Physical Sciences and Mathematics Commons^™

Virginia Wetlands Report Vol. 22, No. 1, Virginia Institute Of Marine Science, Center For Coastal Resources Management

Virginia Wetlands Reports

Sea Level Rise & Other Coastal Hazards - Living on the Edge Tidal Wetlands and Sea Level Rise: Where’s the Marsh?

Supporting Information For "The Molecular Basis Of High-Altitude Adaptation In Deer Mice", Jay F. Storz, Stephen J. Sabatino, Federico G. Hoffmann, Eben J. Gering, Hideaki Moriyama, Nuno Ferrand, Bruno Monteiro, Michael W. Nachman

Hideaki Moriyama Publications

Figure S1: Variation in Site-Specific Levels of Altitudinal Differentiation across the 5′ α- Globin Gene of P. maniculatus

Figure S2: Relationship between Pairwise Linkage Disequilibrium and Distance in bp

Genbank Accession Numbers

Table S1: Amino Acid Variation in the α-Globin Genes of High- and Low-Altitude Deer Mice: Amino acid replacement polymorphisms in deer mice where the derived variant is present at a frequency of >0.100 in the high-altitude sample.

Table S2: Additional Information on Sequenced Loci: Primer sequences for nuclear loci in P. maniculatus.

The Molecular Basis Of High-Altitude Adaptation In Deer Mice, Jay F. Storz, Stephen J. Sabatino, Federico G. Hoffmann, Eben J. Gering, Hideaki Moriyama, Nuno Ferrand, Bruno Monteiro, Michael W. Nachman

Hideaki Moriyama Publications

Elucidating genetic mechanisms of adaptation is a goal of central importance in evolutionary biology, yet few empirical studies have succeeded in documenting causal links between molecular variation and organismal fitness in natural populations. Here we report a population genetic analysis of a two-locus a-globin polymorphism that underlies physiological adaptation to high-altitude hypoxia in natural populations of deer mice, Peromyscus maniculatus. This system provides a rare opportunity to examine the molecular underpinnings of fitness-related variation in protein function that can be related to a well-defined selection pressure. We surveyed DNA sequence variation in the duplicated α -globin genes of P. maniculatus …

Generalized Mixture Models, Semi-Supervised Learning, And Unknown Class Inference, Samuel J. Frame, Sreenivasa Rao Jammalamadaka

Statistics

In this paper, we discuss generalized mixture models and related semi-supervised learning methods, and show how they can be used to provide explicit methods for unknown class inference. After a brief description of standard mixture modeling and current model-based semi-supervised learning methods, we provide the generalization and discuss its computational implementation using three-stage expectation–maximization algorithm.

Benchmarks For Traceability?, Alex Dekhtyar, Jane Huffman Hayes, Giuliano Antoniol

Computer Science and Software Engineering

This position paper discusses the need for and the organization of a traceability benchmark. We establish the basic principles of organization of such a benchmark. We then observe the nature of traceability tasks in three areas of Software Engineering: independent verification and validation, software maintenance, and reverse engineering. Based on this, we derive the desiderata for a traceability benchmark addressing the needs of all three areas.

Doping Golden Buckyballs: Cu@Au16- And Cu@Au17- Cluster Anions, Lei-Ming Wang, Satya S. Bulusu, Hua-Jin Zhai, Xiao Cheng Zeng, Wang

Xiao Cheng Zeng Publications

The discovery of the unique catalytic effects of gold nanoparticles on oxide substrates[1] has stimulated a flurry of research into the structures and properties of free gold nanoclusters, which may hold the key to elucidating the catalytic mechanisms of supported gold clusters. One of the most remarkable results has been the discovery of planar gold cluster anions (Au_n^-) of up to twelve gold atoms and the 2D to 3D transition for clusters with n larger than 12.[2]– [4] Among larger gold clusters, Au₂₀ has been found to be a perfect tetrahedron.[5] A more recent study of …

Invasive Cordgrasses - Spartina Species - Estuarine Invaders!, Vanessa Howard

Center for Lakes and Reservoirs Publications and Presentations

Brochure on invasive Spartina

Angular Spectrum Representation For The Propagation Of Arbitrary Coherent And Partially Coherent Beams Through Atmospheric Turbulence, Greg Gbur, Olga Korotkova

Physics Articles and Papers

An angular spectrum representation is applied for a description of statistical properties of arbitrary beamlike fields propagating through atmospheric turbulence. The Rytov theory is used for the characterization of the perturbation of the field by the atmosphere. In particular, we derive expressions for the cross-spectral density of a coherent and a partially coherent beam of arbitrary type in the case when the power spectrum of atmospheric fluctuations is described by the von Karman model. We illustrate the method by applying it to the propagation of several model beams through the atmosphere.

