cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19728380.v1
title: Additional file 2 of Identification and validation of an epigenetically regulated long noncoding RNA model for breast cancer metabolism and prognosis

description: Additional file 2: Table S2. Differentially methylated genes between cancer tissues and normal tissues.
DOI: 10.6084/m9.figshare.12751332
title: Additional file 2 of Patient specific circulating tumor DNA fingerprints to monitor treatment response across multiple tumors

description: Additional file 2: Table S2. 414 genes and 3331 variants from CIViC knowledge base (02-mar-2020 version).
DOI: 10.6084/m9.figshare.8032247
title: Additional file 1: of Disentangling the roles of maternal and paternal age on birth prevalence of Down syndrome and other chromosomal disorders using a Bayesian modeling approach

description: Model 1. Maternal Age Random-walk (CAR). OpenBUGS code and data that can be used to repeat the analyses for Model 1. (TXT 1 kb)
DOI: 10.6084/m9.figshare.8032247.v2
title: Additional file 1: of Disentangling the roles of maternal and paternal age on birth prevalence of Down syndrome and other chromosomal disorders using a Bayesian modeling approach

description: Model 1. Maternal Age Random-walk (CAR). OpenBUGS code and data that can be used to repeat the analyses for Model 1. (TXT 1 kb)
DOI: 10.6084/m9.figshare.8032247.v1
title: Additional file 1: of Disentangling the roles of maternal and paternal age on birth prevalence of down syndrome and other chromosomal disorders using a Bayesian modeling approach

description: Model 1. Maternal Age Random-walk (CAR). OpenBUGS code and data that can be used to repeat the analyses for Model 1. (TXT 1 kb)
DOI: 10.6084/m9.figshare.8032262
title: Additional file 3: of Disentangling the roles of maternal and paternal age on birth prevalence of Down syndrome and other chromosomal disorders using a Bayesian modeling approach

description: Model 3. Fully Conditional Random-walk (CAR). OpenBUGS code and data that can be used to repeat the analyses for Model 3. (TXT 67 kb)
DOI: 10.6084/m9.figshare.21664098
title: Raw datasets from Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents

description: The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is <i>Xenograpsus testudinatus,</i> a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, <i>X. testudinatus</i> occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of <i>X. testudinatus</i> that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by <i>Epsilonproteobacteria</i>. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.
DOI: 10.6084/m9.figshare.22188034.v1
title: An approach combining deep learning and molecule docking for drug discovery of cathepsin L

description: Cathepsin L (CTSL) is a promising therapeutic target for metabolic disorders and COVID-19. However, there are still no clinically available CTSL inhibitors. Our objective is to develop an approach for the discovery of potential reversible covalent CTSL inhibitors. The authors combined Chemprop, a deep learning-based strategy, and the Schrödinger CovDock algorithm to identify potential CTSL inhibitors. First, they used Chemprop to train a deep learning model capable of predicting whether a molecule would inhibit the activity of CTSL and performed predictions on ZINC20 in-stock librarie (~9.2 million molecules). Then, they selected the top-200 predicted molecules and performed the Schrödinger covalent docking algorithm to explore the binding patterns to CTSL (PDB: 5MQY). The authors then calculated the binding energies using Prime MM/GBSA and examined the stability between the best two molecules and CTSL using 100ns molecular dynamics simulations. The authors found five molecules that showed better docking results than the well-known cathepsin inhibitor odanacatib. Notably, two of these molecules, ZINC-35287427 and ZINC-1857528743, showed better docking results with CTSL compared to other cathepsins. Our approach enables drug discovery from large-scale databases with little computational consumption, which will save the cost and time required for drug discovery.
DOI: 10.6084/m9.figshare.12751329
title: Additional file 1 of Patient specific circulating tumor DNA fingerprints to monitor treatment response across multiple tumors

description: Additional file 1: Table S1. Mutations of eight hotspot tumor genes in the pre-designed ctDNA panel.
DOI: 10.6084/m9.figshare.12751329.v1
title: Additional file 1 of Patient specific circulating tumor DNA fingerprints to monitor treatment response across multiple tumors

description: Additional file 1: Table S1. Mutations of eight hotspot tumor genes in the pre-designed ctDNA panel.
DOI: 10.6084/m9.figshare.8032262.v1
title: Additional file 3: of Disentangling the roles of maternal and paternal age on birth prevalence of down syndrome and other chromosomal disorders using a Bayesian modeling approach

