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Articles 1 - 30 of 54
Full-Text Articles in Physical Sciences and Mathematics
Graphs Of Bounded Degree And The P-Harmonic Boundary, Michael J. Puls
Graphs Of Bounded Degree And The P-Harmonic Boundary, Michael J. Puls
Publications and Research
Let p be a real number greater than one and let G be a connected graph of bounded degree. We introduce the p-harmonic boundary of G and use it to characterize the graphs G for which the constant functions are the only p-harmonic functions on G. We show that any continuous function on the p-harmonic boundary of G can be extended to a function that is p-harmonic on G. We also give some properties of this boundary that are preserved under rough-isometries. Now let Gamma be a finitely generated group. As an application of our results, we characterize the vanishing …
Hybrid Micro-/Nanogels For Optical Sensing And Intracellular Imaging, Weitai Wu, Shuiqin Zhou
Hybrid Micro-/Nanogels For Optical Sensing And Intracellular Imaging, Weitai Wu, Shuiqin Zhou
Publications and Research
Hybrid micro-/nanogels are playing an increasing important part in a diverse range of applications, due to their tunable dimensions, large surface area, stable interior network structure, and a very short response time. We review recent advances and challenges in the developments of hybrid micro-/nanogels toward applications for optical sensing of pH, temperature, glucose, ions, and other species as well as for intracellular imaging. Due to their unique advantages, hybrid micro-/nanogels as optical probes are attracting substantial interests for continuous monitoring of chemical parameters in complex samples such as blood and bioreactor fluids, in chemical research and industry, and in food …
The Mycobacterium Tuberculosis Drugome And Its Polypharmacological Implications, Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Phillip E. Bourne
The Mycobacterium Tuberculosis Drugome And Its Polypharmacological Implications, Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Phillip E. Bourne
Publications and Research
We report a computational approach that integrates structural bioinformatics, molecular modelling and systems biology to construct a drug-target network on a structural proteome-wide scale. The approach has been applied to the genome of Mycobacterium tuberculosis (M.tb), the causative agent of one of today’s most widely spread infectious diseases. The resulting drug-target interaction network for all structurally characterized approved drugs bound to putative M.tb receptors, we refer to as the ‘TB-drugome’. The TB-drugome reveals that approximately one-third of the drugs examined have the potential to be repositioned to treat tuberculosis and that many currently unexploited M.tb receptors may be chemically druggable …
Upper Cretaceous Peay Bentonites (North-Central Wyoming): Provenance And Tectonics Interpretation From Ash Composition, Nazrul I. Khandaker, Carl F. Vondra, Karl E. Seifert, Malek Shami, Rochelle Cardinale, Thakur Chaturgan
Upper Cretaceous Peay Bentonites (North-Central Wyoming): Provenance And Tectonics Interpretation From Ash Composition, Nazrul I. Khandaker, Carl F. Vondra, Karl E. Seifert, Malek Shami, Rochelle Cardinale, Thakur Chaturgan
Publications and Research
The Peay bentonites belong to the basal Frontier Formation (Bighorn Basin, north-central Wyoming), primarily outcrop in the Bighorn Basin, rest on an extensively bioturbated sandstone unit, the Peay Sandstone, and are generally the thinner bentonitic unit. Beds of very light gray to greenish gray bentonite are also abundant in the lower Frontier units between Kaycee and Mayoworth (Powder River Basin) and are very rarely as much as 3 m thick. Bentonite occurs within the interstratified shale, sandstone, and siltstone sequences of the lower Frontier unit throughout much of the southwestern Powder River Basin. The purpose of this study is to …
Tensorial Reconstruction At The Integrand Level, G. Heinrich, Giovanni Ossola, T. Reiter, F. Tramontano
Tensorial Reconstruction At The Integrand Level, G. Heinrich, Giovanni Ossola, T. Reiter, F. Tramontano
Publications and Research
