cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p9fjcm8n
title: Water Temperature Mapping of the Skykomish, Snoqualmie, and Middle Fork Snoqualmie Rivers, Washington—Longitudinal Stream Temperature Profiles, Significant Thermal Features, and Airborne Thermal Infrared and RGB Imagery Mosaics

description: The Skykomish, Snoqualmie, and Middle Fork Snoqualmie River Basins have historically provided critical spawning, rearing, and core habitat for several salmonid species. These salmonid species include natural populations of Chinook salmon (O. tshawytscha), steelhead trout (O. mykiss), and bull trout (Salvelinus confluentus)—listed as “Threatened” under the Endangered Species Act—as well as coho salmon (O. kisutch)—listed as a ”Species of concern”—pink salmon (O. gorbuscha), chum salmon (O. keta), and native char (S. malma) (Solomon and Boles, 2002; Stohr and others, 2011; Svrjcek and others, 2013; Snohomish County Surface Water Management and the Sustainable Lands Strategy Executive Committee [SWM], 2017; U.S. Fish and Wildlife Service, 2022). Because of the thermal constraints on salmonids and other aquatic species, the Washington Department of Ecology maintains temperature criteria for waters designated for aquatic life uses. These standards range between 12 degrees Celsius (°C) and 17.5 °C, referring to the highest permissible 7-day average of the daily maximum temperatures (7-DADMax), and vary depending on the habitat classification and time of year (Washington Department of Ecology, 2020). Over the past two decades, however, summer 7-DADMax water temperatures within the Skykomish, Snoqualmie, and Middle Fork Snoqualmie Rivers have frequently exceeded these temperature criteria, as well as the 23 °C threshold above which temperatures can be lethal to salmonids (Stohr and others, 2011; Svrjcek and others, 2013; Kubo and leDoux, 2016).
DOI: 10.6084/m9.figshare.12450356.v1
title: Additional file 4 of Parallel isotope differential modeling for instationary 13C fluxomics at the genome scale

description: Additional file 4. The trajectory of all mass isotopomers and the derivatives of EMUs of different sizes inE.coli for 3 set of flux distribution.
DOI: 10.6084/m9.figshare.8255924.v1
title: Transcriptome-wide identification of microRNAs and functional insights inferred from microRNA—target pairs in <i>Physalis angulata</i> L

description: <i>Physalis angulata</i> L., a member of the family Solanaceae, is widely used as the folk medicine in various countries. Continuous research efforts are devoted to the discovery of the effective medicinal ingredients from <i>Physalis angulata</i>. However, due to the limited resources of genome and transcriptome sequencing data, only a few studies have been performed at the gene regulatory level. In this study, the transcriptomes of five organs (roots, stems, leaves, flowers and fruits) of <i>Physalis angulata</i> were reported. Based on the transcriptome assembly containing 196,117 unique transcripts, a total of 17,556 SSRs (simple sequence repeats) were identified, which could be useful RNA-based barcoding for discrimination of the plants closely relative to <i>Physalis angulata</i>. Additionally, 24 transcripts were discovered to be the potential microRNA (miRNA) precursors which encode a total of 31 distinct mature miRNAs. Some of these precursors showed organ-specific expression patterns. Target prediction revealed 116 miRNA–target pairs, involving 31 miRNAs and 83 target transcripts in <i>Physalis angulata</i>. Taken together, our results could serve as the data resource for in-depth studies on the molecular regulatory mechanisms related to the production of medicinal ingredients in <i>Physalis angulata</i>.
DOI: 10.6084/m9.figshare.8310182.v1
title: Additional file 13: of Comparative physiology and transcriptome analysis allows for identification of lncRNAs imparting tolerance to drought stress in autotetraploid cassava

description: Table S10. The 104 DE lncRNAs specific to 2Ă plants in response to drought stress. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.12450335
title: Additional file 1 of Parallel isotope differential modeling for instationary 13C fluxomics at the genome scale

description: Additional file 1. A genome-scale metabolic network ofSynechococcus2973 modified fromimSyn593.
DOI: 10.6084/m9.figshare.17693363
title: Additional file 1 of Conjoint analysis of circulating tumor cells and solid tumors for exploring potential prognostic markers and constructing a robust novel predictive signature for breast cancer

