cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5121472
title: Supplementary Material for: Identification and Overexpression of a Bifunctional Aldehyde/Alcohol Dehydrogenase Responsible for Ethanol Production in <i>Thermoanaerobacter mathranii </i>

description: <i>Thermoanaerobacter mathranii </i>contains four genes, <i>adhA, adhB, bdhA </i>and<i> adhE, </i>predicted to code for alcohol dehydrogenases involved in ethanol metabolism. These alcohol dehydrogenases were characterized as NADP(H)-dependent primary alcohol dehydrogenase (AdhA), secondary alcohol dehydrogenase (AdhB), butanol dehydrogenase (BdhA) and NAD(H)-dependent bifunctional aldehyde/alcohol dehydrogenase (AdhE), respectively. Here we observed that AdhE is an important enzyme responsible for ethanol production in <i>T. mathranii</i> based on the constructed <i>adh</i> knockout strains. An <i>adhE</i> knockout strain fails to produce ethanol as a fermentation product, while other <i>adh</i> knockout strains showed no significant difference from the wild type. Further analysis revealed that the Δ<i>adhE</i> strain was defective in aldehyde dehydrogenase activity, but still maintained alcohol dehydrogenase activity. This showed that AdhE is the major aldehyde dehydrogenase in the cell and functions predominantly in the acetyl-CoA reduction to acetaldehyde in the ethanol formation pathway. Finally, AdhE was conditionally expressed from a xylose-induced promoter in a recombinant strain (BG1E1) with a concomitant deletion of a lactate dehydrogenase. Overexpressions of AdhE in strain BG1E1 with xylose as a substrate facilitate the production of ethanol at an increased yield.
DOI: 10.6084/m9.figshare.5121478
title: Supplementary Material for: Chromosomal Homologies among Vampire Bats Revealed by Chromosome Painting (Phyllostomidae, Chiroptera)

description: Substantial effort has been made to elucidate karyotypic evolution of phyllostomid bats, mostly through comparisons of G-banding patterns. However, due to the limited number of G-bands in respective karyotypes and to the similarity of non-homologous bands, an accurate evolutionary history of chromosome segments remains questionable. This is the case for vampire bats (Desmodontinae). Despite several proposed homologies, banding data have not yet provided a detailed understanding of the chromosomal changes within vampire genera. We examined karyotype differentiation of the 3 species within this subfamily using whole chromosomal probes from <i>Phyllostomus hastatus </i>(Phyllostominae) and <i>Carollia brevicauda </i>(Carolliinae). Painting probes of <i>P. hastatus </i>respectively detected 22, 21 and 23 conserved segments in <i>Diphylla ecaudata</i>,<i> Diaemus youngi</i>, and <i>Desmodus rotundus</i> karyotypes, whereas 27, 27 and 28 were respectively detectedwith <i>C. brevicauda </i>paints. Based on the evolutionary relationships proposed by morphological and molecular data, we present probable chromosomal synapomorphies for vampire bats and propose chromosomes that were present in the common ancestor of the 5 genera analyzed. Karyotype comparisons allowed us to relate a number of conserved chromosomal segments among the 5 species, providing a broader database for understanding karyotype evolution in the family.
DOI: 10.6084/m9.figshare.5121466
title: Supplementary Material for: Species Differences in Reactivity of Mouse and Rat Astrocytes in vitro

description: Reactive astrogliosis constitutes a major obstacle to neuronal regeneration and is characterized by rearrangement and upregulation of expression of cytoskeletal proteins, increased proliferation and hypertrophy. Many approaches have been attempted to mimic astrogliosis by inducing reactive astrocytes in vitro. Such research is usually performed using astrocytes derived from <i>Mus musculus</i> or <i>Rattus norvegicus</i>, and results compared between species on the assumption that these cells behave equivalently. Therefore, we compared reactivity between mouse and rat astrocytes in scratch wound assays to gain further insight into how comparable these cell culture models are. Proliferation and migration, as well as expression of the cytoskeletal proteins glial fibrillary acidic protein (GFAP) and vimentin, were compared by immunocytochemistry and immunoblot. Further, we investigated migration of proliferating cells by 5-ethynyl-2′-deoxyuridine staining. Substantial differences in GFAP expression and proliferation between astrocytes of the two species were found: rat astrocytes showed different cytoskeletal morphology, expressed significantly more GFAP and vimentin of different molecular size and were more proliferative than comparable mouse astrocytes. Our results suggest that rat and mouse astrocytes may respond differently to various reactivity-triggering stimuli, which needs to be considered when general conclusions are drawn regarding effects of factors regulating astrocyte reactivity.
DOI: 10.6084/m9.figshare.5121478.v1
title: Supplementary Material for: Chromosomal Homologies among Vampire Bats Revealed by Chromosome Painting (Phyllostomidae, Chiroptera)

