bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Bioluminescence in Photobacterium leiognathi Strain KNH6
Authors: Dunn Anne K. , Rader Bethany A. , Stabb Eric V. , Mandel Mark J. 
Published: September 2015

ABSTRACT

Bacterial bioluminescence is taxonomically restricted to certain proteobacteria, many of which belong to the
Vibrionaceae
. In the most well-studied cases, pheromone signaling plays a key role in regulation of light production. However, previous reports have indicated that certain
Photobacterium
strains do not use this regulatory method for controlling luminescence. In this study, we combined genome sequencing with genetic approaches to characterize the regulation of luminescence in
Photobacterium leiognathi
strain KNH6, an extremely bright isolate. Using transposon mutagenesis and screening for decreased luminescence, we identified insertions in genes encoding components necessary for the luciferase reaction (
lux
,
lum
, and
rib
operons) as well as in nine other loci. These additional loci encode gene products predicted to be involved in the tricarboxylic acid (TCA) cycle, DNA and RNA metabolism, transcriptional regulation, and the synthesis of cytochrome
c
, peptidoglycan, and fatty acids. The mutagenesis screen did not identify any mutants with disruptions of predicted pheromone-related loci. Using targeted gene insertional disruptions, we demonstrate that under the growth conditions tested, luminescence levels do not appear to be controlled through canonical pheromone signaling systems in this strain.

IMPORTANCE
Despite the long-standing interest in luminous bacteria, outside a few model organisms, little is known about the regulation and function of luminescence. Light-producing marine bacteria are widely distributed and have diverse lifestyles, suggesting that the control and significance of luminescence may be similarly diverse. In this study, we apply genetic tools to the study of regulation of light production in the extremely bright isolate
Photobacterium leiognathi
KNH6. Our results suggest an unusual lack of canonical pheromone-mediated control of luminescence and contribute to a better understanding of alternative strategies for regulation of a key bacterial behavior. These experiments lay the groundwork for further study of the regulation and role of bioluminescence in
P. leiognathi
.
Interactions of the Metalloregulatory Protein SloR from Streptococcus mutans with Its Metal Ion Effectors and DNA Binding Site
Authors: Spatafora Grace , Corbett John , Cornacchione Louis , Daly William , Galan Diego , Wysota Michael , Tivnan Patrick , Collins Justin , Nye Dillon , Levitz Talya , Breyer Wendy A. , Glasfeld Arthur 
Published: September 2015

ABSTRACT

Streptococcus mutans
is the causative agent of dental caries, a significant concern for human health, and therefore an attractive target for therapeutics development. Previous work in our laboratory has identified a homodimeric, manganese-dependent repressor protein, SloR, as an important regulator of cariogenesis and has used site-directed mutagenesis to map functions to specific regions of the protein. Here we extend those studies to better understand the structural interaction between SloR and its operator and its effector metal ions. The results of DNase I assays indicate that SloR protects a 42-bp region of DNA that overlaps the
sloABC
promoter on the
S. mutans
UA159 chromosome, while electrophoretic mobility shift and solution binding assays indicate that each of two SloR dimers binds to this region. Real-time semiquantitative reverse transcriptase PCR (real-time semi-qRT-PCR) experiments were used to determine the individual base pairs that contribute to SloR-DNA binding specificity. Solution studies indicate that Mn
2+
is better than Zn
2+
at specifically activating SloR to bind DNA, and yet the 2.8-Å resolved crystal structure of SloR bound to Zn
2+
provides insight into the means by which selective activation by Mn
2+
may be achieved and into how SloR may form specific interactions with its operator. Taken together, these experimental observations are significant because they can inform rational drug design aimed at alleviating and/or preventing
S. mutans
-induced caries formation.

