A heuristic optimization method for mitigating the impact of a virus attack

Taking precautions before or during the start of a virus outbreak can heavily reduce the number of infected. The question which individuals should be immunized in order to mitigate the impact of the virus on the rest of population has received quite some attention in the literature. The dynamics of the of a virus spread through a population is often represented as information spread over a complex network. The strategies commonly proposed to determine which nodes are to be selected for immunization often involve only one centrality measure at a time, while often the topology of the network seems to suggest that a single metric is insufficient to capture the influence of a node entirely. In this work we present a generic method based on a genetic algorithm (GA) which does not rely explicitly on any centrality measures during its search but only exploits this type of information to narrow the search space. The fitness of an individual is defined as the estimated expected number of infections of a virus following SIR dynamics. The proposed method is evaluated on two contact networks: the Goodreau's Faux Mesa high school and the US air transportation network. The GA method manages to outperform the most common strategies based on a single metric for the air transportation network and its performance is comparable with the best performing strategy for the high school network.Comment: To appear in the proceedings of the International Conference on Computational Science (ICCS) in Barcelona. 11 pages, 5 figure

Does settlement plate material matter? The influence of substrate type on fouling community development

Benthic community composition and ascidian abundance can differ dramatically between adjacent man-made and natural substrates. Although multiple factors, including light exposure, surface orientation, predation exposure, and habitat type, are known to contribute to these patterns, few studies have directly tested the influence of substrate identity on community development. We compared fouling communities on settlement plates composed of commonly occurring natural (granite) and artificial (concrete, high density polyethylene, and PVC) marine materials deployed from late May to mid November 2014 from a floating dock in Newcastle, NH. We sought to determine if observed patterns resulted from differential recruitment onto substrate materials or post-settlement survival and growth. To do this, half of the plates were cleaned during bi-weekly examinations, and half were left un-cleaned. Preliminary analyses indicate that community composition differs between substrate types. These results will help us understand how substrate features contribute to non-native species establishment and habitat dominance, and may inform decisions regarding material usage in marine construction. These findings also underline the importance of settlement substrate choice in scientific studies, as plate material may influence experimental conclusions

Towards an artificial therapy assistant: Measuring excessive stress from speech

The measurement of (excessive) stress is still a challenging endeavor. Most tools rely on either introspection or expert opinion and are, therefore, often less reliable or a burden on the patient. An objective method could relieve these problems and, consequently, assist diagnostics. Speech was considered an excellent candidate for an objective, unobtrusive measure of emotion. True stress was successfully induced, using two storytelling\ud sessions performed by 25 patients suffering from a stress disorder. When reading either a happy or a sad story, different stress levels were reported using the Subjective Unit of Distress (SUD). A linear regression model consisting of the high-frequency energy, pitch, and zero crossings of the speech signal was able to explain 70% of the variance in the subjectively reported stress. The results demonstrate the feasibility of an objective measurement of stress in speech. As such, the foundation for an Artificial Therapeutic Agent is laid, capable of assisting therapists through an objective measurement of experienced stress

