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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Xiaofei, Nan; Gang, Fu; Zhengdong, Zhao; Sheng, Liu; +7 Authors

    AbstractBackgroundIt is commonly believed that including domain knowledge in a prediction model is desirable. However, representing and incorporating domain information in the learning process is, in general, a challenging problem. In this research, we consider domain information encoded by discrete or categorical attributes. A discrete or categorical attribute provides a natural partition of the problem domain, and hence divides the original problem into several non-overlapping sub-problems. In this sense, the domain information is useful if the partition simplifies the learning task. The goal of this research is to develop an algorithm to identify discrete or categorical attributes that maximally simplify the learning task.ResultsWe consider restructuring a supervised learning problem via a partition of the problem space using a discrete or categorical attribute. A naive approach exhaustively searches all the possible restructured problems. It is computationally prohibitive when the number of discrete or categorical attributes is large. We propose a metric to rank attributes according to their potential to reduce the uncertainty of a classification task. It is quantified as a conditional entropy achieved using a set of optimal classifiers, each of which is built for a sub-problem defined by the attribute under consideration. To avoid high computational cost, we approximate the solution by the expected minimum conditional entropy with respect to random projections. This approach is tested on three artificial data sets, three cheminformatics data sets, and two leukemia gene expression data sets. Empirical results demonstrate that our method is capable of selecting a proper discrete or categorical attribute to simplify the problem, i.e., the performance of the classifier built for the restructured problem always beats that of the original problem.ConclusionsThe proposed conditional entropy based metric is effective in identifying good partitions of a classification problem, hence enhancing the prediction performance.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Europe PubMed Central
    Article . 2011
    Data sources: PubMed Central
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    BMC Bioinformatics
    Article
    License: CC BY
    Data sources: UnpayWall
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    BMC Bioinformatics
    Article . 2011 . Peer-reviewed
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Europe PubMed Central
      Article . 2011
      Data sources: PubMed Central
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      BMC Bioinformatics
      Article
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      BMC Bioinformatics
      Article . 2011 . Peer-reviewed
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    Authors: Clark, Robert; Krishnan, Venkatesh; Schoof, Michael; Rodriguez, Irving; +3 Authors

    The goal of controlling ovarian cancer metastasis formation has elicited considerable interest in identifying the tissue microenvironments involved in cancer cell colonization of the omentum. Omental adipose is a site of prodigious metastasis in both ovarian cancer models and clinical disease. This tissue is unusual for its milky spots, comprised of immune cells, stromal cells, and structural elements surrounding glomerulus-like capillary beds. The present study shows the novel finding that milky spots and adipocytes play distinct and complementary roles in omental metastatic colonization. In vivo assays showed that ID8, CaOV3, HeyA8, and SKOV3ip.1 cancer cells preferentially lodge and grow within omental and splenoportal fat, which contain milky spots, rather than in peritoneal fat depots. Similarly, medium conditioned by milky spot–containing adipose tissue caused 75% more cell migration than did medium conditioned by milky spot–deficient adipose. Studies with immunodeficient mice showed that the mouse genetic background does not alter omental milky spot number and size, nor does it affect ovarian cancer colonization. Finally, consistent with the role of lipids as an energy source for cancer cell growth, in vivo time-course studies revealed an inverse relationship between metastatic burden and omental adipocyte content. Our findings support a two-step model in which both milky spots and adipose have specific roles in colonization of the omentum by ovarian cancer cells.

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    Other literature type . 2013
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      Europe PubMed Central
      Other literature type . 2013
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Xin-Xing Zhang; Andrei Tokmakoff;

    The solvent-protein interactions are important for protein biological functions, especially for a coupled folding and binding system as insulin. By monitoring the conformational change of insulin dimers during dissociation with temperature jump (T-jump) IR spectroscopy, we show that co-solvents can significantly destabilize the dimers by perturbing their hydrophobic center. Transition from native to intermediate dimer state is observed as the buried residues exposed to solvents at the presence of 10% DMSO and with α–helices unfolding when ethanol is present, which reduces the dissociation time dramatically to 20% and 50% of the value in the D(2)O solution, respectively. We propose a self-consistent analysis using complementary methods for resolving this coupled folding and binding process is resolved with, and obtain a much larger rate of monomer association than the intermediate folding. Our results demonstrate that the conformational changes are critical in the dimer formation and are highly affected by co-solvents.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    Europe PubMed Central
    Other literature type . 2020
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    The Journal of Physical Chemistry Letters
    Article . 2020 . Peer-reviewed
    License: STM Policy #29
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Europe PubMed Central
      Other literature type . 2020
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      The Journal of Physical Chemistry Letters
      Article . 2020 . Peer-reviewed
      License: STM Policy #29
      Data sources: Crossref
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Lemasters, John J.; Holmuhamedov, Ekhson;

