cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5121847.v1
title: Supplementary Material for: Knock-Out of β-Glucosidase 2 Has No Influence on Dextran Sulfate Sodium-Induced Colitis

description: <i>Background/Aims:</i> The non-lysosomal glucosylceramidase, β-glucosidase (Gba2), hydrolyzes glucosylceramide to glucose and ceramide (Cer). Cer is a potent second-messenger lipid that plays an important role in signaling cascades involved in apoptosis. The aim of this study was to investigate whether Gba2 knock-out (Gba2<sup>–/–</sup>) affects the extent of dextran sulfate sodium (DSS)-induced colitis in mice. <i>Methods:</i> Acute colitis was induced in wild-type (WT) and Gba2<sup>–/–</sup> mice by administration of 2% DSS in drinking water. After 7 days, mice underwent colonoscopy and were sacrificed. <i>Results:</i> Both DSS-treated WT (n = 10) and Gba2<sup>–/–</sup> (n = 12) mice showed elevated histological and endoscopic scores compared to respective H<sub>2</sub>O controls (n = 9 each). However, no significant differences between the DSS groups were detected. Flow cytometric analysis of propidium iodide staining, cleavage of caspases-3 and -8, indicative for apoptosis, as well as Cer levels were not altered in DSS-treated WT or Gba2<sup>–/–</sup> mice. Gba2<sup>–/–</sup> resulted in slightly decreased expression of glucocerebrosidase (Gba1) as well as in upregulation of proteins being involved in cellular regeneration, such as STAT3 (signal transducer and activator of transcription), JNK and iNOS, upon DSS treatment. <i>Conclusion:</i> We demonstrate that Gba2<sup>–/–</sup> does not affect the extent of DSS-induced inflammation in mice, however, it might be involved in tissue regeneration in response to toxic agents.
DOI: 10.6084/m9.figshare.5121835
title: Supplementary Material for: Deleterious Effect of Hyperoxia at Birth on White Matter Damage in the Newborn Rat

description: White matter damage (WMD) remains the leading cause of cerebral palsy in children born prematurely. The release of an excessive amount of reactive oxygen species is recognized as a risk factor for WMD. We hypothesize that free radical injury during reoxygenation at birth may be harmful to the immature white matter and may underlie, at least in part, the pathogenesis of WMD. We tested this hypothesis in rat pups delivered from normoxic pregnant rats, and by investigating an animal model based on protracted antenatal hypoxia in the pregnant rat and mimicking the main features of human WMD in rat pups. From embryonic day (E)5 to E21, the pregnant rats were placed in a chamber supplied with a gas mixture that either induced hypoxia (Fi<i>O</i><sub>2</sub> = 10%) or maintained normoxia (Fi<i>O</i><sub>2</sub> = 21%). On E21, the dams were removed from the chamber and housed under either normoxia (Fi<i>O</i><sub>2</sub> = 21%), hyperoxia (Fi<i>O</i><sub>2</sub> = 60%) or slowly reoxygenated (Fi<i>O</i><sub>2</sub> from 15% at E21 to 21% at postnatal day 7). Postnatal hyperoxia was associated with a significantly increased density of activated microglial cells (+105%) and TUNEL (terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labeling)-positive cells (+85%) within the developing white matter. Myelin content (–31%) and mature oligodendrocyte density (–37%) in the normal developing white matter were significantly decreased by postnatal hyperoxia. Postnatal hyperoxia significantly potentiated the myelination delay and oligodendroglial dysmaturation induced by antenatal hypoxia. In contrast, progressive reoxygenation at birth did not induce any change in white matter inflammation, myelination and cell death as compared with normoxic controls, and prevented most of the WMD observed following antenatal hypoxia. This study demonstrates a deleterious effect of hyperoxia at birth on the developing white matter in normal rat pups. Postnatal hyperoxia worsened the WMD induced by antenatal hypoxia. Hyperoxia at birth should be avoided in preterm infants at risk of WMD.
DOI: 10.6084/m9.figshare.5121850.v1
title: Supplementary Material for: Activation of KCNQ2/3 Potassium Channels by Novel Pyrazolo[1,5-a]pyrimidin-7(4H)-One Derivatives

