bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gut Microbiome-Mediated Changes in Bone Metabolism Upon Infrared Light Exposure in Rats
Authors: Lu Yueying , Yang Jianlou , Fu Yuming , Liu Hong 
Published: June 2020

Abstract
Background Adequate sunlight exposure helps reduce bone loss and is important to bone health. Currently, about 90% of the world population spends a major portion of daily life under artificial lighting. Unlike sunlight, LED white light, the main source of artificial lighting, has no infrared radiation, which is known to be beneficial to human health. In artificial lighting environments, infrared supplementation may be used to simulate the effects of sunlight on bone metabolism. Results Here, we supplemented white LED exposure with infrared light in normal and ovariectomized rats for three consecutive months and examined bone turnover, bone mass, and bone density. We also analyzed the structure and function of gut microbiota in the rats. Infrared supplementation significantly reduced the abundance of Saccharibacteria and increased the abundance of Clostridiaceae 1 and Erysipelotrichaceae bacteria. Our results indicate that changes in the gut microbiome correlate well with bone mass and bone metabolism.Conclusions Our work demonstrates that infrared supplementation can have a positive effect on rat bone metabolism by affecting gut microbiota. Our findings will be important considerations in the future design of healthy lighting environments that prevent or possibly ameliorate osteoporosis.
The Association Between Obesity and Weight Loss after Bariatric Surgery on the Vaginal Microbiota
Authors: Raglan Olivia , MacIntyre David A. , Mitra Anita , Lee Yun S. , Smith Ann , Assi Nada , Nautiyal Jaya , Purkayastha Sanjay , Gunter Marc J , Gabra Hani , Marchesi Julian R. , Bennett Phillip R. , Kyrgiou Maria 
Published: June 2020

Abstract
Background: Obesity and vaginal microbiome (VMB) dysbiosis are each risk factors for adverse reproductive and oncological health outcomes in women. Here we investigated the relationship between obesity, vaginal bacterial composition, local inflammation and bariatric surgery.Methods: Vaginal bacterial composition assessed by high-throughput sequencing of bacterial 16S rRNA genes and local cytokine levels measured using a multiplexed Magnetic Luminex Screening Assay were compared between 67 obese and 42 non-obese women. We further assessed temporal changes in the microbiota and cytokines in a subset of 27 women who underwent bariatric surgery. Results: The bacterial component of the vaginal microbiota in obese women was characterised by a lower prevalence of a Lactobacillus-dominant VMB and higher prevalence of a high diversity (Lactobacillus spp., and Gardnerella- spp. depleted) VMB, compared with non-obese subjects (p<0.001). Obese women had higher relative abundance of Dialister species (p<0.001), Anaerococcus vaginalis (p=0.021) and Prevotella timonensis (p=0.020) and decreased relative abundance of Lactobacillus crispatus (p=0.014). Local vaginal IL-1β, IL-4, IL-6, IL-8, IFNγ, MIP-1α, and TNFα levels were all higher among obese women, however only IL-1β and IL-8 correlated with VMB species diversity. In a subset of obese women undergoing bariatric surgery, there were no significant overall differences in VMB following surgery, however 75% of these women remained obese at six months. Prior to surgery there was no relationship between body mass index (BMI) and VMB structure, however post-surgery women with a Lactobacillus-dominant VMB had a significantly lower BMI than those with a high diversity VMB.Conclusions: Obese women have a significantly different vaginal microbiota composition with increased levels of local inflammation compared to non-obese women. Bariatric surgery does not change the VMB, however, those with the greatest weight loss six-months post-surgery are most likely to have a Lactobacillus-dominant VMB.
Development and Validation of a New Scoring System for the Early Diagnosis of Tuberculous Meningitis in Adults
Authors: LU Yuying , ZHANG Chen , HU Zhongyang , YAO Guang , ZHANG Qinghua , ZHU Haixia , YAO Huan , WANG Zhen , SONG Zhi , CHEN Ru , Liu Ding 
Published: June 2020

