706 research outputs found

    Network-based prediction of metabolic enzymes' subcellular localization

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    Motivation: Revealing the subcellular localization of proteins within membrane-bound compartments is of a major importance for inferring protein function. Though current high-throughput localization experiments provide valuable data, they are costly and time-consuming, and due to technical difficulties not readily applicable for many Eukaryotes. Physical characteristics of proteins, such as sequence targeting signals and amino acid composition are commonly used to predict subcellular localizations using computational approaches. Recently it was shown that protein–protein interaction (PPI) networks can be used to significantly improve the prediction accuracy of protein subcellular localization. However, as high-throughput PPI data depend on costly high-throughput experiments and are currently available for only a few organisms, the scope of such methods is yet limited

    Patients With Generalized Joint Hypermobility Have Thinner Superior Hip Capsules and Greater Hip Internal Rotation on Physical Examination

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    PURPOSE: To compare preoperative hip range of motion (ROM), hip capsular thickness on magnetic resonance imaging (MRI), and bony morphology on radiographs and computed tomography (CT) between patients with and without joint hypermobility as measured by the Beighton Test score (BTS), with subanalysis based on sex and age. METHODS: Consecutive patients who underwent hip arthroscopy for a diagnosis of femoroacetabular impingement syndrome with or without dysplasia were retrospectively reviewed. Patient BTS, hip ROM, demographics, surgical data, morphologic measures on radiographs and CT, and MRI findings including hip capsule thickness at various locations were compiled. Multiple statistical tests were performed, including multivariable linear or logistic regression models, while controlling for BTS, age, and sex. RESULTS: In total, 99 patients were included with a mean age of 29 ± 9.9 years; 62 (62.6%), were female. Forty patients (40.4%) had a BTS ≥4. Female patients (P \u3c .001) and younger patients (26.7 vs 30.9 years, P = .030) were more likely to have a BTS ≥4. Male patients had significantly thicker superior capsules (3.4 mm vs. 2.8 mm, P = .034). BTS was not associated with capsular thickness when controlling for sex. On CT, femoral version (18.9° vs 11.4°, P \u3c .001), and McKibben index (37.8° vs. 28.2°, P \u3c .001) were significantly greater in those with a BTS ≥4. Patients with a BTS ≥4 had more hip internal rotation at 90° of flexion (15.0° vs 10.0°, P \u3c .001), when prone (30.0° vs 20.0°, P = .004), and in extension (10.0° vs. 5.0°, P \u3c .001). CONCLUSIONS: All female patients, regardless of Beighton score, and all patients with a BTS ≥4 indicated for primary hip arthroscopy for femoroacetabular impingement syndrome with or without dysplasia were more likely to have thinner superior hip capsules on MRI and greater hip internal rotation on exam. Bony morphologic differences exist between sexes and between patients with and without hypermobility, likely contributing to differences in ROM. LEVEL OF EVIDENCE: III, retrospective cohort study

    Basket Cases and Breadbaskets: Sacred Rice and Agricultural Development in Postcolonial Africa

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    Author's final manuscript.Based on ethnographic research among rural Diola in Guinea-Bissau, I provide a broad view of the history and interpenetration of rice in social, political, religious, and ecological domains, while chronicling the current difficulties of residents in this region who are no longer able to grown enough of it. These farmers’ experiences are unfolding at a time of revitalized attention to agricultural development in Africa, particularly under the auspices of the New Green Revolution for Africa. I examine the premises that constitute the resuscitated effort to address the plight of African farmers. I argue that the totalizing quality of rice in Diola and other rice-cultivating societies requires a development approach that takes into account dimensions of agrarian life not encapsulated by the high- modernist and anti-political orientation of the New Green Revolution for Africa

    Analyzing the discharge regime of a large tropical river through remote sensing, ground-based climatic data, and modeling

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    This study demonstrates the potential for applying passive microwave satellite sensor data to infer the discharge dynamics of large river systems using the main stem Amazon as a test case. The methodology combines (1) interpolated ground-based meteorological station data, (2) horizontally and vertically polarized temperature differences (HVPTD) from the 37-GHz scanning multichannel microwave radiometer (SMMR) aboard the Nimbus 7 satellite, and (3) a calibrated water balance/water transport model (WBM/WTM). Monthly HVPTD values at 0.25° (latitude by longitude) resolution were resampled spatially and temporally to produce an enhanced HVPTD time series at 0.5° resolution for the period May 1979 through February 1985. Enhanced HVPTD values were regressed against monthly discharge derived from the WBM/WTM for each of 40 grid cells along the main stem over a calibration period from May 1979 to February 1983 to provide a spatially contiguous estimate of time-varying discharge. HVPTD-estimated flows generated for a validation period from March 1983 to February 1985 were found to be in good agreement with both observed arid modeled discharges over a 1400-km section of the main stem Amazon. This span of river is bounded downstream by a region of tidal influence and upstream by low sensor response associated with dense forest canopy. Both the WBM/WTM and HVPTD-derived flow rates reflect the significant impact of the 1982–1983 El Niño-;Southern Oscillation (ENSO) event on water balances within the drainage basin

