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Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco
No full textAbstract
Background
Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now.
Description
We present the Nicotiana attenuata Data Hub ( Na DH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata . The Na DH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. We implemented several visualization tools, including a modified version of the Electronic Fluorescent Pictograph (eFP) browser, co-expression networks and the Interactive Tree Of Life (iTOL) for studying gene expression divergence among duplicated homologous. In addition, the Na DH allows researchers to query phylogenetic trees of 16,305 gene families and provides tools for analyzing their evolutionary history. Furthermore, we also implemented tools to identify co-expressed genes and metabolites, which can be used for predicting the functions of genes. Using the transcription factor NaMYB8 as an example, we illustrate that the tools and data in Na DH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites.
Conclusion
The Na DH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes in Nicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. Because N. attenuata shares many genome-wide features with other Nicotiana species including cultivated tobacco, and hence Na DH can be a resource for exploring the function and evolution of genes in Nicotiana species in general. The Na DH can be accessed at: http://nadh.ice.mpg.de/
Assessment of quality of care among in-patients with postpartum haemorrhage and severe pre-eclampsia at st. Francis hospital nsambya: a criteria-based audit
No full textAbstract
Background
The maternal mortality ratio of Uganda is still high and the leading causes of maternal mortality are postpartum haemorrhage (PPH), severe pre-eclampsia and eclampsia. Criteria-based audit (CBA) is a way of improving quality of care that has not been commonly used in low income countries. This study aimed at finding out the quality of care provided to patients with these conditions and to find out if the implementation of recommendations from the audit cycle resulted in improvement in quality of care.
Methods
This study was a CBA following a time series study design. It was done in St. Francis Hospital Nsambya and it involved assessment of adherence to standards of care for PPH, severe pre-eclampsia and eclampsia. An initial audit was done for 3 consecutive months, then findings were presented to health workers and recommendations made; we implemented the recommendations in a subsequent month and this comprised three interventions namely continuing medical education (CME), drills and displaying guidelines; a re-audit was done in the proceeding 3 consecutive months and analysis compared adherence rates of the initial audit with those of the re-audit.
Results
Pearson Chi-Square test revealed that the adherence rates of 7 out of 10 standards of care for severe pre-eclampsia/eclampsia were statistically significantly higher in the re-audit than in the initial audit; also, the adherence rates of 3 out of 4 standards of care for PPH were statistically significantly higher in the re-audit than in the initial audit.
Conclusion
The giving of feedback on quality of care and the implementation of recommendations made during the CBA including CME, drills and displaying guidelines was associated with improvements in the quality of care for patients with PPH, severe pre-eclampsia and eclampsia
D-dimer is an essential accompaniment of circulating tumor cells in gastric cancer
No full textAbstract
Background
Fibrinogen (FIB) is an important source of fibrin, which plays a crucial role in circulating tumor cells (CTCs) extravasation and distant metastasis development. We hypothesize it\u2019s stable final product, plasma D-dimer, may be associated with CTCs appearance and can reflect the metastatic phenotype in cancer patients.
Methods
We first verified our hypothesis in different murine gastric cancer metastasis models in vivo, plasma D-dimer and fibrinogen as well as its degradation products were directly examined in three metastasis immune-deficient mouse models and in controls. Next, we gathered and analyzed the result of plasma D-dimer levels and CTCs numbers in 41 advanced primary gastric cancer (GC) patients. A follow-up study was conducted in these patients.
Results
In three in vivo murine metastasis models, plasma D-dimer levels were extremely elevated in a hematogenous and intraperitoneal murine model of metastasis compared with a subcutaneous tumor model and the control group, supporting our previous hypothesis. While in 41 GC patients, the result displayed that plasma D-dimer levels were remarkably increased in patients with distant metastases, especially in visceral metastases patients. Additionally, linear association was shown between D-dimer level and CTCs numbers ( R
2
\u2009=\u20090.688, p \u2009<\u20090.001), additionally, plasma D-dimer represent a better survival predictor than CTCs.
