bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1
Authors: Dobrzanski Tatiane , Pobre Vânia , Moreno Leandro Ferreira , Barbosa Helba Cirino de Souza , Monteiro Rose Adele , de Oliveira Pedrosa Fábio , de Souza Emanuel Maltempi , Arraiano Cecília Maria , Steffens Maria Berenice Reynaud 
Published: February 2020

Abstract
Background
Herbaspirillum seropedicae is a diazotrophic bacterium from the β-proteobacteria class that colonizes endophytically important gramineous species, promotes their growth through phytohormone-dependent stimulation and can express nif genes and fix nitrogen inside plant tissues. Due to these properties this bacterium has great potential as a commercial inoculant for agriculture. The H. seropedicae SmR1 genome is completely sequenced and annotated but despite the availability of diverse structural and functional analysis of this genome, studies involving small non-coding RNAs (sRNAs) has not yet been done. We have conducted computational prediction and RNA-seq analysis to select and confirm the expression of sRNA genes in the H. seropedicae SmR1 genome, in the presence of two nitrogen independent sources and in presence of naringenin, a flavonoid secreted by some plants.

Results
This approach resulted in a set of 117 sRNAs distributed in riboswitch, cis-encoded and trans-encoded categories and among them 20 have Rfam homologs. The housekeeping sRNAs tmRNA, ssrS and 4.5S were found and we observed that a large number of sRNAs are more expressed in the nitrate condition rather than the control condition and in the presence of naringenin. Some sRNAs expression were confirmed in vitro and this work contributes to better understand the post transcriptional regulation in this bacterium.

Conclusions
H. seropedicae SmR1 express sRNAs in the presence of two nitrogen sources and/or in the presence of naringenin. The functions of most of these sRNAs remains unknown but their existence in this bacterium confirms the evidence that sRNAs are involved in many different cellular activities to adapt to nutritional and environmental changes.
QTL mapping of yield component traits on bin map generated from resequencing a RIL population of foxtail millet (Setaria italica)
Authors: Liu Tianpeng , He Jihong , Dong Kongjun , Wang Xuewen , Wang Wenwen , Yang Peng , Ren Ruiyu , Zhang Lei , Zhang Zhengsheng , Yang Tianyu 
Published: February 2020

Abstract
Background
Foxtail millet (Setaria italica) has been developed into a model genetical system for deciphering architectural evolution, C4 photosynthesis, nutritional properties, abiotic tolerance and bioenergy in cereal grasses because of its advantageous characters with the small genome size, self-fertilization, short growing cycle, small growth stature, efficient genetic transformation and abundant diverse germplasm resources. Therefore, excavating QTLs of yield component traits, which are closely related to aspects mentioned above, will further facilitate genetic research in foxtail millet and close cereal species.

Results
Here, 164 Recombinant inbreed lines from a cross between Longgu7 and Yugu1 were created and 1,047,978 SNPs were identified between both parents via resequencing. A total of 3413 bin markers developed from SNPs were used to construct a binary map, containing 3963 recombinant breakpoints and totaling 1222.26 cM with an average distance of 0.36 cM between adjacent markers. Forty-seven QTLs were identified for four traits of straw weight, panicle weight, grain weight per plant and 1000-grain weight. These QTLs explained 5.5–14.7% of phenotypic variance. Thirty-nine favorable QTL alleles were found to inherit from Yugu1. Three stable QTLs were detected in multi-environments, and nine QTL clusters were identified on Chromosome 3, 6, 7 and 9.

Conclusions
A high-density genetic map with 3413 bin markers was constructed and three stable QTLs and 9 QTL clusters for yield component traits were identified. The results laid a powerful foundation for fine mapping, identifying candidate genes, elaborating molecular mechanisms and application in foxtail millet breeding programs by marker-assisted selection.
Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity
Authors:   On behalf of the IBESS group, Hendriks Amber C. A. , Reubsaet Frans A. G. , Kooistra-Smid A. M. D. ( Mirjam) , Rossen John W. A. , Dutilh Bas E. , Zomer Aldert L. , van den Beld Maaike J. C. 
Published: February 2020

Abstract
Background
We investigated the association of symptoms and disease severity of shigellosis patients with genetic determinants of infecting Shigella and entero-invasive Escherichia coli (EIEC), because determinants that predict disease outcome per individual patient could be used to prioritize control measures. For this purpose, genome wide association studies (GWAS) were performed using presence or absence of single genes, combinations of genes, and k-mers. All genetic variants were derived from draft genome sequences of isolates from a multicenter cross-sectional study conducted in the Netherlands during 2016 and 2017. Clinical data of patients consisting of binary/dichotomous representation of symptoms and their calculated severity scores were also available from this study. To verify the suitability of the methods used, the genetic differences between the genera Shigella and Escherichia were used as control.

