Digital Commons Network^™

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

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 …

Alternation Rate In Perceptual Bistability Is Maximal At And Symmetric Around Equi-Dominance, Rubén Moreno-Bote, Asya Shpiro, John Rinzel, Nava Rubin

Publications and Research

When an ambiguous stimulus is viewed for a prolonged time, perception alternates between the different possible interpretations of the stimulus. The alternations seem haphazard, but closer inspection of their dynamics reveals systematic properties in many bistable phenomena. Parametric manipulations result in gradual changes in the fraction of time a given interpretation dominates perception, often over the entire possible range of zero to one. The mean dominance durations of the competing interpretations can also vary over wide ranges (from less than a second to dozens of seconds or more), but finding systematic relations in how they vary has proven difficult. Following …

Enumeration Refactoring: A Tool For Automatically Converting Java Constants To Enumerated Types, Raffi 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

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, …

Percept Strength At The Onset Of Bistable Perception, Asya Shpiro, John Rinzel, Nava Rubin

Publications and Research

No abstract provided.

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 …

A Genealogical Review Of The Worldview Framework In African-Centered Psychology, Karanja Keita Carroll

Publications and Research

Of all the subject/content areas within Africana Studies, African-centered (African/Africana/Black) psychology has been instrumental in advancing culturally-specific theory and research. Central to the field of African-centered psychology is the usage of worldview as the conceptual and philosophical framework. This essay provides a genealogical review of the worldview framework as discussed within African-centered psychology. A focus is on understanding the developmental history and usage of worldview as it relates to producing culturally-specific theory and research consistent with the aims and goals of African-centered psychology and Africana Studies.

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

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

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

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

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.

Analysis Of Large Scale Spatial Variability Of Soil Moisture Using A Geostatistical Method, Tarendra Lakhankar, Andrew S. Jones, Cynthia L. Combs, Manajit Sengupta, Thomas H. Vonder Haar, Reza Khanbilvardi

Publications and Research

Spatial and temporal soil moisture dynamics are critically needed to improve the parameterization for hydrological and meteorological modeling processes. This study evaluates the statistical spatial structure of large-scale observed and simulated estimates of soil moisture under pre- and post-precipitation event conditions. This large scale variability is a crucial in calibration and validation of large-scale satellite based data assimilation systems. Spatial analysis using geostatistical approaches was used to validate modeled soil moisture by the Agriculture Meteorological (AGRMET) model using in situ measurements of soil moisture from a state-wide environmental monitoring network (Oklahoma Mesonet). The results show that AGRMET data produces larger …

Comparative Analysis On Applicability Of Satellite And Meteorological Data For Prediction Of Malaria In Endemic Area In Bangladesh, Atiqur Rahman, Leonid Roytman, Mitch Goldberg, Felix Kogan

Publications and Research

Relationships between yearly malaria incidence and (1) climate data from weather station and (2) satellite-based vegetation health (VH) indices were investigated for prediction of malaria vector activities in Bangladesh. Correlation analysis of percent of malaria cases with Advanced Very High Resolution Radiometer- (AVHRR-) based VH indices represented by the vegetation condition index (VCI—moisture condition) and the temperature condition index (TCI—estimates thermal condition) and with rainfall, relative humidity, and temperature from ground-based meteorological stations. Results show that climate data from weather stations are poorly correlated and are not applicable to estimate prevalence in Bangladesh. The study also has shown that AVHRR-based …

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

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.

The Future Of Natural Selection Knowledge Measurement: A Reply To Anderson Et Al. (2010), Ross Nehm, Irvin Sam Schonfeld

Publications and Research

The development of rich, reliable, and robust measures of the composition, structure, and stability of student thinking about core scientific ideas (such as natural selection) remains a complex challenge facing science educators. In their recent article (Nehm & Schonfeld 2008), the authors explored the strengths, weaknesses, and insights provided by a detailed exploration of three commonly used measures of student thinking about natural selection in a large sample of underrepresented minority students. One of their core findings was that all of the tools they studied--including the CINS--have strengths and weaknesses that must be carefully taken into consideration by those …

Single Magnetic Molecule Between Conducting Leads: Effect Of Mechanical Rotations, Reem Jaafar, Eugene M. Chudnovsky, Dmitry A. Garanin

Publications and Research

We study spin-rotation effects in a magnetic molecule bridge d between two conducting leads. Dy- namics of the total angular momentum couples spin tunneling to the mechanical rotations. Landau- Zener spin transition produced by the time-dependent magne tic field generates a unique pattern of mechanical oscillations that can be detected by measuring t he electronic tunneling current through the molecule.

Dynamical Decompactification And Three Large Dimensions, Brian Greene, Daniel N. Kabat, Stefanos Marnerides

Publications and Research

We study string gas dynamics in the early universe and seek to realize the Brandenberger - Vafa mechanism - a goal that has eluded earlier works - that singles out three or fewer spatial dimensions as the number which grow large cosmologically. Considering wound string interactions in an impact parameter picture, we show that a strong exponential suppression in the interaction rates for d > 3 spatial dimensions reflects the classical argument that string worldsheets generically intersect in at most four spacetime dimensions. This description is appropriate in the early universe if wound strings are heavy - wrapping long cycles - …

Edges And Diffractive Effects In Casimir Energies, Daniel N. Kabat, Dimitra Karabali, V P. Nair