description: The voltage-gated M-type potassium channel, encoded mainly by the KCNQ2/3 genes, plays an important role in the control of neuronal excitability. Mutations in the KCNQ2 gene lead to a form of neonatal epilepsy in humans termed ‘benign familial neonatal convulsions’, which is characterized by hyperexcitability of neurons. KCNQ openers or activators are expected to decrease the firing of overactive neurons and are thus conducive to the treatment of epilepsy and pain. Here, we report that four novel synthesized derivatives of pyrazolo[1,5-a]pyrimidin-7(4H)-one (PPO) named QO-26, QO-28, QO-40 and QO-41 potently augmented KCNQ2/3 channels expressed in Chinese hamster ovary cells and shifted the half-maximal activation voltage (V<sub>1/2</sub>) in the hyperpolarizing direction. The V<sub>1/2</sub> was negatively shifted in a concentration-dependent manner. The compounds markedly slowed both KCNQ2/3 channel activation and deactivation kinetics. Structure-activity relationship studies suggest that trifluoromethyl at the C-2 position, phenyl or naphthyl at the C-3 position, and trifluoromethyl or chloromethyl at the C-5 position are essential for the activity. These results suggest the four PPO derivatives act as KCNQ2/3 channel openers, providing a new dimension for the design and development of more potent channel openers.
DOI: 10.6084/m9.figshare.5121838
title: Supplementary Material for: A Non-Parametric Method for Building Predictive Genetic Tests on High-Dimensional Data

description: <i>Objective:</i> Predictive tests that capitalize on emerging genetic findings hold great promise for enhanced personalized healthcare. With the emergence of a large amount of data from genome-wide association studies (GWAS), interest has shifted towards high-dimensional risk prediction.<i>Methods:</i> To form predictive genetic tests on high-dimensional data, we propose a non-parametric method, called the ‘forward ROC method’. The method adopts a computationally efficient algorithm to search for environment risk factors, genetic predictors on the entire genome, and their possible interactions for an optimal risk prediction model, without relying on prior knowledge of known risk factors. An efficient yet powerful procedure is also incorporated into the method to handle missing data. <i>Results:</i>Through simulations and real data applications, we found our proposed method outperformed the existing approaches. We applied the new method to the Wellcome Trust rheumatoid arthritis GWAS dataset with a total of 460,547 markers. The results from the risk prediction analysis suggested important roles of <i>HLA-DRB1 </i>and <i>PTPN22</i> in predicting rheumatoid arthritis. <i>Conclusion:</i> We proposed a powerful and robust approach for high-dimensional risk prediction. The new method will facilitate future risk prediction that considers a large number of predictors and their interaction for improved performance.
DOI: 10.6084/m9.figshare.5121841.v1
title: Supplementary Material for: Chromosomal Variants in Klinefelter Syndrome

description: Klinefelter syndrome (KS) describes the phenotype of the most common sex chromosome abnormality in humans and occurs in one of every 600 newborn males. The typical symptoms are a tall stature, narrow shoulders, broad hips, sparse body hair, gynecomastia, small testes, absent spermatogenesis, normal to moderately reduced Leydig cell function, increased secretion of follicle-stimulating hormone, androgen deficiency, and normal to slightly decreased verbal intelligence. Apart from that, amongst others, osteoporosis, varicose veins, thromboembolic disease, or diabetes mellitus are observed. Some of the typical features can be very weakly pronounced so that the affected men often receive the diagnosis only at the adulthood by their infertility. With a frequency of 4%, KS is described to be the most common genetic reason for male infertility. The most widespread karyotype in affected patients is 47,XXY. Apart from that, various other karyotypes have been described, including 46,XX in males, 47,XXY in females, 47,XX,der(Y), 47,X,der(X),Y, or other numeric sex chromosome abnormalities (48,XXXY, 48,XXYY, and 49,XXXXY). The focus of this review was to abstract the different phenotypes, which come about by the various karyotypes and to compare them to those with a ‘normal’ KS karyotype. For that the patients have been divided into 6 different groups: Klinefelter patients with an additional isochromosome Xq, with additional rearrangements on 1 of the 2 X chromosomes or accordingly on the Y chromosome, as well as XX males and true hermaphrodites, 47,XXY females and Klinefelter patients with other numeric sex chromosome abnormalities. In the latter, an almost linear increase in height and developmental delay was observed. Men with an additional isochromosome Xq show infertility and other minor features of ‘normal’ KS but not an increased height. Aside from the infertility, in male patients with other der(X) as well as der(Y) rearrangements and in XXY women no specific phenotype is recognizable amongst others due to the small number of cases. The phenotype of XX males depends on the presence of <i>SRY</i> (sex-determining region Y) and the level of X inactivation at which <i>SRY</i>-negative patients are generally rarely observed.
DOI: 10.6084/m9.figshare.5121826
title: Supplementary Material for: Modifiers and Subtype-Specific Analyses in Whole-Genome Association Studies: A Likelihood Framework

