cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2074408.v1
title: A reevaluation of <i>Brachyprosopus broomi</i> and <i>Chelydontops altidentalis</i>, dicynodonts (Therapsida, Anomodontia) from the middle Permian <i>Tapinocephalus</i> Assemblage Zone of the Karoo Basin, South Africa

description: <i>Brachyprosopus broomi</i> was described in 1937 based on a specimen from the <i>Tapinocephalus</i> Assemblage Zone (Karoo Basin, South Africa), but it was largely overlooked by subsequent workers. We have identified several new specimens that show that <i>Brachyprosopus</i> is a valid taxon. An autapomorphy for the taxon is a curled lateral edge of the squamosal that forms a lateral wall of the external adductor fossa. Other important characters are absence of anterior median palatal ridges; maxillary tooth rows bounded laterally by a shelf; unfused vomers; raised margins of the interpterygoid vacuity; broad intertemporal region; pineal boss; dentary tables; and a long, wide posterior dentary sulcus that extends posterior to the dentary teeth. <i>Chelydontops altidentalis</i> is a junior synonym of <i>B. broomi</i>. A phylogenetic analysis places <i>Brachyprosopus</i> among basal dicynodonts, not as a close relative of <i>Endothiodon</i>. It is noteworthy that some characters, such as well-developed medial maxillary tooth rows and the shape of the palatines, are shared by <i>Brachyprosopus, Pristerodon, Endothiodon</i>, and <i>Niassodon</i>, hinting that a final resolution of relationships among toothed dicynodonts remains to be achieved. Most <i>Brachyprosopus</i> specimens are from the upper Abrahamskraal Formation (Moordenaars and Karelskraal members). One specimen is from low in the Koonap Formation, just above the lowermost maroon mudrocks of the Beaufort Group, and an exact correlation between this level and the strata of the Abrahamskraal Formation is uncertain. Therefore, it is likely that the stratigraphic range of <i>Brachyprosopus</i> extends throughout the <i>Tapinocephalus</i> zone and possibly down into the <i>Eodicynodon</i> Assemblage Zone. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Angielczyk, K. D., B. S. Rubidge, M. O. Day, and F. Lin. 2016. A reevaluation of <i>Brachyprosopus broomi</i> and <i>Chelydontops altidentalis</i>, dicynodonts (Therapsida, Anomodontia) from the middle Permian <i>Tapinocephalus</i> Assemblage Zone of the Karoo Basin, South Africa. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1078342.
DOI: 10.6084/m9.figshare.2951263.v453
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2074399
title: Comminuted meat products—consumption, composition, and approaches to healthier formulations

description: Comminuted meat products are significant contributors to consumer fat and salt intakes, which are currently above World Health Organization recommended levels. Reducing fat and salt in comminuted meat products may therefore have a significant positive effect on public health in countries with a high consumption of these meats. As an example, the processed meat intake and the fat and salt levels of various comminuted meat products in Ireland and the UK are presented. The review focuses on substitution of fat and salt (including nitrite) with ingredients that yield products with acceptable organoleptic properties and have proven human health benefits.
DOI: 10.6084/m9.figshare.2951263.v454
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2074399.v1
title: Comminuted meat products - consumption, composition and approaches to healthier formulations

description: Comminuted meat products are significant contributors to consumer fat and salt intakes, which are currently above World Health Organization recommended levels. Reducing fat and salt in comminuted meat products may therefore have a significant positive effect on public health in countries with a high consumption of these meats. As an example, the processed meat intake and the fat and salt levels of various comminuted meat products in Ireland and the UK are presented. The review focuses on substitution of fat and salt (including nitrite) with ingredients that yield products with acceptable organoleptic properties and have proven human health benefits.
DOI: 10.6084/m9.figshare.2951263.v455
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2074387
title: Novel small RNA (sRNA) landscape of the starvation-stress response transcriptome of <i>Salmonella enterica</i> serovar typhimurium

