bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-Genome Sequencing Analysis of Methicillin-Resistant Staphylococcus simulans Causing Surgical Site Infection
Authors: Chen Jian , Fang Qiang 
Published: June 2016

ABSTRACT

Staphylococcus simulans
is a normal part of the microbiota in humans and animals and is rarely associated with human invasive infections. We present here the genome sequence of
S. simulans
CJ16, which caused the first case of surgical site infection. Adhesion proteins, including fibronectin-binding protein (FnbA), elastin-binding protein (EbpS), and cell wall-anchored protein (SasA, SasF, and SasH), were detected in the genome, which might promote the survival of
S. simulans
on human skin and pathogenesis of infections.
Whole-Genome Sequencing of a Haarlem Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate from Medellín, Colombia
Authors: Alvarez N. , Haft D. , Hurtado U. A. , Robledo J. , Rouzaud F. 
Published: June 2016

ABSTRACT

Colombia is one of the 105 countries that has reported at least one case of extensively drug-resistant tuberculosis (XDR-TB). The
Mycobacterium tuberculosis
Haarlem genotype is ubiquitous worldwide. Here, we report the high-quality draft genome sequence of a Colombian Haarlem XDR-TB clinical isolate composed of 4,329,127 bp with 4,386 genes.
Draft Genome Sequence of Sphingobium yanoikuyae TJ, a Halotolerant Di-
n
-Butyl-Phthalate-Degrading Bacterium
Authors: Jin Decai , Zhu Ying , Wang Xinxin , Kong Xiao , Liu Huijun , Wang Yafeng , Deng Ye , Jia Minghong 
Published: June 2016

ABSTRACT

Sphingobium yanoikuyae
TJ is a halotolerant di-
n
-butyl-phthalate-degrading bacterium, isolated from the Haihe estuary in Bohai Bay, Tianjin, China. Here, we report the 5.1-Mb draft genome sequence of this strain, which will provide insights into the diversity of
Sphingobium
spp. and the mechanism of phthalate ester degradation in the estuary.
Penicillin-Binding Protein Transpeptidase Signatures for Tracking and Predicting β-Lactam Resistance Levels in Streptococcus pneumoniae
Authors: Li Yuan , Metcalf Benjamin J. , Chochua Sopio , Li Zhongya , Gertz Robert E. , Walker Hollis , Hawkins Paulina A. , Tran Theresa , Whitney Cynthia G. , McGee Lesley , Beall Bernard W. 
Published: June 2016

ABSTRACT
β-Lactam antibiotics are the drugs of choice to treat pneumococcal infections. The spread of β-lactam-resistant pneumococci is a major concern in choosing an effective therapy for patients. Systematically tracking β-lactam resistance could benefit disease surveillance. Here we developed a classification system in which a pneumococcal isolate is assigned to a “PBP type” based on sequence signatures in the transpeptidase domains (TPDs) of the three critical penicillin-binding proteins (PBPs), PBP1a, PBP2b, and PBP2x. We identified 307 unique PBP types from 2,528 invasive pneumococcal isolates, which had known MICs to six β-lactams based on broth microdilution. We found that increased β-lactam MICs strongly correlated with PBP types containing divergent TPD sequences. The PBP type explained 94 to 99% of variation in MICs both before and after accounting for genomic backgrounds defined by multilocus sequence typing, indicating that genomic backgrounds made little independent contribution to β-lactam MICs at the population level. We further developed and evaluated predictive models of MICs based on PBP type. Compared to microdilution MICs, MICs predicted by PBP type showed essential agreement (MICs agree within 1 dilution) of >98%, category agreement (interpretive results agree) of >94%, a major discrepancy (sensitive isolate predicted as resistant) rate of <3%, and a very major discrepancy (resistant isolate predicted as sensitive) rate of <2% for all six β-lactams. Thus, the PBP transpeptidase signatures are robust indicators of MICs to different β-lactam antibiotics in clinical pneumococcal isolates and serve as an accurate alternative to phenotypic susceptibility testing.

