cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22631445
title: Additional file 5 of Stalled oligodendrocyte differentiation in IDH-mutant gliomas

description: Additional file 5: Table S4. Hypermethylation in myelination program but hypomethylation in regulators of OPC specification in PM gliomas.
DOI: 10.6084/m9.figshare.22631439.v1
title: Additional file 3 of Stalled oligodendrocyte differentiation in IDH-mutant gliomas

description: Additional file 3: Table S2. Frequencies of cell populations in single cell RNA-seq samples analyzed.
DOI: 10.6084/m9.figshare.22631436
title: Additional file 2 of Stalled oligodendrocyte differentiation in IDH-mutant gliomas

description: Additional file 2: Table S1. Morphological subtypes found in the PM gliomas.
DOI: 10.6084/m9.figshare.22631445.v1
title: Additional file 5 of Stalled oligodendrocyte differentiation in IDH-mutant gliomas

description: Additional file 5: Table S4. Hypermethylation in myelination program but hypomethylation in regulators of OPC specification in PM gliomas.
DOI: 10.6084/m9.figshare.22631436.v1
title: Additional file 2 of Stalled oligodendrocyte differentiation in IDH-mutant gliomas

description: Additional file 2: Table S1. Morphological subtypes found in the PM gliomas.
DOI: 10.6084/m9.figshare.14767224.v1
title: Additional file 1 of Comparison of mitochondrial genome and development of specific PCR primers for identifying two scuticociliates, Pseudocohnilembus persalinus and Uronema marinum

description: Additional file 1: Table S1. Ka/Ks values of 25 common encoding genes of P. persalinus and U. marinum.
DOI: 10.6084/m9.figshare.14767230.v1
title: Additional file 1 of Identification of a tumor microenvironment-related seven-gene signature for predicting prognosis in bladder cancer

description: Additional file 1: Table S1. GO analysis of 4 TME-related co-expression modules (magenta, brown, purple and yellow).
DOI: 10.34740/kaggle/dsv/7590209
title: Vietnam SARS-CoV-2 | COVID-19 Data
DOI: 10.6084/m9.figshare.14778262.v2
title: Single-cell immune checkpoint landscape of PBMCs stimulated with <i>Candida albicans</i>

description: Immune checkpoints play various important roles in tumour immunity, which usually contribute to T cells’ exhaustion, leading to immunosuppression in the tumour microenvironment. However, the roles of immune checkpoints in infectious diseases, especially fungal infection, remain elusive. Here, we reanalyzed a recent published single-cell RNA-sequencing (scRNA-seq) data of peripheral blood mononuclear cells (PBMCs) stimulated with <i>Candida albicans</i> (<i>C. albicans</i>), to explore the expression patterns of immune checkpoints after <i>C. albicans</i> bloodstream infection. We characterized the heterogeneous pathway activities among different immune cell subpopulations after <i>C. albicans</i> infection. The CTLA-4 pathway was up-regulated in stimulated CD4<sup>+</sup> and CD8<sup>+</sup> T cells, while the PD-1 pathway showed high activity in stimulated plasmacytoid dendritic cell (pDC) and monocytes. Importantly, we found that immunosuppressive checkpoints <i>HAVCR2</i> and <i>LAG3</i> were only expressed in stimulated NK and CD8<sup>+</sup> T cells, respectively. Their viabilities were validated by flow cytometry. We also identified three overexpressed genes (<i>ISG20</i>, <i>LY6E</i>, <i>ISG15</i>) across all stimulated cells. Also, two monocyte-specific overexpressed genes (<i>SNX10</i>, <i>IDO1</i>) were screened out in this study. Together, these results supplemented the landscape of immune checkpoints in fungal infection, which may serve as potential therapeutic targets for <i>C. albicans</i> infection. Moreover, the genes with the most relevant for <i>C. albicans</i> infection were identified in this study.
DOI: 10.5066/f72z13k4
title: USGS National Assessment of Oil and Gas Project -  Mississippian Barnett Shale, Bend Arch-Fort Worth Basin Province Assessment Units

