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Search Results: 1 - 10 of 297582 matches for " J. Gustafson "
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Why the Kemeny Time is a Constant
Karl Gustafson,Jeffrey J. Hunter
Mathematics , 2015,
Abstract: We present a new fundamental intuition for why the Kemeny feature of a Markov chain is a constant. This new perspective has interesting further implications
Grid Cells, Place Cells, and Geodesic Generalization for Spatial Reinforcement Learning
Nicholas J. Gustafson ,Nathaniel D. Daw
PLOS Computational Biology , 2011, DOI: 10.1371/journal.pcbi.1002235
Abstract: Reinforcement learning (RL) provides an influential characterization of the brain's mechanisms for learning to make advantageous choices. An important problem, though, is how complex tasks can be represented in a way that enables efficient learning. We consider this problem through the lens of spatial navigation, examining how two of the brain's location representations—hippocampal place cells and entorhinal grid cells—are adapted to serve as basis functions for approximating value over space for RL. Although much previous work has focused on these systems' roles in combining upstream sensory cues to track location, revisiting these representations with a focus on how they support this downstream decision function offers complementary insights into their characteristics. Rather than localization, the key problem in learning is generalization between past and present situations, which may not match perfectly. Accordingly, although neural populations collectively offer a precise representation of position, our simulations of navigational tasks verify the suggestion that RL gains efficiency from the more diffuse tuning of individual neurons, which allows learning about rewards to generalize over longer distances given fewer training experiences. However, work on generalization in RL suggests the underlying representation should respect the environment's layout. In particular, although it is often assumed that neurons track location in Euclidean coordinates (that a place cell's activity declines “as the crow flies” away from its peak), the relevant metric for value is geodesic: the distance along a path, around any obstacles. We formalize this intuition and present simulations showing how Euclidean, but not geodesic, representations can interfere with RL by generalizing inappropriately across barriers. Our proposal that place and grid responses should be modulated by geodesic distances suggests novel predictions about how obstacles should affect spatial firing fields, which provides a new viewpoint on data concerning both spatial codes.
NeuroTerrain – a client-server system for browsing 3D biomedical image data sets
Carl Gustafson, William J Bug, Jonathan Nissanov
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-40
Abstract: Here we describe the basic architecture of a client-server 3D visualization system, consisting of a thin Java client built on a development kit, and a computationally robust, high-performance server written in ANSI C++. The Java client components (NetOStat) support arbitrary-angle viewing and run on readily available desktop computers running Mac OS X, Windows XP, or Linux as a downloadable Java Application. Using the NeuroTerrain Software Development Kit (NT-SDK), sophisticated atlas browsing can be added to any Java-compatible application requiring as little as 50 lines of Java glue code, thus making it eminently re-useable and much more accessible to programmers building more complex, biomedical data analysis tools. The NT-SDK separates the interactive GUI components from the server control and monitoring, so as to support development of non-interactive applications. The server implementation takes full advantage of data center's high-performance hardware, where it can be co-localized with centrally-located, 3D dataset repositories, extending access to the researcher community throughout the Internet.The combination of an optimized server and modular, platform-independent client provides an ideal environment for viewing complex 3D biomedical datasets, taking full advantage of high-performance servers to prepare images and subsets of associated meta-data for viewing, as well as the graphical capabilities in Java to actually display the data.Volumetric anatomical atlases have become more prevalent as desktop computers have grown more powerful and have been provided with greater storage capacity. Digital atlases can be superior to print atlases in a number of ways: true 3D atlases are not restricted to just the limited number of sectional views typically presented in a print atlas but can be resliced in any arbitrary orientation [1]; the user can create spatially coded annotations or segmentation regions to share with other researchers [1]; they can be used as a can
PCR-Based EST Mapping in Wheat (Triticum aestivum L.)
TATIK CHIKMAWATI,MIFTAHUDIN,J. PERRY GUSTAFSON
Biodiversitas , 2009,
Abstract: Mapping expressed sequence tags (ESTs) to hexaploid wheat is aimed to reveal the structure and function of the hexaploid wheat genome. Sixty eight ESTs representing 26 genes were mapped into all seven homologous chromosome groups of wheat (Triticum aestivum L) using a polymerase chain reaction technique. The majority of the ESTs were mapped to homologous chromosome group 2, and the least were mapped to homologous chromosome group 6. Comparative analysis between the EST map from this study and the EST map based on RFLPs showed 14 genes that have been mapped by both approaches were mapped to the same arm of the same homologous chromosome, which indicated that using PCR-based ESTs was a reliable approach in mapping ESTs in hexaploid wheat.
The effect of wheat-rye translocation 1BL.1RS in a different quality genetic background on biological traits in wheat
Dimitrijevi? Miodrag,Petrovi? Sofija,Gustafson Perry J.