description: <i>Objective:</i> We propose new statistical methods for analyzing genetic case/control association data in which cases can be further classified into subtypes, for example, based on clinical features. The primary utility of our work is the ability to distinguish between subtype-specific and modifier effects of genetic variants within a single testing framework. <i>Methods:</i> A range of disease/subtype causal models are defined for genetic variants involving subtype-specific and modifier effects. We present a log-linear modeling framework enabling comparison between these causal models and selection of the best-fit model. <i>Results:</i> We evaluate and compare the analytic power and model selection performance of the proposed work with standard two-group-based association tests. Simulation studies demonstrate that our approach has similar or greater power than the traditional approach over a range of causal models. We also report empirical findings about the impact of misspecification of subtype frequency during model selection, and extend the application of the proposed work to the cross-disorder association studies of multiple diseases. <i>Conclusion:</i> Whether a variant is a disease risk factor, is subtype specific, or modifies disease features has important consequences for the interpretation and follow-up of genetic associations. Our framework provides a simple, systematic way to evaluate and describe associations involving such subtype-specific or modifier effects.
DOI: 10.6084/m9.figshare.5121829
title: Supplementary Material for: Involvement of Neuronal Nitric Oxide Synthase in Ongoing Fetal Brain Injury following Near-Term Rabbit Hypoxia-Ischemia

description: Neuronal nitric oxide synthase (nNOS) and nitric oxide (NO) are implicated in neuronal injury following acute hypoxia-ischemia (HI). Our hypothesis was that NO from nNOS is responsible for ongoing mitochondrial dysfunction in near-term fetal HI. Recently, we synthesized new selective nNOS inhibitors that prevent the cerebral palsy phenotype in our animal model. We tested the efficacy of a selective nNOS inhibitor (JI-8) in fetal brains after in utero HI in our rabbit model. Brain slices at 29 days gestation were obtained after in utero HI, and immediately cultured in medium containing JI-8 or saline for 3–6 days. Mitochondrial membrane integrity and function were determined by flow cytometry using rhodamine 123 and JC-1, and cell death by using propidium iodide. JI-8 decreased NO production in brain slices and also showed significant preservation of mitochondrial function at both 3 and 6 days (p &lt; 0.05) when compared with saline and inducible NOS inhibitor 1400W. There was no difference in cell death. In conclusion, nNOS is involved in ongoing mitochondrial dysfunction after in utero HI. The subacute brain slice model could be a tool for studying the mechanisms involved in ongoing neuronal injury, and for rapidly assessing potential neuroprotectants.
DOI: 10.6084/m9.figshare.5121832
title: Supplementary Material for: Neuronal Nitric Oxide Synthase Inhibition Prevents Cerebral Palsy following Hypoxia-Ischemia in Fetal Rabbits: Comparison between JI-8 and 7-Nitroindazole

description: Cerebral palsy and death are serious consequences of perinatal hypoxia-ischemia (HI). Important concepts can now be tested using an animal model of cerebral palsy. We have previously shown that reactive oxygen and nitrogen species are produced in antenatal HI. A novel class of neuronal nitric oxide synthase (nNOS) inhibitors have been designed, and they ameliorate postnatal motor deficits when administered prior to the hypoxic-ischemic insult. This study asks how the new class of inhibitors, using JI-8 (K<sub>i</sub> for nNOS: 0.014 µ<i>M</i>) as a representative, compare with the frequently used nNOS inhibitor 7-nitroindazole (7-NI; K<sub>i</sub>: 0.09 ± 0.024 µ<i>M</i>). A theoretical dose equivalent to 75 K<sub>i</sub> of JI-8 or equimolar 7-NI was administered to pregnant rabbit dams 30 min prior to and immediately after 40 min of uterine ischemia at 22 days gestation (70% term). JI-8 treatment resulted in a significant decrease in NOS activity (39%) in fetal brain homogenates acutely after HI, without affecting maternal blood pressure and heart rate. JI-8 treatment resulted in 33 normal kits, 2 moderately and 13 severely affected kits and 5 stillbirths, compared with 8 normal, 3 moderately affected and 5 severely affected kits and 10 stillbirths in the 7-NI group. In terms of neurobehavioral outcome, 7-NI was not different from saline treatment, while JI-8 was superior to saline and 7-NI in its protective effect (p &lt; 0.05). In the surviving kits, JI-8 significantly improved the locomotion score over both saline and 7-NI scores. JI-8 was also significantly superior to saline in preserving smell, muscle tone and righting reflex function, but 7-NI did not show significant improvement. Furthermore, a 100-fold increase in the dose (15.75 µmol/kg) of 7-NI significantly decreased systolic blood pressure in the dam, while JI-8 did not. The new class of inhibitors such as JI-8 shows promise in the prevention of cerebral palsy and is superior to the previously more commonly used nNOS inhibitor.
DOI: 10.6084/m9.figshare.5121823
title: Supplementary Material for: <i>CDH3</i>-Related Syndromes: Report on a New Mutation and Overview of the Genotype-Phenotype Correlations

