Evolution of Anolis Lizard Dewlap Diversity

BACKGROUND: The dewlaps of Anolis lizards provide a classic example of a complex signaling system whose function and evolution is poorly understood. Dewlaps are flaps of skin beneath the chin that are extended and combined with head and body movements for visual signals and displays. They exhibit extensive morphological variation and are one of two cladistic features uniting anoles, yet little is known regarding their function and evolution. We quantified the diversity of anole dewlaps, investigated whether dewlap morphology was informative regarding phylogenetic relationships, and tested two separate hypotheses: (A) similar Anolis habitat specialists possess similar dewlap configurations (Ecomorph Convergence hypothesis), and (B) sympatric species differ in their dewlap morphologies to a greater extent than expected by chance (Species Recognition hypothesis). METHODOLOGY/PRINCIPAL FINDINGS: We found that dewlap configurations (sizes, patterns and colors) exhibit substantial diversity, but that most are easily categorized into six patterns that incorporate one to three of 13 recognizable colors. Dewlap morphology is not phylogenetically informative and, like other features of anoles, exhibits convergence in configurations. We found no support for the Ecomorph Convergence hypothesis; species using the same structural habitat were no more similar in dewlap configuration than expected by chance. With one exception, all sympatric species in four communities differ in dewlap configuration. However, this provides only weak support for the Species Recognition hypothesis because, due to the great diversity in dewlap configurations observed across each island, few cases of sympatric species with identical dewlaps would be expected to co-occur by chance alone. CONCLUSIONS/SIGNIFICANCE: Despite previous thought, most dewlaps exhibit easily characterizable patterns and colorations. Nevertheless, dewlap variation is extensive and explanations for the origin and evolution of this diversity are lacking. Our data do not support two hypothesized explanations for this diversity, but others such as sexual selection remain to be tested

Robust Poisson Surface Reconstruction

Abstract. We propose a method to reconstruct surfaces from oriented point clouds with non-uniform sampling and noise by formulating the problem as a convex minimization that reconstructs the indicator func-tion of the surface’s interior. Compared to previous models, our recon-struction is robust to noise and outliers because it substitutes the least-squares fidelity term by a robust Huber penalty; this allows to recover sharp corners and avoids the shrinking bias of least squares. We choose an implicit parametrization to reconstruct surfaces of unknown topology and close large gaps in the point cloud. For an efficient representation, we approximate the implicit function by a hierarchy of locally supported basis elements adapted to the geometry of the surface. Unlike ad-hoc bases over an octree, our hierarchical B-splines from isogeometric analysis locally adapt the mesh and degree of the splines during reconstruction. The hi-erarchical structure of the basis speeds-up the minimization and efficiently represents clustered data. We also advocate for convex optimization, in-stead isogeometric finite-element techniques, to efficiently solve the min-imization and allow for non-differentiable functionals. Experiments show state-of-the-art performance within a more flexible framework.

Associations between Cardiorespiratory Fitness and Health-Related Quality of Life

© 2009 Sloan et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2

RosettaDock has been increasingly used in protein docking and design strategies in order to predict the structure of protein-protein interfaces. Here we test capabilities of RosettaDock 3.2, part of the newly developed Rosetta v3.2 modeling suite, against Docking Benchmark 3.0, and compare it with RosettaDock v2.3, the latest version of the previous Rosetta software package. The benchmark contains a diverse set of 116 docking targets including 22 antibody-antigen complexes, 33 enzyme-inhibitor complexes, and 60 ‘other’ complexes. These targets were further classified by expected docking difficulty into 84 rigid-body targets, 17 medium targets, and 14 difficult targets. We carried out local docking perturbations for each target, using the unbound structures when available, in both RosettaDock v2.3 and v3.2. Overall the performances of RosettaDock v2.3 and v3.2 were similar. RosettaDock v3.2 achieved 56 docking funnels, compared to 49 in v2.3. A breakdown of docking performance by protein complex type shows that RosettaDock v3.2 achieved docking funnels for 63% of antibody-antigen targets, 62% of enzyme-inhibitor targets, and 35% of ‘other’ targets. In terms of docking difficulty, RosettaDock v3.2 achieved funnels for 58% of rigid-body targets, 30% of medium targets, and 14% of difficult targets. For targets that failed, we carry out additional analyses to identify the cause of failure, which showed that binding-induced backbone conformation changes account for a majority of failures. We also present a bootstrap statistical analysis that quantifies the reliability of the stochastic docking results. Finally, we demonstrate the additional functionality available in RosettaDock v3.2 by incorporating small-molecules and non-protein co-factors in docking of a smaller target set. This study marks the most extensive benchmarking of the RosettaDock module to date and establishes a baseline for future research in protein interface modeling and structure prediction