IMPORTANCE
This report focuses on investigating the SloR protein as a regulator of essential metal ion transport and virulence gene expression in the oral pathogen
Streptococcus mutans
and on revealing the details of SloR binding to its metal ion effectors and binding to DNA that together facilitate this expression. We used molecular and biochemical approaches to characterize the interaction of SloR with Mn
2+
and with its SloR recognition element to gain a clearer picture of the regulatory networks that optimize SloR-mediated metal ion homeostasis and virulence gene expression in
S. mutans
. These experiments can have a significant impact on caries treatment and/or prevention by revealing the
S. mutans
SloR-DNA binding interface as an appropriate target for the development of novel therapeutic interventions.
Transcriptome Profiling of the Endophyte Burkholderia phytofirmans PsJN Indicates Sensing of the Plant Environment and Drought Stress
Authors: Sheibani-Tezerji Raheleh , Rattei Thomas , Sessitsch Angela , Trognitz Friederike , Mitter Birgit 
Published: September 2015

ABSTRACT

It is widely accepted that bacterial endophytes actively colonize plants, interact with their host, and frequently show beneficial effects on plant growth and health. However, the mechanisms of plant-endophyte communication and bacterial adaption to the plant environment are still poorly understood. Here, whole-transcriptome sequencing of
B. phytofirmans
PsJN colonizing potato (
Solanum tuberosum
L.
) plants was used to analyze
in planta
gene activity and the response of strain PsJN to plant stress. The transcriptome of PsJN colonizing
in vitro
potato plants showed a broad array of functionalities encoded in the genome of strain PsJN. Transcripts upregulated in response to plant drought stress were mainly involved in transcriptional regulation, cellular homeostasis, and the detoxification of reactive oxygen species, indicating an oxidative stress response in PsJN. Genes with modulated expression included genes for extracytoplasmatic function (ECF) group IV sigma factors. These cell surface signaling elements allow bacteria to sense changing environmental conditions and to adjust their metabolism accordingly. TaqMan quantitative PCR (TaqMan-qPCR) was performed to identify ECF sigma factors in PsJN that were activated in response to plant stress. Six ECF sigma factor genes were expressed in PsJN colonizing potato plants. The expression of one ECF sigma factor was upregulated whereas that of another one was downregulated in a plant genotype-specific manner when the plants were stressed. Collectively, our study results indicate that endophytic
B. phytofirmans
PsJN cells are active inside plants. Moreover, the activity of strain PsJN is affected by plant drought stress; it senses plant stress signals and adjusts its gene expression accordingly.

IMPORTANCE
In recent years, plant growth-promoting endophytes have received steadily growing interest as an inexpensive alternative to resource-consuming agrochemicals in sustainable agriculture. Even though promising effects are recurrently observed under controlled conditions, these are rarely reproducible in the field or show undesirably strong variations. Obviously, a better understanding of endophyte activities in plants and the influence of plant physiology on these activities is needed to develop more-successful application strategies. So far, research has focused mainly on analyzing the plant response to bacterial inoculants. This prompted us to study the gene expression of the endophyte
Burkholderia phytofirmans
PsJN in potato plants. We found that endophytic PsJN cells express a wide array of genes and pathways, pointing to high metabolic activity inside plants. Moreover, the strain senses changes in the plant physiology due to plant stress and adjusts its gene expression pattern to cope with and adapt to the altered conditions.
Experiences with, perceptions of and attitudes towards traditional Korean medicine (TKM) in patients with chronic fatigue: a qualitative, one-on-one, in-depth interview study
Authors: Son Haeng-Mi , Park Eun Young , Kim Duck Hee , Kim Eunjeong , Shin Mi-Suk , Kim Tae-Hun 
Published: September 2015

ObjectivesTo explore perceptions and experiences of patients with chronic fatigue with traditional Korean medicine (TKM) and their motivation for choosing TKM.DesignQualitative, one-on-one, in-depth interview study.SettingPrimary TKM hospitals in Seoul, Incheon and Daejeon, South Korea.Results15 patients with chronic fatigue were interviewed in this study. Patients with chronic fatigue experienced physical and psychological symptoms that resulted in severe difficulties associated with routine daily activities. The motivations for choosing TKM were primarily dissatisfaction with conventional medicine and previous positive experiences with TKM. While undergoing TKM treatment, patients found that TKM practitioners considered fatigue to be a treatable illness; also, patients felt comfortable with the doctor–patient relationship in TKM.ConclusionsHealthcare providers need to be concerned about the symptoms of chronic fatigue to a degree that is in line with the patient's own perceptions. Korean patients with chronic fatigue choose TKM as an alternative to fulfil their long-term needs that were unmet by conventional medicine, and they are greatly positively influenced by TKM. TKM may present a possible therapy to alleviate symptoms of diseases that conventional medicine does not address and is an approach that has a considerable effect on Korean patients.
Fertility outcome analysis after surgical management of tubal ectopic pregnancy: a retrospective cohort study
Authors: Li Jingwei , Jiang Kailei , Zhao Fujie 
Published: September 2015

