cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3405892
title: The guanylate cyclase-C signaling pathway is down-regulated in inflammatory bowel disease

description: <b><i>Objective.</i></b> Activation of membrane receptor guanylate cyclase-C (GC-C) is implicated in gastrointestinal fluid and electrolyte balance, preservation of intestinal barrier integrity, anti-trophic effects and inhibition of pain sensation. To evaluate GC-C signaling, we examined the regulation of GC-C (<i>GUCY2C</i>/<i>Gucy2c</i>) and its endogenous ligands guanylin (GN/<i>GUCA2A</i>/<i>Guca2a</i>) and uroguanylin (UGN/<i>GUCA2B</i>/<i>Guca2b</i>) in colonic Crohn’s disease (CD), ulcerative colitis (UC) and in rats with 2,4,6-Trinitrobenzene sulphonic acid (TNBS) colitis. Correlation analyses between expression of <i>GUCA2A</i> and <i>GUCY2C</i> and expression of inflammatory cytokines (<i>IL1A,</i> <i>IL1B,</i> <i>TNFA</i> and <i>IFNG</i>) were conducted. Additionally, expression of transcription factors for <i>GUCA2A</i> and <i>GUCY2C,</i> and the GC-C signaling pathway, were examined. <b><i>Material and methods.</i></b> Biopsies from active UC/CD, un-inflamed UC/CD and healthy controls, and inflamed and healthy rat colon were investigated with gene expression microarray, immunohistochemistry (IHC) and <i>in situ</i> hybridization (ISH). <b><i>Results.</i></b> <i>GUCA2A</i>/<i>Guca2a,</i> <i>GUCA2B,</i> <i>GUCY2C</i>/<i>Gucy2c,</i> transcription factors, as well as several cyclic guanosine-3′,5′-monophosphate downstream mediators were all significantly down-regulated in both inflamed colonic inflammatory bowel disease (IBD) mucosa and TNBS colitis. Expression of <i>GUCA2A</i> and <i>GUCY2C</i> negatively correlated to expression of inflammatory cytokines. IHC and ISH confirmed microarray results for <i>GUCA2A</i>/<i>Guca2a</i> and <i>GUCY2C</i>/<i>Gucy2c</i> in inflamed samples. We identified a highly significant positive correlation between the expression of the transcription factor caudal type homeobox 2 (<i>CDX2</i>) and the expression of the downstream target gene <i>GUCY2C.</i> <b><i>Conclusions.</i> GUCA2A,</b> <i>GUCA2B</i> and <i>GUCY2C</i> as well as several steps of the GC-C signaling pathway are down-regulated in IBD. This may have implications in IBD pathogenesis.
DOI: 10.6084/m9.figshare.3405892.v2
title: The guanylate cyclase-C signaling pathway is down-regulated in inflammatory bowel disease

description: <b><i>Objective.</i></b> Activation of membrane receptor guanylate cyclase-C (GC-C) is implicated in gastrointestinal fluid and electrolyte balance, preservation of intestinal barrier integrity, anti-trophic effects and inhibition of pain sensation. To evaluate GC-C signaling, we examined the regulation of GC-C (<i>GUCY2C</i>/<i>Gucy2c</i>) and its endogenous ligands guanylin (GN/<i>GUCA2A</i>/<i>Guca2a</i>) and uroguanylin (UGN/<i>GUCA2B</i>/<i>Guca2b</i>) in colonic Crohn’s disease (CD), ulcerative colitis (UC) and in rats with 2,4,6-Trinitrobenzene sulphonic acid (TNBS) colitis. Correlation analyses between expression of <i>GUCA2A</i> and <i>GUCY2C</i> and expression of inflammatory cytokines (<i>IL1A,</i> <i>IL1B,</i> <i>TNFA</i> and <i>IFNG</i>) were conducted. Additionally, expression of transcription factors for <i>GUCA2A</i> and <i>GUCY2C,</i> and the GC-C signaling pathway, were examined. <b><i>Material and methods.</i></b> Biopsies from active UC/CD, un-inflamed UC/CD and healthy controls, and inflamed and healthy rat colon were investigated with gene expression microarray, immunohistochemistry (IHC) and <i>in situ</i> hybridization (ISH). <b><i>Results.</i></b> <i>GUCA2A</i>/<i>Guca2a,</i> <i>GUCA2B,</i> <i>GUCY2C</i>/<i>Gucy2c,</i> transcription factors, as well as several cyclic guanosine-3′,5′-monophosphate downstream mediators were all significantly down-regulated in both inflamed colonic inflammatory bowel disease (IBD) mucosa and TNBS colitis. Expression of <i>GUCA2A</i> and <i>GUCY2C</i> negatively correlated to expression of inflammatory cytokines. IHC and ISH confirmed microarray results for <i>GUCA2A</i>/<i>Guca2a</i> and <i>GUCY2C</i>/<i>Gucy2c</i> in inflamed samples. We identified a highly significant positive correlation between the expression of the transcription factor caudal type homeobox 2 (<i>CDX2</i>) and the expression of the downstream target gene <i>GUCY2C.</i> <b><i>Conclusions.</i> GUCA2A,</b> <i>GUCA2B</i> and <i>GUCY2C</i> as well as several steps of the GC-C signaling pathway are down-regulated in IBD. This may have implications in IBD pathogenesis.
DOI: 10.6084/m9.figshare.3405826
title: Protected Areas buffer the Brazilian semi-arid biome from Climate Change

