cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3121924
title: Regulation of poly(A) RNA retention in the nucleus as a survival strategy of plants during hypoxia

description: Last finding indicates that post-transcriptional processes are significant in low-oxygen conditions, but their nature is poorly understood. Here, we localized poly(A) RNA and mRNA coding proteins involved and not involved with resistance to hypoxia in <i>Lupinus luteus</i> and <i>Arabidopsis thaliana</i> during submergence and after recovery of aerobic conditions. We showed a strong nuclear accumulation of poly(A) RNA and 6 of 7 studied mRNAs with a concurrent strong reduction in RNA polymerase II transcription during hypoxia. In this study, the nucleus did not accumulate mRNA of the <i>ADH1</i> (alcohol dehydrogenase 1) gene, which is a core hypoxia gene. The RNA accumulation in the nucleus is among the mechanisms of post-transcriptional gene regulation that prevents translation. However re-aeration was accompanied by a strong increase in the amount of the mRNAs in the cytoplasm and a simultaneous decrease in nuclear mRNAs. This finding indicates that the nucleus is a storage site for those of mRNAs which are not involved in the response to hypoxia for use by the plants after the hypoxic stress. In this study, the highest intensity of RNA accumulation occurred in Cajal bodies (CBs); the intensity of accumulation was inversely correlated with transcription. Under hypoxia, <i>ncb-1</i> mutants of <i>Arabidopsis thaliana</i> with a complete absence of CBs died sooner than wild type (WT), accompanied by a strong reduction in the level of poly(A) RNA in the nucleus. These results suggest that the CBs not only participate in the storage of the nuclear RNA, but they also could take part in its stabilization under low-oxygen conditions.
DOI: 10.6084/m9.figshare.3121927
title: Tables about use of open data in Spain

description: Tables whit data about the consumption practices of Spanish citizens of open data published by public institutions
DOI: 10.6084/m9.figshare.3121924.v1
title: Regulation of poly(A) RNA retention in the nucleus as a survival strategy of plants during hypoxia

description: Last finding indicates that post-transcriptional processes are significant in low-oxygen conditions, but their nature is poorly understood. Here, we localized poly(A) RNA and mRNA coding proteins involved and not involved with resistance to hypoxia in <i>Lupinus luteus</i> and <i>Arabidopsis thaliana</i> during submergence and after recovery of aerobic conditions. We showed a strong nuclear accumulation of poly(A) RNA and 6 of 7 studied mRNAs with a concurrent strong reduction in RNA polymerase II transcription during hypoxia. In this study, the nucleus did not accumulate mRNA of the <i>ADH1</i> (alcohol dehydrogenase 1) gene, which is a core hypoxia gene. The RNA accumulation in the nucleus is among the mechanisms of post-transcriptional gene regulation that prevents translation. However re-aeration was accompanied by a strong increase in the amount of the mRNAs in the cytoplasm and a simultaneous decrease in nuclear mRNAs. This finding indicates that the nucleus is a storage site for those of mRNAs which are not involved in the response to hypoxia for use by the plants after the hypoxic stress. In this study, the highest intensity of RNA accumulation occurred in Cajal bodies (CBs); the intensity of accumulation was inversely correlated with transcription. Under hypoxia, <i>ncb-1</i> mutants of <i>Arabidopsis thaliana</i> with a complete absence of CBs died sooner than wild type (WT), accompanied by a strong reduction in the level of poly(A) RNA in the nucleus. These results suggest that the CBs not only participate in the storage of the nuclear RNA, but they also could take part in its stabilization under low-oxygen conditions.
DOI: 10.6084/m9.figshare.3121927.v2
title: Tables about use of open data in Spain

description: Tables whit data about the consumption practices of Spanish citizens of open data published by public institutions
DOI: 10.6084/m9.figshare.3121927.v1
title: The consumption practices of Spanish citizens of open data published by public institutions - Tables

description: Tabla con datos que avalan el estudio.
DOI: 10.6084/m9.figshare.3121915
title: Detecting and Localizing Differences in Functional Time Series Dynamics: A Case Study in Molecular Biophysics

