bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncharacterized Bacterial Structures Revealed by Electron Cryotomography
Authors: Dobro Megan J. , Oikonomou Catherine M. , Piper Aidan , Cohen John , Guo Kylie , Jensen Taylor , Tadayon Jahan , Donermeyer Joseph , Park Yeram , Solis Benjamin A. , Kjær Andreas , Jewett Andrew I. , McDowall Alasdair W. , Chen Songye , Chang Yi-Wei , Shi Jian , Subramanian Poorna , Iancu Cristina V. , Li Zhuo , Briegel Ariane , Tocheva Elitza I. , Pilhofer Martin , Jensen Grant J. 
Published: June 2017

ABSTRACT
Electron cryotomography (ECT) can reveal the native structure and arrangement of macromolecular complexes inside intact cells. This technique has greatly advanced our understanding of the ultrastructure of bacterial cells. We now view bacteria as structurally complex assemblies of macromolecular machines rather than as undifferentiated bags of enzymes. To date, our group has applied ECT to nearly 90 different bacterial species, collecting more than 15,000 cryotomograms. In addition to known structures, we have observed, to our knowledge, several uncharacterized features in these tomograms. Some are completely novel structures; others expand the features or species range of known structure types. Here, we present a survey of these uncharacterized bacterial structures in the hopes of accelerating their identification and study, and furthering our understanding of the structural complexity of bacterial cells.

IMPORTANCE
Bacteria are more structurally complex than is commonly appreciated. Here we present a survey of previously uncharacterized structures that we observed in bacterial cells by electron cryotomography, structures that will initiate new lines of research investigating their identities and roles.
Anaerobic Cysteine Degradation and Potential Metabolic Coordination in Salmonella enterica and Escherichia coli
Authors: Loddeke Melissa , Schneider Barbara , Oguri Tamiko , Mehta Iti , Xuan Zhenyu , Reitzer Larry 
Published: June 2017

ABSTRACT

Salmonella enterica
has two CyuR-activated enzymes that degrade cysteine, i.e., the aerobic CdsH and an unidentified anaerobic enzyme;
Escherichia coli
has only the latter. To identify the anaerobic enzyme, transcript profiling was performed for
E. coli
without
cyuR
and with overexpressed
cyuR
. Thirty-seven genes showed at least 5-fold changes in expression, and the
cyuPA
(formerly
yhaOM
) operon showed the greatest difference. Homology suggested that CyuP and CyuA represent a cysteine transporter and an iron-sulfur-containing cysteine desulfidase, respectively.
E. coli
and
S. enterica
Δ
cyuA
mutants grown with cysteine generated substantially less sulfide and had lower growth yields. Oxygen affected the CyuR-dependent genes reciprocally;
cyuP-lacZ
expression was greater anaerobically, whereas
cdsH-lacZ
expression was greater aerobically. In
E. coli
and
S. enterica
, anaerobic
cyuP
expression required
cyuR
and cysteine and was induced by
l
-cysteine,
d
-cysteine, and a few sulfur-containing compounds. Loss of either CyuA or RidA, both of which contribute to cysteine degradation to pyruvate, increased
cyuP-lacZ
expression, which suggests that CyuA modulates intracellular cysteine concentrations. Phylogenetic analysis showed that CyuA homologs are present in obligate and facultative anaerobes, confirming an anaerobic function, and in archaeal methanogens and bacterial acetogens, suggesting an ancient origin. Our results show that CyuA is the major anaerobic cysteine-catabolizing enzyme in both
E. coli
and
S. enterica
, and it is proposed that anaerobic cysteine catabolism can contribute to coordination of sulfur assimilation and amino acid synthesis.

