bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequences of Isolates of Enterococcus faecium Sequence Type 117, a Globally Disseminated Multidrug-Resistant Clone
Authors: Tedim Ana P. , Lanza Val F. , Manrique Marina , Pareja Eduardo , Ruiz-Garbajosa Patricia , Cantón Rafael , Baquero Fernando , Coque Teresa M. , Tobes Raquel 
Published: March 2017

ABSTRACT

The emergence of nosocomial infections by multidrug-resistant sequence type 117 (ST117)
Enterococcus faecium
has been reported in several European countries. ST117 has been detected in Spanish hospitals as one of the main causes of bloodstream infections. We analyzed genome variations of ST117 strains isolated in Madrid and describe the first ST117 closed genome sequences.
Draft Genome Sequences of 24 Lactococcus lactis Strains
Authors: Backus Lennart , Wels Michiel , Boekhorst Jos , Dijkstra Annereinou R. , Beerthuyzen Marke , Kelly William J. , Siezen Roland J. , van Hijum Sacha A. F. T. , Bachmann Herwig 
Published: March 2017

ABSTRACT

The lactic acid bacterium
Lactococcus lactis
is widely used for the production of fermented dairy products. Here, we present the draft genome sequences of 24
L. lactis
strains isolated from different environments and geographic locations.
Factors related to receipt of non-cancer-related transurethral prostatectomy: findings from a large prospective study of 106 769 middle-aged and older Australian men
Authors: Joshy Grace , Soga Kay , Korda Rosemary J , Patel Manish I , Banks Emily 
Published: March 2017

BackgroundTransurethral prostatectomy (TURP) is a common surgical intervention for chronic lower urinary tract symptoms (LUTS). Little large-scale evidence exists on factors related to receipt of non-cancer-related TURP.MethodsA prospective study of men aged ≥45 years participating in the 45 and Up Study, a large Australian cohort study, without prior prostatectomy and/or bowel/genital/urinary-tract cancer; questionnaire data were linked to hospitalisations and deaths. HRs for TURP were estimated in relation to multiple factors, adjusting for confounders.ResultsThere were 3416 incident TURPs among 106 769 men (median follow-up 5.8 years), with rates of 1.8, 5.3, 9.1 and 11.4/1000 person-years for ages 45–54, 55–64, 65–74 and ≥75 years, respectively. Age-adjusted rates of TURP varied markedly according to baseline LUTS from 2.2/1000 person-years with no/mild symptoms to 30.7/1000 person-years with severe symptoms. Annual household income ≥$70 000 versus <$20 000, having private health insurance and living in major cities were associated with higher TURP rates; there were no significant differences according to baseline diabetes, stroke, high blood pressure or cardiovascular disease. Men reporting severe versus no physical functioning limitation, high versus low psychological distress or poor versus excellent self-rated health were 36–51% more likely to undergo procedures overall, but were 24–37% less likely to undergo procedures following additional adjustment for need (baseline LUTS).ConclusionsTURP rates were most strongly related to baseline LUTS and age, consistent with appropriate health services targeting. Lower TURP rates in men experiencing socioeconomic disadvantage and with poor health/disability, after accounting for baseline LUTS, suggest inequity and factors such as frailty and risks related to surgery.
Northern Shanghai Study: cardiovascular risk and its associated factors in the Chinese elderly—a study protocol of a prospective study design
Authors: Ji Hongwei , Xiong Jing , Yu Shikai , Chi Chen , Fan Ximin , Bai Bin , Zhou Yiwu , Teliewubai Jiadela , Lu Yuyan , Xu Henry , Zhang Yi , Xu Yawei 
Published: March 2017

