bluuebunny/crossref_metadata_2025_split huggingface dataset:
fosI
Is a New Integron-Associated Gene Cassette Encoding Reduced Susceptibility to Fosfomycin
Authors: Pelegrino Karla de Oliveira , Campos Juliana Coutinho , Sampaio Suely Carlos Ferreira , Lezirovitz Karina , Seco Bruna Mara , Pereira Mayne de Oliveira , Rocha Darlan Augusto da Costa , Jové Thomas , Nicodemo Antonio Carlos , Sampaio Jorge Luiz Mello 
Published: November 2015

ABSTRACT

In this work, we demonstrate that the
fosI
gene encodes a predicted small protein with 134 amino acids and determines reduced susceptibility to fosfomycin. It raised the MIC from 0.125 to 6 μg/ml when the pBRA100 plasmid was introduced into
Escherichia coli
TOP10 and to 16 μg/ml when the gene was cloned into the pBC_SK(−) vector and expressed in
E. coli
TOP10.
Discovery and Characterization of Human-Urine Utilization by Asymptomatic-Bacteriuria-Causing Streptococcus agalactiae
Authors: Ipe Deepak S. , Ben Zakour Nouri L. , Sullivan Matthew J. , Beatson Scott A. , Ulett Kimberly B. , Benjamin William H. , Davies Mark R. , Dando Samantha J. , King Nathan P. , Cripps Allan W. , Schembri Mark A. , Dougan Gordon , Ulett Glen C. 
Published: November 2015

ABSTRACT

Streptococcus agalactiae
causes both symptomatic cystitis and asymptomatic bacteriuria (ABU); however, growth characteristics of
S. agalactiae
in human urine have not previously been reported. Here, we describe a phenotype of robust growth in human urine observed in ABU-causing
S. agalactiae
(ABSA) that was not seen among uropathogenic
S. agalactiae
(UPSA) strains isolated from patients with acute cystitis. In direct competition assays using pooled human urine inoculated with equal numbers of a prototype ABSA strain, designated ABSA 1014, and any one of several UPSA strains, measurement of the percentage of each strain recovered over time showed a markedly superior fitness of ABSA 1014 for urine growth. Comparative phenotype profiling of ABSA 1014 and UPSA strain 807, isolated from a patient with acute cystitis, using metabolic arrays of >2,500 substrates and conditions revealed unique and specific
l
-malic acid catabolism in ABSA 1014 that was absent in UPSA 807. Whole-genome sequencing also revealed divergence in malic enzyme-encoding genes between the strains predicted to impact the activity of the malate metabolic pathway. Comparative growth assays in urine comparing wild-type ABSA and gene-deficient mutants that were functionally inactivated for the malic enzyme metabolic pathway by targeted disruption of the
maeE
or
maeK
gene in ABSA demonstrated attenuated growth of the mutants in normal human urine as well as synthetic human urine containing malic acid. We conclude that some
S. agalactiae
strains can grow in human urine, and this relates in part to malic acid metabolism, which may affect the persistence or progression of
S. agalactiae
ABU.
Inactivation of Peroxiredoxin 6 by the Pla Protease of Yersinia pestis
Authors: Zimbler Daniel L. , Eddy Justin L. , Schroeder Jay A. , Lathem Wyndham W. 
Published: November 2015

ABSTRACT

Pneumonic plague represents the most severe form of disease caused by
Yersinia pestis
due to its ease of transmission, rapid progression, and high mortality rate. The
Y. pestis
outer membrane Pla protease is essential for the development of pneumonic plague; however, the complete repertoire of substrates cleaved by Pla in the lungs is not known. In this study, we describe a proteomic screen to identify host proteins contained within the bronchoalveolar lavage fluid of mice that are cleaved and/or processed by
Y. pestis
in a Pla-dependent manner. We identified peroxiredoxin 6 (Prdx6), a host factor that contributes to pulmonary surfactant metabolism and lung defense against oxidative stress, as a previously unknown substrate of Pla. Pla cleaves Prdx6 at three distinct sites, and these cleavages disrupt both the peroxidase and phospholipase A
2
activities of Prdx6. In addition, we found that infection with wild-type
Y. pestis
reduces the abundance of extracellular Prdx6 in the lungs compared to that after infection with Δ
pla
Y. pestis
, suggesting that Pla cleaves Prdx6 in the pulmonary compartment. However, following infection with either wild-type or Δ
pla Y. pestis
, Prdx6-deficient mice exhibit no differences in bacterial burden, host immune response, or lung damage from wild-type mice. Thus, while Pla is able to disrupt Prdx6 function
in vitro
and reduce Prdx6 levels
in vivo
, the cleavage of Prdx6 has little detectable impact on the progression or outcome of pneumonic plague.
Dissecting the Structural Elements for the Activation of β-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae
Authors: Hou Jing , Zheng Heping , Chruszcz Maksymilian , Zimmerman Matthew D. , Shumilin Igor A. , Osinski Tomasz , Demas Matt , Grimshaw Sarah , Minor Wladek 
Published: November 2015

