bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Transfer Agents in Plant Pathogenic Bacteria: Comparative Mobilomics, Genomic Survey and Recombinogenic Impacts
Authors: Jibrin Mustafa O , Minsavage Gerald V. , Goss Erica M. , Roberts Pamela D. , Jones Jeffrey B 
Published: August 2019

Abstract
Background Gene transfer agents (GTAs) are phage-like mediators of gene transfer in bacterial species. Typically, strains of a bacteria species which have GTA shows more recombination than strains without GTAs. GTA-mediated gene transfer activity has been shown for few bacteria, with Rhodobacter capsulatus being the prototypical GTA. GTA have not been previously studied in plant pathogenic bacteria. A recent study inferring recombination in strains of the bacterial spot xanthomonads identified a Nigerian lineage which showed unusual recombination background. We initially set out to understand genomic drivers of recombination in this genome by focusing on mobile genetic elements. Results We identified a unique cluster which was present in the Nigerian strain but absent in other sequenced strains of bacterial spot xanthomonads. The protein sequence of a gene within this cluster contained the GTA_TIM domain that is present in bacteria with GTA. We identified GTA clusters in other Xanthomonas species as well as species of Agrobacterium and Pantoea. Recombination analyses showed that generally, strains of Xanthomonas with GTA have more inferred recombination events than strains without GTA, which could lead to genome divergence.Conclusion This study identified GTA clusters in species of the plant pathogen genera Xanthomonas, Agrobacterium and Pantoea which we have named XpGTA, AgGTA and PaGTA respectively. Our recombination analyses suggest that Xanthomonas strains with GTA generally have more inferred recombination events than strains without GTA. The study is important in understanding the drivers of evolution of bacterial plant pathogens.
Evaluation of drug-specific multigene markers to predict aromatase inhibitor efficacy in advanced breast cancer: a cohort study from Danish Breast Cancer Cooperative Group
Authors: Buhl Ida Kappel , Christensen Troels Dreier , Buhl Anna Sofie Kappel , Christensen Ib Jarle , Balslev Eva , Knop Ann Søegaard , Ejlertsen Bent , Kümler Iben , Danø Hella , Luczak Adam Andrzej , Langkjer Sven Tyge , Linnet Søren , Jakobsen Erik Hugger , Bogovic Jurij , Glavicic Vesna , Buhl Ulla Hald , Knudsen Steen , Jensen Peter Buhl , Nielsen Dorte 
Published: August 2019

Abstract
Background
Even with positive oestrogen receptor (ER+) status some advanced breast cancer (ABC) patients fail to benefit from endocrine therapy (ET). A method that previously predicted other drugs in various cancers was evaluated. Here multigene markers based on aromatase inhibitor (AI) effect in vitro were used for prediction of AI benefit in ER+ ABC patients. Simultaneously effects of long-term ET on predictive efficacy was evaluated.
Methods
The Drug Response Predictors (DRPs) are based on correlations between baseline gene expression and growth inhibition patterns of exemestane, anastrozole and letrozole, respectively, in the National Cancer Institute 60 cell lines. The genes were controlled for expression in 3,500 tumours.
In a Danish Breast Cancer Cooperative Group cohort of 695 ABC patients with complete gene expression and time-to-progression (TTP) data, 414 received an AI as monotherapy. Hereof, 57 received anastrozole, 166 received exemestane, and 327 received letrozole.
mRNA was isolated from archival formalin-fixed paraffin embedded tumour tissue and run on microarray and 60% of the tumours were from time of primary diagnosis. Medical records of the patients were assessed for TTP for all treatments given for ABC.
Results
The DRPs were tested in subsets 1) with no adjuvant ET and 2) with adjuvant ET. In 1) the anastrozole DRP predicted benefit of anastrozole (hazard ratio (HR) was 0.21 upper 95%-confidence interval limit (CI) 0.76, p=0.023) but not in 2). Dichotomised by a DRP of 50, the anastrozole DRP did predict benefit (HR=0.16, upper 95%-CI 0.75, p=0.026). Only in 1) the exemestane DRP predicted benefit of exemestane (HR=0.57, upper 95%-CI 1.00, p=0.0497). The letrozole DRP had no predictive value. Additionally, we tested each DRPs ability to predict other AIs. Only the anastrozole DRP predicted benefit of overall AI treatment, in 1) with an HR of 0.76 (upper 95%-CI 0.99, p=0.044) and in 2) with an HR of 0.71 (upper 95%-CI 0.92, p=0.015). The anastrozole DRP did though not predict benefit of letrozole. All tests are one-sided, alpha=5%.
Conclusions
Among the DRPs for AIs, the anastrozole DRP was strongest with clinically relevant prediction of TTP in AI treated ER+ ABC patients.
Trial registration: ClinicalTrials.gov NCT01861496.
Stomatal and non-stomatal limitations to photosynthesis of Populus euphratica Oliv. leaves in an extremely arid area of northwestern China
Authors: Gao Guanlong , Feng Qi , Liu Xiande 
Published: August 2019