IntroductionCardiovascular (CV) diseases are the leading cause of death and disability in the world. Increasing lifespans and ageing populations also contribute to an increasing CV burden. However, in China, there were few well-designed cohort studies focusing on the elderly population, let alone an established CV risk score. The objective of this study is to establish a CV risk score based on a community-dwelling Chinese elderly population, determining the profile of the associated CV risk factors and target organ damages (TODs), so as to guide the later intervention.Methods and analysisThe Northern Shanghai Study is an ongoing prospective community-based study. After enrolment, clinical examination, anthropometric measurement and a questionnaire will be administered to each participant at baseline and after every 2 years in the follow-up. Our tests and examinations include: blood/urine sample and biochemical measurements, office blood pressure recording, carotid ultrasonograph, echocardiograph, pulse wave velocity, pulse wave analysis, 4-limb blood pressure recording, body mass index, etc. Baseline measurement will also include the assessments on TODs and the conventional CV risk factors. In the follow-up, the incidence of CV events and mortality will be recorded. The Northern Shanghai Risk Score will be calculated, with considerations on CV risk factors and TODs.Ethics and disseminationThis study was approved by the Shanghai Tenth People's Hospital Institutional Review Board. All participants signed a written consent form.Trial registration numberNCT02368938; Pre-results.
Evaluation of an alternative care provider clinic for severe sleep-disordered breathing: a study protocol for a randomised controlled trial
Authors: Ip-Buting Ada , Kelly Jenny , Santana Maria J , Penz Erika D , Flemons W Ward , Tsai Willis H , Fraser Kristin L , Hanly Patrick J , Pendharkar Sachin R 
Published: March 2017

IntroductionDespite the high prevalence of sleep-disordered breathing (SDB) and the significant health consequences associated with untreated disease, access to diagnosis and treatment remains a challenge. Even patients with severe SDB (severe obstructive sleep apnoea or hypoventilation), who are at particularly high risk of adverse health effects, are subject to long delays. Previous research has demonstrated that, within a sleep clinic, management by alternative care providers (ACPs) is effective for patients with milder forms of SDB. The purpose of this study is to compare an ACP-led clinic (ACP Clinic) for patients with severe SDB to physician-led care, from the perspective of clinical outcomes, health system efficiency and cost.Methods and analysisThe study is a randomised, controlled, non-inferiority study in which patients who are referred with severe SDB are randomised to management by a sleep physician or by an ACP. ACPs will be supervised by sleep physicians for safety. The primary outcome is positive airway pressure (PAP) adherence after 3 months of therapy. Secondary outcomes include: long-term PAP adherence; clinical response to therapy; health-related quality of life; patient satisfaction; healthcare usage; wait times from referral to treatment initiation and cost-effectiveness. The economic analysis will be performed using the perspective of a publicly funded healthcare system.Ethics and disseminationEthics approval was obtained from the Conjoint Health Research Ethics Board (ID: REB13-1280) at the University of Calgary. Results from this study will be disseminated through presentations at scientific conferences and publication in peer-reviewed journals.Trial registration numberNCT02191085; Pre-results.
Listening to paediatric primary care nurses: a qualitative study of the potential for interprofessional oral health practice in six federally qualified health centres in Massachusetts and Maryland
Authors: Bernstein Judith , Gebel Christina , Vargas Clemencia , Geltman Paul , Walter Ashley , Garcia Raul , Tinanoff Norman 
Published: March 2017

ObjectivesTo explore the opportunities for interprofessional collaboration (IPC) to improve paediatric oral health in federally qualified health centres (FQHCs), to identify challenges to IPC-led integration of oral health prevention into the well-child visit and to suggest strategies to overcome barriers.SampleNurse managers (NMs), nurse practitioners (NPs), paediatric clinical staff and administrators in six FQHCs in two states were interviewed using a semistructured format.DesignGrounded theory research. Topics included feasibility of integration, perceived barriers and strategies for incorporating oral health into paediatric primary care.MeasurementsQualitative data were coded and analysed using NVivo 10 to generate themes iteratively.ResultsNurses in diverse roles recognised the importance of oral health prevention but were unaware of professional guidelines for incorporating oral health into paediatric encounters. They valued collaborative care, specifically internal communication, joint initiatives and training and partnering with dental schools or community dental practices. Barriers to IPC included inadequate training, few opportunities for cross-communication and absence of charting templates in electronic health records.ConclusionsNMs, NPs and paediatric nursing staff all value IPC to improve patients' oral health, yet are constrained by lack of oral health training and supportive charting and referral systems. With supports, they are willing to take on responsibility for introducing oral health preventive measures into the well-child visit, but will require IPC approaches to training and systems changes. IPC teams in the health centre setting can work together, if policy and administrative supports are in place, to provide oral health assessments, education, fluoride varnish application and dental referrals, decrease the prevalence of early childhood caries and increase access to a dental home for low-income children.
Mortality, greenhouse gas emissions and consumer cost impacts of combined diet and physical activity scenarios: a health impact assessment study
Authors: Tainio Marko , Monsivais Pablo , Jones Nicholas RV , Brand Christian , Woodcock James 
Published: March 2017

