bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of rs556621 Polymorphism with Development of Stroke in Patients with Cardiovascular Pathology
Authors: Nikulina S. Yu. , Shulman V. A. , Chernova A. A. , Prokopenko S. V. , Nikulin D. A. , Platunova I. M. , Tretyakova S. S. , Maksimov V. N. , Gurazheva A. A. 
Published: November 2019

Aim. To study the association of single nucleotide polymorphism rs556621 (G> T) with development of stroke in patients of the East Siberian population with cardiovascular pathology and risk factors.Material and methods. The study involved 260 patients (157 men and 103 women) with stroke (mean age 57.0 [51.0-62.0]) and 272 patients (170 men and 102 women) of the control group (mean age 55.0 [51.0-62.0]). The examination of the main group included: collection of complaints, anamnesis, clinical examination, computed tomography of the brain, electrocardiography, echocardioscopy, ultrasound duplex scanning of extracranial brachiocephalic arteries, daily blood pressure and heart rate monitoring, analysis of the blood coagulation system. The patients of the main group have arterial hypertension, paroxysmal supraventricular tachycardias, dyslipidemia, atherosclerosis of the brachiocephalic arteries, disorders of the hemostatic system. The control group was studied in the framework of the HAPIEE international project. Molecular genetic research was performed by real-time polymerase chain reaction.Results. There were no statistically significant differences in the frequencies of genotypes and single nucleotide polymorphism rs556621 alleles (G>T) in the subgroup of patients with stroke and those in the control group. The frequency of the rare TT genotype among patients with stroke was 13.3%±4.16, among healthy individuals – 8.8±3.37% (p=0.1). Gender differences when comparing the frequencies of genotypes and alleles were also not detected (p>0.05). The frequencies of the TT genotype were approximately the same in the subgroup of patients with arterial hypertension (13.1%±4.22) and in the control group (7.4±5.25%; p>0.05). No significant differences were observed in the frequencies of the rare genotype of the studied polymorphism in the subgroup of patients with supraventricular tachycardias (20.0±14.37%), hypercoagulability (15.9±7.64%) and the control group (8.8±3.37%), p>0.05. A statistically significant relationship was found between the rare genotype TT of single nucleotide polymorphism rs556621 (G>T) and the development of stroke in patients with dyslipidemia and atherosclerotic lesions of the coronary arteries (p=0.041; odds ratio 1.86, 95% confidence interval 1.02-3.41).Conclusion. The genotype of TTs of single nucleotide polymorphism rs556621 (G> T) increases the risk of developing stroke in patients with dyslipidemia and atherosclerosis of the brachiocephalic arteries compared with carriers of the GG and GT genotypes. The obtained data are recommended to be considered when prescribing lipid-lowering and antithrombotic therapy.
Pilot study of expanded newborn screening for 573 genes related to severe diseases in China: results from 1173 newborns
Authors: Luo Xiaomei , Sun Yu , Xu Feng , Guo Jun , Li Lin , Lin Zhiwei , Ye Jun , Gu Xuefan , Yu Yongguo 
Published: November 2019

Abstract
Background: Current newborn screening (NBS) in China is mainly aimed at detecting biochemical levels of metabolites in the blood, which may generate false positive/negative results. To explore whether next-generation sequencing (NGS) for dried blood spots can increase the detecting rate, we carried out a pilot study using NGS in 1,173 newborns who had been tested by traditional NBS. With a focus on inherited metabolic diseases (IMDs), our team investigated the current frequencies of genes related to common inherited metabolic diseases in this cohort. Methods: We designed an NGS panel of 573 genes related to severe diseases and performed NBS in 1,173 individuals who had been screened by tandem mass spectrometry (MS/MS) as well as for phenylalanine (Phe), thyroid-stimulating hormone (TSH), 17-α-hydroxyprogesterone (17-OHP), and glucose-6-phosphate dehydrogenase (G6PD) abnormalities in a traditional biochemical NBS conducted in September 2016. We compared the biochemical results to the genetic variants and investigated the carrier frequencies of 77 genes related to disorders by MS/MS in these newborns.Results: The biochemical results showed that four newborns (all male) were positive for G6PD by enzymatic assay, while the other biochemical findings including MS/MS, Phe, TSH and 17-OHP were negative. Genetic analysis results revealed that all the four newborns with positive G6PD values harbored hemizygous G6PD mutations. The NGS results also revealed an individual (ID 84123) carrying two SLC22A5 mutations (c.760C>T/p.R254* and c.1400C>G/p.S467C) common in Chinese patients with carnitine deficiency, which were later verified to be in trans, who was biochemically negative in 2016. The MS/MS results in 2019 showed free carnitine deficiency, consistent with the genetic analysis findings. The top five genes with the highest carrier frequencies in these newborns were PAH (1.77%), ETFDH (1.24%), MMACHC (1.15%), SLC25A13 (0.98%), and GCDH (0.80%). Conclusions: Our study provided data combing biochemical results with genetic variants in 1,173 newborns and confirmed a primary carnitine deficiency patient with false-negative biochemical results. This is also the first study to report the carrier frequencies of 77 IMD-causing genes in China.
Comparison of gabapentin and oxycodone-acetaminophen used for pre-emptive analgesia in patients undergoing double-port thoracoscopic pulmonary surgery: a randomized, double-blind, controlled trial.
Authors: Li Li , Li XiJuan , Shen JinMei , Zhou LiJun 
Published: November 2019