    AbstractDespite a detailed understanding of their metabolism, mitochondria often behave anomalously. In particular, global suppression of mitochondrial metabolism and metabolite exchange occurs in apoptosis, ischemia and anoxia, cytopathic hypoxia of sepsis and multiple organ failure, alcoholic liver disease, aerobic glycolysis in cancer cells (Warburg effect) and unstimulated pancreatic beta cells. Here, we propose that closure of voltage-dependent anion channels (VDAC) in the mitochondrial outer membrane accounts for global mitochondrial suppression. In anoxia, cytopathic hypoxia and ethanol treatment, reactive oxygen and nitrogen species, cytokines, kinase cascades and increased NADH act to inhibit VDAC conductance and promote selective oxidation of membrane-permeable respiratory substrates like short chain fatty acids and acetaldehyde. In cancer cells, highly expressed hexokinase binds to and inhibits VDAC to suppress mitochondrial function while stimulating glycolysis, but an escape mechanism intervenes when glucose-6-phosphate accumulates and dissociates hexokinase from VDAC. Similarly, glucokinase binds mitochondria of insulin-secreting beta cells, possibly blocking VDAC and suppressing mitochondrial function. We propose that glucose metabolism leads to glucose-6-phosphate-dependent unbinding of glucokinase, relief of VDAC inhibition, release of ATP from mitochondria and ATP-dependent insulin release. In support of the overall proposal, ethanol treatment of isolated rat hepatocytes inhibited mitochondrial respiration and accessibility to adenylate kinase in the intermembrane space, effects that were overcome by digitonin permeabilization of the outer membrane. Overall, these considerations suggest that VDAC is a dynamic regulator, or governator, of global mitochondrial function both in health and disease.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Biochimica et Biophy...arrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Biochimica et Biophy...arrow_drop_down
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Selena Ahmed; Shauna Downs; Jessica Fanzo;

    The food system is responsible for some of society's most pressing sustainability challenges. Dietary guidelines are one policy tool to help address the multiple sustainability challenges associated with food systems through dietary recommendations that better support environmental and human well-being. This article develops and applies a sustainability framework scoring tool comprised of four key dimensions (environmental, economic, human health, and sociocultural and political) and 32 sub-dimensions of sustainable food systems for the analysis and modification of national dietary guidelines. Two coders pilot tested the framework to quantify the occurrence of sustainability dimensions and sub-dimensions in national and regional dietary guidelines of 12 randomly selected high-income and upper-middle income countries including Albania, Australia, Brazil, the Grenadines, Grenada, Qatar, Netherlands, Nordic Countries, St. Vincent, Sweden, Thailand, the United Kingdom, and the United States. Sustainability Dimension Scores (SDS) were calculated as a percentage of the occurrence of the eight sub-dimensions comprising each sustainability dimension and Total Sustainability Scores (TSS) were calculated as a percentage of the occurrence of the 32 sub-dimensions in each guideline. Inter-rater reliability of TSS and SDS indicated high validity of applying the sustainability framework for dietary guidelines. SDS varied between the four sustainability dimensions with human health being the most represented in the dietary guidelines examined, as hypothesized (average SDS score of 83%; range from 50 to 100%). Significant differences (p < 0.0001) were found in mean SDS between the four sustainability dimensions. Overall, results indicate that the ecological (average SDS score of 31%; range from 0 to 100%) economic (average SDS score of 29%; range from 0 to 100%), and socio-cultural and political (average SDS score of 44%; range of 0–100%) dimensions of sustainability are underrepresented in the examined national dietary guidelines with significant differences in SDS between guidelines (p < 0.0001). TSS varied by country between 12 and 74% with a mean score of 36% (± 20%). Brazil had the highest TSS (74%) followed by Australia (69%). The sustainability framework presented here can be applied by policy makers, researchers, and practitioners to identify gaps and opportunities to modify national dietary guidelines and associated programs for transforming food systems through diets that support planetary health.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Frontiers in Sustain...arrow_drop_down
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    Frontiers in Sustainable Food Systems
    Article . 2019 . Peer-reviewed
    License: CC BY
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    Frontiers in Sustainable Food Systems
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    DOAJ-Articles
    Article . 2019
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      Frontiers in Sustainable Food Systems
      Article . 2019 . Peer-reviewed
      License: CC BY
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      Frontiers in Sustainable Food Systems
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      DOAJ-Articles
      Article . 2019
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Cory W, Morin; Andrew C, Comrie; Kacey, Ernst;