description: Motivated by the problem of inferring the molecular dynamics of DNA in solution, and linking them with its base-pair composition, we consider the problem of comparing the dynamics of functional time series (FTS), and of localizing any inferred differences in frequency and along curvelength. The approach we take is one of Fourier analysis, where the complete second-order structure of the FTS is encoded by its spectral density operator, indexed by frequency and curvelength. The comparison is broken down to a hierarchy of stages: at a global level, we compare the spectral density operators of the two FTS, across frequencies and curvelength, based on a Hilbert–Schmidt criterion; then, we localize any differences to specific frequencies; and, finally, we further localize any differences along the length of the random curves, that is, in physical space. A hierarchical multiple testing approach guarantees control of the averaged false discovery rate over the selected frequencies. In this sense, we are able to attribute any differences to distinct dynamic (frequency) and spatial (curvelength) contributions. Our approach is presented and illustrated by means of a case study in molecular biophysics: how can one use molecular dynamics simulations of short strands of DNA to infer their temporal dynamics at the scaling limit, and probe whether these depend on the sequence encoded in these strands? Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3121915.v1
title: Detecting and Localizing Differences in Functional Time Series Dynamics: A Case Study in Molecular Biophysics

description: Motivated by the problem of inferring the molecular dynamics of DNA in solution, and linking them with its base-pair composition, we consider the problem of comparing the dynamics of functional time series (FTS), and of localizing any inferred differences in frequency and along curvelength. The approach we take is one of Fourier analysis, where the complete second-order structure of the FTS is encoded by its spectral density operator, indexed by frequency and curvelength. The comparison is broken down to a hierarchy of stages: at a global level, we compare the spectral density operators of the two FTS, across frequencies and curvelength, based on a Hilbert–Schmidt criterion; then, we localize any differences to specific frequencies; and, finally, we further localize any differences along the length of the random curves, that is, in physical space. A hierarchical multiple testing approach guarantees control of the averaged false discovery rate over the selected frequencies. In this sense, we are able to attribute any differences to distinct dynamic (frequency) and spatial (curvelength) contributions. Our approach is presented and illustrated by means of a case study in molecular biophysics: how can one use molecular dynamics simulations of short strands of DNA to infer their temporal dynamics at the scaling limit, and probe whether these depend on the sequence encoded in these strands? Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3121894
title: EGB-promoted electrochemical synthesis of 6-thioxo-[1,3,5]-triazinane-2,4 dione derivatives

description: A simple method for the synthesis of 6-thioxo-[1,3,5]-triazinane-2,4-dione derivatives was reported. The electrogenerated cyanomethyl base obtained from electroreduction of neat acetonitrile assisted the reaction between thiourea derivatives and alkyl or aryl isocyanate. This protocol had the advantage of giving good yields using mild conditions. The obtained products have been identified by spectroscopic data, mass spectrometry, and high-resolution mass spectra or elemental analysis.
DOI: 10.6084/m9.figshare.3121921.v1
title: Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the Nematode Intestine

description: The intestine of parasitic nematodes has proven an important target for therapies aimed at prevention and treatment of diseases caused by these pathogens in humans, animals and plants. We have developed a unique research model with the intestine of <i>Ascaris suum</i>, the large round worm of swine and humans, that will enhance biological research on this tissue. To expand utility of this model, we quantitatively compared expression of 15,382 coding RNAs and 277 noncoding, micro RNAs (miRNAs) among three contiguous regions of the adult <i>A. suum</i> intestine. Differentially expressed transcripts were identified among regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. We further identified 64 exon splice variants (from 47 genes) that are differentially expressed among these regions. A total of 2,063 intestinal mRNA transcripts were predicted to be targeted by intestinal miRNA, and negative correlation coefficients for miRNA:mRNA abundances predicted 22 likely influential miRNAs and 503 likely associated miRNA:mRNA pairs. <i>A. suum</i> intestinal miRNAs were identified that are conserved with intestinal miRNAs from <i>C. elegans</i> (10 mature sequences and 13 seed sequences conserved), and prospective intestinal miRNAs from the murine gastrointestinal nematode, <i>Heligmosomoides polygyrus</i> (5 mature and 11 seeds). Most of the conserved intestinal miRNAs were also high abundance miRNAs. The data provide the most comprehensive compilation of constitutively and differentially expressed genes along the length of the intestine for any nematode species. The information will guide prospective development of many hypotheses on nematode intestinal functions encoded by mRNAs, miRNAs and interactions between these RNA populations.
DOI: 10.6084/m9.figshare.3121921.v3
title: Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the Nematode Intestine