Abstract
Background This study was designed to determine whether gabapentin is not inferior to the oxycodone-acetaminophen group used as pre-emptive analgesia in reducing post-operative pain. The post-operative pain of patients undergoing thoracoscopic pulmonary surgery, a routine operation procedure, is also a clinical problem that urgently needs to be further explored. We hypothesized that gabapentin is not inferior to oxycodone-acetaminophen.Methods Ninety patients were randomly divided into group A,n=30; group B,n=30; and group C,n=30. Patients in group A received oral gabapentin (300 mg) 2 h before surgery, similarly patients in group B received oral oxycodone-acetaminophen (330mg);Group C did not take any oral drugs; all patients were given self-controlled intravenous analgesia after surgery. NRS scores post-operative, opioid consumption 48 hours post-operative, analgesic-related adverse events, post-operative chronic pain after 2 months, were recorded.Results The NRS scores and opioid consumption 48 hours post-operative of intervention groups were significantly lower than the control group, and did not increase analgesic-related adverse events. The incidence of chronic pain 2 months post-operative in groups A and B was significantly lower than group C.Conclusion Oral gabapentin and oxycodone-acetaminophen alleviated the pain post-operative, reduced opioid consumption post-operative,promoted the recovery.
Biodegradation of recalcitrant compounds and phthalates by a consortium of Liometopum apiculatum gut microbiota
Authors: González-Escobar Jorge L. , Pereyra-Camacho Marco A. , Léon-Rodríguez Antonio De , Grajales-Lagunes Alicia , Reyes-Agüero Antonio , Chagolla-López Alicia , Rosa Ana Paulina Barba de la 
Published: November 2019

Abstract
Liometopum apiculatum ants species are widely distributed in arid and semi-arid ecosystems where there is a relative food shortage. They have established an ecological balance involving symbiotic interactions, which have allowed them to survive through mechanisms that are still unknown. The aim of this study was to explore the metabolic potential of isolated bacteria from L. apiculatum using substrate assimilation and enzymatic activity assay. Results revealed a complex bacteria consortium belonging to Proteobacteria, Firmicutes, and Actinobacteria phylum. These symbionts showed activities associated with biopolymers degradation, suggesting their important role in nutrients release stored in plant-derived material. By other hand, some microorganisms had a high capacity for degradation of phthalate esters. These results not only revealed the important contribution of the symbionts in L apiculatum ants feeding habits, but also they showed a promising source of enzymes with high potential for biotechnological applications such as lignocellulosic biomass hydrolysis and bioremediation.
A comprehensive assessment of automatic logistic regression model selection methods
Authors: Ehwerhemuepha Louis , Rakovski Cyril 
Published: November 2019

