A biologist's guide to Bayesian phylogenetic analysis.

Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. Here, we summarize the major features of Bayesian phylogenetic inference and discuss Bayesian computation using Markov chain Monte Carlo (MCMC), the diagnosis of an MCMC run, and ways of summarising the MCMC sample. We discuss the specification of the prior, the choice of the substitution model, and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software and provide recommendations as to their use

Guidance on noncorticosteroid systemic immunomodulatory therapy in noninfectious uveitis: fundamentals of care for uveitis (focus) initiative

Topic: An international, expert-led consensus initiative to develop systematic, evidence-based recommendations for the treatment of noninfectious uveitis in the era of biologics. Clinical Relevance: The availability of biologic agents for the treatment of human eye disease has altered practice patterns for the management of noninfectious uveitis. Current guidelines are insufficient to assure optimal use of noncorticosteroid systemic immunomodulatory agents. Methods: An international expert steering committee comprising 9 uveitis specialists (including both ophthalmologists and rheumatologists) identified clinical questions and, together with 6 bibliographic fellows trained in uveitis, conducted a Preferred Reporting Items for Systematic Reviews and Meta-Analyses protocol systematic reviewof the literature (English language studies from January 1996 through June 2016; Medline [OVID], the Central Cochrane library, EMBASE,CINAHL,SCOPUS,BIOSIS, andWeb of Science). Publications included randomized controlled trials, prospective and retrospective studies with sufficient follow-up, case series with 15 cases or more, peer-reviewed articles, and hand-searched conference abstracts from key conferences. The proposed statements were circulated among 130 international uveitis experts for review.Atotal of 44 globally representativegroupmembersmet in late 2016 to refine these guidelines using a modified Delphi technique and assigned Oxford levels of evidence. Results: In total, 10 questions were addressed resulting in 21 evidence-based guidance statements covering the following topics: when to start noncorticosteroid immunomodulatory therapy, including both biologic and nonbiologic agents; what data to collect before treatment; when to modify or withdraw treatment; how to select agents based on individual efficacy and safety profiles; and evidence in specific uveitic conditions. Shared decision-making, communication among providers and safety monitoring also were addressed as part of the recommendations. Pharmacoeconomic considerations were not addressed. Conclusions: Consensus guidelines were developed based on published literature, expert opinion, and practical experience to bridge the gap between clinical needs and medical evidence to support the treatment of patients with noninfectious uveitis with noncorticosteroid immunomodulatory agents

T-Cell Memory Responses Elicited by Yellow Fever Vaccine are Targeted to Overlapping Epitopes Containing Multiple HLA-I and -II Binding Motifs

The yellow fever vaccines (YF-17D-204 and 17DD) are considered to be among the safest vaccines and the presence of neutralizing antibodies is correlated with protection, although other immune effector mechanisms are known to be involved. T-cell responses are known to play an important role modulating antibody production and the killing of infected cells. However, little is known about the repertoire of T-cell responses elicited by the YF-17DD vaccine in humans. In this report, a library of 653 partially overlapping 15-mer peptides covering the envelope (Env) and nonstructural (NS) proteins 1 to 5 of the vaccine was utilized to perform a comprehensive analysis of the virus-specific CD4+ and CD8+ T-cell responses. The T-cell responses were screened ex-vivo by IFN-γ ELISPOT assays using blood samples from 220 YF-17DD vaccinees collected two months to four years after immunization. Each peptide was tested in 75 to 208 separate individuals of the cohort. The screening identified sixteen immunodominant antigens that elicited activation of circulating memory T-cells in 10% to 33% of the individuals. Biochemical in-vitro binding assays and immunogenetic and immunogenicity studies indicated that each of the sixteen immunogenic 15-mer peptides contained two or more partially overlapping epitopes that could bind with high affinity to molecules of different HLAs. The prevalence of the immunogenicity of a peptide in the cohort was correlated with the diversity of HLA-II alleles that they could bind. These findings suggest that overlapping of HLA binding motifs within a peptide enhances its T-cell immunogenicity and the prevalence of the response in the population. In summary, the results suggests that in addition to factors of the innate immunity, "promiscuous" T-cell antigens might contribute to the high efficacy of the yellow fever vaccines. © 2013 de Melo et al