IMPORTANCE
The human pathogen
Streptococcus pneumoniae
is a leading cause of morbidity and mortality worldwide. β-Lactam antibiotics such as penicillin and ceftriaxone are the drugs of choice to treat pneumococcal infections. Some pneumococcal strains have developed β-lactam resistance through altering their penicillin-binding proteins (PBPs) and have become a major concern in choosing effective patient therapy. To systematically track and predict β-lactam resistance, we obtained the sequence signatures of PBPs from a large collection of clinical pneumococcal isolates using whole-genome sequencing data and found that these “PBP types” were predictive of resistance levels. Our findings can benefit the current era of strain surveillance when whole-genome sequencing data often lacks detailed resistance information. Using PBP positions that we found are always substituted within highly resistant strains may lead to further refinements. Sequence-based predictions are accurate and may lead to the ability to extract critical resistance information from nonculturable clinical specimens.
Effect of a hospital outreach intervention programme on decreasing hospitalisations and medical costs in patients with chronic obstructive pulmonary disease in China: protocol of a randomised controlled trial
Authors: Yan Jin , Wang Lianhong , Liu Chun , Yuan Hong , Wang Xiaowan , Yu Baorong , Luo Qian 
Published: June 2016

IntroductionPatients with chronic obstructive pulmonary disease (COPD) often have multiple hospitalisations because of exacerbation. Evidence shows disease management programmes are one of the most cost-effective measures to prevent re-hospitalisation for COPD exacerbation, but lack implementation and economic appraisal in China. The aims of the proposed study are to determine whether a hospital outreach invention programme for disease management can decrease hospitalisations and medical costs in patients with COPD in China. Economic appraisal of the programme will also be carried out.Methods and analysisA randomised single-blinded controlled trial will be conducted. 220 COPD patients with exacerbations will be recruited from the Third Xiangya Hospital, Central South University, China. After hospital discharge they will be randomly allocated into an intervention or a control group. Participants in the intervention group will attend a 3-month hospital-based pulmonary rehabilitation intervention and then receive a home-based programme. Both groups will receive identical usual discharge care before discharge from hospital. The primary outcomes will include rate of hospitalisation and medical cost, while secondary outcomes will include mortality, self-efficacy, self-management, health status, quality of life, exercise tolerance and pulmonary function, which will be evaluated at baseline and at 3, 12 and 24 months after the intervention. Cost-effectiveness analysis will be employed for economic appraisal.Ethics and disseminationThe study has been approved by the institutional review board (IRB) of the Third Xiangya Hospital, Central South University (IRB2014-S159). Findings will be shared widely through conference presentations and peer-reviewed publications. Furthermore, the results of the programme will be submitted to health authorities and policy reform will be recommended.Trial registration numberChi CTR-TRC-14005108; Pre-results.
Associations of alcoholic beverage preference with cardiometabolic and lifestyle factors: the NQplus study
Authors: Sluik Diewertje , Brouwer-Brolsma Elske M , de Vries Jeanne H M , Geelen Anouk , Feskens Edith J M 
Published: June 2016

ObjectivesThe preference for a specific alcoholic beverage may be related to an individual's overall lifestyle and health. The objective was to investigate associations between alcoholic beverage preference and several cardiometabolic and lifestyle factors, including adiposity, cholesterol, glycated haemoglobin (HbA1c), liver enzymes and dietary patterns.DesignCross-sectional study.SettingThe Dutch Longitudinal Nutrition Questionnaires plus (NQplus) Study.Participants1653 men and women aged 20–77 years.MethodsDiet, including alcohol, was assessed by Food Frequency Questionnaire. Based on the average number of reported glasses of alcoholic beverage, a person was classified as having a preference for beer, wine, spirit/no specific preference, or as a non-consumer. Mixed linear models were used to calculate crude and adjusted means of cardiometabolic and lifestyle factors across alcoholic beverage preference categories.Primary outcome measuresAnthropometric measures, blood pressure, lipids, HbA1c, albumin, creatinine, uric acid, liver enzymes and dietary patterns.ResultsIn the study population, 43% had a wine preference, 13% a beer preference, 29% had a spirit or no specific preference, and 15% did not consume alcohol. Men who preferred wine had lowest measures of adiposity; the preference for alcoholic beverages was not associated with adiposity measures in women. Wine consumers had higher high density lipoprotein-cholesterol, lower HbA1cand were more likely to follow the ‘Salad’ pattern. Beer consumers had highest levels of triglycerides and liver enzymes, and had higher scores for the ‘Meat’ and ‘Bread’ pattern.ConclusionsFew differences in dietary patterns across alcoholic beverage preference categories were observed. Those differences in cardiometabolic parameters that were observed according to alcoholic beverage preference, suggested that wine consumers have a better health status than beer consumers.
Physicians' occupational stress, depressive symptoms and work ability in relation to their working environment: a cross-sectional study of differences among medical residents with various specialties working in German hospitals
Authors: Bernburg Monika , Vitzthum Karin , Groneberg David A , Mache Stefanie 
Published: June 2016