    Alphavirus Entry and Membrane Fusion

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    The study of enveloped animal viruses has greatly advanced our understanding of the general properties of membrane fusion and of the specific pathways that viruses use to infect the host cell. The membrane fusion proteins of the alphaviruses and flaviviruses have many similarities in structure and function. As reviewed here, alphaviruses use receptor-mediated endocytic uptake and low pH-triggered membrane fusion to deliver their RNA genomes into the cytoplasm. Recent advances in understanding the biochemistry and structure of the alphavirus membrane fusion protein provide a clearer picture of this fusion reaction, including the protein’s conformational changes during fusion and the identification of key domains. These insights into the alphavirus fusion mechanism suggest new areas for experimental investigation and potential inhibitor strategies for anti-viral therapy

    Network analysis of human protein location

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    <p>Abstract</p> <p>Background</p> <p>Understanding cellular systems requires the knowledge of a protein's subcellular localization (SCL). Although experimental and predicted data for protein SCL are archived in various databases, SCL prediction remains a non-trivial problem in genome annotation. Current SCL prediction tools use amino-acid sequence features and text mining approaches. A comprehensive analysis of protein SCL in human PPI and metabolic networks for various subcellular compartments is necessary for developing a robust SCL prediction methodology.</p> <p>Results</p> <p>Based on protein-protein interaction (PPI) and metabolite-linked protein interaction (MLPI) networks of proteins, we have compared, contrasted and analysed the statistical properties across different subcellular compartments. We integrated PPI and metabolic datasets with SCL information of human proteins from LOCATE and GOA (Gene Ontology Annotation) and estimated three statistical properties: Chi-square (χ<sup>2</sup>) test, Paired Localisation Correlation Profile (PLCP) and network topological measures. For the PPI network, Pearson's chi-square test shows that for the same SCL category, twice as many interacting protein pairs are observed than estimated when compared to non-interacting protein pairs (χ<sup>2 </sup>= 1270.19, <it>P-value </it>< 2.2 × 10<sup>-16</sup>), whereas for MLPI, metabolite-linked protein pairs having the same SCL are observed 20% more than expected, compared to non-metabolite linked proteins (χ<sup>2 </sup>= 110.02, <it>P-value </it>< 2.2 x10<sup>-16</sup>). To address the issue of proteins with multiple SCLs, we have specifically used the PLCP (Pair Localization Correlation Profile) measure. PLCP analysis revealed that protein interactions are majorly restricted to the same SCL, though significant cross-compartment interactions are seen for nuclear proteins. Metabolite-linked protein pairs are restricted to specific compartments such as the mitochondrion (<it>P-value </it>< 6.0e-07), the lysosome (<it>P-value </it>< 4.7e-05) and the Golgi apparatus (<it>P-value </it>< 1.0e-15). These findings indicate that the metabolic network adds value to the information in the PPI network for the localisation process of proteins in human subcellular compartments.</p> <p>Conclusions</p> <p>The MLPI network differs significantly from the PPI network in its SCL distribution. The PPI network shows passive protein interaction, possibly due to its high false positive rate, across different subcellular compartments, which seem to be absent in the MLPI network, as the MLPI network has evolved to maintain high substrate specificity for proteins.</p

    Sushi in the United States, 1945-1970

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    Sushi first achieved widespread popularity in the United States in the mid-1960s. Many accounts of sushi’s US establishment foreground the role of a small number of key actors, yet underplay the role of a complex web of large-scale factors that provided the context in which sushi was able to flourish. This article critically reviews existing literature, arguing that sushi’s US popularity arose from contingent, long-term, and gradual processes. It examines US newspaper accounts of sushi during 1945–1970, which suggest the discursive context for US acceptance of sushi was considerably more propitious than generally acknowledged. Using California as a case study, the analysis also explains conducive social and material factors, and directs attention to the interplay of supply- and demand-side forces in the favorable positioning of this “new” food. The article argues that the US establishment of sushi can be understood as part of broader public acceptance of Japanese cuisine

    The correlation-consistent composite approach: Application to the G3/99 test set

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    Article discussing research on the correlation consistent composite approach (ccCA) and an application to the G3/99 test set
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