description: Data used to model satellite-derived Normalized Difference Vegetation Index (NDVI) in response to precipitation in deforested and non-deforested areas of the Brazilian semi-arid Caatinga biome.
DOI: 10.6084/m9.figshare.3405826.v1
title: Protected Areas buffer the Brazilian semi-arid biome from Climate Change

description: Data used to model satellite-derived Normalized Difference Vegetation Index (NDVI) in response to precipitation in deforested and non-deforested areas of the Brazilian semi-arid Caatinga biome.
DOI: 10.6084/m9.figshare.3405808
title: River Discharge Calculator

description: River Discharge Calculator is a user friendly program that implements a numerical method to improve the efficiency of river discharge measurement, proposed in the accompanying preprint submitted to the Journal of Hydrological Engineering (ASCE), May 2016. In this work we propose a simple computational scheme with the pragmatic purpose of augmenting the efficiency of river discharge measurements. Observing the functional form of the velocity profile versus depth, applying polynomial regression for each vertical, and finally interpolating between the verticals, we arrive at a continuous approximation for the velocity across the entire vertical section, which turns out to be rather robust to removal of individual measurement points. In particular, numerical data analysis shows that the number of measurements can be significantly reduced without a significant loss of precision of the discharge estimate. This procedure has been tested on the data obtained experimentally on Exu, Capibaribe and Ipojuca rivers, in the state of Pernambuco, northeast of Brazil, with different stream flow patterns demonstrating multiple local velocity maxima on and below the surface.
DOI: 10.6084/m9.figshare.3405787
title: Dose response curve shows better survival of TAT.ARC protein transduced primary cortical neurons in comparison to TAT beta galactosidase transduced neurons after oxygen glucose deprivation

description: Primary mice cortical neuronal cultures on DIV10. OGD for 150 min. Analysis of cell survival after 24h. Exogenous ARC protein transduction leads to a dose-dependent increase in neuronal survival following OGD compared to TAT.β-Gal-treated neurons. 4 independent experiments.
DOI: 10.6084/m9.figshare.3405787.v1
title: Dose response curve shows better survival of TAT.ARC protein transduced primary cortical neurons in comparison to TAT beta galactosidase transduced neurons after oxygen glucose deprivation

description: Primary mice cortical neuronal cultures on DIV10. OGD for 150 min. Analysis of cell survival after 24h. Exogenous ARC protein transduction leads to a dose-dependent increase in neuronal survival following OGD compared to TAT.β-Gal-treated neurons. 4 independent experiments.
DOI: 10.6084/m9.figshare.3405691
title: Proteomics for OSF and OSCC.xls

description: Based on the Unused ProtScore &gt;1.3 (95%) as threshold with at least more than one peptide above the 95% confidence, a total of 1998 proteins were identified from 14237 distinct peptides among three tissue samples. 71.7% proteins were identified with at least two peptides and 56.2% proteins were identified with three or more peptides. (Quantitative Proteomic Analysis for the Identification of Candidate Biomarkers in Buccal Squamous Cell Carcinoma Arising in Background of Oral Submucous Fibrosis)
DOI: 10.6084/m9.figshare.3405691.v1
title: Proteomics for OSF and OSCC.xls

description: Based on the Unused ProtScore &gt;1.3 (95%) as threshold with at least more than one peptide above the 95% confidence, a total of 1998 proteins were identified from 14237 distinct peptides among three tissue samples. 71.7% proteins were identified with at least two peptides and 56.2% proteins were identified with three or more peptides. (Quantitative Proteomic Analysis for the Identification of Candidate Biomarkers in Buccal Squamous Cell Carcinoma Arising in Background of Oral Submucous Fibrosis)
DOI: 10.6084/m9.figshare.3405691.v3
title: Proteomics for OSF and OSCC.xls

