Milwaukee, WI, United States
Milwaukee, WI, United States

Time filter

Source Type

Tamrakar S.,UW Milwaukee | Richmond P.,University of Sheffield | D'Souza R.M.,UW Milwaukee
Simulation | Year: 2017

Agent-based models (ABMs) are increasingly being used to study population dynamics in complex systems, such as the human immune system. Previously, Folcik et al. (The basic immune simulator: an agent-based model to study the interactions between innate and adaptive immunity. Theor Biol Med Model 2007; 4: 39) developed a Basic Immune Simulator (BIS) and implemented it using the Recursive Porous Agent Simulation Toolkit (RePast) ABM simulation framework. However, frameworks such as RePast are designed to execute serially on central processing units and therefore cannot efficiently handle large model sizes. In this paper, we report on our implementation of the BIS using FLAME GPU, a parallel computing ABM simulator designed to execute on graphics processing units. To benchmark our implementation, we simulate the response of the immune system to a viral infection of generic tissue cells. We compared our results with those obtained from the original RePast implementation for statistical accuracy. We observe that our implementation has a 13× performance advantage over the original RePast implementation. © The Author(s) 2016.


Patch S.K.,UW Milwaukee | Hull D.,Bostwick Laboratories Inc. | Thomas M.,Medical College of Wisconsin | Griep S.,University of Southern California | And 2 more authors.
Physics in Medicine and Biology | Year: 2015

Applying the thermoacoustic (TA) effect to diagnostic imaging was first proposed in the 1980s. The object under test is irradiated by high-power pulses of electromagnetic energy, which heat tissue and cause thermal expansion. Outgoing TA pressure pulses are detected by ultrasound transducers and reconstructed to provide images of the object. The TA contrast mechanism is strongly dependent upon the frequency of the irradiating electromagnetic pulse. When very high frequency (VHF) electromagnetic irradiation is utilized, TA signal production is driven by ionic content. Prostatic fluids contain high levels of ionic metabolites, including citrate, zinc, calcium, and magnesium. Healthy prostate glands produce more ionic metabolites than diseased glands. VHF pulses are therefore expected to generate stronger TA signal in healthy prostate glands than in diseased glands. A benchtop system for performing ex vivo TA computed tomography with VHF energy is described and images are presented. The system utilizes irradiation pulses of 700 ns duration exceeding 20 kW power. Reconstructions frequently visualize anatomic landmarks such as the urethra and verumontanum. TA reconstructions from three freshly excised human prostate glands with little, moderate, and severe cancerous involvement are compared with histology. TA signal strength is negatively correlated with percent cancerous involvement in this small sample size. For the 45 regions of interest analyzed, a reconstruction value of 0.4 mV provides 100% sensitivity but only 29% specificity. Thissample size is far too small to draw sweeping conclusions, but the results warrant a larger volume study including comparison of TA images to the gold standard, histology. © 2015 Institute of Physics and Engineering in Medicine.


Patch S.K.,UW Milwaukee | Rao N.,Medical College of Wisconsin | Kelly H.,Medical College of Wisconsin | Jacobsohn K.,Medical College of Wisconsin | See W.A.,Medical College of Wisconsin
Physiological Measurement | Year: 2011

The specific heat capacity of tissue is a critical parameter for thermal therapies that act over a long period of time. It is also critical for thermoacoustic signal generation. We present ex vivo measurements of specific heat capacity performed by a dual-pin probe with tight temperature control of the specimen. One 30 mm × 1.28 mm probe heats steadily for 30 s, while another measurement probe measures temperatures 6 mm away from the center of the heater probe. Specific heat values ranging from 2.9 to 4 J cm -3 °C -1 were measured on 20 lobes from ten fresh prostate specimens with varying degrees of cancerous involvement as confirmed by histology. © 2011 Institute of Physics and Engineering in Medicine.


