273 research outputs found

    Real value prediction of protein solvent accessibility using enhanced PSSM features

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    <p>Abstract</p> <p>Background</p> <p>Prediction of protein solvent accessibility, also called accessible surface area (ASA) prediction, is an important step for tertiary structure prediction directly from one-dimensional sequences. Traditionally, predicting solvent accessibility is regarded as either a two- (exposed or buried) or three-state (exposed, intermediate or buried) classification problem. However, the states of solvent accessibility are not well-defined in real protein structures. Thus, a number of methods have been developed to directly predict the real value ASA based on evolutionary information such as position specific scoring matrix (PSSM).</p> <p>Results</p> <p>This study enhances the PSSM-based features for real value ASA prediction by considering the physicochemical properties and solvent propensities of amino acid types. We propose a systematic method for identifying residue groups with respect to protein solvent accessibility. The amino acid columns in the PSSM profile that belong to a certain residue group are merged to generate novel features. Finally, support vector regression (SVR) is adopted to construct a real value ASA predictor. Experimental results demonstrate that the features produced by the proposed selection process are informative for ASA prediction.</p> <p>Conclusion</p> <p>Experimental results based on a widely used benchmark reveal that the proposed method performs best among several of existing packages for performing ASA prediction. Furthermore, the feature selection mechanism incorporated in this study can be applied to other regression problems using the PSSM. The program and data are available from the authors upon request.</p

    On character table of Clifford groups

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    Based on a presentation of Cn\mathcal{C}_n and the help of [GAP], we construct the character table of the Clifford group Cn\mathcal{C}_n for n=1,2,3n=1,2,3. As an application, we can efficiently decompose the (higher power of) tensor product of the matrix representation in those cases. Our results recover some known results in [HWW, WF] and reveal some new phenomena. We prove that the trivial character is the only linear character for Cn\mathcal{C}_n and hence Cn\mathcal{C}_n equals to its commutator subgroup when n3n\geq 3. A few conjectures about Cn\mathcal{C}_n for general nn are proposed.Comment: 13 pages; comments and suggestions are welcom

    Motor neuron-derived Thsd7a is essential for zebrafish vascular development via the Notch-dll4 signaling pathway.

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    BackgroundDevelopment of neural and vascular systems displays astonishing similarities among vertebrates. This parallelism is under a precise control of complex guidance signals and neurovascular interactions. Previously, our group identified a highly conserved neural protein called thrombospondin type I domain containing 7A (THSD7A). Soluble THSD7A promoted and guided endothelial cell migration, tube formation and sprouting. In addition, we showed that thsd7a could be detected in the nervous system and was required for intersegmental vessels (ISV) patterning during zebrafish development. However, the exact origin of THSD7A and its effect on neurovascular interaction remains unclear.ResultsIn this study, we discovered that zebrafish thsd7a was expressed in the primary motor neurons. Knockdown of Thsd7a disrupted normal primary motor neuron formation and ISV sprouting in the Tg(kdr:EGFP/mnx1:TagRFP) double transgenic zebrafish. Interestingly, we found that Thsd7a morphants displayed distinct phenotypes that are very similar to the loss of Notch-delta like 4 (dll4) signaling. Transcript profiling further revealed that expression levels of notch1b and its downstream targets, vegfr2/3 and nrarpb, were down-regulated in the Thsd7a morphants. These data supported that zebrafish Thsd7a could regulate angiogenic sprouting via Notch-dll4 signaling during development.ConclusionsOur results suggested that motor neuron-derived Thsd7a plays a significant role in neurovascular interactions. Thsd7a could regulate ISV angiogenesis via Notch-dll4 signaling. Thus, Thsd7a is a potent angioneurin involved in the development of both neural and vascular systems

    Modification of Vertical Earth Pressure Formulas for High Fill Cut-and-Cover Tunnels Experimental and Numerical Methods

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    Te high-flled cut-and-cover tunnel (HFCCT) is a solution to reclaim more useable lands due to the unique landforms of Loess Plateau in northwestern China. Because of the ultrahigh backfll, the estimation of vertical earth pressure will signifcantly afect the design and safety of the cut-and-cover tunnel (CCT). Te current methods for estimating the vertical earth pressure are either to overestimate or underestimate the vertical earth pressure on the top of HFCCT. To more precisely estimate the vertical earth pressure distribution, the vertical earth pressure based on the soil column pressure, �h (h: the height of backfll above the CCT), needs to be properly modifed. Considering diferent infuential factors, four corresponding coefcients are proposed: �0: crosssectional shape of CCT efect, �1: stifness of backfll efect, �2: width of CCT efect, and �3: coupling efect of slope angle, �, and the ratio of B/D. It is found that �0 has little infuence; the �3 and �1 reduce and �2 amplifes the �h. Te corresponding general forms for these coefcients are determined based on fnite element analysis results. A general equation for estimating vertical earth pressure for the HFCCT including these four coefcients is proposed. Meanwhile, this general form is verifed by the numerical analysis results and experimental results for diferent cases. Terefore, this proposed equation is applicable to estimate the vertical earth pressure for existing or newly designed HFCCT. Furthermore, this proposed method can signifcantly reduce the computational work in engineering analysis

    Green tea inhibited the elimination of nephro-cardiovascular toxins and deteriorated the renal function in rats with renal failure

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    Chronic kidney disease (CKD) is a major health problem worldwide. Indoxyl sulfate (IS) and p-cresyl sulfate (PCS) are highly protein-bound nephro-cardiovascular toxins, which are not efficiently removed through hemodialysis. The renal excretions of IS and PCS were mediated by organic anion transporters (OATs) such as OAT1 and OAT3. Green tea (GT) is a popular beverage containing plenty of catechins. Previous pharmacokinetic studies of teas have shown that the major molecules present in the bloodstream are the glucuronides/sulfates of tea catechins, which are putative substrates of OATs. Here we demonstrated that GT ingestion significantly elevated the systemic exposures of endogenous IS and PCS in rats with chronic renal failure (CRF). More importantly, GT also significantly increased the levels of serum creatinine (Cr) and blood urea nitrogen (BUN) in CRF rats. Mechanism studies indicated that the serum metabolites of GT (GTM) inhibited the uptake transporting functions of OAT1 and OAT3. In conclusion, GT inhibited the elimination of nephro-cardiovascular toxins such as IS and PCS, and deteriorated the renal function in CRF rats

    Performance evaluation on the implementation of Pre-established Medical Processes for nurse practitioners in the hospitals

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    In 2015, Taiwan announced the establishment of “Pre-established Medical Processes” and related regulations to assist nurse practitioners in the clinical tasks, maintain medical quality and patient safety, and provide protection in clinical practice. However, the effectiveness of implementation still needs to be improved and strengthened. This study adopts the TAM and the TTF as the research framework, and a cross-sectional design. The questionnaires are administered to the professional nurse practitioners in the hospitals of central Taiwan. A total of 300 questionnaires were distributed, and Smart PLS 3.0 and SPSS 24.0 were both applied to verify interpretability. The questionnaire recovery rate was 88.3%, and the overall predictive power was 65.2%. Technological characteristics and TTF had a significant impact on perceived usefulness
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