ABSTRACT

β-Ketoacyl-(acyl carrier protein) reductase (FabG) catalyzes the key reductive reaction in the elongation cycle of fatty acid synthesis (FAS), which is a vital metabolic pathway in bacteria and a promising target for new antibiotic development. The activation of the enzyme is usually linked to the formation of a catalytic triad and cofactor binding, and crystal structures of FabG from different organisms have been captured in either the active or inactive conformation. However, the structural elements which enable activation of FabG require further exploration. Here we report the findings of structural, enzymatic, and binding studies of the FabG protein found in the causative agent of cholera,
Vibrio cholerae
(vcFabG). vcFabG exists predominantly as a dimer in solution and is able to self-associate to form tetramers, which is the state seen in the crystal structure. The formation of the tetramer may be promoted by the presence of the cofactor NADP(H). The transition between the dimeric and tetrameric states of vcFabG is related to changes in the conformations of the α4/α5 helices on the dimer-dimer interface. Two glycine residues adjacent to the dimer interface (G92 and G141) are identified to be the hinge for the conformational changes, while the catalytic tyrosine (Y155) and a glutamine residue that forms hydrogen bonds to both loop β4-α4 and loop β5-α5 (Q152) stabilize the active conformation. The functions of the aforementioned residues were confirmed by binding and enzymatic assays for the corresponding mutants.

IMPORTANCE
This paper describes the results of structural, enzymatic, and binding studies of FabG from
Vibrio cholerae
(vcFabG). In this work, we dissected the structural elements responsible for the activation of vcFabG. The structural information provided here is essential for the development of antibiotics specifically targeting bacterial FabG, especially for the multidrug-resistant strains of
V. cholerae
.
GroEL2 of Mycobacterium tuberculosis Reveals the Importance of Structural Pliability in Chaperonin Function
Authors: Chilukoti Neeraja , Kumar C. M. Santosh , Mande Shekhar C. 
Published: November 2015

ABSTRACT

Intracellular protein folding is mediated by molecular chaperones, the best studied among which are the chaperonins GroEL and GroES. Conformational changes and allosteric transitions between different metastable states are hallmarks of the chaperonin mechanism. These conformational transitions between three structural domains of GroEL are anchored at two hinges. Although hinges are known to be critical for mediating the communication between different domains of GroEL, the relative importance of hinges on GroEL oligomeric assembly, ATPase activity, conformational changes, and functional activity is not fully characterized. We have exploited the inability of
Mycobacterium tuberculosis
GroEL2 to functionally complement an
Escherichia coli
groEL
mutant to address the importance of hinge residues in the GroEL mechanism. Various chimeras of
M. tuberculosis
GroEL2 and
E. coli
GroEL allowed us to understand the role of hinges and dissect the consequences of oligomerization and substrate binding capability on conformational transitions. The present study explains the concomitant conformational changes observed with GroEL hinge variants and is best supported by the normal mode analysis.

