cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16778477
title: Additional file 2 of Taxonomy-aware, sequence similarity ranking reliably predicts phage–host relationships

description: Additional file 2: Table S1. Distribution of Phirbo, BLAST and WIsH scores among interacting and non-interacting virus-prokaryote pairs obtained from Edwards et al. and Galiez et al. data sets. Score ranges were summarized separately for 16,757 interacting and non-interacting virus-host pairs from Edwards et al., and 26,024 interacting and non-interacting virus-host pairs from Galiez et al. Table S2. Number of virus-host pairs evaluated by Phirbo, BLAST, and WIsH in Edwards et al. and Galiez et al. data sets. Table S3. Phages assigned by BLAST to multiple, equally-scored host species. Phirbo differentiated between host species and provided the highest score to primary host species. Table S4. Host prediction accuracy of Phirbo, BLAST, and WIsH over virus contig length. Table S5. Phage sequence coverage of 485 phages correctly assigned by BLAST and Phirbo to their host species. Sequence coverage was calculated for each phage as the sum of the lengths of its non-overlapping high scoring pairs to the genome of the correct host species, divided by the size of the query phage genome. Prophages were assumed to have sequence coverage greater than or equal to 30%. Table S6. Summary of taxonomic affiliations of 236 phages that had sequence coverage &lt; 30% with the host species genomes. Table S7. Protein families present in sequence regions of 236 phage genomes that were used by BLAST and/or Phirbo in host prediction. The table provides information on each protein family (prokaryotic Virus Orthologous Group (pVOG)) used by BLAST and Phirbo, including: (i) pVOG description and functional assignment (manually curated), (ii) pVOG count (number of times a given pVOG was present in the phage genome, as well as in sequences used by BLAST or Phirbo), (iii) pVOG percentage (pVOG count divided by pVOG count in the genome), and (iii) P-value of pVOG enrichment. Table S8. RNA families present in sequence regions of 236 phage genomes that were used by BLAST and Phirbo in host prediction. The table provides information on each Rfam family used by BLAST and Phirbo. Table S9. Comparison of Phirbo’s host prediction performance between BLAST-based and Mash-based rankings of prokaryotic species.
DOI: 10.6084/m9.figshare.16778433
title: Additional file 6 of Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation

description: Additional file 6: Table S6. qRT-PCR primer information.
DOI: 10.6084/m9.figshare.16778430
title: Additional file 5 of Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation

description: Additional file 5: Table S5. Differentially expressed genes (DEGs) related hormone metabolism and biosynthesis.
DOI: 10.6084/m9.figshare.16778427
title: Additional file 4 of Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation

description: Additional file 4: Table S4. Differentially expressed protein kinases (PKs) of M. denudata buds in response to cold acclimation.
DOI: 10.6084/m9.figshare.16778424
title: Additional file 3 of Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation

description: Additional file 3: Table S3. Differentially expressed transcription factors (TFs) of M. denudata buds in response to cold acclimation.
DOI: 10.6084/m9.figshare.16778421
title: Additional file 2 of Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation

description: Additional file 2: Table S2. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed genes (DEGs) for M. denudata buds in response to cold acclimation.
DOI: 10.6084/m9.figshare.16778418
title: Additional file 1 of Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation

description: Additional file 1: Table S1. Gene Ontology (GO) analysis of the differentially expressed genes (DEGs) for M. denudata buds in response to cold acclimation.
DOI: 10.6084/m9.figshare.16778417
title: Additional file 4 of Impact of human gene annotations on RNA-seq differential expression analysis

description: Additional file 4 All metrics (Microsoft Excel).
DOI: 10.6084/m9.figshare.16778411
title: Additional file 2 of Impact of human gene annotations on RNA-seq differential expression analysis

description: Additional file 2 Comparison of characteristic features across the count dataset (HTML).
DOI: 10.6084/m9.figshare.16778406
title: Additional file 3 of Compositional variation of the human fecal microbiome in relation to azo-reducing activity: a pilot study