Abstract
Background
The absence of a sufficiently accurate and efficient diagnosis of tuberculous meningitis (TBM) is major obstacle to delayed treatment, and its non-specific clinical manifestations easily mimic the central nervous system infections caused by other causes, including virus, bacteria, and cryptococcus. This study aims to develop and validate a diagnostic score system for TBM in HIV-uninfected adults by simultaneously comparing TBM with viral meningitis (VM), bacterial meningitis (BM), and cryptococcal meningitis (CM).
Methods
Twenty-nine factors (including clinical, laboratory and imaging) were assessed among 382 patients who satisfied inclusion criteria for TBM (n = 113), VM (n = 143), BM (n = 65) and CM (n = 61). Independent predictors for the diagnosis of TBM were obtained by logistic regression to establish a diagnostic scoring system. The performance of this scoring system was evaluated using a prospective validation cohort.
Results
Nine factors independently associated with the diagnosis of TBM: symptom duration (10–30 days), systemic symptoms, evidence of extra-central nervous system tuberculosis, cerebrospinal fluid (CSF) leukocyte count (100-500∗106 /mL), CSF neutrophil proportion (20%-75%), CSF protein (> 1 g/L), low serum sodium (< 137 mmol/L), meningeal enhancement, and brain parenchymal nodules (tuberculomas). The CSF neutrophil proportion was assigned a score of 2 and all other factors were assigned a score of 1. A score of at least five was suggestive of TBM with a sensitivity of 85.8% and a specificity of 87.7%, and the area under the receiver operating characteristic curve (AUC) was 0.927. When applied prospectively to an additional 72 patients (21 with TBM, 27 with VM, 14 with BM, and 10 with CM), the sensitivity, specificity, accuracy, and AUC values of this scoring model were 90.5%, 86.3%, 87.5%, and 0.944, respectively.
Conclusions
For differential diagnosis between TBM and other causes of meningitis (VM,CM and BM), we developed and validated a new weighted scoring system. The application of this scoring system can help diagnose TBM more efficiently in the early stage.
Diagnostic value of four coagulation function indicators for distinguishing between tuberculous pleural effusions and malignant pleural effusions due to lung adenocarcinoma
Authors: Li Rui cheng , Gao Zhaowei , Lin Fang , Wang Xi , Gu Bingquan , Fan Yanni , Lu Yanzhi , Ding Congcong , Ma Haihang , Dong Ke , Zhang Huizhong 
Published: June 2020

Abstract
Background: Coagulation function indicators are often used to evaluate patients’ coagulation function.They are rarely used in disease diagnosis;their use is limited to somecoagulopathies. We described the pattern of coagulation function indicators in patients with pleural effusions and determined the diagnostic value of different abnormal patterns of these indicators for distinguishing tuberculous pleural effusions (TPEs) from malignant pleural effusions associated with lung adenocarcinoma (AD-MPEs).Methods: Patients with AD-MPEs or TPEs participated in this retrospective study.Coagulation functionindicators, including activated partial thromboplastin time, prothrombin time (PT), fibrinogen (FIB), thrombin time, fibrinogen degradation products (FDP), and D-dimer(D-D), were measured; their levels and abnormal patterns were analyzed separately and in combination,to determine the diagnostic performance of individual and combined values and the optimal diagnostic model.Results: One hundred patients with AD-MPEs and 84 patients with TPEs participated.PT, FIB, FDP, and D-Dlevels in patients with TPE were significantly higher than those in patients with AD-MPE (all P<0.01).Receiver operating characteristiccurves revealed that PT, FIB, FDP, and D-Dvalues, particularly FDP and D-D, could distinguish betweenAD-MPE and TPE. The diagnostic performance was better for the combination of the four indicators than for any single indicator (Youden’s index: 0.513; area under the curve: 0.810).The proportion of patients with abnormal patterns of all four indicators was significantly higher in those with TPE than in those with AD-MPE (P<0.001).Conclusions: Thecombined values of PT, FIB, FDP, and D-Dhave diagnostic value for distinguishing TPE from AD-MPE.
What mechanisms drive uptake of family planning when integrated with childhood immunisation in Ethiopia? A realist evaluation
Authors: Krishnaratne Shari , Hamon Jessie K. , Hoyt Jenna , Chantler Tracey , Landegger Justine , Spilotros Nathaly , Demissie Shiferaw Dechasa , Mohammed Siraj , Webster Jayne 
Published: June 2020