Conclusions
Plasma D-dimer is an essential accompaniment of CTCs in GC that is easy to measure and lower in cost, and can be used in the detection of hematogenous metastasis
Predictors of long term use of psychiatric services of patients with recent-onset schizophrenia: 12\ua0years follow-up
No full textAbstract
Background
The aim of study was to investigate predictors of long term use of psychiatric services of patients with recent-onset schizophrenia.
Methods
A cohort of 50 clinically stable patients with recent-onset schizophrenia was included in a randomized controlled trial comparing early integrated treatment with treatment as usual. Recent onset was defined as emergence of psychotic symptoms for the first time during the preceding 2\ua0years. The follow up period was from the date of randomization and until 12\ua0years after termination of treatment trial, 14\ua0years forward.
Results
Score on Brief psychiatric rating scale both at baseline and after 2\ua0years of treatment, suicide attempts during 2\ua0years of treatment and being an inpatient during 2\ua0years of treatment were significant predictors of long term use of services.
Conclusion
High score on Brief psychiatric rating scale, suicide attempts and being admitted as inpatient early in the course of schizophrenia are possible predictors of long term use of services.
Trial registration
ClinicalTrials.gov NCT00184509 . Registered 15 September 2005
Physical activity levels and associated socio-demographic factors in Bangladeshi adults: a cross-sectional study
No full textAbstract
Background
Low level of physical activity (PA) has become an important public health problem even in low-income countries. The objectives of this study were to measure PA levels, determine the prevalence of low PA and identify socio-demographic factors associated with it in Bangladeshi adults.
Methods
Data from 792 (urban, 395; rural, 397) Bangladeshi adults (25\u201364 years) were included in this population-based cross-sectional study conducted in 2011. Global Physical Activity Questionnaire version 2 (GPAQ-2) was used to measure PA. The metabolic equivalent task (MET) in minutes per week was calculated to determine total PA. Participants were categorized into low, moderate and high PA groups. Logistic regression was used to assess socio-demographic factors associated with low level of PA.
Results
Median MET-minute of total PA per week was almost double in the rural area (1720) than the urban area (960). The overall prevalence of low PA was 50.3% (95% CI: 46.8\u201353.8), urban 59.5% (54.7\u201364.3) and rural 41.9% (37.0\u201346.8). Women in general were more inactive (women 63.1% [58.3\u201367.9], men 39.3% [34.6\u201344.0]). The main contributions to total PA were from work (urban 40.0%, rural 77.0%) and active commute (57.0%, 21.0%). Leisure-time PA represented a very small proportion (<3.0%). Multiple logistic regressions found a significant association of urban residence (OR\u2009=\u20092.2; 95% CI: 1.5\u20133.2), women (2.1; 1.4\u20133.9), oldest age group 55\u201364 years (15.6; 7.5\u201332.2) compared to youngest age group 25\u201334 years, graduation or further education (8.6; 4.1\u201317.7), and higher socio-economic class (2.4; 1.4\u20134.2) compared to poor with insufficient PA.
Conclusions
This study identifies low PA in a rural and urban population in Bangladesh and that further large-scale population studies are warranted
Innovation contests to promote sexual health in china: a qualitative evaluation
No full textAbstract
Background
Innovation contests call on non-experts to help solve problems. While these contests have been used extensively in the private sector to increase engagement between organizations and clients, there is little data on the role of innovation contests to promote health campaigns. We implemented an innovation contest in China to increase sexual health awareness among youth and evaluated community engagement in the contest.
Methods
The sexual health image contest consisted of an open call for sexual health images, contest promotion activities, judging of entries, and celebrating contributions. Contest promotion activities included in-person and social media feedback, classroom didactics, and community-driven activities. We conducted 19 semi-structured interviews with a purposive sample to ensure a range of participant scores, experts and non-expert participants, submitters and non-submitters. Transcripts of each interview were coded with Atlas.ti and evaluated by three reviewers.