description: Substantial effort has been made to elucidate karyotypic evolution of phyllostomid bats, mostly through comparisons of G-banding patterns. However, due to the limited number of G-bands in respective karyotypes and to the similarity of non-homologous bands, an accurate evolutionary history of chromosome segments remains questionable. This is the case for vampire bats (Desmodontinae). Despite several proposed homologies, banding data have not yet provided a detailed understanding of the chromosomal changes within vampire genera. We examined karyotype differentiation of the 3 species within this subfamily using whole chromosomal probes from <i>Phyllostomus hastatus </i>(Phyllostominae) and <i>Carollia brevicauda </i>(Carolliinae). Painting probes of <i>P. hastatus </i>respectively detected 22, 21 and 23 conserved segments in <i>Diphylla ecaudata</i>,<i> Diaemus youngi</i>, and <i>Desmodus rotundus</i> karyotypes, whereas 27, 27 and 28 were respectively detectedwith <i>C. brevicauda </i>paints. Based on the evolutionary relationships proposed by morphological and molecular data, we present probable chromosomal synapomorphies for vampire bats and propose chromosomes that were present in the common ancestor of the 5 genera analyzed. Karyotype comparisons allowed us to relate a number of conserved chromosomal segments among the 5 species, providing a broader database for understanding karyotype evolution in the family.
DOI: 10.6084/m9.figshare.5121481.v1
title: Supplementary Material for: A Balanced Translocation t(6;14)(q25.3;q13.2) Leading to Reciprocal Fusion Transcripts in a Patient with Intellectual Disability and Agenesis of Corpus Callosum

description: We identified a male patient presenting with intellectual disability and agenesis of the corpus callosum, carrying an apparently balanced, reciprocal, de novo translocation t(6;14)(q25.3;q13.2). Breakpoint mapping, using array painting, identified 2 interesting candidate genes, <i>ARID1B</i> and <i>MRPP3</i>, disrupted in the patient. Unexpectedly, the rearrangement produced 3 in-frame reciprocal fusion transcripts that were further characterized. Formation of fusion transcripts is mainly reported in acquired malignancies and is very rarely observed in patients with intellectual disability (ID) and/or multiple congenital malformations (MCA). Additional experimental results suggest that <i>ARID1B</i>, a gene involved in chromatin remodeling, constitutes a good candidate for the central nervous system phenotype present in the patient.
DOI: 10.6084/m9.figshare.5121463
title: Supplementary Material for: Trophoblast Glycoprotein: Possible Candidate Mediating Podocyte Injuries in Glomerulonephritis

description: <i>Background:</i> Trophoblast glycoprotein (Tpbg), a 72-kDa transmembrane glycoprotein, is known to regulate the phenotypes of epithelial cells by modifying actin organization and cell motility. Recently, a microarray study showed that Tpbg is upregulated in Thy1 glomerulonephritis (Thy1 GN). We hypothesized that Tpbg regulates cytoskeletal rearrangement and modulates phenotypic alteration in podocytes under pathological conditions. <i>Methods:</i> We examined Tpbg expression in Thy1 GN and Tpbg function in mouse podocytes. <i>Results:</i> We demonstrated that Tpbg is upregulated in the injured podocytes of Thy1 GN. In vitro, immunofluorescence studies revealed that Tpbg colocalized with the focal adhesion protein, vinculin, in parallel with stress fiber formation. This colocalization was observed even when actin filaments were depolymerized with cytochalasin D. Tpbg localization at focal adhesions was induced by dominant-active RhoA and suppressed by the ROCK1 inhibitor Y-26732. In addition, transforming growth factor-β increased Tpbg expression at focal adhesions concurrently with rearrangement of stress fibers. Stress fiber formation was suppressed in differentiated podocytes transfected with full-length Tpbg. Furthermore, knockdown of Tpbg using small interfering RNA decreased podocyte motility. <i>Conclusion:</i>Our findings suggest a novel role of Tpbg in the phenotypic alteration of injured podocytes, and we accordingly propose a new mechanism of glomerular injury in glomerulonephritis.
DOI: 10.6084/m9.figshare.5121460
title: Supplementary Material for: Renal Replacement Therapy for Prevention of Contrast-Induced Acute Kidney Injury: A Meta-Analysis of Randomized Controlled Trials