We present a new approach to the reduction of one-loop amplitudes obtained by reconstructing the tensorial expression of the scattering amplitudes. The reconstruction is performed at the integrand level by means of a sampling in the integration momentum. There are several interesting applications of this novel method within existing techniques for the reduction of one-loop multi-leg amplitudes: to deal with numerically unstable points, such as in the vicinity of a vanishing Gram determinant; to allow for a sampling of the numerator function based on real values of the integration momentum; to optimize the numerical reduction in the case of long …
An Application Of Statistical Technique To Correct Satellite Data Due To Orbit Degradation, Md Zahidur Rahman, Leonid Roytman, Run Jesmin
An Application Of Statistical Technique To Correct Satellite Data Due To Orbit Degradation, Md Zahidur Rahman, Leonid Roytman, Run Jesmin
Publications and Research
This paper apply an statistical technique to correct radiometric data measured by Advanced Very High Resolution Radiometers(AVHRR) onboard the National Oceanic and Atmospheric Administration (NOAA) Polar Orbiting Environmental Satellites(POES). This paper study Normalized Difference Vegetation Index (NDVI) stability in the NOAA/NESDIS Global Vegetation Index (GVI) data for the period 1982-2003. AVHRR weekly data for the five NOAA afternoon satellites NOAA-7, NOAA-9, NOAA-11, NOAA-14, and NOAA-16 are used for the China dataset, for it includes a wide variety or different ecosystems represented globally. GVI has found wide use for studying and monitoring land surface, atmosphere, and recently for analyzing climate and …
Drug Off-Target Effects Predicted Using Structural Analysis In The Context Of A Metabolic Network Model, Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson
Drug Off-Target Effects Predicted Using Structural Analysis In The Context Of A Metabolic Network Model, Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson
Publications and Research
Recent advances in structural bioinformatics have enabled the prediction of protein-drug off-targets based on their ligand binding sites. Concurrent developments in systems biology allow for prediction of the functional effects of system perturbations using large-scale network models. Integration of these two capabilities provides a framework for evaluating metabolic drug response phenotypes in silico. This combined approach was applied to investigate the hypertensive side effect of the cholesteryl ester transfer protein inhibitor torcetrapib in the context of human renal function. A metabolic kidney model was generated in which to simulate drug treatment. Causal drug off-targets were predicted that have previously been …
Enumeration Refactoring: A Tool For Automatically Converting Java Constants To Enumerated Types, Raffi T. Khatchadourian, Benjamin Muskalla
Enumeration Refactoring: A Tool For Automatically Converting Java Constants To Enumerated Types, Raffi T. Khatchadourian, Benjamin Muskalla
Publications and Research
Java 5 introduces several new features that significantly improve older Java technology. We consider the new enum construct, which provides language support for enumerated types. Before Java 5, programmers needed to employ various patterns to compensate for the absence of enumerated types in Java. Unfortunately, these compensation patterns lack several highly desirable properties of the enum construct, notably type-safety. We demonstrate an automated refactoring tool called Convert Constants to Enum for transforming legacy Java code to use the new enumeration construct. An interprocedural type inferencing algorithm that tracks the flow of enumerated values drives the approach, and the tool is …
Scattering Amplitudes From Unitarity-Based Reduction Algorithm At The Integrand-Level, P. Mastrolia, Giovanni Ossola, T. Reiter, F. Tramontano
Scattering Amplitudes From Unitarity-Based Reduction Algorithm At The Integrand-Level, P. Mastrolia, Giovanni Ossola, T. Reiter, F. Tramontano
Publications and Research