description: Based on the Unused ProtScore &gt;1.3 (95%) as threshold with at least more than one peptide above the 95% confidence, a total of 1998 proteins were identified from 14237 distinct peptides among three tissue samples. 71.7% proteins were identified with at least two peptides and 56.2% proteins were identified with three or more peptides. (Quantitative Proteomic Analysis for the Identification of Candidate Biomarkers in Buccal Squamous Cell Carcinoma Arising in Background of Oral Submucous Fibrosis)
DOI: 10.6084/m9.figshare.3405691.v2
title: Proteomics for OSF and OSCC.xls

description: Based on the Unused ProtScore &gt;1.3 (95%) as threshold with at least more than one peptide above the 95% confidence, a total of 1998 proteins were identified from 14237 distinct peptides among three tissue samples. 71.7% proteins were identified with at least two peptides and 56.2% proteins were identified with three or more peptides. (Quantitative Proteomic Analysis for the Identification of Candidate Biomarkers in Buccal Squamous Cell Carcinoma Arising in Background of Oral Submucous Fibrosis)
DOI: 10.6084/m9.figshare.3405685.v3
title: Literature visualisation: Bibliometric of groundwater research in Jakarta

description: The following data is our latest update. It is included in the analysis for our paper on RIOJournal (submitted 27/05/2016). <br>
DOI: 10.6084/m9.figshare.3405685.v2
title: Literature visualisation: Bibliometric of groundwater research in Jakarta

description: The following data is our latest update. It is included in the analysis for our paper on RIOJournal (submitted 27/05/2016). <br>
DOI: 10.6084/m9.figshare.3405676
title: Forced KLF4 expression increases the generation of mature plasma cells and uncovers a network linked with plasma cell stage

description: A role of the transcription factor Krüppel-like factor 4 (KLF4) in the generation of mature plasma cells (PC) is unknown. Indeed, KLF4 is critical in controlling the differentiation of various cell linages, particularly monocytes and epithelial cells. KLF4 is expressed at low levels in pro-B cells and its expression increases as they mature into pre-B cells, resting naïve B cells and memory B cells. We show here that KLF4 is expressed in human bone marrow plasma cells and its function was studied using an <i>in vitro</i> model of differentiation of memory B cells into long lived plasma cells. KLF4 is rapidly lost when memory B cells differentiate into highly cell cycling plasmablasts, poorly cycling early plasma cells and then quiescent long-lived plasma cells. A forced expression of KLF4 in plasmablasts enhances the yield of their differentiation into early plasma cell and long lived plasma cells, by inhibiting apoptosis and upregulating previously unknown plasma cell pathways.
DOI: 10.6084/m9.figshare.3405676.v1
title: Forced KLF4 expression increases the generation of mature plasma cells and uncovers a network linked with plasma cell stage

description: A role of the transcription factor Krüppel-like factor 4 (KLF4) in the generation of mature plasma cells (PC) is unknown. Indeed, KLF4 is critical in controlling the differentiation of various cell linages, particularly monocytes and epithelial cells. KLF4 is expressed at low levels in pro-B cells and its expression increases as they mature into pre-B cells, resting naïve B cells and memory B cells. We show here that KLF4 is expressed in human bone marrow plasma cells and its function was studied using an <i>in vitro</i> model of differentiation of memory B cells into long lived plasma cells. KLF4 is rapidly lost when memory B cells differentiate into highly cell cycling plasmablasts, poorly cycling early plasma cells and then quiescent long-lived plasma cells. A forced expression of KLF4 in plasmablasts enhances the yield of their differentiation into early plasma cell and long lived plasma cells, by inhibiting apoptosis and upregulating previously unknown plasma cell pathways.
DOI: 10.6084/m9.figshare.3405670
title: Estimation Under Cross-Classified Sampling With Application to a Childhood Survey

description: The cross-classified sampling design consists in drawing samples from a two-dimensional population, independently in each dimension. Such design is commonly used in consumer price index surveys and has been recently applied to draw a sample of babies in the French Longitudinal Survey on Childhood, by crossing a sample of maternity units and a sample of days. We propose to derive a general theory of estimation for this sampling design. We consider the Horvitz–Thompson estimator for a total, and show that the cross-classified design will usually result in a loss of efficiency as compared to the widespread two-stage design. We obtain the asymptotic distribution of the Horvitz–Thompson estimator and several unbiased variance estimators. Facing the problem of possibly negative values, we propose simplified nonnegative variance estimators and study their bias under a super-population model. The proposed estimators are compared for totals and ratios on simulated data. An application on real data from the French Longitudinal Survey on Childhood is also presented, and we make some recommendations. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3405670.v2
title: Estimation Under Cross-Classified Sampling With Application to a Childhood Survey