Results
The isolates obtained were representative of the population structure encountered in other Western European countries. No association was found between single genes or combinations of genes and separate symptoms or disease severity scores. Our benchmark characteristic, genus, resulted in eight associated genes and > 3,000,000 k-mers, indicating adequate performance of the algorithms used.

Conclusions
To conclude, using several microbial GWAS methods, genetic variants in Shigella spp. and EIEC that can predict specific symptoms or a more severe course of disease were not identified, suggesting that disease severity of shigellosis is dependent on other factors than the genetic variation of the infecting bacteria. Specific genes or gene fragments of isolates from patients are unsuitable to predict outcomes and cannot be used for development, prioritization and optimization of guidelines for control measures of shigellosis or infections with EIEC.
Circular RNA expression profile and its potential regulative role in human abdominal aortic aneurysm
Authors: Zhou Min , Shi Zhenyu , Cai Liang , Li Xu , Ding Yong , Xie Tianchen , Fu Weiguo 
Published: February 2020

Abstract
Background
This study aimed to identify the differentially expressed circular RNAs (circRNAs) between human abdominal aortic aneurysm (AAA) and the control group.

Methods
High-throughput sequencing was applied to determine the circRNA expression profiles of 4 paired aortic samples. Real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was carried out to testify 6 randomly selected dysregulated circRNAs. Kyoto Encyclopedia of Genes and Genomes and Gene ontology (GO) analysis were conducted for functional annotation of the parental genes. Additionally, interaction networks between circRNA and 5 putative microRNA (miRNA) partners were constructed.

Results
Finally, 411 differentially expressed circRNAs were discovered, including 266 downregulated and 145 upregulated circRNAs. Compared with the control group, the expression level of hsa (Homo sapiens) _circ_0005360 (LDLR) and hsa_circ_0002168 (TMEM189) were proved significantly lower in the AAA group by qRT-PCR. Regarding upregulated circRNAs, the most enriched GO molecular function, biological process and cellular component terms were poly(A) RNA binding, negative regulation of transcription from RNA polymerase II promoter and nucleoplasm, respectively. Moreover, circRNA/miRNA interaction networks showed that hsa_circ_0005360/miR-181b and hsa_circ_0002168/miR-15a axis might have a regulative role in human AAA.

Conclusions
This study revealed new circRNAs potentially related to the pathogenesis of AAA. Further experimental studies are warranted to clarify the potential molecular mechanisms.
Comparison of different rating scales for the use in Delphi studies: different scales lead to different consensus and show different test-retest reliability
Authors: Lange Toni , Kopkow Christian , Lützner Jörg , Günther Klaus-Peter , Gravius Sascha , Scharf Hanns-Peter , Stöve Johannes , Wagner Richard , Schmitt Jochen 
Published: February 2020

