cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19652754.v1
title: 10x Single-Cell RNAseq Colon (Reference)

description: Human epithelial, B, and stromal cells from the colon in a SingleCellExperiment object with labels. These data can be used as a reference set for training cell-type annotation classifiers. These three different cell-types were combined from the following original studies: <br> Epithelial cells: Wang, Y., Song, W., Wang, J., Wang, T., Xiong, X., Qi, Z., ... & Chen, Y. G. (2020). Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. <em>Journal of Experimental Medicine</em>, <em>217</em>(2). <br> B cells: Huang, B., Chen, Z., Geng, L., Wang, J., Liang, H., Cao, Y., ... & Zhang, Y. (2019). Mucosal profiling of pediatric-onset colitis and IBD reveals common pathogenics and therapeutic pathways. <em>Cell</em>, <em>179</em>(5), 1160-1176. <br> Stromal cells: Kinchen, J., Chen, H. H., Parikh, K., Antanaviciute, A., Jagielowicz, M., Fawkner-Corbett, D., ... & Simmons, A. (2018). Structural remodeling of the human colonic mesenchyme in inflammatory bowel disease. <em>Cell</em>, <em>175</em>(2), 372-386.
DOI: 10.6084/m9.figshare.24587328.v5
title: Exome-wide MTR scores computed with RGC-ME data for all possible missense variants in canonical transcripts

description: Exome-wide missense tolerance ratio (MTR) scores computed with RGC-ME exome sequencing data for all possible missense variants in canonical transcripts. Coordinates are in hg38. Variants are labeled “uid” and follow the format CHR:POS:REF:ALT. Other fields include: Ensembl v100 transcript ID, gene name, gene ID, exon number, amino acid position (“aa_position”), adjusted tri-nucleotide context mutation rate (“adj_rate”), and protein length. Parameters for computing MTR at each variant include the expected (“synExp” and “misExp”, resulting in the MTR denominator “expMTR”) and observed (“synObs” and “misObs”, resulting in the MTR numerator “obsMTR”) counts of missense and synonymous variants in each 31-codon window centered on possible missense variants exome-wide using data from 822K related individuals. Computed MTR values for all missense variants, p-value from binomial test, and FDR corrected q-value are included. MTRPercentile_exome and MTRPercentile_transcript represent the percentile rank of MTR score across the exome and per transcript, respectively. Regions with long, continuous regions of median MTR=0 as defined by segmentation were removed as likely artifacts stemming from lack of high-quality observed variants. A small number of genes retained MTR=0 segments because there were sufficiently high counts of observed synonymous variants relative to the lack of missense variants.<br>
DOI: 10.6084/m9.figshare.28793246.v1
title: <b>Research on Multi-Parameter Optimization of Coupled Models Using PINN Based on Numerical Mode</b>

description: Traditional data assimilation methods may lead to erroneous parameter estimation due to system parameter compensation effects. In recent years, with the emergence of neural network technology, particularly the introduction of Physics-Informed Neural Networks (PINN), it has become possible to effectively embed physical models into neural networks to optimize biased parameters. However, the traditional PINN-RK framework is limited to solving models that couple a single physical quantity, which integrates Runge-Kutta nodes into the neural network loss function. The study introduces a novel PINN-MCS framework based on PINN-RK. The PINN-MCS can flexibly integrate neural networks with multivariable coupled models. To improve performance when optimizing multiple parameters simultaneously, we set the initial learning rate based on the sensitivity of the parameters in the physical model. This strategy has been proven in the study to accelerate the overall parameter convergence. This research conducted perfect twin and biased twin experiments on a Five Variable Coupled Climate Model. In the perfect twin experiment, system bias arises from imperfect parameter values. The experimental results show that the PINN-MCS framework can efficiently optimize parameters with various sensitivities to the true values. In the biased twin experiment, system bias arises from imperfect numerical discretization schemes. The results show that after optimizing the initial parameters using observational data generated by the imperfect dynamical core, the optimized parameters can compensate for the system bias introduced by the numerical scheme, improving the model's predictive performance.
DOI: 10.6084/m9.figshare.6823373.v1
title: RPS Sistem Informasi Manajemen

