Correspondence between environmental gradients and summer littoral fish assemblages in low salinity reaches of the Chesapeake Bay, USA

Patterns in the assemblage structure of littoral fishes occupying the gradient between riverine and estuarine ecosystems were revealed through multivariate analysis of 5 annual summer seine surveys in 4 tributary systems of the lower Chesapeake Bay. Catch per unit effort of fishes was quantified and environmental variables measured to characterize assemblage structure and population responses along large-scale (km) environmental gradients. Results of two-way indicator species analysis (TWINSPAN), detrended correspondence analysis (DCA) and detrended canonical correspondence analysis (DCCA) suggested the presence of 4 intergrading assemblages of littoral beach fishes: permanent tidal freshwater, lower tidal freshwater, oligohaline estuary and mesohaline estuary. Littoral fish assemblages were ordered along a large-scale spatial gradient between tidal freshwater and mesohaline river reaches during summer, when relatively stable hydrological conditions create a well-defined salinity gradient. Large-scale distribution of these fishes along the liver axis corresponded with salinity (and its correlates) up to the interface, and with structural attributes of the habitat (nearshore sediment grain size, presence of submerged aquatic vegetation, woody debris) in the permanent tidal freshwater river reaches. The permanent tidal freshwater reaches were more riverine in character, and were typified by speciose and relatively stable assemblages dominated by resident secondary division freshwater fishes and the juveniles of several diadromous species. Although the resident fauna is certainly derivative of more upland, non-tidal streams. patterns of association suggest distinct ecological relationships may exist for species co-occurring in tidal freshwater habitats

Improved approximation algorithms for inventory problems

We give new approximation algorithms for the submodular joint replenishment problem and the inventory routing problem, using an iterative rounding approach. In both problems, we are given a set of N items and a discrete time horizon of T days in which given demands for the items must be satisfied. Ordering a set of items incurs a cost according to a set function, with properties depending on the problem under consideration. Demand for an item at time t can be satisfied by an order on any day prior to t, but a holding cost is charged for storing the items during the intermediate period; the goal is to minimize the sum of the ordering and holding cost. Our approximation factor for both problems is [Formula Presented]; this improves exponentially on the previous best results

Scaling properties of protein family phylogenies

One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of balance) of a large set of protein phylogenies with a set of species phylogenies. The comparative analysis shows that both sets of phylogenies share remarkably similar scaling behavior, suggesting the universality of branching rules and of the evolutionary processes that drive biological diversification from gene to species level. In order to explain such generality, we propose a simple model which allows us to estimate the proportion of evolvability/robustness needed to approximate the scaling behavior observed in the phylogenies, highlighting the relevance of the robustness of a biological system (species or protein) in the scaling properties of the phylogenetic trees. Thus, the rules that govern the incapability of a biological system to diversify are equally relevant both at the gene and at the species level.Comment: Replaced with final published versio

Proximity to Sports Facilities and Sports Participation for Adolescents in Germany

Objectives - To assess the relationship between proximity to specific sports facilities and participation in the corresponding sports activities for adolescents in Germany. Methods - A sample of 1,768 adolescents aged 11–17 years old and living in 161 German communities was examined. Distances to the nearest sports facilities were calculated as an indicator of proximity to sports facilities using Geographic Information Systems (GIS). Participation in specific leisure-time sports activities in sports clubs was assessed using a self-report questionnaire and individual-level socio-demographic variables were derived from a parent questionnaire. Community-level socio-demographics as covariates were selected from the INKAR database, in particular from indicators and maps on land development. Logistic regression analyses were conducted to examine associations between proximity to the nearest sports facilities and participation in the corresponding sports activities. Results - The logisitic regression analyses showed that girls residing longer distances from the nearest gym were less likely to engage in indoor sports activities; a significant interaction between distances to gyms and level of urbanization was identified. Decomposition of the interaction term showed that for adolescent girls living in rural areas participation in indoor sports activities was positively associated with gym proximity. Proximity to tennis courts and indoor pools was not associated with participation in tennis or water sports, respectively. Conclusions - Improved proximity to gyms is likely to be more important for female adolescents living in rural areas

Effectiveness and efficiency of primary care based case management for chronic diseases: rationale and design of a systematic review and meta-analysis of randomized and non-randomized trials [CRD32009100316]