Clay Mineralization Of The Neogene Aged Volcanics Of The Northeastern Si̇vri̇hi̇sar (Mülk-Demi̇rci̇), Zehra Karakaş, Baki Varol, Sonay Boyraz

Bulletin of the Mineral Research and Exploration

No abstract provided.

Determining The Effectiveness Of The 3d Alice Programming Environment At The Computer Science I Level, Edward R. Sykes

Faculty Publications and Scholarship

Student retention in Computer Science is becoming a serious concern among Educators in many colleges and universities. Most institutions currently face a significant drop in enrolment in Computer Science. A number of different tools and strategies have emerged to address this problem (e.g., BlueJ, Karel Robot, etc.). Although these tools help to minimize attrition, they have not made significant improvements to this widespread problem. A newcomer to the scene called Alice has been met with positive results by captivating student interest through its rich 3D visual programming environment. During the fall of 2005, Alice, a newly published textbook, and numerous …

Plan Of Management For The Kalbarri Blue Holes Fish Habitat Protection Area, Department Of Fisheries

Fisheries management papers

The FHPA has been declared to protect and conserve an example of a near-shore reef community. In order to achieve this aim, and encourage the appreciation and conservation of fish, a number of management strategies have been identified which restrict recreational and commercial fishing. The FHPA is approximately 420 metres long and approximately 130 metres wide at the southern end and 140 metres wide at the northern end.

Periodic Solutions Of Functional Dynamic Equations With Infinite Delay, Li Bi, Meng Fan, Martin Bohner

Mathematics and Statistics Faculty Research & Creative Works

In this paper, sufficient criteria are established for the existence of periodic solutions of some functional dynamic equations with infinite delays on time scales, which generalize and incorporate as special cases many known results for differential equations and for difference equations when the time scale is the set of the real numbers or the integers, respectively. The approach is mainly based on the Krasnosel'skilatin small letter i with breve fixed point theorem, which has been extensively applied in studying existence problems in differential equations and difference equations but rarely applied in studying dynamic equations on time scales. This study shows …

Refuge Update – March/April 2010, Volume 7, Number 2

RefugeUpdate (USFWS-NWRS)

Table of Contents:

First, We Inventory by Bill O’Brian
The Legacy We Carry On By Greg Siekaniec
Straight from the Secretary
FOCUS: Maintenance
CMS Is Coming to a Web Site Near You
Protecting Wildlife, Producing Energy

In-Use Stocks Of Iron In The State Of Connecticut, Usa, Matthew Eckelman, Jason Rauch, Robert Gordon

Yale School of the Environment Publications Series

A “bottom-up” study was conducted for in-use stocks of iron in the State of Connecticut for the base year of 2000. The study covers 145 product types in the four major categories of transportation, buildings, equipment, and infrastructure. The method of calculation, as well as the allocation of iron in different use categories is discussed. The total result of 9,300 kg of iron per capita is slightly higher than that from a previous study for the city of New Haven, but below the results of national top-down analyses. Possible reasons for these discrepancies are considered. A sensitivity analysis and an …

Flow And Fates Of Discarded Copper In Sofia, Bulgaria, And New Haven Ct, Usa, Diana Dimitrova, Jason Rauch, Robert Gordon, T. E. Graedel

Yale School of the Environment Publications Series

In order to better understand the fate of copper following its use, the discard flows of copper were analyzed in Sofia, Bulgaria, and New Haven, CT, USA. These cities were chosen to compare discard copper generation and recovery between a city in a developed country and a city in a developing country. The comparison between these two cities can be problematic due to their different relative sizes, and generalizing the results to other cities cannot be done without some error. However, as the first study of its kind, this study provides insights into the relative copper recovery rates indifferent socioeconomic …

Variational Analysis In Bilevel Programming, S Dempe, J Dutta, Boris S. Mordukhovich

Mathematics Research Reports

The paper is devoted to applications of advanced tools of modern variational analysis and generalized differentiation to problems of optimistic bilevel programming. In this way, new necessary optimality conditions are derived for two major classes of bilevel programs: those with partially convex and with fully convex lower-level problems. We provide detailed discussions of the results obtained and their relationships with known results in this area.