Are isomeric alkenes used in species recognition among neo-tropical stingless bees (Melipona spp)

The majority of our understanding of the role of cuticular hydrocarbons (CHC) in recognition is based largely on temperate ant species and honey bees. The stingless bees remain relatively poorly studied, despite being the largest group of eusocial bees, comprising more than 400 species in some 60 genera. The Meliponini and Apini diverged between 80-130 Myr B.P. so the evolutionary trajectories that shaped the chemical communication systems in ants, honeybees and stingless bees may be very different. Therefore, the main aim of this study was to study if a unique species CHC signal existed in Neotropical stingless bees, as shown for many temperate species, and if so what compounds are involved. This was achieved by collecting CHC data from 24 colonies belonging to six species of Melipona from North-eastern Brazil and comparing this new data with all previously published CHC studies on Melipona. We found that each of the eleven Melipona species studied so far each produced a unique species CHC signal based around their alkene isomer production. A remarkable number of alkene isomers, up to 25 in M. asilvai, indicated the diversification of alkene positional isomers among the stingless bees. The only other group to have really diversified in alkene isomer production are the primitively eusocial Bumblebees (Bombus spp), which are the sister group of the stingless bees. Furthermore, among the eleven Neotropical Melipona species we could detect no effect of the environment on the proportion of alkane production as has been suggested for some other species

Effects of preoperative feeding with a whey protein plus carbohydrate drink on the acute phase response and insulin resistance. A randomized trial

<p>Abstract</p> <p>Background</p> <p>Prolonged preoperative fasting increases insulin resistance and current evidence recommends carbohydrate (CHO) drinks 2 hours before surgery. Our hypothesis is that the addition of whey protein to a CHO-based drink not only reduces the inflammatory response but also diminish insulin resistance.</p> <p>Methods</p> <p>Seventeen patients scheduled to cholecystectomy or inguinal herniorraphy were randomized and given 474 ml and 237 ml of water (CO group) or a drink containing CHO and milk whey protein (CHO-P group) respectively, 6 and 3 hours before operation. Blood samples were collected before surgery and 24 hours afterwards for biochemical assays. The endpoints of the study were the insulin resistance (IR), the prognostic inflammatory and nutritional index (PINI) and the C-reactive protein (CRP)/albumin ratio. A 5% level for significance was established.</p> <p>Results</p> <p>There were no anesthetic or postoperative complications. The post-operative IR was lower in the CHO-P group when compared with the CO group (2.75 ± 0.72 vs 5.74 ± 1.16; p = 0.03). There was no difference between the two groups in relation to the PINI. The CHO-P group showed a decrease in the both CRP elevation and CRP/albumin ratio (p < 0.05). The proportion of patients who showed CRP/albumin ratio considered normal was significantly greater (p < 0.05) in the CHO-P group (87.5%) than in the CO group (33.3%).</p> <p>Conclusions</p> <p>Shortening the pre-operative fasting using CHO and whey protein is safe and reduces insulin resistance and postoperative acute phase response in elective moderate operations.</p> <p>Trial registration</p> <p>ClinicalTrail.gov <a href="http://www.clinicaltrials.gov/ct2/show/NCT01354249">NCT01354249</a></p

An unusual presentation of adenoid cystic carcinoma of the minor salivary glands with cranial nerve palsy: a case study