Abstract
Background: Current studies of variable selection methods are based on small datasets for which the true underlying predictors and corresponding effect sizes may not be known precisely. We designed and implemented a large-scale simulation study to assess the ability of stepwise logistic regression variable selection and lasso regression methods to identify the correct underlying model. Methods: We simulated data based on a random multivariate distribution over an extensive range of covariate correlation structures, sample sizes, number of covariates, number of true predictors, and effect sizes. We considered correlation structures reflecting the scenarios of independence across all covariates; two low correlation blocks and a block of zero correlation; three blocks of high correlation, low correlation and zero correlation; and two blocks of high correlation with low cross block correlation and a block of zero correlation respectively. Results: Our results show that the performances of stepwise regression, lasso regression, and random forest algorithm (as measured by the AUC, detection of true predictors, selection of noise variables, and effect size estimation) are affected by the number of true predictor variables, the correlation between the variables in the dataset, and the sample size. The number of noise variables in the dataset, although significant in some cases, has only a marginal effect on a variety of model performance statistic. Our results show that stepwise regression procedures are more likely to capture a true predictor, more likely to correctly estimate the true effect sizes, and more likely to have lower false discovery rates. Moreover, stepwise model selection based on the BIC criteria obtained the highest average AUC (0.7515) closely followed by lasso regression, stepwise model selection based on the AIC criteria, ridge regression, and random forest algorithm. Conclusions: Stepwise procedures for variable selection are robust in the selection of the true underly predictor variables, estimation of corresponding effect sizes, and predictive model performance. Recommendations suggesting that stepwise procedures should be abandoned may be misguided.
The influence of pre-pregnancy body mass index and gestational weight gain on pregnancy outcomes in two-child women
Authors: Chen Hanqing , Zou Suhua , Li Zhuyu , Yang Jianbo , Cai Jian , Wang Zilian 
Published: November 2019

Abstract
Background Pre-pregnancy body mass index and gestational weight gain were related to perinatal outcomes. It was not know the changes of pre-pregnancy body mass index, weight gain during pregnancy and its effect on perinatal outcomes in two-child women.Methods This was a retrospective study. Data of single term women delivered in the First Affiliated Hospital of Sun Yat-sen University were collected from July 2017 to June 2018. Gestational weight gain criteria of the American Institute of Medical Research and pre-pregnancy body mass index classes were used to evaluate the effects on pregnancy outcomes.Results A total of 3049 cases were enrolled in the study. Overweight cases was 9.0% and obesity was 2.4%. The weight gain of the two-child women was less than that of primipara(12.4±3.9vs13.3±4.0kg, P<0.001). The proportion of primipara with excessive weight gain was higher compared to two-child women(20.1%versus17.3%, P<0.001). There were 40.0% overweight primipara and 55.2% of two-child women had excessive weight gain. And 40.5% primipara and 54.5% two-child women of obesity had excessive weight gain during pregnancy. Obese primipara increased the risk of pre-eclampsia (aOR2.38, 95%CI 0.76-7.46). And the odds of diabetes mellitus and large for gestational age also increased in this group (aOR3.49, 95%CI 1.46-8.35 and aOR7.65, 95%CI 1.83-31.97, respectively). Two-child women had similar results. Underweight primipara with excessive weight gain increased the pre-eclampsia risk (aOR2.26, 95%CI 0.29-17.46). Normal weight and overweight/obese primipara also had similar results. But in two-child women, only overweight/obesity increased the risk of pre-eclampsia (aOR2.01, 95%CI 0.41-9.98). Underweight two-child women with less weight gain increased the risk of diabetes(aOR2.06, 95%CI 0.43-9.8). Two-child women with overweight/obese increased the odds of LGA even if they had less weight gain(aOR2.58, 95%CI 0.11-63.22). Normal weight primipara and two-child women with overweight and obese with excessive weight gain had similar results. On the other way, underweight primipara with less weight gain increased the risk of SGA(aOR1.74, 95%CI 0.81-3.76).Conclusions Gestational weight gain of two-child women was less than primipara. Overweight/obese women with excessive weight gain of two-child women increased the risk of adverse outcomes.
Evaluation of High-Resolution Melting Curve Analysis (HRM) assay for Detection of Pseudomonas aeruginosa PASGNDM699: A dangerous New Delhi metallo-β-lactamase (NDM) strain
Authors: Dehbashi Sanaz , Tahmasebi Hamed , Arabestani Mohammad 
Published: November 2019