Genetika , 2008, DOI: 10.2298/gensr0803261d
Abstract: A sample of 139 varieties of common wheat (Triticum aestivum L.), predominantly Serbian winter wheat varieties originated in the Institute of Field and Vegetable Crops in Novi Sad, has been examined for presence of 1BL/1RS wheat-rye translocation. Two genotype groups consisted of varieties possessing and lacking the translocation have been compared. Stem rust, leaf rust, powdery mildew as well as, winter hardiness were studied. The influence of 1BL/1RS translocation was also studied in a light of wheat seed storage protein (glutenin and gliadin) genetic background composition. Genotypes having the translocation appeared to be more tolerant to stem rust, and leaf rust, but more susceptible to powdery mildew. These effects were slightly modified depending on the examined genetic background, but the effect of the rye 1RS translocated chromosome arm was the main cause for the observed differences.
Colour connections in e+e- -annihilation
C. Friberg,G. Gustafson,J. H?kkinen
Physics , 1996, DOI: 10.1016/S0550-3213(97)00064-3
Abstract: We have a very limited knowledge about how the confinement mechanism works in processes like $\epea\epe\ra\epq\epqa\ggn\ldots\ggn$, when there are identical colour charges. In this case the partons can be connected by a string or a cluster chain in several different ways. We do not know if in such a situation Nature chooses a particular configuration at random, or if some configuration is dynamically favoured. Also in the perturbative parton cascade we have no well founded recipe for describing the interference effects, which correspond to non planar diagrams and are caused by identical colour charges. We have studied two different models, and are in particular interested in the possibility that a colour singlet gluon system hadronizes isolated from the remainder of the state. Using double tagged events with heavy $\epc\epca$ or $\epb\epba$ quarks, it appears to be possible to find a significant signal, if such events appear in Nature. If this type of (re)connected states appear in Z decays it may also be an indication that reconnection might appear between the decay products of two W's in the reaction $\epea\epe\ra\gwp\gwm\ra\epq_1\epqa_2\epQ_1\epQa_2$ at LEP2. This would be important e.g. for a precision measurement of the W mass.
Kikuchi-Fujimoto Disease in a 30-Year-Old Caucasian Female
David J. Archibald,Matthew L. Carlson,Ray O. Gustafson
International Journal of Otolaryngology , 2009, DOI: 10.1155/2009/901537
Abstract: Kikuchi-Fujimoto disease is a rare, self-limited, histiocytic, necrotizing lymphadenitis first described in Japan in 1972. Necrosis of lymph node tissue is caused by apoptosis and may be virally induced. It commonly presents with cervical lymphadenitis and fever. Despite its low incidence, Kikuchi-Fujimoto disease should be considered in patients with persistent lymphadenopathy. Originally thought to occur only in young Asian women, it is now recognized in other geographic regions. We report a 30-year-old white woman with Kikuchi-Fujimoto disease. We discuss the clinical features, differential diagnosis, radiography, pathology, and outcome.
An investigation of the sub-grid variability of trace gases and aerosols for global climate modeling
Y. Qian, W. I. Gustafson Jr.,J. D. Fast
Atmospheric Chemistry and Physics (ACP) & Discussions (ACPD) , 2010,
Abstract: One fundamental property and limitation of grid based models is their inability to identify spatial details smaller than the grid cell size. While decades of work have gone into developing sub-grid treatments for clouds and land surface processes in climate models, the quantitative understanding of sub-grid processes and variability for aerosols and their precursors is much poorer. In this study, WRF-Chem is used to simulate the trace gases and aerosols over central Mexico during the 2006 MILAGRO field campaign, with multiple spatial resolutions and emission/terrain scenarios. Our analysis focuses on quantifying the sub-grid variability (SGV) of trace gases and aerosols within a typical global climate model grid cell, i.e. 75×75 km2. Our results suggest that a simulation with 3-km horizontal grid spacing adequately reproduces the overall transport and mixing of trace gases and aerosols downwind of Mexico City, while 75-km horizontal grid spacing is insufficient to represent local emission and terrain-induced flows along the mountain ridge, subsequently affecting the transport and mixing of plumes from nearby sources. Therefore, the coarse model grid cell average may not correctly represent aerosol properties measured over polluted areas. Probability density functions (PDFs) for trace gases and aerosols show that secondary trace gases and aerosols, such as O3, sulfate, ammonium, and nitrate, are more likely to have a relatively uniform probability distribution (i.e. smaller SGV) over a narrow range of concentration values. Mostly inert and long-lived trace gases and aerosols, such as CO and BC, are more likely to have broad and skewed distributions (i.e. larger SGV) over polluted regions. Over remote areas, all trace gases and aerosols are more uniformly distributed compared to polluted areas. Both CO and O3 SGV vertical profiles are nearly constant within the PBL during daytime, indicating that trace gases are very efficiently transported and mixed vertically by turbulence. But, simulated horizontal variability indicates that trace gases and aerosols are not well mixed horizontally in the PBL. During nighttime the SGV for trace gases is maximum at the surface, and quickly decreases with height. Unlike the trace gases, the SGV of BC and secondary aerosols reaches a maximum at the PBL top during the day. The SGV decreases with distance away from the polluted urban area, has a more rapid decrease for long-lived trace gases and aerosols than for secondary ones, and is greater during daytime than nighttime. The SGV of trace gases and aerosols is generally larger than for meteorological quantities. Emissions can account for up to 50% of the SGV over urban areas such as Mexico City during daytime for less-reactive trace gases and aerosols, such as CO and BC. The impact of emission spatial variability on SGV decays with altitude in the PBL and is insignificant in the free troposphere. The emission variability affects SGV more significantly during daytime