<p>Abstract</p> <p>Background</p> <p>Adenoid Cystic Carcinoma (ACC) is a rare tumor entity and comprises about 1% of all malignant tumor of the oral and maxillofacial region. It is slow growing but a highly invasive cancer with a high recurrence rate. Intracranial ACC is even more infrequent and could be primary or secondary occurring either by direct invasion, hematogenous spread, or perineural spread. We report the first case of the 5^thand 6^thnerve palsy due to cavernous sinus invasion by adenoid cystic carcinoma.</p> <p>Case presentation</p> <p>A 49-year-old African American female presented to the emergency room complaining of severe right-sided headache, photophobia, dizziness and nausea, with diplopia. The patient had a 14 year history migraine headaches, hypertension, and mild intermittent asthma. Physical examination revealed right lateral rectus muscle palsy with esotropia. There was numbness in all three divisions of the right trigeminal nerve. Motor and sensory examination of extremities was normal. An MRI of the brain/brain stem was obtained which showed a large mass in the clivus extending to involve the nasopharynx, pterygoid plate, sphenoid and right cavernous sinuses.</p> <p>Biopsy showed an ACC tumor with a cribriform pattern of the minor salivary glands. The patient underwent total gross surgical resection and radiation therapy.</p> <p>Conclusion</p> <p>This is a case of ACC of the minor salivary glands with intracranial invasion. The patient had long history of headaches which changed in character during the past year, and symptoms of acute 5^thand 6^thcranial nerve involvement. Our unique case demonstrates direct invasion of cavernous sinus and could explain the 5^thand 6^thcranial nerve involvement as histopathology revealed no perineural invasion.</p

Dietary availability patterns of the brazilian macro-regions

<p>Abstract</p> <p>Introduction</p> <p>Epidemiological studies have raised concerns about the role of dietary patterns on the risk of chronic diseases and also in the formulation of better informed nutrition policies.</p> <p>Objective</p> <p>The development of a dietary availability patterns according to geographic regions in Brazil.</p> <p>Methodology</p> <p>The 2002-2003 Brazilian Household Budget Survey was conducted in 48,470 households. Dietary availability patterns were identified by Principal Component Analysis using as a unit of analysis the survey's Primary Sampling Units (PSUs) and purchased amounts for 21 food groups. Each of the extracted dietary availability patterns was regressed on socioeconomics categories.</p> <p>Results</p> <p>There were no differences in dietary availability patterns between urban and rural areas. In all regions, a rice and beans pattern was identified. This pattern explained 15% to 28% of the variance dependent on the region of the country. In South, Southeast and Midwest regions, a mixed pattern including at least 10 food groups explaining 8% to 16% of the variance. In the North region (Amazon forest included) the first pattern was based on fish and nuts and then it was designed as regional pattern. In multiple linear regression the rice and beans pattern was associated with the presence of adolescents in the households, except for North region, whereas the presence of adolescents was associated with the Regional pattern. A mixed patterns were associated with a higher income and education (p < 0.05), except in the South region.</p> <p>Conclusion</p> <p>The rice and beans and regional dietary availability patterns, both considered healthy eating patterns are still important in the country. Brazil has taken many actions to improve nutrition as part of their public health policies, the data of the Household Budget Survey could help to recognize the different food choices in the large regions of the country.</p

Dental caries in Uruguayan adults and elders: findings from the first Uruguayan National Oral Health Survey

This study aimed to assess dental caries status and associated factors in Uruguayan adults and elders using data from the first Uruguayan National Oral Health Survey. Data were representative of the country as a whole. Socio-demographic information was collected with a closed questionnaire. Dental caries was assessed by clinical examination using the DMFT index. The final sample consisted of 769 participants. Mean DMFT was 15.20 and 24.12 for the 35-44 and 65-74-year age groups, respectively. Mean number of decayed teeth was 1.70 in adults and 0.66 in elders. Multivariate analyses showed higher prevalence of dental caries associated with age 65-74 years, low socioeconomic status, use of public dental services, presence of gingivitis; for decayed teeth, age 35-44 years, low socioeconomic status, use of public dental services, infrequent tooth brushing, need for oral health care, and presence of root caries showed higher severity. Uruguayan adults and elders from disadvantaged backgrounds concentrated a heavier burden of dental caries