description: Model 3. Fully Conditional Random-walk (CAR). OpenBUGS code and data that can be used to repeat the analyses for Model 3. (TXT 67 kb)
DOI: 10.6084/m9.figshare.8032262.v2
title: Additional file 3: of Disentangling the roles of maternal and paternal age on birth prevalence of Down syndrome and other chromosomal disorders using a Bayesian modeling approach

description: Model 3. Fully Conditional Random-walk (CAR). OpenBUGS code and data that can be used to repeat the analyses for Model 3. (TXT 67 kb)
DOI: 10.6084/m9.figshare.8032265
title: Additional file 1: of Investigation and genome-wide association study for Fusarium crown rot resistance in Chinese common wheat

description: Table S1. Resistance to FCR of wheat cultivars inoculated by F.pg in four environments. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8032271.v1
title: Additional file 4: of Disentangling the roles of maternal and paternal age on birth prevalence of down syndrome and other chromosomal disorders using a Bayesian modeling approach

description: 5 year age categories. Fully conditional modeling of maternal and paternal ages as 5â year age categories. OpenBUGS code and data that can be used to repeat the analyses for the 5â year age categories. The data are arranged so that the DIC is comparable to the other fully conditional models (TXT 37 kb)
DOI: 10.6084/m9.figshare.8032274
title: Additional file 2: of Investigation and genome-wide association study for Fusarium crown rot resistance in Chinese common wheat

description: Table S2. Information for FCR disease index and correlation coefficients among environments. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8032280.v1
title: Additional file 5: of Disentangling the roles of maternal and paternal age on birth prevalence of down syndrome and other chromosomal disorders using a Bayesian modeling approach

description: Linear. Fully conditional modeling of maternal and paternal ages as linear. OpenBUGS code and data that can be used to repeat the analyses for maternal and paternal ages as linear. (TXT 65 kb)
DOI: 10.6084/m9.figshare.8032286
title: Additional file 6: of Disentangling the roles of maternal and paternal age on birth prevalence of Down syndrome and other chromosomal disorders using a Bayesian modeling approach

description: Curvilinear. Fully conditional modeling of maternal and paternal ages as curvilinear. OpenBUGS code and data that can be used to repeat the analyses for maternal and paternal ages as curvilinear. (TXT 66 kb)
DOI: 10.25625/2zip7m/3tqlll
title: INFO_dummy_caterpillar_data.txt

description: :unav
DOI: 10.25625/2zip7m/juippa
title: dummy_caterpillar_data.tab

description: :unav
DOI: 10.6084/m9.figshare.21664098.v1
title: Raw datasets from Cellular mechanisms underlying extraordinary sulphide tolerance in a crustacean holobiont from hydrothermal vents

description: The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulphide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is <i>Xenograpsus testudinatus,</i> a brachyuran crab endemic to marine sulphur-rich vent systems. Despite the toxicity of hydrogen sulphide, <i>X. testudinatus</i> occupies an ecological niche in a sulphide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of <i>X. testudinatus</i> that are the major site of sulphide detoxification. Here sulphide is oxidized to thiosulphate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulphate and hypotaurine is mediated by the sodium-independent sulphate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by <i>Epsilonproteobacteria</i>. Our results suggest that thiotaurine synthesized in gills is used by sulphide-oxidizing endo-symbiotic bacteria, creating an effective sulphide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.
DOI: 10.6084/m9.figshare.21664098.v2
title: Raw datasets from Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents

description: The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is <i>Xenograpsus testudinatus,</i> a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, <i>X. testudinatus</i> occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of <i>X. testudinatus</i> that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by <i>Epsilonproteobacteria</i>. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.
DOI: 10.6084/m9.figshare.8032781.v1
title: Additional file 2: of Adjuvant radiotherapy and chemotherapy for patients with breast phyllodes tumors: a systematic review and meta-analysis

description: Table S1. Quality assessment of the included studies. Table S2. Subgroup analysis of metastasis rate of radiotherapy. Table S3. Subgroup analysis of disease-free survival rate. Table S4. Subgroup analysis of overall survival rate. (ZIP 73 kb)
DOI: 10.25625/2zip7m
title: Predation of dummy caterpillars (CRC990 EFForTS - Landscape Assessment)

description: Predation rates on dummies imitating caterpillars made from plasticine. Dummy caterpillars were deployed in 126 plots in the lowlands of Sumatra in 4 land use systems (forest, shrublands, rubber plantations, oil palm plantations). Dummies were exposed for 48 h in subplots B,C,D,E. Predation and predator identity were assessed via unique bitemarks in the plasticine.
DOI: 10.25625/2zip7m/eivwvv
title: INFO_predation_data.txt