AbstractBackgroundConsensus-orientated Delphi studies are increasingly used in various areas of medical research using a variety of different rating scales and criteria for reaching consensus. We explored the influence of using three different rating scales and different consensus criteria on the results for reaching consensus and assessed the test-retest reliability of these scales within a study aimed at identification of global treatment goals for total knee arthroplasty (TKA).MethodsWe conducted a two-stage study consisting of two surveys and consecutively included patients scheduled for TKA from five German hospitals. Patients were asked to rate 19 potential treatment goals on different rating scales (three-point, five-point, nine-point). Surveys were conducted within a 2 week period prior to TKA, order of questions (scales and treatment goals) was randomized.ResultsEighty patients (mean age 68 ± 10 years; 70% females) completed both surveys. Different rating scales (three-point, five-point and nine-point rating scale) lead to different consensus despite moderate to high correlation between rating scales (r = 0.65 to 0.74). Final consensus was highly influenced by the choice of rating scale with 14 (three-point), 6 (five-point), 15 (nine-point) out of 19 treatment goals reaching the pre-defined 75% consensus threshold. The number of goals reaching consensus also highly varied between rating scales for other consensus thresholds. Overall, concordance differed between the three-point (percent agreement [p] = 88.5%, weighted kappa [k] = 0.63), five-point (p = 75.3%, k = 0.47) and nine-point scale (p = 67.8%, k = 0.78).ConclusionThis study provides evidence that consensus depends on the rating scale and consensus threshold within one population. The test-retest reliability of the three rating scales investigated differs substantially between individual treatment goals. This variation in reliability can become a potential source of bias in consensus studies. In our setting aimed at capturing patients’ treatment goals for TKA, the three-point scale proves to be the most reasonable choice, as its translation into the clinical context is the most straightforward among the scales. Researchers conducting Delphi studies should be aware that final consensus is substantially influenced by the choice of rating scale and consensus criteria.
Hepatitis C screening, diagnosis, and cascade of care among people aged > 40 years in Brasilia, Brazil
Authors: Carvalho-Louro Daniela Mariano , Soares Eric Bassetti , Trevizoli Jose Eduardo , Marra Thayna Moreira Gomes , da Cunha Alexandre Lima Rodrigues , Rodrigues Marcelo Palmeira , Carvalho-Furtado Adriana Claudia Lopes , dos Santos Beatriz Taynara Araujo , de Assis da Rocha Neves Francisco 
Published: February 2020

Abstract
Background
Identifying patients with hepatitis C virus (HCV) infection and enhancing the cascade of care are essential for eliminating HCV infection. This study aimed to estimate the prevalence of positive anti-HCV serology in Brasilia, Brazil, and evaluate the efficiency of the cascade of care for HCV-positive individuals.

Methods
This cross-sectional study analyzed 57,697 rapid screening tests for hepatitis C in individuals aged > 40 years between June 2018 and June 2019. HCV-positive patients were contacted and scheduled to undergo the HCV RNA viral test, genotyping, and transient elastography.

Results
The prevalence of positive serology was 0.27%. Among 161 patients with positive anti-HCV serology, 124 (77%) were contacted, 109 (67.7%) were tested for HCV RNA viral load, and 69 (42.8%) had positive results. Genotype 1 (75%) was the most prevalent genotype. Among 65 patients (94.2%) who underwent transient elastography, 30 (46.2%) presented with advanced fibrosis. Additionally, of the 161 patients, 55 (34.1%) were referred for treatment, but only 39 (24.2%) complied, with 36 (22.4%) showing sustained virological response. By the end of the study, 16 patients were still awaiting to receive medication.

Conclusions
The prevalence of HCV-positive patients was low in Brasilia, and the gaps in the cascade of care for these patients were significantly below the targets of HCV infection elimination. This study opens new avenues for eliminating HCV infection and suggests that partnerships with clinical laboratories to conduct anti-HCV tests are a useful strategy to improve HCV diagnosis.

Trial registration
Research Ethics Committee of the Faculty of Health Sciences of the University of Brasília - UNB (CAAE number 77818317.2.0000.0030) and by the Ethics Committee of the Health Science Teaching and Research Foundation - FEPECS/SES/DF (CAAE number 77818317.2.3001.5553).
Hydroxychloroquine may reduce risk of Pneumocystis pneumonia in lupus patients: a Nationwide, population-based case-control study
Authors: Yeo Kai-Jieh , Chen Hsin-Hua , Chen Yi-Ming , Lin Ching-Heng , Chen Der-Yuan , Lai Chih-Ming , Chao Wen-Cheng 
Published: February 2020

Abstract
Background
Pneumocystis pneumonia (PCP) is increasingly being diagnosed in patients with systemic lupus erythematosus (SLE), and hydroxychloroquine (HCQ) has been found to possess antifungal activities. We hence aimed to investigate the association between HCQ and PCP risk among patients with SLE.