ObjectivesThis study aimed to analyse and compare differences in occupational stress, depressive symptoms, work ability and working environment among residents working in various medical specialties.Methods435 German hospital residents in medical training working in 6 different medical specialties participated in a cross-sectional survey study. Physicians were asked about their working conditions and aspects of mental health and work ability. The Copenhagen Psychosocial Questionnaire, the Work Ability Index, the ICD-10 Symptom Rating and the Perceived Stress Questionnaire were used to measure working conditions, mental health and work ability.ResultsResults show that up to 17% of the physicians reported high levels of occupational distress and 9% reported high levels of depressive symptoms. 11% of the hospital physicians scored low in work ability. Significant differences between medical specialties were demonstrated for occupational distress, depressive symptoms, work ability, job demands and job resources. Surgeons showed consistently the highest levels of perceived distress but also the highest levels of work ability and lowest scores for depression. Depressive symptoms were rated with the highest levels by anaesthesiologists. Significant associations between physicians’ working conditions, occupational distress and mental health-related aspects are illustrated.ConclusionsStudy results demonstrated significant differences in specific job stressors, demands and resources. Relevant relations between work factors and physicians' health and work ability are discussed. These findings should be reinvestigated in further studies, especially with a longitudinal study design. This work suggests that to ensure physicians' health, hospital management should plan and implement suitable mental health promotion strategies. In addition, operational efficiency through resource planning optimisation and work process improvements should be focused by hospital management.
Endovascular therapy for Acute ischemic Stroke Trial (EAST): study protocol for a prospective, multicentre control trial in China
Authors: Miao Zhongrong , Huo Xiaochuan , Gao Feng , Liao Xiaoling , Wang Chunjuan , Peng Ya , Cao Yibin , Chen Shengli , Zhang Meng , Jiang Changchun , Peng Xiaoxiang , Song Cunfeng , Wei Liping , Zhu Qiyi , Guo Zaiyu , Liu Li , Lin Hang , Yang Hua , Wu Wei , Liang Hui , Xu Anding , Chen Kangning , Zhao Xingquan , Pan Yuesong , Li Hao , Liu Liping , Wang Yilong , Wang Yongjun ,   EAST investigators
Published: June 2016

Background and purpose5 recent trials have shown the benefit of endovascular treatment for acute ischaemic stroke (AIS) due to large vessel occlusion of the anterior circulation. This study aims to evaluate the safety and efficacy of Solitaire thrombectomy in patients with moderate-to-severe stroke in the Chinese population, which has a high prevalence of intracranial atherosclerosis.Methods and analysisThis multicentre prospective control study will involve 17 stroke centres in China, and plans to recruit 150 patients in the intervention group, and 150 patients in the medical group, in which patients meet enrolment criteria but refuse intervention. Patients with AIS due to large vessel occlusion indicated for treatment with Solitaire stent retriever within 12 hours of symptom onset, and who meet the inclusion and exclusion criteria, will be enrolled in this study. The primary efficacy endpoint is functional independence as defined by a modified Rankin Scale (mRS) score ≤2 at 90 days or by functional improvement as defined by mRS, using shift analysis. The procedural efficacy endpoint is arterial recanalisation of the occluded target vessel measured by a modified Thrombolysis in Cerebral Infarction (mTICI) score equal or superior to 2b right following the use of the study device. The primary safety endpoint is symptomatic intracranial haemorrhage (sICH) within 24±3 hours postprocedure.Ethics and disseminationThe protocol was approved by the Ethics Committee at the coordinating centre and by the local Institutional Review Board of each participating centre.Trial registration numberNCT02350283.
Clinical findings and treatment outcomes for cats diagnosed with patent ductus arteriosus in the UK: a retrospective study of 19 cases (2004–2012)
Authors: Wustefeld‐Janssens B. G. , Burrow R. , Mõtsküla P. , Martin M. , Dukes‐McEwan J. 
Published: June 2016

