
title: Data_Vallecillo_et_al_Reliability_of_animal_counts_and implications_for_the_interpretation_of_trends.xlsx

description: Groups size estimation by 24 observers using animal counting simulation software Wildlife Counts<br>
DOI: 10.6084/m9.figshare.3561966.v1
title: Appendix B. Derivations of conventional and autocorrelated kernel-density estimators.

description: Derivations of conventional and autocorrelated kernel-density estimators.
DOI: 10.6084/m9.figshare.12084687.v1
title: TCGA Pan-Cancer cytolic score, T effecror score and IFNG score

description: TCGA Pan-Cancer cytolic score, T effecror score and IFNG score.
DOI: 10.6084/m9.figshare.1381854.v1
title: LocationInteractions_EID2

description: <pre>Location interactions indicate the possibility of a species being found in a location.</pre> Locations were interpreted at two levels: country and region. Regions correspond to first administrative divisions (e.g., states (USA), departments (France,) home nations of the United Kingdom, etc.) Evidence for these interactions was extracted from NCBI sequences database and NCBI PubMed database. This dataset comprises the following fields: 1 Species: name of species.<br>2 Species classification: the taxonomic classification of the Species.<br>3 Country: official name of the country<br>4 Region: where available the official name of the region (sub-country) part of the location is listed under this header. 5 Sequences count: Total number of nucleotide sequences supporting the interaction. 6 Publication count: Total number of PubMed publications supporting the interaction. 7 Sequences: semi colon separated list of the nucleotide sequence identifiers (GIs) that can be used to retrieve these sequences from the NCBI Nucleotide database. For readability purposes this list was restricted to a maximum of 100 identifiers. 8 Publications: semi colon separated list of the PubMed citation identifiers (PMIDs) that can be used to retrieve these publications from the NCBI PubMed database. For readability purposes this list was restricted to a maximum of 100 identifiers.
DOI: 10.6084/m9.figshare.14458608.v1
title: Supplementary Material for: Air Pollution Is Associated with Cognitive Deterioration of Alzheimer’s Disease

description: <b><i>Introduction:</i></b> Dementia is one of the major causes of disability and dependency among older people worldwide. Alz­heimer’s disease (AD), the most common cause of dementia among the elderly, has great impact on the health-care system of developed nations. Several risk factors are suggestive of an increased risk of AD, including APOE-ε4, male, age, diabetes mellitus, hypertension, and low social engagement. However, data on risk factors of AD progression are limited. Air pollution is revealed to be associated with increasing dementia incidence, but the relationship between air pollution and clinical AD cognitive deterioration is unclear. <b><i>Methods:</i></b> We conducted a case-control and city-to-city study to compare the progression of AD patients in different level of air-polluted cities. Clinical data of a total of 704 AD patients were retrospectively collected, 584 residences in Kaohsiung and 120 residences in Pingtung between 2002 and 2018. An annual interview was performed with each patient, and the Clinical Dementia Rating score (0 [normal] to 3 [severe stage]) was used to evaluate their cognitive deterioration. Air pollution data of Kaohsiung and Pingtung city for 2002–2018 were retrieved from Taiwan Environmental Protection Administration. Annual Pollutant Standards Index (PSI) and concentrations of particulate matter (PM<sub>10</sub>), sulfur dioxide (SO<sub>2</sub>), ozone (O<sub>3</sub>), nitrogen dioxide (NO<sub>2</sub>), and carbon monoxide (CO) were obtained. <b><i>Results:</i></b> The PSI was higher in Kaohsiung and compared with Pingtung patients, Kaohsiung patients were exposed to higher average annual concentrations of CO, NO<sub>2</sub>, PM<sub>10</sub>, and SO<sub>2</sub>. AD patients living in Kaohsiung suffered from faster cognitive deterioration in comparison with Pingtung patients (log-rank test: <i>p</i> = 0.016). When using multivariate Cox proportional hazards regression analysis, higher levels of CO, NO<sub>2</sub>, PM<sub>10</sub>, and SO<sub>2</sub> exposure were associated with increased risk of AD cognitive deterioration. Among all these air pollutants, high SO<sub>2</sub> exposure has the greatest impact while O<sub>3</sub> has a neutral effect on AD cognitive deterioration. <b><i>Conclusions:</i></b> Air pollution is an environment-related risk factor that can be controlled and is associated with cognitive deterioration of AD. This finding could contribute to the implementation of public intervention strategies of AD.
DOI: 10.6084/m9.figshare.21746669.v1
title: Segmentation of sandplain lupin weeds from morphologically similar narrow-leafed lupins in the field

