bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis of the fungal pathogen Rosellinia necatrix during infection of a susceptible avocado rootstock identifies potential mechanisms of pathogenesis
Authors: Zumaquero Adela , Kanematsu Satoko , Nakayashiki Hitoshi , Matas Antonio , Martínez-Ferri Elsa , Barceló-Muñóz Araceli , Alfaro Fernando Pliego , Lopez-Herrera Carlos , Cazorla Francisco , Prieto Clara Pliego 
Published: December 2019

Abstract
Background
White root rot disease caused by Rosellinia necatrix is one of the most important threats affecting avocado productivity in tropical and subtropical climates. Control of this disease is complex and nowadays, lies in the use of physical and chemical methods, although none have proven to be fully effective. Detailed understanding of the molecular mechanisms underlying white root rot disease has the potential of aiding future developments in disease resistance and management. In this regard, this study used RNA-Seq technology to compare the transcriptomic profiles of R. necatrix during infection of susceptible avocado `Dusa´ roots with that obtained from the fungus cultured in rich medium.

Results
The transcriptomes from three biological replicates of R. necatrix colonizing avocado roots (RGA) and R. necatrix growing on potato dextrose agar media (RGPDA) were analyzed using Illumina sequencing. A total of 12,104 transcripts were obtained, among which 1,937 were differentially expressed genes (DEG), 137 exclusively expressed in RGA and 160 in RGPDA. During the root infection process, genes involved in the production of fungal toxins, detoxification and transport of toxic compounds, hormone biosynthesis, gene silencing and plant cell wall degradation were overexpressed. Interestingly, 24 out of the 137 contigs expressed only during R. necatrix growth on avocado roots, were predicted as candidate effector proteins (CEP) with a probability above 60%. The PHI (Pathogen Host Interaction) database revealed that three of the R. necatrix CEP showed homology with previously annotated effectors, already proven experimentally via pathogen-host interaction.

Conclusions
The analysis of the full-length transcriptome of R. necatrix during the infection process is suggesting that the success of this fungus to infect roots of diverse crops might be attributed to the production of different compounds which, singly or in combination, interfere with defense or signaling mechanisms shared among distinct plant families. The transcriptome analysis of R. necatrix during the infection process provides useful information and facilitates further research to a more in -depth understanding of the biology and virulence of this emergent pathogen. In turn, this will make possible to evolve novel strategies for white root rot management in avocado.
Enterococcal periprosthetic joint infection: clinical and microbiological findings from a 8-year retrospective cohort study
Authors: Renz Nora , Trebse Rihard , Akgün Doruk , Perka Carsten , Trampuz Andrej 
Published: December 2019

Abstract
Background: Treatment of enterococcal periprosthetic joint infections (PJI) is challenging due to non-standardized management strategies and lack of biofilm-active antibiotics. The optimal surgical and antimicrobial therapy are unknown. Therefore, we evaluated characteristics and outcome of enterococcal PJI. Methods: Consecutive patients with enterococcal PJI from two specialized orthopedic institutions were retrospectively analyzed. Both institutions are following the same diagnostic and treatment concepts. The probability of relapse-free survival was estimated using Kaplan-Meier survival curves and compared by log-rank test. Treatment success was defined by absence of relapse or persistence of PJI due to enterococci or death related to enterococcal PJI. Clinical success was defined by the infection-free status, no subsequent surgical intervention for persistent or perioperative infection after re-implantation and no PJI-related death within 3 months. Results: Included were 75 enterococcal PJI episodes, involving 41 hip, 30 knee, 2 elbow and 2 shoulder prostheses. PJI occurred postoperatively in 61 episodes (81%), hematogenously in 13 (17%) and by contiguous spread in one. E. faecalis grew in 64 episodes, E. faecium in 10 and E. casseliflavus in one. Additional microorganism(s) were isolated in 38 patients (51%). Enterococci were susceptible to vancomycin in 73 of 75 isolates (97%), daptomycin in all 75 isolates, and fosfomycin in 21 of 22 isolates (96%). The outcome data was available for 66 patients (88%). The treatment success after 3 years was 83.7% (95% confidence interval [CI]; 76.1-96.7%) and the clinical success was 67.5% (95% CI; 57.3-80.8%). In 11 patients (17%), a new PJI episode caused by a different pathogen occurred. All failures occurred within the three years of surgery. Conclusion: About half of enterococcal PJI were polymicrobial infections. The treatment success was high (84%). All treatment failures occurred within the first three years after revision surgery. Interestingly, 17% of patients experienced a new PJI caused by another pathogen at a later stage. Trial registration: The study was retrospectively registered with the public clinical trial identification NCT0253022 at https://www.clinicaltrials.gov on 15 July 2015.
Predictive factors for the presence of invasive components in patients diagnosed with ductal carcinoma in situ based on preoperative biopsy
Authors: Lee Kwan Ho , Han Jeong Woo , Kim Eun Young , Yun Ji Sup , Park Yong Lai , Park Chan Heun 
Published: December 2019