ObjectivesTo compare the subsequent fertility and risk of recurrence of an ectopic pregnancy (EP) in women who had had an EP, according to the type of surgical treatment they received—that is, salpingectomy, salpingostomy or tubal anastomosis.MethodsA retrospective cohort study was carried out between January 2003 and September 2011 of 618 patients admitted to hospital with tubal EP and who had received surgical treatment (salpingectomy, n=434; salpingostomy, n=112; and tube anastomosis, n=72). Main outcomes included the first intrauterine pregnancy (IUP) and recurrent EP.ResultsThe crude IUP rates up to 24 months after surgery were 55.5% for salpingectomy, 50.9% for salpingostomy and 40.3% for tubal anastomosis treatments. In the multivariate-adjusted model, with the patients receiving salpingectomy as the reference group, HR for patients after salpingostomy and tubal anastomosis treatments for IUP were 0.912 (95% CI 0.762 to 2.017) and 0.619 (95% CI 0.328 to 0.927), respectively. The 2-year cumulative recurrent EP rates were found to be 8.1% for salpingectomy, 6.3% for salpingostomy and 16.7% for tubal anastomosis treatments. Taking the patients receiving salpingectomy as the reference group, the patients who received tubal anastomosis had a positively higher risk of recurrent EP (HR=2.280; 95% CI 1.121 to 4.636) in univariate analysis. Adjustment for other potential confounders only slightly attenuated the HR.ConclusionsThe patients with an EP receiving tubal anastomosis treatments appeared to have a lower 2-year rate of IUP and a higher risk of recurrent EP after adjustment for other potential risk factors.
Diet and physical activity for children's health: a qualitative study of Nepalese mothers’ perceptions
Authors: Oli Natalia , Vaidya Abhinav , Subedi Madhusudan , Eiben Gabriele , Krettek Alexandra 
Published: September 2015

ObjectivesNon-communicable diseases account for 50% of all deaths in Nepal and 25% result from cardiovascular diseases. Previous studies in Nepal indicate a high burden of behavioural cardiovascular risk factors, suggesting a low level of knowledge, attitude and practice/behaviour regarding cardiovascular health. The behavioural foundation for a healthy lifestyle begins in early childhood, when mothers play a key role in their children's lives. This qualitative study, conducted in a Nepalese peri-urban community, aimed to explore mothers’ perception of their children's diet and physical activity.DesignWe notated, tape-recorded and transcribed all data collected from six focus group discussions, and used qualitative content analysis for evaluation and interpretation.SettingThe study was conducted in the Jhaukhel-Duwakot Health Demographic Surveillance Site in the Bhaktapur district of Nepal.ParticipantsLocal health workers helped recruit 61 women with children aged 5–10 years. We distributed participants among six different groups according to educational status.ResultsAlthough participants understood the importance of healthy food, they misunderstood its composition, perceiving it as unappetising and appropriate only for sick people. Furthermore, participants did not prioritise their children's physical activities. Moreover, mothers believed they had limited control over their children's dietary habits and physical activity. Finally, they opined that health educational programmes would help mothers and recommended various intervention strategies to increase knowledge regarding a healthy lifestyle.ConclusionsOur data reveal that mothers of young children in a peri-urban community of Nepal lack adequate and accurate understanding about the impact of a healthy diet and physical activity. Therefore, to prevent future cardiovascular disease and other non-communicable diseases among children, Nepal needs health education programmes to improve mothers’ cardiovascular health knowledge, attitude and behaviour.
Comparison of the university hospital and county hospitals in western Sweden to identify potential weak links in the early chain of care for acute stroke: results of an observational study
Authors: Wireklint Sundström Birgitta , Herlitz Johan , Hansson Per Olof , Brink Peter 
Published: September 2015

