bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kobuviruses carried by Rattus norvegicus in Guangdong, China
Authors: You Fang-Fei , Zhang Min-Yi , He Huan , He Wen-Qiao , Li Yong-Zhi , Chen Qing 
Published: April 2020

Abstract
Background
Murine kobuviruses (MuKV) are newly recognized picornaviruses first detected in murine rodents in the USA in 2011. Little information on MuKV epidemiology in murine rodents is available. Therefore, we conducted a survey of the prevalence and genomic characteristics of rat kobuvirus in Guangdong, China.

Results
Fecal samples from 223 rats (Rattus norvegicus) were collected from Guangdong and kobuviruses were detected in 12.6% (28) of samples. Phylogenetic analysis based on partial 3D and complete VP1 sequence regions showed that rat kobuvirus obtained in this study were genetically closely related to those of rat/mouse kobuvirus reported in other geographical areas. Two near full-length rat kobuvirus genomes (MM33, GZ85) were acquired and phylogenetic analysis of these revealed that they shared very high nucleotide/amino acids identity with one another (95.4%/99.4%) and a sewage-derived sequence (86.9%/93.5% and 87.5%/93.7%, respectively). Comparison with original Aichivirus A strains, such human kobuvirus, revealed amino acid identity values of approximately 80%.

Conclusion
Our findings indicate that rat kobuvirus have distinctive genetic characteristics from other Aichivirus A viruses. Additionally, rat kobuvirus may spread via sewage.
Silver diamine fluoride (SDF) used in childhood caries management has potent antifungal activity against oral Candida species
Authors: Fakhruddin Kausar Sadia , Egusa Hiroshi , Ngo Hien Chi , Panduwawala Chamila , Pesee Siripen , Venkatachalam Thenmozhi , Samaranayake Lakshman Perera 
Published: April 2020

Abstract
Background
The microbiome of Severe-Early Childhood Caries (S-ECC), is characterized by an ecosystem comprising bacterial and fungal species, with a predominance of Candida species. Hence, an anti-cariogen effective against both bacteria and fungi would be valuable in the management of S-ECC.
Here we evaluate the antifungal effect of silver diamine fluoride (SDF) against 35-clinical yeast isolates (Ten-each of C. albicans, C. krusei, C. tropicalis and five C. glabrata strains) from dentinal caries-lesions from S-ECC.

Results
Disc-diffusion and time-kill assays as well as MIC50 and MIC90 evaluations against therapeutic concentrations confirmed the broad-spectrum anti-candidal potency of SDF. Ultrastructural images revealed morphologic aberrations of yeast-cell walls on exposure to SDF. All C. krusei and C. glabrata isolates were significantly more sensitive to SDF, relative to the standard antifungal fluconazole. Further, SDF appears to effectively abrogate filamentation of C. albicans even at very low concentrations.

Conclusions
Our data, for the first time, elucidate the antifungal potency of SDF, in addition to its known antibacterial activity, in the management of S-ECC.
Identification of a virulence tal gene in the cotton pathogen, Xanthomonas citri pv. malvacearum strain Xss-V2–18
Authors: Haq Fazal , Xie Shiwang , Huang Kunxuan , Shah Syed Mashab Ali , Ma Wenxiu , Cai Lulu , Xu Xiameng , Xu Zhengyin , Wang Sai , Zou Lifang , Zhu Bo , Chen Gongyou 
Published: April 2020

Abstract
Background
Bacterial blight of cotton (BBC), which is caused by the bacterium Xanthomonas citri pv. malvacearum (Xcm), is a destructive disease in cotton. Transcription activator-like effectors (TALEs), encoded by tal-genes, play critical roles in the pathogenesis of xanthomonads. Characterized strains of cotton pathogenic Xcm harbor 8–12 different tal genes and only one of them is functionally decoded. Further identification of novel tal genes in Xcm strains with virulence contributions are prerequisite to decipher the Xcm-cotton interactions.

