bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethnicity-specific transcriptomic variation in immune cells and correlation with disease activity in systemic lupus erythematosus
Authors: Andreoletti Gaia , Lanata Cristina , Paranjpe Ishan , Jain Tia , Nititham Joanne , Taylor Kimberly , Combes Alexis , Maliskova Lenka , Ye Chun , Katz Patricia , Dall'Era Maria , Yazdany Jinoos , Criswell Lindsey , Sirota Marina 
Published: November 2020

Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease in which outcomes vary among different racial groups. We leverage cell-sorted RNA-seq data (CD14 + monocytes, B cells, CD4 + T cells, and NK cells) from 120 SLE patients (63 Asian and 57 White individuals) and apply a four-tier approach to identify SLE subgroups within this multiethnic cohort: unsupervised clustering, differential expression analyses, gene co-expression analyses, and machine learning. K-means clustering on each cell-type resulted in three clusters for CD4 and CD14, and two for B and NK cells. Correlation analysis revealed significant positive associations between the transcriptomic clusters and clinical parameters including disease activity and ethnicity. We then explored differentially expressed genes between Asian and White groups for each cell-type. The shared differentially expressed genes across all cells were involved in SLE or other autoimmune-related pathways. Co-expression analysis identified similarly regulated genes across samples and grouped these genes into modules. Samples were grouped into groups base on their disease activity and ethnicity. Random forest classification of disease activity in the White and Asian cohorts showed the best classification in CD4 + T cells in White. The results from these analyses will help stratify patients based on their gene expression signatures to enable SLE precision medicine.
Effect of Microbial Fermentation on Nutritional and Safety Value of Cassava-Based Food
Authors: Halake Niguse Hotessa 
Published: November 2020

Abstract
Background: Cassava is a potential energy-rich food crops to make different food products in developing countries but limited by a shortage of protein content and the presence of toxic cyanogenic glycosides.Methods: Cassava-teff flour fermented with three pure starter cultures of Saccharomyces cerevisiae, Lactobacillus plantarum and Lactobacillus coryneformis. Two different inoculum levels (0.5 and 1.5 ml) were used. 300 g of cassava-teff flour were fermented with each of single starter cultures at 24 and 48 h. Results: The analysis of pH, crude protein and cyanide content indicates fermentation samples with Lactobacillus plantarum and Lactobacillus coryneformis for 48 h with 1.5 ml inoculums resulted in highest pH reduction. Similarly, highest reduction cyanide was recorded with 1.5 ml inoculums of Lactobacillus coryneformis and Lactobacillus plantarum, while the least cyanide reduction was recorded in fermentation samples of Saccharomyces cerevisiae at 24 h of 1 ml of inoculum level, but this value is higher when compared upon boiling (47.77 mg/kg). The highest levels of crude protein were observed fermentation samples with 1.5 ml inoculum of Saccharomyces cerevisiae for 48 h. Regarding palatability, the panelist preferred that fermentation sample with 1.5 ml inoculums of Lactobacillus plantarum and Lactobacillus coryneformis at 48 h having the best taste with the score of 4.90 ± 0.17 and 4.87 ± 0.23 respectively over the control, while sample fermented with Saccharomyces cerevisiae was preferred in terms of flavor, texture and overall acceptability with score of 4.87 ± 0.23, 4.73 ± 0.11 and 4.67 ± 0.12 respectively over the control. Conclusions: Therefore, microbial fermentation is a promising candidate for improving nutritional and safety value of cassava- based food and suggested as a choice of the processing method, as this method significantly reduced cyanide content, increased protein content and improved sensory properties of injera.
Bacterial Meningitis among Adult Patients at University of Gondar Comprehensive Specialized Referral Hospital: Prevalence and Antimicrobial Susceptibility Patterns
Authors: Tigabu Abiye , Jember Abiyot , Nega Temesgen , Wubishet Getachew , Misganaw Hana , Goshu Tigist , Negash Markos 
Published: November 2020