ObjectiveTo identify weak links in the early chain of care for acute stroke.Setting9 emergency hospitals in western Sweden, each with a stroke unit, and the emergency medical services (EMS).ParticipantsAll patients hospitalised with a first and a final diagnosis of stroke−between 15 December 2010 and 15 April 2011. The university hospital in the city of Gothenburg was compared with 6 county hospitals.Primary and secondary measures(1) The system delay, that is, median delay time from call to the EMS until diagnosis was designated as the primary end point. Secondary end points were: (2) the system delay time from call to the EMS until arrival in a hospital ward, (3) the use of the EMS, (4) priority at the dispatch centre and (5) suspicion of stroke by the EMS nurse.ResultsIn all, 1376 acute patients with stroke (median age 79 years; 49% women) were included. The median system delay from call to the EMS until (1) diagnosis (CT scan) and (2) arrival in a hospital ward was 3 h and 52 min and 4 h and 22 min, respectively. The system delay (1) was significantly shorter in county hospitals. (3) The study showed that 76% used the EMS (Gothenburg 71%; the county 79%; p<0.0001). (4) Priority 1 was given at the dispatch centre in 54% of cases. (5) Stroke was suspected in 65% of cases. A prenotification was sent in 32% (Gothenburg 52%; the county 20%; p<0.0001).ConclusionsSystem delay is still long and only a small fraction of patients received thrombolysis. Three of four used the EMS (more frequent in the county). They were given the highest priority at the dispatch centre in half of the cases. Stroke was suspected in two-thirds of the cases, but a prenotification was seldom sent to the hospital.
Disparities in the completion of steps to kidney transplantation: protocol for a systematic review
Authors: Traino Heather M , Nonterah Camilla W , Cyrus John W , Gillespie Avrum , Urbanski Megan , Adair-Kriz Michael 
Published: September 2015

IntroductionDisparities in access to transplantation have been well documented. The extant literature, however, focuses largely on disparities and related barriers for African-American patients and none has used the steps to transplantation as a guiding framework. This review will catalogue disparities in the steps to transplantation as well as the barriers and facilitators to completion of each step identified in the extant literature. The results of the review will be used to generate recommendations for future research to improve equity in access to kidney transplantation.Methods and analysisStandard procedures will be used in the conduct of the review. Searches will be performed using the following electronic databases: PubMed/Medline, PsycINFO, CINHAL, EMBASE, Cochrane library and Web of Science. Reports of original research will be eligible for inclusion if they are published from 2005 to present, written or available in English language, performed in the USA, enrol adult participants (18 years of age or more), and employ descriptive or observational designs. Two authors will independently screen retrieved articles for inclusion. MaxQDA will be used for data analysis and management. All included reports will be coded for article characteristics; disparities identified; barriers and motivators of completion of steps to transplantation; and proposed solutions to disparities and barriers. Each report will be coded independently by two authors and discrepancies resolved by discussion among the full team. A qualitative approach to data analysis is planned. Risk of bias will be assessed using standard procedures.Ethics and disseminationThe findings will provide crucial information on the current status of disparities in access to transplantation. PRISMA guidelines will be followed in reporting the results of the review. It is anticipated that these results will inform research which seeks to increase parity in access to transplantation.Systematic review registrationPROSPERO CRD42014015027.
Service availability and association betweenMutuellesand medical care usage for under-five children in rural Rwanda: a statistical analysis with repeated cross-sectional data
Authors: Mejía-Guevara Iván , Hill Kenneth , Subramanian S V , Lu Chunling 
Published: September 2015

