cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3145138
title: Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element

description: Many viruses contain RNA elements that modulate splicing and/or promote nuclear export of their RNAs. The RNAs of the major human pathogen, hepatitis B virus (HBV) contain a large (~600 bases) composite <i>cis</i>-acting 'post-transcriptional regulatory element' (PRE). This element promotes expression from these naturally intronless transcripts. Indeed, the related woodchuck hepadnavirus PRE (WPRE) is used to enhance expression in gene therapy and other expression vectors. These PRE are likely to act through a combination of mechanisms, including promotion of RNA nuclear export. Functional components of both the HBV PRE and WPRE are 2 conserved RNA <i>cis</i>-acting stem-loop (SL) structures, SLα and SLβ. They are within the coding regions of polymerase (P) gene, and both P and X genes, respectively. Based on previous studies using mutagenesis and/or nuclear magnetic resonance (NMR), here we propose 2 covariance models for SLα and SLβ. The model for the 30-nucleotide SLα contains a G-bulge and a CNGG(U) apical loop of which the first and the fourth loop residues form a CG pair and the fifth loop residue is bulged out, as observed in the NMR structure. The model for the 23-nucleotide SLβ contains a 7-base-pair stem and a 9-nucleotide loop. Comparison of the models with other RNA structural elements, as well as similarity searches of human transcriptome and viral genomes demonstrate that SLα and SLβ are specific to HBV transcripts. However, they are well conserved among the hepadnaviruses of non-human primates, the woodchuck and ground squirrel.
DOI: 10.6084/m9.figshare.3145240.v2
title: echr_dataset.zip

description: European Court of Human Rights Dataset<br>Cite https://peerj.com/articles/cs-93<br>
DOI: 10.6084/m9.figshare.3145111
title: MicroRNA-495 Regulates Migration and Invasion in Prostate Cancer Cells Via Targeting Akt and mTOR Signaling

description: Abnormal microRNA (miR) expressions were implicated in prostate cancer progression. We identified a novel miR-495, which was downregulated in prostate cancer, but not normal prostate cell lines. MiR-495 directly targeted the 3′-UTR of Akt and mTOR mRNAs. Expression of miR-495 in prostate cancer cells significantly downregulated Akt and mTOR, which further inhibited cancer cell proliferation, migration, and invasion <i>in vitro</i>. Function of miR-495 <i>in vivo</i> was examined in mouse xenograft model and was found to significantly inhibit the growth of tumors, mediated by repressing Akt and mTOR. Our report supported miR-495 as a novel tumor suppressor microRNA in prostate cancer.
DOI: 10.6084/m9.figshare.3145240.v4
title: echr_dataset.zip

description: European Court of Human Rights Dataset<br>Cite https://peerj.com/articles/cs-93<br>
DOI: 10.6084/m9.figshare.3145111.v1
title: MicroRNA-495 Regulates Migration and Invasion in Prostate Cancer Cells Via Targeting Akt and mTOR Signaling

description: Abnormal microRNA (miR) expressions were implicated in prostate cancer progression. We identified a novel miR-495, which was downregulated in prostate cancer, but not normal prostate cell lines. MiR-495 directly targeted the 3′-UTR of Akt and mTOR mRNAs. Expression of miR-495 in prostate cancer cells significantly downregulated Akt and mTOR, which further inhibited cancer cell proliferation, migration, and invasion <i>in vitro</i>. Function of miR-495 <i>in vivo</i> was examined in mouse xenograft model and was found to significantly inhibit the growth of tumors, mediated by repressing Akt and mTOR. Our report supported miR-495 as a novel tumor suppressor microRNA in prostate cancer.
DOI: 10.6084/m9.figshare.3145138.v1
title: Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element.

