bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics of Mycoplasma pneumoniae isolated from children with pneumonia: South Korea, 2010–2016
Authors: Lee Joon Kee , Seong Moon-Woo , Shin Dongjin , Kim Jong-Il , Han Mi Seon , Yeon Youbin , Cho Sung Im , Park Sung Sup , Choi Eun Hwa 
Published: November 2019

Abstract
Background
Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017.

Results
The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. The phylogenetic tree constructed with 78 genomes including 30 genomes from Korea formed two clusters and further divided into two sub-clusters. eBURST analysis revealed two clonal complexes according to P1 typing results showing higher diversity among P1 type 2 strains.

Conclusions
The comparative whole genome approach was able to define high genetic identity, unique structural diversity, and phylogenetic associations among the 78 M. pneumoniae strains isolated worldwide.
Overexpression of OsPUB41, a Rice E3 ubiquitin ligase induced by cell wall degrading enzymes, enhances immune responses in Rice and Arabidopsis
Authors: Kachewar Neha Rajendra , Gupta Vishal , Ranjan Ashish , Patel Hitendra Kumar , Sonti Ramesh V. 
Published: November 2019

Abstract
Background
Cell wall degrading enzymes (CWDEs) induce plant immune responses and E3 ubiquitin ligases are known to play important roles in regulating plant defenses. Expression of the rice E3 ubiquitin ligase, OsPUB41, is enhanced upon treatment of leaves with Xanthomonas oryzae pv. oryzae (Xoo) secreted CWDEs such as Cellulase and Lipase/Esterase. However, it is not reported to have a role in elicitation of immune responses.

Results
Expression of the rice E3 ubiquitin ligase, OsPUB41, is induced when rice leaves are treated with either CWDEs, pathogen associated molecular patterns (PAMPs), damage associated molecular patterns (DAMPs) or pathogens. Overexpression of OsPUB41 leads to induction of callose deposition, enhanced tolerance to Xoo and Rhizoctonia solani infection in rice and Arabidopsis respectively. In rice, transient overexpression of OsPUB41 leads to enhanced expression of PR genes and SA as well as JA biosynthetic and response genes. However, in Arabidopsis, ectopic expression of OsPUB41 results in upregulation of only JA biosynthetic and response genes. Transient overexpression of either of the two biochemically inactive mutants (OsPUB41C40A and OsPUB41V51R) of OsPUB41 in rice and stable transgenics in Arabidopsis ectopically expressing OsPUB41C40A failed to elicit immune responses. This indicates that the E3 ligase activity of OsPUB41 protein is essential for induction of plant defense responses.

Conclusion
The results presented here suggest that OsPUB41 is possibly involved in elicitation of CWDE triggered immune responses in rice.
Factors associated with the rates of coronary artery bypass graft and percutaneous coronary intervention
Authors: Kim Agnus M. , Park Jong Heon , Cho Seongcheol , Kang Sungchan , Yoon Tae Ho , Kim Yoon 
Published: November 2019

AbstractBackgroundKorea has seen a rapid increase in the use of percutaneous coronary intervention (PCI) with the ratio of PCI to coronary artery bypass graft (CABG) the highest in the world. This study was performed to examine the factors associated with the rates of CABG and PCI.MethodsThe data were acquired from the National Health Insurance database in Korea in 2013. We calculated the age-sex standardized rates of CABG and PCI. We examined the factors associated with the CABG and PCI rates by performing a regression analysis.ResultsThe rate of CABG showed a negative association with the deprivation index score, and other factors, such as the number of providers or hospital beds, did not show any significant association with the CABG rate. The rate of PCI had a strong negative association with the number of cardiothoracic surgeons and a strong positive association with the number of hospital beds.ConclusionsThe positive association between the PCI rate and the number of hospital beds suggests that the use of PCI may be driven by the supply of beds, and the inverse association between the PCI rate and the number of cardiothoracic surgeons indicates the overuse of PCI due to lack of the providers of CABG. Policy measures should be taken to optimize the use of revascularization procedures, the choice of which should primarily be based on the patient’s need.
The magnitude and correlates of esophageal Varices among newly diagnosed cirrhotic patients undergoing screening fibre optic endoscope before incident bleeding in North-Western Tanzania; a cross-sectional study
Authors: Gunda Daniel W. , Kilonzo Semvua B. , Mamballah Zakhia , Manyiri Paulina M. , Majinge David C. , Jaka Hyasinta , Kidenya Benson R. , Mazigo Humphrey D. 
Published: November 2019