ObjectiveTo compare the association betweenMutuelles enrolment and medical care utilisation among under-five rural children between 2005 and 2010; that is, before and after substantial improvements in service availability took place in rural areas.MethodsWe tracked the change in service availability between 2005 and 2010. Using the nationally representative population-based Rwanda Demographic and Health Surveys 2005 and 2010, we conducted a statistical analysis using multilevel logistic random-effects models. We includedMutuellesenrollees and uninsured children who had diarrhoea, cough or fever in the previous 2 weeks of the surveys. The final sample size was 4071 children.ResultsWe observed a substantial increase in the availability of health facilities, medical staff and child health services from 2005 to 2010. In both years, under-five children withMutuelleswere more likely to use medical care than uninsured children. Children in 2010 had a higher probability of using medical care than their counterparts in 2005, regardless of the children's poverty orMutuellesstatus.Mutuellesenrollees in 2010 had the highest probability of using care among children in both years. The findings were robust to model specifications and estimation methods.ConclusionsThis study suggests the importance of strengthening service provision at the supply side in promoting equitable utilisation of childcare with prepayment schemes.
Comparing clinical quality indicators for asthma management in children with outcome measures used in randomised controlled trials: a protocol
Authors: Choong Miew Keen , Tsafnat Guy , Hibbert Peter , Runciman William B , Coiera Enrico 
Published: September 2015

IntroductionClinical quality indicators are necessary to monitor the performance of healthcare services. The development of indicators should, wherever possible, be based on research evidence to minimise the risk of bias which may be introduced during their development, because of logistic, ethical or financial constraints alone. The development of automated methods to identify the evidence base for candidate indicators should improve the process of indicator development. The objective of this study is to explore the relationship between clinical quality indicators for asthma management in children with outcome and process measurements extracted from randomised controlled clinical trial reports.Methods and analysisNational-level indicators for asthma management in children will be extracted from the National Quality Measures Clearinghouse (NQMC) database and the National Institute for Health and Care Excellence (NICE) quality standards. Outcome measures will be extracted from published English language randomised controlled trial (RCT) reports for asthma management in children aged below 12 years. The two sets of measures will be compared to assess any overlap. The study will provide insights into the relationship between clinical quality indicators and measurements in RCTs. This study will also yield a list of measurements used in RCTs for asthma management in children, and will find RCT evidence for indicators used in practice.Ethics and disseminationEthical approval is not necessary because this study will not include patient data. Findings will be disseminated through peer-reviewed publications.
The Deyo-Charlson and Elixhauser-van Walraven Comorbidity Indices as predictors of mortality in critically ill patients
Authors: Ladha Karim S , Zhao Kevin , Quraishi Sadeq A , Kurth Tobias , Eikermann Matthias , Kaafarani Haytham M A , Klein Eric N , Seethala Raghu , Lee Jarone 
Published: September 2015

ObjectivesOur primary objective was to compare the utility of the Deyo-Charlson Comorbidity Index (DCCI) and Elixhauser-van Walraven Comorbidity Index (EVCI) to predict mortality in intensive care unit (ICU) patients.SettingObservational study of 2 tertiary academic centres located in Boston, Massachusetts.ParticipantsThe study cohort consisted of 59 816 patients from admitted to 12 ICUs between January 2007 and December 2012.Primary and secondary outcomeFor the primary analysis, receiver operator characteristic curves were constructed for mortality at 30, 90, 180, and 365 days using the DCCI as well as EVCI, and the areas under the curve (AUCs) were compared. Subgroup analyses were performed within different types of ICUs. Logistic regression was used to add age, race and sex into the model to determine if there was any improvement in discrimination.ResultsAt 30 days, the AUC for DCCI versus EVCI was 0.65 (95% CI 0.65 to 0.67) vs 0.66 (95% CI 0.65 to 0.66), p=0.02. Discrimination improved at 365 days for both indices (AUC for DCCI 0.72 (95% CI 0.71 to 0.72) vs AUC for EVCI 0.72 (95% CI 0.72 to 0.72), p=0.46). The DCCI and EVCI performed similarly across ICUs at all time points, with the exception of the neurosciences ICU, where the DCCI was superior to EVCI at all time points (1-year mortality: AUC 0.73 (95% CI 0.72 to 0.74) vs 0.68 (95% CI 0.67 to 0.70), p=0.005). The addition of basic demographic information did not change the results at any of the assessed time points.ConclusionsThe DCCI and EVCI were comparable at predicting mortality in critically ill patients. The predictive ability of both indices increased when assessing long-term outcomes. Addition of demographic data to both indices did not affect the predictive utility of these indices. Further studies are needed to validate our findings and to determine the utility of these indices in clinical practice.