cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19919869
title: Additional file 1 of Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades

description: Additional file 1: Figure S1. Expression profiles of UVC exposed R. varieornatus. Gene expression profiles of R. varieornatus specimens exposed to 2.5kJ/m2 UVC shown as a heatmap. TPM values were Z-scaled to between samples. Expression and sample profiles were clustered with by Ward method based on Spearman correlation and the cluster number is indicated on the right side of the heatmap (Cluster numbers from one to eight). Samples are indicated in the following format: Short or long, time point, replicate number. Figure S2. Phylogenetic analysis OG0000230 orthologs within Tardigrada. Phylogenetic tree of tardigrade OG0000230 orthologs and bacterial orthologs. Amino acid sequences were aligned with Mafft, and the phylogenetic tree was constructed with FastTree with 1000 bootstraps (-boot, -gamma). CAHS genes were used as an out-group. Figure S3. Multiple alignment of R. varieornatus and H. exemplaris OG0000231 orthologs. The amino acid sequences of OG0000231 orthologs were submitted to multiple alignment by constraint-based multiple alignment tool from NCBI. Figure S4. Metal-binding property and structural detail of g12777 globular domain. [a,b] The crystal structures of catalytic domain of g12777 complexed with Mn2+ [a] andZn2+ [b]. All crystallographically observed metal ion binding sites are indicated. [c] Topology diagram of g12777 catalytic domain. [d] Close-up view of the Zn2+-binding site. The residues comprising binding site 1(D92, D98, D161, and D163) and the disulfide bond (C91 and C97) are indicated. [e] Conservation of residues. All OG0000231 orthologs were submitted to MEME search. [f] Conserved resides of g12777. The conserved resides are colored according to the bit scores obtained from MEME analysis. [g] Ca2+and Zn2+ ion binding affinity measured by isothermal titration calorimetry. The upper two panels indicate the raw data, while the bottom two panel represent the integrated heat values corrected for the heat of dilution and fit to a one-site binding model (solid line); red: Ca2+, cyan: Zn2+. Time is in seconds. Figure S5. Localization of other OG0000231 orthologs. The localization of top six highly expressed OG0000231 orthologs were validated using the same method of Figure 3a. All of these orthologs showed localization mainly to the Golgi apparatus. The images have been adjusted for visualization. Figure S6. Comparison of peroxidase function with Bovine liver catalase. The peroxidase function of g12777 + Mn2+ was compared to those of Bovine liver catalase (BLC). p-value &lt; 0.001 (Welch’s t-test).
DOI: 10.6084/m9.figshare.19919869.v1
title: Additional file 1 of Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades

description: Additional file 1: Figure S1. Expression profiles of UVC exposed R. varieornatus. Gene expression profiles of R. varieornatus specimens exposed to 2.5kJ/m2 UVC shown as a heatmap. TPM values were Z-scaled to between samples. Expression and sample profiles were clustered with by Ward method based on Spearman correlation and the cluster number is indicated on the right side of the heatmap (Cluster numbers from one to eight). Samples are indicated in the following format: Short or long, time point, replicate number. Figure S2. Phylogenetic analysis OG0000230 orthologs within Tardigrada. Phylogenetic tree of tardigrade OG0000230 orthologs and bacterial orthologs. Amino acid sequences were aligned with Mafft, and the phylogenetic tree was constructed with FastTree with 1000 bootstraps (-boot, -gamma). CAHS genes were used as an out-group. Figure S3. Multiple alignment of R. varieornatus and H. exemplaris OG0000231 orthologs. The amino acid sequences of OG0000231 orthologs were submitted to multiple alignment by constraint-based multiple alignment tool from NCBI. Figure S4. Metal-binding property and structural detail of g12777 globular domain. [a,b] The crystal structures of catalytic domain of g12777 complexed with Mn2+ [a] andZn2+ [b]. All crystallographically observed metal ion binding sites are indicated. [c] Topology diagram of g12777 catalytic domain. [d] Close-up view of the Zn2+-binding site. The residues comprising binding site 1(D92, D98, D161, and D163) and the disulfide bond (C91 and C97) are indicated. [e] Conservation of residues. All OG0000231 orthologs were submitted to MEME search. [f] Conserved resides of g12777. The conserved resides are colored according to the bit scores obtained from MEME analysis. [g] Ca2+and Zn2+ ion binding affinity measured by isothermal titration calorimetry. The upper two panels indicate the raw data, while the bottom two panel represent the integrated heat values corrected for the heat of dilution and fit to a one-site binding model (solid line); red: Ca2+, cyan: Zn2+. Time is in seconds. Figure S5. Localization of other OG0000231 orthologs. The localization of top six highly expressed OG0000231 orthologs were validated using the same method of Figure 3a. All of these orthologs showed localization mainly to the Golgi apparatus. The images have been adjusted for visualization. Figure S6. Comparison of peroxidase function with Bovine liver catalase. The peroxidase function of g12777 + Mn2+ was compared to those of Bovine liver catalase (BLC). p-value &lt; 0.001 (Welch’s t-test).
DOI: 10.6084/m9.figshare.19786027
title: 10X_Mouse_brain