Abstract
Background: Bacterial meningitis is a bacterial infection that causes inflammation of the membranes that surround the brain and spinal cord. The most frequent causes of bacterial meningitis are N. meningitidis, Streptococcus pneumonia, Listeria monocytogenes, and Homophiles influenza. This study aimed to determine bacterial meningitis and their antibiotic susceptibility patterns among adult patients.Methods: A retrospective cross-sectional study was conducted on 3,683 patients to determine bacterial meningitis and their antibiotic susceptibility patterns from 2011 to 2020. Cerebrospinal fluid samples were collected and inoculated on blood and chocolate agar plates, and then incubated at 37oc for 24 hours. Bacterial identification performed using morphological characters, gram stain, and standardized biochemical tests. Records of 3,683 culture results were collected and reviewed using a checklist from the registration book. Finally, data was entered, cleared, and checked using Epi-info version 7 and exported to SPSS version 20 for analysis. Logistic regression used for statistical association. The results were displayed using tables and figures. P-value < 0.05 at 95% CI was considered as statistically significant.Results: Of the 3,683 patients, the overall prevalence of bacterial meningitis was 1.28% (47/3683). Of them, bacterial meningitis in males was 0.9% (33/3683) whereas, it was 0.38% (14/3683) in females. Bacterial meningitis among inpatients, 1.16% (43/3683) was higher than their outpatient counterparts, 0.12% (4/3683). Ceftriaxone, chloramphenicol, ciprofloxacin, vancomycin, clindamycin, and erythromycin were the most effective antibiotics whereas penicillin, tetracycline, and cotrimoxazole were the least effective antibiotics for isolates. Being male in sex (P = 0.048, AOR = 0.53, CI = 0.283-0.993) was significantly associated with bacterial meningitis.Conclusions: The prevalence of bacterial meningitis among adult patients was 1.28%, which is considerably high. Being male in gender is a risk factor for bacterial meningitis. Therefore, infection preventive measures are required with a particular focus on adult patients. Further research is needed to explore the epidemiology and risk factors of meningitis.
The association between deficiency of nutrient intake on resting metabolic rate (RMR) in overweight and obese women: a cross-sectional study
Authors: Sajjadi Seyedeh Forough , Mirzababaei Atieh , Abdollahi Afsoun , Shiraseb Farideh , Mirzaei Khadijeh - 
Published: November 2020

Abstract
Background: The double burden of malnutrition is an emerging public health concern nowadays which a correlation with Obesity. The aim of this study was to examine the relationship between resting metabolic rate (RMR) and dietary intake of zinc, vitamin C, and riboflavin based on Nutrient Adequacy Ratios (NAR) in overweight and obese women.Methods: We enrolled 293 overweight and obese women in this cross-sectional study. BMI, body fat mass, fat-free mass, insulin level were assessed. RMR was measured using indirect calorimetry. NAR was measured by calculating the ratio of daily individual intakes to the standard recommended amounts.Results: the RMR/FFM showed a significant association with riboflavin (β=1.59; 95% CI: 1.04-23.26, P=0.04) and zinc (β=0.78; 95% CI: 1.04-4.61, P=0.03) in the crude model. Moreover, differences in vitamin C and RMR/FFM was marginal significant (β=0.75; 95% CI: 0.95-4.77, P=0.06). After adjust for confounders the riboflavin association change to marginal significance (β=1.52; 95% CI: 0.91-23.04, P=0.06). After controlling for potential confounders, the associations change between zinc and RMR/FFM (β=0.66; 95% CI: 0.78-4.86, P=0.15) and between RMR/FFM and vitamin C (β=0.48; 95% CI: 0.66-3.96, P=0.28).Conclusion: Our study showed a significant association between dietary intake of zinc, riboflavin, and vitamin C and change in RMR/FFM in overweight and obese women.
Vitamin A5/X, a new food to lipid hormone concept for a nutritional ligand to control RXR-mediated signaling
Authors: Krezel Wojciech , Rivas Aurea , Szklenar Monika , Ciancia Marion , Alvarez Rosana , Lera Angel R. de , Rühl Ralph 
Published: November 2020