Abstract
On the basis of successive measurements of leaf gas exchange during the main growing seasons of Populus euphratica Oliv. in 2013 and 2014, respectively, we analyzed the stomatal and non-stomatal limitations to photosynthesis under natural conditions in an extremely arid region of northwestern China. Our results showed that (1) the distribution patterns of net photosynthesis (Pn) and stomatal conductance (gs) were similar, both of which increased in the morning, peaked at around noon, and then decreased. This contrasted with the observed changes in sub-stomatal CO2 concentrations (Ci). (2) The phenomenon of midday depression of photosynthesis (MDP) was obvious from July to September during the two years. At the beginning of MDP, the stomatal limitation to photosynthesis (Ls) peaked, where its predominance was supported by Ci being at a minimum. Thereafter, Ls decreased and Ci/gs increased sharply, indicating that the non-stomatal limitation to photosynthesis predominated. (3) Both the Ls and relative stomatal limitation to photosynthesis (RLs) increased in the morning, and then decreased, whereas Ci/gs presented contrary changes. (4) The RLs values were greater than the Ls values, which was mainly due to the nonlinearity of the Pn/Ci curve, which often leads to large overestimations. (5) The Ls values in our study were much greater than those from other studies under natural conditions. The most probable reason was that the extremely high temperature and scarce water resource caused the stomata to close to reduce transpiration, resulting in the stomatal limitation to photosynthesis being more intense.
How to evaluate the HbeAg-positive during the natural course of Chronic Hepatitis B in clinic? A cross-sectional study
Authors: Zheng JinLi , Huang Yang , Yang Lingpeng , Jiang Li 
Published: August 2019

Abstract
Background

The previous studies showed the correlation between HBsAg and serum HBV DNA levels was weak or missing.

Objective

The study aims to investigate the correlation between HBeAg and HBV DNA levels, and to find an alternative tool to evaluate the HBV DNA level for clinicians.

Methods

A total of 1020 patients with CHB were enrolled in this cross-sectional study. We divided the patients into four groups as: HBeAg positivity and negativity groups, and high and low HBV DNA levels groups. Further, as per the levels of serum HBV DNA, we performed subgroups’ analyses for the HBeAg-positive and HBeAg-negative groups.

Results

Results showed that the ALT, ALB and HBeAg are independent factors to estimate the serum HBV DNA in CHB patients. But diagnosing the high levels of HBV DNA is not credible (the AUC=0.622, Fig1-A). In HBeAg-positive group, when the level of HBeAg is higher than 16.15 S/CO, we can predict the patient with high levels of HBV DNA (> 2000 IU/ml, AUC=0.787, Fig1-C) and the patients were 4 folds to have the high levels of HBV DNA than the HBeAg-negativ (table3). The levels of ALT and TB are the independent risk factors for the patients in HBeAg-negative group. When the levels of ALT and TB are higher 36.5 IU/L and 11.15 umol/L,respectively, the patient would have a high levels of HBV DNA (> 2000 IU/ml, AUC=0.609, Fig2-B).

Conclusion

HBeAg is an independent factor that reflects the levels of serum HBV DNA with a strong correlation, but it is not accurate to evaluate the levels of serum HBV DNA by the HBeAg-positive. On the other hand, the patients with HBeAg-negative are not mean having a low levels of HBV DNA, which can be evaluated by the levels of ALT and TB.
The comparative evaluation of the neurosurgery books used in Poland - theoretical foundation and study results
Authors: Pawlicka Aleksandra , Tomaszewska Renata , Smuczyński Wojciech , Śniegocki Maciej 
Published: August 2019

Abstract
• Background: The aim of the study was to carry out comparative evaluation of the books used in Poland for teaching neurosurgery to undergraduates, and find the most valuable one. Comparative textbook evaluation has not been of great scientific interest in the country yet.