description: This is a set of 10X visum platform st dataset from mouse brain h5ad file dataset with preprocessing.
DOI: 10.6084/m9.figshare.17149208.v7
title: CRISPR/Cas12a-based assay for the rapid and high-sensitivity detection of Streptococcus agalactiae colonization in pregnant women with premature rupture of membrane.xlsx

description: <b>Aims: </b><i>Streptococcus agalactiae</i> (GBS) is a leading infectious cause of neonatal morbidity and mortality. It is essential to establish a rapid and sensitive method for the detection of GBS.<b>Methods and Results:</b> This study developed a CRISPR-GBS assay that combines recombinase polymerase amplification (RPA) and CRISPR/Cas12a for GBS detection. The detection process can be completed within 35 min, compared to 85 min for quantitative real-time PCR (qPCR) assay and 48-72h for culture method. The limit of detection (LoD) was as low as 5 copies μL<sup>-1</sup> and no cross-reaction with other microorganisms was observed. The clinical performance of CRISPR-GBS assay was assessed using vaginal or cervical swab samples collected from 179 pregnant women with premature rupture of membrane. Compared with the culture-based matrix-assisted laser desorption ionization time-of-flight mass spectrometry (culture-MS) method, the CRISPR-GBS assay demonstrated a sensitivity of 96.64% (144/149, 95% confidence interval [CI] = 92.39–98.56%) and a specificity of 100 % (30/30, 95% CI = 88.65–100%). It also had a high concordance rate of 98.88% with the qPCR assay. <b>Conclusions:</b> The established CRISPR-GBS platform can detect GBS in a rapid, accurate, easy-to-operate and cost-efficient manner. <b>Significance and Impact of the Study: </b>The CRISPR-GBS assay has promising prospects as a clinically useful point-of-care test for intrapartum screening of GBS infection. <b></b>
DOI: 10.6084/m9.figshare.19919822
title: SPLITseqVignette_gencodeV35-vM25_combined_transcriptome_splici_fl61

description: make_splici_txome( gtf_path = "combined_gene_annotations.gtf", genome_path = "combined_genome.fa", read_length = 66, flank_trim_length = 5, output_dir = "/pine/scr/j/m/jmsimon", file_name_prefix = "SPLITseqVignette_gencodeV35-vM25_combined_transcriptome_splici", dedup_seqs = FALSE ) <br>
DOI: 10.6084/m9.figshare.19919822.v1
title: SPLITseqVignette_gencodeV35-vM25_combined_transcriptome_splici_fl61

description: make_splici_txome( gtf_path = "combined_gene_annotations.gtf", genome_path = "combined_genome.fa", read_length = 66, flank_trim_length = 5, output_dir = "/pine/scr/j/m/jmsimon", file_name_prefix = "SPLITseqVignette_gencodeV35-vM25_combined_transcriptome_splici", dedup_seqs = FALSE ) <br>
DOI: 10.6084/m9.figshare.19785988
title: 10X_genomics_data

description: This is a set of 10X genomics spatial omix dataset with preprocessed into h5ad files.
DOI: 10.25442/hku.18623522.v3
title: The Belt and Road Initiative on Twitter: An Annotated Dataset

description: This repository stores a collection of 500,711 posts (tweets) and 714,794 reposting threads (retweets) related to the BRI on Twitter. The dataset was collected through Twitter APIs using the terms: “belt and road”, “one belt one road”, ‘new silk road”, “maritime silk road”, and “silk road economic belt”, which includ the phrases and their hashtag format to download data. The time series of the dataset is from 7 September 2013 to 30 November 2021. Furthermore, the dataset has been annotated in terms of languages, sentiment, and geopolitical entities by using text analytics in language detection, neural machine translation, lexicon-based sentiment analysis, and web automation. To facilitate insights discovery, we classified the dataset into four databases in which can be analyzed separately and used by researchers related to various fields, such as social science, network science, sociology, and others to study the dynamic activities on Twitter, trends on keywords, users’ characteristics, as well as the social networks on citing patterns.
DOI: 10.5281/zenodo.6592049
title: ground truths for mesmerize-core tests