description: The hydrogen index (HI) is a parameter obtained from Rock-Eval data which reflects general hydrocarbon generation and maturation trends in petroleum systems. In the Mississippian Barnett Shale, the hydrogen index was used to map general boundaries between regions of oil and gas generation within the extents of the formation. Hydrogen index values were obtained via Rock-Eval analyses of Barnett Shale core samples. In this system, HI values greater than 100 represent primarily oil generation and HI values less than 100 represent primarily gas generation. Secondary gas generation is indicated by HI values less than 50. In addition, the 100 HI line was utilized to establish part of the assessment unit (AU) boundaries for the 2015 assessment of shale gas and shale oil resources of the Barnett Shale in the Bend Arch-Fort Worth Basin Province. The AU represents the fundamental boundary used in the National and Global Assessment Project for the assessment of undiscovered oil and gas resources.
DOI: 10.6084/m9.figshare.5341093.v1
title: Early Cretaceous K-rich rhyolites from the Duolong Cu–Au deposit, southern Qiangtang, China: evidence for crustal growth

description: We report new zircon U–Pb age, Hf isotopic, and major and trace element data for rhyolites from the Duolong Ore Concentration Area of the Southern Qiangtang Terrane. Building on previous studies, we constrain the tectonic setting and propose a model to explain the geodynamics and crustal growth during regional magmatism in the Early Cretaceous. The analysed rhyolites yield laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) zircon U–Pb ages of 115 and 118 Ma. The rocks are K-rich (K<sub>2</sub>O = 6.66–9.93 wt.%; K<sub>2</sub>O/Na<sub>2</sub>O = 8.2–19.7 wt.%), alkaline and peraluminous (A/CNK = 1.02–1.46), and are characterized by high SiO<sub>2</sub> contents (72.8–78.8 wt.%) similar to highly fractionated I-type granites. Fractionation of Fe–Ti oxides, plagioclase, hornblende, Ti-bearing phases, apatite, monazite, allanite and zircon contributed to the variations in major and trace element chemistry. High K<sub>2</sub>O contents are likely due to partial melting of the continental crust. The samples have positive zircon <i>ε</i>Hf(<i>t</i>) values ranging from +7.1 to +11.2. These features, together with young zircon Hf crustal model ages of 489–721 Ma, indicate that the K-rich rhyolites were derived from juvenile lower crust with an input of a mantle-derived component. We suggest that the Early Cretaceous K-rich rhyolites formed in a continental arc setting during northward subduction of Bangong Co–Nujiang oceanic lithosphere. Basaltic magma underplating was responsible for vertical crustal growth, triggered by slab roll-back in the Duolong Ore Concentration Area in the Early Cretaceous.
DOI: 10.6084/m9.figshare.14773819
title: Additional file 1 of BRS1 mediates plant redox regulation and cold responses

description: Additional file 1: Table S1. Identification of DEGs in BRS1 mutants. Table S2. Proteins identified by BRS1-GFP pull-down.
DOI: 10.6084/m9.figshare.14773822.v1
title: Additional file 2 of BRS1 mediates plant redox regulation and cold responses

description: Additional file 2: Figure S1. The seedling hypocotyl phenotypes of WS2, brs1-1 and brs1-1D. a. The seedling phenotypes of WS2, brs1-1 and brs1-1D grown on 1/2 MS medium under long-day conditions. Photos captured 7 DAG. Scale bar = 1 cm. b. The hypocotyl phenotypes of WS2, brs1-1 and brs1-1D seedlings grown on 1/2 MS medium in the dark. Photos captured 5 DAG. Scale bar = 1 cm. c. Comparison of hypocotyl lengths in (a). Means ± SD are shown from three independent experiments, n≥ 20 in each experiment. The asterisks indicate a statistically significant difference (Student’s t-test, *p &lt; 0.05). d. Comparison of the hypocotyl lengths in (b). Means ± SD are shown from three independent experiments, n ≥ 20 in each experiment. The asterisks indicate a statistically significant difference (Student’s t-test, *p &lt; 0.05). Figure S2. The expression analysis of BRS1 homologs in wild type and BRS1 mutants. RNA sequencing was used to calculate the expression levels (FPKM value) of five BRS1 homologs: SCPL22, SCPL23, SCPL25, SCPL26 and SCPL27 in WS2, brs1-1 and brs1-1D plants. Mean ± SD is shown. The asterisks indicate a statistically significant difference (Student’s t-test, *p &lt; 0.05).
DOI: 10.6084/m9.figshare.25136972
title: VolRes-Raikoke-ACP-2024-data