description: The intestine of parasitic nematodes has proven an important target for therapies aimed at prevention and treatment of diseases caused by these pathogens in humans, animals and plants. We have developed a unique research model with the intestine of <i>Ascaris suum</i>, the large round worm of swine and humans, that will enhance biological research on this tissue. To expand utility of this model, we quantitatively compared expression of 15,382 coding RNAs and 277 noncoding, micro RNAs (miRNAs) among three contiguous regions of the adult <i>A. suum</i> intestine. Differentially expressed transcripts were identified among regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. We further identified 64 exon splice variants (from 47 genes) that are differentially expressed among these regions. A total of 2,063 intestinal mRNA transcripts were predicted to be targeted by intestinal miRNA, and negative correlation coefficients for miRNA:mRNA abundances predicted 22 likely influential miRNAs and 503 likely associated miRNA:mRNA pairs. <i>A. suum</i> intestinal miRNAs were identified that are conserved with intestinal miRNAs from <i>C. elegans</i> (10 mature sequences and 13 seed sequences conserved), and prospective intestinal miRNAs from the murine gastrointestinal nematode, <i>Heligmosomoides polygyrus</i> (5 mature and 11 seeds). Most of the conserved intestinal miRNAs were also high abundance miRNAs. The data provide the most comprehensive compilation of constitutively and differentially expressed genes along the length of the intestine for any nematode species. The information will guide prospective development of many hypotheses on nematode intestinal functions encoded by mRNAs, miRNAs and interactions between these RNA populations.
DOI: 10.6084/m9.figshare.3121921.v2
title: Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the nematode intestine

description: The intestine of parasitic nematodes has proven an important target for therapies aimed at prevention and treatment of diseases caused by these pathogens in humans, animals and plants. We have developed a unique research model with the intestine of <i>Ascaris suum</i>, the large round worm of swine and humans, that will enhance biological research on this tissue. To expand utility of this model, we quantitatively compared expression of 15,382 coding RNAs and 277 noncoding, micro RNAs (miRNAs) among 3 contiguous regions of the adult <i>A. suum</i> intestine. Differentially expressed transcripts were identified among regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. We further identified 64 exon splice variants (from 47 genes) that are differentially expressed among these regions. A total of 2,063 intestinal mRNA transcripts were predicted to be targeted by intestinal miRNA, and negative correlation coefficients for miRNA:mRNA abundances predicted 22 likely influential miRNAs and 503 likely associated miRNA:mRNA pairs. <i>A. suum</i> intestinal miRNAs were identified that are conserved with intestinal miRNAs from <i>C. elegans</i> (10 mature sequences and 13 seed sequences conserved), and prospective intestinal miRNAs from the murine gastrointestinal nematode, <i>Heligmosomoides polygyrus</i> (5 mature and 11 seeds). Most of the conserved intestinal miRNAs were also high abundance miRNAs. The data provide the most comprehensive compilation of constitutively and differentially expressed genes along the length of the intestine for any nematode species. The information will guide prospective development of many hypotheses on nematode intestinal functions encoded by mRNAs, miRNAs and interactions between these RNA populations.
DOI: 10.6084/m9.figshare.3121885
title: Selective binding and lateral clustering of <b>α</b>5<b>β</b>1 and <b>α</b>v<b>β</b>3 integrins: Unraveling the spatial requirements for cell spreading and focal adhesion assembly