ObjectiveTo quantify changes in mortality, greenhouse gas (GHG) emissions and consumer costs for physical activity and diet scenarios.DesignFor the physical activity scenarios, all car trips from <1 to <8 miles long were progressively replaced with cycling. For the diet scenarios, the study population was assumed to increase fruit and vegetable (F&V) consumption by 1–5 portions of F&V per day, or to eat at least 5 portions per day. Health effects were modelled with the comparative risk assessment method. Consumer costs were based on fuel cost savings and average costs of F&V, and GHG emissions to fuel usage and F&V production.SettingWorking age population for England.ParticipantsData from the Health Survey for England, National Travel Survey and National Diet and Nutrition Survey.Primary outcomes measuredChanges in premature deaths, consumer costs and GHG emissions stratified by age, gender and socioeconomic status (SES).ResultsPremature deaths were reduced by between 75 and 7648 cases per year for the physical activity scenarios, and 3255 and 6187 cases per year for the diet scenarios. Mortality reductions were greater among people of medium and high SES in the physical activity scenarios, whereas people with lower SES benefited more in the diet scenarios. Similarly, transport fuel costs fell more for people of high SES, whereas diet costs increased most for the lowest SES group. Net GHG emissions decreased by between 0.2 and 10.6 million tons of carbon dioxide equivalent (MtCO2e) per year for the physical activity scenarios and increased by between 1.3 and 6.3 MtCO2e/year for the diet scenarios.ConclusionsIncreasing F&V consumption offers the potential for large health benefits and reduces health inequalities. Replacing short car trips with cycling offers the potential for net benefits for health, GHG emissions and consumer costs.
Understanding the acceptability and adherence to paediatric antiretroviral treatment in the new formulation of pellets (LPV/r): the protocol of a realist evaluation
Authors: Nebot Giralt Ariadna , Nöstlinger Christiana , Lee Janice , Salami Olawale , Lallemant Marc , Ouma Onyango , Nyamongo Isaac , Marchal Bruno 
Published: March 2017

BackgroundImproving access to paediatric HIV treatment requires both large-scale treatment programmes and medication that is adapted to infants and children's needs. The WHO recommends lopinavir/ritonavir as first-line antiretroviral therapy for all HIV-infected children younger than 3 years. There is currently little evidence on the acceptability of, and adherence to, a formulation of this combination treatment if given in the form of pellets. This protocol presents how we will carry a realist evaluation to assess the factors that contribute to the acceptability and adherence to the new pellets formulation in 3 hospitals in Kenya.MethodsWe structured the protocol along the realist evaluation cycle following 4 steps: (1) the initial programme theory, (2) the study design, (3) the data collection methods and (4) the data analysis plan. Theories of behavioural sciences were reviewed for frames that could provide insights into how using such new formulations may contribute to better acceptability and adherence.Ethics and disseminationThis study was approved by the Institutional Review Board of the Institute of Tropical Medicine, the Ethical Committee of the University Hospital Antwerp and the Kenyatta National Hospital/University of Nairobi Ethics and Research Committee. We aim to disseminate the findings through international conferences and peer-reviewed journals and to share them with Drugs for Neglected Diseases initiative's (DNDi) programme managers and with the Kenyan healthcare providers.DiscussionIn developing this study, we encountered some challenges. First, methods to measure the acceptability of any formulation and adherence to it are not standardised. The second challenge is common in realist evaluation and relates to how to choose from different potentially interesting theoretical frameworks. We identified relevant and empirically tested theories from behavioural science that may be helpful in our study. We will test them in 3 settings by exploring the multilevel factors that influence acceptability and adherence of this new paediatric Antiretroviral (ARV) formulation.
Rapid detection ofcfiAmetallo-β-lactamase-producingBacteroides fragilisby the combination of MALDI-TOF MS and CarbaNP
Authors: Ho Pak-Leung , Yau Chong-Yee , Ho Lok-Yan , Chen Jonathan H K , Lai Eileen L Y , Lo Stephanie W U , Tse Cindy W S , Chow Kin-Hung 
Published: March 2017