Abstract
Background:Maternal and child health are key priorities among the Sustainable Development Goals , which include a particular focus on reducing morbidity and mortality among women of reproductive age, newborns, and children under the age of five. Two key components of maternal and child health are family planning (FP) and immunisation. Providing these services through an integrated delivery system could increase the uptake of vaccines and modern contraceptive methods (MCMs) particularly during the post-partum period. Methods:A realist evaluation was conducted in two woredas in Ethiopia to determine the key mechanisms and their triggers that drive successful implementation and service uptake of an intervention of integrated delivery of immunisations and FP. This evaluation included the: 1) development of an initial programme theory; 2) review of relevant published theories; 3) analysis of project monitoring data; 4) analysis of qualitative data from 23 semi-structured interviews to determine key mechanisms and drivers; and 5) development of a revised programme theory comprised of context-mechanism-actor-outcome (CAMO) and context-mechanism-intervention-actor-outcome (CIAMO) configurations based on empirical findings. Results:The proportion of women who brought their children for immunisation and received MCMs was 63.0% (4,260/6,764) overall [74.3% (2,944/3,961) in Assosa woreda and 46.9% (1,316/2,803) in Bambasi woreda]. Key contextual factors identified were: a strong belief in values among religious leaders and community members that challenged FP; a lack of support for FP from male partners based on religious values; and the use of trained Health Extension Workers (HEWs) to deliver FP services. Within these contexts, intervention components that focused on the alignment of religious texts with FP, the promotion of FP by religious leaders, and the training of HEWs and health care workers on FP counselling and service delivery, influenced the implementation of the intervention and triggered several mechanisms of acceptability, access, and adoption of innovations. Conclusions:Linking context and intervention components to the mechanisms they triggered helped explain the intervention outcomes, and more broadly how and for who the intervention worked. This enabled the development of a programme theory that could be used to inform the integrated delivery of FP services in similar contexts.
L2MXception: An Improved Xception Network for Classification of Peach diseases
Authors: Yao Na , Ni Fuchuan , Wang Ziyan , Luo Jun , Sung Wing-Kin , Luo Chaoxi , Li Guoliang 
Published: June 2020

Abstract
Background: Peach diseases can cause severe yield reduction and decreased quality for peach production. Rapid and accurate detection and identification of peach diseases is of great importance. Deep learning has been applied to detect peach diseases using imaging data. However,peach disease image data is difficult to collect and samples are imbalance. Results: This paper proposed an improved Xception network named as L2MXception which ensembles regularization term of L2-norm and mean. With the peach disease image dataset collected, results on six mainstream deep learning models were compared in details and an improved loss function was integrated with regularization term L2-norm and mean (L2M Loss). Experiments showed that the Xception model with L2M Loss outperformed the current best method for peach disease prediction. Compared to the original Xception model, the validation accuracy of L2MXception was up to 93.85%, increased by 28.48%. Conclusions: The proposed L2MXception network may have great potential in early identification of peach diseases.
Systematic modification of N-glycosylation sites in cellobiohydrolase Cel7A from Trichoderma reesei reveals higher activity and binding affinity on crystalline cellulose
Authors: Kołaczkowski Bartłomiej Maciej , Schaller Kay S. , Sørensen Trine Holst , Peters Günther H. J. , Jensen Kenneth , Krogh Kristian B. R. M. , Westh Peter 
Published: June 2020

Abstract
Background: Cellobiohydrolase from glycoside hydrolase family 7 is a major component of commercial enzymatic mixtures for lignocellulosic biomass degradation. For many years, Trichoderma reesei Cel7A (TrCel7A) has served as a model to understand structure-function relationships of processive cellobiohydrolases. The architecture of TrCel7A includes an N-glycosylated catalytic domain, which is connected to a carbohydrate-binding module through a flexible, O-glycosylated linker. Depending on the fungal expression host, glycosylation can vary not only in glycoforms, but also in site occupancy, leading to a complex pattern of glycans, which can affect the enzyme’s stability and kinetics. Results: Two expression hosts, Aspergillus oryzae and Trichoderma reesei, were utilized to successfully express wild-types TrCel7A (WTAo and WTTr) and the triple N-glycosylation site deficient mutants TrCel7A N45Q, N270Q, N384Q (ΔN-glycAo and ΔN-glycTr). Also, we expressed single N-glycosylation site deficient mutants TrCel7A (N45QAo, N270QAo, N384Ao). The TrCel7A enzymes were studied by steady-state kinetics under both substrate- and enzyme-saturating conditions using different cellulosic substrates. The Michaelis constant (KM) was consistently found to be lowered for the variants with reduced N-glycosylation content, and for the triple deficient mutants, it was less than half of the WTs value on some substrates. The ability of the enzyme to combine productively with sites on the cellulose surface followed a similar pattern on all tested substrates. Thus, site density (number of sites per gram cellulose) was 30-60 % higher for the single deficient variants compared to the WT, and about two-fold larger for the triple deficient enzyme. Molecular dynamic simulation of the N-glycan mutants TrCel7A reveled higher number of contacts between CD and cellulose crystal upon removal of glycans at position N45 and N384. Conclusions: We propose that the marked kinetic changes did not rely on alterations in the overall fold of Cel7A but reflected modifications of substrate accessibility. The presence of N-glycans with extended structures increased KM and decreased attack site density of TrCel7A likely due to steric hindrance effect and distance between the enzyme and the cellulose surface, preventing the enzyme from achieving optimal conformation. This knowledge could be applied to modify enzyme glycosylation to engineer enzyme with higher activity on the insoluble substrates.
Surgical Choice for Patients With Stage I Non-small-cell Lung Cancer ≤ 2 Cm: An Analysis From Surveillance, Epidemiology, and End Results Database
Authors: Zhao Weigang , Chen Tangbing , Yang Yi 
Published: June 2020

