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Top-C: A Task-Oriented Parallel C Interface, Gene D. Cooperman 2011 Northeastern University

Top-C: A Task-Oriented Parallel C Interface, Gene D. Cooperman

Gene D. Cooperman

The goal of this work is to simplify parallel application development, and thus ease the learning barriers faced by non-experts. It is especially useful where there is little data-parallelism to be recognized by a compiler. The applications programmer need learn the intricacies of only one primary subroutine in order to get the full benefits of the parallel interface. The applications programmer defines a high level concept, the task, that depends only on his application, and not on any particular parallel library. The task is defined by its three phases: (a) the task input, (b) sequential code to execute the task ...


Doubly Robust Estimates For Binary Longitudinal Data Analysis With Missing Response And Missing Covariates, Baojiang Chen, Xiao-Hua Zhou 2011 University of Washington

Doubly Robust Estimates For Binary Longitudinal Data Analysis With Missing Response And Missing Covariates, Baojiang Chen, Xiao-Hua Zhou

UW Biostatistics Working Paper Series

Longitudinal studies often feature incomplete response and covariate data. Likelihood-based methods such as the EM algorithm give consistent estimators for model parameters when data are missing at random provided that the response model and the missing covariate model are correctly specified; but we do not need to specify the missing data mechanism. An alternative method is the weighted estimating equation which gives consistent estimators if the missing data and response models are correctly specified; but we do not need to specify the distribution of the covariates that have missing values. In this paper we develop a doubly robust estimation method ...


Semiparametric Estimation Of The Covariate-Specific Roc Curve In Presence Of Ignorable Verification Bias, Danping Liu, Xiao-Hua Zhou 2011 University of Washington - Seattle Campus

Semiparametric Estimation Of The Covariate-Specific Roc Curve In Presence Of Ignorable Verification Bias, Danping Liu, Xiao-Hua Zhou

UW Biostatistics Working Paper Series

Covariate-specific ROC curves are often used to evaluate the classification accuracy of a medical diagnostic test or a biomarker, when the accuracy of the test is associated with certain covariates. In many large-scale screening tests, the gold standard is subject to missingness due to high cost or harmfulness to the patient. In this paper, we propose a semiparametric estimation method for the covariate-specific ROC curves with a partial missing gold standard. A location-scale model is constructed for the test result to model the covariates' effect, but the residual distributions are left unspecified. Thus the baseline and link functions of the ...


Evaluating Markers For Treatment Selection Based On Survival Time, Xiao Song, Xiao-Hua Zhou 2011 University of Geogia

Evaluating Markers For Treatment Selection Based On Survival Time, Xiao Song, Xiao-Hua Zhou

UW Biostatistics Working Paper Series

For many medical conditions there are several treatment options available to patients. We consider evaluating markers based on a simple treatment selection policy that incorporates information on the patient's marker value exceeding a threshold. Although traditional regression methods may assess the effect of the marker and treatment on outcomes, it is appealing to quantify more directly the potential impact on the population of using the marker to select treatment. A useful tool is the selection impact (SI) curve proposed by Song and Pepe (2004, \textit{Biometrics} \textbf{60}, 874--883) for binary outcomes. However, this approach does not deal with ...


Non-Homogeneous Markov Process Models With Incomplete Observations: Application To A Dementia Disease Study, Xiao-Hua Zhou, Baojiang Chen 2011 University of Washington

Non-Homogeneous Markov Process Models With Incomplete Observations: Application To A Dementia Disease Study, Xiao-Hua Zhou, Baojiang Chen

UW Biostatistics Working Paper Series

Identifying risk factors for transition rates among normal cognition, mildly cognitive impairment, dementia and death in an Alzheimer's disease study is very important. It is known that transition rates among these states are strongly time dependent. While Markov process models are often used to describe these disease progressions, the literature mainly focuses on time homogeneous processes, and limited tools are available for dealing with non-homogeneity. Further, patients may choose when they want to visit the clinics, which creates informative observations. In this paper, we develop methods to deal with non-homogeneous Markov processes through time scale transformation when observation times ...