Abstract
Background: Vitamin A is a family of derivatives synthesized from carotenoids acquired from the diet and can be converted in animals to bioactive forms essential for life. The vitamin A1 (all-trans-retinol / ATROL) and provitamin A1 (all-trans-β,β-carotene / ATBC) are precursors of all-trans-retinoic acid acting as a ligand for the retinoic acid receptors. The contribution of ATROL and ATBC to formation of 9-cis-13,14-dihydroretinoic acid (9CDHRA), the only endogenous retinoid acting as retinoid X receptor ligand remains unknown. Methods: Novel and well know retinoids and carotenoids were synthesized via organic chemical synthesis. Further, novel and well know retinoids / carotenoids were administered to in vitro oligodendrocyte cell culture and to in vivo oral supplemented mice with following HPLC-MS / UV-Vis based metabolomic evaluation of these administered retinoids / carotenoids. In addition, working memory analyses were performed in a mouse study. Results: In this study, we show that ATROL and ATBC are at best only weak and non-selective precursors of 9CDHRA. Instead, we identify 9-cis-13,14-dihydroretinol (9CDHROL) and 9-cis-13,14-dihydro-β,β-carotene (9CDHBC) as novel direct nutritional precursors of 9CDHRA, which are present endogenously in humans and the human food chain matrix. We also propose that the endogenous carotenoid 9-cis-β,β-carotene (9CBC) can also act as weak, indirect precursor of 9CDHRA via hydrogenation to 9CDHBC and further metabolism to 9CDHROL and/or 9CDHRA.Conclusion: In summary, since classical vitamin A1 is not an efficient 9CDHRA precursor, we conclude that this group of molecules constitutes as a new class of vitamin or a new independent member of the vitamin A family, named “Vitamin A5/X”.
Effects of Shaoyao-Gancao-Fuzi Decoction on the Pharmacokinetics of CYP3A4-Mediated Tofacitinib in Rats
Authors: Lin Li , Wang Yuan , Shao Sennan , Lin Wen , Huang Dan , Pan Ronghua , Xia Yufeng 
Published: November 2020

Abstract
Background: The combination of traditional Chinese medicine and western medicine is commonly accepted in clinics in China. Shaoyao-Gancao-Fuzi decoction (SGFD) has been extensively used to dispel wind, eliminate dampness and treat paralysis. Tofacitinib is approved for the treatment of rheumatoid arthritis. SGFD and tofacitinib could be used together for the treatment of rheumatoid arthritis.Methods: A cocktail approach was employed to assess the effects of SGFD on the activities of CYP450s. After pretreatment for 2 weeks with SGFD, a cocktail solution was given to rats 24 h after the last dose of saline or SGFD. Additionally, the pharmacokinetic profiles of oral administration of tofacitinib in rats, with or without SGFD pre-treatment were investigated.Results: The results showed that SGFD could induce the activity of CYP1A2 and inhibit the activity of CYP3A4. Furthermore, SGFD could significantly affect the pharmacokinetics of tofacitinib. Compared with control group, the AUC0-∞ of tofacitinib was increased from 13669.53 ± 4986.83 to 28706.69 ± 9563.13 ng/mL*h (p < 0.01), and the Cmax was increased from 8359.66 ± 1512.22 to 11332.51 ± 2791.90 ng/mL (p < 0.05).Conclusions: The system exposure of tofacitinib was increased by SGFD. The mechanism might be through inhibiting the activity of CYP3A4 and reducing the metabolism of tofacitinib in rats. The study will provide better guidance for the safe clinical use of SGFD and tofacitinib.
Differentiating Curculigo Orchioides Rhizoma and Curculigo glabrescens Rhizoma by a Unique New Compound
Authors: Liu Yu-shi , Guo Yi-ping , Liu Juan-ru , Bao Xiao-hong , Zhou Juan , Pan Jia , Liu Fei , Liu Juan , Wu Zhong , Guo Li 
Published: November 2020

Abstract
Background: Market research found that Curculigo glabrescens Rhizoma (CGR) is the major counterfeit of the Curculigo orchioides Rhizoma (COR). C. orchioides Gaertn and C. glabrescens (Ridl.) Merr. belong to the same family and genus, with close plant relationships and high genetic similarity, and rhizomes of the herbs part have less distinguished characteristics, which make the identification difficult.Methods: In order to distinguish COR from CGR more accurately and conveniently, HPLC method was used to establish a characteristic chromatogram of the two herbs, and a unique component in CGR was discovered for first time. Based on that, the characteristic component was systematically separated and purified.Results: The unique component was a new neolignans and named glabrescenin, which could specifically distinguish COR from CGR. The HPLC method we used could establish a characteristic chromatography of CGR.Conclusion: This study was conducive to the quality control of Curculigo, and could promote the correct application of genuine COR in clinical practice.
Ecological Perturbations Impact Species-Specific Gene Expression of the Oral Microbiota
Authors: Belstrøm Daniel , Constancias Florentin , Drautz-Moses Daniela I , Schuster Stephan C , Veleba Mark , Mahé Frédéric , Givskov Michael 
Published: November 2020