IMPORTANCE
Sulfur-containing compounds such as cysteine and sulfide are essential and reactive metabolites. Exogenous sulfur-containing compounds can alter the thiol landscape and intracellular redox reactions and are known to affect several cellular processes, including swarming motility, antibiotic sensitivity, and biofilm formation. Cysteine inhibits several enzymes of amino acid synthesis; therefore, increasing cysteine concentrations could increase the levels of the inhibited enzymes. This inhibition implies that control of intracellular cysteine levels, which is the immediate product of sulfide assimilation, can affect several pathways and coordinate metabolism. For these and other reasons, cysteine and sulfide concentrations must be controlled, and this work shows that cysteine catabolism contributes to this control.
Burden of vision loss associated with eye disease in China 1990–2020: findings from the Global Burden of Disease Study 2015
Authors: Wang Bingsong , Congdon Nathan , Bourne Rupert , Li Yichong , Cao Kai , Zhao Aiping , Yusufu Mayinuer , Dong Wenlan , Zhou Maigeng , Wang Ningli 
Published: June 2017

AimsTo assess the burden of vision loss due to eye disease in China between 1990 and 2015, and to predict the burden in 2020.MethodsData from the GBD 2015 (Global Burden of Diseases, Injuries, and Risk Factors Study 2015) were used. The main outcome measures were prevalence and years lived with disability (YLDs) for vision loss due to cataract, glaucoma, macular degeneration, other vision loss, refraction and accommodation disorders and trachoma.ResultsPrevalence for eye diseases increased steadily from 1990 to 2015, and will increase until 2020. From 1990 to 2015, the most common eye disorder was refraction and accommodation disorders. From 1990 to 2015, the vision loss burden due to eye disease decreased for those aged 0–14 years, and increased for those aged 15 years and above, with the most notable increases occurring among those aged 50 years and above. China ranked 10th when comparing YLDs for vision loss due to eye disease with the other members of the G20 (Group of Twenty, an international forum for the governments from 20 major economies) . Age-standardised YLD rates for vision loss due to eye disease declined in all 19 countries, except for China. The burden from vision loss due to eye disease ranked 12th and 11th among all causes of health loss in China in 1990 and 2015, respectively.ConclusionAlone among major economies, China has experienced an increase in the burden of age-standardised vision loss from eye disease over the last two decades. In the future, China may expect a growing burden of vision loss due to population growth and ageing.
Use of standardised patients to assess quality of healthcare in Nairobi, Kenya: a pilot, cross-sectional study with international comparisons
Authors: Daniels Benjamin , Dolinger Amy , Bedoya Guadalupe , Rogo Khama , Goicoechea Ana , Coarasa Jorge , Wafula Francis , Mwaura Njeri , Kimeu Redemptar , Das Jishnu 
Published: June 2017

IntroductionThe quality of clinical care can be reliably measured in multiple settings using standardised patients (SPs), but this methodology has not been extensively used in Sub-Saharan Africa. This study validates the use of SPs for a variety of tracer conditions in Nairobi, Kenya, and provides new results on the quality of care in sampled primary care clinics.MethodsWe deployed 14 SPs in private and public clinics presenting either asthma, child diarrhoea, tuberculosis or unstable angina. Case management guidelines and checklists were jointly developed with the Ministry of Health. We validated the SP method based on the ability of SPs to avoid detection or dangerous situations, without imposing a substantial time burden on providers. We also evaluated the sensitivity of quality measures to SP characteristics. We assessed quality of practice through adherence to guidelines and checklists for the entire sample, stratified by case and stratified by sector, and in comparison with previously published results from urban India, rural India and rural China.ResultsAcross 166 interactions in 42 facilities, detection rates and exposure to unsafe conditions were both zero. There were no detected outcome correlations with SP characteristics that would bias the results. Across all four conditions, 53% of SPs were correctly managed with wide variation across tracer conditions. SPs paid 76% less in public clinics, but proportions of correct management were similar to private clinics for three conditions and higher for the fourth. Kenyan outcomes compared favourably with India and China in all but the angina case.ConclusionsThe SP method is safe and effective in the urban Kenyan setting for the assessment of clinical practice. The pilot results suggest that public providers in this setting provide similar rates of correct management to private providers at significantly lower out-of-pocket costs for patients. However, comparisons across countries are sensitive to the tracer condition considered.
Protocol for a qualitative synthesis of barriers and facilitators in implementing guidelines for diagnosis of tuberculosis
Authors: Ochodo Eleanor , Kredo Tamara , Young Taryn , Wiysonge Charles Shey 
Published: June 2017