description: The files included here were used to produced the figures of this paper.
DOI: 10.6084/m9.figshare.25136972.v1
title: VolRes-Raikoke-ACP-2024-data

description: The files included here were used to produced the figures of this paper.
DOI: 10.6084/m9.figshare.5341195
title: UV-Curable Polyurethane-Acrylate-Ag/TiO<sub>2</sub> Nanocomposites with Superior UV Light Antibacterial Activity

description: Polyurethane acrylate (PUA)-Ag/TiO<sub>2</sub> nanocomposites were synthesized via in-situ polymerization. The well-dispersed Ag/TiO<sub>2</sub> nanorods (NRs) serve as photoinitiator. Meanwhile, the PUA-Ag/TiO<sub>2</sub> nanocomposite films exhibit superior activity towards the photocatalytic degradation of <i>Escherichia coli (E. Coli)</i> under UV light. The excellent UV-curing and antibacterial activity can be ascribed to the synergistic effect of Ag and TiO<sub>2</sub>, which promotes the effective electron/holes separation and thus generates various reactive species. Thin films with these nanoparticles are more hydrophilic after UV illumination. And the antibacterial mechanism of the UV-Curable Polyurethane-Acrylate-Ag/TiO2 Nanocomposites was proposed.
DOI: 10.25549/usctheses-ouc11258018
title: Microsoft Word - Dissertation_Diana Younan_v0531-2017.docx
DOI: 10.25549/usctheses-c40-381680
title: etd-ShinPeterS-5383-08-screamingshapes
DOI: 10.6084/m9.figshare.12156975
title: Generalized Spatially Varying Coefficient Models

description: In this article, we introduce a new class of nonparametric regression models, called generalized spatially varying coefficient models (GSVCMs), for data distributed over complex domains. For model estimation, we propose a nonparametric quasi-likelihood approach using the bivariate penalized spline approximation technique. We show that our estimation procedure is able to handle irregularly-shaped spatial domains with complex boundaries. Under some regularity conditions, the estimator for the coefficient function is proved to be consistent in the <i>L</i><sub>2</sub> sense and its convergence rate is established. We develop a numerically stable algorithm using penalized iteratively reweighted least squares method to estimate the coefficient functions in GSVCMs. To gain efficiency in the computation for large-scale data, we further propose a QR decomposition-based algorithm, which requires only sub-blocks of the design matrix to be computed at a time, so that it allows efficient estimation of GSVCMs for large datasets with modest computer hardware. The finite sample performance of the GSVCM and its estimation method is examined by simulations studies. The proposed method is also illustrated by an analysis of the crash data in Florida. Supplementary materials for this article are available online.
DOI: 10.25549/usctheses-ouc11258024
title: 00001.tif
DOI: 10.25549/usctheses-ouc11258025
title: 00001.tif
DOI: 10.25549/usctheses-ouc11258028
title: Microsoft Word - 20170502_MJL_ThesisPaper_v3.doc
DOI: 10.6084/m9.figshare.14773861
title: Additional file 5 of CCDC114, DNAI2 and TOP2A involves in the effects of tibolone treatment on postmenopausal endometrium

description: Additional file 5: Table S4. The obtained drug-gene interactions information from GDIdb database.
DOI: 10.6084/m9.figshare.14773822
title: Additional file 2 of BRS1 mediates plant redox regulation and cold responses