description: <i>Background:</i> Contrast-induced acute kidney injury (CI-AKI) is an important cause of acute renal injury. Several clinical trials using renal replacement therapy (RRT) for prevention of CI-AKI yielded conflicting results. We performed a meta-analysis to assess the efficacy of prophylactic RRT on CI-AKI. <i>Methods:</i> Randomized controlled trials on CI-AKI using RRT were identified without language restriction in Cochrane library, Pubmed and Embase. Data extracted from literature were analyzed with Review manager and Stata software. <i>Results:</i> Nine randomized controlled trials involving 751 patients were included. Heterogeneity was found across trials (p &lt; 0.00001). A random effect model was used to combine the data. RRT reduced the risk of CI-AKI by 26% compared with the control group, but statistical significance was not reached (risk ratio (RR) 0.74, 95% CI 0.35–1.60, p = 0.45). Subgroup analysis of modality indicated that hemodialysis was ineffective in reducing the risk of CI-AKI (RR 1.21, 95% CI 0.63–2.32, p = 0.57), while CRRT decreased the incidence of CI-AKI (RR 0.22, 95% CI 0.07–0.64, p = 0.006). Subgroup analysis according to the CKD stage did not record heterogeneity across trials. RRT increased the odds of CI-AKI in CKD stage 3 patients (RR 1.53, 95% CI 0.07–0.64, p = 0.01), but decreased the occurrence of CI-AKI in patients with CKD stage higher than 3 (RR 0.74, 95% CI 0.35–1.60, p = 0.45). The pooled RR of the need for permanent dialysis demonstrated an insignificant trend towards benefit in patients treated with RRT (RR 0.61, 95% CI 0.26–1.40, p = 0.24). RRT reduced in-hospital mortality compared with control group (RR 0.33, 95% CI 0.14–0.77, p = 0.01). <i>Conclusion:</i> RRT fails to reduce the incidence of CI-AKI in CKD stage 3 patients, but may be beneficial in patients with more advanced renal function. CRRT is more effective than hemodialysis for prevention of CI-AKI. RRT is effective in reducing the in-hospital mortality of CI-AKI patients.
DOI: 10.6084/m9.figshare.5121466.v1
title: Supplementary Material for: Species Differences in Reactivity of Mouse and Rat Astrocytes in vitro

description: Reactive astrogliosis constitutes a major obstacle to neuronal regeneration and is characterized by rearrangement and upregulation of expression of cytoskeletal proteins, increased proliferation and hypertrophy. Many approaches have been attempted to mimic astrogliosis by inducing reactive astrocytes in vitro. Such research is usually performed using astrocytes derived from <i>Mus musculus</i> or <i>Rattus norvegicus</i>, and results compared between species on the assumption that these cells behave equivalently. Therefore, we compared reactivity between mouse and rat astrocytes in scratch wound assays to gain further insight into how comparable these cell culture models are. Proliferation and migration, as well as expression of the cytoskeletal proteins glial fibrillary acidic protein (GFAP) and vimentin, were compared by immunocytochemistry and immunoblot. Further, we investigated migration of proliferating cells by 5-ethynyl-2′-deoxyuridine staining. Substantial differences in GFAP expression and proliferation between astrocytes of the two species were found: rat astrocytes showed different cytoskeletal morphology, expressed significantly more GFAP and vimentin of different molecular size and were more proliferative than comparable mouse astrocytes. Our results suggest that rat and mouse astrocytes may respond differently to various reactivity-triggering stimuli, which needs to be considered when general conclusions are drawn regarding effects of factors regulating astrocyte reactivity.
DOI: 10.6084/m9.figshare.5121451
title: Supplementary Material for: Chronic Occlusion of the Left Main Coronary Artery: Importance of Collaterals

description: Chronic occlusion of the left coronary artery is an infrequent finding in patients undergoing coronary angiography. These patients usually present symptoms of angina or heart failure. We describe a patient who was training regularly without cardiac symptoms until ventricular fibrillation suddenly occurred during a long-distance run. A chronic left main stem occlusion with well-developed right-to-left coronary collaterals was demonstrated by angiography. Up to this event, the collateral flow had been sufficient to allow physical exercise at a high performance level without symptoms. The patient later underwent coronary bypass surgery and recovered completely.
DOI: 10.6084/m9.figshare.5121454
title: Supplementary Material for: Possible Association of <i>SLC22A2</i> Polymorphisms with Aspirin-Intolerant Asthma

