Physical Sciences and Mathematics Commons^™

Bayesian Meta-Analysis Models For Microarray Data: A Comparative Study, Erin M. Conlon, Joon J. Song, Anna Liu

Anna Liu

Background With the growing abundance of microarray data, statistical methods are increasingly needed to integrate results across studies. Two common approaches for meta-analysis of microarrays include either combining gene expression measures across studies or combining summaries such as p-values, probabilities or ranks. Here, we compare two Bayesian meta-analysis models that are analogous to these methods. Results Two Bayesian meta-analysis models for microarray data have recently been introduced. The first model combines standardized gene expression measures across studies into an overall mean, accounting for inter-study variability, while the second combines probabilities of differential expression without combining expression values. Both models produce …

Tragedy Of The Foss Commons? Investigating The Institutional Designs Of Free/Libre And Open Source Software Projects, Charles M. Schweik, Robert English

National Center for Digital Government

Free/Libre and Open Source Software projects (FOSS) are a form of Internetbased commons. Since 1968, when Garrett Hardin published his famous article “Tragedy of the Commons” in the journal Science, there has been significant interest in understanding how to manage commons appropriately, particularly in environmental fields. An important distinction between natural resource commons and FOSS commons is that the “tragedy” to be avoided in natural resources is overharvesting and the potential destruction of the resource. In FOSS commons the “tragedy” to be avoided is project abandonment and a “dead” project. Institutions – defined as informal norms, more formalized rules, and …

Identifying Success And Tragedy Of Floss Commons: A Preliminary Classification Of Sourceforge.Net Projects, Robert English, Charles M. Schweik

National Center for Digital Government

Free/Libre and Open Source Software (FLOSS) projects are a form of commons where individuals work collectively to produce software that is a public, rather than a private, good. The famous phrase “Tragedy of the Commons” describes a situation where a natural resource commons, such as a pasture, or a water supply, gets depleted because of overuse. The tragedy in FLOSS commons is distinctly different -- it occurs when collective action ceases before a software product is produced or reaches its full potential. This paper builds on previous work about defining success in FLOSS projects by taking a collective action perspective. …

Core-Like Particles Of An Enveloped Animal Virus Can Self-Assemble Efficiently On Artificial Templates, Nl Goicochea, M De, Vm Rotello, S Mukhopadhyay, B Dragnea

Vincent Rotello

Alphaviruses are animal viruses holding great promise for biomedical applications as drug delivery vectors, functional imaging probes, and nanoparticle delivery vesicles because of their efficient in vitro self-assembly properties. However, due to their complex structure, with a protein capsid encapsulating the genome and an outer membrane composed of lipids and glycoproteins, the in-vitro self-assembly of virus-like particles, which have the functional virus coat but carry an artificial cargo, can be challenging. Fabrication of such alphavirus-like particles is likely to require a two-step process: first, the assembly of a capsid structure around an artificial core, second the addition of the membrane …

Triply-Periodic Smectic Liquid Crystals, Christian Santangelo, Randall D. Kamien

Christian Santangelo

Twist-grain-boundary phases in smectics are the geometrical analogs of the Abrikosov flux lattice in superconductors. At large twist angles, the nonlinear elasticity is important in evaluating their energetics. We analytically construct the height function of a π∕2 twist-grain-boundary phase in smectic-A liquid crystals, known as Schnerk’s first surface. This construction, utilizing elliptic functions, allows us to compute the energy of the structure analytically. By identifying a set of heretofore unknown defects along the pitch axis of the structure, we study the necessary topological structure of grain boundaries at other angles, concluding that there exist a set of privileged angles and …

Asymptotic Calculation Of Discrete Non-Linear Wave Interactions, Pg Kevrekidis

Mathematics and Statistics Department Faculty Publication Series

We illustrate how to compute asymptotic interactions between discrete solitary waves of dispersive equations, using the approach proposed by Manton [N.S. Manton, Nucl. Phys. B 150 (1979) 397]. We also discuss the complications arising due to discreteness and showcase the application of the method in non-linear Schrödinger, as well as in Klein-Gordon lattices, finding excellent agreement with direct numerical computations.