description: The cross-classified sampling design consists in drawing samples from a two-dimensional population, independently in each dimension. Such design is commonly used in consumer price index surveys and has been recently applied to draw a sample of babies in the French Longitudinal Survey on Childhood, by crossing a sample of maternity units and a sample of days. We propose to derive a general theory of estimation for this sampling design. We consider the Horvitz–Thompson estimator for a total, and show that the cross-classified design will usually result in a loss of efficiency as compared to the widespread two-stage design. We obtain the asymptotic distribution of the Horvitz–Thompson estimator and several unbiased variance estimators. Facing the problem of possibly negative values, we propose simplified nonnegative variance estimators and study their bias under a super-population model. The proposed estimators are compared for totals and ratios on simulated data. An application on real data from the French Longitudinal Survey on Childhood is also presented, and we make some recommendations. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3405670.v1
title: Estimation under cross-classified sampling with application to a childhood survey

description: The cross-classified sampling design consists in drawing samples from a two-dimension population, independently in each dimension. Such design is commonly used in consumer price index surveys and has been recently applied to draw a sample of babies in the French Longitudinal Survey on Childhood, by crossing a sample of maternity units and a sample of days. We propose to derive a general theory of estimation for this sampling design. We consider the Horvitz-Thompson estimator for a total, and show that the cross-classified design will usually result in a loss of efficiency as compared to the widespread two-stage design. We obtain the asymptotic distribution of the Horvitz-Thompson estimator, and several unbiased variance estimators. Facing the problem of possibly negative values, we propose simplified non-negative variance estimators and study their bias under a super-population model. The proposed estimators are compared for totals and ratios on simulated data. An application on real data from the French Longitudinal Survey on Childhood is also presented, and we make some recommendations. Supplementary materials are available online.
DOI: 10.6084/m9.figshare.3405628
title: SUMO-interacting motifs (SIMs) in Polo-like kinase 1-interacting checkpoint helicase (PICH) ensure proper chromosome segregation during mitosis

description: Polo-like kinase 1 (Plk1)-interacting checkpoint helicase (PICH) localizes at the centromere and is critical for proper chromosome segregation during mitosis. However, the precise molecular mechanism of PICH's centromeric localization and function at the centromere is not yet fully understood. Recently, using <i>Xenopus</i> egg extract assays, we showed that PICH is a promiscuous SUMO binding protein. To further determine the molecular consequence of PICH/SUMO interaction on PICH function, we identified 3 SUMO-interacting motifs (SIMs) on PICH and generated a SIM-deficient PICH mutant. Using the conditional expression of PICH in cells, we found distinct roles of PICH SIMs during mitosis. Although all SIMs are dispensable for PICH's localization on ultrafine anaphase DNA bridges, only SIM3 (third SIM, close to the C-terminus end of PICH) is critical for its centromeric localization. Intriguingly, the other 2 SIMs function in chromatin bridge prevention. With these results, we propose a novel SUMO-dependent regulation of PICH's function on mitotic centromeres.
DOI: 10.6084/m9.figshare.3405628.v1
title: SUMO-interacting motifs (SIMs) in Polo-like kinase 1-interacting checkpoint helicase (PICH) ensure proper chromosome segregation during mitosis

description: Polo-like kinase 1 (Plk1)-interacting checkpoint helicase (PICH) localizes at the centromere and is critical for proper chromosome segregation during mitosis. However, the precise molecular mechanism of PICH's centromeric localization and function at the centromere is not yet fully understood. Recently, using <i>Xenopus</i> egg extract assays, we showed that PICH is a promiscuous SUMO binding protein. To further determine the molecular consequence of PICH/SUMO interaction on PICH function, we identified 3 SUMO-interacting motifs (SIMs) on PICH and generated a SIM-deficient PICH mutant. Using the conditional expression of PICH in cells, we found distinct roles of PICH SIMs during mitosis. Although all SIMs are dispensable for PICH's localization on ultrafine anaphase DNA bridges, only SIM3 (third SIM, close to the C-terminus end of PICH) is critical for its centromeric localization. Intriguingly, the other 2 SIMs function in chromatin bridge prevention. With these results, we propose a novel SUMO-dependent regulation of PICH's function on mitotic centromeres.
DOI: 10.6084/m9.figshare.3405622
title: Cellular localization of Sun4p and its interaction with proteins in the yeast birth scar