description: Small RNAs (sRNAs) are short (∼50–200 nucleotides) noncoding RNAs that regulate cellular activities across bacteria. <i>Salmonella enterica</i> starved of a carbon-energy (C) source experience a host of genetic and physiological changes broadly referred to as the starvation-stress response (SSR). In an attempt to identify novel sRNAs contributing to SSR control, we grew log-phase, 5-h C-starved and 24-h C-starved cultures of the virulent <i>Salmonella enterica</i> subspecies enterica serovar Typhimurium strain SL1344 and comprehensively sequenced their small RNA transcriptomes. Strikingly, after employing a novel strategy for sRNA discovery based on identifying dynamic transcripts arising from “gene-empty” regions, we identify 58 wholly undescribed <i>Salmonella</i> sRNA genes potentially regulating SSR averaging an ∼1,000-fold change in expression between log-phase and C-starved cells. Importantly, the expressions of individual sRNA loci were confirmed by both comprehensive transcriptome analyses and northern blotting of select candidates. Of note, we find 43 candidate sRNAs share significant sequence identity to characterized sRNAs in other bacteria, and ∼70% of our sRNAs likely assume characteristic sRNA structural conformations. In addition, we find 53 of our 58 candidate sRNAs either overlap neighboring mRNA loci or share significant sequence complementarity to mRNAs transcribed elsewhere in the SL1344 genome strongly suggesting they regulate the expression of transcripts via antisense base-pairing. Finally, in addition to this work resulting in the identification of 58 entirely novel <i>Salmonella enterica</i> genes likely participating in the SSR, we also find evidence suggesting that sRNAs are significantly more prevalent than currently appreciated and that <i>Salmonella</i> sRNAs may actually number in the thousands.
DOI: 10.6084/m9.figshare.2074384
title: Tumor suppressor properties of the splicing regulatory factor RBM10

description: RBM10 is an RNA binding protein and alternative splicing regulator frequently mutated in lung adenocarcinomas. Recent results indicate that RBM10 inhibits proliferation of lung cancer cells by promoting skipping of exon 9 of the gene NUMB, a frequent alternative splicing change in lung cancer generating a negative regulator of Notch signaling. Complementing these observations, we show that knock down of RBM10 in human cancer cells enhances growth of mouse tumor xenografts, confirming that RBM10 acts as a tumor suppressor, while knock down of an oncogenic mutant version of RBM10 reduces xenograft tumor growth. A RBM10 mutation found in lung cancer cells, V354E, disrupts RBM10-mediated regulation of NUMB alternative splicing, inducing the cell proliferation-promoting isoform. We now show that 2 natural RBM10 isoforms that differ by the presence or absence of V354 in the second RNA Recognition Motif (RRM2), display similar regulatory effects on NUMB alternative splicing, suggesting that V354E actively disrupts RBM10 activity. Structural modeling localizes V354 in the outside surface of one α-helix opposite to the RNA binding surface of RBM10, and we show that the mutation does not compromise binding of the RRM2 domain to NUMB RNA regulatory sequences. We further show that other RBM10 mutations found in lung adenocarcinomas also compromise regulation of NUMB exon 9. Collectively, our previous and current results reveal that RBM10 is a tumor suppressor that represses Notch signaling and cell proliferation through the regulation of NUMB alternative splicing.
DOI: 10.6084/m9.figshare.2074384.v1
title: Tumor suppressor properties of the splicing regulatory factor RBM10

description: RBM10 is an RNA binding protein and alternative splicing regulator frequently mutated in lung adenocarcinomas. Recent results indicate that RBM10 inhibits proliferation of lung cancer cells by promoting skipping of exon 9 of the gene NUMB, a frequent alternative splicing change in lung cancer generating a negative regulator of Notch signaling. Complementing these observations, we show that knock down of RBM10 in human cancer cells enhances growth of mouse tumor xenografts, confirming that RBM10 acts as a tumor suppressor, while knock down of an oncogenic mutant version of RBM10 reduces xenograft tumor growth. A RBM10 mutation found in lung cancer cells, V354E, disrupts RBM10-mediated regulation of NUMB alternative splicing, inducing the cell proliferation-promoting isoform. We now show that 2 natural RBM10 isoforms that differ by the presence or absence of V354 in the second RNA Recognition Motif (RRM2), display similar regulatory effects on NUMB alternative splicing, suggesting that V354E actively disrupts RBM10 activity. Structural modeling localizes V354 in the outside surface of one α-helix opposite to the RNA binding surface of RBM10, and we show that the mutation does not compromise binding of the RRM2 domain to NUMB RNA regulatory sequences. We further show that other RBM10 mutations found in lung adenocarcinomas also compromise regulation of NUMB exon 9. Collectively, our previous and current results reveal that RBM10 is a tumor suppressor that represses Notch signaling and cell proliferation through the regulation of NUMB alternative splicing.
DOI: 10.6084/m9.figshare.2951263.v456
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2074387.v2
title: Novel small RNA (sRNA) landscape of the starvation-stress response transcriptome of <i>Salmonella enterica</i> serovar typhimurium