Results
In this study, we identified six tal genes in Xss-V2–18, a highly-virulent strain of Xcm from China, and assessed their role in BBC. RFLP-based Southern hybridization assays indicated that Xss-V2–18 harbors the six tal genes on a plasmid. The plasmid-encoded tal genes were isolated by cloning BamHI fragments and screening clones by colony hybridization. The tal genes were sequenced by inserting a Tn5 transposon in the DNA encoding the central repeat region (CRR) of each tal gene. Xcm TALome evolutionary relationship based on TALEs CRR revealed relatedness of Xss-V2–18 to MSCT1 and MS14003 from the United States. However, Tal2 of Xss-V2–18 differs at two repeat variable diresidues (RVDs) from Tal6 and Tal26 in MSCT1 and MS14003, respectively, inferred functional dissimilarity. The suicide vector pKMS1 was then used to construct tal deletion mutants in Xcm Xss-V2–18. The mutants were evaluated for pathogenicity in cotton based on symptomology and growth in planta. Four mutants showed attenuated virulence and all contained mutations in tal2. One tal2 mutant designated M2 was further investigated in complementation assays. When tal2 was introduced into Xcm M2 and expressed in trans, the mutant was complemented for both symptoms and growth in planta, thus indicating that tal2 functions as a virulence factor in Xcm Xss-V2–18.

Conclusions
Overall, the results demonstrated that Tal2 is a major pathogenicity factor in Xcm strain Xss-V2–18 that contributes significantly in BBC. This study provides a foundation for future efforts aimed at identifying susceptibility genes in cotton that are targeted by Tal2.
LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network
Authors: Xue Lingzi , Sun Mintao , Wu Zhen , Yu Lu , Yu Qinghui , Tang Yaping , Jiang Fangling 
Published: April 2020

AbstractBackgroundFruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks.ResultsHere, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, ‘LA1698’ (cracking-resistant, CR) and ‘LA2683’ (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 (Peroxide, POD), Solyc01g008710.3 (Mannan endo-1,4-beta-mannosidase, MAN), Solyc08g077910.3 (Expanded, EXP), Solyc09g075330.3 (Pectinesterase, PE), Solyc07g055990.3 (Xyloglucan endotransglucosylase-hydrolase 7, XTH7), Solyc12g011030.2 (Xyloglucan endotransglucosylase-hydrolase 9, XTH9), Solyc10g080210.2 (Polygalacturonase-2, PG2), Solyc08g081010.2 (Gamma-glutamylcysteine synthetase, gamma-GCS), Solyc09g008720.2 (Ethylene receptor, ER), Solyc11g042560.2 (Ethylene-responsive transcription factor 4, ERF4) etc. In addition, the lncRNAs (XLOC_16662 and XLOC_033910, etc) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking.ConclusionsThis study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H2O2) signal transduction and many cell wall-related mRNAs (EXP, PG, XTH), as well as some lncRNAs (XLOC_16662 and XLOC_033910, etc.).
Identification and validation of mutation points associated with waxy phenotype in cassava
Authors: do Carmo Cátia Dias , Sousa Massaine Bandeira e , dos Santos Silva Priscila Patrícia , Oliveira Gilmara Alvarenga Fachardo , Ceballos Hernán , de Oliveira Eder Jorge 
Published: April 2020

Abstract
Background
The granule-bound starch synthase I (GBSSI) enzyme is responsible for the synthesis of amylose, and therefore, its absence results in individuals with a waxy starch phenotype in various amylaceous crops. The validation of mutation points previously associated with the waxy starch phenotype in cassava, as well as the identification of alternative mutant alleles in the GBSSI gene, can allow the development of molecular-assisted selection to introgress the waxy starch mutation into cassava breeding populations.

Results
A waxy cassava allele has been identified previously, associated with several SNPs. A particular SNP (intron 11) was used to develop SNAP markers for screening heterozygote types in cassava germplasm. Although the molecular segregation corresponds to the expected segregation at 3:1 ratio (dominant gene for the presence of amylose), the homozygotes containing the SNP associated with the waxy mutation did not show waxy phenotypes. To identify more markers, we sequenced the GBSS gene from 89 genotypes, including some that were segregated from a cross with a line carrying the known waxy allele. As a result, 17 mutations in the GBSSI gene were identified, in which only the deletion in exon 6 (MeWxEx6-del-C) was correlated with the waxy phenotype. The evaluation of mutation points by discriminant analysis of principal component analysis (DAPC) also did not completely discriminate the waxy individuals. Therefore, we developed Kompetitive Allele Specific PCR (KASP) markers that allowed discrimination between WX and wx alleles. The results demonstrated the non-existence of heterozygous individuals of the MeWxEx6-del-C deletion in the analyzed germplasm. Therefore, the deletion MeWxEx6-del-C should not be used for assisted selection in genetic backgrounds different from the original source of waxy starch. Also, the alternative SNPs identified in this study were not associated with the waxy phenotype when compared to a panel of accessions with high genetic diversity.