    Background: Climate influences dengue ecology by affecting vector dynamics, agent development, and mosquito/human interactions. Although these relationships are known, the impact climate change will have on transmission is unclear. Climate-driven statistical and process-based models are being used to refine our knowledge of these relationships and predict the effects of projected climate change on dengue fever occurrence, but results have been inconsistent. Objective: We sought to identify major climatic influences on dengue virus ecology and to evaluate the ability of climate-based dengue models to describe associations between climate and dengue, simulate outbreaks, and project the impacts of climate change. Methods: We reviewed the evidence for direct and indirect relationships between climate and dengue generated from laboratory studies, field studies, and statistical analyses of associations between vectors, dengue fever incidence, and climate conditions. We assessed the potential contribution of climate-driven, process-based dengue models and provide suggestions to improve their performance. Results and Discussion: Relationships between climate variables and factors that influence dengue transmission are complex. A climate variable may increase dengue transmission potential through one aspect of the system while simultaneously decreasing transmission potential through another. This complexity may at least partly explain inconsistencies in statistical associations between dengue and climate. Process-based models can account for the complex dynamics but often omit important aspects of dengue ecology, notably virus development and host–species interactions. Conclusion: Synthesizing and applying current knowledge of climatic effects on all aspects of dengue virus ecology will help direct future research and enable better projections of climate change effects on dengue incidence. Citation: Morin CW, Comrie AC, Ernst KC. 2013. Climate and dengue transmission: evidence and implications. Environ Health Perspect 121:1264–1272; http://dx.doi.org/10.1289/ehp.1306556

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    Authors: Xia, Zongping; Liu, Yuechueng;

    AbstractGreen fluorescence protein (GFP)-based fluorescence resonance energy transfer (FRET) is increasingly used in investigation of inter- and intramolecular interactions in living cells. In this report, we present a modified method for FRET quantification in cultured cells using conventional fluorescence microscopy. To reliably measure FRET, three positive control constructs in which a cyan fluorescence protein and a yellow fluorescence protein were linked by peptides of 15, 24, or 37 amino acid residues were prepared. FRET was detected using a spectrofluorometer, a laser scanning confocal microscope, and an inverted fluorescence microscope. Three calculation methods for FRET quantification using fluorescence microscopes were compared. By normalization against expression levels of GFP fusion proteins, the modified method gave consistent FRET values that could be compared among different cells with varying protein expression levels. Whole-cell global analysis using this method allowed FRET measurement with high spatial resolutions. Using such a procedure, the interaction of synaptic proteins syntaxin and the synaptosomal associated protein of 25 kDa (SNAP-25) was examined in PC12 cells, which showed strong FRET on plasma membranes. These results demonstrate the effectiveness of the modified method for FRET measurement in live cell systems.

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    Biophysical Journal
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    Biophysical Journal
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      Biophysical Journal
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    Authors: Rees, MG; Davis, MI; Shen, M; Titus, S; +5 Authors