description: Additional file 3. An Excel file with multiple sheets, representing relative abundance ofdifferent taxa (phyla, classes, order, family, genera).
DOI: 10.6084/m9.figshare.16778403
title: Additional file 2 of Compositional variation of the human fecal microbiome in relation to azo-reducing activity: a pilot study

description: Additional file 2. QIIME output in Biological Observation Matrix (biom) data format for allsamples.
DOI: 10.6084/m9.figshare.16778397
title: Additional file 2 of Whole genome copy number analyses reveal a highly aberrant genome in TP53 mutant lung adenocarcinoma tumors

description: Additional file 2. Recurrent aberrant regions and associated genes.
DOI: 10.6084/m9.figshare.16778393
title: Additional file 1 of Transcriptomic analysis of the seminal vesicle response to the reproductive toxicant acrylamide

description: Additional file 1: Tables A1-A9. This additional file contains all supplemental tables for this manuscript.
DOI: 10.6084/m9.figshare.16778384
title: Additional file 1 of Electroretinography and contrast sensitivity, complementary translational biomarkers of sensory deficits in the visual system of individuals with fragile X syndrome

description: Additional file 1.
DOI: 10.6084/m9.figshare.16778382
title: Additional file 1 of Novel chemotherapeutic agent FX-9 activates NF-κB signaling and induces G1 phase arrest by activating CDKN1A in a human prostate cancer cell line

description: Additional file 1.
DOI: 10.6084/m9.figshare.16778360
title: Additional file 1 of Hsa-mir-548 family expression in human reproductive tissues

description: Additional file 1: Supplementary Table S1. Human hsa-mir-548 family pre-miRNA sequence locations in human genome. Supplementary Table S2. Hsa-mir-548 family miRNAs expressed in reproductive tissues. Supplementary Table S3. Reactome pathways of predicted miRNA targets
DOI: 10.6084/m9.figshare.16778062
title: FeO_w90-w45.7z

description: Abundance and distribution of oxide abundances and Mg# values generated from KAGUYA multiband imager (MI) spectra<br>
DOI: 10.6084/m9.figshare.16778557
title: Childhood malnutrition and Hypomineralized molar defects , a cross sectional study.

description: Data of cross sectional study entitled <b>Childhood malnutrition and Hypomineralized molar defects , a cross sectional study.<br></b><b> </b>
DOI: 10.15151/esrf-es-514133778
title: Structure of metalloproteins, membrane proteins, filamentous sarcomer proteins, and virus particles

description: Our work focusses on biological nitrogen fixation by Nitrogenase, on metalloenzymes and integral membrane proteins of bacterial and archaeal respiratory systems (Andrade/Einsle/Wohlwend), the working mechanism and regulation of medically relevant membrane proteins and complexes and their defects leading to pathologies (Hunte), bacterial antibiotic resistance factors and viral and bacterial proteins bound to their targets or inhibitors, and their interactions with glycans (Stehle), human S100 proteins involved in nutritional immunity, USP18 enforcing the endogenous antiviral interferon response, and the respiratory complex NQR of V. cholerae (Fritz), LDL lipoprotein particles with low resolution data collection and phasing to find envelopes of parts of membrane proteins escaping conventional methods (Baumstark/Lunin), and on multi-domain components of the sarcomeric filamentous protein titin and their binding to the E3 ubiquitin ligase MuRF1 and the central myosin rod-domain (Mayans).
DOI: 10.15151/esrf-es-514135427
title: SAARLAND BAG: ATOMIC MECHANISMS OF ACTION OF MEMBRANE PROTEINS AND BIOSYNTHETIC ENZYMES

description: Projects are focussed primarily within the framework of the DFG-funded excellence network program on "Ca2+signals: Molecular Mechanisms und Integrative Functions" at Saarland University and a new joint multidisciplinary initiative of the University with the Helmholtz Institute of Pharmaceutical Research Saarland on natural bioactive compounds including their interactions with their target proteins. These projects involve the structure determination of membrane proteins and soluble proteins.
DOI: 10.15151/esrf-es-514141163
title: Berlin-Karlsruhe - Macromolecular Crystallography BAG - Structural Biology of light responsive, signal transducing and metalloproteins