IMPORTANCE
Conformational changes and allosteric transitions are hallmarks of the chaperonin mechanism. We have exploited the inability of
M. tuberculosis
GroEL2 to functionally complement a strain of
E. coli
in which
groEL
expression is repressed to address the importance of hinges. The significance of conservation at the hinge regions stands out as a prominent feature of the GroEL mechanism in binding to GroES and substrate polypeptides. The hinge residues play a significant role in the chaperonin activity
in vivo
and
in vitro
.
Clustering of pain and its associations with health in people aged 50 years and older: cross-sectional results from the North Staffordshire Osteoarthritis Project
Authors: Lacey R J , Strauss V Y , Rathod T , Belcher J , Croft P R , Natvig B , Wilkie R , McBeth J 
Published: November 2015

ObjectiveMost pain in patients aged ≥50 years affects multiple sites and yet the predominant mode of presentation is single-site syndromes. The aim of this study was to investigate if pain sites form clusters in this population and if any such clusters are associated with health factors other than pain.SettingSix general practices in North Staffordshire, UK.DesignCross-sectional, postal questionnaire, study.ParticipantsCommunity-dwelling adults aged ≥50 years registered at the general practices.Main outcomes measuresNumber of pain sites was measured by asking participants to shade sites of pain lasting ≥1 day in the past 4 weeks on a blank body manikin. Health factors measured included anxiety and depression (Hospital and Anxiety Depression Scale), cognitive complaint (Sickness Impact Profile) and sleep. Pain site clustering was investigated using latent class analysis. Association of clusters with health factors, adjusted for age, sex, body mass index and morbidities, was analysed using multinomial regression models.Results13 986 participants (adjusted response 70.6%) completed a questionnaire, of whom 12 408 provided complete pain data. Four clusters of participants were identified: (1) low number of pain sites (36.6%), (2) medium number of sites with no back pain (31.5%), (3) medium number of sites with back pain (17.9%) and (4) high number of sites (14.1%). Compared to Cluster 1, other clusters were associated with poor health. The strongest associations (relative risk ratios, 95% CI) were with Cluster 4: depression (per unit change in score) 1.11 (1.08 to 1.14); cognitive complaint 2.60 (2.09 to 3.24); non-restorative sleep 4.60 (3.50 to 6.05).ConclusionsThese results indicate that in a general population aged ≥50 years, pain forms four clusters shaped by two dimensions—number of pain sites (low, medium, high) and, within the medium cluster, the absence or presence of back pain. The usefulness of primary care treatment approaches based on this simple classification should be investigated.
Funding allocation to surgery in low and middle-income countries: a retrospective analysis of contributions from the USA
Authors: Gutnik Lily , Dieleman Joseph , Dare Anna J , Ramos Margarita S , Riviello Robert , Meara John G , Yamey Gavin , Shrime Mark G 
Published: November 2015

ObjectiveThe funds available for global surgical delivery, capacity building and research are unknown and presumed to be low. Meanwhile, conditions amenable to surgery are estimated to account for nearly 30% of the global burden of disease. We describe funds given to these efforts from the USA, the world's largest donor nation.DesignRetrospective database review. US Agency for International Development (USAID), National Institute of Health (NIH), Foundation Center and registered US charitable organisations were searched for financial data on any organisation giving exclusively to surgical care in low and middle income countries (LMICs). For USAID, NIH and Foundation Center all available data for all years were included. The five recent years of financial data per charitable organisation were included. All nominal dollars were adjusted for inflation by converting to 2014 US dollars.SettingUSA.ParticipantsUSAID, NIH, Foundation Center, Charitable Organisations.Primary and secondary outcome measuresCumulative funds appropriated to global surgery.Results22 NIH funded projects (totalling $31.3 million) were identified, primarily related to injury and trauma. Six relevant USAID projects were identified—all obstetric fistula care totalling $438 million. A total of $105 million was given to universities and charitable organisations by US foundations for 12 different surgical specialties. 95 US charitable organisations representing 14 specialties totalled revenue of $2.67 billion and expenditure of $2.5 billion.Conclusions and relevanceCurrent funding flows to surgical care in LMICs are poorly understood. US funding predominantly comes from private charitable organisations, is often narrowly focused and does not always reflect local needs or support capacity building. Improving surgical care, and embedding it within national health systems in LMICs, will likely require greater financial investment. Tracking funds targeting surgery helps to quantify and clarify current investments and funding gaps, ensures resources materialise from promises and promotes transparency within global health financing.
Protocol for the design of an instrument to measure preadolescent children's self-report of covert aggression and bullying
Authors: Nelson Helen Jean , Kendall Garth Edward , Burns Sharyn , Schonert-Reichl Kimberly 
Published: November 2015