Quantifying the sub-grid variability of trace gases and aerosols based on WRF-Chem simulations
Y. Qian,W. I. Gustafson Jr.,J. D. Fast
Atmospheric Chemistry and Physics Discussions , 2010, DOI: 10.5194/acpd-10-10777-2010
Abstract: One fundamental property and limitation of grid based models is their inability to identify spatial details smaller than the grid cell size. While decades of work have gone into developing sub-grid treatments for clouds and land surface processes in climate models, the quantitative understanding of sub-grid processes and variability for aerosols and their precursors is much poorer. In this study, WRF-Chem is used to simulate the trace gases and aerosols over central Mexico during the 2006 MILAGRO field campaign, with multiple spatial resolutions and emission/terrain scenarios. Our analysis focuses on quantifying the sub-grid variability (SGV) of trace gases and aerosols within a typical global climate model grid cell, i.e. 75×75 km2. Our results suggest that a simulation with 3-km horizontal grid spacing adequately reproduces the overall transport and mixing of trace gases and aerosols downwind of Mexico City, while 75-km horizontal grid spacing is insufficient to represent local emission and terrain-induced flows along the mountain ridge, subsequently affecting the transport and mixing of plumes from nearby sources. Therefore, the coarse model grid cell average may not correctly represent aerosol properties measured over polluted areas. Probability density functions (PDFs) for trace gases and aerosols show that secondary trace gases and aerosols, such as O3, sulfate, ammonium, and nitrate, are more likely to have a relatively uniform probability distribution (i.e. smaller SGV) over a narrow range of concentration values. Mostly inert and long-lived trace gases and aerosols, such as CO and BC, are more likely to have broad and skewed distributions (i.e. larger SGV) over polluted regions. Over remote areas, all trace gases and aerosols are more uniformly distributed compared to polluted areas. Both CO and O3 SGV vertical profiles are nearly constant within the PBL during daytime, indicating that trace gases are very efficiently transported and mixed vertically by turbulence. But, simulated horizontal variability indicates that trace gases and aerosols are not well mixed horizontally in the PBL. During nighttime the SGV for trace gases is maximum at the surface, and quickly decreases with height. Unlike the trace gases, the SGV of BC and secondary aerosols reaches a maximum at the PBL top during the day. The SGV decreases with distance away from the polluted urban area, has a more rapid decrease for long-lived trace gases and aerosols than for secondary ones, and is greater during daytime than nighttime. The SGV of trace gases and aerosols is generally la
Modeling organic aerosols in a megacity: comparison of simple and complex representations of the volatility basis set approach
M. Shrivastava,J. Fast,R. Easter,W. I. Gustafson Jr.
Atmospheric Chemistry and Physics (ACP) & Discussions (ACPD) , 2011, DOI: 10.5194/acp-11-6639-2011
Abstract: The Weather Research and Forecasting model coupled with chemistry (WRF-Chem) is modified to include a volatility basis set (VBS) treatment of secondary organic aerosol formation. The VBS approach, coupled with SAPRC-99 gas-phase chemistry mechanism, is used to model gas-particle partitioning and multiple generations of gas-phase oxidation of organic vapors. In addition to the detailed 9-species VBS, a simplified mechanism using 2 volatility species (2-species VBS) is developed and tested for similarity to the 9-species VBS in terms of both mass and oxygen-to-carbon ratios of organic aerosols in the atmosphere. WRF-Chem results are evaluated against field measurements of organic aerosols collected during the MILAGRO 2006 campaign in the vicinity of Mexico City. The simplified 2-species mechanism reduces the computational cost by a factor of 2 as compared to 9-species VBS. Both ground site and aircraft measurements suggest that the 9-species and 2-species VBS predictions of total organic aerosol mass as well as individual organic aerosol components including primary, secondary, and biomass burning are comparable in magnitude. In addition, oxygen-to-carbon ratio predictions from both approaches agree within 25 %, providing evidence that the 2-species VBS is well suited to represent the complex evolution of organic aerosols. Model sensitivity to amount of anthropogenic semi-volatile and intermediate volatility (S/IVOC) precursor emissions is also examined by doubling the default emissions. Both the emission cases significantly under-predict primary organic aerosols in the city center and along aircraft flight transects. Secondary organic aerosols are predicted reasonably well along flight tracks surrounding the city, but are consistently over-predicted downwind of the city. Also, oxygen-to-carbon ratio predictions are significantly improved compared to prior studies by adding 15 % oxygen mass per generation of oxidation; however, all modeling cases still under-predict these ratios downwind as compared to measurements, suggesting a need to further improve chemistry parameterizations of secondary organic aerosol formation.
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