Samurai is a tool for the automated numerical evaluation of one-loop corrections to any scattering amplitudes within the dimensional-regularization scheme. It is based on the decomposition of the integrand according to the OPP-approach, extended to accommodate an implementation of the generalized d-dimensional unitarity-cuts technique, and uses a polynomial interpolation exploiting the Discrete Fourier Transform. samurai can process integrands written either as numerator of Feynman diagrams or as product of tree-level amplitudes. We discuss some applications, among which the 6- and 8-photon scattering in QED, and the 6-quark scattering in QCD. samurai has been implemented as a Fortran90 library, publicly available, …
Optimizing Radiology Peer Review: A Mathematical Model For Selecting Future Cases Based On Prior Errors, Yun Robert Sheu, Elie Feder, Igor Balsim, Victor F. Levin, Andrew G. Bleicher, Barton F. Branstetter Iv
Optimizing Radiology Peer Review: A Mathematical Model For Selecting Future Cases Based On Prior Errors, Yun Robert Sheu, Elie Feder, Igor Balsim, Victor F. Levin, Andrew G. Bleicher, Barton F. Branstetter Iv
Publications and Research
Introduction: Peer review is an essential process for physicians because it facilitates improved quality of patient care and continuing physician learning and improvement. However, peer review often is not well received by radiologists, who note that it is time intensive, subjective, and lacks demonstrable impact on patient care. Current advances in peer review include the RADPEER system with its standardization of discrepancies and incorporation of the peer review process into the PACS itself. Our purpose was to build on RADPEER and similar systems by using a mathematical model to optimally select the types of cases to be reviewed, for each …
Sensitivity Analysis Of B-Factor In Microwave Emission Model For Soil Moisture Retrieval: A Case Study For Smap Mission, Dugwon Seo, Tarendra Lakhankar, Reza Khanbilvardi
Sensitivity Analysis Of B-Factor In Microwave Emission Model For Soil Moisture Retrieval: A Case Study For Smap Mission, Dugwon Seo, Tarendra Lakhankar, Reza Khanbilvardi
Publications and Research
Sensitivity analysis is critically needed to better understand the microwave emission model for soil moisture retrieval using passive microwave remote sensing data. The vegetation b-factor along with vegetation water content and surface characteristics has significant impact in model prediction. This study evaluates the sensitivity of the b-factor, which is function of vegetation type. The analysis is carried out using Passive and Active L and S-band airborne sensor (PALS) and measured field soil moisture from Southern Great Plains experiment (SGP99). The results show that the relative sensitivity of the b-factor is 86% in wet soil condition and 88% in high vegetated …
Smap-Ws: A Parallel Web Service For Structural Proteome-Wide Ligand-Binding Site Comparison, Jingyuan Ren, Lei Xie, Wilfred W. Li, Philip E. Bourne
Smap-Ws: A Parallel Web Service For Structural Proteome-Wide Ligand-Binding Site Comparison, Jingyuan Ren, Lei Xie, Wilfred W. Li, Philip E. Bourne
Publications and Research
The proteome-wide characterization and analysis of protein ligand-binding sites and their interactions with ligands can provide pivotal information in understanding the structure, function and evolution of proteins and for designing safe and efficient therapeutics. The SMAP web service (SMAP-WS) meets this need through parallel computations designed for 3D ligand-binding site comparison and similarity searching on a structural proteome scale. SMAP-WS implements a shape descriptor (the Geometric Potential) that characterizes both local and global topological properties of the protein structure and which can be used to predict the likely ligand-binding pocket [Xie,L. and Bourne,P.E. (2007) A robust and efficient algorithm for …
Tredd—A Database For Tandem Repeats Over The Edit Distance, Dina Sokol, Firat Atagun
Tredd—A Database For Tandem Repeats Over The Edit Distance, Dina Sokol, Firat Atagun
Publications and Research
A ‘tandem repeat’ in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats are common in the genomes of both eukaryotic and prokaryotic organisms. They are significant markers for human identity testing, disease diagnosis, sequence homology and population studies. In this article, we describe a new database, TRedD, which contains the tandem repeats found in the human genome. The database is publicly available online, and the software for locating the repeats is also freely available. The definition of tandem repeats used by TRedD is a new and innovative definition based upon …
