cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12737193.v1
title: Additional file 7 of Evaluating the effect of TLR4-overexpressing on the transcriptome profile in ovine peripheral blood mononuclear cells

description: Additional file 7. Expression levels of the seven selected genes in each samples detected by real-time PCR and its correlation with RNA-seq.
DOI: 10.6084/m9.figshare.6445796.v1
title: Geometry-Sensitive Ensemble Mean based on Wasserstein Barycenters: Proof-of-Concept on Cloud Simulations

description: An ensemble of forecasts generated by different model simulations provides rich information for meteorologists about impending weather such as precipitating clouds. One major form of forecasts presents cloud images created by multiple ensemble members. Common features identified from these images are often used as the consensus prediction of the entire ensemble, while the variation among the images indicates forecast uncertainty. However, the large number of images and the possibly tremendous extent of dissimilarity between them pose cognitive challenges for decision making. In this paper, we develop novel methods for summarizing an ensemble of forecasts represented by cloud images and call them collectively the <i>Geometry-Sensitive Ensemble Mean</i> (GEM) toolkit. Conventional pixel-wise or feature-based averaging either loses interesting geometry information or focuses narrowly on some pre-chosen characteristics of the clouds to be forecasted. In GEM, we represent a cloud simulation by a Gaussian mixture model, which captures cloud shapes effectively without making special assumptions. Furthermore, using a state-of-the-art optimization algorithm, we compute the Wasserstein barycenter for a set of distributional entities, which can be considered as the consensus mean or centroid under the Wasserstein metric. Experimental results on two sets of ensemble simulated images are provided. Supplemental materials for the article are available online.
DOI: 10.17632/hz9s4nwncf.1
title: Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems

description: Graphical Processor Units (GPUs) are nowadays widely used in all-atom molecular simulations because of the advantage of efficient partitioning of atom pairs between the kernels to compute the contributions to energy and forces, thus enabling the treatment of very large systems. Extension of time- and size-scale of computations is also sought through the development of coarse-grained (CG) models, in which atoms are merged into extended interaction sites. Implementation of CG codes on the GPUs, particularly the multiple-GPU platforms is, however, a challenge due to more complicated potentials and removing the explicit solvent, forcing developers to do interaction- rather than space-domain decomposition. In this paper, we propose a design of a multi-GPU coarse-grained simulator and report the implementation of the heavily coarse-grained physics-based UNited RESidue (UNRES) model of polypeptide chains. By moving all computations to GPUs and keeping the communication with CPUs to a minimum, we managed to achieve almost 5-fold speed-up with 8 A100 GPU accelerators for systems with over 200,000 amino-acid residues, this result making UNRES the best scalable coarse-grained software and enabling us to do laboratory-time millisecond-scale simulations of such cell components as tubulin within days of wall-clock time.
DOI: 10.17632/3sndbd4p84.1
title: Automated Personality Prediction

description: This is a dataset of preprocessed texts from Reddit Platform and their corresponding Big Five Scores for 1608 users of the platform with more than 27,000 comments.
DOI: 10.17632/k4b2rrff95.1
title: Data

description: Research data
DOI: 10.6084/m9.figshare.12737445
title: Additional file 1 of Integrated single-molecule long-read sequencing and Illumina sequencing reveal the resistance mechanism of Psathyrostachys huashanica in response to barley yellow dwarf virus-GAV

description: Additional file 1: Table S1. Summary of PacBio Polymerase Reads Subreads. Table S2. Summary statistics of the trimmed and error-corrected PacBio isoforms by RNA-seq dataset. Table S3. Summary statistics of RNA-seq raw reads and clean reads from twelve libraries. Table S4. Summary statistics of the identification of transcription factors and transcriptional regulators from RNA-seq. Table S5. Primers used in RT-qPCR for validation of RNA-seq data.
DOI: 10.17632/m83ntz92jh.1
title: Biologic Treatment Outcomes in Refractory Chronic Urticaria: A Systematic Review

description: Chronic Urticaria is an allergic condition of the skin characterized by recurrent, pruritic wheals and angioedema spanning at least 6 weeks. Initial treatment involves the use of oral antihistamine therapy, with adjunct leukotriene receptor antagonist therapy in severe cases. Systemic biologics are often reserved for patient’s refractory to initial therapy. This systematic review examines the treatment outcomes of systemic biologics in patients with refractory chronic urticaria.
DOI: 10.6084/m9.figshare.12737460
title: Additional file 1 of Correction to: An analytical pipeline for identifying and mapping the integration sites of HIV and other retroviruses