description: <i>Background:</i> Aspirin-intolerant asthma (AIA) is a clinical syndrome characterized by acute bronchoconstriction following the ingestion of aspirin. Solute carrier family 22, member 2 (SLC22A2), also known as organic cation transporter 2 (OCT2), is predominantly expressed in the luminal membrane of airway epithelial cells and has been shown to mediate the transport of prostaglandins on the cyclooxygenase pathway which is regulated by aspirin blockage. Recently, SLC22A2-mediated uptake inhibition by several nonsteroidal anti-inflammatory drugs and decreased SLC22A2 transport activity by its genetic variants have been elucidated in asthma. <i>Methods:</i> To investigate the associations between AIA and genetic polymorphisms of the <i>SLC22A2</i> gene, 18 variants were genotyped in 163 AIA subjects and 429 aspirin-tolerant asthma (ATA) controls. Logistic analyses were used to evaluate p values for the associations of <i>SLC22A2</i> polymorphisms with AIA. <i>Results:</i> One common polymorphism in intron 5, i.e. <i>rs316021</i>, was significantly associated with susceptibility to AIA (p<i> = </i>0.004, <i>P</i><sup>corr</sup> <i>= </i>0.05, OR = 0.60, 95% CI = 0.43–0.85 in a codominant model). The minor allele frequency of <i>rs316021</i> in the AIA group was significantly lower than that in the ATA controls. In addition, a polymorphism in intron 4 <i>(rs3912161)</i> and a haplotype <i>(SLC22A2-ht3)</i> showed significantly stronger association signals with the FEV<sub>1</sub> fall rate induced by aspirin provocation in AIA subjects compared with ATA controls (p <i>= </i>0.004, <i>P</i><sup>corr</sup><i> = </i>0.05). <i>Conclusion:</i> Our findings suggest that <i>SLC22A2</i> could be a susceptibility gene for aspirin intolerance in asthmatics.
DOI: 10.6084/m9.figshare.5121457
title: Supplementary Material for: Sex and the Frontal Cortex: A Developmental CT Study in the Spotted Hyena

description: The purpose of this study was to examine developmental and individual variation in total endocranial volume and regional brain volumes, including the anterior cerebrum, posterior cerebrum and cerebellum/brain stem, in the spotted hyena <i>(Crocuta crocuta)</i>. The spotted hyena is a highly gregarious animal noted for living in large, hierarchically organized groups. The social lives of male and female spotted hyenas do not differ until after puberty, when males disperse from the natal group, while females remain philopatric. Here we sought to determine whether the divergent life histories of male and female spotted hyenas are linked to differences in brain size or organization. Three-dimensional virtual endocasts were created using computed tomography from 46 spotted hyenas skulls (23 females, 22 males, 1 unknown sex) ranging in age from 1 day to 18 years. Brain volume and skull length were highly correlated (r = 0.91), and both reached asymptotic values by 34 months of age. Analyses of total endocranial volume (relative to skull length) and cerebellum/brain stem volume (relative to total endocranial volume) revealed no sex differences. However, relative anterior cerebrum volume, comprised mainly of frontal cortex, was significantly greater in adult males than adult females, and relative posterior cerebrum volume was greater in adult females than adult males. We hypothesize that the demands of neural processing underlying enhanced social cognition required for successful male transfer between matriarchical social groups at dispersal may be greater than cognitive demands on philopatric females.
DOI: 10.6084/m9.figshare.5121460.v1
title: Supplementary Material for: Renal Replacement Therapy for Prevention of Contrast-Induced Acute Kidney Injury: A Meta-Analysis of Randomized Controlled Trials

description: <i>Background:</i> Contrast-induced acute kidney injury (CI-AKI) is an important cause of acute renal injury. Several clinical trials using renal replacement therapy (RRT) for prevention of CI-AKI yielded conflicting results. We performed a meta-analysis to assess the efficacy of prophylactic RRT on CI-AKI. <i>Methods:</i> Randomized controlled trials on CI-AKI using RRT were identified without language restriction in Cochrane library, Pubmed and Embase. Data extracted from literature were analyzed with Review manager and Stata software. <i>Results:</i> Nine randomized controlled trials involving 751 patients were included. Heterogeneity was found across trials (p &lt; 0.00001). A random effect model was used to combine the data. RRT reduced the risk of CI-AKI by 26% compared with the control group, but statistical significance was not reached (risk ratio (RR) 0.74, 95% CI 0.35–1.60, p = 0.45). Subgroup analysis of modality indicated that hemodialysis was ineffective in reducing the risk of CI-AKI (RR 1.21, 95% CI 0.63–2.32, p = 0.57), while CRRT decreased the incidence of CI-AKI (RR 0.22, 95% CI 0.07–0.64, p = 0.006). Subgroup analysis according to the CKD stage did not record heterogeneity across trials. RRT increased the odds of CI-AKI in CKD stage 3 patients (RR 1.53, 95% CI 0.07–0.64, p = 0.01), but decreased the occurrence of CI-AKI in patients with CKD stage higher than 3 (RR 0.74, 95% CI 0.35–1.60, p = 0.45). The pooled RR of the need for permanent dialysis demonstrated an insignificant trend towards benefit in patients treated with RRT (RR 0.61, 95% CI 0.26–1.40, p = 0.24). RRT reduced in-hospital mortality compared with control group (RR 0.33, 95% CI 0.14–0.77, p = 0.01). <i>Conclusion:</i> RRT fails to reduce the incidence of CI-AKI in CKD stage 3 patients, but may be beneficial in patients with more advanced renal function. CRRT is more effective than hemodialysis for prevention of CI-AKI. RRT is effective in reducing the in-hospital mortality of CI-AKI patients.
DOI: 10.6084/m9.figshare.5121463.v1
title: Supplementary Material for: Trophoblast Glycoprotein: Possible Candidate Mediating Podocyte Injuries in Glomerulonephritis

