DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning

<p>Abstract</p> <p>Background</p> <p>Accurate identification of protein domain boundaries is useful for protein structure determination and prediction. However, predicting protein domain boundaries from a sequence is still very challenging and largely unsolved.</p> <p>Results</p> <p>We developed a new method to integrate the classification power of machine learning with evolutionary signals embedded in protein families in order to improve protein domain boundary prediction. The method first extracts putative domain boundary signals from a multiple sequence alignment between a query sequence and its homologs. The putative sites are then classified and scored by support vector machines in conjunction with input features such as sequence profiles, secondary structures, solvent accessibilities around the sites and their positions. The method was evaluated on a domain benchmark by 10-fold cross-validation and 60% of true domain boundaries can be recalled at a precision of 60%. The trade-off between the precision and recall can be adjusted according to specific needs by using different decision thresholds on the domain boundary scores assigned by the support vector machines.</p> <p>Conclusions</p> <p>The good prediction accuracy and the flexibility of selecting domain boundary sites at different precision and recall values make our method a useful tool for protein structure determination and modelling. The method is available at <url>http://sysbio.rnet.missouri.edu/dobo/</url>.</p

Study on the Creep Characteristics of Sandstone under Coupled Stress-water Pressure

Long-term interaction between stress and water pressure leads to creep damage of reservoir bank slope. As a result there will be instability of the bank slopes in many water conservancy projects. The rock mass creeping effect of coupled stress-water pressure was studied by using a typical sandstone rock from the Three Gorges reservoir area. The experiment was conducted by using the rock immersion-air-drying cyclic load rheometer device (designed and manufactured by our research team). Based on the experimental results, the following key points were observed: 1) the creep strain and the steady-state creep rate was increasing when the water pressure increased (at the same stress level). Under the same water pressure, the increase in the axial pressure resulted in the increase in the creep strain and steady creep rate of the sandstone specimens. 2) the increase in the axial pressure increased the creep strain and steady-state creep rate of the sandstone specimens while the water pressure increased. The mechanical properties of the sandstone specimens were affected by the water pressure. 3) the water infiltrates through the pore surfaces. As a result, the rate of deformation will increase while the bearing capacity and long-term strength of the rock decrease. This paper provides a solid theoretical foundation for the evaluation and prediction of reservoir geological hazards

The Neutrophil/Lymphocyte Ratio is Associated with Different Stages of Development of Coronary Artery Disease

Introduction: Inflammation plays a role in coronary artery disease (CAD). The neutrophil/lymphocyte ratio (NLR), monocyte/lymphocyte ratio (MLR) and platelet/lymphocyte ratio (PLR) are blood parameters associated with inflammation. We aimed to perform a systematic comparison and study the predictive values of these inflammatory parameters with respect to CAD stage. Method: A total of 513 patients who had undergone coronary angiography (CAG) were retrospectively analyzed. Clinical status, lipid profiles, CAG scans and hematological parameters were collected. NLR, MLR and PLR were calculated. All patients were classified into a normal coronary group (n=133), coronary atherosclerosis (CA) group (n=149), chronic coronary syndrome (CCS) group (n=175) or acute myocardial infarction (AMI) group (n=56). NLR, MLR and PLR were compared among groups. Results: NLR and MLR were higher in the CCS and AMI groups. PLR was higher in the AMI group. The AMI group had higher NLR, PLR and MLR than the CCS group. Logistic regression analysis revealed that NLR (OR:1.227, 95% CI: 1.016–1.482. P<0.05) had a strong significant correlation with CAD. Area under the ROC curve of NLR was 0.580 (95% CI=0.516–0.644) in predicting CCS and 0.727 (95% CI=0.642–0.811) in predicting AMI. Conclusion: NLR may be associated with the occurrence and progression of CAD, and may serve as a marker of inflammation

Study on the Time-lag Failure of Sandstone With Different Degrees of Unloading Damage

The unloading effect of rock mass excavation is an inevitable practice, and it’s often characterized by a relatively large-scale engineering hazard with a noticeable time lag.A set of unloading triaxial tests were conducted on a sandstone rock to establish the deformation law and the threshold time. Based on the renormalization group theory, the unloading sandstone model was developed by considering the interaction between particles. Similarly, a logistic model was used to predict the unloading damage of sandstone. The unloading time lag damage of sandstone rock was predicted by using the damage threshold. The research shows that: (1) The higher the degree of unloading, the shorter the time-lag failure. (2) The damage range of critical values was optimized. (3) The error between the predicted value and the experimental value of the time threshold was almost less than 5 %, the prediction result was found to be good, and the employed logistic evolution model was reasonable. The findings of this research provide a prediction method and precise information about the mechanism of unloading time lag deformation. Therefore, it can be used as a reference for excavation-support design of underground structures

Effect of the Water-Rock Interaction on the Creep Mechanical Properties of the Sandstone Rock