Patent ductus arteriosus (PDA) is infrequently reported in cats and represents between 1–7.3 per cent of left to right shunting cardiac congenital anomalies. The objective of this study was to report the presenting complaints, clinical examination findings, diagnostic findings, treatment outcomes and survival times in cats diagnosed with a PDA in the UK. Medical records from three major UK referral centres were searched for cats that were diagnosed with PDA from January 2004 to December 2012. Data obtained for analysis included: signalment, clinical examination findings including murmur characteristics, diagnostic imaging findings, treatment outcomes and survival times. Nineteen cats were included in the analysis. The most common reason for referral was investigation of an incidentally detected heart murmur without clinical signs (13/19; 68 per cent). Pulmonary arterial hypertension (PAH) was diagnosed in seven (37 per cent) cats and those cats with PAH were significantly more likely to present with signs of disease (P=0.004). Median survival time in cats that were diagnosed with PDA and died due to cardiac causes was 898 days (interquartile range 459–1011 days). The median survival time of those cats that had an additional congenital anomaly was significantly shorter to those cats without a congenital anomaly (P=0.008).
Comparing the effects of first‐line antiepileptic drugs on the gait of dogs with idiopathic epilepsy
Authors: Suiter E. J. , Packer R. M. A. , Volk H. A. 
Published: June 2016

Idiopathic epilepsy (IE) is a common chronic neurological disease of the dog. Previous studies of anti‐epileptic drug (AED) treatment have indicated that acceptable AED adverse effects are as important to owners as reductions in seizure frequency. AEDs in both dogs and human beings are frequently associated with the adverse‐effect ataxia. The aim of this study was to compare ataxia levels in dogs with IE treated chronically with phenobarbitone or imepitoin, the two currently available first‐line AED treatments. The gait of 6 imepitoin‐treated dogs, 8 phenobarbitone‐treated dogs and 10 age‐matched healthy control dogs were compared. Fifty strides from a walking gait were analysed for each dog, quantifying ataxia via the variability in six established gait parameters. Three variables differed significantly between groups: lateral distance between (i) pelvic paw placements, (ii) thoracic paw placements and (iii) stance time, which were significantly more variable in the phenobarbitone‐treated dogs than imepitoin‐treated or control dogs. These results indicate that dogs treated with phenobarbitone experience ataxia compared with controls and imepitoin‐treated dogs. Conversely, there was no difference between imepitoin‐treated dogs and controls. These results along with further research are needed to quantify AEDs adverse effects, to help vets and owners make more informed drug‐choices.
By-product of passion fruit seed (Passiflora edulis) in the diet of commercial laying hens
Authors: Zanetti Leonardo Henrique , Murakami Alice Eiko , Diaz-Vargas Mayra , Flávia Quiles Garcia Guerra Ana , Ospina-Rojas Ivan Camilo , Matumoto Pintro Paula Toshimi , Cruz-Polycarpo Valquíria Cação 
Published: June 2016

This study evaluated the effects of the inclusion of the by-product passion fruit seed (BPFS) in the diet of laying hens on performance, blood variables, quality, and lipid oxidation in eggs. A total of 384 Hy-line W36 layers (32 wk old) were distributed in a completely randomized design, with six treatments (control, 2.5%, 5.0%, 7.5%, 10.0%, and 12.5% inclusion of BPFS), eight replicates and eight birds each. The productive performance was evaluated for three cycles of 28 d each. There was no difference (P > 0.05) in egg production and feed conversion. However, feed intake showed increased linearly (P < 0.05). The egg weight, egg mass, percentage of eggshell, eggshell thickness, and Haugh unit did not differ (P > 0.05); however, the specific gravity of eggs increased (P < 0.05). Total cholesterol and blood triglycerides decreased linearly (P < 0.05). To evaluate the lipid yolk oxidation, a 6 × 5 × 2 factorial design (six levels of BPFS × five storage periods × two temperatures) was used. There was an interaction (P < 0.05) among the levels of BPFS, time, and storage temperature with the lowest oxidation level of 12.5% when eggs were refrigerated. The BPFS can be included at a level up to 5.0% without compromising bird performance and 12.5% for egg quality, and this level reduced yolk lipid oxidation.
Comparison of apparent ileal and total tract digestibility of calcium in calcium sources for pigs
Authors: Zhang F. , Ragland D. , Adeola O. 
Published: June 2016

