One-Dimensional and Two-Dimensional Simulations of Helical Homopolymers: A Comparative Analysis of Energy Stabilization and Efficiency​

The purpose of our work is to analyze the results of a two-dimensional parallel tempering Monte Carlo simulation of a coarse-grained helical homopolymer. The two-dimensional simulation allows Hamiltonian exchanges across both temperature and torsion values, while the one-dimensional simulation exclusively exchanges across temperature values. The genesis of each simulation is defined by a randomly configured polymer; as time progresses, randomly generated movements of monomers decrease the structure’s energy until equilibrium is reached. Equilibrium is determined by finding the absolute minimum of the data series, computing the mean of all remaining data, and finding the intersection between the rolling average and the post-minimum mean. Data collected after equilibration is used to understand polymer behavior for each model and simulated temperature. This data aids in constructing a hyperphase diagram to visualize phase transitions of the simulated polymers. Simulation efficiencies as a function of both equilibration time and steps per new structure are calculated to compare the efficacy of the 2D parallel exchange scheme versus the 1D. Incorporating the two-dimensional Hamiltonian exchange into parallel tempering simulations lead to an average seven-fold increase in the rate at which new structures are generated in this model and a decrease in the equilibration time by as much as 95%

One-Dimensional and Two-Dimensional Simulations of Helical Homopolymers: A Comparative Analysis of Energy Stabilization and Efficiency

The purpose of our work is to analyze the results of a two-dimensional parallel tempering simulation of a coarse-grained helical homopolymer. We aim to measure the efficiency of the simulation and apply this efficiency to the theoretical protein free energy landscape.The stable states for helical homopolymers will be analyzed using the folding funnel theory of free energy landscapes for given polymer configurations. The genesis of each simulation is defined by a randomly configured polymer; as time progresses, the energy of each structure decreases until equilibrium is reached. Data collected after equilibrium is reached is used to understand polymer behavior for each model and simulated temperature. A rolling average algorithm has been designed to establish the time step at which energy stabilization is reached for each model. The simulation is considered to be stable when the rolling average of the energy is within a set fraction of the standard deviation of the rolling window based on the standard deviation and mean of previous windows. Efficiency and equilibration time of the 1D and 2D simulations are compared to determine the value of the two dimensional exchange scheme and analyze the free energy landscape of the polymer configuration

Faculty members engaging in transformative PETE: a feminist perspective

The purpose of this study was to describe sport pedagogy faculty members’ (FMs) efforts at engaging in transformative physical education teacher education (T-PETE). T-PETE stresses the importance of FMs creating social change through their pedagogical approach and begins by asking preservice teachers (PTs) to reflect on their perspectives and practices (Tinning, 2017 Tinning, R. (2017). Transformative pedagogies and physical education. In C. Ennis (Ed.), The Routledge handbook of physical education pedagogies (pp. 295–306). New York: Taylor & Francis. [Google Scholar]. Transformative pedagogies and physical education. In C. Ennis (Ed.), The Routledge handbook of physical education pedagogies (pp. 295–306). New York: Taylor & Francis; Ukpokodu, 2009. The practice of transformative pedagogy. Journal on Excellence in College Teaching, 20(2), 43–67.). Participants were three white, female, able-bodied, lesbian/gay sport pedagogy FMs. The study was conducted in the United States. Feminist theory and feminist pedagogy drove data collection and analysis. Data were collected by employing a series of qualitative methods. An inductive and deductive analysis revealed that FMs had specific T-PETE goals, content, and pedagogies. Furthermore, several factors served to facilitate and limit the FMs’ effectiveness when engaging in T-PETE. The findings suggest that program-wide PETE reform is necessary in the United States for creating social change, and influencing PTs perspectives and practices. In addition, they suggest that American PETE programs might benefit from greater diversity among the FMs who staff them

What definition is used to describe second impact syndrome in sports? A systematic and critical review

Concern about what has been termed, “second impact syndrome” (SIS) is a major factor determining return-to-play decisions after concussion. However, definitions of SIS vary. We used Scopus to conduct a systematic review and categorize the definitions used to describe SIS. Of the 91 sources identified, 79 (87%) clearly specified that SIS involved either cerebral edema or death after a concussion when a prior concussion had not resolved. Twelve articles (13%) could be interpreted as merely the events of two consecutive concussions. Among the articles that listed mortality rates, nearly all (33/35, 94%) said the rate of death was “high” (e.g., 50% to 100%). Our review found that most articles define SIS as a syndrome requiring catastrophic brain injury after consecutive concussive episodes. Given that it is unclear how common it is to have a second concussion while not fully recovered from a first concussion, the actual mortality rate of SIS is unknown.http://journals.lww.com/acsm-csmr2018-01-31hb2017Sports Medicin

Somatic mutations and clonal dynamics in healthy and cirrhotic human liver.