description: Coordination of the specific functions of α5β1 and αvβ3 integrins is crucial for the precise regulation of cell adhesion, spreading and migration, yet the contribution of differential integrin-specific crosstalk to these processes remains unclear. To determine the specific functions of αvβ3 and α5β1 integrins, we used nanoarrays of gold particles presenting immobilized, integrin-selective peptidomimetic ligands. Integrin binding to the peptidomimetics is highly selective, and cells can spread on both ligands. However, spreading is faster and the projected cell area is greater on α5β1 ligand; both depend on ligand spacing. Quantitative analysis of adhesion plaques shows that focal adhesion size is increased in cells adhering to αvβ3 ligand at 30 and 60 nm spacings. Analysis of αvβ3 and α5β1 integrin clusters indicates that fibrillar adhesions are more prominent in cells adhering to α5β1 ligand, while clusters are mostly localized at the cell margins in cells adhering to αvβ3 ligand. αvβ3 integrin clusters are more pronounced on αvβ3 ligand, though they can also be detected in cells adhering to α5β1 ligand. Furthermore, α5β1 integrin clusters are present in cells adhering to α5β1 ligand, and often colocalize with αvβ3 clusters. Taken together, these findings indicate that the activation of αvβ3 integrin by ligand binding is dispensable for initial adhesion and spreading, but essential to formation of stable focal adhesions.
DOI: 10.6084/m9.figshare.3121888
title: Data from: A rank test for bivariate event time outcomes when one event is a surrogate

description: In many clinical settings, improving patient survival is of interest but a practical surrogate, such as time to disease progression, is instead used as a clinical trial's primary endpoint. A time-to-first endpoint (e.g. death or disease progression) is commonly analyzed but may not be adequate to summarize patient outcomes if a subsequent event contains important additional information. We consider a surrogate outcome very generally, as one correlated with the true endpoint of interest. Settings of interest include those where the surrogate indicates a beneficial outcome so that the usual time-to-first endpoint of death or surrogate event is nonsensical. We present a new two-sample test for bivariate, interval-censored time-to-event data, where one endpoint is a surrogate for the second, less frequently observed endpoint of true interest. This test examines whether patient groups have equal clinical severity. If the true endpoint rarely occurs, the proposed test acts like a weighted logrank test on the surrogate; if it occurs for most individuals, then our test acts like a weighted logrank test on the true endpoint. If the surrogate is a useful statistical surrogate, our test can have better power than tests based on the surrogate that naively handle the true endpoint. In settings where the surrogate is not valid (treatment affects the surrogate but not the true endpoint), our test incorporates the information regarding the lack of treatment effect from the observed true endpoints and hence is expected to have a dampened treatment effect compared to tests based on the surrogate alone.
DOI: 10.6084/m9.figshare.3121894.v1
title: EGB-Promoted Electrochemical Synthesis of 6-Thioxo-[1,3,5]- Triazinane-2,4 Dione Derivatives

description: A simple method for the synthesis of 6-Thioxo-[1,3,5]-triazinane-2,4-dione derivatives was reported. The electrogenerated cyanomethyl base obtained from electroreduction of neat acetonitrile assisted the reaction between thiourea derivatives and alkyl or aryl isocyanate. This protocol had the advantage of giving good yields using mild conditions. The obtained products have been identified according to their spectroscopic data, by mass spectrometry and high-resolution mass spectra or elemental analysis.
DOI: 10.6084/m9.figshare.3121882
title: Epigenome-Microbiome crosstalk: A potential new paradigm influencing neonatal susceptibility to disease

description: Preterm birth is the leading cause of infant morbidity and mortality. Necrotizing enterocolitis (NEC) is an inflammatory bowel disease affecting primarily premature infants, which can be lethal. Microbial intestinal colonization may alter epigenetic signatures of the immature gut establishing inflammatory and barrier properties predisposing to the development of NEC. We hypothesize that a crosstalk exists between the epigenome of the host and the initial intestinal colonizing microbiota at critical neonatal stages. By exposing immature enterocytes to probiotic and pathogenic bacteria, we showed over 200 regions of differential DNA modification, which were specific for each exposure. Reciprocally, using a mouse model of prenatal exposure to dexamethasone we demonstrated that antenatal treatment with glucocorticoids alters the epigenome of the host. We investigated the effects on the expression profiles of genes associated with inflammatory responses and intestinal barrier by qPCR-based gene expression array and verified the DNA modification changes in 5 candidate genes by quantitative methylation specific PCR (qMSP). Importantly, by 16S RNA sequencing-based phylogenetic analysis of intestinal bacteria in mice at 2 weeks of life, we showed that epigenome changes conditioned early microbiota colonization leading to differential bacterial colonization at different taxonomic levels. Our findings support a novel conceptual framework in which epigenetic changes induced by intrauterine influences affect early microbial colonization and intestinal development, which may alter disease susceptibility.
DOI: 10.6084/m9.figshare.3121882.v1
title: Epigenome-Microbiome crosstalk: A potential new paradigm influencing neonatal susceptibility to disease