Contribution Of Soil Moisture Feedback To Hydroclimatic Variability, Nir Krakauer, B. I. Cook, M. J. Puma
Contribution Of Soil Moisture Feedback To Hydroclimatic Variability, Nir Krakauer, B. I. Cook, M. J. Puma
Publications and Research
While a variety of model experiments and analyses of observations have explored the impact of soil moisture variation on climate, it is not yet clear how large or detectable soil moisture feedback is across spatial and temporal scales. Here, we study the impact of dynamic versus climatological soil moisture in the GISS GCM ModelE (with prescribed sea-surface temperatures) on the variance and on the spatial and temporal correlation scale of hydrologically relevant climate variables (evaporation, precipitation, temperature, cloud cover) over the land surface. We also confirm that synoptic variations in soil moisture have a substantial impact on the mean climate …
Identification And Quantitation Of 3,4-Methylenedioxy-N-Methylamphetamine (Mdma, Ecstasy) In Human Urine By 1h Nmr Spectroscopy. Application To Five Cases Of Intoxication, Jonathan Liu, John Decatur, Gloria Proni, Elise Champeil
Identification And Quantitation Of 3,4-Methylenedioxy-N-Methylamphetamine (Mdma, Ecstasy) In Human Urine By 1h Nmr Spectroscopy. Application To Five Cases Of Intoxication, Jonathan Liu, John Decatur, Gloria Proni, Elise Champeil
Publications and Research
Identification of 3,4-methylenedioxy-N-methylamphetamine (MDMA, ecstasy) in five cases of intoxication using nuclear magnetic resonance (NMR) spectroscopy of human urine is reported. A new water suppression technique PURGE (Presaturation Utilizing Relaxation Gradients and Echoes) was used. A calibration curve was obtained using spiked samples. The method gave a linear response (correlation coefficient of 0.992) over the range 0.01–1 mg/mL. Subsequently, quantitation of the amount of MDMA present in the samples was performed. The benefit and reliability of NMR investigations of human urine for cases of intoxication with MDMA are discussed.
On The Feasibility Of A Timely Transition To A More Sustainable Energy Future, Micha Tomkiewicz
On The Feasibility Of A Timely Transition To A More Sustainable Energy Future, Micha Tomkiewicz
Publications and Research
The paper uses the framework of the IPAT equation, as applied to CO2 emission, to decompose the various driving forces in the global energy use. Data from recent history are superimposed on projections of SRES IPCC scenarios to determine if enough sustainable capacity can be built to prevent irreversible ecological deterioration. The conclusion from the analysis is that, in agreement with the IPCC 4th report, until about 2030 there are no large differences between a sustainable scenario and the one that resembles “business as usual”. The sharp divergence that follows stems from different estimates in population growth and in the …
What The 2007 Tac Market Design Game Tells Us About Effective Auction Mechanisms, Jinzhong Niu, Kai Cai, Simon Parsons, Peter Mcburney, Enrico Gerding
What The 2007 Tac Market Design Game Tells Us About Effective Auction Mechanisms, Jinzhong Niu, Kai Cai, Simon Parsons, Peter Mcburney, Enrico Gerding
Publications and Research
This paper analyzes the entrants to the 2007 TAC Market Design Game. We present a classification of the entries to the competition, and use this classification to compare these entries. The paper also attempts to relate market dynamics to the auction rules adopted by these entries and their adaptive strategies via a set of post-tournament experiments. Based on this analysis, the paper speculates about the design of effective auction mechanisms, both in the setting of this competition and in the more general case.
Tr-2010005: Securing Bgp Through Existing Infrastructure And Contractual Chains (Ccbgp), Yuri Cantor, Nancy Griffeth, Bilal Khan, Ping Ji
Tr-2010005: Securing Bgp Through Existing Infrastructure And Contractual Chains (Ccbgp), Yuri Cantor, Nancy Griffeth, Bilal Khan, Ping Ji
Computer Science Technical Reports
No abstract provided.