description: Rancangan Pembelajaran Studi untuk mata kuliah Sistem Informasi Manajemen yang ditujukan kepada mahasiswa Manajemen tingkat sarjana.<br>
DOI: 10.6084/m9.figshare.12162492.v1
title: GTT-1-protein-032.dcd

description: Trajectories dataTrajectories of WW domain
DOI: 10.6084/m9.figshare.23507517.v3
title: ContScout supporting data

description: Script and supporting data for Balint et al "ContScout: Sensitive detection and removal of contamination from annotated genomes"
DOI: 10.17632/sxf9kkb6t2
title: Survey Data on Bullying Involvement among School-going Adolescents in India

description: The data was collected from 169 school-going adolescents of grades six to twelve from two cities in South India. The survey forms comprised the demographic profile sheet, Adolescent Peer Relations Questionnaire (Parada, 2000), and Online Victimization Scale for Adolescents - General Online Victimization subscale (Tynes et al., 2010). The Adolescent Peer Relations Questionnaire by Parada (2000) consists of 36 items to assess bullying experiences in the past year of school life. It is used to measure bullying and victimization experiences across three dimensions that are physical, verbal, and social. Each of the six subscales in this questionnaire is measured with six items. The Online Victimization Scale for Adolescents by Tynes et al. (2010) consists of 21 items across four subscales, general online victimization, sexual online victimization, individual online racial discrimination, and vicarious online racial discrimination. The present data set used the General Online Victimization subscale which consists of eight items.
DOI: 10.6084/m9.figshare.105471.v1
title: Forming of adaptation of students’ organism to the cold factor by the methods of active conditioning to the cold in the process of physical education in the institute of higher

description: A research purpose was a ground of the system forming of adaptation to the cold of organism of students which master speciality the "Cryogenic technique and technologies». 25 students of the first course took part in research. The level of adaptation possibilities of organism is found out to the cold for students. Offered and tested technology of improvement of these indexes. Medical tests, which allow to define the measure of adaptability of organism to cold a factor, design of method of adaptation this factor, were utillized. Methodical advices are recommended in relation to facilities of adaptation to the cold of organism in home terms within the framework of observance of healthy way of life. It is set that endurance and firmness to the sharp overfalls of temperatures is arrived at by implementation of exercises in the conditions of sharp fluctuations in a temperature: physical exercises in winter were executed in an apartment and then outdoors. It is also suggested to utillize a contrasting shower. It is set that the level of adaptation to the cold substantially became better: unsatisfactorily - 51,7 %, satisfactorily - 28,8 %, well-19,5 %.
DOI: 10.6084/m9.figshare.19351730.v1
title: data2.csv

description: Data 2 contains the data of Fig. 4.
DOI: 10.6084/m9.figshare.19391063.v4
title: Effects of Spartina invasions on blue carbon sequestration in China