The Power Method Transformation: Its Probability Density Function, Distribution Function, And Its Further Use For Fitting Data, Todd C. Headrick, Rhonda K. Kowalchuk

Todd Christopher Headrick

The power method polynomial transformation is a popular algorithm used for simulating non-normal distributions because of its simplicity and ease of execution. The primary limitations of the power method transformation are that its probability density function (pdf) and cumulative distribution function (cdf) are unknown. In view of this, the power method’s pdf and cdf are derived in general form. More specific properties are also derived for determining if a given transformation will also have an associated pdf in the context of polynomials of order three and five. Numerical examples and parametric plots of power method densities are provided to confirm …

Causal Effect Models For Realistic Individualized Treatment And Intention To Treat Rules, Mark J. Van Der Laan, Maya L. Petersen

Maya Petersen

Marginal structural models (MSM) are an important class of models in causal inference. Given a longitudinal data structure observed on a sample of n independent and identically distributed experimental units, MSM model the counterfactual outcome distribution corresponding with a static treatment intervention, conditional on user-supplied baseline covariates. Identification of a static treatment regimen-specific outcome distribution based on observational data requires, beyond the standard sequential randomization assumption, the assumption that each experimental unit has positive probability of following the static treatment regimen. The latter assumption is called the experimental treatment assignment (ETA) assumption, and is parameter-specific. In many studies the ETA …

Inter-Rater Reliability Of Pressure Ulcer Staging: Ordinal Probit Bayesian Hierarchical Model That Allows For Uncertain Rater Response, Byron J. Gajewski, Sara Hart, Sandra Bergquist-Beringer , Nancy Dunton

Byron J Gajewski

This article describes a method for estimating the inter-rater reliability of pressure ulcer (PU) staging (stages I-IV) from raters in National Database of Nursing Quality Indicators (NDNQI) participating hospitals. The method models ordinal spanning data utilizing an ordinal probit Bayesian hierarchical model (BHM) across several hospitals in which raters monitor patient's PUs. An ulcer that cannot be accurately assessed because the base of the wound cannot be seen is defined as unstageable. Our novel approach allows for an unstageable PU rating to be included in the analysis. We compare the ordinal probit BHM to an approximate random-effects (standard approach in …

Quantum Mechanics In Vectorial Relativity, Jorge A. Franco, Jose G. Quintero

Jorge A Franco

In previous work it was shown that assumptions, y’= y and z’= z, within Lorentz Transformations (LT) were needless, and therefore groundless. Achieved development of LT without assumptions, brought about a unique relativistic mass definition, m = M0 /(1-v2/c2)3/2. Also, in a subsequent work, based on this definition of mass, a new and general expression of relativistic Energy was devised E = 2M0 – m(c2 – 2v2), valid for particles with null or non-null masses at rest. Remember that it reduces to Einstein’s equation, E = m.c2 for particles with null mass at rest (i.e. photons) and to Newtonian Energy, …

Gravitational Forces In Vectorial Relativity, Jorge A. Franco

Jorge A Franco

It is known that Kepler’s Laws can be derived from the Newton’s Law of Universal Gravitation. For doing this, mass is considered as an invariable parameter. Although this consideration works wonderfully to solve most of problems in astronomy calculations, as well as in all physics, when astral body’s speeds are so high and very precise measurements are required, the referred Kepler Laws do not cope enough what is expected. That’s why the General Theory of Relativity materialized. As it was indirectly pointed out by Einstein in 1905, Newton and Kepler Laws do not consider the relativistic variation of mass with …

Statistical Evaluation Of Evidence For Clonal Allelic Alterations In Array-Cgh Experiments, Colin B. Begg, Kevin Eng, Adam Olshen, E S. Venkatraman

Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series

In recent years numerous investigators have conducted genetic studies of pairs of tumor specimens from the same patient to determine whether the tumors share a clonal origin. These studies have the potential to be of considerable clinical significance, especially in clinical settings where the distinction of a new primary cancer and metastatic spread of a previous cancer would lead to radically different indications for treatment. Studies of clonality have typically involved comparison of the patterns of somatic mutations in the tumors at candidate genetic loci to see if the patterns are sufficiently similar to indicate a clonal origin. More recently, …

Enantioselective 1,3-Dipolar Cycloadditions Of Diazoacetates With Electron-Deficient Olefins, Mukund P. Sibi, Levi M. Stanley, Takahiro Soeta

Levi M. Stanley

A general strategy for highly enantioselective 1,3-dipolar cycloaddition of diazoesters to β-substituted, α-substituted, and α,β-disubstituted α,β-unsaturated pyrazolidinone imides is described. Cycloadditions utilizing less reactive α,β-disubstituted dipolarophiles require elevated reaction temperatures, but still provide the corresponding pyrazolines with excellent enantioselectivities. Finally, an efficient synthesis of (−)-manzacidin A employing this cycloaddition methodology as a key step is illustrated.

Modified Kubelka-Munk Equations For Localized Waves Inside A Layered Medium, Kasper Van Wijk

CGISS Publications and Presentations

We present a pair of coupled partial differential equations to describe the evolution of the average total intensity and intensity flux of a wave field inside a randomly layered medium. These equations represent a modification of the Kubelka-Munk equations, or radiative transfer. Our modification accounts for wave interference (e.g., localization), which is neglected in radiative transfer. We numerically solve the modified Kubelka-Munk equations and compare the results to radiative transfer as well as to simulations of the wave equation with randomly located thin layers.