Abstract
Background: New Delhi metallo-β-lactamase (NDM-1) is a broad spectrum β-lactamase that is able to inactivate all β-lactams except aztreonam, as is typical of metallo-β-lactamases. NDM-1 producers in Pseudomonas aeruginosa, especially PASGNDM699 strain, cause a range of infections such as urinary tract, diarrhoea and soft tissue infections. The aim of this study was to Standardization of High-Resolution Melting Curve Analysis (HRM) assay for detection of P. aeruginosa, especially PASGNDM699 strain.
Methods: The HRM method was done on standard strains of P. aeruginosa strains. 9-fold Serial dilutions of known DNA concentrations, extracted from standard isolates were prepared and tested by Real Time Melting curve and HRM assay. Data analysis was performed using the StepOne Software v2.3 and HRM Software v3.0.1 (Applied Biosystems, Ltd).
Results: Based on the results of the Real Time PCR assay and melt curve analysis, melting point temperatures of the N-1, N-2 and N-3 amplicon for isolates identified as NDM strains were 87.57°C, 76.92°C and 82.97°C, respectively. Furthermore, melting point temperatures of the blaVIM, blaSPM and blaSIM amplicon for isolates identified as MBL strains were 84.56°C, 85.35°C and 86.62°C, respectively. Due to the analytical specificity of the primers, all dilutions with a similar Tm and melt peaks were obtained in the melting curves. Moreover, the analytical sensitivity of NDM primer were able to detected 100CFU/mL, 103CFU/mL and 104CFU/mL of standard DAN by N-1, N-2 and N-3 primers, respectively. Also, according to analytical sensitivity of MBL primers, blaVIM was able detected of 100CFU/mL, blaSPM primer 105CFU/mL and blaSIM primer 102CFU/mL of PASGNDM699 strain. HRM results showed that N-1 primers with 55 bp and blaVIM primers with 124 bp had the highest sensitivity and specificity for P. aeruginosa PASGNDM699 strain identification.
Conclusion: The data from our study indicated that the sensitivity and specificity of the HRM method linked to the primer length and the fluorescent dye. Further, we can identify antibiotic resistance in substrates such as P. aeruginosa PASGNDM699 by software analysis and melting curve analysis.
No association of vitamin D binding protein gene polymorphisms with ulcerative colitis in Chinese patients
Authors: Qiu Fubin , Zhang Lijuan , Wang Jing , Li Rui , Yang Linxue 
Published: November 2019

Abstract
Object Vitamin D (VD) deficiency has been reported in patients with ulcerative colitis (UC), and polymorphism in the gene encoding the vitamin D binding protein (DBP) can affect the characteristics of DBP, thus affecting the level and function of VD in vivo . Previous studies have rarely reported on the potential relationship between DBP polymorphisms and UC. To investigate the associations between genetic variants in DBP genes and UC susceptibility in the Han Chinese population, in order to discern whether any differences exist between this population and those of other countries.Methods In this case-control study, the genotyping of DBP rs4588 and rs7041 polymorphisms was conducted using polymerase chain reaction (PCR)-ligase detection reactions, and the rs4588 and rs7041 genotypes were detected by PCR-restriction fragment length polymorphism.Results In our case-control cohort, no significant difference was observed in the UC risk for either of the two SNPs (rs4588 and rs7401) in the DBP genes ( P > 0.05). No association between UC susceptibility and the DBP gene haplotypes was found either.Conclusions Our results suggest that the two SNPs (rs4588 and rs7401) in the DBP genes may have no correlation with susceptibility to UC in the Chinese Han population. But interestingly, haplotype GC, which contains the rs4588 and rs7041 variants in the DBP gene, may affect the level of oxidative stress in UC patients, especially the level of MDA.
Loss of region-specific glial homeostatic signature in prion diseases
Authors: Makarava Natallia , Chang Jennifer Chen-Yu , Molesworth Kara , Baskakov Ilia V 
Published: November 2019