description: Hypotrichosis with juvenile macular dystrophy (HJMD) and ectodermal dysplasia, ectrodactyly and macular dystrophy (EEM) are both caused by mutations in the <i>CDH3</i> gene. In this report, we describe a family with EEM syndrome caused by a novel <i>CDH3</i> gene mutation and review the mutation spectrum and limb abnormalities in both EEM and HJMD. A protein structure model showing the localization of different mutations causing both syndromes is presented. The <i>CDH3 </i>gene was sequenced and investigation of the mutations performed using a protein structure model. The conservation score was calculated by ConSurf. We identified a novel <i>CDH3</i> gene mutation, p.G277V, which resides in a conserved residue located on a β-strand in the second cadherin domain. Review of the data on previously published mutations showed intra-familial and inter-familial variations in the severity of the limb abnormalities. Syndactyly was the most consistent clinical finding present in all the patients regardless of mutation type. The results of our study point to a phenotypic continuum between HJMD and EEM. It is important for genetic counseling to keep in mind the possible clinical/phenotypic overlap between these 2 syndromes and to be aware of the possible risk of limb abnormalities in future pregnancies in families with HJMD syndrome. <i>CDH3</i> gene mutation screening is recommended in patients with both these syndromes as part of the work-up in order to offer appropriate genetic counseling.
DOI: 10.6084/m9.figshare.5121829.v1
title: Supplementary Material for: Involvement of Neuronal Nitric Oxide Synthase in Ongoing Fetal Brain Injury following Near-Term Rabbit Hypoxia-Ischemia

description: Neuronal nitric oxide synthase (nNOS) and nitric oxide (NO) are implicated in neuronal injury following acute hypoxia-ischemia (HI). Our hypothesis was that NO from nNOS is responsible for ongoing mitochondrial dysfunction in near-term fetal HI. Recently, we synthesized new selective nNOS inhibitors that prevent the cerebral palsy phenotype in our animal model. We tested the efficacy of a selective nNOS inhibitor (JI-8) in fetal brains after in utero HI in our rabbit model. Brain slices at 29 days gestation were obtained after in utero HI, and immediately cultured in medium containing JI-8 or saline for 3–6 days. Mitochondrial membrane integrity and function were determined by flow cytometry using rhodamine 123 and JC-1, and cell death by using propidium iodide. JI-8 decreased NO production in brain slices and also showed significant preservation of mitochondrial function at both 3 and 6 days (p &lt; 0.05) when compared with saline and inducible NOS inhibitor 1400W. There was no difference in cell death. In conclusion, nNOS is involved in ongoing mitochondrial dysfunction after in utero HI. The subacute brain slice model could be a tool for studying the mechanisms involved in ongoing neuronal injury, and for rapidly assessing potential neuroprotectants.
DOI: 10.6084/m9.figshare.5121820
title: Supplementary Material for: Skeletal Muscle Gene Expression Profile Is Modified by Dietary Protein Source and Calcium during Energy Restriction