Conclusion
Although the GBSSI gene can exhibit several mutations in cassava, only the deletion in exon 6 (MeWxEx6-del-C) was correlated with the waxy phenotype in the original AM206–5 source.
High plasma levels of pro-inflammatory factors interleukin-17 and interleukin-23 are associated with poor outcome of cardiac-arrest patients: a single center experience
Authors: Zhuang Yu-Gang , Chen Yuan-Zhuo , Zhou Shu-Qin , Peng Hu , Chen Yan-Qing , Li Dong-Jie 
Published: April 2020

Abstract
Background
Systemic inflammation is an important feature of post-cardiac arrest syndrome (PCAS). This study was designed to determine whether the plasma concentrations of some circulating pro-inflammatory cytokines (interleukin-17 [IL-8], IL-22, IL-23 and IL-33) are of value in predicting the outcome of patients after return of spontaneous circulation (ROSC) during the post–cardiac arrest period.

Methods
This was a prospective observational clinical study. In total, 21 patients (survivors, n = 10; non-survivors, n = 11) who experienced cardiac arrest and successful ROSC with expected survival of at least 7 days were consecutively enrolled from January 2016 to December 2017. Of the 21 enrolled patients, ten survived were designated “survivors”. The other eleven patients died between 2 days and 1 months post ROSC. Venous blood was drawn at three time-points: baseline (< 1 h post ROSC), 2 days post ROSC and 7 days post ROSC. Plasma IL-8, IL-22, IL-23 and IL-33 were determined using commercial enzyme-linked immunosorbent assays.

Results
Plasma creatinine levels, but aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels, were elevated in non-survivors compared with survivors. Plasma levels of IL-17, IL-22, IL-23 and IL-33 of the 21 total patients did not change at 2 or 7 days post ROSC compared to baseline. In survivors, the plasma levels of IL-17 and IL-23 at 2 or 7 days post ROSC were lower than baseline. In non-survivors, plasma levels of IL-17 increased compared with baseline. Receiver operating characteristic curve analysis showed that the plasma levels of IL-17 and IL-23 at 2 or 7 days post ROSC were able to predict the mortality of PCAS patients, and positively correlated with Acute Physiology and Chronic Health Evaluation (APACHE)-II score and time to ROSC.

Conclusion
These results provide the first evidence that the elevated plasma IL-17 and IL-23 levels are associated with poor outcome in PCAS patients. The role of IL-17/IL-23 axis post ROSC is worth paying attention to in PCAS patients.

Trial registration
Clinicaltrial.govNCT02297776, 2014-11-21.
The interaction between serum uric acid and triglycerides level on blood pressure in middle-aged and elderly individuals in China: result from a large national cohort study
Authors: Zhang Lin , Li Jin-long , Guo Lei-lei , Li Hong , Li Dan , Xu Guang 
Published: April 2020

Abstract
Background
The purpose of the research was to explore the extent of interaction between triglycerides (TG) and serum uric acid (SUA) level with blood pressure (BP) in middle-aged and elderly individuals in China.

Methods
Data were selected from the China Health and Retirement Longitudinal Study (CHARLS), a cross-sectional study. 3345(46.99%) men with average ages of 60.24 ± 9.24 years and 3774 (53.01%) women with average ages of 59.91 ± 9.95 years were included in the study. Differences between gender, or between categories of blood pressure levels were evaluated by t-test or chi-square test. The adjusted associations between various characteristics and BP status were first compared using linear regression models, as appropriate. Then, A general linear model adjusted for confounding factors (socio-demographic characteristics [age, educational levels, marital status, place of residence], health behaviors [cigarette smoking, alcohol drinking, eating habits, social and leisure activities, accidental injury, physical activities], medical history [history of cardiovascular diseases, hepatitis history, antidiabetic drugs, history of antilipidemic medication, anti-hypertensive therapy], metabolic measures [C-reactive protein (CRP), hemoglobin A1c (HbA1c), fasting plasma glucose (FPG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), estimated glomerular filtration rate (eGFR), body mass index (BMI)]) was used to examine the synergistic effect of SUA and TG level on BP in middle-aged and elderly individuals in China.

