Open Access. Powered by Scholars. Published by Universities.®

Physical Sciences and Mathematics Commons™

Open Access. Powered by Scholars. Published by Universities.®

2009

Models

Articles 1 - 10 of 10

Full-Text Articles in Physical Sciences and Mathematics

Venn, A Tool For Titrating Sequence Conservation Onto Protein Structures, Jay Vyas, Michael R. Gryk, Martin R. Schiller Oct 2009

Venn, A Tool For Titrating Sequence Conservation Onto Protein Structures, Jay Vyas, Michael R. Gryk, Martin R. Schiller

Life Sciences Faculty Research

Residue conservation is an important, established method for inferring protein function, modularity and specificity. It is important to recognize that it is the 3D spatial orientation of residues that drives sequence conservation. Considering this, we have built a new computational tool, VENN that allows researchers to interactively and graphically titrate sequence homology onto surface representations of protein structures. Our proposed titration strategies reveal critical details that are not readily identified using other existing tools. Analyses of a bZIP transcription factor and receptor recognition of Fibroblast Growth Factor using VENN revealed key specificity determinants. Weblink: http://sbtools.uchc.edu/venn/.

Go to article

Failure To Replicate A Genetic Association May Provide Important Clues About Genetic Architecture, Casey S. Greene, Nadia M. Penrod, Scott M. Williams, Jason H. Moore Jun 2009

Failure To Replicate A Genetic Association May Provide Important Clues About Genetic Architecture, Casey S. Greene, Nadia M. Penrod, Scott M. Williams, Jason H. Moore

Dartmouth Scholarship

Replication has become the gold standard for assessing statistical results from genome-wide association studies. Unfortunately this replication requirement may cause real genetic effects to be missed. A real result can fail to replicate for numerous reasons including inadequate sample size or variability in phenotype definitions across independent samples. In genome-wide association studies the allele frequencies of polymorphisms may differ due to sampling error or population differences. We hypothesize that some statistically significant independent genetic effects may fail to replicate in an independent dataset when allele frequencies differ and the functional polymorphism interacts with one or more other functional polymorphisms. To …

Go to article

Field Line Distribution Of Density At L=4.8 Inferred From Observations By Cluster, R E. Denton, P Décréau, M J. Engebretson, F Darrouzet Feb 2009

Field Line Distribution Of Density At L=4.8 Inferred From Observations By Cluster, R E. Denton, P Décréau, M J. Engebretson, F Darrouzet

Dartmouth Scholarship

For two events observed by the CLUSTER space- craft, the field line distribution of mass density ρ was inferred from Alfve ́n wave harmonic frequencies and compared to the electron density ne from plasma wave data and the oxy- gen density nO+ from the ion composition experiment. In one case, the average ion mass M≡ρ/ne was about 5amu (28 October 2002), while in the other it was about 3 amu (10 September 2002). Both events occurred when the CLUSTER 1 (C1) spacecraft was in the plasmatrough. Nevertheless, the electron density ne was significantly lower for the first event (ne =8 …

Go to article

Periodic Traveling Waves In Sirs Endemic Models, Tong Li, Yi Li, Herbert W. Hethcote Jan 2009

Periodic Traveling Waves In Sirs Endemic Models, Tong Li, Yi Li, Herbert W. Hethcote

Yi Li

Mathematical models are used to determine if infection wave fronts could occur by traveling geographically in a loop around a region or continent. These infection wave fronts arise by Hopf bifurcation for some spatial models for infectious disease transmission with distributed-contacts. Periodic traveling waves are shown to exist for the spatial analog of the SIRS endemic model, in which the temporary immunity is described by a delay, but they do not exist in a similar spatial SIRS endemic model without a delay. Specifically, we found that the ratio of the delay ω in the recovered class and the average infectious …

Go to article

Periodic Traveling Waves In Sirs Endemic Models, Tong Li, Yi Li, Herbert W. Hethcote Jan 2009

Periodic Traveling Waves In Sirs Endemic Models, Tong Li, Yi Li, Herbert W. Hethcote

Mathematics and Statistics Faculty Publications

Mathematical models are used to determine if infection wave fronts could occur by traveling geographically in a loop around a region or continent. These infection wave fronts arise by Hopf bifurcation for some spatial models for infectious disease transmission with distributed-contacts. Periodic traveling waves are shown to exist for the spatial analog of the SIRS endemic model, in which the temporary immunity is described by a delay, but they do not exist in a similar spatial SIRS endemic model without a delay. Specifically, we found that the ratio of the delay ω in the recovered class and the average infectious …

Go to article

Logistic Models With Missing Categorical Covariates, Jeremiah Rounds Jan 2009

Logistic Models With Missing Categorical Covariates, Jeremiah Rounds

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

We present an EM based solution to missing categorical covariates in Binomial models with logit links using an assumption that experimental units are drawn from a Multinomial population of infinite size. We further address the problem of separation of points inducing large variances on parameter estimates by the use of a novel score-modification based on Firth's bias-reduction score-modification. We simulate to address questions about estimate bias, distribution, and appropriate parameter coverage by Wald intervals.