description: Yeast harbor several proteins with predicted glucanase activity that are potentially involved in cell wall remodeling during different processes, including mitosis. Here, we showed that 2 of these putative glucanases, Sun4p and Dse2p, co-localize to the yeast birth scar, dependently on presence of the third glucanase, Egt2p. The absence of these glucanases results in inefficient mother-daughter cell separation. The Sun4p, Dse2p and Egt2p localize to the daughter side of the bud neck, possibly forming a complex, and are involved in the separation of the virgin daughter from the mother cell during mitosis. The formation of properly assembled birth scars that delimitate cell wall area restricted in the next budding is dependent on the presence of Aim44p and its transcriptional regulator, Swi5p. <i>AIM44</i> or <i>SWI5</i> deletion caused the “budding within the birth scar” phenotype, together with altered localization of the birth scar proteins Sun4p and Dse2p, indicating the impairment of birth scar protein complexes.
DOI: 10.6084/m9.figshare.3405622.v1
title: Cellular localization of Sun4p and its interaction with proteins in the yeast birth scar

description: Yeast harbor several proteins with predicted glucanase activity that are potentially involved in cell wall remodeling during different processes, including mitosis. Here, we showed that 2 of these putative glucanases, Sun4p and Dse2p, co-localize to the yeast birth scar, dependently on presence of the third glucanase, Egt2p. The absence of these glucanases results in inefficient mother-daughter cell separation. The Sun4p, Dse2p and Egt2p localize to the daughter side of the bud neck, possibly forming a complex, and are involved in the separation of the virgin daughter from the mother cell during mitosis. The formation of properly assembled birth scars that delimitate cell wall area restricted in the next budding is dependent on the presence of Aim44p and its transcriptional regulator, Swi5p. <i>AIM44</i> or <i>SWI5</i> deletion caused the “budding within the birth scar” phenotype, together with altered localization of the birth scar proteins Sun4p and Dse2p, indicating the impairment of birth scar protein complexes.
DOI: 10.6084/m9.figshare.3405619
title: Increased expression of SIRT2 is a novel marker of cellular senescence and is dependent on wild type p53 status

description: Sirtuins (SIRT) belonging to the NAD+ dependent histone deacetylase III class of enzymes have emerged as master regulators of metabolism and longevity. However, their role in prevention of organismal aging and cellular senescence still remains controversial. In the present study, we now report upregulation of SIRT2 as a specific feature associated with stress induced premature senescence but not with either quiescence or cell death. Additionally, increase in SIRT2 expression was noted in different types of senescent conditions such as replicative and oncogene induced senescence using multiple cell lines. Induction of SIRT2 expression during senescence was dependent on p53 status as depletion of p53 by shRNA prevented its accumulation. Chromatin immunoprecipitation revealed the presence of p53 binding sites on the SIRT2 promoter suggesting its regulation by p53, which was also corroborated by the SEAP reporter assay. Overexpression or knockdown of SIRT2 had no effect on stress induced premature senescence, thereby indicating that SIRT2 increase is not a cause of senescence; rather it is an effect linked to senescence-associated changes. Overall, our results suggest SIRT2 as a promising marker of cellular senescence at least in cells with wild type p53 status.
DOI: 10.6084/m9.figshare.3405619.v1
title: Increased expression of SIRT2 is a novel marker of cellular senescence and is dependent on wild type p53 status

description: Sirtuins (SIRT) belonging to the NAD+ dependent histone deacetylase III class of enzymes have emerged as master regulators of metabolism and longevity. However, their role in prevention of organismal aging and cellular senescence still remains controversial. In the present study, we now report upregulation of SIRT2 as a specific feature associated with stress induced premature senescence but not with either quiescence or cell death. Additionally, increase in SIRT2 expression was noted in different types of senescent conditions such as replicative and oncogene induced senescence using multiple cell lines. Induction of SIRT2 expression during senescence was dependent on p53 status as depletion of p53 by shRNA prevented its accumulation. Chromatin immunoprecipitation revealed the presence of p53 binding sites on the SIRT2 promoter suggesting its regulation by p53, which was also corroborated by the SEAP reporter assay. Overexpression or knockdown of SIRT2 had no effect on stress induced premature senescence, thereby indicating that SIRT2 increase is not a cause of senescence; rather it is an effect linked to senescence-associated changes. Overall, our results suggest SIRT2 as a promising marker of cellular senescence at least in cells with wild type p53 status.