description: We study structure-function relationships in several groups of proteins, of which many are involved in signal transduction or energy conversion. In our work on biocatalytic splitting of molecular hydrogen into protons and electrons, we analyse in particular the membrane bound [NiFe]hydrogenase, a protein of the remarkable small subgroup of hydrogenases which is active under aerobic conditions. We study the signaling mechanisms of phytochromes by focusing on the structures of photocycle intermediates and analysing domain movements. We analyse the structures of various G-protein coupled receptors (GPCRs; e.g. melanocortin-4 receptor, Ghrelin receptor), either alone or in complex with their cognate G-proteins or selected effector proteins (arrestins), to understand their signaling mechanisms. Other areas of our research include various microbial rhodopsins, cytomegalovirus proteins and their complexes, and DNA photolyases, in particular bacterial (6-4) photolyases.
DOI: 10.15151/esrf-es-517788359
title: Monitoring of biotransformations and biosynthesis of iron oxide-based nanoparticles in cells using XAS and XES

description: The purpose of this proposal is to study and monitor the biotransformations of iron oxide-based nanoheterostructures for applications in biomedicine, over time, at the cellular environment. On one hand, their therapeutic efficacy and toxicity depend on how they transform in the organism after administration and how they degrade, where the excess of iron is regulated by ferritin-like proteins in homeostasis processes. On the other hand, remagnetization and recrystallization of magnetic phases can occur from the biosynthesis of degraded elements inside cells. We therefore propose a time-comprehensive study by means of X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) of the nanoparticles in the cellular environment at different stages of tissue maturation. The electronic structure of Fe and other elements that take part of the nanostructures (Co and Zn) will be probed to track the different phases formed during their degradation or re-biosynthesis inside cells.
DOI: 10.15151/esrf-es-517790861
title: Synthesis and single-crystal X-ray diffraction characterization of novel yttrium carbides under high pressure

description: The systematic investigation of transition metal carbides chemistry under high pressure will allow to produce new forms of polycarbon entities and to understand how their formation alter the physico-chemical properties. Here we propose to investigate the Y-C system up to 120 GPa by single crystal X-ray diffraction (SC-XRD) at ID15b beamline. The main objectives of this proposal are to i) synthesize novel yttrium carbides including novel Raman-discovered Y-C solid, ii) determine their crystal structure in-situ by employing synchrotron single-crystal X-ray diffraction and, iii) establish the produced compounds’ equation of state and find out if they are recoverable to atmospheric pressure.
DOI: 10.15151/esrf-es-517494519
title: Revealing Fe speciation and its impact on catalytic activity in MFI and CHA zeolite structures during methane non-oxidative coupling by oper

description: Non-oxidative coupling of methane is a direct route for natural gas monetization. We have developed a series of Fe-doped zeolite catalysts and discovered that their catalytic performance highly depends on the Fe species confined in zeolites with different topologies (CHA and MFI). Herein, we propose operando HERFD-XANES/XES measurements by using a pulse reactor at ID26, which will help us elucidate the evolution of Fe species at a high temporal resolution during methane non-oxidative coupling process. We will perform a detailed qualitative and quantitative analysis of Fe speciation by using HERFD-XANES with a focus on the pre-edge features, and identify the specific ligands (C or O) linked to Fe-centers by XES. This information will allow us to directly link the structure and evolution of active sites to their catalytic activity under real reaction conditions and therefore will provide a comprehensive understanding of the catalyst activation and deactivation mechanisms.
DOI: 10.5281/zenodo.5558333
title: Dataset for study: The association between reactive strength index and reactive strength index modified with approach jump performance

description: This is the underlying dataset for study: The association between reactive strength index and reactive strength index modified with approach jump performance.
DOI: 10.5281/zenodo.5558332
title: Dataset for study: The association between reactive strength index and reactive strength index modified with approach jump performance

description: This is the underlying dataset for study: The association between reactive strength index and reactive strength index modified with approach jump performance.
DOI: 10.6084/m9.figshare.16778674
title: Supplementary Tables.xlsx