Faraday Waves In Bose-Einstein Condensates, Ai Nicolin, R Carretero-Gonzalez, Pg Kevrekidis

Mathematics and Statistics Department Faculty Publication Series

Motivated by recent experiments on Faraday waves in Bose-Einstein condensates we investigate both analytically and numerically the dynamics of cigar-shaped Bose-condensed gases subject to periodic modulation of the strength of the transverse confinement. We offer a fully analytical explanation of the observed parametric resonance, based on a Mathieu-type analysis of the non-polynomial Schrödinger equation. The theoretical prediction for the pattern periodicity versus the driving frequency is directly compared to the experimental data, yielding good qualitative and quantitative agreement between the two. These results are corroborated by direct numerical simulations of both the one-dimensional non-polynomial Schrödinger equation and of the fully …

Mobility Of Discrete Solitons In Quadratically Nonlinear Media, H Susanto, Pg Kevrekidis, R Carretero-Gonzalez, Ba Malomed, Dj Frantzeskakis

Mathematics and Statistics Department Faculty Publication Series

We study the mobility of solitons in lattices with quadratic (χ(2), alias second-harmonic-generating) nonlinearity. Using the notion of the Peierls-Nabarro potential and systematic numerical simulations, we demonstrate that, in contrast with their cubic (χ(3)) counterparts, the discrete quadratic solitons are mobile not only in the one-dimensional (1D) setting, but also in two dimensions (2D), in any direction. We identify parametric regions where an initial kick applied to a soliton leads to three possible outcomes: staying put, persistent motion, or destruction. On the 2D lattice, the solitons survive the largest kick and attain the largest speed along the diagonal direction.

Solitary Waves Under The Competition Of Linear And Nonlinear Periodic Potentials, Z Rapti, Pg Kevrekidis, Vv Konotop, Ckrt Jones

Mathematics and Statistics Department Faculty Publication Series

In this paper, we study the competition of the linear and nonlinear lattices and its effects on the stability and dynamics of bright solitary waves. We consider both lattices in a perturbative framework, whereby the technique of Hamiltonian perturbation theory can be used to obtain information about the existence of solutions, and the same approach, as well as eigenvalue count considerations, can be used to obtain detailed conditions about their linear stability. We find that the analytical results are in very good agreement with our numerical findings and can also be used to predict features of the dynamical evolution of …

Symplectic Symmetries Of 4-Manifolds, Wm Chen, S Kwasik

Mathematics and Statistics Department Faculty Publication Series

A study of symplectic actions of a finite group G on smooth 4-manifolds is initiated. The central new idea is the use of G-equivariant Seiberg–Witten–Taubes theory in studying the structure of the fixed-point set of these symmetries. The main result in this paper is a complete description of the fixed-point set structure (and the action around it) of a symplectic cyclic action of prime order on a minimal symplectic 4-manifold with . Comparison of this result with the case of locally linear topological actions is made. As an application of these considerations, the triviality of many such actions on …

Nasa’S S'Cool Program, Rob Snyder

STEM Earth Central

NASA's S'COOL program gives students an opportunity to provide "ground truth" measurements to help NASA verify that data collected by CERES (Clouds and the Earth's Radiant Energy System) instruments. The CERES instrumentation has been launched into polar obits on three satellites

Global Warming Or Climate Hysteria?, Richard Yuretich

STEM Earth Central

No abstract provided.

Eratosthenes' Proportion - Measure The Diameter Of The Earth, Stephen E. Schneider

STEM Earth Central

Objective: To use a midday shadow on or close to the day of an Equinox to calculate Earth’s Polar Circumference.

True Scale Solar System Models, Stephen E. Schneider

STEM Earth Central

Objectives:

To construct a true scale model of the solar system

To understand the size of Earth relative to the Solar System

To comprehend the sizes of planets versus the spaces between them

Planet Longitudes, Stephen E. Schneider

STEM Earth Central

Objectives:

To apply the concept of Longitude to the location of planets in their orbits.

To predict what planets can be seen in the night sky on any date.

Measuring Carbon Dioxide With Btb, Stephen E. Schneider

STEM Earth Central

No abstract provided.

The Earth's Energy Balance, Richard Yuretich

STEM Earth Central

No abstract provided.

Overview: Exploring Earth System Science, Richard F. Yuretich, Stephen E. Schneider, Rob Snyder, Morton Sternheim

STEM Earth Central

Earth Science topics that can be used in other science teaching

Mapping, GPS, GIS applications, geology, water, environmental issues

Hands-on activities and relevant internet resources

Designing and conducting research project

Applications to teaching in the K12 classroom

Curriculum concept component

Optional extensions

The Hydrologic Cycle, Richard Yuretich

STEM Earth Central

No abstract provided.

