cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5123020.v1
title: Supplementary Material for: Post-Transcriptional Regulation of the Alginate Biosynthetic Gene algD by the Gac/Rsm System in Azotobacter vinelandii

description: <i>Azotobacter vinelandii </i>is a soil bacterium that produces the polysaccharide alginate. The two-component system GacS/GacA is required for alginate synthesis since a mutation in <i>gacS </i>or <i>gacA </i>significantly reduced the level of transcripts of <i>algD</i>, the gene encoding GDP-mannose dehydrogenase, a key enzyme of the alginate biosynthetic pathway. In many γ-proteobacteria, GacA homologs control the expression of small regulatory RNAs of the RsmZ/Y/X (CsrB/CsrC) family that interact with RsmA (CsrA) proteins. These proteins bind to their target mRNAs acting as translational repressors. The interaction of Rsm/Csr small RNAs with RsmA/CsrA counteract its repressor activity. In this study, one <i>rsmA</i> gene, seven <i>rsmZ</i> and two <i>rsmY</i> homologs were identified in the <i>A. vinelandii</i> genome. Two of the <i>rsmZ</i> homologs, named <i>rsmZ1</i> and <i>rsmZ2</i>, together with <i>rsmA</i>, were characterized. Northern blot analysis was carried out to show that in <i>A. vinelandii, </i>GacA activates <i>rsmZ1</i> and <i>rsmZ2</i> transcription. We also showed that either overexpression of <i>rsmA</i> or inactivation of <i>rsmZ1</i> or <i>rsmZ2</i> diminished the production of alginate. In addition, interaction of RsmA with RsmZ1, RsmZ2 and the <i>algD </i>mRNA was demonstrated in vitro. These results show that GacS/A regulates alginate biosynthesis by post-transcriptional control of <i>algD </i>expression through the Rsm system.
DOI: 10.6084/m9.figshare.5123002
title: Supplementary Material for: Oculomotor Nerve Palsy following Cardiac Tamponade with Churg-Strauss Syndrome: A Case Report

description: A 57-year-old man with a history of more than 10 years of bronchial asthma and chronic sinusitis complained of double vision which developed 18 days after cardiac tamponade with eosinophil-rich fluid (eosinophils 30%). He had oculomotor nerve palsy, and a blood test revealed eosinophilia (12,700/mm<sup>3</sup>) and elevation of both C-reactive protein and rheumatoid factor. He was diagnosed as having Churg-Strauss syndrome. His symptoms were relieved by corticosteroid therapy. Our case and previous cases in the literature revealed that oculomotor nerve palsy in Churg-Strauss syndrome is associated with pupil involvement and may be relieved by corticosteroid treatment.
DOI: 10.6084/m9.figshare.5123008
title: Supplementary Material for: No Consensus on Definition Criteria for Stroke Registry Common Data Elements

description: <i>Background:</i> Stroke registries contribute to the conduct of clinical research and to the assessment of health care quality control. Efforts to compare clinical outcomes and quality indicators between centers are dependent on standardized data elements, but it is unknown how stroke physicians define common data elements, such as hypertension or diabetes, when collecting data for registries at their centers. <i>Methods:</i> We conducted an internet-based survey of 91 centers affiliated with a university to assess their definitions of common data elements (CDEs) and compared their responses with standardized definitions, including those from the American College of Cardiology (ACC). <i>Results:</i> More than half (52%) of centers completed the survey. There was only modest agreement among respondents regarding definitions of CDEs in the survey and even less agreement on how the respondents’ definitions compared to ACC standards. <i>Conclusions:</i> Surveyed respondents do not agree on the definitions of CDEs, making comparisons between centers problematic. Standardized definitions of CDEs are needed to improve data collection for patient care and clinical research.
DOI: 10.6084/m9.figshare.5123014.v1
title: Supplementary Material for: Current National Patterns of Comorbid Diabetes among Acute Ischemic Stroke Patients