Abstract
Background
Bleeding esophageal varices is a deadly complication of liver cirrhosis. Guidelines recommend an early diagnosis of esophageal varices before incident bleeding by screening all patients diagnosed with liver cirrhosis. Though it has been reported elsewhere that the presence of esophageal varices varies widely among cirrhotic patients this has not been assessed in Tanzania since endoscopy is not readily available for routine use in our setting. This study was designed to determine the prevalence of esophageal varices and assess the utility of clinical parameters in predicting the presence of varices among cirrhotic patients in northwestern Tanzania.

Methods
A cross-sectional analysis of adult patients with liver cirrhosis was done at Bugando Medical Centre. Demographic, clinical, laboratory and endoscopic data were collected and analyzed using STATA 13. The presence of esophageal varices was detected using endoscopic examination and associated factors were assessed by logistic regression. The predictive value of clinical predictors was also assessed by calculating sensitivity and specificity.

Results
A total of 223 patients were enrolled, where 88 (39.5%; 95%CI: 33.0–45.9) had esophageal varices. The varices were independently associated with increased age (OR: 1.02; 95%CI: 1.0–1.04; p = 0.030); increased splenic diameter (OR:1.3; 95%CI:1.2–1.5; p <  0.001), increased portal vein diameter (OR:1.2; 95%CI: 1.07–1.4; p = 0.003), having ascites (OR: 3.0; 95%CI: 1.01–8.7; p = 0.046), and advanced liver disease (OR: 2.9; 95%CI: 1.3–6.7; p = 0.008). PSDR least performed in predicting varices, (AUC: 0.382; 95%CI: 0.304–0.459; cutoff: < 640; Sensitivity: 58.0%; 95%CI: 46.9–68.4; specificity: 57.0%; 95%CI: 48.2–65.5). SPD had better prediction; (AUC: 0.713; 95%CI: 0.646–0.781; cut off: > 15.2 cm; sensitivity: 65.9%; (95% CI: 55–75.7 and specificity:65.2%; 95%CI: 56.5–73.2), followed by PVD, (AUC: 0.6392; 95%CI: 0.566–0.712;cutoff: > 1.45 cm; sensitivity: 62.5%; 95CI: 51.5–72.6; specificity: 61.5%; 95%CI: 52.7–69.7).

Conclusion
Esophageal varices were prevalent among cirrhotic patients, most of which were at risk of bleeding. The non-invasive prediction of varices was not strong enough to replace endoscopic diagnosis. However, the predictors in this study can potentially assist in the selection of patients at high risk of having varices and prioritize them for endoscopic screening and appropriate management.
Characteristics of febrile urinary tract infections in older male adults
Authors: Smithson Alex , Ramos Javier , Niño Esther , Culla Alex , Pertierra Ubaldo , Friscia Michele , Bastida Maria Teresa 
Published: November 2019

