Path-integral virial estimator for reaction rate calculation based on the quantum instanton approximation

The quantum instanton approximation is a type of quantum transition state theory that calculates the chemical reaction rate using the reactive flux correlation function and its low order derivatives at time zero. Here we present several path-integral estimators for the latter quantities, which characterize the initial decay profile of the flux correlation function. As with the internal energy or heat capacity calculation, different estimators yield different variances (and therefore different convergence properties) in a Monte Carlo calculation. Here we obtain a virial-type estimator by using a coordinate scaling procedure rather than integration by parts, which allows more computational benefits. We also consider two different methods for treating the flux operator, i.e., local-path and global-path approaches, in which the latter achieves a smaller variance at the cost of using second-order potential derivatives. Numerical tests are performed for a one-dimensional Eckart barrier and a model proton transfer reaction in a polar solvent, which illustrates the reduced variance of the virial estimator over the corresponding thermodynamic estimator.Comment: 23 pages, 5 figures, 1 tabl

PLIT: An alignment-free computational tool for identification of long non-coding RNAs in plant transcriptomic datasets

Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate identification of lncRNAs in RNA-seq datasets is crucial for exploring their characteristic functions in the genome as most coding potential computation (CPC) tools fail to accurately identify them in transcriptomic data. Well-known CPC tools such as CPC2, lncScore, CPAT are primarily designed for prediction of lncRNAs based on the GENCODE, NONCODE and CANTATAdb databases. The prediction accuracy of these tools often drops when tested on transcriptomic datasets. This leads to higher false positive results and inaccuracy in the function annotation process. In this study, we present a novel tool, PLIT, for the identification of lncRNAs in plants RNA-seq datasets. PLIT implements a feature selection method based on L1 regularization and iterative Random Forests (iRF) classification for selection of optimal features. Based on sequence and codon-bias features, it classifies the RNA-seq derived FASTA sequences into coding or long non-coding transcripts. Using L1 regularization, 31 optimal features were obtained based on lncRNA and protein-coding transcripts from 8 plant species. The performance of the tool was evaluated on 7 plant RNA-seq datasets using 10-fold cross-validation. The analysis exhibited superior accuracy when evaluated against currently available state-of-the-art CPC tools

Graph-search Based UNet-d For The Analysis Of Endoscopic Images

While object recognition in deep neural networks (DNN) has shown remarkable success in natural images, endoscopic images still cannot be fully analysed using DNNs, since analysing endoscopic images must account for occlusion, light reflection and image blur. UNet based deep convolutional neural networks (DNNs) offer great potential to extract high-level spatial features, thanks to its hierarchical nature with multiple levels of abstraction, which is especially useful for working with multimodal endoscopic images with white light and fluoroscopy in the diagnosis of esophageal disease. However, the currently reported inference time for DNNs is above 200ms, which is unsuitable to integrate into robotic control loops. This work addresses real-time object detection and semantic segmentation in endoscopic devices. We show that endoscopic assistive diagnosis can approach satisfy detection rates with a fast inference time

Trends of sputum-smear positive tuberculosis in Zimbabwe: 2008–2011

Abstract Background Tuberculosis (TB) has remained one of the major public health problems in Zimbabwe with an estimated incidence rate of 552 per 100,000 persons in 2013. The aim of this study was to describe the trends in acid-fast bacilli (AFB) sputum-smear positive (SSP) TB overall and within subpopulations for the period during 2008–2011 in Zimbabwe. Results of this study will contribute towards the evaluation and implementation of targeted TB control interventions. Methods A cross-sectional study design was used to analyze 40, 110 SSP TB patient records routinely collected during 2008–2011. Incidence trends of SSP TB were described by province, sex, and age group. A Mantel–Haenszel Chi Statistic was calculated to compare each provincial SSP TB notification rate to the national SSP TB notification rate. Results SSP TB notification rates were higher in the two main urban provinces, the western provinces and Manicaland. The 25–44 year age group accounted for the largest proportion of notified SSP TB. However, the 55–64 year and 65+ age groups had SSP TB notification rates in 2011 higher than the 2008 value. Finally, the average SSP TB notification rate in males was 23 % higher than in females. Conclusion The findings of this study suggest that TB control has successfully decreased the notification rate of SSP TB in Zimbabwe during 2008–2011. However, the disproportionate distribution of SSP TB among different regions and subpopulations of the country highlights the need for more targeted interventions to accelerate the decline of TB in Zimbabwe.http://deepblue.lib.umich.edu/bitstream/2027.42/115461/1/13104_2015_Article_1568.pd

Mechanical Evidence of the Orbital Angular Momentum to Energy Ratio of Vortex Beams