description: Many viruses contain RNA elements that modulate splicing and/or promote nuclear export of their RNAs. The RNAs of the major human pathogen, hepatitis B virus (HBV) contain a large (∼600 bases) composite <i>cis</i>-acting ‘post-transcriptional regulatory element’ (PRE). This element promotes expression from these naturally intronless transcripts. Indeed, the related woodchuck hepadnavirus PRE (WPRE) is used to enhance expression in gene therapy and other expression vectors. These PRE are likely to act through a combination of mechanisms, including promotion of RNA nuclear export. Functional components of both the HBV PRE and WPRE are two conserved RNA <i>cis</i>-acting stem-loop (SL) structures, SLα and SLβ. They are within the coding regions of polymerase (P) gene, and both P and X genes, respectively. Based on previous studies using mutagenesis and/or nuclear magnetic resonance (NMR), here we propose two covariance models for SLα and SLβ. The model for the 30-nucleotide SLα contains a G-bulge and a CNGG(U) apical loop of which the first and the fourth loop residues form a CG pair and the fifth loop residue is bulged out, as observed in the NMR structure. The model for the 23-nucleotide SLβ contains a 7-base-pair stem and a 9-nucleotide loop. Comparison of the models with other RNA structural elements, as well as similarity searches of human transcriptome and viral genomes demonstrate that SLα and SLβ are specific to HBV transcripts. However, they are well conserved among the hepadnaviruses of non-human primates, the woodchuck and ground squirrel.
DOI: 10.6084/m9.figshare.3145108
title: Peripheral circadian clocks are diversely affected by adrenalectomy

description: Glucocorticoids are considered to synchronize the rhythmicity of clock genes in peripheral tissues; however, the role of circadian variations of endogenous glucocorticoids is not well defined. In the present study, we examined whether peripheral circadian clocks were impaired by adrenalectomy. To achieve this, we tested the circadian rhythmicity of core clock genes (<i>Bmal1, Per1-3, Cry1, RevErbα, Rora</i>), clock-output genes (<i>Dbp, E4bp4</i>) and a glucocorticoid- and clock-controlled gene (<i>Gilz</i>) in liver, jejunum, kidney cortex, splenocytes and visceral adipose tissue (VAT). Adrenalectomy did not affect the phase of clock gene rhythms but distinctly modulated clock gene mRNA levels, and this effect was partially tissue-dependent. Adrenalectomy had a significant inhibitory effect on the level of <i>Per1</i> mRNA in VAT, liver and jejunum, but not in kidney and splenocytes. Similarly, adrenalectomy down-regulated mRNA levels of <i>Per2</i> in splenocytes and VAT, <i>Per3</i> in jejunum, <i>RevErbα</i> in VAT and <i>Dbp</i> in VAT, kidney and splenocytes, whereas the mRNA amounts of <i>Per1</i> and <i>Per2</i> in kidney and <i>Per3</i> in VAT and splenocytes were up-regulated. On the other hand, adrenalectomy had minimal effects on <i>Rora</i> and <i>E4bp4</i> mRNAs. Adrenalectomy also resulted in decreased level of <i>Gilz</i> mRNA but did not alter the phase of its diurnal rhythm. Collectively, these findings suggest that adrenalectomy alters the mRNA levels of core clock genes and clock-output genes in peripheral organs and may cause tissue-specific modulations of their circadian profiles, which are reflected in changes of the amplitudes but not phases. Thus, the circulating corticosteroids are necessary for maintaining the high-amplitude rhythmicity of the peripheral clocks in a tissue-specific manner.
DOI: 10.6084/m9.figshare.3145108.v1
title: Peripheral circadian clocks are diversely affected by adrenalectomy

description: Glucocorticoids are considered to synchronize the rhythmicity of clock genes in peripheral tissues; however, the role of circadian variations of endogenous glucocorticoids is not well defined. In the present study, we examined whether peripheral circadian clocks were impaired by adrenalectomy. To achieve this, we tested the circadian rhythmicity of core clock genes (<i>Bmal1, Per1-3, Cry1, RevErbα, Rora</i>), clock-output genes (<i>Dbp, E4bp4</i>) and a glucocorticoid- and clock-controlled gene (<i>Gilz</i>) in liver, jejunum, kidney cortex, splenocytes and visceral adipose tissue (VAT). Adrenalectomy did not affect the phase of clock gene rhythms but distinctly modulated clock gene mRNA levels, and this effect was partially tissue-dependent. Adrenalectomy had a significant inhibitory effect on the level of <i>Per1</i> mRNA in VAT, liver and jejunum, but not in kidney and splenocytes. Similarly, adrenalectomy down-regulated mRNA levels of <i>Per2</i> in splenocytes and VAT, <i>Per3</i> in jejunum, <i>RevErbα</i> in VAT and <i>Dbp</i> in VAT, kidney and splenocytes, whereas the mRNA amounts of <i>Per1</i> and <i>Per2</i> in kidney and <i>Per3</i> in VAT and splenocytes were up-regulated. On the other hand, adrenalectomy had minimal effects on <i>Rora</i> and <i>E4bp4</i> mRNAs. Adrenalectomy also resulted in decreased level of <i>Gilz</i> mRNA but did not alter the phase of its diurnal rhythm. Collectively, these findings suggest that adrenalectomy alters the mRNA levels of core clock genes and clock-output genes in peripheral organs and may cause tissue-specific modulations of their circadian profiles, which are reflected in changes of the amplitudes but not phases. Thus, the circulating corticosteroids are necessary for maintaining the high-amplitude rhythmicity of the peripheral clocks in a tissue-specific manner.
DOI: 10.6084/m9.figshare.3145138.v3
title: Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element