description: Additional file 1: Table S1. Primary antibodies used in our study.
DOI: 10.6084/m9.figshare.13498719.v1
title: Repeatability and agreement of corneal thickness measurements by three methods of pachymetry in small incision lenticule extraction eyes

description: <b>Background</b>: The accurate evaluation of corneal thickness (CT) post small incision lenticule extraction (SMILE) is clinically relevant to reduce the risk of complications. We aimed to analyze repeatability and agreement of central corneal thickness (CCT), thinnest corneal thickness (TCT), and mid-peripheral corneal thickness (MPCT) measurements using Scheimpflug imaging, anterior segment swept-source optical coherence tomography (AS-SS-OCT, CASIA 1000, Tomey), and ultrasound pachymetry (USP, SP-3000, Tomey) in eyes with previous SMILE. <b>Methods</b>: Ninety-one eyes of 91 patients were included. Within-subject standard deviation (Sw), test-retest repeatability (TRT), intraclass correlation coefficient (ICC), and coefficient of variation (CoV) were used to evaluate repeatability. Agreement was assessed by repeat-measurement analysis of variance and Bland–Altman analysis. <b>Results</b>: The above three instruments revealed that Sw was &lt;5.91 µm, CoV was &lt;1.08%, TRT was &lt;16.38 µm, and ICC was &gt;0.94. The 95% limits of agreement were relatively narrow and Bland–Altman plots were more concentrated at the CCT, at the TCT, and at the CT<sub>2mm</sub>. However, it was shown to be wide at the CT<sub>5mm</sub>. <b>Conclusions</b>: The three devices provide good repeatability of CT measurements in patients who undergone SMILE. Agreement between measurements at the CCT, TCT, and CT<sub>2mm</sub> were high, but measurement agreements among CT<sub>5mm</sub> revealed poor agreement.
DOI: 10.6084/m9.figshare.17163156
title: Additional file 1 of Machine learning approaches for the genomic prediction of rheumatoid arthritis and systemic lupus erythematosus

description: Additional file 1
DOI: 10.6084/m9.figshare.17163156.v1
title: Additional file 1 of Machine learning approaches for the genomic prediction of rheumatoid arthritis and systemic lupus erythematosus

description: Additional file 1
DOI: 10.6084/m9.figshare.12450704
title: Additional file 10 of Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

description: Additional file 10. Excel spreadsheet of the heterozygous sites and inter-individual polymorphic sites of nrITS sequences. * represents the sequence from Genbank. △ = CGGAGATC.
DOI: 10.6084/m9.figshare.20315037
title: Gene expression of the white-rot fungus <i>Lenzites gibbosa</i> during wood degradation

description: To determine the wood degradation mechanism and its key genes and biological processes of <i>Lenzites gibbosa</i>, we sequenced 15 transcriptomes of mycelial samples under woody environment at 3, 5, 7, and 11 d (D3, D5, D7, and D11) and nonwoody environment (control). All the transcripts were annotated as much as possible in eight databases to determine their function. The key genes and biological processes relating to wood degradation were predicted and screened. The expression of 11 key genes during wood degradation after 5 d of sawdust treatment was detected by quantitative polymerase chain reaction (PCR). A total of 2069 differentially expressed genes (DEGs) were obtained in 10 differential groups. Comparing wood with nonwood treatment condition, the key genes were those participating in oxidation-reduction process, they were oxidoreductase and peroxidase genes and their regulator genes; these genes mainly focused on the three biological processes of carbohydrate metabolism, lignin catabolism, and secondary metabolite biosynthesis, transport, and catabolism. The mostly enriched subcategories in molecular function were oxidoreductase activity, peroxidase activity, and heme binding in Gene Ontology (GO) annotation. One cellulose and hemicellulose degradation pathway and seven pathways related to lignin-derived aromatic compound degradation or the later degradation of lignin were found. In conclusion, during the process of <i>L. gibbosa</i> growing on wood, gene expression at the transcriptional level indicated that lignin catabolism and hyphal growth were promoted, but the metabolism of carbon and carbohydrates including cellulose in lignocellulose in overall trend was inhibited to some extent. The results have important reference value for the study of degradation mechanism of wood white rot.
DOI: 10.17630/0b976971-8f36-48d1-a662-e13f4629400d
title: Angle resolved photoemission spectroscopy of delafossite metals (thesis data)