IntroductionCovert bullying in schools is associated with a range of academic, social, emotional and physical health problems. Much research has focused on bullying, but there remains a gap in understanding about covert aggression and how to most accurately and reliably measure children's own reports of this behaviour. This paper reviews relevant literature and outlines a research project that aims to develop a self-report instrument that effectively measures covert aggression and bullying. It is anticipated that this research will result in a standardised instrument that is suitable for exploring preadolescent children's experiences of covert aggressive behaviour. The data collected by the instrument will enhance health and education professionals understanding of covert bullying behaviours and will inform the design and evaluation of interventions.Methods and analysisRelational developmental systems theory will guide the design of an online self-report instrument. The first phase of the project will include a critical review of the research literature, focus groups with children aged 8–12 years (grades 4–6) in Perth, Western Australia, and expert review. The instrument will be explored for content and face validity prior to the assessment of convergent and discriminant validity, internal consistency and test-retest reliability.Ethics and disseminationThe study has been approved by the Curtin University of Human Research Ethics Committee (RDHS-38-15) and by the Executive Principal of the participating school.
Comparison of transient associations of air pollution and AMI hospitalisation in two cities of Alberta, Canada, using a case-crossover design
Authors: Wang Xiaoming , Kindzierski Warren , Kaul Padma 
Published: November 2015

ObjectiveTo investigate reproducibility of outcomes for short-term associations between ambient air pollutants and acute myocardial infarction (AMI) hospitalisation in 2 urban populations.DesignUsing a time-stratified design, we conducted independent case-crossover studies of AMI hospitalisation events over the period 1999–2010 in the geographically close and demographically similar cities of Calgary and Edmonton, Alberta, Canada. Patients with his/her first AMI hospitalisation event were linked with air pollution data from the National Ambient Pollution Surveillance database and meteorological data from the National Climatic Data Center database. Patients were further divided into subgroups to examine adjusted pollution effects. Effects of pollution levels with 0–3-day lag were modelled using conditional logistic regression and adjusted for daily average ambient temperature, dew point temperature and wind speed.SettingPopulation-based studies in Calgary/Edmonton.Participants12 066/10 562 first-time AMI hospitalisations in Calgary/Edmonton.Main outcome measuresAssociation (adjusted OR) between daily ambient air pollution levels and hospitalisation for AMI.ResultsAmong 600 potential air pollution effect variables investigated for the Calgary (Edmonton) population, only 1.17% (0.67%) was statistically significant by using the traditional 5% criterion. None of the effect variables were reproduced in the 2 cities, despite their geographic closeness (within 300 km of each other), and demographic and air pollution similarities.ConclusionsComparison of independent investigations of the effect of air pollution on risk of AMI hospitalisation in Calgary and Edmonton, Alberta, indicated that none of the air pollutants investigated—CO, NO, NO2, O3and particulate matter (PM2.5)—showed consistent positive associations with increased risk of AMI hospitalisation.
Oxfordshire Women and Their Children's Health (OxWATCH): protocol for a prospective cohort feasibility study
Authors: Harrison S , Petrovic G , Chevassut A , Brook L , Higgins N , Kenworthy Y , Selwood M , Snelgar T , Arnold L , Boardman H , Heneghan C , Leeson P , Redman C , Granne I 
Published: November 2015