description: 1. Coastal wetlands are large reservoirs of soil carbon (C) and have been invaded globally by the exotic species <i>Spartina alterniflora</i>. However, the effects of these invasions on blue C sequestration remain unclear. 2. Here, we conducted a meta-analysis of 2479 soil organic C (SOC) observations collected from 91 field studies in coastal China, the world’s largest introduced range for <i>S. alterniflora</i>. 3. Our results show that <i>S. alterniflora</i> invasions had no significant effect on SOC in vegetated native coastal wetlands in China. <i>S. alterniflora</i> increased the SOC in the top 30 cm of salt marshes after invading only one of the nine types of native marshes, the native marsh was dominated by a dwarf succulent species, <i>Suaeda salsa</i>, in the northern subtropics, and decreased the SOC in the top 60 cm of mangrove habitats after invasion in the southern subtropics. <i>S. alterniflora</i> invasions did not significantly affect the SOC in salt marshes or mangroves dominated by other native species. Therefore, the C sequestration capacity of <i>S. alterniflora</i> does not differ from those of most native dominant species. Moreover, the SOC in <i>S. alterniflora</i>-invaded ecosystems increased on only a decadal-scale and then decreased, rather than increasing monotonically as was previously thought. 4. 1. <i>Synthesis and applications</i>. Our findings reveal that<i> S. alterniflora</i> invasions apparently increase the blue C sink in China only in native ecosystems dominated by specific species in specific regions and only over short time periods. Therefore, the expansion of <i>S. alterniflora</i> should not be considered as a natural climate solution to increase C sink in coastal China. Instead, future efforts are required to eradicate <i>S. alterniflora</i> preferentially in the coastal wetlands where<i> S. alterniflora</i> invasions do not increase C sinks, and to conserve and restore native coastal wetlands nationwide for increasing both ecological integrity and C sinks and mitigate climate change.
DOI: 10.17632/whfbxx4mnb
title: Una alianza arquitectónica: El papel del museo entre la cultura y la ciudad

description: This article explores the relevance of museum architecture as a scenario for the encounter between culture and the city. Since the museum institution is the main institution in charge of acquiring, preserving, studying and exhibiting objects of cultural value and, understanding the city as an urban ensemble comprising several buildings, complex road systems and a relevant group of individuals, the museum is conceived as an essential space and a transcendent link in the meeting of both concepts. As an essential and articulating piece between the museum and the urban fabric, the vestibule conditions the relationship of the museum with both the city and society. From its form, implantation, scale and incubation of spaces of transit or permanence, architecture stipulates, conditions, improves or rejects certain exchanges. While these are morphological, spatial, volumetric and temporal decisions, they are also urban, political and social. In this context, it is interesting to emphasize that, in the end, architecture is the means through which the architect gives his opinion and decides, for better or worse, how this relationship will be.
DOI: 10.6084/m9.figshare.1569814.v1
title: BIOL 2050 - Lab 3: Sweep nets and transect tape

description: The objective was to use a distance based sampling method to determine the abundance and richness of insects inhabiting a given area. Using a combination of the sweep net method and transect method we were able to actively collect walking and flying insects. The dataset for this experiment was collected on Thursday, October 1 2015 between 3 and 4:00 pm within the grasslands of York University's Keele Campus. This region is isolated from human acitivity. The weather was sunny with a temperature of 15 degrees celsius. The direct sunlight allowed for clear visualization of organisms captured by the sweep net. The materials included in the study were: a stop watch to record time, notebook and pen to record data, transect tape for distance measurement and sweep net for gathering insects. The approach taken was carefully selected prior to the execution of this method. The grasslands were divided into 2 regions, mowed and non-mowed. This study had a total of 10 trials (n=10), 5 trials involved the mowed land and 5 trials involved the non-mowed land. This study involved the participation of all 4 group members (Adilah Ismail, Amrutha Balamurugan, Harshvir Hehar and Olivia Kazmierczak). Harshvir Hehar was responsible for laying out the transect tape to a distance of 20 m. All 10 placements of the transect tape were made cautiously to prevent abstraction of organisms from the same region. Adilah Ismail was responsible for gathering the insects using a sweep net. The sweep net was forcefully moved back and forth in a figure eight motion to extract as many insects as possible. The sweeping motion was kept consistent amongst both the mowed and non-mowed regions. High rising plants were not given any mercy. After sweeping, the net was flipped over so that the open portion of the net was facing the sky and then it was closed off using Adilah's hand to prevent insects from escaping. At this point the abundance and RTUs were counted. Amrutha Balamurugan recorded the time with a stopwatch. The time spent sampling was slightly different for each replicate (with an average time of 23.6 seconds). Olivia Kazmierczak recorded all the data in her notebook. After each trial all organisms captured were released to prevent recounting and restore them into their natural habitat. Overall this sampling method was slightly destructive. There were high concerns of reducing population. It did however, reveal a correlation between the region (mowed vs non-mowed) and abundance of a certain species.
DOI: 10.6084/m9.figshare.17942513.v1
title: Extended Data 2: tRNA phylogeny of trypanosomatids