IntroductionDespite the introduction of new tests and guidelines for diagnosis of tuberculosis (TB), worldwide case detection rate of TB is still suboptimal. This could be in part explained by the poor implementation of TB diagnostic guidelines. We aim to identify, appraise and synthesise qualitative evidence exploring the barriers and facilitators to implementing TB diagnostic guidelines.Methods and analysisA systematic review of qualitative studies will be conducted. Relevant electronic databases will be searched and studies included based on predefined inclusion criteria. We will also search reference lists, grey literature, conduct forward citation searches and contact relevant content experts. An adaptation of the Critical Appraisal Skills Programme tool will be used to assess the methodological quality of included studies. Two authors will review the search output, extract data and assess methodological quality independently, resolving any disagreements by consensus. We will use the thematic framework analysis approach based on the Supporting the Use of Research Evidence thematic framework to analyse and synthesise our data. We will apply the Confidence in the Evidence from Reviews of Qualitative research approach to transparently assess our confidence in the findings of the systematic review.Ethics and disseminationThis protocol has been registered with the International Prospective Register of Systematic Reviews (PROSPERO), registration number CRD42016039790Trial registration numberPROSPERO 2016: CRD42016039790. Available fromhttp://www.crd.york.ac.uk/PROSPERO/
Defining and measuring suspicion of sepsis: an analysis of routine data
Authors: Inada-Kim Matthew , Page Bethan , Maqsood Imran , Vincent Charles 
Published: June 2017

ObjectivesTo define the target population of patients who have suspicion of sepsis (SOS) and to provide a basis for assessing the burden of SOS, and the evaluation of sepsis guidelines and improvement programmes.DesignRetrospective analysis of routinely collected hospital administrative data.SettingSecondary care, eight National Health Service (NHS) Acute Trusts.ParticipantsHospital Episode Statistics data for 2013–2014 was used to identify all admissions with a primary diagnosis listed in the ‘suspicion of sepsis’ (SOS) coding set. The SOS coding set consists of all bacterial infective diagnoses.ResultsWe identified 47 475 admissions with SOS, equivalent to a rate of 17 admissions per 1000 adults in a given year. The mortality for this group was 7.2% during their acute hospital admission. Urinary tract infection was the most common diagnosis and lobar pneumonia was associated with the most deaths. A short list of 10 diagnoses can account for 85% of the deaths.ConclusionsPatients with SOS can be identified in routine administrative data. It is these patients who should be screened for sepsis and are the target of programmes to improve the detection and treatment of sepsis. The effectiveness of such programmes can be evaluated by examining the outcomes of patients with SOS.
Socioeconomic status and geographical factors associated with active listing in primary care: a cross-sectional population study accounting for multimorbidity, age, sex and primary care
Authors: Ranstad Karin , Midlöv Patrik , Halling Anders 
Published: June 2017

BackgroundSocioeconomic status and geographical factors are associated with health and use of healthcare. Well-performing primary care contributes to better health and more adequate healthcare. In a primary care system based on patient’s choice of practice, this choice (listing) is a key to understand the system.ObjectiveTo explore the relationship between population and practices in a primary care system based on listing.MethodsCross-sectional population-based study. Logistic regressions of the associations between active listing in primary care, income, education, distances to healthcare and geographical location, adjusting for multimorbidity, age, sex and type of primary care practice.Setting and subjectsPopulation over 15 years (n=123 168) in a Swedish county, Blekinge (151 731 inhabitants), in year 2007, actively or passively listed in primary care. The proportion of actively listed was 68%.Main outcome measureActively listed in primary care on 31 December 2007.ResultsHighest ORs for active listing in the model including all factors according to income had quartile two and three with OR 0.70 (95% CI 0.69 to 0.70), and those according to education less than 9 years of education had OR 0.70 (95% CI 0.68 to 0.70). Best odds for geographical factors in the same model had municipality C with OR 0.85 (95% CI 0.85 to 0.86) for active listing. Akaike’s Information Criterion (AIC) was 124 801 for a model including municipality, multimorbidity, age, sex and type of practice and including all factors gave AIC 123 934.ConclusionsHigher income, shorter education, shorter distance to primary care or longer distance to hospital is associated with active listing in primary care.Multimorbidity, age, geographical location and type of primary care practice are more important to active listing in primary care than socioeconomic status and distance to healthcare.
Interfacility transfer of pregnant women using publicly funded emergency call centre-based ambulance services: a cross-sectional analysis of service logs from five states in India
Authors: Singh Samiksha , Doyle Pat , Campbell Oona MR , Oakley Laura , Rao GV Ramana , Murthy GVS 
Published: June 2017