• Methods: Based on the textbook functions theory and textbook evaluation forms created by other researchers, an entirely new textbook evaluation tool was created. The form checks if the desired functions are performed in a textbook. The tool was used to evaluate the books selected for the study. Altogether, there were 9 neurosurgery books and 3 reference books of different fields. Then, the study results were compared with the list of the books found valuable by several neurosurgery-teaching institutions in the world.

• Results: It turned out that the best textbook amongst the studied ones was ‘Handbook of Neurosurgery’ by Greenberg. Schirmer’s ‘Neurochirurgie’ came second. ‘Zarys Neurochirurgii’ by Ząbek, which was the third best book, proved to be the most valuable textbook amongst the ones written by Polish authors.

• Conclusions: Although Greenberg’s book scored the highest in the evaluation process and is the textbook that institutions choose and recommend the most often, there is still a lot to be done in order to make it serve all the desired textbook functions well. If the Polish neurosurgery textbooks were re-issued and modernised, they could compete with the most valued foreign books.
Farmers’ Exposure to Climate Hazards and Reforestation in Selected African Villages: An Endogenous-Switching Regression Model
Authors: Oyekale Tolulope Olayemi , Oyekale Abayomi 
Published: August 2019

Abstract
Background: Deforestation remains a serious concern for Africa’s economic development and global climatic stability. Emphases are now placed on promoting some essential adaptive and mitigation strategies among smallholder farmers. This paper analyzed the effect of exposure to climate-related hazards on tree planting among smallholder farmers in nine selected African countries. The data were from baseline surveys which were conducted by the CGIAR’s research programme on Climate Change, Agriculture and Food Security (CCAFS). The included countries were Burkina Faso, Ethiopia, Ghana, Kenya, Mali, Niger, Senegal, Tanzania and Uganda. Data were analyzed with Endogenous Switching regression considering the endogeneity potentials of climate-hazard exposure.
Results: The results showed that Uganda and Ethiopia had the highest average numbers of tree planting with 1.082 and 1.000 respectively, while Senegal (89.86%), Kenya (87.77%), Burkina Faso (82.86%) and Ethiopia (82.86%) had the highest exposure to climate-related hazards. Endogenous Switching regression results showed that climate hazard exposure was truly endogenous going by statistical significance of the Wald Chi Square test (p<0.05) and it was significantly influenced by female household headship, perception of more droughts, floods and low ground water. The number of tree that were planted increased significantly (p<0.05) with climate hazard exposure, degraded land areas, asset indices and residence in East Africa, while it reduced with female household headship. In addition, Average Treatment Effect (ATE) result indicated that an average household will plant 0.745 trees more when it had been previously exposed to climate shocks while Average Treatment Effect on the Treated (ATET) revealed that an average household that was exposed to climate hazards would plant 0.54 more trees than it would if it had not been exposed to hazards.
Conclusion: The major implication of the findings is that without having previously experienced some climatic adversities, farmers may not see the need to engage in tree planting as a mitigating strategy. It was concluded that many farmers had been affected by climate-related shocks and efforts to safeguard future climate through tree planting should be gender sensitive and concentrated among previously affected farmers.
Clinical Value and Potential Mechanisms Exploration of GOLGA8B in Hepatocellular Carcinoma: A Comprehensive Investigation Based on Real-Time Quantitative Polymerase Chain Reaction, RNA-seq, Microarray and Immunohistochemistry
Authors: Ma Fu-chao , Zhai Gao-qiang , Wu Hua-yu , He Rong-quan , Sun Qi , Huo Zeng-yu , Chen Gang , Dang Yi-wu 
Published: August 2019

Abstract
Introduction

Recent studies found that GOLGA8B plays an essential role in different cancers. However, the role GOLGA8B plays in the carcinogenesis and development of hepatocellular carcinoma (HCC) remains unclear. This study explores the clinical significance and prospective mechanisms of GOLGA8B in HCC.