description: Dataset for weed detection used in the paper "Segmentation of sandplain lupin weeds from morphologically similar narrow-leafed lupins in the field". <br> The scripts developed are available on GitHub at mdanilevicz/WeedDetectionML. <br> This repository contains five datasets collected in the field by drone or smartphone in Western Australia, Australia. The images for <strong>field-1, field-2, grow-1</strong> and <strong>grow-2</strong> datasets were collected using the DJI Phantom 4 unoccupied aerial vehicle (UAV) RGB camera. The images were collected between 12 and 2 PM under overcast or clear sky conditions. The details for the image collection can be seen in Table 3. The images were collected with 75% side overlap and 80% front overlap, with five ground control points distributed across the field to increase GPS accuracy. Additionally, 217 images with 4879 sandplain lupins labelled among narrow-leafed lupins were downloaded from the Weed-AI database and named <strong>ext-1 </strong>dataset. <br> In this repository you will find the RGB images, plant-soil segmentation mask obtained using CIVE vegetation index and weed-crop-soil segmentation mask. <br> Detailed methods fro dataset generation is available on the paper, and github repositories. <br> <br>
DOI: 10.6084/m9.figshare.4286423
title: Birth of the cool: a two-centuries decline in emotional expression in Anglophone fiction

description: The presence of emotional words and content in stories has been shown to enhance a story’s memorability, and its cultural success. Yet, recent cultural trends run in the opposite direction. Using the Google Books corpus, coupled with two metadata-rich corpora of Anglophone fiction books, we show a decrease in emotionality in English-speaking literature starting plausibly in the nineteenth century. We show that this decrease cannot be explained by changes unrelated to emotionality (such as demographic dynamics concerning age or gender balance, changes in vocabulary richness, or changes in the prevalence of literary genres), and that, in our three corpora, the decrease is driven almost entirely by a decline in the proportion of <i>positive</i> emotion-related words, while the frequency of <i>negative</i> emotion-related words shows little if any decline. Consistently with previous studies, we also find a link between ageing and negative emotionality at the individual level.
DOI: 10.6084/m9.figshare.4675837.v2
title: Providing and exporting grant data with Europe PMC

description: Europe PMC provides a Grant Finder tool that allows to search through grants awarded by Europe PMC Funder's group.<br>This presentation focuses on details of providing and exporting grant data for funders. The video details advanced search option, e.g. retrieving information about all manuscripts deposited to Europe PMC Plus specific to one of the funders.
DOI: 10.25442/hku.24949091.v2
title: Greenspace data cube for 2020_Part3

description: Greenspace data cube for 2020
DOI: 10.6084/m9.figshare.1259023.v2
title: FISHERY INDUCES SPERM DEPLETION AND REDUCTION IN MALE REPRODUCTIVE POTENTIAL FOR CRAB SPECIES UNDER MALE-BIASED HARVEST STRATEGY

description: 10.1371/journal.pone.0115525 Paper data PLOS ONE Pardo et al. FUNDING : FONDECYT 1110445
DOI: 10.6084/m9.figshare.3519203.v1
title: Appendix A. Equations to determine biomass of mangrove trees and downed wood at Montecristi National Park.