ObjectiveTo estimate the proportion of interfacility transfers (IFTs) transported by ‘108’ ambulances and to compare the characteristics of the IFTs and non-IFTs to understand the pattern of use of ‘108’ services for pregnant women in India.DesignA cross-sectional analysis of ‘108’ ambulance records from five states for the period April 2013 to March 2014. Data were obtained from the call centre database for the pregnant women, who called ‘108’.Main outcomesProportion of all pregnancies and institutional deliveries in the population who were transported by ‘108’, both overall and for IFT. Characteristics of the women transported; obstetric emergencies, the distances travelled and the time taken for both IFT and non-IFT.ResultsThe ‘108’ ambulances transported 6 08 559 pregnant women, of whom 34 993 were IFTs (5.8%) in the five states. We estimated that ‘108’ transferred 16.5% of all pregnancies and 20.8% of institutional deliveries. Only 1.2% of all institutional deliveries in the population were transported by ‘108’ for IFTs—lowest 0.6% in Gujarat and highest 3.0% in Himachal Pradesh. Of all ‘108’ IFTs, only 8.4% had any pregnancy complication. For all states combined, on adjusted analysis, IFTs were more likely than non-IFTs to be for older and younger women or from urban areas, and less likely to be for women from high-priority districts, from backward or scheduled castes, or women below the poverty line. Obstetric emergencies were more than twice as likely to be IFTs as pregnant women without obstetric emergencies (OR=2.18, 95% CI 2.09 to 2.27). There was considerable variation across states.ConclusionOnly 6% institutional deliveries made use of the ‘108’ ambulance for IFTs in India. The vast majority did not have any complication or emergency. The ‘108’ service may need to consider strategies to prioritise the transfer of women with obstetric emergency and those requiring IFT, over uncomplicated non-IFT.
Global prevalence of diabetes mellitus in patients with tuberculosis: a systematic review and meta-analysis protocol
Authors: Tankeu Aurel T , Bigna Jean Joël , Nansseu Jobert Richie , Endomba Francky Teddy A , Wafeu Guy Sadeu , Kaze Arnaud D , Noubiap Jean Jacques 
Published: June 2017

IntroductionDiabetes mellitus (DM) is an important risk factor for active tuberculosis (TB), which also adversely affect TB treatment outcomes. The escalating global DM epidemic is fuelling the burden of TB and should therefore be a major target in the strategy for ending TB. This review aims to estimate the global prevalence of DM in patients with TB.Methods and analysisThis systematic review will include cross-sectional, case–control or cohort studies of populations including patients diagnosed with TB that have reported the prevalence of DM using one of the fourth standard recommendations for screening and diagnosis. This protocol is written in accordance with recommendations from the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols 2015 statement. Relevant abstracts published in English/French from inception to 31 December 2016 will be searched in PubMed, Excerpta Medica Database and online journals. Two investigators will independently screen, select studies, extract data and assess the risk of bias in each study. The study-specific estimates will be pooled through a random-effects meta-analysis model to obtain an overall summary estimate of the prevalence of diabetes across the studies. Heterogeneity will be assessed, and we will pool studies judged to be clinically homogenous. On the other hand, statistical heterogeneity will be evaluated by the χ² test on Cochrane’s Q statistic. Funnel-plots analysis and Egger’s test will be used to investigate publication bias. Results will be presented by continent or geographic regions.Ethics and disseminationThis study is based on published data. An ethical approval is therefore not required. This systematic review and meta-analysis is expected to inform healthcare providers as well as general population on the co-occurrence of DM and TB. The final report will be published as an original article in a peer-reviewed journal, and will also be presented at conferences and submitted to relevant health authorities. We also plan to update the review every 5 years.Protocolregistration numberPROSPERO International Prospective Register of Systematic Reviews (CRD42016049901).
Cohort profile: the Right to Care Clinical HIV Cohort, South Africa
Authors: Fox Matthew P , Maskew Mhairi , Brennan Alana T , Evans Denise , Onoya Dorina , Malete Given , MacPhail Patrick , Bassett Jean , Ebrahim Osman , Mabotja Dikeledi , Mashamaite Sello , Long Lawrence , Sanne Ian 
Published: June 2017