description: Additional file 2: Figure S1. The seedling hypocotyl phenotypes of WS2, brs1-1 and brs1-1D. a. The seedling phenotypes of WS2, brs1-1 and brs1-1D grown on 1/2 MS medium under long-day conditions. Photos captured 7 DAG. Scale bar = 1 cm. b. The hypocotyl phenotypes of WS2, brs1-1 and brs1-1D seedlings grown on 1/2 MS medium in the dark. Photos captured 5 DAG. Scale bar = 1 cm. c. Comparison of hypocotyl lengths in (a). Means ± SD are shown from three independent experiments, n≥ 20 in each experiment. The asterisks indicate a statistically significant difference (Student’s t-test, *p &lt; 0.05). d. Comparison of the hypocotyl lengths in (b). Means ± SD are shown from three independent experiments, n ≥ 20 in each experiment. The asterisks indicate a statistically significant difference (Student’s t-test, *p &lt; 0.05). Figure S2. The expression analysis of BRS1 homologs in wild type and BRS1 mutants. RNA sequencing was used to calculate the expression levels (FPKM value) of five BRS1 homologs: SCPL22, SCPL23, SCPL25, SCPL26 and SCPL27 in WS2, brs1-1 and brs1-1D plants. Mean ± SD is shown. The asterisks indicate a statistically significant difference (Student’s t-test, *p &lt; 0.05).
DOI: 10.6084/m9.figshare.14773855.v1
title: Additional file 3 of CCDC114, DNAI2 and TOP2A involves in the effects of tibolone treatment on postmenopausal endometrium

description: Additional file 3: Table S2. Results of topological properties analysis for nodes in PPI network.
DOI: 10.6084/m9.figshare.14773864.v1
title: Additional file 6 of CCDC114, DNAI2 and TOP2A involves in the effects of tibolone treatment on postmenopausal endometrium

description: Additional file 6: Table S5. Validation of the predictive drugs in Pubmed.
DOI: 10.25549/usctheses-ouc11258038
title: 00001.tif
DOI: 10.6084/m9.figshare.14773852
title: Additional file 2 of CCDC114, DNAI2 and TOP2A involves in the effects of tibolone treatment on postmenopausal endometrium

description: Additional file 2: Table S1. The enriched biological processes terms and KEGG pathways for DEGs.
DOI: 10.6084/m9.figshare.14773819.v1
title: Additional file 1 of BRS1 mediates plant redox regulation and cold responses

description: Additional file 1: Table S1. Identification of DEGs in BRS1 mutants. Table S2. Proteins identified by BRS1-GFP pull-down.
DOI: 10.6084/m9.figshare.14773858.v1
title: Additional file 4 of CCDC114, DNAI2 and TOP2A involves in the effects of tibolone treatment on postmenopausal endometrium

description: Additional file 4: Table S3. The enriched GO terms and KEGG pathways for genes in significant modules identified from PPI network.
DOI: 10.6084/m9.figshare.14773861.v1
title: Additional file 5 of CCDC114, DNAI2 and TOP2A involves in the effects of tibolone treatment on postmenopausal endometrium

description: Additional file 5: Table S4. The obtained drug-gene interactions information from GDIdb database.
DOI: 10.6084/m9.figshare.14773852.v1
title: Additional file 2 of CCDC114, DNAI2 and TOP2A involves in the effects of tibolone treatment on postmenopausal endometrium

description: Additional file 2: Table S1. The enriched biological processes terms and KEGG pathways for DEGs.
DOI: 10.25549/usctheses-c40-381686
title: etd-ShinPeterS-5383-14-freshmintz
DOI: 10.6084/m9.figshare.21065552.v1
title: Transcriptome analysis of strawberry (<i>Fragaria</i> × <i>ananasa</i>) responsive to <i>Colletotrichum gloeosporioides</i> inoculation and mining of resistance genes

