bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetics of Lactococci
Authors: Gaudu Philippe , Yamamoto Yuji , Jensen Peter Ruhdal , Hammer Karin , Lechardeur Delphine , Gruss Alexandra 
Published: July 2019

ABSTRACT

Lactococcus lactis
is the best characterized species among the lactococci, and among the most consumed food-fermenting bacteria worldwide. Thanks to their importance in industrialized food production, lactococci are among the lead bacteria understood for fundamental metabolic pathways that dictate growth and survival properties. Interestingly, lactococci belong to the Streptococcaceae family, which includes food, commensal and virulent species. As basic metabolic pathways (e.g., respiration, metal homeostasis, nucleotide metabolism) are now understood to underlie virulence, processes elucidated in lactococci could be important for understanding pathogen fitness and synergy between bacteria. This chapter highlights major findings in lactococci and related bacteria, and covers five themes: distinguishing features of lactococci, metabolic capacities including the less known respiration metabolism in Streptococcaceae, factors and pathways modulating stress response and fitness, interbacterial dialogue
via
metabolites, and novel applications in health and biotechnology.
Rifting of the northern margin of the Indian craton in the Early Cretaceous: Insight from the Aulis Trachyte of the Lesser Himalaya (Nepal)
Authors: Bhandari Saunak , Xiao Wenjiao , Ao Songjian , Windley Brian F. , Zhu Rixiang , Li Rui , Wang Hao Y.C. , Esmaeili Rasoul 
Published: July 2019

Abstract
To reconstruct the early tectonic history of the Himalayan orogen before final India-Asia collision, we carried out geochemical and geochronological studies on the Early Cretaceous Aulis Trachyte of the Lesser Himalaya. The trace-element geochemistry of the trachytic lava flows suggests formation in a rift setting, and zircon U-Pb ages indicate that volcanism occurred in Early Cretaceous time. The felsic volcanics show enrichment of more incompatible elements and rare earth elements, a pattern that is identical to the trachyte from the East African Rift (Kenya rift), with conspicuous negative anomalies of Nb, P, and Ti. Although much of the zircon age data are discordant, they strongly suggest an Early Cretaceous eruption age, which is in agreement with the fossil age of intravolcanic siltstones. The Aulis Trachyte provides the first corroboration of Cretaceous rifting in the Lesser Himalaya as suggested by paleomagnetic data associated with the concept that the northern margin of India separated as a microcontinent and drifted north in the Neo-Tethys before terminal collision of India with Asia.
Hamstring rehabilitation in elite track and field athletes: applying the British Athletics Muscle Injury Classification in clinical practice
Authors: Macdonald Ben , McAleer Stephen , Kelly Shane , Chakraverty Robin , Johnston Michael , Pollock Noel 
Published: July 2019

RationaleHamstring injuries are common in elite sports. Muscle injury classification systems aim to provide a framework for diagnosis. The British Athletics Muscle Injury Classification (BAMIC) describes an MRI classification system with clearly defined, anatomically focused classes based on the site of injury: (a) myofascial, (b) muscle–tendon junction or (c) intratendinous; and the extent of the injury, graded from 0 to 4. However, there are no clinical guidelines that link the specific diagnosis (as above) with a focused rehabilitation plan.ObjectiveWe present an overview of the general principles of, and rationale for, exercise-based hamstring injury rehabilitation in British Athletics. We describe how British Athletics clinicians use the BAMIC to help manage elite track and field athletes with hamstring injury. Within each class of injury, we discuss four topics: clinical presentation, healing physiology, how we prescribe and progress rehabilitation and how we make the shared decision to return to full training. We recommend a structured and targeted diagnostic and rehabilitation approach to improve outcomes after hamstring injury.
Poor health, physical workload and occupational social class as determinants of health-related job loss: results from a prospective cohort study in the UK
Authors: Sewdas Ranu , van der Beek Allard J , Boot Cecile R L , D’Angelo Stefania , Syddall Holly E , Palmer Keith T , Walker-Bone Karen 
Published: July 2019