Gram Scale Synthesis Of The C(18)-C(34) Fragment Of Amphidinolide C., Nicholas A Morra, Brian L Pagenkopf 2011 Western University

Gram Scale Synthesis Of The C(18)-C(34) Fragment Of Amphidinolide C., Nicholas A Morra, Brian L Pagenkopf

Chemistry Publications

The synthesis of the C(18)-C(34) fragment of amphidinolide C has been achieved via two routes, culminating in both the shortest (11 steps) and highest yielding (26% overall yield) approaches to this segment. The highly convergent approach will facilitate the synthesis of analogues, including the C(18)-C(29) fragment of amphidinolide F. Synthetic highlights include the selective methylation of a diyne, and the highly efficient use of a second generation cobalt catalyst in the Mukaiyama oxidative cyclization to form the trans-THF ring.


Experimental Evidence For The Acceleration Of Thermal Electrons By Ion Cyclotron Waves In The Magnetosphere, A. J. Norris, J.F. E. Johnson, Jan Josef Sojka, G. L. Wrenn, N. Cornilleau-Wehrlin, S. Perraut, A. Roux 2011 Utah State University

Experimental Evidence For The Acceleration Of Thermal Electrons By Ion Cyclotron Waves In The Magnetosphere, A. J. Norris, J.F. E. Johnson, Jan Josef Sojka, G. L. Wrenn, N. Cornilleau-Wehrlin, S. Perraut, A. Roux

Jan J. Sojka

Ion cyclotron waves (ICWs) at frequencies just above f He+ , the helium gyrofrequency, are often observed by the ESA satellites GEOS 1 and GEOS 2. Young et al. (1981) have shown the close connection between these ICWs and the presence of thermal He+ ions in the outer magnetosphere. The purpose of this paper is to provide experimental evidence for the acceleration of thermal electrons by the large amplitude ICWs. The wave power in the ultra low frequency (ULF) range near f He+ is compared with the distribution function of low energy electrons, measured by instruments aboard the GEOS satellites. It ...


Parity Violation In Low-Energy Neutron-Deuteron Scattering, Young-Ho Song, Rimantas Lazauskas, Vladimir Gudkov 2011 University of South Carolina - Columbia

Parity Violation In Low-Energy Neutron-Deuteron Scattering, Young-Ho Song, Rimantas Lazauskas, Vladimir Gudkov

Faculty Publications

Parity-violating effects for low-energy elastic neutron deuteron scattering are calculated for Desplanques,Donoghue, and Holstein (DDH) and effective field theory types of weak potentials in a distorted-wave Bornapproximation, using realistic hadronic strong interaction wave functions, obtained by solving three-bodyFaddeev equations in configuration space. The resulting relation between physical observables and low-energyconstants can be used to fix low-energy constants from experiments. Potential model dependencies ofparity-violating effects are discussed.


Rising Seas, Stormy Skies, Margaret (Peg) A. Van_Patten Ms. 2011 University of Connecticut

Rising Seas, Stormy Skies, Margaret (Peg) A. Van_Patten Ms.

Wrack Lines

Rising seas and more intense storms will affect Connecticut and Long Island Sound if climate change continues at present rates.


Two Features At The Two-Dimensional Freezing Transitions, Ziren Wang, Weikai Qi, Yi Peng, Ahmed M. Alsayed, Yong Chen, Penger Tong, Yiklong Han 2011 Hong Kong University of Science and Technology

Two Features At The Two-Dimensional Freezing Transitions, Ziren Wang, Weikai Qi, Yi Peng, Ahmed M. Alsayed, Yong Chen, Penger Tong, Yiklong Han

Department of Physics Papers

We studied the two-dimensional freezing transitions in monolayers of microgel colloidal spheres with short-ranged repulsions in video-microscopy experiments, and monolayers of hard disks, and Yukawa particles in simulations. These systems share two common features at the freezing points: (1) the bimodal distribution profile of the local orientational order parameter; (2) the two-body excess entropy, s2, reaches −4.5 ± 0.5 kB. Both features are robust and sensitive to the freezing points, so that they can potentially serve as empirical freezing criteria in two dimensions. Compared with the conventional freezing criteria, the first feature has no finite-size ambiguities and ...