Accessibility Of Home Blood Pressure Monitors For Blind And Visually Impaired People, Mark M. Uslan, Darren M. Burton, Thomas E. Wilson, Steven Taylor, Bruce S. Chertow, Jack E. Terry

Physics Faculty Research

Background: The prevalence of hypertension comorbid with diabetes is a significant health care issue. Use of the home blood pressure monitor (HBPM) for aiding in the control of hypertension is noteworthy because of benefits that accrue from following a home measurement regimen. To be usable by blind and visually impaired patients, HBPMs must have speech output to convey all screen information, an easily readable visual display, identifiable controls that are easy to use, and an accessible user manual.

Methods: Data on the physical aspects and the features and functions of nine Food and Drug Administration-approved HBPMs (eight of which were …

Protein Design By Mining And Sampling An Undirected Graphical Model Of Evolutionary Constraints, John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg

Computer Science Technical Reports

Evolutionary pressures on proteins to maintain structure and function have constrained their sequences over time and across species. The sequence record thus contains valuable information regarding the acceptable variation and covariation of amino acids in members of a protein family. When designing new members of a protein family, with an eye toward modified or improved stability or functionality, it is incumbent upon a protein engineer to uncover such constraints and design conforming sequences. This paper develops such an approach for protein design: we first mine an undirected probabilistic graphical model of a given protein family, and then use the model …

Dynamic Polarizabilities Of Rare-Earth-Metal Atoms And Dispersion Coefficients For Their Interaction With Helium Atoms, Xi Chu, Alexander Dalgarno, Gerrit C. Groenenboom

Chemistry and Biochemistry Faculty Publications

The dynamic scalar and tensor polarizabilities of the rare-earth-metal atoms are calculated with time-dependent density functional theory. The frequency-dependent polarizabilities at imaginary frequencies are used to determine the isotropic and orientation-dependent van der Waals coefficients for the interactions of the rare-earth-metal atoms with helium atoms. The static polarizabilities are compared with other theoretical values and with experimental results. The agreement is satisfactory in most cases but there are some exceptions where the discrepancy between theory and experiment is significant. The derived isotropic van der Waals coefficients range between 37 and 50 E(H)a(0)(6) and the orientation-dependent coefficients between 2 and -1 …

Pressure Dissociation Of Integration Host Factor-Dna Complexes Reveals Flexibility-Dependent Structural Variation At The Protein-Dna Interface, Donald F. Senear, Vira Tretyachenko-Ladokhina, Michael L. Opel, Kimberly A. Aeling, G. Wesley Hatfield, Laurie M. Franklin, Reuben C. Darlington, J. B. A. Ross

Chemistry and Biochemistry Faculty Publications

E. coli Integration host factor (IHF) condenses the bacterial nucleoid by wrapping DNA. Previously, we showed that DNA flexibility compensates for structural characteristics of the four consensus recognition elements associated with specific binding (Aeling et al., J. Biol. Chem. 281, 39236-39248, 2006). If elements are missing, high-affinity binding occurs only if DNA deformation energy is low. In contrast, if all elements are present, net binding energy is unaffected by deformation energy. We tested two hypotheses for this observation: in complexes containing all elements, (1) stiff DNA sequences are less bent upon binding IHF than flexible ones; or (2) DNA sequences …

Control, Trust, Privacy, And Security: Evaluating Location-Based Services, L. Perusco, Katina Michael

Faculty of Informatics - Papers (Archive)

Location-based services (LBS) are those applications that utilize the position of an end-user, animal, or thing based on a given device (handheld, wearable, or implanted), for a particular purpose. This article uses scenario planning to identify the possible risks related to location-based services in the context of security and privacy. The original contribution of this article is that the dilemma has been related specifically to LBS, under the privacy-security dichotomy. Here, each side of the dichotomy is divided into three key components that combine to greatly magnify risk. Removing one or more components for each set decreases the privacy or …

Consumer Electronics Control System Based On Hand Gesture Moment Invariants, Prashan Premaratne, Q. Nguyen

Faculty of Informatics - Papers (Archive)

Almost all consumer electronic equipment today uses remote controls for user interfaces. However, the variety of physical shapes and functional commands that each remote control features also raises numerous problems: the difficulties in locating the required remote control, the confusion with the button layout, the replacement issue and so on. The consumer electronics control system using hand gestures is a new innovative user interface that resolves the complications of using numerous remote controls for domestic appliances. Based on one unified set of hand gestures, this system interprets the user hand gestures into pre-defined commands to control one or many devices …