ObjectivesThe aims of the present study were to assess the association and interactions of physical workload and poor health with health-related job loss (HRJL) among older workers, and the association and interactions of occupational social class and poor health with HRJL.MethodsData were used from an existing prospective cohort study, Health and Employment after Fifty, where employed or self-employed workers aged 50–64 years (n=4909) were followed-up between 2014 and 2016. Associations between potential determinants (self-perceived health status, physical workload and occupational social class) and 2-year HRJL were examined by Cox regression analyses. To study whether physical workload or occupational social class moderates the influence of poor health on HRJL, additive and multiplicative interactions were calculated.ResultsOlder workers with poor self-perceived health status had increased risk of HRJL during the 2-year follow-up period (men: HR 2.57 (95%CI: 1.68 to 3.92); women: HR 3.26 (95%CI: 2.33 to 4.55)). Furthermore, men with high physical workload were at increased risk for HRJL (HR 1.63 (95%CI: 1.09 to 2.43)). No significant interactions (p<0.05) were identified between poor health and high physical workload, nor between poor health and lower occupational social class.ConclusionOur study indicates that older workers in poor health, and older workers with a physically demanding job, are at increased risk of HRJL. Having a physically demanding job or working in routine/manual occupations does not moderate the association between poor health and HRJL.
Development of hypotension in patients newly diagnosed with heart failure in UK general practice: retrospective cohort and nested case–control analyses
Authors: Martín-Pérez Mar , Michel Alexander , Ma Mark , García Rodríguez Luis Alberto 
Published: July 2019

ObjectivesHypotension is of particular relevance for patients with heart failure (HF), since almost all HF drugs cause lowering of blood pressure (BP) and it is associated with a poor prognosis. We aimed to investigate hypotension incidence and risk factors in patients with incident HF in the UK.DesignRetrospective cohort study including nested case–control analyses.SettingThe Health Improvement Network UK primary care database.Participants18 677 adult patients with incident HF during 2000–2005 were followed and cases of hypotension (systolic BP ≤90 mm Hg) were identified. Controls were age-matched, sex-matched and date-matched to cases (1:2).Primary and secondary outcome measuresWe estimated hypotension incidence in the full study population and relevant subgroups (eg, sex and age). Potential risk factors for hypotension overall and for multiple versus single hypotensive episodes were evaluated using conditional logistic regression and unconditional regression models, respectively.ResultsDuring a mean follow-up of 3.31 years, 2565 patients (13.7%) developed hypotension. The incidence of hypotension was 3.17 cases per 100 patient years (95% confidence interval (CI): 3.05–3.30), and was markedly increased in women aged 18–39 years (n=32; 17.72 cases per 100 patient-years; 95% CI: 9.69–29.73). Hypotension risk factors included high healthcare utilisation (proxy measure for HF severity and general comorbidity; eg, ≥10 primary care physician visits versus none, odds ratio (OR): 2.29; 95% CI: 1.34–3.90), previous hypotensive episodes (OR: 2.32; 95% CI: 1.84–2.92), renal failure and use of aldosterone antagonists, angiotensin-converting enzyme inhibitors and angiotensin receptor blockers. Risk factors identified for hypotension generally overlapped with those for multiple versus single hypotensive episodes.ConclusionsHypotension occurs frequently in patients with incident HF. Our findings may help identify patients most likely to benefit from close BP monitoring. The increased incidence of hypotension in young women with HF requires investigation.
External validation of the quick Sequential Organ Failure Assessment score for mortality and bacteraemia risk evaluation in Japanese patients undergoing haemodialysis: a retrospective multicentre cohort study
Authors: Nishiwaki Hiroki , Sasaki Sho , Hasegawa Takeshi , Sasai Fumihiko , Kawarazaki Hiroo , Minatoguchi Shun , Uchida Daisuke , Koitabashi Kenichiro , Ozeki Takaya , Koiwa Fumihiko 
Published: July 2019

ObjectivesWe aimed to examine the validity of the quick Sequential Organ Failure Assessment (qSOFA) score for mortality and bacteraemia risk assessment in Japanese haemodialysis patients.DesignThis is a retrospective multicentre cohort study.SettingThe six participating hospitals are tertiary-care institutions that receive patients on an emergency basis and provide primary, secondary and tertiary care. The other participating hospital is a secondary-care institution that receives patients on an emergency basis and provides both primary and secondary care.ParticipantsThis study included haemodialysis outpatients admitted for bacteraemia suspicion, who had blood drawn for cultures within 48 hours of their initial admission.Primary and secondary outcome measuresThe primary outcome measure was overall in-hospital mortality. Secondary outcomes included 28-day in-hospital mortality and the incidence of bacteraemia diagnosed based on blood culture findings. The discrimination, calibration and test performance of the qSOFA score were assessed. Missing data were handled using multiple imputation.ResultsAmong the 507 haemodialysis patients admitted with bacteraemia suspicion between August 2011 and July 2013, the overall in-hospital mortality was 14.6% (74/507), the 28-day in-hospital mortality was 11.1% (56/507) and the incidence of bacteraemia, defined as a positive blood culture, was 13.4% (68/507). For predicting in-hospital mortality among haemodialysis patients, the area under the receiver operating characteristic curve was 0.61 (95% CI 0.56–0.67) for a qSOFA score ≥2. The Hosmer-Lemeshow χ2statistics for the qSOFA score as a predictor of overall and 28-day in-hospital mortality were 5.72 (p=0.02) and 7.40 (p<0.01), respectively.ConclusionOn external validation, the qSOFA score exhibited low diagnostic accuracy and miscalibration for in-hospital mortality and bacteraemia among haemodialysis patients.
Timing Of Primary Surgery for cleft palate (TOPS): protocol for a randomised trial of palate surgery at 6 months versus 12 months of age
Authors: Shaw William , Semb Gunvor , Lohmander Anette , Persson Christina , Willadsen Elisabeth , Clayton-Smith Jill , Trindade Inge Kiemle , Munro Kevin J , Gamble Carrol , Harman Nicola , Conroy Elizabeth J , Weichart Dieter , Williamson Paula 
Published: July 2019

