bluuebunny/crossref_metadata_2025_split huggingface dataset:
KLF4 alleviates cerebral vascular injury by ameliorating vascular endothelial inflammation and regulating tight junction protein expression following ischemic stroke
Authors: Zhang Xinyu , Wang Lu , Han Zhenxiang , Dong Jing , Pang Defang , Fu Yuan , Li Longxuan 
Published: March 2020

Abstract
Background: Although inflammatory cell adhesion molecules (CAMs) and anti-inflammation factor- kruppel-like transcription factor (KLF) 4 have all been reported to be induced after cerebral ischemic stroke (CIS), the close temporal and spatial relationship between expressions of CAMs and KLF4 following CIS, and whether and how CAMs and KLF-4 contribute to development of CIS-induced vascular injury are still unclear. Methods: Here, we first examined the correlation between serum levels of CAMs/KLF4 and infarct volume in acute CIS patients. Then, we determined relationship between CAMs and KLF4 in mice after focal cerebral ischemia. Finally, we investigated the mechanism of KLF4 in protecting against oxygen-glucose deprivation-induced brain endothelial cell injury. Results: Our results demonstrated that patients with moderate to severe CIS had higher serum levels of three CAMs including E-selectin, inter-cellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion molecule 1 (VCAM-1) but lower levels of KLF4 at 48 hours after acute event as compared to patients with minor CIS. The expression levels of three CAMs as well as KLF4 all correlated well with the infarct volume in all the CIS subjects at that time. Although the expressions of three CAMs and KLF4 were all induced in the ischemic hemisphere following focal cerebral ischemia, but the peak timing and distribution patterns of their expression were different: the induction of KLF4 lagged behind that of the CAMs in the ischemic penumbra, furthermore, the dual immunofluorescent studies displayed that high expression of KLF4 was always associated with relatively less cerebral vascular endothelial inflammation response in the ischemic hemisphere, and vice versa. Mechanistic analyses revealed that KLF4 alleviated CIS-induced cerebral vascular injury by regulating endothelial expressions of CAMs, nuclear factor-kB and tight junction proteins.Conclusions: These data indicate that KLF4 confers vascular protection against cerebral ischemic injury, suggesting that circulating CAMs and KLF4 might be used as potential biomarkers for predicting the prognosis of acute ischemic stroke, and also providing a new proof of concept and potential targets for future prevention and treatment of CIS.
Transcriptomic and metabolomic analysis provides insights into anthocyanin and pyocyanin accumulation in pear
Authors: Zhang Zhen , Tian Changping , Zhang Ya , Li Chenzhiyu , Li Xi , Yu Qiang , Wang Shuo , Wang Xinyu , Chen Xuesen , Feng Shouqian 
Published: March 2020

Abstract
Background Pear is one of the most important fruit crops worldwide. Anthocyanins and procyanidins (PAs) are important secondary metabolites that affect the appearance and nutritive quality of pear. However, few studies have focused on the molecular mechanism underlying anthocyanin and PA accumulation in pear . Results We conducted metabolome and transcriptome analyses to identify candidate genes involved in anthocyanin and PA accumulation in young fruits of the pear cultivar ‘Clapp Favorite’ (CF) and its red mutation cultivar ‘Red Clapp Favorite’ ( RCF ). Gene–metabolite correlation analyses revealed a ‘core set’ of 20 genes that were strongly correlated with 10 anthocyanin and seven PA metabolites. Of these, PcGSTF12 was confirmed to be involved in anthocyanin and PA accumulation by complementation of the tt19-7 Arabidopsis mutant. Interestingly, PcGSTF12 was found to be responsible for the accumulation of procyanidin A3, but not petunidin 3, 5-diglucoside, opposite to the function of AtGSTs in Arabidopsis . Transformation with PcGSTF12 greatly promoted or repressed genes involved in anthocyanin and PA biosynthesis, regulation, and transport. Electrophoretic mobility shift and luciferase reporter assays confirmed positive regulation of PcGSTF12 by PcMYB114 . Conclusion These findings identify a core set of genes for anthocyanin and PA accumulation in pear. Of these, PcGSTF12 , was confirmed to be involved in anthocyanin and PA accumulation. Our results also identified an important anthocyanin and PA regulation node comprising two core genes, PcGSTF12 and PcMYB114 . These results provide novel insights into anthocyanin and PA accumulation in pear and represent a valuable data set to guide future functional studies and pear breeding.
Invasive cattle ticks in East Africa: morphological and molecular confirmation of the presence of Rhipicephalus microplus in south-eastern Uganda
Authors: Muhanguzi Dennis , Byaruhanga Joseph , Amanyire Wilson , Ndekezi Christian , Ochwo Sylvester , Nkamwesiga Joseph , Mwiine Frank Nobert , Tweyongyere Robert , Fourie Josephus , Madder Maxime , Schetters Theo , Horak Ivan , Juleff Nick , Jongejan Frans 
Published: March 2020