AbstractBackgroundUrinary tract infections (UTI) are among the most frequent bacterial infections in older adults. The aim of the study was to analyse the existence of differences in clinical features, microbiological data and risk of infection by multidrug-resistant organisms (MDRO) between older and non-older men with febrile UTI (FUTI).MethodsThis was an ambispective observational study involving older males with a FUTI attended in the Emergency Department. Variables collected included age, comorbidity, diagnostic of healthcare-associated (HCA)-FUTI, clinical manifestations, hospitalization, mortality, and microbiological data.ResultsFive hundred fifty-two males with a FUTI, 329 (59.6%) of whom were older adults, were included. Older males had a higher frequency of HCA-FUTI (p <  0.001), increased Charlson scores (p <  0.001), had received previous antimicrobial treatment more frequently (p <  0.001) and had less lower urinary tract symptoms (p <  0.001). Older patients showed a lower frequency of FUTI caused byE. coli(p <  0.001) and a higher rate of those due toEnterobacter spp.(p = 0.003) andP. aeruginosa(p = 0.033). Resistance rates to cefuroxime (p = 0.038), gentamicin (p = 0.043), and fluoroquinolones (p <  0.001)inE. coliisolates and the prevalence of extended-spectrum beta-lactamase and AmpC producingE. coliandKlebsiella spp.strains (p = 0.041) and MDRO (p <  0.001) were increased in older males. Inadequate empirical antimicrobial treatment (p = 0.004), frequency of hospitalization (p <  0.001), and all cause in-hospital mortality (p = 0.007) were higher among older patients. In the multivariate analysis, being admitted from an long term care facility (OR 2.4; 95% CI: 1.06–5.9), having a urinary tract abnormality (OR 2.2; 95% CI: 1.2–3.8) and previous antimicrobial treatment (OR 3.2; 95% CI: 1.9–5.4) were associated to FUTI caused by MDRO.ConclusionsOlder male adults with a FUTI have different clinical characteristics, present specific microbiological features, and antimicrobial resistance rates. In the multivariate analysis being an older male was not associated with an increased risk of FUTI caused by MDRO.
Mathematical modelling for antibiotic resistance control policy: do we know enough?
Authors: Knight Gwenan M. , Davies Nicholas G. , Colijn Caroline , Coll Francesc , Donker Tjibbe , Gifford Danna R. , Glover Rebecca E. , Jit Mark , Klemm Elizabeth , Lehtinen Sonja , Lindsay Jodi A. , Lipsitch Marc , Llewelyn Martin J. , Mateus Ana L. P. , Robotham Julie V. , Sharland Mike , Stekel Dov , Yakob Laith , Atkins Katherine E. 
Published: November 2019

Abstract
Background
Antibiotics remain the cornerstone of modern medicine. Yet there exists an inherent dilemma in their use: we are able to prevent harm by administering antibiotic treatment as necessary to both humans and animals, but we must be mindful of limiting the spread of resistance and safeguarding the efficacy of antibiotics for current and future generations. Policies that strike the right balance must be informed by a transparent rationale that relies on a robust evidence base.

Main text
One way to generate the evidence base needed to inform policies for managing antibiotic resistance is by using mathematical models. These models can distil the key drivers of the dynamics of resistance transmission from complex infection and evolutionary processes, as well as predict likely responses to policy change in silico. Here, we ask whether we know enough about antibiotic resistance for mathematical modelling to robustly and effectively inform policy. We consider in turn the challenges associated with capturing antibiotic resistance evolution using mathematical models, and with translating mathematical modelling evidence into policy.

Conclusions
We suggest that in spite of promising advances, we lack a complete understanding of key principles. From this we advocate for priority areas of future empirical and theoretical research.
Characteristics and outcome of influenza-associated encephalopathy/encephalitis among children in a tertiary pediatric hospital in Italy, 2017–2019
Authors: Mastrolia Maria Vincenza , Rubino Chiara , Resti Massimo , Trapani Sandra , Galli Luisa 
Published: November 2019

Abstract
Background
Influenza is the most frequent cause of acute upper respiratory tract infections during winter season. Although rare, neurological manifestations are known to occur during influenza infection and approximatively three-quarters of cases are in children. In this study, we aimed to characterize the burden and clinical spectrum of influenza-associated encephalopathy and encephalitis in children admitted at a tertiary pediatric hospital in Italy over two influenza seasons (2017–2019).

Methods
We retrospectively analyzed clinical, laboratory, instrumental data and outcome of patients discharged with ICD9-CM 487.0 code.