IntroductionCleft palate is among the most common birth abnormalities. The success of primary surgery in the early months of life is crucial for successful feeding, speech, hearing, dental development and facial growth. Over recent decades, age at palatal surgery in infancy has reduced. This has led to palatal closure in one-stage procedures being carried out around the age of 12 months, but in some cases as early as 6 months. The primary objective of the Timing Of Primary Surgery for Cleft Palate (TOPS)trial is to determine whether surgery for cleft palate performed at 6 or 12 months of age is most beneficial for speech outcomes.Methods and analysisInfants with a diagnosis of non-syndromic isolated cleft palate will be randomised to receive standardised primary surgery (Sommerlad technique) for closure of the cleft at either 6 months or 12 months, corrected for gestational age. The primary outcome will be perceived insufficient velopharyngeal function at 5 years of age. Secondary outcomes measured across 12 months, 3 years and 5 years will include growth, safety of the procedure, dentofacial development, speech, hearing level and middle ear function. Video and audio recordings of speech will be collected in a standardised age-appropriate manner and analysed independently by multiple speech and language therapists. The trial aims to recruit and follow-up 300 participants per arm. Data will be analysed according to the intention-to-treat principle using a 5% significance level. All analyses will be prespecified within a full and detailed statistical analysis plan.Ethics and disseminationEthical approval has been sought in each participating country according to country-specific procedures. Trial results will be presented at conferences, published in peer-reviewed journals and disseminated through relevant patient support groups.Trial registration numberNCT00993551; Pre-results.
IBD prevalence in Lothian, Scotland, derived by capture–recapture methodology
Authors: Jones Gareth-Rhys , Lyons Mathew , Plevris Nikolas , Jenkinson Philip W , Bisset Cathy , Burgess Christopher , Din Shahida , Fulforth James , Henderson Paul , Ho Gwo-Tzer , Kirkwood Kathryn , Noble Colin , Shand Alan G , Wilson David C , Arnott Ian DR , Lees Charlie W 
Published: July 2019

ObjectiveIBD prevalence is estimated to be rising, but no detailed, recent UK data are available. The last reported prevalence estimate in the UK was 0.40% in 2003. We aimed to establish the current, and project future, prevalence in Lothian, Scotland.DesignWe conducted an all-age multiparameter search strategy using inpatient IBD international classification of disease (ICD-10) coding (K50/51)(1997–2018), IBD pathology coding (1990–2018), primary and secondary care prescribing data (2009–2018) and a paediatric registry, (1997–2018) to identify ‘possible’ IBD cases up to 31/08/2018. Diagnoses were manually confirmed through electronic health record review as per Lennard-Jones/Porto criteria. Autoregressive integrated moving average (ARIMA) regression was applied to forecast prevalence to 01/08/2028.ResultsIn total, 24 601 possible IBD cases were identified of which 10 499 were true positives. The point prevalence for IBD in Lothian on 31/08/2018 was 784/100 000 (UC 432/100 000, Crohn’s disease 284/100 000 and IBD unclassified (IBDU) 68/100 000). Capture–recapture methods identified an additional 427 ‘missed’ cases (95% CI 383 to 477) resulting in a ‘true’ prevalence of 832/100 000 (95% CI 827 to 837).Prevalence increased by 4.3% per year between 2008 and 2018 (95% CI +3.7 to +4.9%, p<0.0001). ARIMA modelling projected a point prevalence on 01/08/2028 of 1.02% (95% CI 0.97% to 1.07%) that will affect an estimated 1.53% (95% CI 1.37% to 1.69%) of those >80 years of age.ConclusionsWe report a rigorously validated IBD cohort with all-age point prevalence on 31/08/2018 of 1 in 125, one of the highest worldwide.
Genetic variants and copy number changes in soft tissue leiomyosarcoma detected by targeted amplicon sequencing
Authors: Rao Uma , Schoedel Karen Elizabeth , Petrosko Patricia , Sakai Nozomi , LaFramboise William 
Published: July 2019