Abstract
Background: Rhipicephalus microplus, an invasive tick species of Asian origin and the main vector of Babesia species, is considered one of the most widespread ectoparasites of livestock. The tick has spread from its native habitats on translocated livestock to large parts of the tropical world, where it has replaced some of the local populations of Rhipicephalus decoloratus ticks. Although the tick was reported in Uganda 70 years ago, it has not been found in any subsequent surveys. This study was carried out to update the national tick species distribution on livestock in Uganda as a basis for tick and tick-borne disease control, with particular reference to R.microplus.Methods: The study was carried out in Kadungulu, Serere district, south-eastern Uganda, which is dominated by small scale livestock producers. All the ticks collected from 240 cattle from six villages were identified microscopically. Five R. microplus specimens were further processed for phylogenetic analysis and species confirmation.Results: The predominant tick species found on cattle was Rhipicephalus appendiculatus (86.9 %; n=16,509). Other species found were Amblyomma variegatum (7.2 %; n=1,377), Rhipicephalus evertsi (2.3 %; n=434) and R. microplus (3.6 %; n= 687). Phylogenetic analysis of the 12S rRNA, 16S rRNA and ITS2 gene sequences of R. microplus confirmed the morphological identification.Conclusions: It is concluded that R. microplus has replaced Rhipicephalus decoloratus in the sampled villages in Kadungulu sub county, since the latter was not any longer found in this area. There is currently no livestock movement policy in force in Uganda, which could possibly limit the further spread of R. microplus ticks. Future surveys, but also retrospective surveys of museum specimens, will reveal the extent of distribution of R. microplus in Uganda and also for how long this tick has been present on livestock without being noticed.
On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments
Authors: Assefa Alemu Takele , Vandesompele Jo , Thas Olivier 
Published: March 2020

Abstract
Background: In gene expression studies, RNA sample pooling is sometimes considered because of budget constraints or lack of sufficient input material. Using microarray technology, RNA sample pooling strategies have been reported to optimize both the cost of data generation as well as the statistical power for differential gene expression (DGE) analysis. For RNA sequencing, with its different quantitative output in terms of counts and tunable dynamic range, the adequacy and empirical validation of RNA sample pooling strategies have not yet been evaluated. In this study, we comprehensively assessed the utility of pooling strategies in RNA-seq experiments using empirical and simulated RNA-seq datasets. Results: The data generating model in pooled experiments is defined mathematically to evaluate the the mean and variability of gene expression estimates. The model is further used to examine the trade-off between the statistical power of testing for DGE and the data generating costs. Empirical assessment of pooling strategies is done through analysis of RNA-seq datasets under various pooling and non-pooling experimental settings. Simulation study is also used to rank experimental scenarios with respect to the rate of false and true discoveries in DGE analysis. The results demonstrate that pooling strategies in RNA-seq studies can be both cost-effective and powerful when the number of pools, pool size and sequencing depth are optimally defined. Conclusion: For high within-group gene expression variability, small RNA sample pools are effective to reduce the variability and compensate for the loss of the number of replicates. Unlike the typical cost-saving strategies, such as reducing sequencing depth or number of biological samples, an adequate pooling strategy is effective in maintaining the power of testing for DGE for genes with low to medium abundance levels, along with a substantial reduction of the total cost of the experiment. In general, pooling RNA samples or pooling RNA samples in conjunction with moderate reduction of the sequencing depth can be good options to optimize cost and maintain power.
Integrated bioinformatics analysis of aberrantly-methylated differentially-expressed genes and pathways in age-related macular degeneration
Authors: Shen Yinchen , Li Mo , Liu Kun , Xu Xiaoyin , Zhu Shaopin , Wang Ning , Guo Wenke , Zhao Qianqian , Lu Ping , Yu Fudong , Xu Xun 
Published: March 2020