Results
Fifteen children (13.1% of those discharged with a diagnosis of influenza infection in the study period), had influenza-associated central nervous system (CNS) manifestations. Eight patients (53.3%) were diagnosed as influenza encephalitis, 7 (46.7%) as influenza encephalopathy. Median age was 27 months. In children under 2 years of age (40% of all cases) altered consciousness was the most frequent neurological manifestation while respiratory symptoms were present at admission in all cases. Younger children also required intensive care support more frequently. Five subjects (33.3%) presented comorbidity. None of the patients had received seasonal influenza vaccination. The median time from onset of respiratory signs to onset of neurological manifestations was 24 h. Cerebrospinal fluid (CSF) analysis was normal in most patients and polymerase chain reaction for influenza virus RNA on CSF, when performed, was negative in all samples. Neuroradiological investigations, performed in 5 children, reported cortical and subcortical white matter signal alterations. Oseltamivir was administered only in 2 cases. Fourteen patients recovered without sequelae, and only a 2-year-old girl had minimal impairment in fine motor skills at discharge.

Conclusions
All children presenting acute neurological features during influenza season should be evaluated for influenza-associated CNS complications even if the respiratory involvement is mild. Absence of underlying diseases or other risk factors are not protective factors against CNS influenza-associated complications. The lack of CSF pleocytosis does not exclude CNS involvement. Children under 2 years of age are at higher risk of requiring intensive care support.
American tegumentary leishmaniasis diagnosis using L. (V.) braziliensis fixed promastigotes: a comparative performance of serological tests and spontaneous cure identification
Authors: Mendes Andresa Pereira Oliveira , Oliveira Beatriz Coutinho , Pereira Allana Maria S. , Castro Maria Carolina Accioly Brelaz , Souza Marina Assis , Brito Maria Edileuza Felinto , Araújo Fernanda Fortes , Teixeira-Carvalho Andrea , Martins-Filho Olindo Assis , Pereira Valeria Rêgo Alves 
Published: November 2019

Abstract
Background
The present study aimed to demonstrate the applicability of a flow cytometry-based serology approach to identify spontaneous cure by the detection of immunoglobulin G, and also, the diagnosis and cure criterion by the IgG1 isotype in American Tegumentary Leishmaniasis – ATL caused by L. (V.) braziliensis. Also, a comparison between flow cytometry with the serological conventional technique was performed.

Methods
Forty five individuals were included in study. They were assessed in two moments: First, 8 subjects spontaneously cured of ATL, 8 healthy individuals and 15 patients who had a positive diagnosis for ATL were selected before treatment to identify spontaneous cure by immunoglobulin G detection. Secondly, 14 patients who were positive for ATL were selected and had their blood collected before and 1, 2 and 5 years after treatment, respectively, for the diagnostic tests (ELISA and flow cytometry) and cure criterion evaluation using the IgG1 isotype.

Results
The analysis of the mean percentage of positive fluorescent parasites (PPFP) along with the titration curves of IgG anti-fixed promastigotes of L.(V.)braziliensis, confirmed the applicability of this method for monitoring spontaneous cure in ATL with outstanding co-positivity (100%) and co-negativity (100%) performance indexes. Regarding the results of the comparison between flow cytometry and ELISA it was seen that there was a better accuracy of the first one in relation to the other. When IgG1 applicability was evaluated, it was observed that before treatment, 36.8% of the patients were negative; in patients 1 year post-treatment, 82.3%; 2 years post-treatment, 27.2% and in patients 5 years post-treatment, 87.5%. The overall analysis of the results suggests that flow cytometry can be applied to ATL detection, and that the use of IgG1 isotype has possibilities to contribute as a more specific diagnostic method.