description: Equations to determine biomass of mangrove trees and downed wood at Montecristi National Park.
DOI: 10.6084/m9.figshare.21867942.v7
title: ASD

description: Research conducted with parents of children or adolescents with ASD of both sexes.
DOI: 10.6084/m9.figshare.768500.v3
title: Changes in transcript abundance for cuticular proteins and other genes three hours after a blood meal in Anopheles gambiae

description: Logfiles generated by the blacktie-automated execution of the 'Tuxedo Protocol'-based RNA-seq analysis published in: "<em>Changes in transcript abundance for cuticular proteins and other genes three hours after a blood meal in Anopheles gambiae</em>"
DOI: 10.6084/m9.figshare.24939168.v1
title: Dataset for extended-wavelength diffuse reflectance spectroscopy dataset of animal tissues for bone-related biomedical applications

description: Two extended-wavelength diffuse reflectance spectroscopy datasets from ovine and porcine specimens for bone-related biomedical applications
DOI: 10.6084/m9.figshare.16814359.v1
title: Metabolomic Analysis of Carbohydrate and Amino Acid Changes Induced by Hypoxia in Naked Mole-Rat Brain and Liver

description: These are raw metabolomics file (.mzXML) for 4 hrs hypoxia vs. normoxia treated naked mole-rat and mice. Liver (Li) and brain (br) were examined. n=4 per treatment group. Metabolite identification library is included.
DOI: 10.6084/m9.figshare.22266952.v1
title: urban secne point cloud dataset

description: urban scene point cloud dataset
DOI: 10.6084/m9.figshare.678328.v35
title: About "Categories and Sheaves" (tex)
DOI: 10.6084/m9.figshare.28767860.v1
title: KABARAK UNIVERSITY RESEARCH ETHICS (KUREC) COMMITTEE PERMIT

description: KUREC is the body that approves all research projects conducted by Kabarak University students & staff. Attached is the KUREC permit for this research project
DOI: 10.6084/m9.figshare.5123164.v1
title: Supplementary Material for: MIP-3α Expression in Macrophages Is NOD Dependent

description: <i>Background:</i> The first identified susceptibility gene for Crohn’s disease, <i>NOD2</i>, acts as a sensor for the bacterial-wall peptidoglycan fragment muramyl dipeptide (MDP) and activates the transcription factor nuclear factor-ĸB (NF-ĸB). Upon NF-ĸB activation, intestinal macrophages (IMACs) induce expression of macrophage inflammatory protein (MIP)-3α to attract memory T lymphocytes. We therefore investigated the influence of NOD2 ligation of IMAC differentiation and functional MIP-3α induction. <i>Methods:</i> Human embryonal kidney HEK293 cells were transfected with NOD2 wild-type (NOD2<sup>WT</sup>) and the NOD2 SNP13 variant (NOD2<sup>L1007fsinsC</sup>) and stimulated with MDP. Recruitment of CD45R0<sup>+</sup> and Th17 cells was determined by immunohistochemistry. <i>Results:</i> Endogenous NOD2 stimulation was followed by a dose-dependent increase in MIP-3α secretion in MONO-MAC-6 (MM6) cells. MIP-3α mRNA was also significantly (* p &lt; 0.05) induced in HEK293 transfected with NOD2<sup>WT</sup> via MDP ligation. In vivo cell-cell contacts between IMACs and CD45R0<sup>+</sup> memory T cells as well as recruitment of Th17 cells in patients of NOD2 variants were unchanged as compared to wild-type patients. <i>Conclusion:</i> Our data demonstrate a dose-dependent increase in MIP-3α secretion in the human myeloid cell line MM6 upon MDP. However, MIP-3α-driven recruitment of Th17 cells or CD45R0<sup>+</sup> memory T lymphocytes is not affected in patients carrying heterozygous NOD2 variants.
DOI: 10.6084/m9.figshare.5589775.v1
title: Phylogenetic tree used in analysis from Variation in recombination frequency and distribution across eukaryotes: patterns and processes

description: Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate <i>itself</i> evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies.This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.
DOI: 10.15482/usda.adc/1504518
title: Vegetation, rainfall simulation, and overland flow experiments before and after tree removal in woodland-encroached sagebrush steppe: the SageSTEP hydrology study
DOI: 10.6084/m9.figshare.28711649.v1
title: <b>Park et al. 2025. </b><b>Sub-seasonal impact of El Niño–Southern Oscillation on development of the Indian Ocean Dipole</b>

description: Dataset used in Park et al. 2025. Sub-seasonal impact of El Niño–Southern Oscillation on development of the Indian Ocean Dipole
DOI: 10.6084/m9.figshare.20696866.v2
title: CTMD.xlsx

description: Relevant data of cable temperature mapping model