Abstract
Background In patients diagnosed with ductal carcinoma in situ (DCIS) with needle biopsy before surgery, invasive component (IC) is often found in the postoperative tissue, which results in altered post-surgical care. However, there are no clinically available factors to predict IC, and few MRI studies are available for the detection of IC in DCIS patients. The purpose of this study was to evaluate which risk factors can predict IC preoperatively.Methods Patients with a DCIS diagnosis based on preoperative biopsy, who underwent breast surgery Kangbuk Samsung Hospital between Jan 2005 and June 2018, were retrospectively evaluated. Clinico-pathological and breast MRI factors were compared between DCIS and DCIS with IC in postsurgical specimens.Results Of the 431 patients with a preoperative diagnosis of DCIS, 34 (7.9%) showed IC during the postoperative pathological investigations, and 217 (50.3%) underwent breast MRI. Among MRI-related factors, Mass-like enhancement on MRI was the sole but significant predictor of IC (HR=0.26, C.I.=0.07-0.93, p=0.038), while nipple-areolar complex invasion, enhancement peak and pattern were not statistically significant. Nuclear grade was the only significant predictor of IC in the analysis of other clinico-pathological factors (HR=2.39, C.I.=1.05-5.42, p=0.038 in univariate analysis, HR=2.86, C.I.=1.14-7.14, p=0.025 in multivariate analysis).Conclusions Mass-like enhancement on MRI and high nuclear grade were associated with IC in patients with preoperative diagnosis of DCIS. Considering the high sensitivity of breast MRI for IC, further evaluation of the predictive value of MRI in preoperative DCIS patients is desirable.
Factors Affecting HBV Vaccination in a Medical Training College in Kenya: A Mixed Methods Study
Authors: Maina Anne , Bii Leah 
Published: December 2019

Abstract
Background : Hepatitis B Virus (HBV) is highly endemic in Sub-Saharan Africa with 70 to 90% of the population becoming infected before the age of 40 years. Healthcare workers (HCWs) including healthcare students (HCSs) are at an increased risk of contracting HBV due to occupational exposure. HCSs are especially at a high risk because of their inexperience with infection control procedures and insufficient knowledge about the level of risk when dealing with patients. Despite the availability of an effective vaccine, and its recommendation by Kenya’s Ministry of Health, few HCW and students are vaccinated. The aim of this study was to evaluate the influence of awareness, attitude, practices, and access factors on hepatitis B vaccination uptake by HCSs at Kenya Medical Training College (KMTC). Methods : This was a concurrent mixed methods study. For the quantitative arm, a structured questionnaire was used to assess the awareness, knowledge, attitudes and practices towards HBV disease and vaccination. Accessibility of the HBV vaccine in the participating campuses was also assessed. Two FGDs were carried out: one comprised of student representatives of the participating campuses while the second comprised of members of staff. Quantitative data was analysed using STATA (version 15) while NVIVO (version 11) was used for qualitative data. Results: Out of 634 students invited to participate in the study, 487 participated (response rate 76.8%). Majority of the respondents were from Nairobi Campus (44.2%) and from the Department of Nursing (31.2%). HBV vaccine uptake rate was 85.8% while the non-vaccination rate was 14.3%. Full vaccination was reported by only 20.2% of respondents. The major reason for not receiving the recommended doses was the unavailability of the vaccine when students went for it. The qualitative study revealed challenges in the implementation of the vaccination program at KMTC. Conclusions Full vaccination rates remained low despite good knowledge of HBV infection and positive attitude towards vaccination. There is therefore need to streamline vaccination programs in medical colleges to ensure availability and accessibility of the vaccine to healthcare students. Key words: HBV vaccination, Vaccine Uptake, Health Care Students, Kenya
Explaining the successes and failures of tuberculosis treatment programs; a tale of two regions in rural Eastern Uganda
Authors: Izudi Jonathan , Tamwesigire Imelda K , Bajunirwe Francis 
Published: December 2019