description: ground truths for mesmerize-core tests
DOI: 10.5281/zenodo.5914847
title: Berkeley Lab Feedstock to Function tool property database

description: Property prediction database for melting point, boiling point, flash point, yield sooting index, and heat of combustion as they appear in the Feedstock to Function website.
description: This work was supported by the Bioenergy Technologies Office of the U.S. Department of Energy through Contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the US Department of Energy. This research also used resources of the Oak Ridge Leadership Computing Facility, which is a Department of Energy Office of Science User Facility supported under Contract DE-AC05-00OR22725.
DOI: 10.5281/zenodo.5914846
title: Berkeley Lab Feedstock to Function tool property database

description: Property prediction database for melting point, boiling point, flash point, yield sooting index, and heat of combustion as they appear in the Feedstock to Function website.
description: This work was supported by the Bioenergy Technologies Office of the U.S. Department of Energy through Contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the US Department of Energy. This research also used resources of the Oak Ridge Leadership Computing Facility, which is a Department of Energy Office of Science User Facility supported under Contract DE-AC05-00OR22725.
DOI: 10.5281/zenodo.6592084
title: ground truths for mesmerize-core tests

description: ground truths for mesmerize-core tests
DOI: 10.34740/kaggle/dsv/3717444
title: Russian Invasion of Ukraine
DOI: 10.6073/pasta/582d2d04d70921a55357e55f201fe7d1
title: CME01 The Consumer Size Manipulation Experiment (ConSME) at Konza Prairie

description: Herbivores of varying size classes exist with the grassland biome (large mammals, small mammals, insects), however their independent and interactive effects on grassland plant species composition and function are understudied. Here we aim to tease apart the effects of three size classes of herbivores within the Konza Prairie system, and whether these effects vary across fire regimes.
DOI: 10.6073/pasta/50a6f3ed9841383ca0e264fe511a21ff
title: NUT01 Nutrient Network: Investigating the roles of nutrient availability and vertebrate herbivory on grassland structure and function at Konza Prairie

description: The goals and focal research questions are copied below from the Nutrient Network website. More information can be found at nutnet.org. NutNet focal research questions: (1) How general is our current understanding of productivity-diversity relationships? (2) To what extent are plant production and diversity co-limited by multiple nutrients in herbacoues-dominated communities? (3) Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? NutNet goals: (1) To collect data from a broad range of sites in a consistent manner to allow direct comparisons of environment-productivity-diversity relationships among systems around the world. This is currently occurring at each site in the network and, when these data are compiled, will allow us to provide new insights into several important, unanswered questions in ecology. (2) To implement a cross-site experiment requiring only nominal investment of time and resources by each investigator, but quantifying community and ecosystem responses in a wide range of herbaceous-dominated ecosystems (i.e., desert grasslands to arctic tundra).
DOI: 10.48370/ofd/ocpcoz/47xbqh
title: m-2653.tif

description: :unav
DOI: 10.48370/ofd/ocpcoz/lewisi
title: FMW Fuscoporia gilva (Schwein.) T. Wagner & M. Fisch. M-2653.JPG

description: :unav
DOI: 10.48370/ofd/jtle4x/dtdzqu
title: m-2622.tif

description: :unav
DOI: 10.48370/ofd/ocpcoz/rusode
title: FMW Fuscoporia gilva (Schwein.) T. Wagner & M. Fisch. M-2653 (2).JPG

description: :unav
DOI: 10.48370/ofd/jtle4x/zjsued
title: FMW Fuscoporia gilva (Schwein.) T. Wagner & M. Fisch. M-2622 (3).JPG

description: :unav
DOI: 10.48370/ofd/ocpcoz/qjj2wf
title: FMW Fuscoporia gilva (Schwein.) T. Wagner & M. Fisch. M-2653 (3).JPG

description: :unav
DOI: 10.48370/ofd/psku3u/znd88t
title: m-2614.tif

description: :unav
DOI: 10.48370/ofd/jtle4x/gmen9x
title: FMW Fuscoporia gilva (Schwein.) T. Wagner & M. Fisch. M-2622 (2).JPG

description: :unav
DOI: 10.48370/ofd/ocpcoz
title: Fuscoporia gilva (Schwein.) T. Wagner M. Fisch., 2653