description: Additional file 1:.
DOI: 10.17632/kzkjkt7mx2.1
title: Sport DB 2.0

description: Sport DB 2.0 is a collection of 168 cardiorespiratory datasets, acquired through wearable sensors and portable devices from 130 subjects while practicing 11 different sports during training and competition. Each dataset consists of demographic data (sex, age, weight, height, smoking habit, alcohol consumption, caffeine consumption, weekly training rate, presence of diseases and dietary supplement consumption), cardiorespiratory signals (electrocardiogram, heart-rate series, RR-interval series, and/or breathing-rate series), and training note data (sport-dependent training protocol). Cardiorespiratory signals were acquired through the BioHarness 3.0 by Zephyr, the KardiaMobile by AliveCor, the Kardia 6L by AliveCor, the Polar M400 by Polar, and heart-rate sensor H7 by Polar, on the playing field or gym following a specific acquisition protocol for each sport. Sport DB 2.0 may be useful to support research activity finalized to investigate the cardiorespiratory pathophysiological mechanisms triggered by sport, to develop automatic algorithms for monitoring athletes’ health while practicing sports, to validate the reliability of wearable sensors and portable devices in sport, and to develop data analytics techniques and artificial intelligence applications to support sport sciences.
DOI: 10.17632/sgbkzf2jt5.1
title: Disconnection from deeper layers of life

description: This code conducts a comprehensive analysis of the relationship between the recognition of one's eternal soul and its impact on the perceived depth of life's meaning and purpose. Here's a breakdown of the code:

Generating Random Data:

Random data for recognition levels of the eternal soul is generated, ensuring variability.
The impact on the perceived depth of life's meaning and purpose is calculated, introducing a slight random deviation to simulate real-life complexity.
Creating a DataFrame:

A pandas DataFrame is created to organize and structure the generated data.
The DataFrame includes columns for Recognition Levels and Impact on Purpose.
Saving Data to CSV:

The generated data is saved to a CSV file named 'recognition_impact_data.csv' for future reference or external use.
Data Visualization:

The scatter plot is generated using Matplotlib, visually representing the relationship between Recognition Levels and Impact on Purpose.
The x-axis represents the levels of recognition of the eternal soul, while the y-axis illustrates the corresponding impact on life's meaning and purpose.
Statistical Analysis:

A correlation matrix is calculated, providing insights into the linear relationships between recognition levels and impact on purpose.
Linear regression is employed to model and analyze the predictive power of recognition levels on life's meaning, and the R-squared value quantifies how well the model explains the observed variations.
Displaying Results:

The correlation matrix and linear regression R-squared value are printed to the console, providing quantitative measures of the relationship and predictive accuracy.
DOI: 10.17632/nyrvy6379f.1
title: Doru luteipes action against Spodoptera frugiperda

description: In Brazil, the common earwig Doru luteipes (Scudder) (Dermaptera: Forficulidae) is considered an important biocontrol agent for the maize crop, consuming the fall armyworm Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae) eggs and caterpillars from 1st to 3rd instar. Despite this, several aspects of the interaction between both species have not yet been studied. We aim to evaluate the non-consumption effects of earwigs on the oviposition of moths, the earwig’s predatory preference between eggs and neonates and its functional response on S. frugiperda eggs. In no-choice tests between plants with or without the presence of the predator, S. frugiperda moths deposited a smaller number of eggs on plants with risk of predation. In choice-based tests, earwigs initially attacked newborn caterpillars, but preferred to feed on eggs. Males and females fed more on eggs with increasing supply density and consumption was adjusted to the type II functional response curve. D. luteipes males were more efficient predators than females when exposed to higher egg densities. These findings clarify aspects of the predatory role of D. luteipes on S. frugiperda that had not yet been addressed and confirm that the earwig is an important biological control agent, potentially capable of impacting the colonization and population growth of S. frugiperda in maize crops, if there were conditions favorable to its early arrival.
DOI: 10.6084/m9.figshare.12737460.v1
title: Additional file 1 of Correction to: An analytical pipeline for identifying and mapping the integration sites of HIV and other retroviruses