description: The data files are embargoed until 03/06/2021. This folder contains the data underpinning all the experimental plots in the thesis "Angle resolved photoemission spectroscopy of delafossite metals." If you would like to use the data, please get in touch at veronika.sunko@protonmail.com. All the data contained in the Figure X.YY are stored in a file named FigXpYY.txt. If the Figure contains multiple datasets, they are named FigXpYY_i, for the i-th data set. The data which appear on multiple figures in the thesis are included only once, and named after the first figure in which they appear. All the data are stored in IGOR Text format, and can be directly loaded in IGOR Pro with correct axis scaling. The appropriate scaling for use with other software is provided below each data set in the individual files. For example," X SetScale/P x -20, 0.5 ,"deg", Fig1_1" means the first data point in data set called Fig1_1 has the X value of -20, the difference between adjacent points is 0.5, and the units on the axis are deg. Comparing the data in the files with the figures in the thesis, their labels and captions, should provide enough information to uniquely identify the data sets. In a few cases this may be non-trivial; for those additional explanation is provided in ReadMe.xls.
DOI: 10.25387/g3.7207718
title: Supplemental Material for Lai et al., 2018

description: This dataset provides information about whole genome bisulphite sequencing (WGBS) and RNA-seq. The plant material is cucumber shoot species that were subjected to photoperiod treatment. <b>Figure S1 </b>The overwhelming majority of the CHH-DmCs showed levels of methylation changes ranging from 0.3-0.6, while CG- and CHG-DmCs had less extensive changes.<b>Figure S2</b> Gene classification of DEGs resulting from the long-day treatment based on GO terms.
DOI: 10.6084/m9.figshare.17693363.v1
title: Additional file 1 of Conjoint analysis of circulating tumor cells and solid tumors for exploring potential prognostic markers and constructing a robust novel predictive signature for breast cancer

description: Additional file 1: Table S1. Primary antibodies used in our study.
DOI: 10.6084/m9.figshare.12450752.v1
title: Additional file 6 of Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

description: Additional file 6. Excel spreadsheet of the numbers of nucleotide substitutions and sequence distance in 32 complete cp genomes (Sheet1). The upper triangle shows the number of nucleotide substitutions and the lower triangle indicates the number of sequence distance in complete cp genomes.
DOI: 10.6084/m9.figshare.12450773
title: Additional file 5 of Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)

description: Additional file 5 Results of heritability analyses within each subspecies.
DOI: 10.6084/m9.figshare.17163008.v1
title: Additional file 2 of OmicsOne: associate omics data with phenotypes in one-click

description: Additional file 2: Table S1. The analysis results of OmicsOne applied on the proteome dataset of HGSOC
DOI: 10.6084/m9.figshare.12450773.v1
title: Additional file 5 of Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)

description: Additional file 5 Results of heritability analyses within each subspecies.
DOI: 10.17630/592cc7e7-85bb-4bdc-a229-2250bfb728c5
title: High-resolution photoemission on Sr2RuO4 reveals correlation-enhanced effective spin-orbit coupling and dominantly local self-energies (dataset)
DOI: 10.6084/m9.figshare.12450779.v1
title: Additional file 6 of Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)

description: Additional file 6 Genes showing differences in heritability between subspecies.
DOI: 10.6084/m9.figshare.12450341.v1
title: Additional file 2 of Parallel isotope differential modeling for instationary 13C fluxomics at the genome scale

description: Additional file 2. 3 different sets of the flux distribution of theS.2973 network.
DOI: 10.6084/m9.figshare.12450356
title: Additional file 4 of Parallel isotope differential modeling for instationary 13C fluxomics at the genome scale

description: Additional file 4. The trajectory of all mass isotopomers and the derivatives of EMUs of different sizes inE.coli for 3 set of flux distribution.
DOI: 10.6084/m9.figshare.12450782
title: Additional file 7 of Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)

description: Additional file 7 cis-eQTL results.
DOI: 10.6084/m9.figshare.5634874
title: Analysis of Distributional Variation Through Graphical Multi-Scale Beta-Binomial Models