We measure, in a single experiment, both the radiation pressure and the torque due to a wide variety of propagating acoustic vortex beams. The results validate, for the first time directly, the theoretically predicted ratio of the orbital angular momentum to linear momentum in a propagating beam. We experimentally determine this ratio using simultaneous measurements of both the levitation force and the torque on an acoustic absorber exerted by a broad range of helical ultrasonic beams produced by a 1000-element matrix transducer array. In general, beams with helical phase fronts have been shown to contain orbital angular momentum as the result of the azimuthal component of the Poynting vector around the propagation axis. Theory predicts that for both optical and acoustic helical beams the ratio of the angular momentum current of the beam to the power should be given by the ratio of the beam’s topological charge to its angular frequency. This direct experimental observation that the ratio of the torque to power does convincingly match the expected value (given by the topological charge to angular frequency ratio of the beam) is a fundamental result

An experimental and CFD study of the extreme waves impact on OC3-Hywind Spar Floating offshore wind turbine

The study presents a combined wave tank experiment and Computational Fluid Dynamics(CFD) study on the OC3-Hywind Spar Floating [1] offshore wind turbine under extreme wave conditions. Focused wave is adopted in the present study as one of the effective ways to model the extreme wave. The main objectives of this study are to demonstrate how the focused waves could represent the extreme waves and the difference of focused waves approach and other wave types to model extreme waves, i.e., irregular waves. The experimental tank test was carried out with a 1/74 scale model both in irregular and focused wave conditions in Kelvin Hydrodynamics Laboratory at the University of Strathclyde. The irregular waves are designed by using identical wave spectrum with focused waves in the wave tank, and it will be helpful to determine the viability of using different wave types to represent high amplitude waves. The study provides a comparison of the dynamic responses, motion RAOs of the floater between focused waves and irregular waves. In addition, an in-house CFD code[2][3][4] based on an open-source CFD framework OpenFOAM [5] is adopted to simulate the fluid flow around the Spar-FOWT in a numerical wave tank under regular and focused wave conditions. Firstly, for code validation, the dynamic response of the Spar-FOWT is simulated under regular waves and the results are compared with the existing research [6]. Next, the focused wave with the identical wave spectrum provided by the experimental test is generated in our numerical wave tank without the floating structure. After the validation of the focused wave generation, the wave-structure interaction and the dynamic response of the Spar-FOWT is investigated under the focused wave. The results show good agreement with the tank test which demonstrates the capacity and the fidelity of our CFD tools

Family Relations and Remarriage Post-Divorce and Post-Widowhood in China

Analyzing event history data from the 2010 China Family Panel Studies and 13 qualitative interviews, we examine the complex and gendered relationship between family relations and remarriage in China. Distinct roles are played by the presence of pre-school, school-age and adult children in configuring the remarriage of women and men after divorce and after widowhood. The remarriage of widows but not divorcées is positively associated with the presence of parents and siblings respectively. Remarriage is more likely in the presence of large extended families. Whereas single and remarried divorcé(e)s equally provide care to their children, such care provision is less likely among remarried than single widow(er)s. Compared with their single counterparts, remarried divorcé(e)s and particularly widow(er)s are less likely to receive care from their children. We underline the importance of considering the “linked lives” of family members and comparing distinct life-course circumstances in the study of remarriage. We demonstrate that remarriage is far from an “individualized” institution, and that the state’s privatization of marriage seems to reinforce the “familialization” of remarriage practices in China

Pharmacokinetic modeling of tranexamic acid for patients undergoing cardiac surgery with normal renal function and model simulations for patients with renal impairment

Tranexamic acid (TXA), an effective anti-fibrinolytic agent that is cleared by glomerular filtration, is used widely for cardiopulmonary bypass (CPB) surgery. However, an effective dosing regimen has not been fully developed in patients with renal impairment. The aims of this study were to characterize the inter-patient variability associated with pharmacokinetic parameters and to recommend a new dosing adjustment based on the BART dosing regimen for CPB patients with chronic renal dysfunction (CRD). Recently published data on CPB patients with normal renal function (n = 15) were re-examined with a two-compartment model using the ADAPT5® and NONMEMVII® to identify covariates that explain inter-patient variability and to ascertain whether sampling strategies might affect parameter estimation. A series of simulations was performed to adjust the BART dosing regimen for CPB patients with renal impairment. Based on the two-compartmental model, the number of samples obtained after discontinuation of TXA infusion was found not to be critical in parameter estimation (p > 0.05). Both body weight and creatinine clearance were identified as significant covariates (p < 0.005). Simulations showed significantly higher than normal TXA concentrations in CRD patients who received the standard dosing regimen in the BART trial. Adjustment of the maintenance infusion rate based on the percent reduction in renal clearance resulted in predicted plasma TXA concentrations that were safe and therapeutic (~100 mg·L(-1) ). Our proposed dosing regimen, with consideration of renal function, is predicted to maintain effective target plasma concentrations below those associated with toxicity for patients with renal failure for CPB