Abstract
Background Chronic neuroinflammation is recognized as a major neuropathological hallmark in a broad spectrum of neurodegenerative diseases including Alzheimer’s, Parkinson’s, Frontal Temporal Dementia, Amyotrophic Lateral Sclerosis, and prion diseases. Both microglia and astrocytes exhibit region-specific homeostatic transcriptional identities, which under chronic neurodegeneration, transform into reactive phenotypes in a region- and disease-specific manner. Little is known about region-specific identity of glia in prion diseases. The current study was designed to determine whether the region-specific homeostatic signature of glia changes with the progression of prion diseases, and whether these changes occur in a region-dependent or universal manner. Also of interest was whether different prion strains give rise to different reactive phenotypes. Methods To answer these questions, we analyzed gene expression in thalamus, cortex, hypothalamus and hippocampus of mice infected with 22L and ME7 prion strains using Nanostring Neuroinflammation panel at subclinical, early clinical and advanced stages of the disease. Results We found that at the preclinical stage of the disease, region-specific homeostatic identities were preserved. However, with the appearance of clinical signs, region-specific signatures were partially lost and replaced with a neuroinflammation signature. While the same sets of genes were activated by both prion strains, the timing of neuroinflammation and the degree of activation in different brain regions was strain-specific. Changes in astrocyte function scored at the top of activated pathways. Moreover, clustering analysis suggested that the astrocyte function pathway responded to prion infection prior to activated microglia or neuron and neurotransmission pathways. Conclusions The current work established neuroinflammation gene expression signature associated with prion diseases. Our results illustrate that with the disease progression, the region-specific homeostatic transcriptome signatures are replaced by region-independent neuroinflammation signature, which was common for prion strains with different cell tropism. The prion-associated neuroinflammation signature identified in the current study overlapped only partially with the microglia degenerative phenotype and the disease-associated microglia phenotype reported for animal models of other neurodegenerative diseases.
Calbindin-D9k is a novel risk gene for neurodegenerative disease
Authors: Jung Eui-Man , Yoo Yeong-Min , Park Seon Young , Ahn Changhwan , Jeon Bo-Hui , Hong Eui-Ju , Kim Woo-Yang , Jeung Eui-Bae 
Published: November 2019

Abstract
Background: Calcium homeostasis plays a crucial role in neuronal development and disease. Calbindin-D9k (CaBP-9k) acts as calcium modulators and sensors in various tissues. However, the neurobiological functions of CaBP-9k are unknown.
Methods: We used CaBP-9k knockout (KO) mice to investigate the roles of these proteins in neurodegenerative diseases, such as Alzheimer’s and Parkinson’s diseases.
Results: We found that the brains of CaBP-9k KO mice have increased APP/β-amyloid, Tau, and α-synuclein accumulation and endoplasmic reticulum (ER) stress-induced apoptosis. Neurons deficient for these calbindins had abnormal intracellular calcium levels and responses. ER stress inhibitor TUDCA reduced ER stress-induced apoptosis and restored ER stress- and apoptosis-related gene expression to wild-type levels in CaBP-9k KO mice. Furthermore, treatment with TUDCA rescued the abnormal memory and motor behaviors exhibited by older CaBP-9k KO mice.
Conclusion: Our results suggest that a loss of CaBP-9k may contribute to the onset and progression of neurodegenerative diseases.
Photothermal-assisted antibacterial application of GO-Ag against clinical isolated MDR E. coli
Authors: Chen Yuqing , Wu Wei , Xu Zeqiao , Jiang Cheng , Han Shuang , Ruan Jun , Wang Yong 
Published: November 2019

Abstract
Background: Treatment of multidrug-resistant (MDR) bacterial infection is a great challenge in public health. Herein, we provide a solution to this problem with the use of graphene oxide-silver (GO-Ag) nanocomposites as anti-bacterial agent. Methods: Following established protocols, silver nanoparticles were grown on graphene oxide sheets. Then, a series of in-vitro studies were conducted to validate the antibacterial efficiency of the GO-Ag nanocomposites against clinical MDR Escherichia coli (E. coli) strains. Firstly, minimum inhibitory concentrations (MICs) of different antimicrobials were tested against MDR E. Coli strains. Then, bacteria viability assessments were conducted with different nanomaterials in Luria-Bertani (LB) broth. Afterwards, photothermal irradiation was conducted on MDR E. coli with lower GO-Ag concentration. At last, fluorescent imaging and morphology characterization using scanning electron microscope (SEM) were done to find the possible cause of antibacterial effect. Results: GO-Ag nanocomposites showed the highest antibacterial efficiency among tested antimicrobials. Synergetic antibacterial effect was observed in GO-Ag nanocomposites treated group. The remained bacteria viabilities were 4.4% and 4.1% respectively for different bacteria strains with GO-Ag concentration at 14.0 µg mL-1. In addition, GO-Ag nanocomposites have strong absorption in the near-infrared field and can convert the electromagnetic energy to heat. With the use of this photothermal effect, effective sterilization could be achieved using GO-Ag nanocomposites concentration as low as 7.0 µg mL-1. Fluorescent imaging and morphology characterization were used to analyze bacteria living status, which uncovered that bacteria integrity was disrupted after GO-Ag nanocomposites treatment. Conclusions: GO-Ag nanocomposites are proved to be efficient antibacterial agent against multi-drug resistant E. coli. Their strong antibacterial effect arises from inherent antibacterial property and photothermal effect that provides aid for bacteria killing.