Results
Age-adjusted partial Pearson’s correlation coefficient showed that SUA and TG level positively correlated with both systolic blood pressure (SBP) and diastolic blood pressure (DBP) in both men and women. Multiple linear regression analysis showed the TG level was significantly and positively associated with SBP and DBP in both men (SBP: β =0.068, P = 0.001; DBP: β =0.064, P = 0.002) and women (SBP: β =0.061, P = 0.002; DBP: β =0.084, P = 0.000), but SUA were significantly and positively associated with SBP in both men (SBP: β =0.047, P = 0.013) and women (SBP: β =0.040, P = 0.028), regardless of other confounding factors. After adjusting for related potential confounders, evidence of interaction between SUA and TG level on SBP (men: β = − 1.090, P = 0.726; women: β = − 0.692, P = 0.861) and DBP (men: β = − 1.026, P = 0.572; women: β = − 0.794, P = 0.842) was not observed.

Conclusion
The interaction effect of SUA and TG level on BP was not observed in our study. Moreover, high SUA level was significantly associated with SBP, while high TG level was strongly related to both DBP and SBP.
Clustering of continuous and binary outcomes at the general practice level in individually randomised studies in primary care - a review of 10 years of primary care trials
Authors: Stuart Beth , Becque Taeko , Moore Michael , Little Paul 
Published: April 2020

Abstract
Background
In randomised controlled trials, the assumption of independence of individual observations is fundamental to the design, analysis and interpretation of studies. However, in individually randomised trials in primary care, this assumption may be violated because patients are naturally clustered within primary care practices. Ignoring clustering may lead to a loss of power or, in some cases, type I error.

Methods
Clustering can be quantified by intra-cluster correlation (ICC), a measure of the similarity between individuals within a cluster with respect to a particular outcome. We reviewed 17 trials undertaken by the Department of Primary Care at the University of Southampton over the last ten years. We calculated the ICC for the primary and secondary outcomes in each trial at the practice level and determined whether ignoring practice-level clustering still gave valid inferences. Where multiple studies collected the same outcome measure, the median ICC was calculated for that outcome.

Results
The median intra-cluster correlation (ICC) for all outcomes was 0.016, with interquartile range 0.00–0.03.
The median ICC for symptom severity was 0.02 (interquartile range (IQR) 0.01 to 0.07) and for reconsultation with new or worsening symptoms was 0.01 (IQR 0.00, 0.07). For HADS anxiety the ICC was 0.04 (IQR 0.02, 0.05) and for HADS depression was 0.02 (IQR 0.00, 0.05). The median ICC for EQ. 5D-3 L was 0.01 (IQR 0.01, 0.04).

Conclusions
There is evidence of clustering in individually randomised trials primary care. The non-zero ICC suggests that, depending on study design, clustering may not be ignorable. It is important that this is fully considered at the study design phase.
Examining Interprofessional teams structures and processes in the implementation of a primary care intervention (Health TAPESTRY) for older adults using normalization process theory
Authors: Valaitis Ruta , Cleghorn Laura , Dolovich Lisa , Agarwal Gina , Gaber Jessica , Mangin Derelie , Oliver Doug , Parascandalo Fiona , Ploeg Jenny , Risdon Cathy 
Published: April 2020

Abstract
Background
Many countries are engaged in primary care reforms to support older adults who are living longer in the community. Health Teams Advancing Patient Experience: Strengthening Quality [Health TAPESTRY] is a primary care intervention aimed at supporting older adults that involves trained volunteers, interprofessional teams, technology, and system navigation. This paper examines implementation of Health TAPESTRY in relation to interprofessional teamwork including volunteers.

Methods
This study applied Normalization Process Theory (NPT) and used a descriptive qualitative approach [1] embedded in a mixed-methods, pragmatic randomized controlled trial. It was situated in two primary care practice sites in a large urban setting in Ontario, Canada. Focus groups and interviews were conducted with primary care providers, clinical managers, administrative assistants, volunteers, and a volunteer coordinator. Data was collected at 4 months (June–July 2015) and 12 months (February–March 2016) after intervention start-up. Patients were interviewed at the end of the six-month intervention. Field notes were taken at weekly huddle meetings.