description: Preterm birth is the leading cause of infant morbidity and mortality. Necrotizing enterocolitis (NEC) is an inflammatory bowel disease affecting primarily premature infants, which can be lethal. Microbial intestinal colonization may alter epigenetic signatures of the immature gut establishing inflammatory and barrier properties predisposing to the development of NEC. We hypothesize that a crosstalk exists between the epigenome of the host and the initial intestinal colonizing microbiota at critical neonatal stages. By exposing immature enterocytes to probiotic and pathogenic bacteria, we showed over 200 regions of differential DNA modification, which were specific for each exposure. Reciprocally, using a mouse model of prenatal exposure to dexamethasone we demonstrated that antenatal treatment with glucocorticoids alters the epigenome of the host. We investigated the effects on the expression profiles of genes associated with inflammatory responses and intestinal barrier by qPCR-based gene expression array and verified the DNA modification changes in 5 candidate genes by quantitative methylation specific PCR (qMSP). Importantly, by 16S RNA sequencing-based phylogenetic analysis of intestinal bacteria in mice at 2 weeks of life, we showed that epigenome changes conditioned early microbiota colonization leading to differential bacterial colonization at different taxonomic levels. Our findings support a novel conceptual framework in which epigenetic changes induced by intrauterine influences affect early microbial colonization and intestinal development, which may alter disease susceptibility.
DOI: 10.6084/m9.figshare.3121885.v2
title: Selective binding and lateral clustering of <b>α</b>5<b>β</b>1 and <b>α</b>v<b>β</b>3 integrins: Unraveling the spatial requirements for cell spreading and focal adhesion assembly

description: Coordination of the specific functions of α5β1 and αvβ3 integrins is crucial for the precise regulation of cell adhesion, spreading and migration, yet the contribution of differential integrin-specific crosstalk to these processes remains unclear. To determine the specific functions of αvβ3 and α5β1 integrins, we used nanoarrays of gold particles presenting immobilized, integrin-selective peptidomimetic ligands. Integrin binding to the peptidomimetics is highly selective, and cells can spread on both ligands. However, spreading is faster and the projected cell area is greater on α5β1 ligand; both depend on ligand spacing. Quantitative analysis of adhesion plaques shows that focal adhesion size is increased in cells adhering to αvβ3 ligand at 30 and 60 nm spacings. Analysis of αvβ3 and α5β1 integrin clusters indicates that fibrillar adhesions are more prominent in cells adhering to α5β1 ligand, while clusters are mostly localized at the cell margins in cells adhering to αvβ3 ligand. αvβ3 integrin clusters are more pronounced on αvβ3 ligand, though they can also be detected in cells adhering to α5β1 ligand. Furthermore, α5β1 integrin clusters are present in cells adhering to α5β1 ligand, and often colocalize with αvβ3 clusters. Taken together, these findings indicate that the activation of αvβ3 integrin by ligand binding is dispensable for initial adhesion and spreading, but essential to formation of stable focal adhesions.
DOI: 10.6084/m9.figshare.3121894.v3
title: EGB-promoted electrochemical synthesis of 6-thioxo-[1,3,5]-triazinane-2,4 dione derivatives

description: A simple method for the synthesis of 6-thioxo-[1,3,5]-triazinane-2,4-dione derivatives was reported. The electrogenerated cyanomethyl base obtained from electroreduction of neat acetonitrile assisted the reaction between thiourea derivatives and alkyl or aryl isocyanate. This protocol had the advantage of giving good yields using mild conditions. The obtained products have been identified by spectroscopic data, mass spectrometry, and high-resolution mass spectra or elemental analysis.