description: Many viruses contain RNA elements that modulate splicing and/or promote nuclear export of their RNAs. The RNAs of the major human pathogen, hepatitis B virus (HBV) contain a large (~600 bases) composite <i>cis</i>-acting 'post-transcriptional regulatory element' (PRE). This element promotes expression from these naturally intronless transcripts. Indeed, the related woodchuck hepadnavirus PRE (WPRE) is used to enhance expression in gene therapy and other expression vectors. These PRE are likely to act through a combination of mechanisms, including promotion of RNA nuclear export. Functional components of both the HBV PRE and WPRE are 2 conserved RNA <i>cis</i>-acting stem-loop (SL) structures, SLα and SLβ. They are within the coding regions of polymerase (P) gene, and both P and X genes, respectively. Based on previous studies using mutagenesis and/or nuclear magnetic resonance (NMR), here we propose 2 covariance models for SLα and SLβ. The model for the 30-nucleotide SLα contains a G-bulge and a CNGG(U) apical loop of which the first and the fourth loop residues form a CG pair and the fifth loop residue is bulged out, as observed in the NMR structure. The model for the 23-nucleotide SLβ contains a 7-base-pair stem and a 9-nucleotide loop. Comparison of the models with other RNA structural elements, as well as similarity searches of human transcriptome and viral genomes demonstrate that SLα and SLβ are specific to HBV transcripts. However, they are well conserved among the hepadnaviruses of non-human primates, the woodchuck and ground squirrel.
DOI: 10.6084/m9.figshare.3145138.v2
title: Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element

description: Many viruses contain RNA elements that modulate splicing and/or promote nuclear export of their RNAs. The RNAs of the major human pathogen, hepatitis B virus (HBV) contain a large (~600 bases) composite <i>cis</i>-acting 'post-transcriptional regulatory element' (PRE). This element promotes expression from these naturally intronless transcripts. Indeed, the related woodchuck hepadnavirus PRE (WPRE) is used to enhance expression in gene therapy and other expression vectors. These PRE are likely to act through a combination of mechanisms, including promotion of RNA nuclear export. Functional components of both the HBV PRE and WPRE are 2 conserved RNA <i>cis</i>-acting stem-loop (SL) structures, SLα and SLβ. They are within the coding regions of polymerase (P) gene, and both P and X genes, respectively. Based on previous studies using mutagenesis and/or nuclear magnetic resonance (NMR), here we propose 2 covariance models for SLα and SLβ. The model for the 30-nucleotide SLα contains a G-bulge and a CNGG(U) apical loop of which the first and the fourth loop residues form a CG pair and the fifth loop residue is bulged out, as observed in the NMR structure. The model for the 23-nucleotide SLβ contains a 7-base-pair stem and a 9-nucleotide loop. Comparison of the models with other RNA structural elements, as well as similarity searches of human transcriptome and viral genomes demonstrate that SLα and SLβ are specific to HBV transcripts. However, they are well conserved among the hepadnaviruses of non-human primates, the woodchuck and ground squirrel.
DOI: 10.6084/m9.figshare.3144985
title: Polymorphisms of anti-Müllerian hormone signaling pathway in healthy Singapore women: population differences, endocrine effects and reproductive outcomes

