Weighted ensemble: Recent mathematical developments

The weighted ensemble (WE) method, an enhanced sampling approach based on periodically replicating and pruning trajectories in a set of parallel simulations, has grown increasingly popular for computational biochemistry problems, due in part to improved hardware and the availability of modern software. Algorithmic and analytical improvements have also played an important role, and progress has accelerated in recent years. Here, we discuss and elaborate on the WE method from a mathematical perspective, highlighting recent results which have begun to yield greater computational efficiency. Notable among these innovations are variance reduction approaches that optimize trajectory management for systems of arbitrary dimensionality.Comment: 12 pages, 10 figure

An Empirical Analysis of Children's After School Out-of-Home Activity-Location Engagement Patterns and Time Allocation

At the time of publication R. Paleti and C.R. Bhat were at the University of Texas at Austin; and R.B. Copperman was at Cambridge Systematics, Inc.Children are an often overlooked and understudied population group, whose travel needs are responsible for a significant number of trips made by a household. In addition, children's travel and activity participation during the post-school period have direct implication for adults' activity-travel patterns. A better understanding of children's after school activity-travel patterns and the linkages between parents and children's activity-travel needs is necessary for accurate prediction and forecasting of activity-based travel demand modeling systems. Specifically, this research effort utilizes a multinomial logit model to analyze children's post-school location patterns, and employs a multiple discrete-continuous extreme value (MDCEV) model to study the propensity of children to participate in, and allocate time to, multiple activity episode purpose-location types during the after-school period. The results show that a wide variety of demographic, attitudinal, environmental, and others' activity-travel pattern characteristics impact children's after school activity engagement patterns.Civil, Architectural, and Environmental Engineerin

Clinically recognizable error rate after the transfer of comprehensive chromosomal screened euploid embryos is low

ObjectiveTo determine the clinically recognizable error rate with the use of quantitative polymerase chain reaction (qPCR)–based comprehensive chromosomal screening (CCS).DesignRetrospective study.SettingMultiple fertility centers.Patient(s)All patients receiving euploid designated embryos.Intervention(s)Trophectoderm biopsy for CCS.Main Outcome Measure(s)Evaluation of the pregnancy outcomes following the transfer of qPCR-designated euploid embryos. Calculation of the clinically recognizable error rate.Result(s)A total of 3,168 transfers led to 2,354 pregnancies (74.3%). Of 4,794 CCS euploid embryos transferred, 2,976 gestational sacs developed, reflecting a clinical implantation rate of 62.1%. In the cases where a miscarriage occurred and products of conception were available for analysis, ten were ultimately found to be aneuploid. Seven were identified in the products of conception following clinical losses and three in ongoing pregnancies. The clinically recognizable error rate per embryo designated as euploid was 0.21% (95% confidence interval [CI] 0.10–0.37). The clinically recognizable error rate per transfer was 0.32% (95% CI 0.16–0.56). The clinically recognizable error rate per ongoing pregnancy was 0.13% (95% CI 0.03–0.37). Three products of conception from aneuploid losses were available to the molecular laboratory for detailed examination, and all of them demonstrated fetal mosaicism.Conclusion(s)The clinically recognizable error rate with qPCR-based CCS is real but quite low. Although evaluated in only a limited number of specimens, mosaicism appears to play a prominent role in misdiagnoses. Mosaic errors present a genuine limit to the effectiveness of aneuploidy screening, because they are not attributable to technical issues in the embryology or analytic laboratories

An Exploratory Analysis of Children's Daily Time-Use and Activity Patterns Using the Child Development Supplement (CDS) to the US Panel Study of Income Dynamics (PSID)

This research paper examines the weekday and weekend activity participation characteristics of school-going children. Specifically, the research focuses on the overall time-use of children in different types of activities, as well as on several dimensions characterizing the context of participation in activities. These include the temporal (day of week and participation duration), spatial (location), with-whom (i.e., accompanying individuals), and episode sequencing dimensions. The data for our analysis is drawn from the 2002 Child Development Supplement to the Panel Study of Income Dynamics.Civil, Architectural, and Environmental Engineerin

An Analysis of the Determinants of Children's Weekend Physical Activity Participation

This paper examines the out-of-home, weekend, time-use patterns of children aged 5 through 17 years, with a specific emphasis on their physical activity participation. The impact of several types of factors, including individual and household demographics, neighborhood demographics, built environment characteristics, and activity day variables, on physical activity participation is analyzed using a joint nested multiple discrete-continuous extreme value-binary choice model. The sample for analysis is drawn from the 2000 San Francisco Bay Area Travel Survey. The model developed in the paper can be used to assess the impacts of changing demographics and built environment characteristics on children's physical activity levels.Civil, Architectural, and Environmental Engineerin

Effect of the Built Environment on Motorized and Non-Motorized Trip Making: Substitutive, Complementary, or Synergistic?

At the time of publication J.Y. Guo was at the University of Wisconsin-Madison; and C.R. Bhat and R.B. Copperman were at the University of Texas at Austin.It has become well recognized that non-motorized transportation is beneficial to a community's health as well as its transportation system performance. In view of the limited public resources available for improving public health and/or transportation, the present study aims to (a) assess the expected impact of built environment improvements on the substitutive, complementary, or synergistic use of motorized and non-motorized modes; and (b) examine how the effects of built environment improvements differ for different population groups and for different travel purposes. The bivariate ordered probit models estimated in this study suggest that few built environment factors lead to the substitution of motorized mode use by non-motorized mode use. Rather, factors such as increased bikeway density and street network connectivity have the potential of promoting more non-motorized travel to supplement individuals' existing motorized trips. Meanwhile, the heterogeneity found in individuals' responsiveness to built environment factors indicates that built environment improvements need to be sensitive to the local residents' characteristics.Civil, Architectural, and Environmental Engineerin

FULLDOC: A full reporting debugger for optimized code

. As compilers increasingly rely on optimizations to achieve high performance, the effectiveness of source level debuggers for optimized code continues to falter. Even if values of source variables are computed in the execution of the optimized code, source level debuggers of optimized code are unable to always report the expected values of source variables at breakpoints. In this paper, we present FULLDOC, a debugger that can report all of the expected values of source variables that are computed in the optimized code. FULLDOC uses statically computed information to guide the gathering of dynamic information that enables full reporting. FULLDOC can report expected values at breakpoints when reportability is affected because values have been overwritten early, due to code hoisting or register reuse, or written late, due to code sinking. Our debugger can also report values that are path sensitive in that a value may be computed only along one path or the location of the va..