AimsCarbapenem resistance inBacteroides fragilisis emerging and is mainly attributed to insertion sequence (IS)-mediated activation of the carbapenemase genecfiA. We investigated the use of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and the CarbaNP assay for the rapid identification of these strains.MethodsThis study used the Bruker MALDI Biotype system and the mass spectra models generated by 20B. fragilisreference strains (10cfiA-positive and 10cfiA-negative) in the ClinProTools software to identify 404B. fragilis(71cfiA-positive and 333cfiA-negative) clinical isolates. The ability of the CarbaNP assay to detect IS-mediated activation of thecfiAgene was assessed and the results obtained by molecular analysis were used as reference methods.ResultsThe support vector machine model generated by ClinProTools was found to be the most reliable algorithm for differentiation ofcfiA-positive andcfiA-negativeB. fragilissubgroups. Using the direct transfer method, all but onecfiA-negative isolates were correctly identified to the two subgroups by the model. The correct identification of thecfiA-negative isolate was obtained upon retesting by the extraction method. Of the 81cfiA-positive isolates, PCR and sequencing showed that 30 had an IS element providing the promoter for activation ofcfiA. With regard to the presence of the IS element, the CarbaNP test in thecfiAupstream region had 100% sensitivity, 80.4% specificity, 75.0% positive predictive value and 100% negative predictive value.ConclusionsThe combination of MALDI-TOF MS and the CarbaNP assay can be applied in diagnostic clinical laboratory for rapid identification ofB. fragiliswith IS element-activatedcfiAgene.
Predictors of false-positive stroke thrombectomy transfers
Authors: Yi Julia , Zielinski Danielle , Ouyang Bichun , Conners James , Dafer Rima , Chen Michael 
Published: March 2017

BackgroundMost patients with large vessel occlusion (LVO) stroke need to be transferred to receive thrombectomy. To save time, the decision to transfer often relies on clinical scales as a surrogate for LVO rather than imaging. However, clinical scales have been associated with high levels of diagnostic error. The aim of this study is to define the susceptibility to overdiagnosis of our current transfer decision process by measuring the rate of non-treatment transfers, the most common reasons for no treatment and potential predictors.MethodsClinical and transfer data on consecutive patients transferred to a single endovascular capable centre for possible thrombectomy via stroke code activation were retrospectively reviewed. Whether patients underwent the procedure, why they did not undergo the procedure, and other clinical and logistical predictors were recorded. χ2tests and multivariate logistic regression analysis were performed.ResultsFrom 2015 to 2016, 105/192 transferred patients (54%) did not undergo thrombectomy and the most common reason was absence of a LVO found on CTA after transfer (71/104 (68%)). 14/16 (88%) with a National Institutes of Health Stroke Scale (NIHSS) score <10 did not undergo thrombectomy while 41/78 (52%) with a NIHSS>20 underwent thrombectomy (p<0.001). Helicopter use was associated with no treatment (p=0.004) while arrival within 5 hours was associated with treatment (p<0.001).ConclusionsClinical scales appear to overdiagnose LVO and may be responsible for the majority of our stroke code transfers not undergoing thrombectomy. Primary stroke centres therefore have reason to develop the capability to rapidly acquire and interpret a CTA in patients with suspected LVO prior to transfer. Such efforts may reduce the costs associated with unnecessary thrombectomy transfers.
Detection of human elastase isoforms by the ScheBo Pancreatic Elastase 1 Test
Authors: Tóth Anna Zsófia , Szabó András , Hegyi Eszter , Hegyi Péter , Sahin-Tóth Miklós 
Published: March 2017