description: In order to study the association of genetic polymorphisms of anti-Müllerian hormone (AMH) signaling pathway with endocrine changes and pregnancy outcomes, a total of 213 women of reproductive ages were recruited according to our inclusion and exclusion criteria between November 2011 and September 2014 in Singapore. Genotyping studies were performed using a minor groove binder primer/probe Taqman assay. The allele frequencies of the AMH Ile<sup>49</sup>Ser and AMHR2 −482A &gt; G polymorphisms were analyzed in relation to female reproductive hormone levels, ovarian parameters, menstrual cycle lengths and pregnancy outcomes. AMH Ser allele frequency and AMHR2 G allele frequency of our Singapore population were compared with those of other populations reported in HapMap. The genotype distributions and allele frequencies for the AMH Ile<sup>49</sup>Ser and AMHR2 −482A &gt; G polymorphisms were not associated with estradiol (E2) levels, ovarian parameters, menstrual cycle length, or pregnancy outcomes in our cohort. Our findings suggest that genetic variants in the AMH signal transduction pathway have population differences but do not appear to have significant effects on ovarian, endocrine, metabolic parameters and reproductive outcomes.
DOI: 10.6084/m9.figshare.3144982
title: Is Your Work Traditional or Innovative?

description: Presentation and abstract of a new method for the detection of scientific innovation. Presented at the 2016 Symposium on Science of Science at the Library of Congress.
DOI: 10.6084/m9.figshare.3144985.v1
title: Polymorphisms of anti-Müllerian hormone signaling pathway in healthy Singapore women: population differences, endocrine effects and reproductive outcomes

description: In order to study the association of genetic polymorphisms of anti-Müllerian hormone (AMH) signaling pathway with endocrine changes and pregnancy outcomes, a total of 213 women of reproductive ages were recruited according to our inclusion and exclusion criteria between November 2011 and September 2014 in Singapore. Genotyping studies were performed using a minor groove binder primer/probe Taqman assay. The allele frequencies of the AMH Ile<sup>49</sup>Ser and AMHR2 −482A &gt; G polymorphisms were analyzed in relation to female reproductive hormone levels, ovarian parameters, menstrual cycle lengths and pregnancy outcomes. AMH Ser allele frequency and AMHR2 G allele frequency of our Singapore population were compared with those of other populations reported in HapMap. The genotype distributions and allele frequencies for the AMH Ile<sup>49</sup>Ser and AMHR2 −482A &gt; G polymorphisms were not associated with estradiol (E2) levels, ovarian parameters, menstrual cycle length, or pregnancy outcomes in our cohort. Our findings suggest that genetic variants in the AMH signal transduction pathway have population differences but do not appear to have significant effects on ovarian, endocrine, metabolic parameters and reproductive outcomes.
DOI: 10.6084/m9.figshare.3144961
title: CP11_SelfReport_survey_data_forPLoS.xlsx

description: <br> Anonymous survey data set supporting Hameed et al. 2016 PLoS One article entitled, "<strong>Incidence, Etiology and Risk Factors for Travelers’ Diarrhea during a Hospital Ship-Based Military Humanitarian Mission: Continuing Promise 2011"</strong>
DOI: 10.6084/m9.figshare.3144967
title: CP11_DNBI_MASTER_SHEET_for_PLoS.xlsx

description: Limited de-identified aggregate data set supporting Hameed et al. 2016 PLoS One article entitled, "<strong>Incidence, Etiology and Risk Factors for Travelers’ Diarrhea during a Hospital Ship-Based Military Humanitarian Mission: Continuing Promise 2011"</strong>
DOI: 10.6084/m9.figshare.3144982.v1
title: Is Your Work Traditional or Innovative?

description: Presentation and abstract of a new method for the detection of scientific innovation. Presented at the 2016 Symposium on Science of Science at the Library of Congress.
DOI: 10.6084/m9.figshare.3144967.v1
title: CP11_DNBI_MASTER_SHEET_for_PLoS.xlsx

description: Limited de-identified aggregate data set supporting Hameed et al. 2016 PLoS One article entitled, "<strong>Incidence, Etiology and Risk Factors for Travelers’ Diarrhea during a Hospital Ship-Based Military Humanitarian Mission: Continuing Promise 2011"</strong>
DOI: 10.6084/m9.figshare.3144919
title: Metabolic abnormalities induced by mitochondrial dysfunction in skeletal muscle of the renal carcinoma Eker (TSC2+/−) rat model