description: Additional file 1:.
DOI: 10.6084/m9.figshare.12737319
title: Additional file 2 of The effect of aging on the biological and immunological characteristics of periodontal ligament stem cells

description: Additional file 2. mRNA_differential_expression/groupAvsgroupY_Diff_Analysis.xlsx.
DOI: 10.17632/729d3rj6yp.1
title: Debunking competition - Global Ecologically Unequal Exchange explained by exploitation and control relations

description: Mainstream economic theory argues that competition is the fundamental force regulating the mechanism of production and exchange in the global economy1. Accordingly, countries’ interaction in international trade is presumed to benefit all parties2,3. However, the increasing socioeconomic inequalities across and within countries and global environmental degradation challenge this conventional wisdom4–6. Ecologically Unequal Exchange, among other critical theories, argues that international trade triggers asymmetries in the distribution of benefits and costs between Core and Periphery regions of the global economic system7. Using a combined economic-ecological model, here we show that relations between countries follow dynamics of exploitation and control rather than competition or mutualism. Periphery and semi-periphery present higher environmental intensities, but the burden of such environmental degradation can be directly attributed to handful regions, which acquire and drive most environmental resources. Core regions enhance their economic and environmental performance at the national level by exploiting and controlling Semi-periphery and Periphery regions. Our results demonstrate that green growth and dematerialization policies may be unable to achieve socially fair and environmentally sustainable societies at the global level. We call for abandoning growth-oriented policies to avoid counterproductive efforts in the transition towards sustainability.
DOI: 10.6084/m9.figshare.12737319.v1
title: Additional file 2 of The effect of aging on the biological and immunological characteristics of periodontal ligament stem cells

description: Additional file 2. mRNA_differential_expression/groupAvsgroupY_Diff_Analysis.xlsx.
DOI: 10.17632/56ksxkpbr9.1
title: Data associated with article "Distance- and density-dependent recruitment of common ragwort is not driven by plant-soil feedbacks".

description: This is the supplementary data associated with the article "Distance- and density-dependent recruitment of common ragwort is not driven by plant-soil feedbacks". The detailed description can be found in the original article.

In this study, we established 27 replicated 8 × 8 m2 plots at two sites in The Netherlands. Within each plot, we mapped the positions of rosettes and flowering Jacobaea vulgaris plants. To investigate temporal distribution patterns, we also tracked plant positions repeatedly in three plots at one site during a single season. Using spatial point pattern analysis, we explored distance- and density-dependent effects on J. vulgaris populations. Additionally, we examined whether the observed distance- and density-dependent spatial patterns were soil-mediated. To test this, we collected soil samples from underneath flowering plants and at a distance of 0.5 meter from each flowering plant. These soil samples were used as "home" and "away" soil to trace seed germination, seedling survival, and growth. Furthermore, we measured J. vulgaris biomass in soil collected from patches with high J. vulgaris densities and soil from areas outside these patches.
DOI: 10.17632/mtwr78ktst.1
title: Combined ionizing radiation by gamma-rays and carbon-12 (12C) nuclei caused hyperlocomotion and change in striatal metabolism of rats
DOI: 10.17632/hzrcpjh6y7.1
title: Structural and functional analyses of nermatode-derived antimicrobial peptides provide support for the occurrence of direct mechanisms of worm-microbiota interactions

description: Teladorsagia circumcincta IsoSeq datasets
DOI: 10.17632/kzkjkt7mx2.2
title: Sport DB 2.0

description: Sport DB 2.0 is a collection of 168 cardiorespiratory datasets, acquired through wearable sensors and portable devices from 130 subjects while practicing 11 different sports during training and competition. Each dataset consists of demographic data (sex, age, weight, height, smoking habit, alcohol consumption, caffeine consumption, weekly training rate, presence of diseases and dietary supplement consumption), cardiorespiratory signals (electrocardiogram, heart-rate series, RR-interval series, and/or breathing-rate series), and training note data (sport-dependent training protocol). Cardiorespiratory signals were acquired through the BioHarness 3.0 by Zephyr, the KardiaMobile by AliveCor, the Kardia 6L by AliveCor, the Polar M400 by Polar, and heart-rate sensor H7 by Polar, on the playing field or gym following a specific acquisition protocol for each sport. Sport DB 2.0 may be useful to support research activity finalized to investigate the cardiorespiratory pathophysiological mechanisms triggered by sport, to develop automatic algorithms for monitoring athletes’ health while practicing sports, to validate the reliability of wearable sensors and portable devices in sport, and to develop data analytics techniques and artificial intelligence applications to support sport sciences.
DOI: 10.6084/m9.figshare.19028978
title: Additional file 2 of Rice SIAH E3 Ligases Interact with RMD Formin and Affect Plant Morphology