IntroductionSome specific pregnancy disorders are known to be associated with increased incidence of long-term maternal ill health (eg, gestational diabetes with late onset type 2 diabetes; pre-eclampsia with arterial disease). To what degree these later health conditions are a consequence of the woman's constitution prior to pregnancy rather than pregnancy itself triggering changes in a woman's health is unknown. Additionally, there is little prospective evidence for the impact of pre-pregnancy risk factors on the outcome of pregnancy. To understand the importance of pre-pregnancy health requires the recruitment of women into a long-term cohort study before their first successful pregnancy. The aim of this feasibility study is to test recruitment procedures and acceptability of participation to inform the planning of a future large-scale cohort study.MethodsThe prospective cohort feasibility study will recruit nulliparous women aged 18–40 years. Women will be asked to complete a questionnaire to assess the acceptability of our recruitment and data collection procedures. Baseline biophysical, genetic, socioeconomic, behavioural and psychological assessments will be conducted and samples of blood, urine, saliva and DNA will be collected. Recruitment feasibility and retention rates will be assessed. Women who become pregnant will be recalled for pregnancy and postpregnancy assessments.Ethics and disseminationThe study protocol was approved by South Central Portsmouth REC (Ref: 12/SC/0492). The findings from the study will be disseminated through peer reviewed journals, national and international conference presentations and public events.Trial registration numberhttp://www.clinicaltrials.gov;NCT02419898.
Validity assessment of self-reported medication use by comparing to pharmacy insurance claims
Authors: Fujita Misuzu , Sato Yasunori , Nagashima Kengo , Takahashi Sho , Hata Akira 
Published: November 2015

ObjectivesIn Japan, an annual health check-up and health promotion guidance programme was established in 2008 in accordance with the Act on Assurance of Medical Care for the Elderly. A self-reported questionnaire on medication use is a required item in this programme and has been used widely, but its validity has not been assessed. The aim of this study was to evaluate the validity of this questionnaire by comparing self-reported usage to pharmacy insurance claims.SettingThis is a population-based validation study. Self-reported medication use for hypertension, diabetes and dyslipidaemia is the evaluated measurement. Data on pharmacy insurance claims are used as a reference standard.ParticipantsParticipants were 54 712 beneficiaries of the National Health Insurance of Chiba City.Primary and secondary outcome measuresSensitivity, specificity and κ statistics of the self-reported medication-use questionnaire for predicting actual prescriptions during 1 month (that of the check-up) and 3 months (that of the check-up and the previous 2 months) were calculated.ResultsSensitivity and specificity scores of questionnaire data for predicting insurance claims covering 3 months were, respectively, 92.4% (95% CI 91.9 to 92.8) and 86.4% (95% CI 86.0 to 86.7) for hypertension, 82.6% (95% CI 81.1 to 84.0) and 98.5% (95% CI 98.4 to 98.6) for diabetes, and 86.2% (95% CI 85.5 to 86.8) and 91.0% (95% CI 90.8 to 91.3) for dyslipidaemia. Corresponding κ statistics were 70.9% (95% CI 70.1 to 71.7), 77.1% (95% CI 76.2 to 77.9) and 69.8% (95% CI 68.9 to 70.6). The specificity was significantly higher for questionnaire data covering 3 months compared with data covering 1 month for all 3 conditions.ConclusionsSelf-reported questionnaire data on medication use had sufficiently high validity for further analyses. Item responses showed close agreement with actual prescriptions, particularly those covering 3 months.
A qualitative analysis of New Zealand retailers’ responses to standardised packaging legislation and tobacco industry opposition
Authors: Guthrie John , Hoek Janet , Darroch Ella , Wood Zoë 
Published: November 2015

ObjectivesMany of the approximately 8000 New Zealand retailers selling tobacco are small stores that tobacco companies have represented as victims of policy measures designed to reduce smoking. Despite this depiction, many retailers experience considerable ambivalence in selling tobacco, a product they know harms their customers. We explored how retailers perceived the proposed introduction of standardised (or ‘plain’) packaging and their assessment of arguments made by tobacco companies in submissions on proposed standardised packaging legislation.ParticipantsUsing qualitative in-depth interviews, we recruited and interviewed 23 retailers of dairies (small convenience stores), small supermarkets, and service stations.AnalysesData were analysed using a protocol-driven approach; this stance enabled direct analysis of tobacco companies’ arguments, particularly those purporting to represent retailers’ concerns.ResultsRetailers were concerned about the financial implications of standardised packaging and the effects it may have on their ability to provide rapid and efficient customer service. However, few thought standardised packaging would foster illicit trade or spawn further regulation; most placed public health goals ahead of tobacco companies’ ‘rights’, and many supported government intervention to protect population health.ConclusionsRetailers held ambivalent views on standardised packaging; while they were concerned about short-term effects on their business, they recognised the harm smoking causes. Policymakers and health researchers could collaborate more effectively with retailers by assisting them to create financially viable roles more compatible with public health objectives.