Healthcare utilization of patients accessing an African national treatment program

<p>Abstract</p> <p>Background</p> <p>The roll-out of antiretroviral therapy (ART) in Africa will have significant resource implications arising from its impact on demand for healthcare services. Existing studies of healthcare utilization on HAART have been conducted in the developed world, where HAART is commenced when HIV illness is less advanced.</p> <p>Methods</p> <p>This paper describes healthcare utilization from program entry by treatment-naïve patients in a peri-urban settlement in South Africa. Treatment criteria included a CD4 cell count <200 cells/μl or an AIDS-defining illness. Data on health service utilization were collected retrospectively from the primary-care clinic and secondary and tertiary referral hospitals. Hospital visits were reviewed to determine the clinical reason for each visit.</p> <p>Results</p> <p>212 patients were followed for a median of 490 days. Outpatient visits per 100 patient years of observation (PYO), excluding scheduled primary-care follow-up, fell from 596 immediately prior to ART to 334 in the first 48 weeks on therapy and 245 thereafter. Total inpatient time fell from 2,549 days per 100 PYO pre-ART to 476 in the first 48 weeks on therapy and 73 thereafter. This fall in healthcare utilization occurred at every level of care. The greatest causes of utilization were tuberculosis, cryptococcal meningitis, HIV-related neoplasms and adverse reactions to stavudine. After 48 weeks on ART demand reverted to primarily non-HIV-related causes.</p> <p>Conclusion</p> <p>Utilization of both inpatient and outpatient hospital services fell significantly after commencement of ART for South African patients in the public sector, with inpatient demand falling fastest. Earlier initiation might reduce early on-ART utilization rates.</p

Sex and the city: Differences in disease- and disability-free life years, and active community participation of elderly men and women in 7 cities in Latin America and the Caribbean