PubMed | Medical College of Wisconsin, Avero Diagnostics and UW Milwaukee
Type: Journal Article | Journal: Medical physics | Year: 2017

To demonstrate that very high frequency (VHF) induced thermoacoustics has the potential to provide quantitative images of electrical conductivity in Siemens/meter, much as shear wave elastography provides tissue stiffness in kPa. Quantitatively imaging a large organ requires exciting thermoacoustic pulses throughout the volume and broadband detection of those pulses because tomographic image reconstruction preserves frequency content. Applying the half-wavelength limit to a 200-micron inclusion inside a 7.5 cm diameter organ requires measurement sensitivity to frequencies ranging from 4 MHz down to 10 kHz, respectively. VHF irradiation provides superior depth penetration over near infrared used in photoacoustics. Additionally, VHF signal production is proportional to electrical conductivity, and prostate cancer is known to suppress electrical conductivity of prostatic fluid.A dual-transducer system utilizing a P4-1 array connected to a Verasonics V1 system augmented by a lower frequency focused single element transducer was developed. Simultaneous acquisition of VHF-induced thermoacoustic pulses by both transducers enabled comparison of transducer performance. Data from the clinical array generated a stack of 96-images with separation of 0.3 mm, whereas the single element transducer imaged only in a single plane. In-plane resolution and quantitative accuracy were measured at isocenter.The array provided volumetric imaging capability with superior resolution whereas the single element transducer provided superior quantitative accuracy. Combining axial images from both transducers preserved resolution of the P4-1 array and improved image contrast. Neither transducer was sensitive to frequencies below 50 kHz, resulting in a DC offset and low-frequency shading over fields of view exceeding 15 mm. Fresh human prostates were imaged ex vivo and volumetric reconstructions reveal structures rarely seen in diagnostic images.Quantitative whole-organ thermoacoustic tomography will be feasible by sparsely interspersing transducer elements sensitive to the low end of the ultrasonic range.


Schwartz M.D.,UW Milwaukee | Hanes J.M.,Northern Michigan University | Liang L.,University of Kentucky
Agricultural and Forest Meteorology | Year: 2013

Vegetative canopies play a crucial role in the energy balance and composition of the atmospheric boundary layer via biotic control over evapotranspiration and carbon sources/sinks. Accurately predicting the onset/increase of carbon uptake/transpiration during the spring leaf development period using coarse resolution tower-based and satellite-derived data alone is difficult. Thus, understanding stand-level spatial patterns of spring plant phenological development and the processes that drive them may be crucial for improving landscape level estimates of evapotranspiration and carbon accumulation.In this study, high-resolution spatial and temporal tree phenology data were recorded in field campaigns over approximately 5 weeks during spring 2006 and 2007 (within a 625 m × 275 m area), and over similar periods during spring 2008, 2009, and 2010 (within two 625 m × 625 m areas) near the WLEF eddy covariance flux tower site near Park Falls in northern Wisconsin. Our findings demonstrate that phenological variations between individual trees in a specific microclimate can be adequately represented with a sample of 30 or more individuals. Further, visual phenological observations can be generally related to under-canopy light levels, and for spring phenology measurements in similar microclimates, a sampling interval of every 4 days minimizes data uncertainty and field work expenses. An analysis of the relationships among phenology, climate, and gross primary productivity (GPP) during the spring indicate that the phenology of the dominant tree species is responsible for an overall positive trend in carbon assimilation, but climate is the cause of day-to-day variation. © 2012 Elsevier B.V.


Schwartz M.D.,UW Milwaukee | Hanes J.M.,UW Milwaukee | Liang L.,University of Kentucky
International Journal of Biometeorology | Year: 2013

Phenological observations offer a simple and effective way to measure climate change effects on the biosphere. While some species in northern mixed forests show a highly sensitive site preference to microenvironmental differences (i.e., the species is present in certain areas and absent in others), others with a more plastic environmental response (e.g., Acer saccharum, sugar maple) allow provisional separation of the universal "background" phenological variation caused by in situ (possibly biological/genetic) variation from the microclimatic gradients in air temperature. Moran's I tests for spatial autocorrelation among the phenological data showed significant (α ≤ 0.05) clustering across the study area, but random patterns within the microclimates themselves, with isolated exceptions. In other words, the presence of microclimates throughout the study area generally results in spatial autocorrelation because they impact the overall phenological development of sugar maple trees. However, within each microclimate (where temperature conditions are relatively uniform) there is little or no spatial autocorrelation because phenological differences are due largely to randomly distributed in situ factors. The phenological responses from 2008 and 2009 for two sugar maple phenological stages showed the relationship between air temperature degree-hour departure and phenological change ranged from 0.5 to 1.2 days earlier for each additional 100 degree-hours. Further, the standard deviations of phenological event dates within individual microclimates (for specific events and years) ranged from 2.6 to 3.8 days. Thus, that range of days is inferred to be the "background" phenological variation caused by factors other than air temperature variations, such as genetic differences between individuals. © 2013 ISB.