CLIMATE ANOMALIES AND PRIMARY PRODUCTION IN LAKE SUPERIOR

This dissertation supports the modeling of primary production in Lake Superior by offering site specific kinetics and algorithms developed from lab experiments performed on the natural phytoplankton assemblage of Lake Superior. Functions, developed for temperature, light and nutrient conditions and the maximum specific rate of primary production, were incorporated in a 1D specific primary production model and confirmed to published in-situ measured rates of primary production. An extensive data set (supporting model calibration and confirmation), with a fine spatiotemporal resolution, was developed from field measurements taken bi-weekly during the sampling seasons of 2011, 2012 and 2014; considered to be meteorologically average, extremely warm and cold years, respectively. Samplings were taken at 11 stations along a 26 km transect extending lakeward from Michigan’s Keweenaw Peninsula covering the nearshore to offshore gradient. Measurements included: temperature, solar radiation, transparency, beam attenuation, chlorophyll-a fluorescence, colored dissolved organic matter, suspended solids and phosphorus and carbon constituents. Based on these measurements and application of the developed primary production model, patterns in primary production and driving forces (i.e. temperature, light and nutrients) are described in a seasonal, spatial, and interannual fashion. The signal feature in 2011 was the development of a mid-summer “desert” in the offshore surface waters (a period of suboptimal temperatures coincident with a high degree of phosphorus limitation). The manifestation of the “summer desert”, however, was most extreme during the warm year and nonexistent during the cold year. Offshore primary production in all years manifested a subsurface maximum in the upper area of the metalimnion, distinctly above the deep chlorophyll maximum, with rates of production being highest In 2011 (~20 mg C m-3 d-1) followed by 2012 (~17 mg Cm-3 d-1) and lowest in 2014 (~12 mg Cm-3 d-1). Driven by variances in biomass and forcing conditions, offshore areal primary production manifested differences in seasonal patterns between years as well. In 2011 and 2014 a negatively skewed bell-shape pattern was observed, differing in magnitude and timing. The pattern in 2012 differed from these years in magnitude and timing, manifesting elevated production in April and decreased production in September. Greatest areal production in 2012 occurred in July and August (~320 mg Cm-2 d-1), in 2014 in August (~265 mg Cm-2 d-1) and in 2011 production was greatest in July (253 mg C m-2 d-1). Areal production in the summer of 1998, calculated for EPA’s 19 offshore stations in Lake Superior, manifested comparable rates and averaged 224 ± 90 mg C m-2·d-1. Although in all years the development of the thermal bar (TB) occurred after the spring runoff event, an increase in chlorophyll-a concentration during the presence of the TB was observed in 2012. Rates of primary production during this period, however, decreased while the opposite occurred in 2014, signifying that changes in chlorophyll-a concentration should be interpreted carefully (especially if used to identify spring blooms). The information presented in this work not only offers site specific kinetics, appropriate algorithms in support of primary production modeling and an extensive dataset supporting model calibration and confirmation, it also offers new insights into the dynamics of the Lake Superior ecosystem and the forces driving its function

Mechanisms contributing to the deep chlorophyll maximum in Lake Superior

The seasonal appearance of a deep chlorophyll maximum (DCM) in Lake Superior is a striking phenomenon that is widely observed; however its mechanisms of formation and maintenance are not well understood. As this phenomenon may be the reflection of an ecological driver, or a driver itself, a lack of understanding its driving forces limits the ability to accurately predict and manage changes in this ecosystem. Key mechanisms generally associated with DCM dynamics (i.e. ecological, physiological and physical phenomena) are examined individually and in concert to establish their role. First the prevailing paradigm, “the DCM is a great place to live”, is analyzed through an integration of the results of laboratory experiments and field measurements. The analysis indicates that growth at this depth is severely restricted and thus not able to explain the full magnitude of this phenomenon. Additional contributing mechanisms like photoadaptation, settling and grazing are reviewed with a one-dimensional mathematical model of chlorophyll and particulate organic carbon. Settling has the strongest impact on the formation and maintenance of the DCM, transporting biomass to the metalimnion and resulting in the accumulation of algae, i.e. a peak in the particulate organic carbon profile. Subsequently, shade adaptation becomes manifest as a chlorophyll maximum deeper in the water column where light conditions particularly favor the process. Shade adaptation mediates the magnitude, shape and vertical position of the chlorophyll peak. Growth at DCM depth shows only a marginal contribution, while grazing has an adverse effect on the extent of the DCM. The observed separation of the carbon biomass and chlorophyll maximum should caution scientists to equate the DCM with a large nutrient pool that is available to higher trophic levels. The ecological significance of the DCM should not be separated from the underlying carbon dynamics. When evaluated in its entirety, the DCM becomes the projected image of a structure that remains elusive to measure but represents the foundation of all higher trophic levels. These results also offer guidance in examine ecosystem perturbations such as climate change. For example, warming would be expected to prolong the period of thermal stratification, extending the late summer period of suboptimal (phosphorus-limited) growth and attendant transport of phytoplankton to the metalimnion. This reduction in epilimnetic algal production would decrease the supply of algae to the metalimnion, possibly reducing the supply of prey to the grazer community. This work demonstrates the value of modeling to challenge and advance our understanding of ecosystem dynamics, steps vital to reliable testing of management alternatives