Two experiments were conducted to compare apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of calcium (Ca) in pigs. In experiment 1, three semipurified diets with soybean meal, canola meal, or sunflower meal as the sole source of Ca were formulated. Eighteen cannulated pigs (initial BW = 66 ± 5 kg) were assigned in a randomized complete block design to three treatments and six replicates per treatment. Results indicated that for either Ca or phosphorus (P), the ATTD was not different from the AID in the three diets (Psite = 0.16 and 0.81, respectively). In experiment 2, diets with four Ca concentrations were formulated with calcium carbonate as the Ca source. Sixteen cannulated pigs (initial BW = 73 ± 4 kg) were assigned in a randomized complete block design to four treatments in two experimental periods. The results indicated that the ATTD of Ca was not different from the AID for all diets. Furthermore, the Ca digestibility was not affected by dietary treatments, but the P digestibility was linearly improved (P < 0.01) as dietary Ca and P concentrations increased. Thus, it is concluded that both AID and ATTD can be used to describe the digestibility of Ca for growing–finishing pigs.
miR-196b Is Epigenetically Silenced during the Premalignant Stage of Lung Carcinogenesis
Authors: Tellez Carmen S. , Juri Daniel E. , Do Kieu , Picchi Maria A. , Wang Teresa , Liu Gang , Spira Avrum , Belinsky Steven A. 
Published: June 2016

Abstract
miRNA silencing by promoter hypermethylation may represent a mechanism by which lung cancer develops and progresses, but the miRNAs involved during malignant transformation are unknown. We previously established a model of premalignant lung cancer wherein we treated human bronchial epithelial cells (HBEC) with low doses of tobacco carcinogens. Here, we demonstrate that next-generation sequencing of carcinogen-transformed HBECs treated with the demethylating agent 5-aza-2′deoxycytidine revealed miR-196b and miR-34c-5p to be epigenetic targets. Bisulfite sequencing confirmed dense promoter hypermethylation indicative of silencing in multiple malignant cell lines and primary tumors. Chromatin immunoprecipitation studies further demonstrated an enrichment in repressive histone marks on the miR-196b promoter during HBEC transformation. Restoration of miR-196b expression by transfecting transformed HBECs with specific mimics led to cell-cycle arrest mediated in part through transcriptional regulation of the FOS oncogene, and miR-196b reexpression also significantly reduced the growth of tumor xenografts. Luciferase assays demonstrated that forced expression of miR-196b inhibited the FOS promoter and AP-1 reporter activity. Finally, a case–control study revealed that methylation of miR-196b in sputum was strongly associated with lung cancer (OR = 4.7, P &lt; 0.001). Collectively, these studies highlight miR-196b as a tumor suppressor whose silencing early in lung carcinogenesis may provide a selective growth advantage to premalignant cells. Targeted delivery of miR-196b could therefore serve as a preventive or therapeutic strategy for the management of lung cancer. Cancer Res; 76(16); 4741–51. ©2016 AACR.
PTK6 Inhibition Suppresses Metastases of Triple-Negative Breast Cancer via SNAIL-Dependent E-Cadherin Regulation
Authors: Ito Koichi , Park Sun Hee , Nayak Anupma , Byerly Jessica H. , Irie Hanna Y. 
Published: June 2016

Abstract
Patients with triple-negative breast cancers (TNBC) are at high risk for recurrent or metastatic disease despite standard treatment, underscoring the need for novel therapeutic targets and strategies. Here we report that protein tyrosine kinase 6 (PTK6) is expressed in approximately 70% of TNBCs where it acts to promote survival and metastatic lung colonization. PTK6 downregulation in mesenchymal TNBC cells suppressed migration and three-dimensional culture growth, and enhanced anoikis, resistance to which is considered a prerequisite for metastasis. PTK6 downregulation restored E-cadherin levels via proteasome-dependent degradation of the E-cadherin repressor SNAIL. Beyond being functionally required in TNBC cells, kinase-active PTK6 also suppressed E-cadherin expression, promoted cell migration, and increased levels of mesenchymal markers in nontransformed MCF10A breast epithelial cells, consistent with a role in promoting an epithelial–mesenchymal transition (EMT). SNAIL downregulation and E-cadherin upregulation mediated by PTK6 inhibition induced anoikis, leading to impaired metastatic lung colonization in vivo. Finally, effects of PTK6 downregulation were phenocopied by treatment with a recently developed PTK6 kinase inhibitor, further implicating kinase activity in regulation of EMT and metastases. Our findings illustrate the clinical potential for PTK6 inhibition to improve treatment of patients with high-risk TNBC. Cancer Res; 76(15); 4406–17. ©2016 AACR.