description: To define the origin of stop codon suppressor tRNAs in Blastocrithidia nonstop, all tRNA sequences from trypanosomatid genomes were aligned using MAFFT v7.458 (Katoh and Standley 2013), and the resulting alignment was subjected to phylogenetic analysis. Maximum likelihood analysis was performed in IQTREE v1.4.1 (Nguyen et al., 2015) under GTR+G+H4 model using ultrafast bootstrap and 1,000 replicates.Transfer RNAs (tRNAs) were predicted by tRNAScan-SE v2.0.5 (Chan and Lowe 2019) and Aragorn (Laslett and Canback 2014). <br><br><b>tryp_species_tRNA.xlsx</b> contains the list of reference trypanosomatid species used for the analysis. <b>all_tryp_tRNAs_aligned.fasta </b>represents alignment of the tRNAs.<br><b>tryp_tRNA_tree.newick </b>is the tree file<br>
DOI: 10.17632/8wz5dttyyz
title: Model and Materials of ''Improved Accuracy in Colorectal Cancer Tissue Decomposition through Refinement of Established Deep Learning Solutions''

description: This dataset contains the highest performing trained model definition, weights, and additional materials from the Nature SR study titled ''Improved Accuracy in Colorectal Cancer Tissue Decomposition through Refinement of Established Deep Learning Solutions''. Please refer to the associated article for further details.
DOI: 10.17632/mtmjtgx2gy
title: Dataset related to cold chain logistics sustainability

description: This dataset contains data describing Chinese cold chain logistics managers’ viewpoints of their companies’ sustainability innovation, supply chain resilience, and sustainability performance. The dataset in Excel spreadsheet consists of with 178 rows and 36 columns. Each row represents respondents' responses to questionnaire's items.
DOI: 10.6084/m9.figshare.16959661.v1
title: Databook.xlsx

description: Overall survival, progression-free survival, quality of life, and response rate outcomes in phase 2 and 3 randomized controlled trials evaluating systemic cancer therapy for solid tumours between 2010 and 2020.
DOI: 10.6084/m9.figshare.24799506.v1
title: Data and Analysis for: Ectoparasite load generates habitat specific variation in male color badge intensity and badge size

description: Data and Analysis for: Ectoparasite load generates habitat specific variation in male color badge intensity and badge size
DOI: 10.6084/m9.figshare.29149016.v1
title: FFS

description: The code for training RF algorithm
DOI: 10.17632/9rnchfxs9r
title: Vitrification kits for equine embryos

description: Data for different size equine embryos vitrified in one of three human embryo vitrification kits. All kits gave equivalent pregnancy rates for embryos up to 400 microns in diameter. Embryos &gt;400 microns gave higher pregnancy rates on warming when vitrified using the KITAZATO vitrification kit.
DOI: 10.17632/jyhph4x7b2
title: Data for: Geotechnical characterization of soft soil deposits from Northern Poland

description: Dataset contains physical properties, compressibility parameters and undrained shear strength of deltaic soft soil deposit at Jazowa, northern Poland.
DOI: 10.6084/m9.figshare.10081079.v1
title: OTU table of bulk soil samplesRoot endophytic fungal ‘fingerprinting’ reflects plant spatial co-occurrence patterns in a subtropical forest

description: OTU table of bulk soil samples
DOI: 10.6084/m9.figshare.20343759.v1
title: Supplementary Material for: Teaching radiographic caries detection and treatment planning – a seminar using an audience response system