Efficiency of fat deposition from nonstarch polysaccharides, starch and unsaturated fat in pig

The aim was to evaluate under protein-limiting conditions the effect of different supplemental energy sources: fermentable NSP (fNSP), digestible starch (dStarch) and digestible unsaturated fat (dUFA), on marginal efficiency of fat deposition and distribution. A further aim was to determine whether the extra fat deposition from different energy sources, and its distribution in the body, depends on feeding level. A total of fifty-eight individually housed pigs (48 (sd 4) kg) were used in a 3 x 2 factorial design study, with three energy sources (0.2 MJ digestible energy (DE)/kg0.75 per d of fNSP, dStarch and dUFA added to a control diet) at two feeding levels. Ten pigs were slaughtered at 48 (sd 4) kg body weight and treatment pigs at 106 (sd 3) kg body weight. Bodies were dissected and the chemical composition of each body fraction was determined. The effect of energy sources on fat and protein deposition was expressed relative to the control treatments within both energy intake levels based on a total of thirty-two observations in six treatments, and these marginal differences were subsequently treated as dependent variables. Results showed that preferential deposition of the supplemental energy intake in various fat depots did not depend on the energy source, and the extra fat deposition was similar at each feeding level. The marginal energetic transformation (energy retention; ER) of fNSP, dStarch and dUFA for fat retention (ERfat:DE) was 44, 52 and 49 % (P>0.05), respectively. Feeding level affected fat distribution, but source of energy did not change the relative partitioning of fat deposition. The present results do not support values of energetic efficiencies currently used in net energy-based system

The LyAlpha Line Profiles of Ultraluminous Infrared Galaxies: Fast Winds and Lyman Continuum Leakage

We present new Hubble Space Telescope Cosmic Origins Spectrograph far-ultraviolet (far-UV) spectroscopy and Keck Echellete optical spectroscopy of 11 ultraluminous infrared galaxies (ULIRGs), a rare population of local galaxies experiencing massive gas inflows, extreme starbursts, and prominent outflows. We detect H Lyman alpha emission from 8 ULIRGs and the companion to IRAS09583+4714. In contrast to the P Cygni profiles often seen in galaxy spectra, the H Lyman alpha profiles exhibit prominent, blueshifted emission out to Doppler shifts exceeding -1000 km/s in three HII-dominated and two AGN-dominated ULIRGs. To better understand the role of resonance scattering in shaping the H Lyman alpha line profiles, we directly compare them to non-resonant emission lines in optical spectra. We find that the line wings are already present in the intrinsic nebular spectra, and scattering merely enhances the wings relative to the line core. The H Lyman alpha attenuation (as measured in the COS aperture) ranges from that of the far-UV continuum to over 100 times more. A simple radiative transfer model suggests the H Lyman alpha photons escape through cavities which have low column densities of neutral hydrogen and become optically thin to the Lyman continuum in the most advanced mergers. We show that the properties of the highly blueshifted line wings on the H Lyman alpha and optical emission-line profiles are consistent with emission from clumps of gas condensing out of a fast, hot wind. The luminosity of the H Lyman alpha emission increases non-linearly with the ULIRG bolometric luminosity and represents about 0.1 to 1% of the radiative cooling from the hot winds in the HII-dominated ULIRGs.Comment: Submitted to Ap