BoXHED2.0: Scalable boosting of dynamic survival analysis

Modern applications of survival analysis increasingly involve time-dependent covariates. In healthcare settings, such covariates provide dynamic patient histories that can be used to assess health risks in realtime by tracking the hazard function. Hazard learning is thus particularly useful in healthcare analytics, and the open-source package BoXHED 1.0 provides the first implementation of a gradient boosted hazard estimator that is fully nonparametric. This paper introduces BoXHED 2.0, a quantum leap over BoXHED 1.0 in several ways. Crucially, BoXHED 2.0 can deal with survival data that goes far beyond right-censoring and it also supports recurring events. To our knowledge, this is the only nonparametric machine learning implementation that is able to do so. Another major improvement is that BoXHED 2.0 is orders of magnitude more scalable, due in part to a novel data preprocessing step that sidesteps the need for explicit quadrature when dealing with time-dependent covariates. BoXHED 2.0 supports the use of GPUs and multicore CPUs, and is available from GitHub: www.github.com/BoXHED.Comment: 12 page

Making and Breaking Trust in Forest Collaborative Groups

There has been a recent increase in use of an organized, forest ‘collaborative’ group approach for multi-stakeholder input on federal forestlands in the U.S. West. This approach relies on the creation of shared trust to achieve social agreement. Yet growing critiques suggest a lack of trust in the U.S. Forest Service [Forest Service], between stakeholders, and the collaborative process itself. We conducted three comparative case studies of established forest collaborative groups in Oregon, Washington, and Idaho to ask how trust is created and damaged or broken in this context. We found multiple, interlinked dimensions to trust, including significant reliance on procedural trust, trust of ‘in-groups’ who shared norms for conduct, and distrust of new participants. We also found that trust or distrust in the Forest Service affected other trust and process dynamics within groups. Our research offers new insights into the functions and limitations of a collaborative approach that is increasingly central to federal forest governance; and new empirical knowledge toward recent theoretical developments about trust in natural resource collaboration

Density-functional calculation of ionization energies of current-carrying atomic states

Current-density-functional theory is used to calculate ionization energies of current-carrying atomic states. A perturbative approximation to full current-density-functional theory is implemented for the first time, and found to be numerically feasible. Different parametrizations for the current-dependence of the density functional are critically compared. Orbital currents in open-shell atoms turn out to produce a small shift in the ionization energies. We find that modern density functionals have reached an accuracy at which small current-related terms appearing in open-shell configurations are not negligible anymore compared to the remaining difference to experiment.Comment: 7 pages, 2 tables, accepted by Phys. Rev.

Iterative approach to computational enzyme design

A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the synthesis and screening of a large number of variants. Here, we present an iterative approach that has led to the development of the most catalytically efficient computationally designed enzyme for the Kemp elimination to date. Previously established computational techniques were used to generate an initial design, HG-1, which was catalytically inactive. Analysis of HG-1 with molecular dynamics simulations (MD) and X-ray crystallography indicated that the inactivity might be due to bound waters and high flexibility of residues within the active site. This analysis guided changes to our design procedure, moved the design deeper into the interior of the protein, and resulted in an active Kemp eliminase, HG-2. The cocrystal structure of this enzyme with a transition state analog (TSA) revealed that the TSA was bound in the active site, interacted with the intended catalytic base in a catalytically relevant manner, but was flipped relative to the design model. MD analysis of HG-2 led to an additional point mutation, HG-3, that produced a further threefold improvement in activity. This iterative approach to computational enzyme design, including detailed MD and structural analysis of both active and inactive designs, promises a more complete understanding of the underlying principles of enzymatic catalysis and furthers progress toward reliably producing active enzymes