Materials and methods

The expression of GOLGA8B was detected in tissues of HCC and non-HCC controls. A real-time quantitative polymerase chain reaction analysis was performed to evaluate the mRNA expression of GOLGA8B. RNA-sequencing data and microarray chip data were obtained for further analysis. The role GOLGA8B plays in patients with HCC was also evaluated. An immunohistochemistry (IHC) analysis was also performed to evaluate the protein expression of GOLGA8B. The different GOLGA8B expression resources, including mRNA and protein expression, were integrated by calculating standard mean difference (SMD) and summary of the receiver operator characteristic (sROC). Genes co-expressed GOLGA8B were predicted. Enrichment analyses including Gene ontology (GO) and biological pathway were performed to investigate the essential molecular mechanisms. Hub genes were screened out by a protein-protein interactions network. MicroRNAs which target GOLGA8B at a posttranscriptional level were also predicted.

Results

According to different resources, GOLGA8B manifested a higher expression in tissues of HCC than in non-HCC controls and exhibited clinical values for HCC. The RT-qPCR analysis revealed an increasing trend of GOLGA8B expression in HCC. GOLGA8B expresssion was significantly increased in RNA-sequencing and 7 of 13 microarray chip. IHC analysis also revealed significantly higher expression of GOLGA8B protein. Moreover, GOLGA8B expression was correlated with pathologic tumors and stages according to RNA-sequencing data and IHC analysis. The integrated SMD and sROC of different resources was 0.893 (P=0.004) and 0.79. A total 1303 co-expressed genes were gathered to perform enrichment analyses. The most significant biological pathways of co-expressed genes were spliceosome and mitogen-activated protein kinase signalling (MAPK). Four hub genes (SF3B1, HNRNPA2B1, HNRNPA1 and SRRM2) and five miRNAs (miR-369-3p, miR-203a, miR-374b-5p, miR-139-5p and miR-144-3p) were screened out.

Conclusion

GOLGA8B expression was increased in HCC and may serve as a novel target for HCC diagnosis and treatment.
Meibomian Gland Dysfunction (MGD), as Diagnosed by Non-Contact Infrared Meibography, in Dogs with Ocular Surface Disorders (OSD): A Retrospective Study.
Authors: Vinas Marta , Maggio Federica , D’Anna Nunzio , Rabozzi Roberto , Peruccio Claudio 
Published: August 2019

Abstract
Background: Meibomian gland dysfunction (MGD) is one of the possible conditions underlying ocular surface disorders (OSD). Prevalence of MGD in dogs affected by OSD has not yet been reported. We aimed to evaluate the prevalence of MGD among OSD canine patients, which had been assessed by non-contact infrared meibography and interferometry, and to identify MGD associated factors that might guide its diagnosis. Medical records of canine patients examined for OSD between 2016 and 2019 were reviewed. The frequency of MGD was evaluated within different categories (skull conformation, gender, eye and STT-1). The putative MGD risk factors and frequency of MGD within grades of interferometry were evaluated in a regression analysis model and reported as odd ratios (ORs).Results: One hundred fifty eyes from 81 dogs with OSD were included with median age 75 months (range 3-192) and female representation with 52%. MGD was present in 70% of the examined eyes. MGD risk was higher in males [OR adj = 3.015 (95% CI: 1.395 - 6.514) ( P = 0.005)] and older patients [OR adj = 1.207 (95% CI: 1.081 - 1.348) ( P = 0.001)]. No significant differences were found between left and right eyes ( P = 0.66) or between the two types of skull conformation ( P = 0.477) and MGD presence. MGD was associated to the lowest LL thickness, as assessed by interferometry (grade 0) [OR= 16.00 (95% CI: 2.104 - 121.68) ( P < 0.001)]. STT values were not significantly associated with the presence of MGD ( P > 0.05).Conclusions: MGD is a common underlying pathology in OSD. Being male and higher age are risk factors for MGD. An interferometry grade 0 may guide OSD diagnosis towards MGD.
Does Universal Test and Treat Strategy has an effect on Antiretroviral Therapy Adherence? A Comparative Cross-sectional Study
Authors: Damtie Yitayish , Nigatu Dabere , Tadese Fentaw , Yalew Melaku 
Published: August 2019