Results
We identified stages of community engagement in the contest which contributed to public health impact. Community engagement progressed across a continuum from passive, moderate, active, and finally strong engagement. Engagement was a dynamic process that appeared to have little relationship with formally submitting an image to the contest. Among non-expert participants, contest engagement increased knowledge, healthy attitudes, and empowered participants to share ideas about safe sex with others outside of the contest. Among experts who helped organize the contest, the process of implementing the contest fostered multi-sectoral collaboration and re-oriented public health leadership towards more patient-centered public health campaigns.
Conclusion
The results of this study suggest that innovation contests may be a useful tool for public health promotion by enhancing community engagement and re-orienting health campaigns to make them more patient-centered
The unhealthy food environment does not modify the association between obesity and participation in the Supplemental Nutrition Assistance Program (SNAP) in Los Angeles County
No full textAbstract
Background
Participation in the Supplemental Nutrition Assistance Program (SNAP) has been linked to an increased risk of obesity, but not much is known about the mechanisms behind this association. The objective of this study was to determine if the neighborhood density of unhealthy food outlets modifies the association between obesity and participation in SNAP.
Methods
Data comes from the first wave of the Los Angeles Family and Neighborhood Survey; included are a subsample of adults (18+ years) who were SNAP participants or eligible non-participants ( N \u2009=\u20091,176). We carried out multilevel analyses with obesity (BMI\u2009\u2265\u200930 Kg/m
2
), SNAP participation, and the neighborhood density of unhealthy food outlets as dependent, independent and modifying variables, respectively, controlling for age, gender, race/ethnicity, marital status, working status, mental health, and neighborhood poverty.
Results
SNAP participants had double the odds of obesity compared to eligible non-participants (OR\u2009=\u20092.02; 95%CI\u2009=\u20091.44-2.83). However, the neighborhood density of unhealthy food outlets did not modify this association.
Conclusions
SNAP participation was associated with higher odds of obesity in our primarily Hispanic sample in Los Angeles County, with no effect modification found for the unhealthy portion of the food environment. More research is needed with additional food environment measures to confirm our null findings. Additional research is needed to elucidate the mechanisms linking SNAP participation and obesity as they remain unclear
What patients really think about asthma guidelines: barriers to guideline implementation from the patients\u2019 perspective
No full textAbstract
Background
Treatment of asthma does not always comply with asthma guidelines (AG). This may be rooted in direct or indirect resistance on the doctors\u2019 and/or patients\u2019 side or be caused by the healthcare system. To assess whether patients\u2019 concepts and attitudes are really an implementation barrier for AG, we analysed the patients\u2019 perspective of a \u201cgood asthma therapy\u201d and contrasted their wishes with current recommendations.
Methods
Using a qualitative exploratory design, topic centred focus group (FG) discussions were performed until theoretical saturation was reached. Inclusion criteria were an asthma diagnosis and age above 18. FG sessions were recorded audio-visually and analysed via a mapping technique and content analysis performed according to Mayring (supported by MAXQDA\uae). Participants\u2019 speech times and the proportion of time devoted to different themes were calculated using the Videograph System\uae and related to the content analysis.
Results
Thirteen men and 24 women aged between 20 and 77 from rural and urban areas attended five FG. Some patients had been recently diagnosed with asthma, others years previously or in childhood. The following topics were addressed: (a) concern about or rejection of therapy components, particularly corticosteroids, which sometimes resulted in autonomous uncommunicated medication changes, (b) lack of time or money for optimal treatment, (c) insufficient involvement in therapy choices and (d) a desire for greater empowerment, (e) suboptimal communication between healthcare professionals and (f) difficulties with recommendations conflicting with daily life. Primarily, (g) participants wanted more time with doctors to discuss difficulties and (h) all aspects of living with an impairing condition.
Conclusions
We identified some important patient driven barriers to implementing AG recommendations. In order to advance AG implementation and improve asthma treatment, the patients\u2019 perspective needs to be considered before drafting new versions of AG. These issues should be addressed at the planning stage.