Abstract
Background. Optimally performing tuberculosis (TB) programs are characterized by treatment success rate (TSR) of at least 90%. In rural eastern Uganda, and elsewhere in sub Saharan Africa, TSR varies considerably across district TB programs and the reasons for the differences are unclear. This study explored factors associated with the low and high TSR across four districts in rural eastern Uganda.
Methods. We interviewed District TB and Leprosy Supervisors, Laboratory focal persons, and health facility TB focal persons from four districts in Eastern Uganda as key informants. Interviews were audio recorded, transcribed verbatim, and imported into ATLAs.ti where thematic content analysis was performed and results were summarized into themes.
Results . The emerging themes were categorized as either facilitators of or barriers to treatment success. The emerging facilitators prevailing in the districts with high rates of treatment success were using data to make decisions and design interventions, continuous quality improvement, capacity building, and prioritization of better management of people with TB. The barriers common in districts with low rates of treatment success included lack of motivated and dedicated TB focal persons, scarce or no funding for implementing TB activities , and a poor implementation of community-based directly observed therapy short course.
Conclusion. This study shows that several factors are associated with the differing rates of treatment success in rural eastern Uganda. These factors should be the focus for TB control programs in Uganda and similar settings in order to improve rates of treatment success.
Whole grain food diet slightly reduces cardiovascular risks in obese/overweight adults: a systematic review and meta-analysis
Authors: Wang Weihao , Li Jianan , Chen Xiaoxi , Yu Miao , Pan Qi , Guo Lixin 
Published: December 2019

Abstract
Background: The effects of whole grain diet on cardiovascular risks in obese and overweight adults is not well established. Our goal was to conduct a systematic review and meta-analysis on the effect of whole grain diet on cardiovascular risks in obese/overweight adults. Methods: PubMed, Embase and Cochrane were systematically scanned for randomized controlled trials (RCTs), and studies were selected based on certain inclusion and exclusion criteria. The primary outcome was the effectiveness of whole grain food consumption in reducing body weight. The secondary outcomes were the effect of whole grain food consumption on cardiovascular disease (CVD) risk factors including plasma low-density lipoprotein cholesterol (LDL-C), insulin resistance index, blood pressure, body mass index (BMI), C-reactive protein (CRP), and waist circumference in obese/overweight adults. Results: Our results showed that whole grain consumption was associated with lower body weight (mean difference (MD) =-0.5, 95% confidence intervals (CI) [-0.74, 0.25], I2 = 35%, P < 0.0001) and lower CRP (MD =-0.36, 95% CI [-0.54, -0.18], I2=69%, P<0.0001), compared with the control group. However, there were no significant differences in LDL-C (MD =-0.08, 95% CI [-0.16, 0.00], I2 = 27%, P = 0.05), waist circumference (MD=-0.12, 95% CI [-0.92, 0.68], I2=44%, P=0.76), systolic blood pressure (MD=-0.11, 95% CI [-1.55, 1.33], I2=3%, P=0.88), diastolic blood pressure (MD=-0.44, 95% CI [-1.44, 0.57], I2=15%, P=0.39), and fasting glucose (MD=-0.05, 95% CI [-0.12, 0.01], I2=31%, P=0.11) between the two groups. Conclusion: This study suggests that whole grain food consumption can slightly reduce body weight and CRP in obese/overweight population.
Autism spectrum disorder is associated with gut microbiota disorder in children
Authors: Sun Hairong , You Zhong , Jia Libo , Wang Fang 
Published: December 2019