description: Grzyby makromycetes
DOI: 10.48370/ofd/psku3u/w1dood
title: FMW Fuscoporia gilva (Schwein.) T. Wagner & M. Fisch. M-2614 (2).JPG

description: :unav
DOI: 10.48370/ofd/jtle4x/uhcbsl
title: FMW Fuscoporia gilva (Schwein.) T. Wagner & M. Fisch. M-2622.JPG

description: :unav
DOI: 10.48370/ofd/jtle4x
title: Fuscoporia gilva (Schwein.) T. Wagner M. Fisch., 2622

description: Grzyby makromycetes
DOI: 10.48370/ofd/psku3u/rf8ioo
title: FMW Fuscoporia gilva (Schwein.) T. Wagner & M. Fisch. M-2614.JPG

description: :unav
DOI: 10.48370/ofd/psku3u/j4upk5
title: FMW Fuscoporia gilva (Schwein.) T. Wagner & M. Fisch. M-2614 (3).JPG

description: :unav
DOI: 10.48370/ofd/psku3u
title: Fuscoporia gilva (Schwein.) T. Wagner M. Fisch., 2614

description: Grzyby makromycetes
DOI: 10.6084/m9.figshare.13089479
title: Sources of variation of DNA methylation in rainbow trout: combined effects of temperature and genetic background

description: Phenotypic plasticity is a key component of the ability of organisms to respond to changing environmental conditions. In this study, we aimed to study the establishment of DNA methylation marks in response to an environmental stress in rainbow trout and to assess whether these marks depend on the genetic background. The environmental stress chosen here was temperature, a known induction factor of epigenetic marks in fish. To disentangle the role of epigenetic mechanisms such as DNA methylation in generating phenotypic variations, nine rainbow trout isogenic lines with no genetic variability within a line were used. For each line, half of the eggs were incubated at standard temperature (11°C) and the other half at high temperature (16°C), from eyed-stage to hatching. In order to gain a first insight into the establishment of DNA methylation marks in response to an early temperature regime (control 11°C vs. heated 16°C), we have studied the expression of 8 <i>dnmt3</i> (DNA methyltransferase) genes, potentially involved in <i>de novo</i> methylation, and analysed global DNA methylation in the different rainbow trout isogenic lines using LUMA (LUminometric Methylation Assay). Finally, finer investigation of genome-wide methylation patterns was performed using EpiRADseq, a reduced-representation library approach based on the ddRADseq (Double Digest Restriction Associated DNA) protocol, for six rainbow trout isogenic lines. We have demonstrated that thermal history during embryonic development alters patterns of DNA methylation, but to a greater or lesser extent depending on the genetic background.
DOI: 10.6084/m9.figshare.13312586
title: DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the <i>RB1</i> gene promoter

description: DNA hypermethylation events occur frequently in human cancers, but less is known of the mechanisms leading to their initiation. Retinoblastoma, an intraocular cancer affecting young children, involves bi-allelic inactivation of the <i>RB1</i> gene (<i>RB<sup>−/-</sup></i>). <i>RB1</i> encodes a tumour suppressing, cell cycle regulating transcription factor (<i>pRB)</i> that binds and regulates the <i>RB1</i> core and other <i>E2F</i> responsive promoters with epigenetic functions that include recruitment of histone deacetylases (<i>HDACs</i>). Evidence suggests that bi-allelic epigenetic inactivation/hypermethylation of the <i>RB1</i> core promoter (<i>Pr<sup>E-/E-</sup></i>), is specific to sporadic retinoblastomas (frequency~10%), whereas heritable <i>RB1</i> promoter variants (<i>Pr<sup>−/+</sup></i>, frequency~1-2%) are not associated with known epigenetic phenomena. We report heritable <i>Pr<sup>−/-</sup></i> retinoblastomas with the expected loss of <i>pRB</i> expression, in which hypermethylation consistent with distal boundary displacement (BD) relative to normal peripheral blood DNAs was detected in 4/4 cases. In contrast, proximal <i>BD</i> was identified in <i>16/16 RB<sup>−/-</sup></i> retinoblastomas while multiple boundaries distal of the core promoter was further identified in <i>Pr<sup>E-/E-</sup></i>and <i>Pr<sup>E-/E+</sup></i> retinoblastomas. However, weak or no DNA hypermethylation/<i>BD</i> in peripheral blood DNA was detected in 8/9 <i>Pr<sup>−/+</sup></i> patients, with the exception, a carrier of a microdeletion encompassing several <i>RB1</i> promoter elements. These findings suggest that loss of boundary control may be a critical step leading to epigenetic inactivation of the <i>RB1</i> gene and that novel DNA methylation boundaries/profiles identified in the <i>RB1</i> promoter of <i>Pr<sup>−/-</sup></i> retinoblastomas, may be the result of epigenetic phenomena associated with epimutation in conjunction with loss of <i>pRB</i> expression/binding and/or <i>RB1</i> promoter interactions with boundary control elements.
DOI: 10.6084/m9.figshare.13312586.v3
title: DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the <i>RB1</i> gene promoter