Trial registration
DRKS00000562 (German Clinical Trials Registry)
Recurrent pneumonia among Japanese adults: disease burden and risk factors
No full textAbstract
Background
In Japan and other societies with rapidly aging populations, recurrent pneumonia (RP) is a major clinical problem yet only limited information exists regarding the burden of this disease.
Methods
A prospective study of adult pneumonia was conducted to investigate the incidence of RP and potential risk factors. From February 1, 2012 to January 31, 2013, patients aged\u2009\u2265\u200915\ua0years who were diagnosed with pneumonia were prospectively enrolled in a representative community hospital located in central Japan. Patients were followed for one-year to evaluate the recurrence of pneumonia and characteristics associated with RP. Cox proportional hazards models were constructed to compute adjusted hazard ratios (aHR) and ascertain risk factors significantly associated with RP.
Results
In total, 841 patients with a median age of 73\ua0years (range 15\u2013101\ua0years) were enrolled totaling 1,048 person-years of observation with a median follow-up time of 475\ua0days. A total of 137 patients had at least one recurrent episode with an incidence rate of 13.1 per 100 person-years (95% confidence interval: 11.1\u201315.5). In multivariate analysis, a past history of pneumonia (aHR 1.95, 95% CI: 1.35\u20132.8), chronic pulmonary disease (aHR 1.86, 1.24\u20132.78) and inhaled corticosteroid usage (aHR 1.78, 1.12\u20132.84) and hypnotic/sedative medication usage (aHR 2.06, 1.28\u20133.31) were identified as independent risk factors for recurrent pneumonia, whereas angiotensin converting enzyme-inhibitors usage was associated with a reduction of the risk of RP (aHR 0.22, 0.05\u20130.91). The detection of P. aeruginosa was significantly associated with RP even after adjusting for chronic pulmonary diseases (aHR\u2009=\u20092.37).
Conclusions
Recurrent pneumonia constitutes a considerable proportion of the pneumonia burden in Japan. A past history of pneumonia, chronic pulmonary disease, inhaled corticosteroid and hypnotic/sedative medication usage and detection of P. aeruginosa were identified as independent risk factors for recurrent pneumonia and special attention regarding the use of medications in this vulnerable population is needed to reduce the impact of this disease in aging populations
Study of the variability of scapular inclination and the glenoid version - considerations for preoperative planning: clinical-radiological study
No full textAbstract
Background
Preoperative planning with the aid of imaging methods is a principal factor in successful surgery on the shoulder. This work aims to evaluate the variability of glenoid version, spiralling twist and scapular inclination in relation to the frontal axis. Studies focusing on measuring the variability of scapular inclination in the standardised rest position are lacking in the literature.
Methods
We evaluated 104 CT scans of the shoulder. We measured the glenoid version with respect to the scapular axis at three levels. We measured the scapular inclination angle in relation to the sagittal plane and we determined scapular inclination in relation to the frontal axis. Statistical evaluation was performed using the marginal linear model and parameters were estimated using the generalised least squares method, which enables the dependency of measurements performed on the same subject to be taken into consideration.
Results
The highest values of retroversion are attained by the glenoid in the cranial section (average -9.96\ub0, range -29.7 to +13.2\ub0). Proof of the spiralling twist is the decline in retroversion at the centre of the glenoid (average -2.09\ub0, range -16.7 to +11.6\ub0).
Retroversion decreases further in the inferior direction (average -0.5\ub0, range -20.9 to +17.5\ub0). The average thoracoscapular angle is 45.46\ub0, ranging from 13.1 to 69.0\ub0. The average scapular inclination in relation to the frontal plane is 44.54\ub0, ranging from 21.0 to76.9\ub0.
Conclusions
During preoperative planning, the surgeon should take into consideration not only the glenoid version in relation to the scapular axis, but also the value of the scapular inclination so as to eliminate possible surgical errors, optimise prosthesis implantation and thus decrease the risk of functional restrictions of the joint.
Clinical trial registration
Ethics Committee for Multi-Centric Clinical Trials (EK-554/14,29thApril 2014)