description: <i>Background:</i> Type 2 diabetes rates in the general population have risen with the growing obesity epidemic. Knowledge of temporal patterns and factors associated with comorbid diabetes among stroke patients may enable health practitioners and policy makers to develop interventions aimed at reducing diabetes rates, which may consequently lead to declines in stroke incidence and improvements in stroke outcomes. <i>Methods:</i> Using the Nationwide Inpatient Sample (NIS), a nationally representative data set of US hospital admissions, we assessed trends in the proportion of acute ischemic stroke (AIS) patients with comorbid diabetes from 1997 to 2006. Independent factors associated with comorbid diabetes were evaluated using multivariable logistic regression. <i>Results:</i> Over the study period, the absolute number of AIS hospitalizations declined by 17% (from 489,766 in 1997 to 408,378 in 2006); however, the absolute number of AIS hospitalizations with comorbid type 2 diabetes rose by 27% [from 97,577 (20%) in 1997 to 124,244 (30%) in 2006, p &lt; 0.001]. The rise in comorbid diabetes over time was more pronounced in patients who were relatively younger, Black or ‘other’ race, on Medicaid, or admitted to hospitals located in the South. Factors independently associated with higher odds of diabetes in AIS patients were Black or ‘other’ versus White race, congestive heart failure, peripheral vascular disease, history of myocardial infarction, renal disease and hypertension. <i>Conclusions:</i> Although hospitalizations for AIS in the US decreased from 1997 to 2006, there was a steep rise in the proportion with comorbid diabetes (from 1 in 5 to almost 1 in 3). Specific patient populations may be potential targets for mitigating this trend.
DOI: 10.6084/m9.figshare.5122999
title: Supplementary Material for: 3,4-Methylenedioxymethamphetamine (Ecstasy) Decreases Inflammation and Airway Reactivity in a Murine Model of Asthma

description: <i>Objective:</i> 3,4-Methylenedioxymethamphetamine (MDMA), or ecstasy, is a synthetic drug used recreationally, mainly by young people. It has been suggested that MDMA has a Th cell skewing effect, in which Th1 cell activity is suppressed and Th2 cell activity is increased. Experimental allergic airway inflammation in ovalbumin (OVA)-sensitized rodents is a useful model to study Th2 response; therefore, based on the Th2 skewing effect of MDMA, we studied MDMA in a model of allergic lung inflammation in OVA-sensitized mice. <i>Methods: </i>We evaluated cell trafficking in the bronchoalveolar lavage fluid, blood and bone marrow; cytokine production; L-selectin expression and lung histology. We also investigated the effects of MDMA on tracheal reactivity in vitro and mast cell degranulation. <i>Results:</i> We found that MDMA given prior to OVA challenge in OVA-sensitized mice decreased leukocyte migration into the lung, as revealed by a lower cell count in the bronchoalveolar lavage fluid and lung histologic analysis. We also showed that MDMA decreased expression of both Th2-like cytokines (IL-4, IL-5 and IL-10) and adhesion molecules (L-selectin). Moreover, we showed that the hypothalamus-pituitary-adrenal axis is partially involved in the MDMA-induced reduction in leukocyte migration into the lung. Finally, we showed that MDMA decreased tracheal reactivity to methacholine as well as mast cell degranulation in situ. <i>Conclusions:</i> Thus, we report here that MDMA given prior to OVA challenge in OVA-sensitized allergic mice is able to decrease lung inflammation and airway reactivity and that hypothalamus-pituitary-adrenal axis activation is partially involved. Together, the data strongly suggest an involvement of a neuroimmune mechanism in the effects of MDMA on lung inflammatory response and cell recruitment to the lungs of allergic animals.
DOI: 10.6084/m9.figshare.5123002.v1
title: Supplementary Material for: Oculomotor Nerve Palsy following Cardiac Tamponade with Churg-Strauss Syndrome: A Case Report

description: A 57-year-old man with a history of more than 10 years of bronchial asthma and chronic sinusitis complained of double vision which developed 18 days after cardiac tamponade with eosinophil-rich fluid (eosinophils 30%). He had oculomotor nerve palsy, and a blood test revealed eosinophilia (12,700/mm<sup>3</sup>) and elevation of both C-reactive protein and rheumatoid factor. He was diagnosed as having Churg-Strauss syndrome. His symptoms were relieved by corticosteroid therapy. Our case and previous cases in the literature revealed that oculomotor nerve palsy in Churg-Strauss syndrome is associated with pupil involvement and may be relieved by corticosteroid treatment.
DOI: 10.6084/m9.figshare.5123005
title: Supplementary Material for: Anorexigenic and Orexigenic Hormone Modulation of Mammalian Target of Rapamycin Complex 1 Activity and the Regulation of Hypothalamic Agouti-Related Protein mRNA Expression