Abstract
Background: No consensus was reached on the surgical procedure for patients with stage I non-small-cell lung cancer(NSCLC) ≤ 2 cm. The aim of this study isto investigate the appropriate surgical procedure forstage I NSCLC≤ 2 cm.Methods: Patients with stage I NSCLC ≤ 2 cm received wedge resection, segmentectomy, lobectomy between January 2004 andDecember 2015 were identified using the Surveillance, Epidemiology, and End Results(SEER) database. Data were stratified by age, gender, race, side, location, grade,histology, extent of lymphadenectomy. Overall survival (OS) and lung cancer-specific survival (LCSS) were compared among patients received wedge resection, segmentectomy, lobectomy. Univariate analysis and multivariable Cox regression were performed to identify the prognostic factors ofOS and LCSS. Results:A total of 16511 patients with stage I NSCLC ≤ 2 cm were included in this study, of whom 2945 patients were classified as stage I NSCLC ≤ 1cm.Lobectomy had better OS and LCSS when compared with wedge resection in patients with NSCLC ≤ 2 cm. Only OS favored lobectomy compared with segmentectomy in stage I NSCLC＞1 to 2 cm. Multivariable analysis showed thatsegmentectomy had similar OS and LCSScompared with lobectomy in patients with stage I NSCLC ≤ 2 cm. Lymph node dissection (LND) was associated with better OS in patients with NSCLC≤ 2 cm and better LCSS in patients with stage I NSCLC＞1 to 2 cm.Conclusions:Segmentectomy showed comparable survival compared with lobectomy in patients with stage I NSCLC ≤ 2 cm.LND can provide more accurate pathological stage, may affect survival, and should be recommended for above patients.
CD52 is a prognostic biomarker and correlated with immune features in breast cancer
Authors: Wang Jianxin , Liu Yang , Yang Zhuowen , Sui Yang , Tian Jie , Tao Lin , Yao Jianting , Wu Changjun 
Published: June 2020

Abstract
Background: Breast cancer (BRCA) is the most commonly diagnosed cancer of women, which is aggressive cancer and has a mortality rate. CD52 and its monoclonal antibody (Alemtuzumab) play a critical role in inflammatory diseases, but the relationship between CD52 and BRCA is not clear.Methods: We first used the random forest algorithm to find the most critical genes related to the prognosis of BRCA patients. Then, according to the analysis of RNA sequence and clinical data of the TCGA dataset, we explored the relationship between CD52 with immune response-related pathways and immune metagenes. The pan-cancer analysis shows the importance of CD52 in a variety of tumorsResults:CD52 was related to the prognosis of BRCA patients (p < 0.001). Subsequent analysis based on RNA-seq and clinical data from the TCGA dataset revealed that CD52 is positively correlated with immune response-related pathways and immune metagenes. TIMER analysis showed that CD52 expression was positively correlated with immune infiltrating levels of B, CD4+ T, and CD8+ T cells, macrophages, neutrophils, and dendritic cells (DCs) in BRCA (r = 0.466, r = 0.645, r = 0.483, r = 0.149, r= 0.542,r = 0.665, respectively; p < 0.001). CpG sites (cg16068833, cg19743891, cg19743891, cg16664472, cg19677267, cg22517705, and cg27430637) were negatively correlated with CD52 expression (r = -0.662, r = -0.629, r =- 0.598, r = -0.519, r= -0.492, r = -0.445, respectively; p < 0.001). Furthermore, the expression of CD52 was significantly correlated with the following pathological stages (T stage, N stage, and survival state; p=0.024, p=0.047, and p=0.007, respectively). The results of the pan-cancers study suggest that CD52 may play an important role in the occurrence, development, and prognosis of multiple tumors.Conclusions: These findings suggested that CD52 is a promising immunotherapy target and prognostic prediction value for BRCA.
Kidney Function Change after Transcatheter Aortic Valve Replacement in Patients with Diabetes and/or Hypertension
Authors: Fan Jiaqi , Yu Changjie , Ren Kaida , Lin Wanbing , Ng Stella , Chen Zexin , Lin Xinping , Wang Lihan , Zhu Qifeng , He Yuxin , Jiang Jubo , Liu Xianbao , Wang Jian’an 
Published: June 2020