A Flexible Spatio-Temporal Model For Air Pollution: Allowing For Spatio-Temporal Covariates, Johan Lindstrom, Adam A. Szpiro, Paul D. Sampson, Lianne Sheppard, Assaf Oron, Mark Richards, Tim Larson 2011 Lund University

A Flexible Spatio-Temporal Model For Air Pollution: Allowing For Spatio-Temporal Covariates, Johan Lindstrom, Adam A. Szpiro, Paul D. Sampson, Lianne Sheppard, Assaf Oron, Mark Richards, Tim Larson

UW Biostatistics Working Paper Series

Given the increasing interest in the association between exposure to air pollution and adverse health outcomes, the development of models that provide accurate spatio-temporal predictions of air pollution concentrations at small spatial scales is of great importance when assessing potential health effects of air pollution. The methodology presented here has been developed as part of the Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air), a prospective cohort study funded by the US EPA to investigate the relationship between chronic exposure to air pollution and cardiovascular disease. We present a spatio-temporal framework that models and predicts ambient air pollution by ...


Magnetic Field Dependence Of The Maximum Magnetic Entropy Change, Julia Lyubina, Michael D. Kuz'min, Konstantin Nenkov, Oliver Gutfleisch, Manuel Richter, Deborah L. Schlagel, Thomas A. Lograsso, Karl A. Gschneidner Jr. 2011 IFW Dresden

Magnetic Field Dependence Of The Maximum Magnetic Entropy Change, Julia Lyubina, Michael D. Kuz'min, Konstantin Nenkov, Oliver Gutfleisch, Manuel Richter, Deborah L. Schlagel, Thomas A. Lograsso, Karl A. Gschneidner Jr.

Ames Laboratory Publications

The maximum isothermal entropy change in a magnetic refrigerant with a second-order phase transition is shown to depend on applied magnetic field H as follows: (-ΔS)max = A(H + H0)2/3 – AH02/3 + BH4/3. Here A and B are intrinsic parameters of the cooling material and H0 is an extrinsic parameter determined by the purity and homogeneity of the sample. This theoretical prediction is confirmed by measurements on variously pure poly- and single-crystalline samples of Gd. The Curie point of pure Gd is found to be 295(1) K; however, the maximum of -ΔS ...


Spectra Of "Real-World" Graphs: Beyond The Semicircle Law, Illés J. Farkas, Imre Derényi, Albert-László Barabási, Tamás Vicsek 2011 Eötvös University

Spectra Of "Real-World" Graphs: Beyond The Semicircle Law, Illés J. Farkas, Imre Derényi, Albert-László Barabási, Tamás Vicsek

Albert-László Barabási

Many natural and social systems develop complex networks that are usually modeled as random graphs. The eigenvalue spectrum of these graphs provides information about their structural properties. While the semicircle law is known to describe the spectral densities of uncorrelated random graphs, much less is known about the spectra of real-world graphs, describing such complex systems as the Internet, metabolic pathways, networks of power stations, scientific collaborations, or movie actors, which are inherently correlated and usually very sparse. An important limitation in addressing the spectra of these systems is that the numerical determination of the spectra for systems with more ...


Halting Viruses In Scale-Free Networks, Zoltán Dezső, Albert-László Barabási 2011 University of Notre Dame

Halting Viruses In Scale-Free Networks, Zoltán Dezső, Albert-László Barabási

Albert-László Barabási

The vanishing epidemic threshold for viruses spreading on scale-free networks indicate that traditional methods, aiming to decrease a virus' spreading rate cannot succeed in eradicating an epidemic. We demonstrate that policies that discriminate between the nodes, curing mostly the highly connected nodes, can restore a finite epidemic threshold and potentially eradicate a virus. We find that the more biased a policy is towards the hubs, the more chance it has to bring the epidemic threshold above the virus’ spreading rate. Furthermore, such biased policies are more cost effective, requiring less cures to eradicate the virus.


Bose-Einstein Condensation In Complex Networks, Ginestra Bianconi, Albert-László Barabási 2011 University of Notre Dame

Bose-Einstein Condensation In Complex Networks, Ginestra Bianconi, Albert-László Barabási

Albert-László Barabási

The evolution of many complex systems, including the World Wide Web, business, and citation networks, is encoded in the dynamic web describing the interactions between the system's constituents. Despite their irreversible and nonequilibrium nature these networks follow Bose statistics and can undergo Bose-Einstein condensation. Addressing the dynamical properties of these nonequilibrium systems within the framework of equilibrium quantum gases predicts that the "first-mover-advantage," "fit-get-rich," and "winner-takes-all" phenomena observed in competitive systems are thermodynamically distinct phases of the underlying evolving networks.