The most common causes of chronic liver disease are excess alcohol intake, viral hepatitis and non-alcoholic fatty liver disease, with the clinical spectrum ranging in severity from hepatic inflammation to cirrhosis, liver failure or hepatocellular carcinoma (HCC). The genome of HCC exhibits diverse mutational signatures, resulting in recurrent mutations across more than 30 cancer genes1-7. Stem cells from normal livers have a low mutational burden and limited diversity of signatures8, which suggests that the complexity of HCC arises during the progression to chronic liver disease and subsequent malignant transformation. Here, by sequencing whole genomes of 482 microdissections of 100-500 hepatocytes from 5 normal and 9 cirrhotic livers, we show that cirrhotic liver has a higher mutational burden than normal liver. Although rare in normal hepatocytes, structural variants, including chromothripsis, were prominent in cirrhosis. Driver mutations, such as point mutations and structural variants, affected 1-5% of clones. Clonal expansions of millimetres in diameter occurred in cirrhosis, with clones sequestered by the bands of fibrosis that surround regenerative nodules. Some mutational signatures were universal and equally active in both non-malignant hepatocytes and HCCs; some were substantially more active in HCCs than chronic liver disease; and others-arising from exogenous exposures-were present in a subset of patients. The activity of exogenous signatures between adjacent cirrhotic nodules varied by up to tenfold within each patient, as a result of clone-specific and microenvironmental forces. Synchronous HCCs exhibited the same mutational signatures as background cirrhotic liver, but with higher burden. Somatic mutations chronicle the exposures, toxicity, regeneration and clonal structure of liver tissue as it progresses from health to disease.This work was supported by a Wellcome Trust and Cancer Research UK (CRUK) Grand Challenge Award (C98/A24032). P.J.C. is a Wellcome Trust Senior Clinical Fellow (WT088340MA); S.F.B. was supported by the Swiss National Science Foundation (P2SKP3-171753 and P400PB-180790); M.A.S. is supported by a Rubicon fellowship from NWO (019.153LW.038); the Cambridge Human Research Tissue Bank is supported by the NIHR Cambridge Biomedical Research Centre; and M.H. is supported by a CRUK Clinician Scientist Fellowship (C52489/A19924)

Introduction: Toward an Engaged Feminist Heritage Praxis

We advocate a feminist approach to archaeological heritage work in order to transform heritage practice and the production of archaeological knowledge. We use an engaged feminist standpoint and situate intersubjectivity and intersectionality as critical components of this practice. An engaged feminist approach to heritage work allows the discipline to consider women’s, men’s, and gender non-conforming persons’ positions in the field, to reveal their contributions, to develop critical pedagogical approaches, and to rethink forms of representation. Throughout, we emphasize the intellectual labor of women of color, queer and gender non-conforming persons, and early white feminists in archaeology

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care

One-Dimensional and Two-Dimensional Simulations of Helical Homopolymers: A Comparative Analysis of Efficiency and Funnel Folding

The purpose of our work is to analyze the results of a two-dimensional parallel tempering simulation of a coarse-grained helical homopolymer. We aim to measure the efficiency of the simulation and apply this efficiency to the theoretical protein free energy landscape.The stable states for helical homopolymers will be analyzed using the folding funnel theory of free energy landscapes for given polymer configurations. The genesis of each simulation is defined by a randomly configured polymer; as time progresses, the energy of each structure decreases until equilibrium is reached. Data collected after equilibrium is reached is used to understand polymer behavior for each model and simulated temperature. A rolling average algorithm has been designed to establish the time step at which energy stabilization is reached for each model. The simulation is considered to be stable when the rolling average of the energy is within a set fraction of the standard deviation of the rolling window based on the standard deviation and mean of previous windows. Efficiency and equilibration time of the 1D and 2D simulations are compared to determine the value of the two dimensional exchange scheme and analyze the free energy landscape of the polymer configuration

Optimizing dial-a-ride services in Maryland: Benefits of computerized routing and scheduling

This paper reports on a system developed to address the dial-a-ride problem and an implementation for Maryland where real-world practical constraints are considered in providing customized vehicle routing and scheduling for about 450 trip requests daily. The system, called Mobile Resource Management System (MRMS), allows for dispatch operators to quickly study different operational scenarios and, in a strategic setting, explore tradeoffs between level-of-service and various system characteristics, including fleet composition, fleet size and dispatch rules. Such insights play a key role in making long-term investment decisions or estimating cost of servicing contracts that have service level agreements. Test comparison of manual and MRMS-based routes indicated an estimated annual operational expense reduction of $0.82 million, or about 18% of the total annual expense. In addition to the cost benefits, improved quality of service and the reduction in total vehicle-kilometers traveled leading to environmental benefits are demonstrated