description: Small RNAs (sRNAs) are short (∼50–200 nucleotides) noncoding RNAs that regulate cellular activities across bacteria. <i>Salmonella enterica</i> starved of a carbon-energy (C) source experience a host of genetic and physiological changes broadly referred to as the starvation-stress response (SSR). In an attempt to identify novel sRNAs contributing to SSR control, we grew log-phase, 5-h C-starved and 24-h C-starved cultures of the virulent <i>Salmonella enterica</i> subspecies enterica serovar Typhimurium strain SL1344 and comprehensively sequenced their small RNA transcriptomes. Strikingly, after employing a novel strategy for sRNA discovery based on identifying dynamic transcripts arising from “gene-empty” regions, we identify 58 wholly undescribed <i>Salmonella</i> sRNA genes potentially regulating SSR averaging an ∼1,000-fold change in expression between log-phase and C-starved cells. Importantly, the expressions of individual sRNA loci were confirmed by both comprehensive transcriptome analyses and northern blotting of select candidates. Of note, we find 43 candidate sRNAs share significant sequence identity to characterized sRNAs in other bacteria, and ∼70% of our sRNAs likely assume characteristic sRNA structural conformations. In addition, we find 53 of our 58 candidate sRNAs either overlap neighboring mRNA loci or share significant sequence complementarity to mRNAs transcribed elsewhere in the SL1344 genome strongly suggesting they regulate the expression of transcripts via antisense base-pairing. Finally, in addition to this work resulting in the identification of 58 entirely novel <i>Salmonella enterica</i> genes likely participating in the SSR, we also find evidence suggesting that sRNAs are significantly more prevalent than currently appreciated and that <i>Salmonella</i> sRNAs may actually number in the thousands.
DOI: 10.6084/m9.figshare.2074390.v1
title: MicroRNAs Activate Gene Transcription Epigenetically as an Enhancer Trigger

description: MicroRNAs (miRNAs) are small non-coding RNAs that function as negative gene expression regulators. Emerging evidence shows that, except for function in the cytoplasm, miRNAs are also present in the nucleus. However, the functional significance of nuclear miRNAs remains largely undetermined. By screening miRNA database, we have identified a subset of miRNA that function as enhancer regulator. Here, we found a set of miRNAs show gene-activation function. We focused on miR-24-1 and found that this miRNA unconventionally activates gene transcription by targeting enhancers. Consistently, the activation was completely abolished when the enhancer sequence was deleted by TALEN. Furthermore, we found that miR-24-1 activates enhancer RNA (eRNA) expression, alters histone modification, and increases the enrichment of p300 and RNA Pol II at the enhancer locus. Our results demonstrate a novel mechanism of miRNA as an enhancer trigger.
DOI: 10.6084/m9.figshare.2074387.v1
title: Novel Small RNA (sRNA) Landscape of the Starvation-Stress Response Transcriptome of <i>Salmonella enterica</i> serovar Typhimurium

description: Small RNAs (sRNAs) are short (˜50–200 nucleotides) noncoding RNAs that regulate cellular activities across bacteria. <i>Salmonella enterica</i> starved of a carbon-energy (C) source experience a host of genetic and physiological changes broadly referred to as the starvation-stress response (SSR). In an attempt to identify novel sRNAs contributing to SSR control, we grew log-phase, 5-h C-starved and 24-h C-starved cultures of the virulent <i>Salmonella enterica</i> subspecies enterica serovar Typhimurium strain SL1344 and comprehensively sequenced their small RNA transcriptomes. Strikingly, after employing a novel strategy for sRNA discovery based on identifying dynamic transcripts arising from “gene-empty” regions, we identify 58 wholly undescribed <i>Salmonella</i> sRNA genes potentially regulating SSR averaging an ˜1,000-fold change in expression between log-phase and C-starved cells. Importantly, the expressions of individual sRNA loci were confirmed by both comprehensive transcriptome analyses and northern blotting of select candidates. Of note, we find 43 candidate sRNAs share significant sequence identity to characterized sRNAs in other bacteria, and ˜70% of our sRNAs likely assume characteristic sRNA structural conformations. In addition, we find 53 of our 58 candidate sRNAs either overlap neighboring mRNA loci or share significant sequence complementarity to mRNAs transcribed elsewhere in the SL1344 genome strongly suggesting they regulate the expression of transcripts via antisense base-pairing. Finally, in addition to this work resulting in the identification of 58 entirely novel <i>Salmonella enterica</i> genes likely participating in the SSR, we also find evidence suggesting that sRNAs are significantly more prevalent than currently appreciated and that <i>Salmonella</i> sRNAs may actually number in the thousands.
DOI: 10.6084/m9.figshare.2951263.v457
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2074390.v2
title: MicroRNAs activate gene transcription epigenetically as an enhancer trigger