Contains fulltext : 88751.pdf (publisher's version ) (Open Access)BACKGROUND: Case management is an important component of structured and evidence-based primary care for chronically ill patients. Its effectiveness and efficiency has been evaluated in numerous clinical trials. This protocol describes aims and methods of a systematic review of research on the effectiveness and efficiency of case management in primary care. METHODS/DESIGN: According to this protocol Medline, Embase, CINAHL, PsychInfo, the Cochrane Central Register of Controlled trials, DARE, NHS EED, Science Citation Index, The Royal College of Nursing Database, Dissertation Abstracts, registers of clinical trials and the reference lists of retrieved articles will be searched to identify reports on randomized and non-randomized controlled trials of case management interventions in a primary care setting without limitations on language or publication date. We will further ask experts in the field to avoid missing relevant evidence. Study inclusion and data extraction will be performed independently by two reviewers. After assessing risk of bias according to predefined standards, included studies will be described qualitatively. Subgroup analyses are planned for different chronic diseases and intervention strategies. If appropriate, a quantitative synthesis of data will be performed to provide conclusive evidence about the effectiveness and efficiency of primary care based case management in chronic care. REVIEW REGISTRATION: Centre for Reviews and Dissemination (University of York): CRD32009100316

The Systems Biology Research Tool: evolvable open-source software

BACKGROUND: Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput) experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. RESULTS: We introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT) to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology. CONCLUSION: The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability), to facilitate cooperation among researchers, and to expedite progress in the field of systems biology

Informing the design of a national screening and treatment programme for chronic viral hepatitis in primary care: qualitative study of at-risk immigrant communities and healthcare professionals

n Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise statedThis paper presents independent research funded by the National Institute for Health Research (NIHR) under the Programme Grants for Applied Research programme (RP-PG-1209-10038).

Mechanistic interrogation of combination Bevacizumab/dual PI3K/mTOR inhibitor response in Glioblastoma implementing novel MR and PET imaging biomarkers.

Purpose: Resistance to bevacizumab (BEV) in glioblastoma (GBM) is believed to occur via activation of molecular networks including the mTOR/PI3K pathway. Implementing an MRI/PET molecular imaging biomarker approach, we sought to interrogate response to combining BEV with the mTOR/PI3K inhibitor BEZ235. Methods: Tumors were established by orthotopically implanting U87MG-luc2 in mice. Animals were treated with BEZ235 and/or BEV, and imaged using diffusion weighted-MRI, T2 weighted (T2w), and T2* weighted (T2*w) before and following delivery of superparamagnetic iron oxide (SPIO) contrast. Maps for changes in relaxation rates: ΔR2, ΔR2* and apparent diffusion coefficient (ADC) were calculated. Vessel Size Index (VSI) and micro vessel density index (MDI) were derived. 3´-deoxy-3´-[18F]fluorothymidine ([18F]FLT)- and O-(2-[18F]fluoroethyl)-L-tyrosine ([18F]FET) PET was further performed and tumor endothelium/proliferation markers assessed by immunohistochemistry. Results: Treatment with BEV resulted in a pronounced decrease in tumor volume (T2w MRI). No additive effect on tumour volume was observed in BEV/BEZ235 combination compared with BEV monotherapy. Ki67 proliferation index staining and [18F]FLT uptake studies were used to support observations. Using ΔR2* and ΔR2 values respectively, BEZ235 + BEV combination significantly reduced tumor microvessel volume in comparison to BEV alone. Decreased MDI was further observed in the combination group; supported by von Willebrand Factor (vWF) immunohistochemistry. We observed decreased [18F]FET uptake following BEV, but failed to observe further reduced [18F]FET uptake in the combination cohort. vWF IHC analysis showed mean tumor vessel size increased in all cohorts. Conclusions: Assessing MR imaging biomarker parameters together with [18F]FET and [18F]FLT PET, informed drug combination mechanism of action and provided clues as to potential clinical response. Translation of a BEZ35/BEV combination regimen could support reduction of peritumoral edemaobviating the requirement for steroids. Implementing hypothesis driven molecular imaging studies facilitates the interrogation of drug response in the pre-clinic. These data may more accurately predict the clinical potential of novel therapeutic approaches in oncology