description: This study presents a seminar model for teaching radiographic caries detection and treatment planning at the Faculty of Dentistry, University of Oslo. The seminar is based partly on an audience response system (ARS) and uses patient cases to focus on caries risk assessment and treatment planning. This paper describes the seminar design, implementation, learning outcomes, and observational study of variability in caries registrations and students attitudes to use of ARS. Dental and dental hygiene students participate in two seminar modules. Module 1 aims to develop and increase individual student skills in radiographic caries lesion detection, scoring and differential diagnosis. Students perform trial registrations on bitewings using an ARS with anonymous live polling and scorings are discussed in plenum. Students then perform individual registrations on 12 bitewing pairs. Using digital scoring students detect and grade caries lesions on all proximal and occlusal tooth surfaces. After the session, students use the ARS to repeat scorings on selected tooth surfaces, and results are again discussed in plenum. Module 2 involves group exercises on four patient cases that are later presented in plenum with discussions. In total, 1624 caries registrations performed by 150 students attending the seminar between 2016 and 2018 were assessed for variability between students. As expected, variations in caries registrations were observed between students, mostly related to restored surfaces or tooth surfaces that were otherwise difficult to register. In 2022, 63 dental and dental hygiene students attending the seminar answered a questionnaire about use of ARS. The responses were scored using a five-point Likert scale. Overall, no significant difference in satisfaction with the ARS-based module was observed between dental and dental hygiene students (Chi-squared test, p &gt; 0.05).The majority of the students were positive towards the use of ARS (94%), but some disagreed on the role of ARS in usefulness for understanding the seminar content (3.2%) and in increasing their confidence in radiographic registration of caries (3.2%). The ARS-based module provided a positive, interactive learning environment that ensured student anonymity, interactivity and engagement; and combined with the other seminar module gives students basic skills in caries detection and treatment planning.
DOI: 10.6084/m9.figshare.26973358.v1
title: Japanese Black Rumen Viral genomes

description: The rumen viral genomes were reconstructed by sequencing virus-like particles in the rumens of 37 Japanese Black cattle. The completeness of viral genomes was assessed using CheckV. The Japanese Black Rumen Viral genomes (JBRV) include 22,942 viral operational taxonomic units (vOTUs) of middle-quality or higher (≥5 kb length and ≥50% completeness).
DOI: 10.6084/m9.figshare.27195492.v4
title: Ethics Integration in Software: A Practitioner Survey

description: The integration of ethics into software development faces significant challenges due to market fundamentalism in organizational practices, where profit often takes precedence over ethical considerations. Additionally, the critical influence of practitioners' individual backgrounds on ethical decision-making remains underexplored, highlighting a gap in comprehensive research. This is especially essential to understand due to the demographic imbalance in software roles. This study investigates ethical concerns in software development, focusing on how they are perceived, prioritized, and addressed by demographically different practitioners. By surveying 217 software practitioners across diverse roles, industries, and countries, we identify critical barriers to ethical integration and examine practitioners’ capacity to mitigate these issues. Our findings reveal pronounced demographic disparities, with marginalized groups—including women, BIPOC, and disabled individuals—reporting ethical concerns at higher frequencies. Notably, marginalized practitioners demonstrated heightened sensitivity to ethical implementation and greater empowerment to address them. However, practitioners overall often lack the support needed to address ethical challenges effectively. These insights underscore the urgent need for reforms in software education and development processes that center on diverse perspectives. Such reforms are essential to advancing ethical integration in software development and ensuring responsible computing practices in an increasingly complex technological landscape.
DOI: 10.6084/m9.figshare.5706016.v2
title: Measuring Expert Performance at Manually Classifying Domain Entities under Upper Ontology Classes: Data and Scripts

description: Dataset containing the analysis for the journal paper submission "Measuring Expert Performance at Manually Classifying Domain Entities under Upper Ontology Classes".<br>The output generated by the script can be seen here:http://rpubs.com/matentzn/upperontologyclassification<br>