description: :unav
DOI: 10.25625/2zip7m/fr6l0v
title: bitemark_data.tab

description: :unav
DOI: 10.25625/2zip7m/igfkaj
title: INFO_bitemark_data.txt

description: :unav
DOI: 10.25625/2zip7m/vaswcx
title: predation_data.tab

description: :unav
DOI: 10.6084/m9.figshare.12751335
title: Additional file 3 of Patient specific circulating tumor DNA fingerprints to monitor treatment response across multiple tumors

description: Additional file 3: Table S3. Acquired drug-related mutations in nine patients identified using a pre-designed ctDNA panel.
DOI: 10.6084/m9.figshare.8032781
title: Additional file 2: of Adjuvant radiotherapy and chemotherapy for patients with breast phyllodes tumors: a systematic review and meta-analysis

description: Table S1. Quality assessment of the included studies. Table S2. Subgroup analysis of metastasis rate of radiotherapy. Table S3. Subgroup analysis of disease-free survival rate. Table S4. Subgroup analysis of overall survival rate. (ZIP 73 kb)
DOI: 10.6084/m9.figshare.8032808.v1
title: Additional file 1 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The size of the HCCs dataset. (XLSX 14.3 kb)
DOI: 10.6084/m9.figshare.8032820
title: Additional file 3 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The composition of features. (XLSX 14.2 kb)
DOI: 10.25545/xugv9x
title: Compilation of whole-rock chemical data from the Coldbrook Group and associated plutons (Table S1).

description: This Excel file is the supplementary chemical data file that accompanied the publication for which the full citation is given below. Abstract: The Coldbrook Group is a unique suite of late Ediacaran volcanic and epiclastic rocks deposited in an extensional setting in the Avalonian Caledonia terrane of southern New Brunswick. It is informally divided into a lower part composed of mainly andesitic to dacitic tuffs and epiclastic sedimentary rocks intruded by bimodal plutons, and an upper part composed mainly of mafic flows and tuffs interlayered with but mainly overlain by rhyolitic flows and tuffs and minor epiclastic sedimentary rocks. Recent U–Pb (zircon) dating of four formations in the Coldbrook Group and a subvolcanic granitic dome led to the proposal that the lower and most of the upper Coldbrook Group and associated plutons were formed within &lt;760 kyr at about 551.5 Ma whereas the uppermost rhyolite (Fundy Trail Parkway rhyolite) and underlying basalt of the Hosford Brook Formation formed in a younger event at about 549.5 Ma. Overlapping dates and chemical data also suggest that the subvolcanic granitic domes are the plutonic counterparts of the ca. 551.5 Ma felsic volcanic rocks whereas the other granitic plutons represent extracted melts that evolved separately. Whole-rock geochemical and isotopic data combined with previous field work and map information and integrated with the geochronological data provide new insights into the genesis of these magmas and their change from intermediate to bimodal magmatism. The data indicate that the volcanic and plutonic rocks are mainly tholeiitic and were derived from varying proportions of juvenile melts and recycled older arc lithosphere. The mafic rocks have chemical similarities to flood basalts which inherited some calc-alkalic signatures from older arc-like rocks. Intermediate magmas that formed much of the lower Coldbrook Group had larger lithospheric inputs and thus have mainly calc-alkalic signatures. The Vernon Mountain, Blackall Lake and Silver Hill area rhyolites represent evolved melts derived from the lower Coldbrook Group magmas, and their chemical differences are interpreted to result from melt extraction and solid-liquid dripping magmatic processes. Enhanced extension and thinning led to formation of less lithosphere-contaminated melts that formed the ca. 549.5 Ma bimodal units of the upper Coldbrook Group.
DOI: 10.25545/xugv9x/cbowkl
title: Supplementary+Date+Table+S1.tab

description: :unav
DOI: 10.6084/m9.figshare.8032820.v1
title: Additional file 3 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The composition of features. (XLSX 14.2 kb)
DOI: 10.6084/m9.figshare.8032853.v1
title: Additional file 9 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The running time of different classifiers. (XLSX 12.8 kb)
DOI: 10.6084/m9.figshare.8032832.v1
title: Additional file 5 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The performance of different windows using the HCCs dataset. (XLSX 29.5 kb)
DOI: 10.6084/m9.figshare.8032850
title: Additional file 8 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The results of different methods using the HepG2 dataset. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8032808
title: Additional file 1 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The size of the HCCs dataset. (XLSX 14.3 kb)
DOI: 10.6084/m9.figshare.8032853
title: Additional file 9 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The running time of different classifiers. (XLSX 12.8 kb)
DOI: 10.6084/m9.figshare.8032859
title: Additional file 10: of Identification of genomic regions associated with multi-silique trait in Brassica napus

