Integration of multi-scale biosimulation models via light-weight semantics

Currently, biosimulation researchers use a variety of computational environments and languages to model biological processes. Ideally, researchers should be able to semi- automatically merge models to more effectively build larger, multi-scale models. How- ever, current modeling methods do not capture the underlying semantics of these models sufficiently to support this type of model construction. In this paper, we both propose a general approach to solve this problem, and we provide a specific example that demon- strates the benefits of our methodology. In particular, we describe three biosimulation models: (1) a cardio-vascular fluid dynamics model, (2) a model of heart rate regulation via baroreceptor control, and (3) a sub-cellular-level model of the arteriolar smooth mus- cle. Within a light-weight ontological framework, we leverage reference ontologies to match concepts across models. The light-weight ontology then helps us combine our three models into a merged model that can answer questions beyond the scope of any single model

Using an in vitro System for Maintaining Varroa Destructor Mites on Apis Mellifera Pupae as Hosts: Studies of Mite Longevity and Feeding Behavior

Varroa destructor mites (varroa) are ectoparasites of Apis mellifera honey bees, and the damage they inflict on hosts is likely a causative factor of recent poor honey bee colony performance. Research has produced an arsenal of control agents against varroa mites, which have become resistant to many chemical means of their control, and other means have uncertain efficacy. Novel means of control will result from a thorough understanding of varroa physiology and behavior. However, robust knowledge of varroa biology is lacking; mites have very low survivability and reproduction away from their natural environment and host, and few tested protocols of maintaining mites in vitro are available as standardized methods for varroa research. Here, we describe the \u27varroa maintenance system\u27 (VMS), a tool for maintaining in vitro populations of varroa on its natural host, and present best practices for its use in varroa and host research. Additionally, we present results using the VMS from research of varroa and host longevity and varroa feeding behavior. Under these conditions, from two trials, mites lived an average of 12 and 14 days, respectively. For studies of feeding behavior, female mites inflicted wounds located on a wide range of sites on the host\u27s integument, but preferred to feed from the host\u27s abdomen and thorax. Originally in the phoretic-phase, female mites in VMS had limited reproduction, but positive instances give insights into the cues necessary for initiating reproduction. The VMS is a useful tool for laboratory studies requiring long-term survival of mites, or host-parasite interactions

Chaos in computer performance

Modern computer microprocessors are composed of hundreds of millions of transistors that interact through intricate protocols. Their performance during program execution may be highly variable and present aperiodic oscillations. In this paper, we apply current nonlinear time series analysis techniques to the performances of modern microprocessors during the execution of prototypical programs. Our results present pieces of evidence strongly supporting that the high variability of the performance dynamics during the execution of several programs display low-dimensional deterministic chaos, with sensitivity to initial conditions comparable to textbook models. Taken together, these results show that the instantaneous performances of modern microprocessors constitute a complex (or at least complicated) system and would benefit from analysis with modern tools of nonlinear and complexity science

Winter-to-summer precipitation phasing in southwestern North America : a multicentury perspective from paleoclimatic model-data comparisons

Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Atmospheres 120 (2015): 8052–8064, doi:10.1002/2015JD023085.The phasing of winter-to-summer precipitation anomalies in the North American monsoon (NAM) region 2 (113.25°W–107.75°W, 30°N–35.25°N—NAM2) of southwestern North America is analyzed in fully coupled simulations of the Last Millennium and compared to tree ring reconstructed winter and summer precipitation variability. The models simulate periods with in-phase seasonal precipitation anomalies, but the strength of this relationship is variable on multidecadal time scales, behavior that is also exhibited by the reconstructions. The models, however, are unable to simulate periods with consistently out-of-phase winter-to-summer precipitation anomalies as observed in the latter part of the instrumental interval. The periods with predominantly in-phase winter-to-summer precipitation anomalies in the models are significant against randomness, and while this result is suggestive of a potential for dual-season drought on interannual and longer time scales, models do not consistently exhibit the persistent dual-season drought seen in the dendroclimatic reconstructions. These collective findings indicate that model-derived drought risk assessments may underestimate the potential for dual-season drought in 21st century projections of hydroclimate in the American Southwest and parts of Mexico.NOAA. Grant Number: NA11OAR4310166, NSF. Grant Number: AGS-12432042016-02-1

Planetary Collisions outside the Solar System: Time Domain Characterization of Extreme Debris Disks