description: Strawberry has high nutritional and economic value and is an important horticultural crop widely cultivated worldwide. Strawberry anthracnose is the most harmful disease in strawberry production, which causes huge production losses every year. Mining disease resistance genes and breeding high-quality strawberry varieties are the fundamental way to solve the problem of strawberry anthracnose. In this study, transcriptome analysis and disease resistance-related genes mining were targeted on strawberry anthracnose. The main results are as follows: (1) A total of 100.45 Gb clean reads were obtained, with no less than 6.26 Gb for each sample; (2) The clean reads for each sample were aligned to the reference genome efficiently at 91.30% − 92.27%; (3) 93,042 genes were annotated; (4) 16 anti-anthracnose-related genes were identified, including <i>FaAUX</i>1, <i>FaARF</i>18, <i>FaSAUR</i>50, <i>FaGH</i>3.6, <i>FaAHP</i>1, <i>FaARR</i> (3, 5 and 11), <i>FaPYR</i>1<i>, FaPYL</i>11, <i>FaPP2C</i> (6, 16, 24, 37 and 51) and <i>FaPR</i>1. The above results can provide theoretical guidance for the molecular breeding of disease resistance of strawberry.
DOI: 10.6084/m9.figshare.14773864
title: Additional file 6 of CCDC114, DNAI2 and TOP2A involves in the effects of tibolone treatment on postmenopausal endometrium

description: Additional file 6: Table S5. Validation of the predictive drugs in Pubmed.
DOI: 10.6084/m9.figshare.22631467
title: Additional file 8 of Proteomic profiles and the function of RBP4 in endometrium during embryo implantation phases in pigs

description: Additional file 8.
DOI: 10.6084/m9.figshare.18972775
title: Processed Mouse Vessel Locations from A hydraulic resistance model for interstitial fluid flow in the brain

description: The data from Blinder et al. are provided as a series of points distributed along the centerlines of the vessels. Though penetrating venules and ascending veins are primarily oriented perpendicular to the cortical surface (along the z direction), they occasionally deviate from that orientation and intersect a cross-section at a particular depth more than once. In those cases, we “filter” the data by including only the midpoint of the intersections. Both the filtered and the unfiltered data are provided as Supplemental Material in the accompanying MATLAB file, “Blinder_Coordinates.mat”, where mouse 1, mouse 2, mouse 3, and mouse 4 are labeled “au”, “co”, “db”, and “av”, respectively. Each mouse has a set of coordinates for arterioles (“art”) and venules (“ven”) where columns 1, 2, and 3 correspond to X, Y, and Z coordinates. The substructure “originalstrands” contains the vessel strand index for each of the points in the coordinate set.
DOI: 10.6084/m9.figshare.14773855
title: Additional file 3 of CCDC114, DNAI2 and TOP2A involves in the effects of tibolone treatment on postmenopausal endometrium

description: Additional file 3: Table S2. Results of topological properties analysis for nodes in PPI network.
DOI: 10.6084/m9.figshare.14774249
title: Signatures and Prognostic Values of N6-methyladenosine (m6A) - related Immune Genes in Bladder Cancer

description: In recent years, genes associated with N6-methyladenosine (m6A) modification were found to participate in modulation of multiple tumor biological processes. Concomitantly, the significantly complicated dual effects of tumor microenvironment have been observed on cancer progression. The present study aims to investigate m6A-related immune genes (m6AIGs) for their signatures and prognostic values in bladder cancer (BC). Out of 2856 differentially expressed genes (DEGs) of BC, a total of 85 genes were obtained following intersection of DEGs, immune genes and m6A-related genes. The results of multivariate Cox regression analysis illustrated four genes (BGN, GRK5, IL32, and SREBF1) were significantly associated with the prognosis of BC patients. The BC samples were divided into two types based on the consensus clustering, and the principal component analysis demonstrated a separation between them. It was found that high expression of BGN and GRK5 were linked with advanced T and N stage, and the expression of SREBF1 in early T stage was higher than that in advanced T stage. Subsequently, the nomogram to predict 3- and 5-year survival probability of BC patients was developed and calibrated. GSEA analysis for risk subgroups showed WNT and TGF-beta signaling pathways were involved in regulation of BC progression in high risk level group. In the low risk level group, cytosolic DNA-Sensing cGAS-STING and RIG-I-like receptors signaling pathways were found to be correlated with BC development. These findings provide a novel insight on studies for BC progression.
DOI: 10.25549/usctheses-c3-624637
title: etd-DeeSylviaG-3790~143
DOI: 10.25549/usctheses-c3-624645
title: etd-DeeSylviaG-3790~151
DOI: 10.6084/m9.figshare.14774359.v1
title: Genome-wide characterization, evolution, and expression profiling of FBA gene family in response to light treatments and abiotic stress in <i>Nicotiana tabacum</i>