Methods
Using the 1997–2013 nationwide claim data, we identified 24,343 newly-diagnosed SLE patients. We then identified 58 PCP cases and selected 348 non-PCP controls matching (1:6) by age, sex, disease duration and the year of PCP diagnosis date. The risk of PCP was assessed by determing odds ratios (ORs) with 95% confidence intervals (CIs) by using multivariable conditional logistic regression.

Results
The risk of PCP was associated with moderate to severe renal disease (OR 6.73, 95% CI 1.98–22.92), higher doses of glucocorticoids (≤5 mg/day, reference; 5–10 mg/day, OR 25.88, 95% CI 2.97–225.33; > 10 mg/day, OR 286.58, 95% CI 28.58–> 999), higher 3-month cumulative dose of cyclophosphamide (not use, reference; ≤1.4 g, OR 0.64, 95% CI 0.14–3.01; > 1.4 g, OR 11.52, 95% CI 1.97–67.39) and use of mycophenolate mofetil/mycophenolic acid (OR 50.79, 95% CI 5.32–484.77), whereas 3-month cumulative dose of HCQ was associated with a reduced risk of PCP among patients with SLE (not use, reference; ≤14 g, OR 0.69, 95% CI 0.21–2.24; > 14 g, OR 0.20, 95% CI 0.05–0.71).

Conclusions
This study demonstrated incident PCP was associated with mycophenolate mofetil/mycophenolic acid use and higher doses of cyclophosphamide or glucocorticoid, whereas the use of a higher dose of HCQ was associated with a reduced risk of PCP in lupus patients.
Normothermic and hypothermic oxygenated perfusion for donation after circulatory death in kidney transplantation: do we pay higher risk of severe infection after transplantation?: a case report
Authors: Ravaioli Matteo , Corradetti Valeria , Renzulli Matteo , Germinario Giuliana , Maroni Lorenzo , Odaldi Federica , Fallani Guido , Pezzuto Anna Paola , Parlanti Daniele , Bova Raffaele , Bini Claudia , La Manna Gaetano , Comai Giorgia 
Published: February 2020

Abstract
Background
Normothermic and hypothermic oxygenated perfusion for donation after circulatory death in kidney transplantation are becoming popular in Italy, with the purpose of reducing the risk of primary non function and delayed graft function due to the prolonged warm ischemia time.
Potential complications related to these procedures are currently under investigation and are continuously emerging with the increasing experience. Post-operative infections - in particular graft arteritis - are a rare complication but determine high risk of mortality and of graft loss.
The acute onset of the arterial complications makes it very difficult to find an effective treatment, and early diagnosis is crucial for saving both patient and graft. Prevention of such infections in this particular setting are advisable.

Case presentation
We present a patient with an acute arterial rupture after transplantation of a DCD graft treated in-vivo hypothermic oxygenated perfusion. The cause was a severe arteritis of the renal artery caused by Candida krusei and Pseudomonas aeruginosa. We discussed our treatment and we compared it to the other reported series.

Conclusion
Fungal infections in DCD transplant may be treacherous and strategies to prevent them should be advocated.
Viscerotropic disease and acute uveitis following yellow fever vaccination: a case report
Authors: Volkov Lev , Grard Gilda , Bollaert Pierre-Edouard , Durand Guillaume A. , Cravoisy Aurélie , Conrad Marie , Nace Lionel , Courte Guilhem , Marnai Rémy , Leparc-Goffart Isabelle , Gibot Sébastien 
Published: February 2020

Abstract
Background
Yellow fever vaccine exists for over 80 years and is considered to be relatively safe. However, in rare cases it can produce serious neurotropic and viscerotropic complications. We report a case of a patient who presented both viscerotropic and neurological manifestations after yellow fever vaccination.

Case presentation
We describe the case of a 37 years old man who developed after the yellow fever vaccination a yellow fever vaccine-associated viscerotropic disease followed by acute uveitis. Prolonged detection of yellow fever RNA in blood and urine was consistent with yellow fever vaccine-associated adverse event. The final outcome was good, although with persistent fatigue over a few months.