description: Metabolome and Proteopme analyses with bovine serum.<br><b>Table S1:</b> Metabolome analysis with bovine serum on pregnant days 17, 20, and 22.<b>Table S2:</b> Metabolome analysis with bovine serum on cyclic days 0, 7, 14, and 17.<br><b>Table S3:</b> iTRAQ analysis with bovine serum on pregnant day 20.<br><b>Table S4:</b> iTRAQ analysis with bovine serum on pregnant day 22.<br>
DOI: 10.6084/m9.figshare.13726510.v2
title: Supplementary Material

description: Supplementary Table.
DOI: 10.6084/m9.figshare.13726510.v3
title: Supplementary Material

description: Supplementary Table.
DOI: 10.6084/m9.figshare.13094838
title: Transcriptomic and epigenomic effects of insoluble particles on J774 macrophages

description: Here we report epigenomic and transcriptomic changes in a prototypical J774 macrophage after engulfing talc or titanium dioxide particles in presence of estrogen. Macrophages are the first immune cells to engage and clear particles of various nature. A novel paradigm is emerging, that exposure to so-called ‘inert’ particulates that are considered innocuous is not really free of consequences. We hypothesized that especially the insoluble, non-digestible particles that do not release a known hazardous chemical can be underappreciated agents acting to affect the regulation inside macrophages upon phagocytosis. We performed gene chip microarray profiling and found that talc alone, and especially with oestrogen, has induced a substantially more prominent gene expression change than titanium dioxide; the affected genes were involved in pathways of cell proliferation, immune response and regulation, and, unexpectedly, enzymes and proteins of epigenetic regulation. We therefore tested the DNA methylation profiles of these cells via epigenome-wide bisulphite sequencing and found vast epigenetic changes in hundreds of loci, remarkably after a very short exposure to particles; ELISA assay for methylcytosine levels determined the particles induced an overall decrease in DNA methylation. We found a few loci where both the transcriptional changes and epigenetic changes occurred in the pathways involving immune and inflammatory signalling. Some transcriptomic and epigenomic changes were shared between talc and titanium dioxide, however, it is especially interesting that each of the two particles of similar size and insoluble nature has also induced a specific pattern of gene expression and DNA methylation changes which we report here.
DOI: 10.6084/m9.figshare.13094838.v3
title: Transcriptomic and epigenomic effects of insoluble particles on J774 macrophages

description: Here we report epigenomic and transcriptomic changes in a prototypical J774 macrophage after engulfing talc or titanium dioxide particles in presence of estrogen. Macrophages are the first immune cells to engage and clear particles of various nature. A novel paradigm is emerging, that exposure to so-called ‘inert’ particulates that are considered innocuous is not really free of consequences. We hypothesized that especially the insoluble, non-digestible particles that do not release a known hazardous chemical can be underappreciated agents acting to affect the regulation inside macrophages upon phagocytosis. We performed gene chip microarray profiling and found that talc alone, and especially with oestrogen, has induced a substantially more prominent gene expression change than titanium dioxide; the affected genes were involved in pathways of cell proliferation, immune response and regulation, and, unexpectedly, enzymes and proteins of epigenetic regulation. We therefore tested the DNA methylation profiles of these cells via epigenome-wide bisulphite sequencing and found vast epigenetic changes in hundreds of loci, remarkably after a very short exposure to particles; ELISA assay for methylcytosine levels determined the particles induced an overall decrease in DNA methylation. We found a few loci where both the transcriptional changes and epigenetic changes occurred in the pathways involving immune and inflammatory signalling. Some transcriptomic and epigenomic changes were shared between talc and titanium dioxide, however, it is especially interesting that each of the two particles of similar size and insoluble nature has also induced a specific pattern of gene expression and DNA methylation changes which we report here.
DOI: 10.6084/m9.figshare.13174996
title: A histone H3.3K36M mutation in mice causes an imbalance of histone modifications and defects in chondrocyte differentiation