Determinants of Time to Fatigue during Non-Motorized Treadmill Exercise

Treadmill exercise is commonly used for aerobic and anaerobic conditioning. During non-motorized treadmill exercise, the subject must provide the power necessary to drive the treadmill belt. The purpose of this study was to determine what factors affected the time to fatigue on a pair of non-motorized treadmills. Twenty subjects (10 males/10 females) attempted to complete five minutes of locomotion during separate trials at 3.22, 4.83, 6.44, 8.05, 9.66, and 11.27 km (raised dot) h(sup -1). Total exercise time (less than or equal to 5 min) was recorded. Exercise time was converted to the amount of 15 second intervals completed. Peak oxygen uptake (VO2) was measured using a graded exercise test on a standard treadmill, and anthropometric measures were collected from each subject before entering into the study. A Cox proportional hazards regression model was used to determine significant predictive factors in a multivariate analysis. Non-motorized treadmill speed and absolute peak VO2 were found to be significant predictors of exercise time, but there was no effect of anthropometric characteristics. Gender was found to be a predictor of treadmill time, but this was likely due to a higher peak VO2 in males than in females. These results were not affected by the type of treadmill tested in this study. Coaches and therapists should consider the cardiovascular fitness of an athlete or client when prescribing target speed since these factors are related to the total exercise time than can be achieved on a non-motorized treadmill

Temperature and residence time controls on an estuarine harmful algal bloom : modeling hydrodynamics and Alexandrium fundyense in Nauset estuary

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Estuaries and Coasts 38 (2015): 2240-2258, doi:10.1007/s12237-015-9949-z.A highly resolved, 3-d model of hydrodynamics and Alexandrium fundyense in an estuarine embayment has been developed to investigate the physical and biological controls on a recurrent harmful algal bloom. Nauset estuary on Cape Cod (MA, USA) consists of three salt ponds connected to the ocean through a shallow marsh and network of tidal channels. The model is evaluated using quantitative skill metrics against observations of physical and biological conditions during three spring blooms. The A. fundyense model is based on prior model applications for the nearby Gulf of Maine, but notable modifications were made to be consistent with the Nauset observations. The dominant factors controlling the A. fundyense bloom in Nauset were the water temperature, which regulates organism growth rates, and the efficient retention of cells due to bathymetric constraints, stratification, and cell behavior (diel vertical migration). Spring-neap variability in exchange altered residence times, but for cell retention to be substantially longer than the cell doubling time required both active vertical migration and stratification that inhibits mixing of cells into the surface layer by wind and tidal currents. Unlike in the Gulf of Maine, the model results were relatively insensitive to cyst distributions or germination rates. Instead, in Nauset, high apparent rates of vegetative cell division by retained populations dictated bloom development. Cyst germination occurred earlier in the year than in the Gulf of Maine, suggesting that Nauset cysts have different controls on germination timing. The model results were relatively insensitive to nutrient concentrations, due to eutrophic conditions in the highly impacted estuary or due to limitations in the spatial and temporal resolution of nutrient sampling. Cell loss rates were inferred to be extremely low during the growth phase of the bloom, but increased rapidly during the final phase due to processes that remain uncertain. The validated model allows a quantitative assessment of the factors that contribute to the development of a recurrent harmful algal bloom and provides a framework for assessing similarly impacted coastal systems.This work was supported by the National Science Foundation (OCE-0430724, OCE-0911031, and OCE-1314642) and National Institutes of Health (NIEHS-1P50-ES021923-01) through the Woods Hole Center for Oceans and Human Health, and by National Park Service (NPS) Cooperative Agreement H238015504.2016-03-1

Sub-5 keV electron-beam lithography in hydrogen silsesquioxane resist

We fabricated 9–30 nm half-pitch nested Ls and 13–15 nm half-pitch dot arrays, using 2 keV electron-beam lithography with hydrogen silsesquioxane (HSQ) as the resist. All structures with 15 nm half-pitch and above were fully resolved. We observed that the 9 and 10-nm half-pitch nested Ls and the 13-nm-half-pitch dot array contained some resist residues. We obtained good agreement between experimental and Monte-Carlo-simulated point-spread functions at energies of 1.5, 2, and 3 keV. The long-range proximity effect was minimal, as indicated by simulated and patterned 30 nm holes in negative-tone resist.United States. Dept. of Energy. Office of Basic Energy Sciences (Award DE-SC0001088)National Science Foundation (U.S.) (Grant CMMI-0609241)China Scholarship CouncilNational Science Foundation (U.S.). Graduate Research Fellowshi