After the commencement of the Three Gorges hydropower project, the reservoir water level has been fluctuating by 30 m (145–175 m) annually. The stability of the bank slope has been highlighted since the reservoir water level has been repeated. Apart from that, the long-term effect of the water-rock interaction on the rheological and mechanical properties of the rock was not studied sufficiently. Therefore, a typical sandstone rock was brought from the Three Gorges reservoir area, to meet the purpose of this study. Then, a series of water-rock interaction tests were conducted to simulate the fluctuations in the reservoir water level. Based upon the experimental results, the following points were pointed out: 1) for the first three successive water-rock interaction cycles, the long-term strength of the rock was dramatically reduced. In contrast, the rate of reduction on the long-term strength of the rock was getting a steady state after six successive water rock interactions.2) At the failure stress level, the rock specimens exhibited similar characteristics under different water-rock interaction cycles. 3) The densely compacted micro structures of the sandstone rock were transformed into loose and porous state

Spontaneous Coronary Artery Dissection with Iliac Artery Dissection: A Case Report and Literature Review

Spontaneous coronary artery dissection is a rare cause of acute coronary syndrome or sudden cardiac death. It often occurs in females with no conventional cardiovascular risk factors. Bilateral iliac artery dissection is also a rare disease. This case report describes a patient with spontaneous coronary artery dissection and iliac artery dissection. The authors believe that a conservative approach could be used as an effective therapy for a clinically stable patient

New Method for Determination of Residual Strength Parameters and Critical Damage Value

Residual strength and critical damage parameters are worthy to evaluate the stability of engineered rock masses. In this paper, new thinking, repeated load test on a single specimen was proposed to measure the residual strength of the rock. And author proposed to modify the critical damage value based on residual constitutive energy. The test results showed that: (1) the residual strength of rock is mainly controlled by the confining pressure, without a clear relationship with the confining pressure and stress path of the initial loading failure. (2) The residual strength parameters of the rock specimens under repeated loading test are consistent with the conventional triaxial test. Most importantly, the proposed method is relatively less dispersion, cheap, reliable, and time-saving. (3) The corrected critical damage value was reasonable. Relevant test methods can provide a useful reference for the determination of residual strength parameters and critical damage value

Prolonged mixed phase induced by high pressure in MnRuP

Hexagonally structured MnRuP was studied under high pressure up to 35 GPa from 5 to 300 K using synchrotron X-ray diffraction. We observed that a partial phase transition from hexagonal to orthorhombic symmetry started at 11 GPa. The new and denser orthorhombic phase coexisted with its parent phase for an unusually long pressure range, {\Delta}P ~ 50 GPa. We attribute this structural transformation to a magnetic origin, where a decisive criterion for the boundary of the mixed phase lays in the different distances between the Mn-Mn atoms. In addition, our theoretical study shows that the orthorhombic phase of MnRuP remains steady even at very high pressures up to ~ 250 GPa, when it should transform to a new tetragonal phase.Comment: 15 pages, 5 figures, supplementary materia

Assessing contributions of agricultural and nonagricultural emissions to atmospheric ammonia in a Chinese megacity

Ammonia (NH3) is the predominant alkaline gas in the atmosphere contributing to formation of fine particles—a leading environmental cause of increased morbidity and mortality worldwide. Prior findings suggest that NH3 in the urban atmosphere derives from a complex mixture of agricultural (mainly livestock production and fertilizer application) and nonagricultural (e.g., urban waste, fossil fuel-related emissions) sources; however, a citywide holistic assessment is hitherto lacking. Here we show that NH3 from nonagricultural sources rivals agricultural NH3 source contributions in the Shanghai urban atmosphere. We base our conclusion on four independent approaches: (i) a full-year operation of a passive NH3 monitoring network at 14 locations covering urban, suburban, and rural landscapes; (ii) model-measurement comparison of hourly NH3 concentrations at a pair of urban and rural supersites; (iii) source-specific NH3 measurements from emission sources; and (iv) localized isotopic signatures of NH3 sources integrated in a Bayesian isotope mixing model to make isotope-based source apportionment estimates of ambient NH3. Results indicate that nonagricultural sources and agricultural sources are both important contributors to NH3 in the urban atmosphere. These findings highlight opportunities to limit NH3 emissions from nonagricultural sources to help curb PM2.5 pollution in urban China

Atomic-scale insights into the low-temperature oxidation of methanol over a single-atom Pt1-Co3O4 catalyst

Heterogeneous catalysts with single‐atom active sites offer a means of expanding the industrial application of noble metal catalysts. Herein, an atomically dispersed Pt1‐Co3O4 catalyst is presented, which exhibits an exceptionally high efficiency for the total oxidation of methanol. Experimental and theoretical investigations indicate that this catalyst consists of Pt sites with a large proportion of occupied high electronic states. These sites possess a strong affinity for inactive Co2+ sites and anchor over the surface of (111) crystal plane, which increases the metal–support interaction of the Pt1‐Co3O4 material and accelerates the rate of oxygen vacancies regeneration. In turn, this is determined to promote the coadsorption of the probe methanol molecule and O2. Density functional theory calculations confirm that the electron transfer over the oxygen vacancies reduces both the methanol adsorption energy and activation barriers for methanol oxidation, which is proposed to significantly enhance the dissociation of the CH bond in the methanol decomposition reaction. This investigation serves as a solid foundation for characterizing and understanding single‐atom catalysts for heterogeneous oxidation reactions