Abstract
Background
The kidney function change after Transcatheter Aortic Valve Replacement (TAVR) in diabetes and/or hypertension patients is currently unknown.
Methods
A total of 242 severe Aortic Stenosis patients with diabetes mellitus and/or hypertension who underwent TAVR were analyzed. Patients were categorized into 3 groups based on the percent change [(discharge eGFR – baseline eGFR) x 100/baseline eGFR] in eGFR: improved ≥ 10%, no change, and declined ≥ 10%.
Results
Of these patients, 93 (38.4%) had an improvement in eGFR ≥ 10%, 117 (48.3%) had no changes, and 32 (13.2%) had a decline in eGFR of more than 10%. Patients with unchanged kidney function may be with lower STS scores (5.09 [3.58–8.34] % vs. 7.04 [4.52–9.91] % vs. 7.41 [3.52–10.97] %, p = 0.003), and lower perivascular disease (14.5% vs. 26.9% vs. 40.6%, p = 0.003) when compared with improved and declined kidney function patients, respectively. Patients with improved kidney function had lower eGFR (45.0 [33.9–60.3] mL/min/1.73 m2 vs. 57.4 [43.4–70.7] mL/min/1.73 m2 vs. 56.6 [44.2–76.8] mL/min/1.73 m2, p = 0.000), and lower LVEF (55.1 [40.9–62.0] % vs. 60.4 [53.4–66.1] % vs. 59.9 [52.9–67.8] %, p = 0.002) than the unchanged or declined group, respectively. Moreover, patients with worsening kidney function had higher rate of in-hospital (12.5% vs. 1.7% vs. 0%, p = 0.002) and 30-day (15.6% vs. 1.7% vs. 0%, p = 0.000) mortality. Independent predictors of eGFR changes were STS scores, LVEF, baseline eGFR, and unplanned cardiopulmonary bypass.
Conclusions
Nearly 40% of diabetic and/or hypertensive patients experience an intermediate improvement after TAVR. Patients with declining renal function suffer more terrible outcomes in mortality.
Frequency Distribution of IL-17A G197A (rs2275913) and IL-17F A7488G (rs763780) Polymorphisms Among Healthy Sudanese Population
Authors: Mohamed Nouh Saad , Siddig Emmanuel E. , Ahmed Abdallah E. , Albsheer Musab MA. , Abdelbagi Hanadi , Ali Eman T. , Alsubki Anadel A. , Abdalaziz Sabah A. , Mustafa Madinna , Muneer Mohamed S. , Osman Hussam A. , Osman Maha M. , Ali Mohamed S. , Edris Ali MM. , Ahmed Ayman , Omer Rihab A. 
Published: June 2020

Abstract
Objectives IL-17A G197A and IL-17F A7488G polymorphisms has been identified to be associated with the susceptibility to many diseases. This study aimed to investigate the frequency distribution of IL-17A G197A and IL-17F A7488G polymorphisms among healthy Sudanese population. A descriptive cross-sectional hospital-based molecular study conducted in different sites throughout Sudan. Two ml blood samples were collected from 717 healthy participants. Demographic data and the medical history of the participants were collected.Results Of the 717 participants, 355 (49.5%) were males and 362 (50.5%) were females, their mean age was 30.2 ± 17.2 and 32.2 ± 16.5, respectively. For IL-17A, the most frequent genotype detected among males and females was IL-17A heterozygote allele (AG); 215 (60.6%) and 194 (53.6%), respectively. Whereas, for IL-17F, the most frequent allele among males and females was the homozygote allele (AA); 298 (83.9%) for males and 322 (89.0%) for females. HWE for genotype distributions of IL-17A was showing statistical insignificance for IL-17A among males and females, P value 0.614. While HWE for IL-17F reached the equilibrium level, P value 0.048. The most frequent age group was those aged between 21 to 40 years; 281 (39.2%). Arab constituted the major ethnicity of the study participants; 418 (58.3%), P value 0.034.