description: DNA hypermethylation events occur frequently in human cancers, but less is known of the mechanisms leading to their initiation. Retinoblastoma, an intraocular cancer affecting young children, involves bi-allelic inactivation of the <i>RB1</i> gene (<i>RB<sup>−/-</sup></i>). <i>RB1</i> encodes a tumour suppressing, cell cycle regulating transcription factor (<i>pRB)</i> that binds and regulates the <i>RB1</i> core and other <i>E2F</i> responsive promoters with epigenetic functions that include recruitment of histone deacetylases (<i>HDACs</i>). Evidence suggests that bi-allelic epigenetic inactivation/hypermethylation of the <i>RB1</i> core promoter (<i>Pr<sup>E-/E-</sup></i>), is specific to sporadic retinoblastomas (frequency~10%), whereas heritable <i>RB1</i> promoter variants (<i>Pr<sup>−/+</sup></i>, frequency~1-2%) are not associated with known epigenetic phenomena. We report heritable <i>Pr<sup>−/-</sup></i> retinoblastomas with the expected loss of <i>pRB</i> expression, in which hypermethylation consistent with distal boundary displacement (BD) relative to normal peripheral blood DNAs was detected in 4/4 cases. In contrast, proximal <i>BD</i> was identified in <i>16/16 RB<sup>−/-</sup></i> retinoblastomas while multiple boundaries distal of the core promoter was further identified in <i>Pr<sup>E-/E-</sup></i>and <i>Pr<sup>E-/E+</sup></i> retinoblastomas. However, weak or no DNA hypermethylation/<i>BD</i> in peripheral blood DNA was detected in 8/9 <i>Pr<sup>−/+</sup></i> patients, with the exception, a carrier of a microdeletion encompassing several <i>RB1</i> promoter elements. These findings suggest that loss of boundary control may be a critical step leading to epigenetic inactivation of the <i>RB1</i> gene and that novel DNA methylation boundaries/profiles identified in the <i>RB1</i> promoter of <i>Pr<sup>−/-</sup></i> retinoblastomas, may be the result of epigenetic phenomena associated with epimutation in conjunction with loss of <i>pRB</i> expression/binding and/or <i>RB1</i> promoter interactions with boundary control elements.
DOI: 10.6084/m9.figshare.13134656
title: Extracellular microRNA 3’ end modification across diverse body fluids

description: microRNAs (miRNAs) are small non-coding RNAs that play critical roles in gene regulation. The presence of miRNAs in extracellular biofluids is increasingly recognized. However, most previous characterization of extracellular miRNAs focused on their overall expression levels. Alternative sequence isoforms and modifications of miRNAs were rarely considered in the extracellular space. Here, we developed a highly accurate bioinformatic method, called miNTA, to identify 3’ non-templated additions (NTAs) of miRNAs using small RNA-sequencing data. Using miNTA, we conducted an in-depth analysis of miRNA 3’ NTA profiles in 1047 extracellular RNA-sequencing data sets of 4 types of biofluids. This analysis identified hundreds of miRNAs with 3’ uridylation or adenylation, with the former being more prevalent. Among these miRNAs, up to 53% (22%) had an average 3’ uridylation (adenylation) level of at least 10% in a specific biofluid. Strikingly, we found that 3’ uridylation levels enabled segregation of different types of biofluids, more effectively than overall miRNA expression levels. This observation suggests that 3’ NTA levels possess fluid-specific information relatively robust to batch effects. In addition, we observed that extracellular miRNAs with 3’ uridylations are enriched in processes related to angiogenesis, apoptosis, and inflammatory response, and this type of modification may stabilize base-pairing between miRNAs and their target genes. Together, our study provides a comprehensive landscape of miRNA NTAs in human biofluids, which paves way for further biomarker discoveries. The insights generated in our work built a foundation for future functional, mechanistic, and translational discoveries.