Abstract
Background: The purpose of the present investigation was to use the oral cavity as an in-vivo model to study the impact of internal and external perturbations on bacterial biofilm communities. We tested the hypotheses that bacterial gene expression of the healthy microbiota reflects habituation to site-specific ecological perturbations, and that the perturbation effect of chronic inflammation, i.e. periodontitis, impacts bacterial gene expression not only locally, but also at other sites of the oral cavity. Oral microbial samples were collected from three oral sites – plaque, tongue and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterization of taxonomic composition and to determine species specific bacterial activity as expressed by the ratio of messenger RNA to the corresponding genomic DNA.Results: Here we show the impact of two perturbations – oral site and periodontitis - on bacterial gene expression of the oral microbiota. The oral site was the main determinant of taxonomic composition as well as bacterial gene expression. However, bacterial activity at the three oral sites (plaque, tongue, and saliva) was significantly impacted by periodontitis, with a reduction of the carbohydrate metabolism.Conclusions: Data from the present study characterize the impact of two perturbations – oral site and periodontitis - on bacterial gene expression of the oral microbiota. The oral site was the main determinant of taxonomic composition as well as bacterial gene expression. However, presence of periodontitis had impact on bacterial activity of both plaque but also on tongue and the salivary microbiota. Collectively, data suggest that periodontitis associates with impaired carbohydrate metabolism of the oral microbiota. Future longitudinal and interventional studies are warranted to evaluate the potential pathogenic role of impaired bacterial carbohydrate metabolism not only in periodontitis, but also in other diseases with low grade inflammation, such as type 2 diabetes mellitus.
Co-transplantation of Hypoxia Pretreated Human Adipose Derived Mesenchymal Stem Cells and Cord Blood Mononuclear Cells to Treat Rats with Acute Myocardial Infarction
Authors: Xiang Hang , Xiang Tianyuan , Zhang Hongxia , Xu Ann , Horwedel Matthew John , Zeng Qiang , Li Yang 
Published: November 2020

Abstract
BackgroundHuman adipose derived mesenchymal stem cells (ASCs) are ideal candidates for the treatment of acute myocardial infarction (AMI), due to their favorable availability and regenerative potential. However, in vivo studies showed that ASCs are not resilient at the infarcted area, for a shortage of blood and oxygen supply. Hypoxic pretreatment was proven to be an effective way to enhance cell survival in ischemic atmosphere. Moreover, co-transplantation of stem cells was another promising strategy to improve cardiac function after transplantation. So, we hypothesized that hypoxic pretreated ASCs combined with proangiogenic cord blood mononuclear cells (CBMNCs) would promote treatment efficacy after co-transplantation.MethodsASCs extracted from male volunteer were preconditioned in hypoxic condition (HP-ASC) for 24h, and total RNA were extracted after that. Gene expressions were compared between HP-ASC and ASC. Then, we transplanted stem cells to female Wistar rats which divided into different groups: (1) HP-ASCs group (n=10, 1x106ASCs); (2) HP-ASCs + CBMNCs group (n=10, 0.5×106 ASCs+0.5×106 CBMNCs); (3) CBMNCs group (n=10, 1×106 ASCs); (4) Control group (n=10, 40μL PBS); (5) Sham group (n=10). Echocardiogram was performed before (0d) and after (30d) after cell transplantation. Hearts were harvested at 30d to analyze the infarct size, myocardium apoptosis, stem cells viability and angiogenesis. ResultsIn vitro study showed that HP-ASCs had a wide range of paracrine function, with the incretion growth factors and their receptors, which would support the cell survivals. In addition, HP-ASCs also gained potentials in hypoxic adaptation (increased expression of HO-1 and SDF-1), as well as homing and immigrating abilities (CXCR4, ICAM-1 and ICAM-2). In vivo studies showed that, 30 days after transplantation in AMI rats, the HP-ASCs group had a better improvement in cardiac function; reduction of the infarct size; and decrease of ASCs death than the other groups (HP-ASCs > HP-ASCs + CBMNCs ≧ CBMNCs > PBS) (p<0.05). However, the combined group of HP-ASCs and CBMNCs had more significant angiogenesis than the other groups (HP-ASCs + CBMNCs > CBMNCs > HP-ASCs > PBS) (p <0.05).ConclusionsHP-ASCs alone had a greater potential in improving cardiac function in AMI rats. However, the combination of HP-ASCs and CBMNCs had a better result in angiogenesis.
Data-driven versus theory-driven methods to understand health service implementation problems: A case study of childhood vaccination barriers
Authors: Bonner Carissa , Tuckerman Jane , Kaufman Jessica , Costa Daniel , Durrheim David N , Trevena Lyndal , Thomas Susan , Danchin Margie 
Published: November 2020