description: Table S9. KEGG enrichment of the 2041 genes in the intersection associated regions. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8032916
title: Additional file 5: of Identification of genomic regions associated with multi-silique trait in Brassica napus

description: Table S4. GO enrichment in biological processes (BP) category of the genes. (XLSX 123 kb)
DOI: 10.6084/m9.figshare.8032919.v1
title: Additional file 6: of Identification of genomic regions associated with multi-silique trait in Brassica napus

description: Table S5. GO enrichment in cellular components (CC) category of the genes. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.8032922
title: Additional file 7: of Identification of genomic regions associated with multi-silique trait in Brassica napus

description: Table S6. GO enrichment in molecular function (MF) category of the genes. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.12751338
title: Additional file 4 of Patient specific circulating tumor DNA fingerprints to monitor treatment response across multiple tumors

description: Additional file 4: Table S4. 55 paired data sets for CCF in two consecutive ctDNA detections, treatment regimens, and imaging evaluations.
DOI: 10.6084/m9.figshare.12751338.v1
title: Additional file 4 of Patient specific circulating tumor DNA fingerprints to monitor treatment response across multiple tumors

description: Additional file 4: Table S4. 55 paired data sets for CCF in two consecutive ctDNA detections, treatment regimens, and imaging evaluations.
DOI: 10.6084/m9.figshare.22706072.v1
title: Additional file 4 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

description: Additional file 4: Table S3. Expression level of LUG directly regulated genes in Ler and lug mutant.
DOI: 10.6084/m9.figshare.19728377.v1
title: Additional file 1 of Identification and validation of an epigenetically regulated long noncoding RNA model for breast cancer metabolism and prognosis

description: Additional file 1: Table S1. Differentially methylated sites between cancer tissues and normal tissues for each gene site.
DOI: 10.6084/m9.figshare.10130129.v1
title: Metadata record for: Global sea-surface iodide observations, 1967-2018

description: This dataset contains key characteristics about the data described in the Data Descriptor Global sea-surface iodide observations, 1967-2018. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12751250
title: Additional file 1 of Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan plateau

description: Additional file 1 Table S1. Soil physicochemical properties of the rhizosphere and bulk soils. Data are means ± SD in parentheses, and different letters in the columns indicate significant differences (P &lt; 0.05). Table S2. ANOSIM analyses of separable compartments on archaeal community beta diversity distance matrix. P. crassifoli and P. szechuanica means the rhizosphere soil of Picea crassifolia and Populus szechuanica. Table S3. Comparison of sample differences in abundance of phyla. Data are means ± SD in parentheses. Different letters indicate significant levels (Dunnett test, P &lt; 0.05). For abbreviations, see Table S1. Table S4 Factors affecting the structure of archaeal communities in the rhizosphere and the bulk soil revealed by PERMANOVA. NS means not significant. Table S5. Co-occurrence network topological features statistics in three compartments. For abbreviations, see Table S1. Figure S1. Rarefaction curves comparing the number of sequences with the number of observed OTUs for archaeal communities in each sample. For abbreviations, see Table 1. Figure S2. Principal coordinate analysis (PCoA) ordination of archaeal communities based on MNTD index. For abbreviations, see Table 1. Figure S3. The phylogenetic trees of archaea. The numbers above each split were local support values. Figure S4. Mantel correlogram between the phylogenetic distances of pairwise OTUs and their niche distance of archaea.
DOI: 10.6084/m9.figshare.22706069
title: Additional file 3 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

description: Additional file 3: Table S2. List of MORC7 interacting proteins.
DOI: 10.6084/m9.figshare.12751332.v1
title: Additional file 2 of Patient specific circulating tumor DNA fingerprints to monitor treatment response across multiple tumors

description: Additional file 2: Table S2. 414 genes and 3331 variants from CIViC knowledge base (02-mar-2020 version).
DOI: 10.6084/m9.figshare.22706066.v1
title: Additional file 2 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

description: Additional file 2: Table S1. Genes proximal to MORC7A-unique, MORC7B-unique, MORC7-Pol V Common, and Pol V-unique peaks.
DOI: 10.6084/m9.figshare.8032811
title: Additional file 2 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The size of the HepG2 dataset. (XLSX 10.8 kb)