description: Additional file 2: Table S1. Primers used in this study.
DOI: 10.6084/m9.figshare.19028978.v1
title: Additional file 2 of Rice SIAH E3 Ligases Interact with RMD Formin and Affect Plant Morphology

description: Additional file 2: Table S1. Primers used in this study.
DOI: 10.17632/cpvc2473pt.1
title: UKRmol-scripts: A Perl-based system for the automated operation of the photoionization and electron/positron scattering suite UKRmol+

description: UKRmol-scripts is a set of Perl scripts to automatically run the UKRmol+ codes, a complex software suite based on the R-matrix method to model fixed-nuclei photoionization and electron- and positron-scattering for polyatomic molecules. Starting with several basic parameters, the scripts operatively produce all necessary input files and run all codes for electronic structure and scattering calculations as well as gather the more frequently required outputs. The scripts provide a simple way to run such calculations for many molecular geometries concurrently and collect the resulting data for easier post-processing and visualization. We describe the structure of the scripts and the input parameters as well as provide examples for photoionization and electron and positron collisions with molecules. The codes are freely available from Zenodo.
DOI: 10.6084/m9.figshare.19028946
title: Additional file 1 of Non-additive QTL mapping of lactation traits in 124,000 cattle reveals novel recessive loci

description: Additional file 1: Table S1. Association statistics for most significant variants. Table including association statistics for the most highly associated variant for each QTL identified through GWAS. Table S2. Association statistics for growth and developmental traits. Table including association statistics for five candidate causal mutations in the DOCK8, IL4R, KIAA0556, LRCH4, and RBM34 genes for growth and developmental traits [12].
DOI: 10.6084/m9.figshare.19028946.v1
title: Additional file 1 of Non-additive QTL mapping of lactation traits in 124,000 cattle reveals novel recessive loci

description: Additional file 1: Table S1. Association statistics for most significant variants. Table including association statistics for the most highly associated variant for each QTL identified through GWAS. Table S2. Association statistics for growth and developmental traits. Table including association statistics for five candidate causal mutations in the DOCK8, IL4R, KIAA0556, LRCH4, and RBM34 genes for growth and developmental traits [12].
DOI: 10.6084/m9.figshare.12737546
title: Additional file 2 of Responses of leaf morphology, NSCs contents and C:N:P stoichiometry of Cunninghamia lanceolata and Schima superba to shading

description: Additional file 2.
DOI: 10.6084/m9.figshare.12737546.v1
title: Additional file 2 of Responses of leaf morphology, NSCs contents and C:N:P stoichiometry of Cunninghamia lanceolata and Schima superba to shading

description: Additional file 2.
DOI: 10.6084/m9.figshare.8019620
title: The autophagic degradation of cytosolic pools of peroxisomal proteins by a new selective pathway