description: Activation of mammalian target of rapamycin 1 (mTORC1) by nutrients, insulin and leptin leads to appetite suppression (anorexia). Contrastingly, increased AMP-activated protein kinase (AMPK) activity by ghrelin promotes appetite (orexia). However, the interplay between these mechanisms remains poorly defined. The relationship between the anorexigenic hormones, insulin and leptin, and the orexigenic hormone, ghrelin, on mTORC1 signalling was examined using S6 kinase phosphorylation as a marker for changes in mTORC1 activity in mouse hypothalamic GT1-7 cells. Additionally, the contribution of AMPK and mTORC1 signalling in relation to insulin-, leptin- and ghrelin-driven alterations to mouse hypothalamic agouti-related protein (AgRP) mRNA levels was examined. Insulin and leptin increase mTORC1 activity in a phosphoinositide-3-kinase (PI3K)- and protein kinase B (PKB)-dependent manner, compared to vehicle controls, whereas increasing AMPK activity inhibits mTORC1 activity and blocks the actions of the anorexigenic hormones. Ghrelin mediates an AMPK-dependent decrease in mTORC1 activity and increases hypothalamic AgRP mRNA levels, the latter effect being prevented by insulin in an mTORC1-dependent manner. In conclusion, mTORC1 acts as an integration node in hypothalamic neurons for hormone-derived PI3K and AMPK signalling and mediates at least part of the assimilated output of anorexigenic and orexigenic hormone actions in the hypothalamus.
DOI: 10.6084/m9.figshare.5122990
title: Supplementary Material for: Effects of Monounsaturated Fatty Acids on Cardiovascular Risk Factors: A Systematic Review and Meta-Analysis

description: The appropriate pattern of macronutrient distribution for dietary protocols aimed at treating or preventing obesity and its associated cardiovascular diseases is still a controversial topic of discussion. Recommendations considering a specific percentage or range for monounsaturated fatty acids (MUFA) are rare. It was the aim of this study to analyze long-term, randomized, controlled dietary intervention trials and to investigate the effects of MUFA on the biomarkers of obesity and cardiovascular risk factors. Dietary regimens with a high amount of MUFA (&gt;12%) were compared to those with ≤12%. The biomarkers taken into account were weight, waist circumference, fat mass, total cholesterol, LDL cholesterol, HDL cholesterol, triacylglycerols, systolic and diastolic blood pressure, as well as C-reactive protein. A total of 12 studies met the inclusion criteria. Data analysis was performed using the Review Manager 5.0.25 software. Significant differences between high- and low-MUFA protocols could be observed with respect to fat mass [–1.94 kg (confidence interval –3.72, –0.17), p = 0.03], systolic blood pressure [–2.26 mm Hg (confidence interval –4.28, –0.25), p = 0.03] and diastolic blood pressure [–1.15 mm Hg (confidence interval –1.96, –0.34), p = 0.005] favoring the dietary protocols with &gt;12% MUFA. Therefore, MUFA might represent a useful tool in the design of dietary regimens for obesity and cardiovascular disease.
DOI: 10.6084/m9.figshare.5122993
title: Supplementary Material for: Vocal Parameters That Indicate Threat Level Correlate with FOS Immunolabeling in Social and Vocal Control Brain Regions

description: Transmitting information via communicative signals is integral to interacting with conspecifics, and some species achieve this task by varying vocalizations to reflect context. Although signal variation is critical to social interactions, the underlying neural control has not been studied. In response to a predator, black-capped chickadees <i>(Poecile atricapilla)</i> produce mobbing calls (<i>chick-a-dee </i>calls) with various parameters, some of which convey information about the threat stimulus. We predicted that vocal parameters indicative of threat would be associated with distinct patterns of neuronal activity within brain areas involved in social behavior and those involved in the sensorimotor control of vocal production. To test this prediction, we measured the syntax and structural aspects of <i>chick-a-dee</i> call production in response to a hawk model and assessed the protein product of the immediate early gene FOS in brain regions implicated in context-specific vocal and social behavior. These regions include the medial preoptic area (POM) and lateral septum (LS), as well as regions involved in vocal motor control, including the dorsomedial nucleus of the intercollicular complex and the HVC. We found correlations linking call rate (previously demonstrated to reflect threat) to labeling in the POM and LS. Labeling in the HVC correlated with the number of D notes per call, which may also signal threat level. Labeling in the call control region dorsomedial nucleus was associated with the structure of D notes and the overall number of notes, but not call rate or type of notes produced. These results suggest that the POM and LS may influence attributes of vocalizations produced in response to predators and that the brain region implicated in song control, the HVC, also influences call production. Because variation in <i>chick-a-dee</i> call rate indicates predator threat, we speculate that these areas could integrate with motor control regions to imbue mobbing signals with additional information about threat level.
DOI: 10.6084/m9.figshare.5122996
title: Supplementary Material for: Performance of Genotype Imputations Using Data from the 1000 Genomes Project

