An automatic mesh generator for coupled 1D–2D hydrodynamic models

Two-dimensional (2D), depth-averaged shallow water equation (SWE) models are routinely used to simulate flooding in coastal areas – areas that often include vast networks of channels and flood-control topographic features and/or structures, such as barrier islands and levees. Adequately resolving these features within the confines of a 2D model can be computationally expensive, which has led to coupling 2D simulation tools to less expensive one-dimensional (1D) models. Under certain 1D–2D coupling approaches, this introduces internal constraints that must be considered in the generation of the 2D computational mesh used. In this paper, we further develop an existing automatic unstructured mesh generation tool for SWE models, ADMESH+, to sequentially (i) identify 1D constraints from the raw input data used in the mesh generation process, namely the digital elevation model (DEM) and land–water delineation data; (ii) distribute grid points along these internal constraints, according to feature curvature and user-prescribed minimum grid spacing; and (iii) integrate these internal constraints into the 2D mesh size function and mesh generation processes. The developed techniques, which include a novel approach for determining the so-called medial axis of a polygon, are described in detail and demonstrated on three test cases, including two inland watersheds with vast networks of channels and a complex estuarine system on the Texas, USA, coast.</p

A Discontinuous Galerkin Finite Element Model for Compound Flood Simulations

Recent tropical cyclones, e.g., Hurricane Harvey (2017), have lead to significant rainfall and resulting runoff with accompanying flooding. When the runoff interacts with storm surge, the resulting floods can be greatly amplified and lead to effects that cannot be modeled by simple superposition of its distinctive sources. In an effort to develop accurate numerical simulations of runoff, surge, and compounding floods, we develop a local discontinuous Galerkin method for modified shallow water equations. In this modification, nonzero sources to the continuity equation are included to incorporate rainfall into the model using parametric rainfall models from literature as well as hindcast data. The discontinuous Galerkin spatial discretization is accompanied with a strong stability preserving explicit Runge Kutta time integrator. Hence, temporal stability is ensured through the CFL condition and we exploit the embarrassingly parallel nature of the developed method using MPI parallelization. We demonstrate the capabilities of the developed method though a sequence of physically relevant numerical tests, including small scale test cases based on laboratory measurements and large scale experiments with Hurricane Harvey in the Gulf of Mexico. The results highlight the conservation properties and robustness of the developed method and show the potential of compound flood modeling using our approach

The problem of shot selection in basketball

In basketball, every time the offense produces a shot opportunity the player with the ball must decide whether the shot is worth taking. In this paper, I explore the question of when a team should shoot and when they should pass up the shot by considering a simple theoretical model of the shot selection process, in which the quality of shot opportunities generated by the offense is assumed to fall randomly within a uniform distribution. I derive an answer to the question "how likely must the shot be to go in before the player should take it?", and show that this "lower cutoff" for shot quality $f$ depends crucially on the number $n$ of shot opportunities remaining (say, before the shot clock expires), with larger $n$ demanding that only higher-quality shots should be taken. The function $f(n)$ is also derived in the presence of a finite turnover rate and used to predict the shooting rate of an optimal-shooting team as a function of time. This prediction is compared to observed shooting rates from the National Basketball Association (NBA), and the comparison suggests that NBA players tend to wait too long before shooting and undervalue the probability of committing a turnover.Comment: 7 pages, 2 figures; comparison to NBA data adde

AUGIST: inferring species trees while accommodating gene tree uncertainty

Summary: AUGIST (accomodating uncertainty in genealogies while inferring species tress) is a new software package for inferring species trees while accommodating uncertainty in gene genealogies. It is written for the Mesquite software system and provides sampling procedures to incorporate uncertainty in gene tree reconstruction while providing confidence estimates for inferred species trees

Neighborhoods of trees in circular orderings

In phylogenetics, a common strategy used to construct an evolutionary tree for a set of species X is to search in the space of all such trees for one that optimizes some given score function (such as the minimum evolution, parsimony or likelihood score). As this can be computationally intensive, it was recently proposed to restrict such searches to the set of all those trees that are compatible with some circular ordering of the set X. To inform the design of efficient algorithms to perform such searches, it is therefore of interest to find bounds for the number of trees compatible with a fixed ordering in the neighborhood of a tree that is determined by certain tree operations commonly used to search for trees: the nearest neighbor interchange (nni), the subtree prune and regraft (spr) and the tree bisection and reconnection (tbr) operations. We show that the size of such a neighborhood of a binary tree associated with the nni operation is independent of the tree’s topology, but that this is not the case for the spr and tbr operations. We also give tight upper and lower bounds for the size of the neighborhood of a binary tree for the spr and tbr operations and characterize those trees for which these bounds are attained

openWAR: An Open Source System for Evaluating Overall Player Performance in Major League Baseball

Within baseball analytics, there is substantial interest in comprehensive statistics intended to capture overall player performance. One such measure is Wins Above Replacement (WAR), which aggregates the contributions of a player in each facet of the game: hitting, pitching, baserunning, and fielding. However, current versions of WAR depend upon proprietary data, ad hoc methodology, and opaque calculations. We propose a competitive aggregate measure, openWAR, that is based upon public data and methodology with greater rigor and transparency. We discuss a principled standard for the nebulous concept of a "replacement" player. Finally, we use simulation-based techniques to provide interval estimates for our openWAR measure.Comment: 27 pages including supplemen

Relationship between stereoscopic vision, visual perception, and microstructure changes of corpus callosum and occipital white matter in the 4-year-old very low birth weight children

Aim. To assess the relationship between stereoscopic vision, visual perception, and microstructure of the corpus callosum (CC) and occipital white matter, 61 children born with a mean birth weight of 1024 g (SD 270 g) were subjected to detailed ophthalmologic evaluation, Developmental Test of Visual Perception (DTVP-3), and diffusion tensor imaging (DTI) at the age of 4. Results. Abnormal stereoscopic vision was detected in 16 children. Children with abnormal stereoscopic vision had smaller CC (CC length: 53±6 mm versus 61±4 mm; p<0.01; estimated CC area: 314±106 mm2 versus 446±79 mm2; p<0.01) and lower fractional anisotropy (FA) values in CC (FA value of rostrum/genu: 0.7±0.09 versus 0.79±0.07; p<0.01; FA value of CC body: 0.74±0.13 versus 0.82±0.09; p=0.03). We found a significant correlation between DTVP-3 scores, CC size, and FA values in rostrum and body. This correlation was unrelated to retinopathy of prematurity. Conclusions. Visual perceptive dysfunction in ex-preterm children without major sequelae of prematurity depends on more subtle changes in the brain microstructure, including CC. Role of interhemispheric connections in visual perception might be more complex than previously anticipated

Inference of population splits and mixtures from genome-wide allele frequency data

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.comComment: 28 pages, 6 figures in main text. Attached supplement is 22 pages, 15 figures. This is an updated version of the preprint available at http://precedings.nature.com/documents/6956/version/