Abstract
Background: Age-related macular degeneration (AMD) represents the leading cause of visual impairment in the aging population. The goal of this study was to identify aberrantly-methylated, differentially-expressed genes (MDEGs) in AMD and explore the involved pathways via integrated bioinformatics analysis.Methods: Data from expression profile GSE29801 and methylation profile GSE102952 were obtained from the Gene Expression Omnibus database. We analyzed differentially-methylated genes and differentially-expressed genes using R software. Functional enrichment and protein–protein interaction (PPI) network analysis were performed using the R package and Search Tool for the Retrieval of Interacting Genes online database. Hub genes were identified using Cytoscape. Results: In total, 827 and 592 genes showed high and low expression, respectively, in GSE29801; 4117 hyper-methylated genes and 511 hypo-methylated genes were detected in GSE102952. Based on overlap, we categorized 153 genes as hyper-methylated, low-expression genes (Hyper-LGs) and 24 genes as hypo-methylated, high-expression genes (Hypo-HGs). Four Hyper-LGs (CKB, PPP3CA, TGFB2, SOCS2) overlapped with AMD risk genes in the Public Health Genomics and Precision Health Knowledge Base. KEGG pathway enrichment analysis indicated that Hypo-HGs were enriched in the calcium signaling pathway, whereas Hyper-LGs were enriched in sphingolipid metabolism. In GO analysis, Hypo-HGs were enriched in fibroblast migration, membrane raft, and coenzyme binding, among others. Hyper-LGs were enriched in mRNA transport, nuclear speck, and DNA binding, among others. In PPI network analysis, 23 nodes and two edges were established from Hypo-HGs, and 151 nodes and 73 edges were established from Hyper-LGs. Hub genes (DHX9, MAPT, PAX6) showed the greatest overlap. Conclusion: This study revealed potentially aberrantly MDEGs and pathways in AMD, which might improve the understanding of this disease.
Development, characterization, and cross-amplification of polymorphic microsatellite markers for North American Trachymyrmex and Mycetomoellerius ants
Authors: Matthews Alix E. , Rowan Chase , Stone Colby , Kellner Katrin , Seal Jon N. 
Published: March 2020

Abstract
Objective
The objective of this study is to develop and identify polymorphic microsatellite markers for fungus-gardening (attine) ants in the genus Trachymyrmex sensu lato . These ants are important ecosystem engineers and have been a model group for understanding complex symbiotic systems, but very little is understood about the intraspecific genetic patterns across most North American attine species. These microsatellite markers will help to better study intraspecific population genetic structure, gene flow, mating habits, and phylogeographic patterns in these species and potentially other congeners.
Results
Using next-generation sequencing techniques, we identified 17 and 12 polymorphic microsatellite markers from T. septentrionalis and Mycetomoellerius (formerly Trachymyrmex ) turrifex , respectively, and assessed the genetic diversity of each marker. We also analyzed the cross-amplification success of the T. septentrionalis markers in two other closely related Trachymyrmex species, and identified 10 and 12 polymorphic markers for T. arizonensis and T. pomonae , respectively.
Impact of brachytherapy technique (2D versus 3D) on outcomes of cervical cancer: A Systematic Review and Meta-analysis
Authors: Kim Yeon Joo , Kang Hyun-Cheol , Kim Young Seok 
Published: March 2020

Abstract
Background: To perform a systematic review and meta-analysis of the impact of brachytherapy (BT) technique (two-dimensional [2D] or three-dimensional image-guided [3D]) on outcomes of cervical cancer patients.Methods: PubMed and Embase databases were searched up to April 16, 2019, for studies which evaluated the effect of 3D-BT compared to 2D-BT in cervical cancer, and endpoints included cumulative incidence of severe toxicity, locoregional recurrence-free survival (LRRFS), progression-free survival (PFS), and overall survival (OS). Hazard ratios (HRs) were pooled in the meta-analysis using the random-effects model.Results: Six studies of 8 cohorts were included in the quantitative synthesis. The pooled hazard ratio (HR) regarding toxicity was evaluated in 5 cohorts in 3 studies, and the HR of 3D-BT compared to 2D-BT was 0.54 (95% confidence interval [CI], 0.37-0.77). All 6 studies were included for the synthesis for LRRFS, and the pooled HR favors 3D-BT (0.61 [95% CI, 0.40-0.93]). For PFS, 3 studies were included for analysis and 3D-BT was superior to 2D-BT (HR = 0.75 [95% CI, 0.0.59–0.96]). Five studies were included for the pooled HR regarding OS, and pooled HR of 3D-BT compared to 2D-BT was 0.65 (95% CI, 0.40–1.06).Conclusions: 3D-BT might reduce severe toxicity and improve LRRFS, and PFS in patients with cervical cancer. 3D-BT should be considered for standard management of cervical cancer, and efforts for adopting this procedure in Korea should be pursued.
A health care record review of early mobility activities after fragility hip fracture: Utilizing the French systematic method to inform future interventions
Authors: Haslam-Larmer Lynn , Woo Kevin , Auais Mohammad , Donnelly Catherine , DePaul Vincent 
Published: March 2020