Reverse Engineering Of Linking Preferences From Network Restructuring, Gergely Palla, Illés Farkas, Imre Derényi, Albert-László Barabási, Tamás Vicsek 2011 Biological Physics Research Group of HAS and Eötvös University

Reverse Engineering Of Linking Preferences From Network Restructuring, Gergely Palla, Illés Farkas, Imre Derényi, Albert-László Barabási, Tamás Vicsek

Albert-László Barabási

We provide a method to deduce the preferences governing the restructuring dynamics of a network from the observed rewiring of the edges. Our approach is applicable for systems in which the preferences can be formulated in terms of a single-vertex energy function with f(k) being the contribution of a node of degree k to the total energy, and the dynamics obeys the detailed balance. The method is first tested by Monte Carlo simulations of restructuring graphs with known energies; then it is used to study variations of real network systems ranging from the coauthorship network of scientific publications to ...


Analysis Of A Large-Scale Weighted Network Of One-To-One Human Communication, Jukka-Pekka Onnela, Jari Saramäki, Jörkki Hyvönen, Gábor Szabó, M. Argollo de Menezes, Kimmo Kaski, Albert-László Barabási, János Kertész 2011 Helsinki University of Technology and Oxford University

Analysis Of A Large-Scale Weighted Network Of One-To-One Human Communication, Jukka-Pekka Onnela, Jari Saramäki, Jörkki Hyvönen, Gábor Szabó, M. Argollo De Menezes, Kimmo Kaski, Albert-László Barabási, János Kertész

Albert-László Barabási

We construct a connected network of 3.9 million nodes from mobile phone call records, which can be regarded as a proxy for the underlying human communication network at the societal level. We assign two weights on each edge to reflect the strength of social interaction, which are the aggregate call duration and the cumulative number of calls placed between the individuals over a period of 18 weeks. We present a detailed analysis of this weighted network by examining its degree, strength, and weight distributions, as well as its topological assortativity and weighted assortativity, clustering and weighted clustering, together with ...


Topology Of Evolving Networks: Local Events And Universality, Réka Albert, Albert-László Barabási 2011 University of Notre Dame

Topology Of Evolving Networks: Local Events And Universality, Réka Albert, Albert-László Barabási

Albert-László Barabási

Networks grow and evolve by local events, such as the addition of new nodes and links, or rewiring of links from one node to another. We show that depending on the frequency of these processes two topologically different networks can emerge, the connectivity distribution following either a generalized power law or an exponential. We propose a continuum theory that predicts these two regimes as well as the scaling function and the exponents, in good agreement with numerical results. Finally, we use the obtained predictions to fit the connectivity distribution of the network describing the professional links between movie actors.


Hierarchical Organization In Complex Networks, Erzsébet Ravasz, Albert-László Barabási 2011 University of Notre Dame

Hierarchical Organization In Complex Networks, Erzsébet Ravasz, Albert-László Barabási

Albert-László Barabási

Many real networks in nature and society share two generic properties: they are scale-free and they display a high degree of clustering. We show that these two features are the consequence of a hierarchical organization, implying that small groups of nodes organize in a hierarchical manner into increasingly large groups, while maintaining a scale-free topology. In hierarchical networks, the degree of clustering characterizing the different groups follows a strict scaling law, which can be used to identify the presence of a hierarchical organization in real networks. We find that several real networks, such as the Worldwideweb, actor network, the Internet ...


Impact Of Non-Poissonian Activity Patterns On Spreading Processes, Alexei Vazquez, Balázs Rácz, András Lukács, Albert-László Barabási 2011 The Simons Center for Systems Biology

Impact Of Non-Poissonian Activity Patterns On Spreading Processes, Alexei Vazquez, Balázs Rácz, András Lukács, Albert-László Barabási

Albert-László Barabási

Halting a computer or biological virus outbreak requires a detailed understanding of the timing of the interactions between susceptible and infected individuals. While current spreading models assume that users interact uniformly in time, following a Poisson process, a series of recent measurements indicates that the intercontact time distribution is heavy tailed, corresponding to a temporally inhomogeneous bursty contact process. Here we show that the non-Poisson nature of the contact dynamics results in prevalence decay times significantly larger than predicted by the standard Poisson process based models. Our predictions are in agreement with the detailed time resolved prevalence data of computer ...


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