Schwartz M.D.,UW Milwaukee | Hanes J.M.,UW Milwaukee | Liang L.,UW Milwaukee
International journal of biometeorology | Year: 2014

Phenological observations offer a simple and effective way to measure climate change effects on the biosphere. While some species in northern mixed forests show a highly sensitive site preference to microenvironmental differences (i.e., the species is present in certain areas and absent in others), others with a more plastic environmental response (e.g., Acer saccharum, sugar maple) allow provisional separation of the universal "background" phenological variation caused by in situ (possibly biological/genetic) variation from the microclimatic gradients in air temperature. Moran's I tests for spatial autocorrelation among the phenological data showed significant (α ≤ 0.05) clustering across the study area, but random patterns within the microclimates themselves, with isolated exceptions. In other words, the presence of microclimates throughout the study area generally results in spatial autocorrelation because they impact the overall phenological development of sugar maple trees. However, within each microclimate (where temperature conditions are relatively uniform) there is little or no spatial autocorrelation because phenological differences are due largely to randomly distributed in situ factors. The phenological responses from 2008 and 2009 for two sugar maple phenological stages showed the relationship between air temperature degree-hour departure and phenological change ranged from 0.5 to 1.2 days earlier for each additional 100 degree-hours. Further, the standard deviations of phenological event dates within individual microclimates (for specific events and years) ranged from 2.6 to 3.8 days. Thus, that range of days is inferred to be the "background" phenological variation caused by factors other than air temperature variations, such as genetic differences between individuals.


Moore J.,UW Milwaukee
Behavioural Processes | Year: 2015

Mathematical models are often held to be valuable, if not necessary, for theories and explanations in the quantitative analysis of behavior. The present review suggests that mathematical models primarily derived from the observation of functional relations do indeed contribute to the scientific value of theories and explanations, even though the final form of the models appears to be highly abstract. However, mathematical models not primarily so derived risk being essentialist in character, based on a particular view of formal causation. Such models invite less effective and frequently mentalistic theories and explanations of behavior. Models may be evaluated in terms of both (a) the verbal processes responsible for their origin and development and (b) the prediction and control engendered by the theories and explanations that incorporate the models, however indirect or abstract that prediction and control may be. Overall, the present review suggests that technological application and theoretical contemplation may be usefully viewed as continuous and overlapping forms of scientific activity, rather than dichotomous and mutually exclusive. © 2015 Elsevier B.V.


Vinyl acetate is formed selectively on supported palladium and palladium-gold alloy catalysts from ethylene, acetic acid and oxygen, were the reaction selectivity on the alloy is improved compared to pure palladium. The pathway for the synthesis of vinyl acetate is explored on a Pd(111) single crystal by monitoring the nature of the surface by infrared spectroscopy. Vinyl acetate is synthesized on Pd(111) by reaction between ethylene and an acetate species to form an acetoxyethyl intermediate, which decomposes via a β-hydride elimination reaction to form vinyl acetate, the so-called Samanos pathway. VAM is formed on a Au/Pd(111) alloy via a similar pathway, but alloy formation appears to result in a change in the rate-limiting step and an acceleration in reaction rate.


Tysoe W.T.,UW Milwaukee
ACS National Meeting Book of Abstracts | Year: 2010

Palladium provides the basis for a number of selective catalysts, notably for the hydrogenation of alkene and alkynes and for the synthesis of vinyl acetate monomers (VAM) from the reaction of ethylene, acetic acid and oxygen, with selectivities approaching 80%. Much of the work in these areas was pioneered by the Lambert group. Although the basic Horuiti-Polanyi pathway for alkene and hydrogenation, in which hydrogen dissociates on the metal surface and adds to the carbon-carbon double bond in a step-wise fashion, was proposed many years ago, surface science strategies have revealed that the detailed reaction pathway is more complex. The discussion will be extended to examining the pathway for VAM synthesis, where it is shown that reaction proceeds via an initial coupling between ethylene and acetate species to form an acetoxyethyl intermediate, which decomposes via a rate-liming beta-hydride elimination pathway to form VAM.

Loading UW Milwaukee collaborators
Loading UW Milwaukee collaborators