Abstract
Background : Poor adherence is a critical problem in managing Human Immunodeficiency Virus (HIV ) -infected patients receiving Antiretroviral Therapy (ART). Evidence of adherence to antiretroviral therapy after initiation of Universal Test and Treat (UTT) strategy was limited in Ethiopia. Hence, this study aimed to compare adherence to antiretroviral therapy before and after the initiation of universal test and treat strategy, including factors affecting adherence among HIV positive adults in Dessie town. Methods: A comparative cross-sectional study was conducted on 594 HIV positive adults selected using consecutive sampling. Interview and patient record review were used to collect data. The data were analyzed using SPSS version 23. Bi-variable and multivariable logistic regression model were used to identify factors associated with ART adherence. Adjusted Odds Ratio (AOR) with 95% Confidence Interval (CI) was used as a measure of association. Statistical significance was declared at a P - value less than 0.05. Result : The overall proportion of ART adherence using Morisky scale and self-reports were 52.3%, 95% CI: (48.4%, 56.2%) and 95%, 95% CI: (93.5%, 96.8%) respectively. Absence of depression (AOR =3.87, 95% CI: (1.96, 7.64)), eating three or more meals per day (AOR =2.65, 95% CI: (1.08, 6.49)) and absence of concomitant illness (AOR =0.42, 95% CI: (0.23, 0.76)) were significantly associated with better ART adherence. Conclusion: The overall proportion of ART adherence measured by Morisky scale was very low while the proportion of ART adherence measured by self-report was high and consistent with the current World Health Organization (WHO) recommendation. Adherence to ART was not affected by the introduction of the UTT strategy in HIV treatment and care program. Depression, meal frequency and concomitant illness were factors associated with ART adherence. Efforts should be made to improve adherence through tailored interventions to overcome factors linked with poor adherence. Key words: Antiretroviral therapy, Adherence, HIV/AIDS, Ethiopia
Metabolomic profiling of oral squamous cell carcinoma reveals glutaminolysis-related proteins: GLS1 and GLUD1 are potential diagnostic and prognostic factors
Authors: Yang Xihu , Jing Yue , Zhu Ni-Sha , Zhang Xiao-Xin , Fu Yong , Chen Sheng , Hu Qin-Gang , Ni Yan-Hong 
Published: August 2019

Abstract
It is essential to explore potential molecular involved in oral squamous cell carcinoma (OSCC) malignant transformation and progression. The purpose of this study was to delineate the metabolic characteristics of OSCC patients. We firstly report GC-MS based metabolic profiling of OSCC tissues from 8 patients, including tumor tissues and its matched normal tissues, then another 81 OSCC patients with prognostic information were used to verify metabolomics results by exam key enzymes expression. A panel including ten metabolite biomarker were identified, which can distinguish OSCC tumor from normal controls. On the base of metabolites with significantly difference, we applied KEGG for further pathway analysis and found OSCC have highly active glutaminolysis metabolism. Therefore, glutaminolysis-related key enzymes GLS1 and GLUD1 were detected by immunohistochemical and results demonstrated that GLS1 and GLUD1 were highly expressed in OSCC. Moreover, Kaplan-Meier survival analysis also showed and GLS1 and GLUD1 expressions were correlated with poor prognosis and tumor progression in OSCC patients. In conclusion, our results indicated that OSCC have highly active glutaminolysis metabolism, and GLS1 and GLUD1 enzymes are potential diagnostic and prognostic factors for OSCC.
Multiple association analysis strategies identified loci and candidate genes for body size on three growth stages in Simmental beef cattle
Authors: An Bingxing , Xu Lei , Xia Jiangwei , Chang Tianpeng , Wang Xiaoqiao , Xu Lingyang , Zhang Lupei , Gao Xue , Li Junya , Gao Huijiang 
Published: August 2019

Abstract
Background: Body size traits as one of the main breeding selection criteria have long since being widely used to monitor cattle growth and evaluate the selection response. Here the volume of body size is indicated by body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS) and cannon bone size (CS). We performed genome-wide association studies (GWAS) for these traits to a broad spectrum of three growth stages (months 6, 12 and 18 after birth) under three statistical models: single-trait GWAS, multi-trait GWAS and LONG-GWAS. The whole genomic single nucleotide polymorphisms (SNPs) were obtained from the Illumina Bovine HD 770K BeadChip genotype on 1217 individuals.
Results: In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. While 21 genes among in these loci appeared to be promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2 and PRIM2 detected by single-trait analyze; SLC37A1, LAP3, PCDH7, MANEA and LHCGR detected by multi-trait analyze; P2RY1, MPZL1, LINGO2, CMIP and WSCD1 detected by LONG-GWAS.
Conclusions: Multiple association analysis strategies were performed for six growth traits on each stage. This research could offer valuable insights to further explore the potential mechanism of growth traits in Simmental beef cattle.