PurposeThe research objectives of the Right to Care Clinical HIV Cohort analyses are to: (1) monitor treatment outcomes (including death, loss to follow-up, viral suppression and CD4 count gain among others) for patients on antiretroviral therapy (ART); (2) evaluate the impact of changes in the national treatment guidelines around when to initiate ART on HIV treatment outcomes; (3) evaluate the impact of changes in the national treatment guidelines around what ART regimens to initiate on drug switches; (4) evaluate the cost and cost-effectiveness of HIV treatment delivery models; (5) evaluate the need for and outcomes on second-line and third-line ART; (6) evaluate the impact of comorbidity with non-communicable diseases on HIV treatment outcomes and (7) evaluate the impact of the switch to initiating all patients onto ART regardless of CD4 count.ParticipantsThe Right to Care Clinical HIV Cohort is an open cohort of data from 10 clinics in two provinces within South Africa. All clinics include data from 2004 onwards. The cohort currently has data on over 115 000 patients initiated on HIV treatment and patients are followed up every 3–6 months for clinical and laboratory monitoring.Findings to dateCohort data includes information on demographics, clinical visit, laboratory data, medication history and clinical diagnoses. The data have been used to identify rates and predictors of first-line failure, to identify predictors of mortality for patients on second-line (eg, low CD4 counts) and to show that adolescents and young adults are at increased risk of unsuppressed viral loads compared with adults.Future plansFuture analyses will inform national models of HIV care and treatment to improve HIV care policy in South Africa.
Are dietary vitamin D, omega-3 fatty acids and folate associated with treatment results in patients with early rheumatoid arthritis? Data from a Swedish population-based prospective study
Authors: Lourdudoss Cecilia , Wolk Alicja , Nise Lena , Alfredsson Lars , Vollenhoven Ronald van 
Published: June 2017

BackgroundDietary intake of vitamin D and omega-3 fatty acids (FA) may be associated with superior response to antirheumatic treatments. In addition, dietary folate intake may be associated with worse response to methotrexate (MTX). The aim of this study was to investigate the association between dietary vitamin D, omega-3 FA, folate and treatment results of disease-modifying antirheumatic drugs (DMARDs) in patients with rheumatoid arthritis (RA).MethodsThis prospective study was based on data from the Epidemiological Investigation of Rheumatoid Arthritis (EIRA) study, and included 727 patients with early RA from 10 hospitals in Sweden. Data on dietary vitamin D, omega-3 FA and folate intake based on food frequency questionnaires were linked with data on European League Against Rheumatism (EULAR) response after 3 months of DMARD treatment. Associations between vitamin D, omega-3 FA, folate and EULAR response were analysed with logistic regression adjusted for potential confounders.ResultsThe majority of patients (89.9%) were initially treated with MTX monotherapy and more than half (56.9%) with glucocorticoids. Vitamin D and omega-3 FA were associated with good EULAR response (OR 1.80 (95% CI 1.14 to 2.83) and OR 1.60 (95% CI 1.02 to 2.53), respectively). Folate was not significantly associated with EULAR response (OR 1.20 (95% CI 0.75 to 1.91)). Similar results were seen in a subgroup of patients who were initially treated with MTX monotherapy at baseline.ConclusionsHigher intake of dietary vitamin D and omega-3 FA during the year preceding DMARD initiation may be associated with better treatment results in patients with early RA. Dietary folate intake was not associated with worse or better response to treatment, especially to MTX. Our results suggest that some nutrients may be associated with enhanced treatment results of DMARDs.