Abstract
Background A fragility hip fracture is a serious injury in older adults. Following a fragility fracture, a large percentage of patients are unable to regain their pre-fracture level of mobility. There are several international guidelines recommending early mobility after surgery. We do not know the utilization of these early mobility recommendations by health care providers within our institution. An evidence to practice gap occurs when there is a failure to implement best practices. Utilization of a systematic method allows for a strategic approach to assessment of an evidence to practice gap. A recent publication of quality standards in Ontario provides an opportunity for a local needs assessment of potential evidence to practice gaps. Objective To identify if there is an evidence to practice gap in health care provider implementation of recommendations for early mobility after fragility hip fracture surgery. Methods A retrospective chart review was performed to document the rates of early mobility activities during the first five days after hip fracture surgery at a large tertiary centre in Toronto, Ontario. Patients with cognitive impairment were included. Results Early mobility activities in this older adult population are initiated in the first five days after surgery to varying degrees. Between 11% - 50% of patients are not participating in early mobility activities, thereby not meeting recommendations. Those with low pre-fracture function and cognitive impairment have lower rates of participation when compared to those with a high pre-fracture function and no cognitive impairment. Conclusions The chart review has identified a paucity of contextual information which may influence health care providers’ behaviours related to early mobility. The chart audit is limited in its ability to assess the systems issues, which may have an influence on the health care provider behaviour. Considering the lack of information in these areas, we have identified that further work is required to explore factors which may be having an impact on the health care provider’s ability to engage the patients in early mobility activities.
Differences in Achilles tendon stiffness in people with gout.
Authors: Otter Simon , Catherine Payne , Anna-Marie Jones , Nick Webborn , Peter Watt 
Published: March 2020

Abstract
Background Chronic gout is associated with weaker foot/leg muscles, altered gait patterns and on-going foot pain. Inflammation associated with gout may change tissue elasticity and ultrasound imaging (US) utilising shear wave elastography (SWE) offers a non-invasive method of quantifying these changes in tendon stiffness and SWE findings have not previously been reported in individuals with gout. We sought to determine differences in Achilles tendon stiffness in people with chronic gout compared to controls (non-gout). Methods A cross sectional study comparing 24 people with gout and 26 age/sex-matched controls. Clinical and demographic data were collated and US imaging used to determine tendon thickness, presence of gouty tophi and/or aggregates and levels of angiogenesis. Ten shear wave elastography (SWE) measures were taken along a longitudinal section of the mid-point of the Achilles tendon bilaterally. Prior to data collection, intra-observer error was good (0.75). Data were summarised using descriptive statistics and a repeated measures ANCOVA was used to compare SWE measures between the two groups for the left and right foot separately after accounting for Body Mass Index (BMI). Results: A small proportion of those with gout presented with intra-tendon aggregates and/or intra-tendon tophi in one or both tendons. There was no statistically significant difference in tendon thickness between groups. Neo-vascularity was present in a third of gout participants. SWE findings demonstrated significantly reduced tendon stiffness in those with gout compared to controls: right Achilles mdiff =1.04 (95% CI (0.38 to 1.7) p=0.003 and left Achilles mdiff = 0.7 (95% CI 0.09 to 1.32) p=0.025. Conclusion: Subjects with chronic gout show significantly reduced Achilles tendon stiffness compared to non-gout controls. From a clinical standpoint, our findings were similar to SWE measurements in subjects with Achilles tendinopathy and who did not have gout.
The effect of a non-invasive biomechanical treatment on subjective and objective measures in patients with knee osteoarthritis- A retrospective analysis on a UK population
Authors: Miles Christopher , Greene Andrew 
Published: March 2020