<p>Abstract</p> <p>Background</p> <p>The world's population is ageing, and four of the top 10 most rapidly ageing developing nations are from the region of Latin America and the Caribbean (LAC).</p> <p>Although an ageing population heralds likely increases in chronic disease, disability-related dependence, and economic burden, the societal contribution of the chronically ill or those with disability is not often measured.</p> <p>Methods</p> <p>We calculated country-specific prevalences of 'disability' (difficulty with at least one activity of daily living), 'disease' and 'co-morbidity' (presence of at least one, and at least two, of seven chronic diseases/conditions, respectively), and 'active community engagement' (using five levels of community participation, from less than weekly community contact to voluntary or paid work) in seven LAC cities. We estimated remaining life expectancy (LE) with and without disability, disease and co-morbidity, and investigated age, sex, and regional variations in disability-free LE. Finally, we modeled the association of disease, co-morbidity and disability with active community participation using an ordinal regression model, adjusted for depression.</p> <p>Results</p> <p>Overall, 77% of the LAC elderly had at least one chronic disease/condition, 44% had co-morbidity and 19% had a disability. The proportion of disability-free LE declined between the youngest (60–64 years) and the eldest (90 years and over) age-groups for both men (from 85% to 55%) and women (from 75% to 45%). Disease-free and co-morbidity-free LE, however, remained at approximately 30% and 62%, respectively, for men (20% and 48% for women), until 80–84 years of age, then increased. Only Bridgetown's participants had statistically significantly longer disability-free LE than the regional average (IRR = 1.08; 95%CI 1.05–1.10; p < 0.001). Only Santiago's participants had disability-free LE which was shorter than the regional average (IRR = 0.94; 95%CI 0.92–0.97; p < 0.001). There was 75% active community participation overall, with more women than men involved in active help (49% vs 32%, respectively) and more men involved in voluntary/paid work (46% vs 25%, respectively). There was either no, or borderline significance in the association between having one or more diseases/conditions and active community engagement for both sexes. These associations were limited by depression (odds ratio [OR] reduced by 15–17% for men, and by 8–11% for women), and only remained statistically significant in men. However, disability remained statistically significantly associated with less community engagement after adjusting for depression (OR = 0.58, 95%CI 0.49–0.69, p < 0.001 for women and OR = 0.50, 95%CI 0.47–0.65, p < 0.001 for men).</p> <p>Conclusion</p> <p>There is an increasing burden of disease and disability with older age across the LAC region. As these nations cope with resulting social and economic demands, governments and civic societies must continue to develop and maintain opportunities for community participation by this increasingly frail, but actively engaged group.</p

Validation of Case-Finding Algorithms Derived from Administrative Data for Identifying Adults Living with Human Immunodeficiency Virus Infection

OBJECTIVE: We sought to validate a case-finding algorithm for human immunodeficiency virus (HIV) infection using administrative health databases in Ontario, Canada. METHODS: We constructed 48 case-finding algorithms using combinations of physician billing claims, hospital and emergency room separations and prescription drug claims. We determined the test characteristics of each algorithm over various time frames for identifying HIV infection, using data abstracted from the charts of 2,040 randomly selected patients receiving care at two medical practices in Toronto, Ontario as the reference standard. RESULTS: With the exception of algorithms using only a single physician claim, the specificity of all algorithms exceeded 99%. An algorithm consisting of three physician claims over a three year period had a sensitivity and specificity of 96.2% (95% CI 95.2%-97.9%) and 99.6% (95% CI 99.1%-99.8%), respectively. Application of the algorithm to the province of Ontario identified 12,179 HIV-infected patients in care for the period spanning April 1, 2007 to March 31, 2009. CONCLUSIONS: Case-finding algorithms generated from administrative data can accurately identify adults living with HIV. A relatively simple "3 claims in 3 years" definition can be used for assembling a population-based cohort and facilitating future research examining trends in health service use and outcomes among HIV-infected adults in Ontario

Sí Se Puede: Using Participatory Research to Promote Environmental Justice in a Latino Community in San Diego, California

Community-based participatory research (CBPR) increasingly is seen as a potent tool for studying and addressing urban environmental health problems by linking place-based work with efforts to help effect policy-level change. This paper explores a successful CBPR and organizing effort, the Toxic Free Neighborhoods Campaign, in Old Town National City (OTNC), CA, United States, and its contributions to both local policy outcomes and changes in the broader policy environment, laying the groundwork for a Specific Plan to address a host of interlocking community concerns. After briefly describing the broader research of which the OTNC case study was a part, we provide background on the Environmental Health Coalition (EHC) partnership and the setting in which it took place, including the problems posed for residents in this light industrial/residential neighborhood. EHC’s strong in-house research, and its training and active engagement of promotoras de salud (lay health promoters) as co-researchers and policy change advocates, are described. We explore in particular the translation of research findings as part of a policy advocacy campaign, interweaving challenges faced and success factors and multi-level outcomes to which these efforts contributed. The EHC partnership's experience then is compared with that of other policy-focused CBPR efforts in urban environmental health, emphasizing common success factors and challenges faced, as these may assist other partnerships wishing to pursue CBPR in urban communities