Luminous debris disks of warm dust in the terrestrial planet zones around solar-like stars are recently found to vary, indicative of ongoing large-scale collisions of rocky objects. We use Spitzer 3.6 and 4.5 {\mu}m time-series observations in 2012 and 2013 (extended to 2014 in one case) to monitor 5 more debris disks with unusually high fractional luminosities ("extreme debris disk"), including P1121 in the open cluster M47 (80 Myr), HD 15407A in the AB Dor moving group (80 Myr), HD 23514 in the Pleiades (120 Myr), HD 145263 in the Upper Sco Association (10 Myr), and the field star BD+20 307 (>1 Gyr). Together with the published results for ID8 in NGC 2547 (35 Myr), this makes the first systematic time-domain investigation of planetary impacts outside the solar system. Significant variations with timescales shorter than a year are detected in five out of the six extreme debris disks we have monitored. However, different systems show diverse sets of characteristics in the time domain, including long-term decay or growth, disk temperature variations, and possible periodicity.Comment: 50 pages, 14 figures, 9 tables; Accepted for publication in the Astrophysical Journa

Synthesis and polymorphism of mixed aluminium-gallium oxides

DSC is grateful to the EPSRC for award of an industrial CASE studentship, partly funded by Johnson Matthey plc. SEA, DMD and JEH thank the ERC (EU FP7 Consolidator Grant 614290 “EXONMR”) for funding. SEA would also like to thank the Royal Society and Wolfson Foundation for a merit award.The synthesis of a new solidsolution of the oxyhydroxide Ga5–xAlxO7(OH) isinvestigated via solvothermalreaction between gallium acetylacetonate and aluminium isopropoxide in1,4-butanediol at 240 °C. A limited compositional range 0 ≤ x ≤ 1.5 is produced, with the hexagonalunit cell parameters refined from powder X-ray diffraction (XRD) showing alinear contraction in unit cell volume with increasing Al content. Solid-state 27Aland 71Ga NMR spectroscopy show a strong preference for Ga to occupythe tetrahedral sites and Al to occupy the octahedral sites. Using isopropanolas the solvent, g-Ga2–xAlxO3defect spinel solid solutions with x ≤ 1.8 can be prepared at 240 °C in24 hours. These materials are nanocrystalline, as evidenced by their broaddiffraction profiles, but the refined cubic lattice parameter shows a linearrelationship with the Ga:Al content and solid-state NMR spectroscopy again showsa preference for Al to occupy the octahedral sites. Thermal decomposition ofthe Ga5–xAlxO7(OH)occurs via poorly ordered materials that resemble e-Ga2–xAlxO3and k-Ga2–xAlxO3,but g-Ga2–xAlxO3transforms above 750 °C to monoclinic b-Ga2–xAlxO3for 0 ≤ x ≤ 1.3 and to hexagonal a-Ga2–xAlxO3for x = 1.8, with intermediate compositions 1.3 < x < 1.8 giving mixturesof the aand b polymorphs.Solid-state NMR spectroscopy shows only the expected octahedral Al for a-Ga2–xAlxO3and, for b-Ga2–xAlxO3,the ~1:2 ratio of tetrahedral:octahedral Al is in good agreement with Rietveldanalysis of the average structures against powder XRD data. Relative energiescalculated by periodic density functional theory (DFT) confirm that there is a~5.2 kJ mol–1 penalty for tetrahedral rather than octahedral Al inGa5–xAlxO7(OH), whereas this penalty is muchlower (~2.0 kJ mol–1) for b-Ga2–xAlxO3,in good qualitative agreement with the experimental NMR spectra.PostprintPeer reviewe

Paleoclimate histories improve access and sustainability in index insurance programs

Proxy-based climate reconstructions can extend instrumental records by hundreds of years, providing a wealth of climate information at high temporal resolution. To date, however, their usefulness for informing climate risk and variability in policy and social applications has been understudied. Here, we apply tree-ring based reconstructions of drought for the last 700 years in a climate index insurance framework to show that additional information from long climate reconstructions significantly improves our understanding of the underlying climate distributions and variability. We further show that this added information can be used to better characterize risk to insurance providers, in many cases providing meaningful reductions in long-term contract costs to farmers in stand-alone policies. The impact of uncertainty on insurance premiums can also be reduced when insurers diversify portfolios, and the availability of long-term climate information from tree rings across a broad geographic range provides an opportunity to characterize spatial correlation in climate risk across geographic regions. Our results are robust to the range of climate variability experienced over the last 400 years and in model simulations of the twenty-first century, even within the context of changing baselines due to low frequency variability and secular climate trends. These results demonstrate the utility of longer-term climate histories in index insurance applications. Furthermore, they make the case from a climate-variability perspective for the continued importance of such approaches to improving the instrumental climate record, even into a non-stationary climate future