AimsLeiomyosarcomas (LMSs) occur in various tissues and harbour potential for metastases. The genomic landscape of LMS is poorly understood. In an effort to improve understanding of the LMS genome, we analysed 11 LMSs of somatic soft tissue including matching tissue of normal phenotype.MethodsDNA derived from microdissected tumour domains and matching normal tissue underwent amplicon sequencing of 409 tumour suppressors and oncogenes using the Ion Torrent Comprehensive Cancer Panel.ResultsGenomic changes were heterogeneous with few recurrent abnormalities detected. Coding variants were identified in genes involved in signal transduction, transcriptional regulation and DNA repair. There were variants in several genes related to angiogenesis andGPR124variants (TEM5) were confirmed by immunohistochemical analysis of a LMS tissue microarray. Surprisingly, there were shared coding variants in tumour and corresponding normal tissue.ConclusionsLMSs are a very heterogeneous population lacking recurrent somatic abnormalities. The presence of damaging mutations in normal tissue may reflect either a germline predisposition or field effect rather than tissue contamination. Hopeful therapeutic targets appear to be those related toAKT/MTORpathway.
RASA1mosaic mutations in patients with capillary malformation-arteriovenous malformation
Authors: Revencu Nicole , Fastre Elodie , Ravoet Marie , Helaers Raphaël , Brouillard Pascal , Bisdorff-Bresson Annouk , Chung Clara W T , Gerard Marion , Dvorakova Veronika , Irvine Alan D , Boon Laurence M , Vikkula Miikka 
Published: July 2019

BackgroundCapillary malformation-arteriovenous malformation is an autosomal dominant disorder, characterised by capillary malformations and increased risk of fast-flow vascular malformations, caused by loss-of-function mutations in theRASA1orEPHB4genes. Around 25% of the patients do not seem to carry a germline mutation in either one of these two genes. Even if other genes could be involved, some individuals may have mutations in the known genes that escaped detection by less sensitive techniques. We tested the hypothesis that mosaic mutations could explain some of previously negative cases.MethodsDNA was extracted from peripheral blood lymphocytes, saliva or vascular malformation tissues from four patients.RASA1andEPHB4coding regions and exon/intron boundaries were analysed by targeted custom gene panel sequencing. A second panel and/or Sanger sequencing were used to confirm the identified mutations.ResultsFour distinct mosaicRASA1mutations, with an allele frequency ranging from 3% to 25%, were identified in four index patients with classical capillary malformation-arteriovenous malformation phenotype. Three mutations were known, one was novel. In one patient, a somatic second hit was also identified. One index case had three affected children, illustrating that the mosaicism was also present in the germline.ConclusionThis study shows thatRASA1mosaic mutations can cause capillary malformation-arteriovenous malformation. Thus, highly sensitive sequencing techniques should be considered as diagnostic tools, especially for patients with no family history. Even low-level mosaicism can cause the classical phenotype and increased risk for offspring. In addition, our study further supports the second-hit pathophysiological mechanism to explain the multifocality of vascular lesions in this disorder.
CCMG practice guideline: laboratory guidelines for next-generation sequencing
Authors: Hume Stacey , Nelson Tanya N , Speevak Marsha , McCready Elizabeth , Agatep Ron , Feilotter Harriet , Parboosingh Jillian , Stavropoulos Dimitri J , Taylor Sherryl , Stockley Tracy L 
Published: July 2019