description: <i>Background:</i> Trophoblast glycoprotein (Tpbg), a 72-kDa transmembrane glycoprotein, is known to regulate the phenotypes of epithelial cells by modifying actin organization and cell motility. Recently, a microarray study showed that Tpbg is upregulated in Thy1 glomerulonephritis (Thy1 GN). We hypothesized that Tpbg regulates cytoskeletal rearrangement and modulates phenotypic alteration in podocytes under pathological conditions. <i>Methods:</i> We examined Tpbg expression in Thy1 GN and Tpbg function in mouse podocytes. <i>Results:</i> We demonstrated that Tpbg is upregulated in the injured podocytes of Thy1 GN. In vitro, immunofluorescence studies revealed that Tpbg colocalized with the focal adhesion protein, vinculin, in parallel with stress fiber formation. This colocalization was observed even when actin filaments were depolymerized with cytochalasin D. Tpbg localization at focal adhesions was induced by dominant-active RhoA and suppressed by the ROCK1 inhibitor Y-26732. In addition, transforming growth factor-β increased Tpbg expression at focal adhesions concurrently with rearrangement of stress fibers. Stress fiber formation was suppressed in differentiated podocytes transfected with full-length Tpbg. Furthermore, knockdown of Tpbg using small interfering RNA decreased podocyte motility. <i>Conclusion:</i>Our findings suggest a novel role of Tpbg in the phenotypic alteration of injured podocytes, and we accordingly propose a new mechanism of glomerular injury in glomerulonephritis.
DOI: 10.6084/m9.figshare.5121451.v1
title: Supplementary Material for: Chronic Occlusion of the Left Main Coronary Artery: Importance of Collaterals

description: Chronic occlusion of the left coronary artery is an infrequent finding in patients undergoing coronary angiography. These patients usually present symptoms of angina or heart failure. We describe a patient who was training regularly without cardiac symptoms until ventricular fibrillation suddenly occurred during a long-distance run. A chronic left main stem occlusion with well-developed right-to-left coronary collaterals was demonstrated by angiography. Up to this event, the collateral flow had been sufficient to allow physical exercise at a high performance level without symptoms. The patient later underwent coronary bypass surgery and recovered completely.
DOI: 10.6084/m9.figshare.5121448
title: Supplementary Material for: Validated Methods of Cough Assessment: A Systematic Review of the Literature

description: <i>Background:</i> Cough is a common symptom for which patients often seek medical advice and consume vast amounts of drugs. It is a real challenge for both the physician and the clinical researcher to evaluate a cough’s clinical importance and its precise response to treatment. <i>Objectives:</i> This systematic literature review has the following objectives: first, to make an inventory of the validated tools for assessing cough, and second, to investigate the extent to which the results of various assessment methods can be correlated. <i>Methods:</i> Two independent investigators searched the Medline, Embase, and Cochrane databases for validation studies on cough assessment tools. <i>Results:</i> Thirty-four studies were included. Several ambulatory cough monitors automatically identify cough and have been validated in a limited number of patients. Three cough-specific quality-of-life scales (Leicester Cough Questionnaire, Cough Quality of Life Questionnaire, and Burden of Cough Questionnaire) have been validated. No validation studies of descriptive scores or visual analogue scales were found. The correlations between quality-of-life scores and cough frequency were good. The correlations between descriptive scores or visual analogue scales and more objective methods, such as cough frequency monitoring or quality-of-life scores, were inconsistent. <i>Conclusion:</i> Cough-specific quality-of-life questionnaires can provide valid outcomes for research into cough. Although the current developments in cough monitoring devices are promising, further studies on a larger scale, under more realistic conditions, and for different patterns of cough are required before they can be recommended for widespread use.