Conclusions
Therefore, this area has great perspectives use for the diagnosis and cure criterion, and also it can be scaled up with the possibility to characterize the different clinical stages of the disease. Together, these findings demonstrate the applicability of a flow cytometry-based serology approach and opens up new avenues of research with this technique, such as the understanding the humoral response in ATL patients.
Acute shock caused by Clonorchis sinensis infection: a case report
Authors: Wang Nan , Tang Bin , Hao Yuhua , Bai Xue , Wang Xuelin , Li Yuxiang , Yang Yong , Li Shicun , Hao Shuo , Wang Xinyu , Liu Mingyuan , Liu Xiaolei 
Published: November 2019

Abstract
Background
Clonorchiasis, caused by Clonorchis sinensis (C. sinensis) infection, is a serious food-borne zoonotic disease that is often asymptomatic or shows only mild symptoms, which leads to delayed treatment and chronic clonorchiasis and results in various complications, such as cholelithiasis, cholangitis, cholecystitis and cholangiocarcinoma. However, acute shock caused by C. sinensis infection has not been reported. Here, for the first time, we describe a fatal case of acute shock caused by C. sinensis infection.

Case presentation
A patient with a history of eating raw or undercooked freshwater fish was hospitalized with acute shock caused by severe abdominal pain. Physical examination suggested acute abdomen with severe abdominal pain and rigidity. Computed tomography (CT) detection indicated acute cholecystitis and cholelithiasis. After cholecystectomy, several liver flukes were found in the drainage tube. Furthermore, morphological analysis and polymerase chain reaction (PCR) identified the pathogen as C. sinensis. The liver gradually restored normal function after anthelmintic therapy with praziquantel.

Conclusions
In this fatal case, C. sinensis infection was the cause of acute shock, which is rarely found in the clinic environment. This report aims to increase awareness of the hazards and complications related to clonorchiasis. The PCR diagnosis method used in this report might be helpful in reducing the misdiagnosis of clonorchiasis and unnecessary cholecystectomy.
Ultrasound assessment of tensile stress in carotid arteries of healthy human subjects with varying age
Authors: Luo Xianghong , Du Lianfang , Li Zhaojun 
Published: November 2019

AbstractBackgroundArterial remodeling is thought to reflect the adaptation of the vessel wall to mechanical and hemodynamic stimuli and contributes to the progression of cardiovascular and cerebrovascular diseases. Tensile stress (TS) is one of the mechanical properties of the artery wall. The purpose of this study was to investigate the tensile stress change (TS) of carotid artery with varying viscoelasticity in healthy subjects within two groups of different ages.MethodsForty-five subjects were recruited and randomly assigned into the group at the age above 50 years and below 50 years. The carotid arteries were examined by ultrasonography, using the techniques of shear wave elastography (SWE), shear wave dispersion (SWD) and radiofrequency (RF) -based ultrasound. The following values, including elastic modulus (SWER) and viscous index (SWDR), as well as the peak and mean TS of the left and right carotid arteries (L-PTS, R-PTS, L-MTS and R-MTS) were measured. The correlations between SWER, SWDR and tensile stress were evaluated.ResultsThe SWERand SWDRof carotid arteries are lower in the subjects ≥50 years old than the subjects younger than 50 years (SWER, 10.29 ± 9.57 kPa VS 17.24 ± 14.07 kPa; SWDR,11.99 ± 3.51 (m/s)/kHz VS 13.97 ± 3.71 (m/s)/kHz,P < 0.05). The R-PTS was lower in the group with younger age (P < 0.05). Pearson correlation analysis showed that SWERof carotid artery was positively correlated with the parameters of tensile stress, R-PTS, R-MTS, L-PTS and L-MTS(r = 0.218,r = 0.359,r = 0.209 andr = 0.369, respectively,P < 0.05). However, SWDRof carotid arteries was not significantly associated with TS.ConclusionUltrasonic shear wave imaging could be used to quantitatively assess carotid viscoelasticity. The carotid TS was related to its elasticity while little related to its viscosity, suggesting that mechanical properties of the arterial wall might be better revealed.Trial registrationDate of our trial registration: 2018-06-11. Registered with the official website of China Clinical Trial Registration Center (ChiCTR1800016590)