description: Fructose 1,6-bisphosphate aldolase (FBA) as a key enzyme play crucial roles in glycolysis, gluconeogenesis and Calvin cycle processes in plants. However, limited information is known regarding <i>FBA</i> genes in <i>Nicotiana tabacum</i>. In this study, 16 <i>FBAs</i> were identified and characterized in <i>Nicotiana tabacum</i>. Phylogenetic analysis revealed that these genes can be categorized as type I (<i>NtFBA1-10</i> located in chloroplast) and type II (<i>NtFBA11-16</i> located in cytoplasm) subfamilies. According to the conserved motifs and gene structure analysis, NtFBA protein sequences had the highly homologous to FBAs in other species. Most members of the <i>NtFBA</i> gene family responded positively to NaHCO<sub>3</sub> stress, especially the expression of <i>NtFBA13/14</i> increased by 642%. In addition, the expression results of <i>NtFBAs</i> under five abiotic stress (light, NaCl, NaHCO<sub>3</sub>, drought, and cold) conditions were showed that <i>NtFBA13/14</i> were highly up-regulated. qRT-PCR results showed that most of the <i>NtFBAs</i> expressed higher in leaves. <i>NtFBA7/8</i> and <i>NtFBA13/14</i> have important significance in photosynthesis and abiotic stress, respectively. This study provides a basis foundation for further elucidating the function of <i>NtFBAs</i> and the <i>N. tabacum</i> mechanism of resistance under abiotic stress.
DOI: 10.25549/usctheses-c3-624640
title: etd-DeeSylviaG-3790~146
DOI: 10.25549/usctheses-c3-624572
title: etd-DeeSylviaG-3790~078
DOI: 10.6084/m9.figshare.11108471
title: The palaeoenvironmental and palaeobiogeographical significance of the Late Permian deep-water brachiopod fauna from Dongpan, South China, including descriptions of <i>Micromartinia</i> He & Weldon gen. nov. (Micromartiniidae He & Weldon fam. nov.) and <i>Minutomarginifera</i> nom. nov.

description: A new genus and species, <i>Micromartinia kwangsiella</i> gen. et sp. nov., is erected based on material from the Talung Formation (upper Changhsingian), Guangxi, South China. Based on a phylogenetic analysis, the new genus is placed in a new family, Micromartiniidae He & Weldon. The genus and family are monotypic. <i>Minutomarginifera nomen novum</i> is proposed to replace <i>Eileenella</i> Racheboeuf in Wongwanich <i>et al.</i>, 2004. <i>Eileenella</i> is a homonym that was first used for an insect genus. A review of the brachiopod fauna of the Talung Formation at Dongpan demonstrates that the species are highly endemic and the fauna has a strongly generic affinity with cool-water faunas outside of South China Basin. The associated fauna and facies also indicate that the Dongpan Section was deposited in a cool-water bathyal setting in the southern part (Youjiang Sub-basin) of the South China Basin. The section was linked to the open ocean in the Late Permian. Compared with the coeval faunas of Duanshan and Shaiwa in the Youjiang Sub-basin, the Dongpan brachiopod fauna was not so strongly influenced by the faunas from the adjacent carbonate platforms, because of the deeper, cool water setting which is hostile to the typical warm-water brachiopods. http://zoobank.org/urn:lsid:zoobank.org:pub:23E02390-C47D-4F09-87AF-012BC47A2F30