Abstract
Background Osteoarthritis is a major cause of pain and disability worldwide, therefore ways of treating this condition are paramount to a successful health system. The purpose of the study was to investigate the changes in spatial-temporal gait parameters and clinical measurements following treatment with a non-invasive biomechanical device on patients with knee osteoarthritis within the UK. Methods A retrospective analysis was carried out on 455 patients with knee osteoarthritis. All patients were evaluated using a computerized gait test and two self-assessment questionnaires (WOMAC and SF-36) at baseline and after 3 and 6 months of treatment. The biomechanical device was individually calibrated for each patient to minimise symptoms whilst walking and train neuromuscular control. Patients used the device for short periods during activities of daily living. Repeated measures statistical analyses were performed to compare differences over time. Results After 6 months of therapy significant improvements were seen in all gait parameters (p<0.01). Specifically, gait velocity, step length and single limb support of the more symptomatic knee improved by 13%, 7.8% and 3%, respectively. These were supported by significant improvements in pain, function and quality of life (48.6%, 45.7% and 22% respectively; p<0.001). A sub-group analysis revealed no baseline differences between those who were recommended joint replacement and those who were not. Both groups improved significantly over time (p<0.05 for all). Conclusions Our results suggest the personalised biomechanical intervention can improve gait patterns, pain, function and quality of life. It may provide an additional solution to managing UK patients suffering from knee osteoarthritis.
Epstein Barr virus genotypes (EBV1/EBV2) in individuals with infectious mononucleosis in the metropolitan area of Belém, Brazil, between 2005 and 2016
Authors: Monteiro Talita Antonia Furtado , Monteiro Talita Antonia Furtado , Costa Iran Barros , Costa Igor Brasil , Corrêa Thais Letícia dos Santos , Coelho Beatriz Monteiro Rodrigues , Polaro Alessandra Alves , Silva Amanda Emanuelle Santos da , Ramos Francisco Lúzio de Paula , Filho Arnaldo Jorge Martins , Monteiro Jose Luiz Furtado , Sousa Rita Catarina Medeiros 
Published: March 2020

Abstract
Background: Two types of Epstein Barr virus (EBV1/EBV2) have been shown to infect humans by causing infectious mononucleosis, their genome being very similar, except for regions of the EBNA genes. This study aimed to describe the EBV genotypes in cases of infectious mononucleosis in the metropolitan region of Belém, Brazil, from 2005 to 2016. Methods: A total of 8.295 suspected cases with symptoms/signs of infectious mononucleosis (MI) were investigated by doctors of infectious diseases at the Evandro Chagas Institute Health Care Service from January 2005 to December 2016. In 3.0% (251/8.295) of the cases were positive by enzymatic immunoassay were submitted to PCR for EBNA3C region to detect the types of EBV. Biochemical testing involving aspartate aminotransferase, alanine aminotransferase and gamma-glutamyl transferase were realized. Results: The identification of EBV types by PCR was verified in 30.3% (76/251) of individuals, being 71.1% (54/76) classified as EBV1, 17.1% (13/76) as EBV2 and 11.8% (9/76) as EBV1+EBV2. The number of women infected with EBV1 was higher (61.1% - 33/54) than for men (38.9% - 21/54), most were over 14 years old (66.7%-36/54). The main symptoms/clinical signs observed in EBV1 infection were: cervical lymphadenopathy (64.8%-35/54), fever (63%-34/54), headache (20.3%-11/54), arthralgia (20.3%-11/54) and exanthema (18.5%-10/54). In EBV2 infection, it was also detected in all age groups, with the exception of two groups, with an average age of 24 years. The presence of fever in 76.9% (10/13) with an average duration of 18 days and lymphadenopathy in 53.8 (7/13) were the most relevant signs/symptoms in EBV2. In contrast, EBV1+EBV2 co-infection was more frequent in the £5 year age group, affecting 20.0% (2/10). Women presented 66.7% (6/9) more positive cases. The symptoms involving EBV1+EBV2 co-infection were more related to fever (66.7%-6/9) and cervical lymphadenopathy (55.6% -5/9). The average of enzymatic values according to type of EBV was statistically significant (p <0.05) in individuals with EBV1 infection in those over 14 years of age. Conclusions: A pioneering study that molecularly identified the genotypes of EBV in 30.3% of cases, with circulation of EBV1, EBV2 and co-infection EBV1+EBV2 in cases of infectious mononucleosis in the northern region of Brazil.