Abstract
BackgroundEffective implementation requires identifying and addressing behavioural barriers to uptake. This study aimed to compare data-driven and theory-driven approaches to understanding implementation issues. We used childhood vaccination coverage as a case study, with international relevance and wide-ranging barriers contributing to low vaccine uptake.MethodsThe study utilised the Behaviour Change Wheel framework, which incorporates both individual and system level barriers to behaviour, and is based on several levels of theory: the three components of the COM-B model (capability, opportunity and motivation) can be mapped to the 14 domains of the Theoretical Domains Framework (TDF), which is based on 84 underlying constructs. We first conducted a review of systematic reviews of parent-level barriers to childhood vaccination. Subsequently we: 1) inductively coded these barriers into a data-driven framework, using thematic analysis; and 2) conducted theory-driven mapping of these barriers to TDF domains and constructs. Coding and mapping were undertaken by two authors independently, and discrepancies were resolved through discussion. The data-driven and theory-driven results were compared.ResultsThe data-driven process coded 583 descriptions of barriers identified from the literature into a framework of 74 barriers in 6 categories. The initial definitions used to compare data-driven barriers with theory-driven domains/constructs led to 89% agreement at the domain level. Resolving discrepancies required further definitions at the construct level. Of the 14 TDF domains, 10 were clearly identified in the data from the barrier reviews. Some domains were not specific enough to differentiate between types of barriers (e.g. Environmental Context and Resources), while other domains were not represented in the review data (e.g. Behavioural Regulation).ConclusionsUsing both data- and theory-driven approaches can help achieve a more comprehensive understanding of barriers to health service implementation. The data-driven categories represented the review data in a clearer way than the theoretical domains, with better differentiation; but the missing domains were useful as a way to identify additional issues to investigate further. Both approaches resulted in a comprehensive list of barriers to vaccination that would not have been achieved using either approach alone. This will inform a diagnostic tool to measure the causes of under-vaccination.
Invasive Mechanical Ventilation May Be an Important Factor of Mortality in Severe/Critical COVID-19 Pneumonia: A Retrospective Cohort Study
Authors: Wei Jing , Shi Lei , Cheng Zhi , Jin Xinye , Zhao Wei , Li Ruyou , Zheng You , Peng Zhihang , Niu Changming , Huang Tingrong , Ji Ningfei , Huang Mao , Chen Xiaolin , Yan Jiaxin , Wu Mingjing , Deng Kaili , Shu Lei , Wang Xueli , Cao Yang , Feng Ganzhu 
Published: November 2020

Abstract
Background: Many of severe COVID-19 patients are admitted to the hospital or even to the Intensive Care Unit(ICU). The present study was aimed to investigated the risk factors in death from COVID-19.Methods: In this retrospective study, all inpatients confirmed severe or critical COVID-19 from two tertiary hospital in Huangshi were included, who had been discharged or died by March19,2020. Demographic,clinical,treatment,laboratory data and information were extracted from electronic medical records and compared between survivors group and non-survivors group. The univariable and multivariable logistic regression analysis was used to analyze the risk factors associated with in-hospital death.Results: 81 patients were included in this study, of whom 55 were discharged and 26 died in hospital. In all patients, 36(44.4%) patients had comorbidity, including hypertension(27[33.3%]), diabetes(11[13.6%]) and coronary heart disease (CHD)(11[13.6%]), and 16(19.8%) patients accompanied with more than 2 kinds of underlying diseases. The proportion of CHD in non-survivors group was significantly higher than that in survivors group(26.9% vs 7.3%, P=0.032), but there were no differences in hypertension, diabetes and COPD between the non-survivors group and the survivors group. Multivariable logistic regression analysis showed increasing odds of in-hospital death associated with aspartate aminotransferase(AST) and invasive mechanical ventilation (IMV) (P<0.001)(P=0.017）.Conclusions: Invasive Mechanical Ventilation may contribute to mortality of severe/critical COVID-19 pneumonia, and with higher AST at admission was one of the indicators of poor prognosis.Trial registration: Chinese Clinical Trial Registration; ChiCTR2000031494; Registered 02 April 2020; http://www.medresman.org