Abstract
Background: The aim of this study was to evaluate the occurrence and clinical characteristics of autism spectrum disorder (ASD) associated to the stable state of the gut microbiota.
Methods: A total of 9 children with ASD and 6 healthy children used as control were selected and feces samples were collected from all of them. The 16S gene ribosomal RNA sequencing was used to analyze the difference in gut microbiota between healthy control children and ASD patients.
Results: The results of 16S sequencing based on operational taxonomic units (OTUs) analysis showed that the ASD group and the healthy control (HC) group had a large difference in the abundance of microbiota at the level of family, genus and species. The abundance of Bacteroidales and Selenomonadales was significantly lower in the ASD group than in the HC group (p=0.0110 and p=0.0076, respectively). The abundance of Ruminococcaceae in the ASD group was higher than that in the HC group (p=0.0285), while the amount of Prevotellaceae was significantly lower in the ASD group than in the HC group (p=0.0111). The Tax4Fun analysis based on Kyoto Encyclopaedia of Genes and Genomes (KEGG) data indicated differentially expressed functional pathway between the ASD group and healthy control group associated to the nervous system, environmental information processing and cellular processing.
Conclusions: The abundance of gut microbiota in the ASD group is different from that in the healthy control children. These differences affect the biological function of the host. These results suggest that a disorder in the gut microbiota may be associated, at least in part, with ASD in children.
Development and external validation of an online clinical prediction model for augmented renal clearance in adult mixed critically ill patients: the ARC predictor
Authors: Gijsen Matthias , Huang Chao-yuan , Flechet Marine , Daele Ruth Van , Declercq Peter , Debaveye Yves , Meersseman Philippe , Meyfroidt Geert , Wauters Joost , Spriet Isabel 
Published: December 2019

Abstract
BackgroundAugmented renal clearance (ARC) might lead to subtherapeutic plasma levels of drugs with predominant renal clearance. Early identification of ARC remains challenging for the intensive care unit (ICU) physician. We developed and validated the ARC predictor, a clinical prediction model for ARC on the next day during ICU stay, and made it available via an online calculator. Its predictive performance was compared with that of two existing models for ARC.MethodsA large multicenter database including medical, surgical and cardiac ICU patients (n = 33258 ICU days) from three Belgian tertiary care academic hospitals was used for the development of the prediction model. Development was based on clinical information available during ICU stay. We assessed performance by measuring discrimination, calibration and net benefit. The final model was externally validated (n = 10259 ICU days) in a single-center population.ResultsARC was found on 19.6% of all ICU days in the development cohort. Six clinical variables were retained in the ARC predictor: day from ICU admission, age, sex, serum creatinine, trauma and cardiac surgery. External validation confirmed good performance with an area under the curve of 0.88 (95% CI 0.87 – 0.88), and a sensitivity and specificity of 84.1 (95% CI 82.5 – 85.7) and 76.3 (95% CI 75.4 – 77.2) at the default threshold probability of 0.2, respectively.ConclusionARC on the next day can be predicted with good performance during ICU stay, using routinely collected clinical information that is readily available at bedside. The ARC predictor is available at www.arcpredictor.com.
Comparison of Inpatient Distribution among Different Medical Alliances in County Region: a Longitudinal Study on a healthcare reform in Rural China
Authors: Ran Yifan , Gao Hongxia , Han Dan , Hou Guilin , Chen Yingchun , Zhang Yan 
Published: December 2019

Abstract
Background: Three types of Medical Alliances (MAs) have been built in most county regions in China. These MAs are led by main three county hospitals to drive the development of township hospitals. This paper aims to evaluate the actual effect of China’s MAs reform in rural area on inpatient distribution especially among different categories of MAs. Methods：We obtained 2008-2015 claims data on enrolled residents from the New Cooperative Medical Scheme (NCMS) in Y County, Hubei Province of China. We considered January 2008–December 2010 as the pre-reform period and January 2011–December 2015 as the post-reform period. Independent sample t-test and single-group interrupted time series analysis (ITSA) were used to compare the number of inpatients per month in the three MAs including 3 county hospitals and 10 township hospitals before and after the reform. Paired t-test and multiple-group ITSA were used between township hospitals within MAs and outside MAs. Results：The MAs reform in Y County increased the number of inpatients and improved the service capacity of both county hospitals and township hospitals within MAs. After the reform, the number of inpatients per month in county hospitals had an upward trend, with a slope of 31.01 person/month (P < 0.000). Approximately 19.99 new inpatients were admitted to township hospitals monthly after the reform (P<0.000). Furthermore, township hospitals within MAs had a substantial increase in the number of inpatients (10.45 new inpatients monthly) compared with those outside MAs. Conclusion: The MAs reform in Y county effectively improved the capability of medical services in the county and decreased health inequality significantly. However, it also caused further imbalance in the county region in terms of the medical institutions among the three county hospitals and the different township hospitals, which contained the risk of new health inequality.
Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia
Authors: Zhao Dahe , Zhang Shengjie , Xue Qiong , Chen Junyu , Zhou Jian , Cheng Feiyue , Li Ming , Zhu Yaxin , Yu Haiying , Hu Songnian , Zheng Yanning , Liu Shuangjiang , Xiang Hua 
Published: December 2019