Tr-2010008: Knowability From A Logical Point Of View, Sergei Artemov, Tudor Protopopescu
Tr-2010008: Knowability From A Logical Point Of View, Sergei Artemov, Tudor Protopopescu
Computer Science Technical Reports
No abstract provided.
Tr-2010009: Solving Linear Systems With Randomized Augmentation Ii, Victor Y. Pan, Guoliang Qian
Tr-2010009: Solving Linear Systems With Randomized Augmentation Ii, Victor Y. Pan, Guoliang Qian
Computer Science Technical Reports
No abstract provided.
Tr-2010014: A Complexity Question In Justification Logic, Antonis Achilleos
Tr-2010014: A Complexity Question In Justification Logic, Antonis Achilleos
Computer Science Technical Reports
No abstract provided.
Tr-2010015: New Progress In Real And Complex Polynomial Root-Finding, Victor Y. Pan, Ai-Long Zheng
Tr-2010015: New Progress In Real And Complex Polynomial Root-Finding, Victor Y. Pan, Ai-Long Zheng
Computer Science Technical Reports
No abstract provided.
A Multidimensional Strategy To Detect Polypharmacological Targets In The Absence Of Structural And Sequence Homology, Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, J. Andrew Mccammon
A Multidimensional Strategy To Detect Polypharmacological Targets In The Absence Of Structural And Sequence Homology, Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, J. Andrew Mccammon
Publications and Research
Conventional drug design embraces the ‘‘one gene, one drug, one disease’’ philosophy. Polypharmacology, which focuses on multi-target drugs, has emerged as a new paradigm in drug discovery. The rational design of drugs that act via polypharmacological mechanisms can produce compounds that exhibit increased therapeutic potency and against which resistance is less likely to develop. Additionally, identifying multiple protein targets is also critical for side-effect prediction. One third of potential therapeutic compounds fail in clinical trials or are later removed from the market due to unacceptable side effects often caused by off-target binding. In the current work, we introduce a multidimensional …
Nearest Neighbor Search With Strong Location Privacy, Stavros Papadopoulos, Spiridon Bakiras, Dimitris Papadias
Nearest Neighbor Search With Strong Location Privacy, Stavros Papadopoulos, Spiridon Bakiras, Dimitris Papadias
Publications and Research
The tremendous growth of the Internet has significantly reduced the cost of obtaining and sharing information about individuals, raising many concerns about user privacy. Spatial queries pose an additional threat to privacy because the location of a query may be sufficient to reveal sensitive information about the querier. In this paper we focus on k nearest neighbor (kNN) queries and define the notion of strong location privacy, which renders a query indistinguishable from any location in the data space. We argue that previous work fails to support this property for arbitrary kNN search. Towards this end, we introduce methods that …
Tr-2010002: Reasoning About Games, Melvin Fitting
Tr-2010002: Reasoning About Games, Melvin Fitting
Computer Science Technical Reports
No abstract provided.
Tr-2010003: The Impossibility Of Definitive Solutions For Some Games, Sergei Artemov
Tr-2010003: The Impossibility Of Definitive Solutions For Some Games, Sergei Artemov
Computer Science Technical Reports
No abstract provided.
Tr-2010004: Tracking Evidence, Sergei Artemov
Tr-2010004: Tracking Evidence, Sergei Artemov
Computer Science Technical Reports
No abstract provided.
Tr-2010006: Graph-Based Clustering And Its Application In Coreference Resolution, Zheng Chen
Tr-2010006: Graph-Based Clustering And Its Application In Coreference Resolution, Zheng Chen
Computer Science Technical Reports
No abstract provided.
Tr-2010007: Robust Knowledge Of Rationality, Sergei Artemov
Tr-2010007: Robust Knowledge Of Rationality, Sergei Artemov
Computer Science Technical Reports
No abstract provided.
Tr-2010010: Robust Knowledge And Rationality, Sergei Artemov
Tr-2010010: Robust Knowledge And Rationality, Sergei Artemov
Computer Science Technical Reports
No abstract provided.