Determination of fecal pancreatic elastase content by ELISA is a reliable, noninvasive clinical test for assessing exocrine pancreatic function. Despite the widespread use of commercial tests, their exact molecular targets remain poorly characterized. This study was undertaken to clarify which human pancreatic elastase isoforms are detected by the ScheBo Pancreatic Elastase 1 Stool Test and whether naturally occurring genetic variants influence the performance of this test. Using recombinantly expressed and purified human pancreatic proteinases, we found that the test specifically measured chymotrypsin-like elastases (CELA) 3A and 3B (CELA3A and CELA3B), while CELA2A was not detected. Inactive proelastases, active elastases, and autolyzed forms were detected with identical efficiency. CELA3B elicited approximately four times higher ELISA signal than CELA3A, and we identified Glu154in CELA3B as the critical determinant of detection. Common genetic variants of CELA3A and CELA3B had no effect on test performance, with the exception of the CELA3B variant W79R, which increased detection by 1.4-fold. Finally, none of the human trypsin and chymotrypsin isoforms were detected. We conclude that the ScheBo Pancreatic Elastase 1 Stool Test is specific for human CELA3A and CELA3B, with most of the ELISA signal attributable to CELA3B.NEW & NOTEWORTHY The ScheBo Pancreatic Elastase 1 Stool Test is widely used to assess pancreatic exocrine function, yet its molecular targets have been poorly defined. We demonstrate that, among the human pancreatic proteinases, the test measures the elastase isoform CELA3B and, to a lesser extent, CELA3A. Genetic variants of the human CELA3 isoforms have no significant effect on test performance.
Ursodeoxycholic acid and lithocholic acid exert anti-inflammatory actions in the colon
Authors: Ward Joseph B. J. , Lajczak Natalia K. , Kelly Orlaith B. , O’Dwyer Aoife M. , Giddam Ashwini K. , Ní Gabhann Joan , Franco Placido , Tambuwala Murtaza M. , Jefferies Caroline A. , Keely Simon , Roda Aldo , Keely Stephen J. 
Published: March 2017

Inflammatory bowel diseases (IBD) comprise a group of common and debilitating chronic intestinal disorders for which currently available therapies are often unsatisfactory. The naturally occurring secondary bile acid, ursodeoxycholic acid (UDCA), has well-established anti-inflammatory and cytoprotective actions and may therefore be effective in treating IBD. We aimed to investigate regulation of colonic inflammatory responses by UDCA and to determine the potential impact of bacterial metabolism on its therapeutic actions. The anti-inflammatory efficacy of UDCA, a nonmetabolizable analog, 6α-methyl-UDCA (6-MUDCA), and its primary colonic metabolite lithocholic acid (LCA) was assessed in the murine dextran sodium sulfate (DSS) model of mucosal injury. The effects of bile acids on cytokine (TNF-α, IL-6, Il-1β, and IFN-γ) release from cultured colonic epithelial cells and mouse colonic tissue in vivo were investigated. Luminal bile acids were measured by gas chromatography-mass spectrometry. UDCA attenuated release of proinflammatory cytokines from colonic epithelial cells in vitro and was protective against the development of colonic inflammation in vivo. In contrast, although 6-MUDCA mimicked the effects of UDCA on epithelial cytokine release in vitro, it was ineffective in preventing inflammation in the DSS model. In UDCA-treated mice, LCA became the most common colonic bile acid. Finally, LCA treatment more potently inhibited epithelial cytokine release and protected against DSS-induced mucosal inflammation than did UDCA. These studies identify a new role for the primary metabolite of UDCA, LCA, in preventing colonic inflammation and suggest that microbial metabolism of UDCA is necessary for the full expression of its protective actions.NEW & NOTEWORTHY On the basis of its cytoprotective and anti-inflammatory actions, the secondary bile acid ursodeoxycholic acid (UDCA) has well-established uses in both traditional and Western medicine. We identify a new role for the primary metabolite of UDCA, lithocholic acid, as a potent inhibitor of intestinal inflammatory responses, and we present data to suggest that microbial metabolism of UDCA is necessary for the full expression of its protective effects against colonic inflammation.