Abstract
Background: The chloride-carbonate-sulfate lakes (also called Soda-Saline lakes) are double-extreme ecological environments with high pH and high salinity values but can also exhibit high biodiversity and high productivity. The diversity of metabolic process that functioned well in such environments remains to be systematically investigated. Deep sequencing and species-level characterization of the microbiome in elemental cycling of carbon and sulfur will provide novel insights into the microbial adaptation in such saline-alkaline lakes. Results: In this study, we characterized environmental factors and performed deep metagenomic sequencing of the brine and sediment samples from nine ponds with different salinities of two chloride-carbonate-sulfate lakes in Inner Mongolia of China. The results showed that the concentration of chloride most significantly influenced the microbial community in both of the brine and sediment environments. Of 385 high-quality metagenome-assembled genomes (MAGs) belonging to archaea (56 Euryarchaeota, 12 Candidatus Nanohaloarchaeota, and 12 Candidatus Woesearchaeota) and bacteria (119 Proteobacteria and 186 other diverse bacterial phyla, including 18 from Candidate Phyla Radiation, CPR), 38 MAGs were observed to be abundant species at least in one of the eighteen niches. These abundant taxa represented most branches of a phylogenomic tree at phylum level. Interestingly, almost half of the abundant MAGs had the potential to drive dissimilatory sulfur cycling, including four autotrophic Ectothiorhodospiraceae MAGs, one Cyanobacteria MAG and nine heterotrophic MAGs with potential to oxidize sulfur, as well as four abundant MAGs containing genes for elemental sulfur respiration, which may increase the ability of environmental adaptation in such saline-alkaline environments. In addition, some subgroups in Ca. Nanohaloarchaeota and Ca. Woesearchaeota of the DPANN superphylum were also observed abundant. We found 1,4-alpha-glucans phosphorylation and complete glycolysis pathway in the abundant Nanohaloarchaeota MAG NHA-1, and this efficient energy regeneration pathway (compared with hydrolysis) may be a key factor for Ca. Nanohaloarchaeota in adaptation to hypersaline environments. Conclusions: The abundant taxa including carbon fixing microbes, versatile heterotrophs and the nanosized DPANN superphyla, and the superiority of energy production and thermodynamics of these abundant species were systematically investigated. This has provided novel insights into the microbial process in chloride-carbonate-sulfate lakes, and further understanding of the metabolic mechanism of adaptation to such extremely alkaline and saline conditions.
The effects of Bacillus spp. use as a dietary probiotic in weaning piglets
Authors: Dumitru Mihaela , Hăbeanu Mihaela , Sorescu Ionuț , Tabuc Cristina 
Published: December 2019

Abstract
Background: This study was conducted to evaluate the effects of supplementation with Bacillus-based probiotic (Bacillus subtilis ATCC 6051a, 1.6x109CFU/ml) on the performance of weaned piglets. Methods: A total of 60 piglets, 30 days±3 days of age, with an initial body weight (BW) of 8.41±0.92 kg were allotted randomly to 3 homogeneous groups (C, E1 and E2, 6 pens/10 piglets, 2 replicates/group) with a supplement of additive (Bs) based on 1% (E1), respectively 3% (E2)/kg feed. The feed was administered ad libitum in the flour form, 2 meals/day. Microbiological analysis and chemical composition of compound feed, the growth performances and diarrhoea incidence were assayed as well. Results: The addition of Bs didn’t influence significantly the BW or average daily gain (ADG). After 16 testing days, ADG was 1.13 times higher in E1 compared with C and with 1.04 times higher compared with E2. The feed intake (ADFI) increased with 1.08-fold in C diet compared with E1 diet. Feed efficiency diet was 1.22 times higher in E1 than C and with 1.05 higher than E2 diet. Conclusions: Addition of Bs-1% decreased diarrhoea incidence (P>0.05) by 7.6% vs. C and 3.8% vs. Bs-3%. 23.4% piglets had soft faeces, 43.75% score 2 (mild diarrhoea) and 32.81% score 3 (severe diarrhoea), no significant difference was noticed between the group (P˂0.05).