description: Damaged or redundant peroxisomes and their luminal cargoes are removed by pexophagy, a selective autophagy pathway. In yeasts, pexophagy depends mostly on the pexophagy receptors, such as Atg30 for <i>Pichia pastoris</i> and Atg36 for <i>Saccharomyces cerevisia</i>e, the autophagy scaffold proteins, Atg11 and Atg17, and the core autophagy machinery. In <i>P. pastoris</i>, the receptors for peroxisomal matrix proteins containing peroxisomal targeting signals (PTSs) include the PTS1 receptor, Pex5, and the PTS2 receptor and co-receptor, Pex7 and Pex20, respectively. These shuttling receptors are predominantly cytosolic and only partially peroxisomal. It remains unresolved as to whether, when and how the cytosolic pools of peroxisomal receptors, as well as the peroxisomal matrix proteins, are degraded under pexophagy conditions. These cytosolic pools exist both in normal and mutant cells impaired in peroxisome biogenesis. We report here that Pex5 and Pex7, but not Pex20, are degraded by an Atg30-independent, selective autophagy pathway. To enter this selective autophagy pathway, Pex7 required its major PTS2 cargo, Pot1. Similarly, the degradation of Pex5 was inhibited in cells missing abundant PTS1 cargoes, such as alcohol oxidases and Fox2 (hydratase-dehydrogenase-epimerase). Furthermore, in cells deficient in PTS receptors, the cytosolic pools of peroxisomal matrix proteins, such as Pot1 and Fox2, were also removed by Atg30-independent, selective autophagy, under pexophagy conditions. In summary, the cytosolic pools of PTS receptors and their cargoes are degraded via a pexophagy-independent, selective autophagy pathway under pexophagy conditions. These autophagy pathways likely protect cells from futile enzymatic reactions that could potentially cause the accumulation of toxic cytosolic products. <b>Abbreviations:</b> ATG: autophagy related; Cvt: cytoplasm to vacuole targeting; Fox2: hydratase-dehydrogenase-epimerase; PAGE: polyacrylamide gel electrophoresis; Pot1: thiolase; PMP: peroxisomal membrane protein; Pgk1: 3-phosphoglycerate kinase; PTS: peroxisomal targeting signal; RADAR: receptor accumulation and degradation in the absence of recycling; RING: really interesting new gene; SDS: sodium dodecyl sulphate; TCA, trichloroacetic acid; Ub: ubiquitin; UPS: ubiquitin-proteasome system Vid: vacuole import and degradation
DOI: 10.6084/m9.figshare.8019620.v1
title: The autophagic degradation of cytosolic pools of peroxisomal proteins by a new selective pathway

description: Damaged or redundant peroxisomes and their luminal cargoes are removed by pexophagy, a selective autophagy pathway. In yeasts, pexophagy depends mostly on the pexophagy receptors, such as Atg30 for <i>Pichia pastoris</i> and Atg36 for <i>Saccharomyces cerevisia</i>e, the autophagy scaffold proteins, Atg11 and Atg17, and the core autophagy machinery. In <i>P. pastoris</i>, the receptors for peroxisomal matrix proteins containing peroxisomal targeting signals (PTSs) include the PTS1 receptor, Pex5, and the PTS2 receptor and co-receptor, Pex7 and Pex20, respectively. These shuttling receptors are predominantly cytosolic and only partially peroxisomal. It remains unresolved as to whether, when and how the cytosolic pools of peroxisomal receptors, as well as the peroxisomal matrix proteins, are degraded under pexophagy conditions. These cytosolic pools exist both in normal and mutant cells impaired in peroxisome biogenesis. We report here that Pex5 and Pex7, but not Pex20, are degraded by an Atg30-independent, selective autophagy pathway. To enter this selective autophagy pathway, Pex7 required its major PTS2 cargo, Pot1. Similarly, the degradation of Pex5 was inhibited in cells missing abundant PTS1 cargoes, such as alcohol oxidases and Fox2 (hydratase-dehydrogenase-epimerase). Furthermore, in cells deficient in PTS receptors, the cytosolic pools of peroxisomal matrix proteins, such as Pot1 and Fox2, were also removed by Atg30-independent, selective autophagy, under pexophagy conditions. In summary, the cytosolic pools of PTS receptors and their cargoes are degraded via a pexophagy-independent, selective autophagy pathway under pexophagy conditions. These autophagy pathways likely protect cells from futile enzymatic reactions that could potentially cause the accumulation of toxic cytosolic products. <b>Abbreviations:</b> ATG: autophagy related; Cvt: cytoplasm to vacuole targeting; Fox2: hydratase-dehydrogenase-epimerase; PAGE: polyacrylamide gel electrophoresis; Pot1: thiolase; PMP: peroxisomal membrane protein; Pgk1: 3-phosphoglycerate kinase; PTS: peroxisomal targeting signal; RADAR: receptor accumulation and degradation in the absence of recycling; RING: really interesting new gene; SDS: sodium dodecyl sulphate; TCA, trichloroacetic acid; Ub: ubiquitin; UPS: ubiquitin-proteasome system Vid: vacuole import and degradation