description: Tuberous sclerosis complex 2 (TSC2) is a mediator of insulin signal transduction, and a loss of function in TSC2 induces hyperactivation of mTORC1 pathway, which leads to tumorigenesis. We have previously demonstrated that Eker rat model, which is heterozygous for a TSC2 mutation, exhibits hyperglycemia and hyperketonemia. The present study was to investigate whether these changes also can affect metabolism in skeletal muscle of the Eker rat. Wild-type (TSC2+/+) and Eker (TSC2+/−) rats underwent an oral glucose tolerance test, and the latter showed decrease in whole-body glucose utilization. Additionally, reductions in the expression of glycolysis-, lipolysis-, and ketone body-related genes in skeletal muscle were observed in Eker rats. Furthermore, ATP content and mitochondrial DNA copy number were lower in skeletal muscle of Eker rats. These data demonstrate that heterozygous to mutation TSC2 not only affects the liver metabolism, but also skeletal muscle metabolism, via mitochondrial dysfunction. Eker rats exhibit glucose intolerance due to the inhibition of glucose uptake at the skeletal muscle, which was explained by low number and dysfunction of mitochondria.
DOI: 10.6084/m9.figshare.3144952
title: Climate change and simulation/gaming: Learning for survival

description: This editorial outlines a number of connections between climate change and simulation/gaming/debriefing. First, the development of this symposium is mentioned, including appreciation for contributors, especially Klaus Eisenack, James Hansen, Dennis Meadows, and Diana Reckien. Second, a wide range of climate change dimensions is outlined, with emphasis on the increasingly important role that simulation/gaming and debriefing should play in educating people to combat climate change. Climate issues include anthropogenic warming, due largely to ever increasing greenhouse gas emissions, resulting in massive and irreversible upheaval of the biosphere and the socio-economic system. Given the direct or indirect negative impact of climate change on health and mortality, due largely to the lethargy of politicians and big business, such people, in a saner world, could be facing accusation of crimes against humanity. The topic of climate change needs to become the backbone of education round the world, with simulation/gaming and debriefing being one of the main methods for learning to survive in ‘pockets of resilience’. Topics for simulation/games and debriefing could include resilience, urgency, climate change science, indicators and effects (feedback loops, rising sea levels, storm severity, food scarcity and security, water, war, denial, nuclear power, irresponsibility of politicians, etc.). Third, the absurdities of the push for growth in a finite world and of the burning of more coal are highlighted. Simulation/gaming and debriefing provide opportunities for learning to survive in a dangerously changing climate.
DOI: 10.6084/m9.figshare.3144961.v1
title: CP11_SelfReport_survey_data_forPLoS.xlsx

description: <br> Anonymous survey data set supporting Hameed et al. 2016 PLoS One article entitled, "<strong>Incidence, Etiology and Risk Factors for Travelers’ Diarrhea during a Hospital Ship-Based Military Humanitarian Mission: Continuing Promise 2011"</strong>
DOI: 10.6084/m9.figshare.3144919.v1
title: Metabolic abnormalities induced by mitochondrial dysfunction in skeletal muscle of the renal carcinoma Eker (TSC2+/−) rat model

description: Tuberous sclerosis complex 2 (TSC2) is a mediator of insulin signal transduction, and a loss of function in TSC2 induces hyperactivation of mTORC1 pathway, which leads to tumorigenesis. We have previously demonstrated that Eker rat model, which is heterozygous for a TSC2 mutation, exhibits hyperglycemia and hyperketonemia. The present study was to investigate whether these changes also can affect metabolism in skeletal muscle of the Eker rat. Wild-type (TSC2+/+) and Eker (TSC2+/−) rats underwent an oral glucose tolerance test, and the latter showed decrease in whole-body glucose utilization. Additionally, reductions in the expression of glycolysis-, lipolysis-, and ketone body-related genes in skeletal muscle were observed in Eker rats. Furthermore, ATP content and mitochondrial DNA copy number were lower in skeletal muscle of Eker rats. These data demonstrate that heterozygous to mutation TSC2 not only affects the liver metabolism, but also skeletal muscle metabolism, via mitochondrial dysfunction. Eker rats exhibit glucose intolerance due to the inhibition of glucose uptake at the skeletal muscle, which was explained by low number and dysfunction of mitochondria.
DOI: 10.6084/m9.figshare.3144895
title: VIOLA Input Questionnaires v1.0

description: This questionnaire aims at capturing how many people talk to an infant during a typical week (short and long forms), as well as capturing stability (is one person always present) and local variability (how many different people are present at a time, how big is the change during a typical day; long forms only). Available languages: FrenchEnglish