PurposeThe purpose of this document is to provide guidance for the use of next-generation sequencing (NGS, also known as massively parallel sequencing or MPS) in Canadian clinical genetic laboratories for detection of genetic variants in genomic DNA and mitochondrial DNA for inherited disorders, as well as somatic variants in tumour DNA for acquired cancers. They are intended for Canadian clinical laboratories engaged in developing, validating and using NGS methods.Methods of statement developmentThe document was drafted by the Canadian College of Medical Geneticists (CCMG) Ad Hoc Working Group on NGS Guidelines to make recommendations relevant to NGS. The statement was circulated for comment to the CCMG Laboratory Practice and Clinical Practice committees, and to the CCMG membership. Following incorporation of feedback, the document was approved by the CCMG Board of Directors.DisclaimerThe CCMG is a Canadian organisation responsible for certifying medical geneticists and clinical laboratory geneticists, and for establishing professional and ethical standards for clinical genetics services in Canada. The current CCMG Practice Guidelines were developed as a resource for clinical laboratories in Canada and should not be considered to be inclusive of all information laboratories should consider in the validation and use of NGS for a clinical laboratory service.
Comparison of endoscopic evacuation, stereotactic aspiration, and craniotomy for treatment of basal ganglia hemorrhage
Authors: Guo Wei , Liu Haixiao , Tan Zhijun , Zhang Xiaoyang , Gao Junmei , Zhang Lei , Guo Hao , Bai Hao , Cui Wenxing , Liu Xunyuan , Wu Xun , Luo Jianing , Qu Yan 
Published: July 2019

BackgroundThe main surgical techniques for spontaneous basal ganglia hemorrhage include stereotactic aspiration, endoscopic aspiration, and craniotomy. However, credible evidence is still needed to validate the effect of these techniques.ObjectiveTo explore the long-term outcomes of the three surgical techniques in the treatment of spontaneous basal ganglia hemorrhage.MethodsFive hundred and sixteen patients with spontaneous basal ganglia hemorrhage who received stereotactic aspiration, endoscopic aspiration, or craniotomy were reviewed retrospectively. Six-month mortality and the modified Rankin Scale score were the primary and secondary outcomes, respectively. A multivariate logistic regression model was used to assess the effects of different surgical techniques on patient outcomes.ResultsFor the entire cohort, the 6-month mortality in the endoscopic aspiration group was significantly lower than that in the stereotactic aspiration group (odds ratio (OR) 4.280, 95% CI 2.186 to 8.380); the 6-month mortality in the endoscopic aspiration group was lower than that in the craniotomy group, but the difference was not significant (OR=1.930, 95% CI 0.835 to 4.465). A further subgroup analysis was stratified by hematoma volume. The mortality in the endoscopic aspiration group was significantly lower than in the stereotactic aspiration group in the medium (≥40–<80 mL) (OR=2.438, 95% CI 1.101 to 5.402) and large hematoma subgroup (≥80 mL) (OR=66.532, 95% CI 6.345 to 697.675). Compared with the endoscopic aspiration group, a trend towards increased mortality was observed in the large hematoma subgroup of the craniotomy group (OR=8.721, 95% CI 0.933 to 81.551).ConclusionEndoscopic aspiration can decrease the 6-month mortality of spontaneous basal ganglia hemorrhage, especially in patients with a hematoma volume ≥40 mL.
Does stress echocardiography add incremental value to baseline ejection fraction for the early identification of candidates for implantable defibrillators?
Authors: Muhrbeck Josephine , Gunyeli Elif , Andersson Eva , Alam Mahbubul , Frykman Viveka , Sjoblom Johanna 
Published: July 2019

ObjectiveA reduction in left ventricular ejection fraction (EF) remains the strongest indicator of increased risk of sudden cardiac death after an acute myocardial infarction (AMI). Guidelines recommend that patients with an EF ≤35%, 6–12 weeks after AMI should be considered for implantable cardioverter defibrillator (ICD) therapy. Stress echocardiography is a safe method to detect viability in a stunned myocardium. The purpose of this study was to investigate if stress echocardiography early after AMI could identify ICD candidates before discharge.MethodsNinety-six patients with EF ≤40% early after AMI were prospectively included in a cohort study, and investigated by baseline and stress echocardiography before discharge. Follow-up echocardiography was performed after 3 months. EF, mitral annular plane systolic excursion (MAPSE) and peak systolic velocity (PSV) were determined for each examination.ResultsThere were 80 (83%) patients who completed the baseline, stress and follow-up echocardiography. Among them there were 32 (40%) patients who met the ICD criteria of EF ≤35% at 3 months. For these patients, EF, MAPSE and PSV were significantly lower than for those patients who recovered. The area under the receiver operating characteristic curve (AUC) was 85% (95% CI 0.74 to 0.94) for baseline EF to predict non-recovery. None of the other variables had a higher AUC.ConclusionPatients who met the ICD criteria of EF ≤35% at 3 months after myocardial infarction had lower EF, MAPSE and PSV on baseline and stress echocardiograph before discharge. Stress echocardiography did not add additional value in predicting non-recovery.