Conclusions
Even if the yellow fever vaccine is relatively safe, physicians should be aware of its possible serious adverse effects.
Mutation Spectrum of Stickler Syndrome Type I and Genotype-phenotype Analysis in East Asian Population: a systematic review
Authors: Wang Dan-Dan , Gao Feng-Juan , Hu Fang-Yuan , Zhang Sheng-Hai , Xu Ping , Wu Ji-Hong 
Published: February 2020

Abstract
Background
Stickler syndrome is the most common genetic cause of rhegmatogenous retinal detachment (RRD) in children, and has a high risk of blindness. Type I (STL1) is the most common subtype, caused by COL2A1 mutations. This study aims to analyze the mutation spectrum of COL2A1 and further elucidate the genotype-phenotype relationships in the East Asian populations with STL1, which is poorly studied at present.

Methods
By searching MEDLINE, Web of Science, CNKI, Wanfang Data, HGMD and Clinvar, all publications associated with STL1 were collected. Then, they were carefully screened to obtain all reported STL1-related variants in COL2A1 and clinical features in East Asian patients with STL1.

Results
There were 274 COL2A1 variants identified in 999 patients with STL1 from 466 unrelated families, and more than half of them were truncation mutations. Of the 107 STL1 patients reported in the East Asian population, it was found that patients with truncation mutations had milder systemic phenotypes, whereas patients with splicing mutations had severer phenotypes. In addition, several recurrent variants (c.3106C > T, c.1833 + 1G > A, c.2710C > T and c.1693C > T) were found.

Conclusions
Genotype-phenotype correlations should certainly be studied carefully, contributed to making personalized follow-up plans and predicting prognosis of this disorder. Genome editing holds great potential for treating inherited diseases caused by pathogenic mutations. In this study, several recurrent variants were found, providing potential candidate targets for genetic manipulation in the future.
Validation of pre-operative risk scores of contrast-induced acute kidney injury in a Chinese cohort
Authors: Yin Wenjun , Zhou Ge , Zhou Lingyun , Liu Mancang , Xie Yueliang , Wang Jianglin , Zuo Shanru , Liu Kun , Hu Can , Chen Linhua , Yang Huiqin , Zuo Xiaocong 
Published: February 2020

AbstractBackgroundPre-operative risk scores are more valuable than post-procedure risk scores because of lacking effective treatment for contrast-induced acute kidney injury (CI-AKI). A number of pre-operative risk scores have been developed, but due to lack of effective external validation, most of them are also difficult to apply accurately in clinical practice. It is necessary to review and validate the published pre-operative risk scores for CI-AKI.Materials and methodsWe systematically searched PubMed and EMBASE databases for studies of CI-AKI pre-operative risk scores and assessed their calibration and discriminatory in a cohort of 2669 patients undergoing coronary angiography or percutaneous coronary intervention (PCI) from September 2007 to July 2017. The definitions of CI-AKI may affect the validation results, so three definition were included in this study, CI-AKI broad1 was defined as an increase in serum creatinine (Scr) of 44.2 μmol/L or 25%; CI-AKI broad2, an increase in Scr of 44.2 μmol/L or 50%; and CI-AKI-narrow, an increase in Scr of 44.2 μmol/L. The calibration of the model was assessed with the Hosmer-Lemeshow test and the discriminatory capacity was identified by C-statistic.ResultsOf the 8 pre-operative risk scores for CI-AKI identified, 7 were single-center study and only 1 was based on multi-center study. In addition, 7 of the scores were just validated internally and only Chen score was externally validated. In the validation cohort of 2669 patients, the incidence of CI-AKI ranged from 3.0%(Liu) to 16.4%(Chen) for these scores. Furthermore, the incidence of CI-AKI was 6.59% (178) for CI-AKI broad1, 1.44% (39) for CI-AKI broad2, and 0.67% (18) for CI-AKI-narrow. For CI-AKI broads, C-statistics varied from 0.44 to 0.57. For CI-AKI-narrow, the Maioli score had the best discrimination and calibration, what’s more, the C-statistics of Maioli, Chen, Liu and Ghani was ≥0.7.ConclusionMost pre-operative risk scores were established based on single-center studies and most of them lacked external validation. For CI-AKI broads, the prediction accuracy of all risk scores was low. The Maioli score had the best discrimination and calibration, when using the CI-AKI-narrow definition.