description: Many scientific studies involve comparing multiple datasets collected under different conditions to identify the difference in the underlying distributions. A common challenge in these multi-sample comparison problems is the presence of overdispersion, or extraneous causes other than the conditions of interest that also contribute to the cross-sample difference, which frequently results in false findings—identified “differences” not replicable in follow-up studies. When proper replicate samples are available under the conditions, one can in principle identify the interesting distributional variation from overdispersion through what we call the “analysis of distributional variation” (ANDOVA). We introduce a fully probabilistic framework for ANDOVA that achieves high computational efficiency. We take a divide-and-conquer multi-scale inference strategy: (i) first transform a general nonparametric ANDOVA task into a collection of ANDOVA tasks on Binomial experiments—each characterizing variations in the distributions at a particular location and scale, (ii) address each Binomial ANDOVA using a Beta-Binomial (BB) model, and (iii) use hierarchical graphical modeling to combine the inference from the BB models. We derive efficient MCMC-free Bayesian inference recipe under this framework through a combination of Laplace approximation-based numerical integration and message passing, and evaluate the performance of our method through extensive simulation. We apply the framework to analyzing DNase-seq data for identifying differences in transcriptional factor binding. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.17163014
title: Additional file 4 of OmicsOne: associate omics data with phenotypes in one-click

description: Additional file 4: Table S3. The analysis results of OmicsOne applied on the glycoproteome dataset of LSCC
DOI: 10.6084/m9.figshare.12450755.v1
title: Additional file 3 of Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)

description: Additional file 3 Results of differential expression and presence-absence variation analyses.
DOI: 10.6084/m9.figshare.8256476
title: microRNA-14 as an efficient suppressor to switch off ecdysone production after ecdysis in insects

description: The precise increase and decrease of hormone ecdysone are critical for accurate development in insects. Most previous works focus on transcriptional activation of ecdysone production; however, little is known about the mechanism of switching off ecdysone biosynthesis after ecdysis. Here, we showed that the precursor microRNA-14 (pre-miR-14) encodes two mature miRNAs in silkworm; both of these two mature miRNAs regulate various genes in the ecdysone-signalling pathway. <i>Bmo-miR-14-5p</i> targets on nine genes whereas <i>Bmo-miR-14-3p</i> targets on two genes in the same pathway. These two mature miRNAs increased immediately after the ecdysis, efficiently suppressing the 20-hydroxyecdysone (20E) biosynthesis, the upstream regulation, and the downstream response genes. Knocking down either of two mature miRNAs or both of them delays moult development, impairing development synchrony in antagomir-treated groups. In addition, overexpressing <i>Bmo-miR-14-5p</i> but not <i>Bmo-miR-14-3p</i> significantly affected the 20E titer and increased the moulting time variation, suggesting that <i>Bmo-miR-14-5p</i>, though it is less abundant, has more potent effects in development regulation than <i>Bmo-miR-14-3p</i>. In summary, we present evidence that a pre-miRNA encodes two mature miRNAs targeting on the same pathway, which significantly improves miRNA regulation efficiencies to programmatically switch off ecdysone biosynthesis.
DOI: 10.6084/m9.figshare.8256476.v1
title: microRNA-14 as an efficient suppressor to switch off ecdysone production after ecdysis in insects

description: The precise increase and decrease of hormone ecdysone are critical for accurate development in insects. Most previous works focus on transcriptional activation of ecdysone production; however, little is known about the mechanism of switching off ecdysone biosynthesis after ecdysis. Here, we showed that the precursor microRNA-14 (pre-miR-14) encodes two mature miRNAs in silkworm; both of these two mature miRNAs regulate various genes in the ecdysone-signalling pathway. <i>Bmo-miR-14-5p</i> targets on nine genes whereas <i>Bmo-miR-14-3p</i> targets on two genes in the same pathway. These two mature miRNAs increased immediately after the ecdysis, efficiently suppressing the 20-hydroxyecdysone (20E) biosynthesis, the upstream regulation, and the downstream response genes. Knocking down either of two mature miRNAs or both of them delays moult development, impairing development synchrony in antagomir-treated groups. In addition, overexpressing <i>Bmo-miR-14-5p</i> but not <i>Bmo-miR-14-3p</i> significantly affected the 20E titer and increased the moulting time variation, suggesting that <i>Bmo-miR-14-5p</i>, though it is less abundant, has more potent effects in development regulation than <i>Bmo-miR-14-3p</i>. In summary, we present evidence that a pre-miRNA encodes two mature miRNAs targeting on the same pathway, which significantly improves miRNA regulation efficiencies to programmatically switch off ecdysone biosynthesis.
DOI: 10.6084/m9.figshare.12450347
title: Additional file 3 of Parallel isotope differential modeling for instationary 13C fluxomics at the genome scale