description: Histone lysine-to-methionine (K-to-M) mutations have been identified as driver mutations in human cancers. Interestingly, these ‘oncohistone’ mutations inhibit the activity of histone methyltransferases. Therefore, they can potentially be used as versatile tools to investigate the roles of histone modifications. In this study, we generated a genetically engineered mouse line in which an H3.3K36M mutation could be induced in the endogenous <i>H3f3b</i> gene. Since H3.3K36M has been identified as a causative mutation of human chondroblastoma, we induced this mutation in the chondrocyte lineage in mouse embryonic limbs. We found that H3.3K36M causes a global reduction in H3K36me2 and defects in chondrocyte differentiation. Importantly, the reduction of H3K36me2 was accompanied by a collapse of normal H3K27me3 distribution. Furthermore, the changes in H3K27me3, especially the loss of H3K27me3 at gene regulatory elements, were associated with the mis-regulated expression of a set of genes important for limb development, including HoxA cluster genes. Thus, through the <i>in vivo</i> induction of the H3.3K36M mutation, we reveal the importance of maintaining the balance between H3K36me2 and H3K27me3 during chondrocyte differentiation and limb development.
DOI: 10.6084/m9.figshare.13094838.v2
title: Transcriptomic and epigenomic effects of insoluble particles on J774 macrophages

description: Here we report epigenomic and transcriptomic changes in a prototypical J774 macrophage after engulfing talc or titanium dioxide particles in presence of estrogen. Macrophages are the first immune cells to engage and clear particles of various nature. A novel paradigm is emerging, that exposure to so-called ‘inert’ particulates that are considered innocuous is not really free of consequences. We hypothesized that especially the insoluble, non-digestible particles that do not release a known hazardous chemical can be underappreciated agents acting to affect the regulation inside macrophages upon phagocytosis. We performed gene chip microarray profiling and found that talc alone, and especially with oestrogen, has induced a substantially more prominent gene expression change than titanium dioxide; the affected genes were involved in pathways of cell proliferation, immune response and regulation, and, unexpectedly, enzymes and proteins of epigenetic regulation. We therefore tested the DNA methylation profiles of these cells via epigenome-wide bisulphite sequencing and found vast epigenetic changes in hundreds of loci, remarkably after a very short exposure to particles; ELISA assay for methylcytosine levels determined the particles induced an overall decrease in DNA methylation. We found a few loci where both the transcriptional changes and epigenetic changes occurred in the pathways involving immune and inflammatory signalling. Some transcriptomic and epigenomic changes were shared between talc and titanium dioxide, however, it is especially interesting that each of the two particles of similar size and insoluble nature has also induced a specific pattern of gene expression and DNA methylation changes which we report here.
DOI: 10.6084/m9.figshare.14185555
title: Epigenome-wide association study for glyphosate induced transgenerational sperm DNA methylation and histone retention epigenetic biomarkers for disease

description: The herbicide glyphosate has been shown to promote the epigenetic transgenerational inheritance of pathology and disease in subsequent great-grand offspring (F3 generation). This generational toxicology suggests the impacts of environmental exposures need to assess subsequent generations. The current study was designed to identify epigenetic biomarkers for glyphosate-induced transgenerational diseases using an epigenome-wide association study (EWAS). Following transient glyphosate exposure of gestating female rats (F0 generation), during the developmental period of gonadal sex determination, the subsequent transgenerational F3 generation, with no direct exposure, were aged to 1 year and animals with specific pathologies identified. The pathologies investigated included prostate disease, kidney disease, obesity, and presence of multiple disease. The sperm were collected from the glyphosate lineage males with only an individual disease and used to identify specific differential DNA methylation regions (DMRs) and the differential histone retention sites (DHRs) associated with that pathology. Unique signatures of DMRs and DHRs for each pathology were identified for the specific diseases. Interestingly, at a lower statistical threshold overlapping sets of DMRs and DHRs were identified that were common for all the pathologies. This is one of the first observations that sperm histone retention can potentially act as a biomarker for specific diseases. The DMR and DHR associated genes were identified and correlated with known pathology specific-associated genes. Observations indicate transgenerational epigenetic biomarkers of disease pathology can be identified in the sperm that appear to assess disease susceptibility. These biomarkers suggest epigenetic diagnostics could potentially be used to facilitate preventative medicine.