Publications and Research

The prototypical Casimir effect arises when a scalar field is confined between parallel Dirichlet boundaries. We study corrections to this when the boundaries themselves have apertures and edges. We consider several geometries: a single plate with a slit in it, perpendicular plates separated by a gap, and two parallel plates, one of which has a long slit of large width, related to the case of one plate being semi-infinite. We develop a general formalism for studying such problems, based on the wavefunctional for the field in the gap between the plates. This formalism leads to a lower dimensional theory defined …

The Mds Mortality Risk Index: The Evolution Of A Method For Predicting 6-Month Mortality In Nursing Home Residents, Davina Porock, Debra Parker-Oliver, Gregory F. Petroski, Marilyn Rantz

Publications and Research

Background: Accurate prognosis is vital to the initiation of advance care planning particularly in a vulnerable, at risk population such as care home residents. The aim of this paper is to report on the revision and simplification of the MDS Mortality Rating Index (MMRI) for use in clinical practice to predict the probability of death in six months for care home residents.

Methods: The design was a secondary analysis of a US Minimum Data Set (MDS) for long term care residents using regression analysis to identify predictors of mortality within six months.

Results: Using twelve easy to collect …

Patterns Of Subnet Usage Reveal Distinct Scales Of Regulation In The Transcriptional Regulatory Network Of Escherichia Coli, Carsten Marr, Fabian J. Theis, Larry S. Liebovitch, Marc-Thorsten Hutt

Publications and Research

The set of regulatory interactions between genes, mediated by transcription factors, forms a species’ transcriptional regulatory network (TRN). By comparing this network with measured gene expression data, one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with fewer …

The Maximum Rectilinear Crossing Number Of The Petersen Graph, Elie Feder, Heiko Harborth, Steven Herzberg, Sheldon Klein

Publications and Research

We prove that the maximum rectilinear crossing number of the Petersen graph is 49. First, we illustrate a picture of the Petersen graph with 49 crossings to prove the lower bound. We then prove that this bound is sharp by carefully analyzing the ten Cs's which occur in the Petersen graph and their properties.

Standardization Of Keyword Search Mode, Di Su

Publications and Research

In spite of its popularity, keyword search mode has not been standardized. Though information professionals are quick to adapt to various presentations of keyword search mode, novice end-users may find keyword search confusing. This article compares keyword search mode in some major reference databases and calls for standardization.

The Genomics Education Partnership: Successful Integration Of Research Into Laboratory Classes At A Diverse Group Of Undergraduate Institutions, Christopher D. Shaffer, Consuelo Alvarez, Cheryl Bailey, Daron Barnard, Satish Bhalla, Chitra Chandrasekaran, Vidya Chandrasekaran, Hui-Min Chung, Douglas R. Dorer, Chunguang Du, Todd T. Eckdahl, Jeff L. Poet, Donald Frohlich, Anya L. Goodman, Yuying Gosser, Charles Hauser, Laura L.M. Hoopes, Diana Johnson, Christopher J. Jones, Marian Kaehler, Gerard Mcneil

Publications and Research

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 …

Analysis Of Large Scale Spatial Variability Of Soil Moisture Using A Geostatistical Method, Tarendra Lakhankar, Andrew S. Jones, Cynthia L. Combs, Manajit Sengupta, Thomas H. Vonder Haar, Reza Khanbilvardi

Publications and Research

Spatial and temporal soil moisture dynamics are critically needed to improve the parameterization for hydrological and meteorological modeling processes. This study evaluates the statistical spatial structure of large-scale observed and simulated estimates of soil moisture under pre- and post-precipitation event conditions. This large scale variability is a crucial in calibration and validation of large-scale satellite based data assimilation systems. Spatial analysis using geostatistical approaches was used to validate modeled soil moisture by the Agriculture Meteorological (AGRMET) model using in situ measurements of soil moisture from a state-wide environmental monitoring network (Oklahoma Mesonet). The results show that AGRMET data produces larger …

Rotational States Of Magnetic Molecules, Eugene M. Chudnovsky, Dmitry A. Garanin

Publications and Research

We study a magnetic molecule that exhibits spin tunneling and is free to rotate about its anisotropy axis. Exact low-energy eigenstates of the molecule that are superpositions of spin and rotational states are obtained. We show that parameter α=2(ℏS)2/(IΔ) determines the ground state of the molecule. Here ℏS is the spin, I is the moment of inertia, and Δ is the tunnel splitting. The magnetic moment of the molecule is zero at α<αc=[1−1/(2S)2]−1 and non-zero at α>αc. At α→∞ the spin of the molecule localizes in one of the directions along the anisotropy axis.

Deflagration With Quantum And Dipolar Effects In A Model Of A Molecular Magnet, Dmitry A. Garanin

Publications and Research

Combination of the thermal effet in magnetic deflagration with resonance spin tunneling controlled by the dipole-dipole interaction in molecular magnets leads to the increase of the deflagration speed in the dipolar window near tunneling resonances.

On The Casimir Interaction Between Holes In A Plate, Daniel N. Kabat, Dimitra Karabali, V P. Nair

Publications and Research

We study the leading long-distance attractive force between two holes in a plate arising from a scalar eld with Dirichlet boundary conditions on the plate. We use a formalism in which the interaction is governed by a non-local eld theory which lives on the two holes. The interaction energy is proportional to Q1Q2=r7 at large separation r, where Q1 and Q2 are certain charges associated with the holes. We compute these charges for round and rectangular holes. We show that the 1=r7 behavior is universal for separations large compared to the linear dimensions of the holes, irrespective of the spin …