    Recent genetic and clinical evidence has implicated glucokinase regulatory protein (GKRP) in the pathogenesis of type 2 diabetes and related traits. The primary role of GKRP is to bind and inhibit hepatic glucokinase (GCK), a critically important protein in human health and disease that exerts a significant degree of control over glucose metabolism. As activation of GCK has been associated with improved glucose tolerance, perturbation of the GCK-GKRP interaction represents a potential therapeutic target for pharmacological modulation. Recent structural and kinetic advances are beginning to provide insight into the interaction of these two proteins. However, tools to comprehensively assess the GCK-GKRP interaction, particularly in the context of small molecules, would be a valuable resource. We therefore developed three robust and miniaturized assays for assessing the interaction between recombinant human GCK and GKRP: an HTRF assay, a diaphorase-coupled assay, and a luciferase-coupled assay. The assays are complementary, featuring distinct mechanisms of detection (luminescence, fluorescence, FRET). Two assays rely on GCK enzyme activity modulation by GKRP while the FRET-based assay measures the GCK-GKRP protein-protein interaction independent of GCK enzymatic substrates and activity. All three assays are scalable to low volumes in 1536-well plate format, with robust Z’ factors (>0.7). Finally, as GKRP sequesters GCK in the hepatocyte nucleus at low glucose concentrations, we explored cellular models of GCK localization and translocation. Previous findings from freshly isolated rat hepatocytes were confirmed in cryopreserved rat hepatocytes, and we further extended this study to cryopreserved human hepatocytes. Consistent with previous reports, there were several key differences between the rat and human systems, with our results suggesting that human hepatocytes can be used to interrogate GCK translocation in response to small molecules. The assay panel developed here should help direct future investigation of the GCK-GKRP interaction in these or other physiologically relevant human systems.

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    Europe PubMed Central
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    PLoS ONE
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    Oxford University Research Archive; PLoS ONE
    Other literature type . Article . 2014 . 2016 . Peer-reviewed
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    PLoS ONE
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      Other literature type . Article . 2014 . 2016 . Peer-reviewed
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    Authors: Etz, Rebecca S; Keith, Rosalind E; Maternick, Anna M; Stein, Karen L; +5 Authors

    Background Diabetes is predicted to increase in incidence by 42% from 1995 to 2025. Although most adults with diabetes seek care from primary care practices, adherence to treatment guidelines in these settings is not optimal. Many practices lack the infrastructure to monitor patient adherence to recommended treatment and are slow to implement changes critical for effective management of patients with chronic conditions. Supporting Practices to Adopt Registry-Based Care (SPARC) will evaluate effectiveness and sustainability of a low-cost intervention designed to support work process change in primary care practices and enhance focus on population-based care through implementation of a diabetes registry. Methods SPARC is a two-armed randomized controlled trial (RCT) of 30 primary care practices in the Virginia Ambulatory Care Outcomes Research Network (ACORN). Participating practices (including control groups) will be introduced to population health concepts and tools for work process redesign and registry adoption at a meeting of practice-level implementation champions. Practices randomized to the intervention will be assigned study peer mentors, receive a list of specific milestones, and have access to a physician informaticist. Peer mentors are clinicians who successfully implemented registries in their practices and will help champions in the intervention practices throughout the implementation process. During the first year, peer mentors will contact intervention practices monthly and visit them quarterly. Control group practices will not receive support or guidance for registry implementation. We will use a mixed-methods explanatory sequential design to guide collection of medical record, participant observation, and semistructured interview data in control and intervention practices at baseline, 12 months, and 24 months. We will use grounded theory and a template-guided approach using the Consolidated Framework for Implementation Research to analyze qualitative data on contextual factors related to registry adoption. We will assess intervention effectiveness by comparing changes in patient-level hemoglobin A1c scores from baseline to year 1 between intervention and control practices. Discussion Findings will enhance our understanding of how to leverage existing practice resources to improve diabetes care in primary care practices by implementing and using a registry. SPARC has the potential to validate the effectiveness of low-cost implementation strategies that target practice change in primary care. Trial registration NCT02318108 Electronic supplementary material The online version of this article (doi:10.1186/s13012-015-0232-2) contains supplementary material, which is available to authorized users.