description: Genotype imputations based on 1000 Genomes (1KG) Project data have the advantage of imputing many more SNPs than imputations based on HapMap data. It also provides an opportunity to discover associations with relatively rare variants. Recent investigations are increasingly using 1KG data for genotype imputations, but only limited evaluations of the performance of this approach are available. In this paper, we empirically evaluated imputation performance using 1KG data by comparing imputation results to those using the HapMap Phase II data that have been widely used. We used three reference panels: the CEU panel consisting of 120 haplotypes from HapMap II and 1KG data (June 2010 release) and the EUR panel consisting of 566 haplotypes also from 1KG data (August 2010 release). We used Illumina 324,607 autosomal SNPs genotyped in 501 individuals of European ancestry. Our most important finding was that both 1KG reference panels provided much higher imputation yield than the HapMap II panel. There were more than twice as many successfully imputed SNPs as there were using the HapMap II panel (6.7 million vs. 2.5 million). Our second most important finding was that accuracy using both 1KG panels was high and almost identical to accuracy using the HapMap II panel. Furthermore, after removing SNPs with MACH Rsq &lt;0.3, accuracy for both rare and low frequency SNPs was very high and almost identical to accuracy for common SNPs. We found that imputation using the 1KG-EUR panel had advantages in successfully imputing rare, low frequency and common variants. Our findings suggest that 1KG-based imputation can increase the opportunity to discover significant associations for SNPs across the allele frequency spectrum. Because the 1KG Project is still underway, we expect that later versions will provide even better imputation performance.
DOI: 10.6084/m9.figshare.5122987
title: Supplementary Material for: Distribution of pH Changes in Mouse Neonatal Hypoxic-Ischaemic Insult

description: We assessed the distribution in brain pH after neonatal hypoxic-ischaemic insult and its correlation with local injury. Postnatal day 7 mice were injected with neutral red and underwent left carotid occlusion and exposure to 8% oxygen. Images captured from the cut surface of snap-frozen brain were used to calculate the pH from the blue-green absorbance ratios. Carotid occlusion alone had no effect, but combined with hypoxia caused rapid, biphasic pH decline, with the first plateau at 15–30 min, and the second at 60–90 min. The ipsilateral dorsal cortex, hippocampus, striatum and thalamus were most affected. Contralateral pH initially showed only 30% of the ipsilateral decline, becoming more acidotic with increasing duration. Systemic blood analysis revealed, compared with hypoxia alone, that combined insult caused a 63% decrease in blood glucose (1.3 ± 0.2 m<i>M</i>), a 2-fold increase in circulating lactate (17.7 ± 2.9 m<i>M</i>), a reduction in CO<sub>2</sub> to 1.9 ± 0.1 kPa and a drop in pH (7.26 ± 0.06). Re-oxygenation resulted in the normalisation of systemic changes, as well as a global alkaline rebound in brain pH at 4–6 h. A topographic comparison of brain injury showed only a partial correlation with pH changes, with the severest injury occurring in the ipsilateral hippocampus and sparing acidic parts of the contralateral cortex.
DOI: 10.6084/m9.figshare.5122990.v1
title: Supplementary Material for: Effects of Monounsaturated Fatty Acids on Cardiovascular Risk Factors: A Systematic Review and Meta-Analysis