Results
Overall, 84 participants were included in 17 focus groups and 13 interviews; 24 field notes were collected. Themes were organized under four NPT constructs of implementation: 1) Coherence- (making sense/understanding of the program’s purpose/value) generating comprehensive assessments of older adults; strengthening health promotion, disease prevention, and self-management; enhancing patient-focused care; strengthening interprofessional care delivery; improving coordination of health and community services. 2) Cognitive Participation- (enrolment/buy-in) tackling new ways of working; attaining role clarity. 3) Collective Action- (enactment/operationalizing) changing team processes; reconfiguring resources. 4) Reflective Monitoring- (appraisal) improving teamwork and collaboration; reconfiguring roles and processes.

Conclusions
This study contributes key strategies for effective implementation of interventions involving interprofessional primary care teams. Findings indicate that regular communication among all team members, the development of procedures and/or protocols to support team processes, and ongoing review and feedback are critical to implementation of innovations involving primary care teams.

Trial registration
ClinicalTrials.gov, no. NCT02283723 November 5, 2014. Prospectively registered.
Primary isolated asymptomatic gastric tuberculosis of the cardia mimicking gastric stromal tumor: a rare case report and literature review
Authors: Lv Mingnan , Tang Kejiang , Meng Yajie , Tian Chuan , Wang Min 
Published: April 2020

Abstract
Background
Primary isolated gastric TB of the cardia presenting as a submucosal tumor is extremely rare.

Case presentation
A 60-year-old female was admitted to our department; endoscopy revealed a smooth protruding lesion in the gastric cardia. The patient was diagnosed with a gastric cardia stromal tumor and the lesion was seen in muscularis propria by endoscopic ultrasonography (EUS). Endoscopic submucosal dissection (ESD) revealed that the lesion was filled with a milky, white liquid and white granulation tissue. Acid-fast specimen staining was negative. Hematoxylin and eosin staining showed patches of caseating necrosis and granulomatous inflammation. Gene sequencing subsequent to polymerase chain reaction (PCR) analysis of the ESD specimen identified Mycobacterium tuberculosis (M. TB) DNA fragments. The patient was put on ATT for 6 months.

Conclusion
Primary isolated gastric TB of the cardia should be suspected in patients without clinical symptoms whose manifestations are similar to those associated with submucosal tumors. TB-PCR may be helpful for further diagnosis.
Baseline levels of dynamic CD4+ T cell adhesion to MAdCAM-1 correlate with clinical response to vedolizumab treatment in ulcerative colitis: a cohort study
Authors: Allner Clarissa , Melde Michaela , Becker Emily , Fuchs Friederike , Mühl Laura , Klenske Entcho , Müller Lisa , Morgenstern Nadine , Fietkau Konstantin , Hirschmann Simon , Atreya Raja , Atreya Imke , Neurath Markus F. , Zundler Sebastian 
Published: April 2020

Abstract
Background
While the number of therapeutic options for treating inflammatory bowel diseases (IBD) is increasing, evidence for rational treatment decisions is scarce in many cases. In particular, appropriate biomarkers to predict the response to the anti-α4β7 integrin antibody vedolizumab are currently lacking.

Methods
We performed a cohort study with 21 patients suffering from ulcerative colitis (UC), in which first-time treatment with vedolizumab was initiated. CD4+ T cells were isolated from the peripheral blood and dynamic adhesion to recombinant mucosal vascular addressin cell adhesion molecule (MAdCAM-)1 in vitro as well as the effect of vedolizumab on such adhesion in vitro was determined. The expression of α4β1 integrin on peripheral blood CD4+ T cells was quantified by flow cytometry. Electronic patient records were reviewed to determine clinical response to vedolizumab.

Results
Dynamic adhesion of peripheral blood CD4+ T cells to MAdCAM-1 and the reduction of adhesion following vedolizumab treatment in vitro were higher and the change in α4β1 expression on CD4+ T cells was different in vedolizumab responders and non-responders. Responders could be identified with high specificity and positive-predictive value.

Conclusions
Determining dynamic adhesion of CD4+ T cells to MAdCAM-1 and the in vitro response to vedolizumab before treatment initiation or dynamic integrin regulation in the early course of treatment seem to be promising tools to predict the clinical response to vedolizumab therapy. Larger prospective studies are warranted.