description: Additional file 3. A medium-scale carbon metabolic network of E.coli.
DOI: 10.6084/m9.figshare.12450347.v1
title: Additional file 3 of Parallel isotope differential modeling for instationary 13C fluxomics at the genome scale

description: Additional file 3. A medium-scale carbon metabolic network of E.coli.
DOI: 10.5519/qd.zhga6i7o
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (118 records)
DOI: 10.17630/594363b9-966c-4c53-89e1-7610be33eba5
title: Triggered Gate Opening and Breathing Effects during Selective CO2 Adsorption by the Flexible Zeolite Merlinoite (dataset)
DOI: 10.6084/m9.figshare.12450752
title: Additional file 6 of Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

description: Additional file 6. Excel spreadsheet of the numbers of nucleotide substitutions and sequence distance in 32 complete cp genomes (Sheet1). The upper triangle shows the number of nucleotide substitutions and the lower triangle indicates the number of sequence distance in complete cp genomes.
DOI: 10.6084/m9.figshare.12450764.v1
title: Additional file 4 of Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)

description: Additional file 4 Heritability of gene expression for full population (Indica and Japonica).
DOI: 10.6084/m9.figshare.17169567.v1
title: Additional file 2 of 8DEstablishment and validation of a hypoxia-related signature predicting prognosis in hepatocellular carcinoma

description: Additional file 2. All immune-related genes downloaded from the Tracking Tumor Immuno-phenotype website.
DOI: 10.6084/m9.figshare.17169610.v1
title: Additional file 4 of A comprehensive gene-centric pleiotropic association analysis for 14 psychiatric disorders with GWAS summary statistics

description: Additional file 4: Table S3. List of all the unique pleiotropic genes and the number of psychiatric disorders which were affected by these genes.
DOI: 10.6084/m9.figshare.12450779
title: Additional file 6 of Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)

description: Additional file 6 Genes showing differences in heritability between subspecies.
DOI: 10.6084/m9.figshare.17169613.v1
title: Additional file 5 of A comprehensive gene-centric pleiotropic association analysis for 14 psychiatric disorders with GWAS summary statistics

description: Additional file 5: Table S4. Unique genes with drug-gene interaction of directional effects on 14 psychiatric disorders.
DOI: 10.6084/m9.figshare.17169607.v1
title: Additional file 3 of A comprehensive gene-centric pleiotropic association analysis for 14 psychiatric disorders with GWAS summary statistics

description: Additional file 3: Table S2. Pleiotropic genes for all pairs of 14 psychiatric disorders identified by PLACO (FDR &lt; 0.05).
DOI: 10.6084/m9.figshare.24769677.v4
title: Data and code<i> </i>for <i>Evolution of compound eye morphology underlies differences in vision between closely related </i><i>Drosophila</i><i> species </i>

description: Unzip each zip file and refer to the README.md file in each subdirectory for further instructions.
DOI: 10.6084/m9.figshare.5635039.v1
title: JADE for Tensor-Valued Observations

description: Independent component analysis is a standard tool in modern data analysis and numerous different techniques for applying it exist. The standard methods however quickly lose their effectiveness when the data are made up of structures of higher order than vectors, namely, matrices or tensors (e.g., images or videos), being unable to handle the high amounts of noise. Recently, an extension of the classic fourth-order blind identification (FOBI) specially suited for tensor-valued observations was proposed and showed to outperform its vector version for tensor data. In this article, we extend another popular independent component analysis method, the joint approximate diagonalization of eigen-matrices (JADE), for tensor observations. In addition to the theoretical background, we also provide the asymptotic properties of the proposed estimator and use both simulations and real data to show its usefulness and superiority over its competitors. Supplementary material including the proofs of the theorems and the codes for running the simulations and the real data example are available online.