description: <i>Background/Aims:</i> The potential of whey protein and calcium to modify skeletal muscle gene expression during energy restriction (ER) was investigated in a model of diet-induced obesity. <i>Methods:</i> Obese C57BL/6J mice received casein (calcium 0.4%) and two different high-calcium (1.8%) whey protein-based [whey protein isolate (WPI) + Ca and α-lactalbumin + Ca] diets for ER. <i>Results:</i> Compared to casein, WPI and α-lactalbumin-based diets altered 208 and 287 genes, respectively, of which 186 genes were common to WPI and α-lactalbumin diets. These genes represented 31 KEGG pathways. The Wnt signaling was the most enriched pathway among the 101 genes regulated by α-lactalbumin only, whereas the 22 genes regulated by WPI only were not associated with KEGG pathways. Unlike casein, WPI and α-lactalbumin diets decreased Aldh1a7, Fasn, leptin, Nr4a3 and Scd1 mRNA expression, indicating dietary protein source-dependent alterations in muscle lipid and fatty acid metabolism. Muscle weight or lean body mass maintenance did not differ between groups although modest changes in hypertrophy/atrophy signaling were found. <i>Conclusion:</i> The skeletal muscle gene expression profile is modified by the dietary protein source and calcium during ER which may explain, at least in part, the greater anti-obesity effect of whey proteins and calcium compared to casein.
DOI: 10.6084/m9.figshare.5121826.v1
title: Supplementary Material for: Modifiers and Subtype-Specific Analyses in Whole-Genome Association Studies: A Likelihood Framework

description: <i>Objective:</i> We propose new statistical methods for analyzing genetic case/control association data in which cases can be further classified into subtypes, for example, based on clinical features. The primary utility of our work is the ability to distinguish between subtype-specific and modifier effects of genetic variants within a single testing framework. <i>Methods:</i> A range of disease/subtype causal models are defined for genetic variants involving subtype-specific and modifier effects. We present a log-linear modeling framework enabling comparison between these causal models and selection of the best-fit model. <i>Results:</i> We evaluate and compare the analytic power and model selection performance of the proposed work with standard two-group-based association tests. Simulation studies demonstrate that our approach has similar or greater power than the traditional approach over a range of causal models. We also report empirical findings about the impact of misspecification of subtype frequency during model selection, and extend the application of the proposed work to the cross-disorder association studies of multiple diseases. <i>Conclusion:</i> Whether a variant is a disease risk factor, is subtype specific, or modifies disease features has important consequences for the interpretation and follow-up of genetic associations. Our framework provides a simple, systematic way to evaluate and describe associations involving such subtype-specific or modifier effects.
DOI: 10.6084/m9.figshare.5121832.v1
title: Supplementary Material for: Neuronal Nitric Oxide Synthase Inhibition Prevents Cerebral Palsy following Hypoxia-Ischemia in Fetal Rabbits: Comparison between JI-8 and 7-Nitroindazole

description: Cerebral palsy and death are serious consequences of perinatal hypoxia-ischemia (HI). Important concepts can now be tested using an animal model of cerebral palsy. We have previously shown that reactive oxygen and nitrogen species are produced in antenatal HI. A novel class of neuronal nitric oxide synthase (nNOS) inhibitors have been designed, and they ameliorate postnatal motor deficits when administered prior to the hypoxic-ischemic insult. This study asks how the new class of inhibitors, using JI-8 (K<sub>i</sub> for nNOS: 0.014 µ<i>M</i>) as a representative, compare with the frequently used nNOS inhibitor 7-nitroindazole (7-NI; K<sub>i</sub>: 0.09 ± 0.024 µ<i>M</i>). A theoretical dose equivalent to 75 K<sub>i</sub> of JI-8 or equimolar 7-NI was administered to pregnant rabbit dams 30 min prior to and immediately after 40 min of uterine ischemia at 22 days gestation (70% term). JI-8 treatment resulted in a significant decrease in NOS activity (39%) in fetal brain homogenates acutely after HI, without affecting maternal blood pressure and heart rate. JI-8 treatment resulted in 33 normal kits, 2 moderately and 13 severely affected kits and 5 stillbirths, compared with 8 normal, 3 moderately affected and 5 severely affected kits and 10 stillbirths in the 7-NI group. In terms of neurobehavioral outcome, 7-NI was not different from saline treatment, while JI-8 was superior to saline and 7-NI in its protective effect (p &lt; 0.05). In the surviving kits, JI-8 significantly improved the locomotion score over both saline and 7-NI scores. JI-8 was also significantly superior to saline in preserving smell, muscle tone and righting reflex function, but 7-NI did not show significant improvement. Furthermore, a 100-fold increase in the dose (15.75 µmol/kg) of 7-NI significantly decreased systolic blood pressure in the dam, while JI-8 did not. The new class of inhibitors such as JI-8 shows promise in the prevention of cerebral palsy and is superior to the previously more commonly used nNOS inhibitor.