Go to article

Relative Importance Of Fuel Management, Ignition Management And Weather For Area Burned: Evidence From Five Landscape-Fire-Succession Models, Geoffrey J. Cary, Mike D. Flannigan, Robert E. Keane, Ross A. Bradstock, Ian D. Davies, James M. Lenihan, Chao Li, Kimberley A. Logan, Russell A. Parsons Jan 2009

Relative Importance Of Fuel Management, Ignition Management And Weather For Area Burned: Evidence From Five Landscape-Fire-Succession Models, Geoffrey J. Cary, Mike D. Flannigan, Robert E. Keane, Ross A. Bradstock, Ian D. Davies, James M. Lenihan, Chao Li, Kimberley A. Logan, Russell A. Parsons

Faculty of Science - Papers (Archive)

The behaviour of five landscape fire models (CAFE, FIRESCAPE, LAMOS(HS), LANDSUM and SEM-LAND) was compared in a standardised modelling experiment. The importance of fuel management approach, fuel management effort, ignition management effort and weather in determining variation in area burned and number of edge pixels burned (a measure of potential impact on assets adjacent to fire-prone landscapes) was quantified for a standardised modelling landscape. Importance was measured as the proportion of variation in area or edge pixels burned explained by each factor and all interactions among them. Weather and ignition management were consistently more important for explaining variation in area …

Go to article

Stable Isotope Metabolic Labeling With A Novel 15n-Enriched Bacteria Diet For Improved Proteomic Analyses Of Mouse Models For Psychopathologies, Yinglong Zhang, Elisabeth T. Frank, B. Hambsch, C. W. Turck, M. Bunck, R. Landgraf, M. S. Kessler, G. Maccarrone, M. Filiou, Hermann Heumann, Stefan Reckow Jan 2009

Stable Isotope Metabolic Labeling With A Novel 15n-Enriched Bacteria Diet For Improved Proteomic Analyses Of Mouse Models For Psychopathologies, Yinglong Zhang, Elisabeth T. Frank, B. Hambsch, C. W. Turck, M. Bunck, R. Landgraf, M. S. Kessler, G. Maccarrone, M. Filiou, Hermann Heumann, Stefan Reckow

Faculty of Science - Papers (Archive)

The identification of differentially regulated proteins in animal models of psychiatric diseases is essential for a comprehensive analysis of associated psychopathological processes. Mass spectrometry is the most relevant method for analyzing differences in protein expression of tissue and body fluid proteomes. However, standardization of sample handling and sample-to-sample variability are problematic. Stable isotope metabolic labeling of a proteome represents the gold standard for quantitative mass spectrometry analysis. The simultaneous processing of a mixture of labeled and unlabeled samples allows a sensitive and accurate comparative analysis between the respective proteomes. Here, we describe a cost-effective feeding protocol based on a newly …

Go to article

Flame, Furnace, Fuel: Creating Kansas City In The Nineteenth Century, Twyla Dell Jan 2009

Flame, Furnace, Fuel: Creating Kansas City In The Nineteenth Century, Twyla Dell

Antioch University Dissertations & Theses

Though this work is a fuel and energy history of Kansas City from 1820 to 1920, it also provides a tool to describe and analyze fuel and energy transitions. The four parts follow the rise and fall of wood, coal and oil as their use grows to a peak and, in the case of wood, declines. The founding and growth of Kansas City as an “instant city” that grew from zero population to over three hundred twenty thousand in a hundred years embodies the increased use of fuels and energy in an urban setting and serves as a case study. …

Go to article

Molecular Modeling Of Para-Benzyne And A Series Of Push-Pull [14]-Pyridoannulenes, Evan B. Wang Jan 2009

Molecular Modeling Of Para-Benzyne And A Series Of Push-Pull [14]-Pyridoannulenes, Evan B. Wang

Honors Theses

Molecular modeling is vital for gaining insight into experimental results and discovering molecular properties not yet characterized by experiment. Depending on the type of molecule under investigation, certain methods will yield more accurate and revealing answers. In the first project, a state-averaged, multireference complete active space (CAS) approach was used for the determination of the vertical excitation energies of valence and Rydberg states of para-benzyne. Orbitals were generated with a 10- and 32-state averaged multiconfigurational self consistent field (MCSCF) approach. Electron correlation was included using multireference configuration interaction with singles and doubles (MR-CISD), including Pople correction for size extensivity (MR-CISD+Q), …

Go to article