description: MicroRNAs (miRNAs) are small non-coding RNAs that function as negative gene expression regulators. Emerging evidence shows that, except for function in the cytoplasm, miRNAs are also present in the nucleus. However, the functional significance of nuclear miRNAs remains largely undetermined. By screening miRNA database, we have identified a subset of miRNA that functions as enhancer regulators. Here, we found a set of miRNAs show gene-activation function. We focused on miR-24-1 and found that this miRNA unconventionally activates gene transcription by targeting enhancers. Consistently, the activation was completely abolished when the enhancer sequence was deleted by TALEN. Furthermore, we found that miR-24-1 activates enhancer RNA (eRNA) expression, alters histone modification, and increases the enrichment of p300 and RNA Pol II at the enhancer locus. Our results demonstrate a novel mechanism of miRNA as an enhancer trigger.
DOI: 10.6084/m9.figshare.2074366
title: Butterflyfish data.xlsx

description: Data sheets with mostly raw data from triangle butterflyfish study. Methods and techniques in manuscript.
DOI: 10.6084/m9.figshare.2074372
title: Butterflyfish data

description: Supporting data for study on chaetodon triangulum carried out in Maldives. All methods and permissions can be found within the manucript.
DOI: 10.6084/m9.figshare.2074372.v1
title: Butterflyfish data

description: Supporting data for study on chaetodon triangulum carried out in Maldives. All methods and permissions can be found within the manucript.
DOI: 10.6084/m9.figshare.2951263.v458
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2074366.v1
title: Butterflyfish data.xlsx

description: Data sheets with mostly raw data from triangle butterflyfish study. Methods and techniques in manuscript.
DOI: 10.6084/m9.figshare.2951263.v459
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2074360
title: Organic/inorganic epitaxy: commensurate epitaxial growth of truxenone on Cu (111)

description: The growth of monolayers of truxenone on Cu (111) is investigated using scanning tunneling microscopy (STM) and low energy electron diffraction (LEED). Two distinct molecular packing motifs are observed which exist individually at low and high coverage, and coexist at intermediate states. In each case a commensurate epitaxial relationship between the molecular surface mesh and the substrate is observed.
DOI: 10.6084/m9.figshare.2074360.v1
title: Organic/inorganic epitaxy: commensurate epitaxial growth of truxenone on Cu (111)

description: The growth of monolayers of truxenone on Cu (111) is investigated using scanning tunneling microscopy (STM) and low energy electron diffraction (LEED). Two distinct molecular packing motifs are observed which exist individually at low and high coverage, and coexist at intermediate states. In each case a commensurate epitaxial relationship between the molecular surface mesh and the substrate is observed.
DOI: 10.6084/m9.figshare.2951263.v460
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2074342
title: Vegetarian, vegan diets and multiple health outcomes: A systematic review with meta-analysis of observational studies

description: <b>Background</b>: Beneficial effects of vegetarian and vegan diets on health outcomes have been supposed in previous studies. <b>Objectives</b>: Aim of this study was to clarify the association between vegetarian, vegan diets, risk factors for chronic diseases, risk of all-cause mortality, incidence, and mortality from cardio-cerebrovascular diseases, total cancer and specific type of cancer (colorectal, breast, prostate and lung), through meta-analysis. <b>Methods</b>: A comprehensive search of Medline, EMBASE, Scopus, The Cochrane Library, and Google Scholar was conducted. <b>Results</b>: Eighty-six cross-sectional and 10 cohort prospective studies were included. The overall analysis among cross-sectional studies reported significant reduced levels of body mass index, total cholesterol, LDL-cholesterol, and glucose levels in vegetarians and vegans versus omnivores. With regard to prospective cohort studies, the analysis showed a significant reduced risk of incidence and/or mortality from ischemic heart disease (RR 0.75; 95% CI, 0.68 to 0.82) and incidence of total cancer (RR 0.92; 95% CI 0.87 to 0.98) but not of total cardiovascular and cerebrovascular diseases, all-cause mortality and mortality from cancer. No significant association was evidenced when specific types of cancer were analyzed. The analysis conducted among vegans reported significant association with the risk of incidence from total cancer (RR 0.85; 95% CI, 0.75 to 0.95), despite obtained only in a limited number of studies. <b>Conclusions</b>: This comprehensive meta-analysis reports a significant protective effect of a vegetarian diet versus the incidence and/or mortality from ischemic heart disease (−25%) and incidence from total cancer (−8%). Vegan diet conferred a significant reduced risk (−15%) of incidence from total cancer.
DOI: 10.6084/m9.figshare.2951263.v461
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.