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    Authors: Dong, Xiaoqiong; Thomas, David D.;

    We have used time-resolved fluorescenceresonance energy transfer (TR-FRET) to study the structural basis of regulation of sarcoplasmic reticulum Ca2+ ATPase (SERCA) by a single-pass transmembrane protein, phospholamban (PLB). SERCA actively sequesters Ca2+ back into the sarcoplasmic reticulum to cause muscle relaxation. In the heart, SERCA is inhibited by unphosphorylated PLB. Physiologically, this inhibition is relieved by either micromolar Ca2+ or phosphorylation of PLB. Dysregulation of SERCA-PLB complex causes Ca2+ mishandling in cardiomyocyte, which is a prominent feature in heart failure. Our goal is to elucidate the structural basis for the regulation of the complex, with an emphasis on the structural rearrangement during relief of inhibition. We have used time-resolved fluorescence resonance energy transfer (TR-FRET) to probe the complex directly by measuring the distances between SERCA (C674) and a series of positions on PLB in co-reconstituted vesicles. Our data supports that the cytoplasmic domain of bound PLB exists in two states. The relief of inhibition is achieved by combined effect of dissociation of the complex and shifting the equilibrium of the two states of bound PLB. Spectroscopy was performed in the Biophysical Spectroscopy Center at the University of Minnesota. This work was funded by NIH grants to DDT (R01 GM27906 and P30 AR0507220).

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    Biophysical Journal
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    Biophysical Journal
    Article . 2014 . Peer-reviewed
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      Biophysical Journal
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    Authors: Xiaofei, Nan; Gang, Fu; Zhengdong, Zhao; Sheng, Liu; +7 Authors

    AbstractBackgroundIt is commonly believed that including domain knowledge in a prediction model is desirable. However, representing and incorporating domain information in the learning process is, in general, a challenging problem. In this research, we consider domain information encoded by discrete or categorical attributes. A discrete or categorical attribute provides a natural partition of the problem domain, and hence divides the original problem into several non-overlapping sub-problems. In this sense, the domain information is useful if the partition simplifies the learning task. The goal of this research is to develop an algorithm to identify discrete or categorical attributes that maximally simplify the learning task.ResultsWe consider restructuring a supervised learning problem via a partition of the problem space using a discrete or categorical attribute. A naive approach exhaustively searches all the possible restructured problems. It is computationally prohibitive when the number of discrete or categorical attributes is large. We propose a metric to rank attributes according to their potential to reduce the uncertainty of a classification task. It is quantified as a conditional entropy achieved using a set of optimal classifiers, each of which is built for a sub-problem defined by the attribute under consideration. To avoid high computational cost, we approximate the solution by the expected minimum conditional entropy with respect to random projections. This approach is tested on three artificial data sets, three cheminformatics data sets, and two leukemia gene expression data sets. Empirical results demonstrate that our method is capable of selecting a proper discrete or categorical attribute to simplify the problem, i.e., the performance of the classifier built for the restructured problem always beats that of the original problem.ConclusionsThe proposed conditional entropy based metric is effective in identifying good partitions of a classification problem, hence enhancing the prediction performance.

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    Europe PubMed Central
    Article . 2011
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    BMC Bioinformatics
    Article . 2011 . Peer-reviewed
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      BMC Bioinformatics
      Article . 2011 . Peer-reviewed
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    Authors: Clark, Robert; Krishnan, Venkatesh; Schoof, Michael; Rodriguez, Irving; +3 Authors

    The goal of controlling ovarian cancer metastasis formation has elicited considerable interest in identifying the tissue microenvironments involved in cancer cell colonization of the omentum. Omental adipose is a site of prodigious metastasis in both ovarian cancer models and clinical disease. This tissue is unusual for its milky spots, comprised of immune cells, stromal cells, and structural elements surrounding glomerulus-like capillary beds. The present study shows the novel finding that milky spots and adipocytes play distinct and complementary roles in omental metastatic colonization. In vivo assays showed that ID8, CaOV3, HeyA8, and SKOV3ip.1 cancer cells preferentially lodge and grow within omental and splenoportal fat, which contain milky spots, rather than in peritoneal fat depots. Similarly, medium conditioned by milky spot–containing adipose tissue caused 75% more cell migration than did medium conditioned by milky spot–deficient adipose. Studies with immunodeficient mice showed that the mouse genetic background does not alter omental milky spot number and size, nor does it affect ovarian cancer colonization. Finally, consistent with the role of lipids as an energy source for cancer cell growth, in vivo time-course studies revealed an inverse relationship between metastatic burden and omental adipocyte content. Our findings support a two-step model in which both milky spots and adipose have specific roles in colonization of the omentum by ovarian cancer cells.

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