description: The appropriate pattern of macronutrient distribution for dietary protocols aimed at treating or preventing obesity and its associated cardiovascular diseases is still a controversial topic of discussion. Recommendations considering a specific percentage or range for monounsaturated fatty acids (MUFA) are rare. It was the aim of this study to analyze long-term, randomized, controlled dietary intervention trials and to investigate the effects of MUFA on the biomarkers of obesity and cardiovascular risk factors. Dietary regimens with a high amount of MUFA (&gt;12%) were compared to those with ≤12%. The biomarkers taken into account were weight, waist circumference, fat mass, total cholesterol, LDL cholesterol, HDL cholesterol, triacylglycerols, systolic and diastolic blood pressure, as well as C-reactive protein. A total of 12 studies met the inclusion criteria. Data analysis was performed using the Review Manager 5.0.25 software. Significant differences between high- and low-MUFA protocols could be observed with respect to fat mass [–1.94 kg (confidence interval –3.72, –0.17), p = 0.03], systolic blood pressure [–2.26 mm Hg (confidence interval –4.28, –0.25), p = 0.03] and diastolic blood pressure [–1.15 mm Hg (confidence interval –1.96, –0.34), p = 0.005] favoring the dietary protocols with &gt;12% MUFA. Therefore, MUFA might represent a useful tool in the design of dietary regimens for obesity and cardiovascular disease.
DOI: 10.6084/m9.figshare.5122999.v1
title: Supplementary Material for: 3,4-Methylenedioxymethamphetamine (Ecstasy) Decreases Inflammation and Airway Reactivity in a Murine Model of Asthma

description: <i>Objective:</i> 3,4-Methylenedioxymethamphetamine (MDMA), or ecstasy, is a synthetic drug used recreationally, mainly by young people. It has been suggested that MDMA has a Th cell skewing effect, in which Th1 cell activity is suppressed and Th2 cell activity is increased. Experimental allergic airway inflammation in ovalbumin (OVA)-sensitized rodents is a useful model to study Th2 response; therefore, based on the Th2 skewing effect of MDMA, we studied MDMA in a model of allergic lung inflammation in OVA-sensitized mice. <i>Methods: </i>We evaluated cell trafficking in the bronchoalveolar lavage fluid, blood and bone marrow; cytokine production; L-selectin expression and lung histology. We also investigated the effects of MDMA on tracheal reactivity in vitro and mast cell degranulation. <i>Results:</i> We found that MDMA given prior to OVA challenge in OVA-sensitized mice decreased leukocyte migration into the lung, as revealed by a lower cell count in the bronchoalveolar lavage fluid and lung histologic analysis. We also showed that MDMA decreased expression of both Th2-like cytokines (IL-4, IL-5 and IL-10) and adhesion molecules (L-selectin). Moreover, we showed that the hypothalamus-pituitary-adrenal axis is partially involved in the MDMA-induced reduction in leukocyte migration into the lung. Finally, we showed that MDMA decreased tracheal reactivity to methacholine as well as mast cell degranulation in situ. <i>Conclusions:</i> Thus, we report here that MDMA given prior to OVA challenge in OVA-sensitized allergic mice is able to decrease lung inflammation and airway reactivity and that hypothalamus-pituitary-adrenal axis activation is partially involved. Together, the data strongly suggest an involvement of a neuroimmune mechanism in the effects of MDMA on lung inflammatory response and cell recruitment to the lungs of allergic animals.
DOI: 10.6084/m9.figshare.5122987.v1
title: Supplementary Material for: Distribution of pH Changes in Mouse Neonatal Hypoxic-Ischaemic Insult

description: We assessed the distribution in brain pH after neonatal hypoxic-ischaemic insult and its correlation with local injury. Postnatal day 7 mice were injected with neutral red and underwent left carotid occlusion and exposure to 8% oxygen. Images captured from the cut surface of snap-frozen brain were used to calculate the pH from the blue-green absorbance ratios. Carotid occlusion alone had no effect, but combined with hypoxia caused rapid, biphasic pH decline, with the first plateau at 15–30 min, and the second at 60–90 min. The ipsilateral dorsal cortex, hippocampus, striatum and thalamus were most affected. Contralateral pH initially showed only 30% of the ipsilateral decline, becoming more acidotic with increasing duration. Systemic blood analysis revealed, compared with hypoxia alone, that combined insult caused a 63% decrease in blood glucose (1.3 ± 0.2 m<i>M</i>), a 2-fold increase in circulating lactate (17.7 ± 2.9 m<i>M</i>), a reduction in CO<sub>2</sub> to 1.9 ± 0.1 kPa and a drop in pH (7.26 ± 0.06). Re-oxygenation resulted in the normalisation of systemic changes, as well as a global alkaline rebound in brain pH at 4–6 h. A topographic comparison of brain injury showed only a partial correlation with pH changes, with the severest injury occurring in the ipsilateral hippocampus and sparing acidic parts of the contralateral cortex.