Global Warming - Some Astrophysical Perspectives, Stephen E. Schneider

STEM Earth Central

No abstract provided.

Ozone: What Is It?, Stephen E. Schneider

STEM Earth Central

No abstract provided.

Map The Campus With Gps, Richard Yuretich, Rob Snyder

STEM Earth Central

Objective: To use a Global Positioning System device to collect data in order to construct a campus map.

Note: These instructions are for a Garmin 72 GPS. Refer to the GPS Basics document, the manual, or an on-line manual at http://www.garmin.com/products/gps72/ for additional information

The Digital Divide Metaphor: Understanding Paths To It Literacy, Enrico Ferro, Natalie C. Helbig, J. Ramon Gil-Garci

National Center for Digital Government

Not having access or having a disadvantaged access to information, in an information-based society may be considered as a handicap (Compaine, 2001). In the last two decades scholars have gradually refined the conceptualization of digital divide, moving from a dichotomous model mainly based on access to a multidimensional model accounting for differences in usage levels and perspectives. While models became more complex, research continued to mainly focus on deepening the understanding of demographic and socioeconomic differences between adopters and non-adopters. In doing so, the process of basic IT skills acquisition has been largely overlooked. This paper presents a metaphorical interpretation …

Petrology, Structural Geology, And Significance Of Mn-Andalusite From The Lower Ortega Quartzite, Tusas Mts., Nm, Usa, Nancy A. Price

Masters Theses 1911 - February 2014

The Proterozoic syn-orogenic supra-crustal package exposed in the Tusas Mountain Range in northern New Mexico includes the anomalously thick, clean, ultramature Ortega Formation quartzite (Bauer and Williams, 1989). A unique Mn-bearing horizon spans the basal contact of the quartzite and contains Mn-andalusite, quartz, hematite, rutile, zircon, monazite, phyllosilicates, and locally kyanite and gahnite in intermittent aluminous, hematite-bearing layers, on the surface of cross-beds, concentrated in high strain zones, and on cleavage planes. Large-scale Mn zoning in Mn-andalusite results from a decrease in Mn content away from localized Mn highs (XMn of up to 0.76) that commonly correspond with the location …

Transfer Function And Impulse Response Synthesis Using Classical Techniques, Sonal S. Khilari

Masters Theses 1911 - February 2014

This thesis project presents a MATLAB based application which is designed to synthesize any arbitrary stable transfer function. Our application is based on the Cauer synthesis procedure. It has an interactive front which allows inputs either in the form of residues and poles of a transfer function, in the form of coefficients of the numerator and denominator of the transfer impedance or in the form of samples of an impulse response. The program synthesizes either a single or double resistively terminated LC ladder network. Our application displays a chart showing the variation of stability of an impulse response with the …

2007 Newsletter, Morton Sternheim

STEM Education Institute Newsletters

NANOTECHNOLOGY Summer 2007 Institute p. 3

EARTH CENTRAL 2007 Ending on a High Note p. 5

PV STEMNET Has a Very Productive Year p. 4

CONFERENCE ON ALTERNATIVE CERTIFICATION FOR SCIENCE TEACHERS: Lessons Learned p. 7

NOYCE SCHOLAR travels to Washington D.C. p. 6

NOYCE SCHOLARS p. 6

STEM RAYS Completes Pilot Phase, Goes Into Full Operation p. 2

IPY STEM Polar Connections p. 4

UMASS K12 ENDS DIALUP SERVICE p. 7

SMET OR STEM: WHAT’S IN A NAME? p. 7

Synthesize A Nanoscale Ferrofluid, Rob Snyder

Nanotechnology Teacher Summer Institutes

The chemical synthesis of a ferrofluid is a nanoscale science activity that originally appears in the Journal of Chemical Education. Access to the following website requires a subscription to the journal. J. Chem. Educ., 76, 943-948 (1999). The article was authored by Jonathan Breitzer and George Lisensky.

Proposal Abstract, Morton Sternheim, Julie Brigham-Grette

IPY STEM Polar Connections

No abstract provided.

Proposal Narrative And References, Morton Sternheim, Julie Brigham-Grette

IPY STEM Polar Connections

No abstract provided.

A Satscan Macro Accessory For Cartography (Smac) Package Implemented With Sas Software, Allyson M. Abrams, Ken P. Kleinman

Public Health Department Faculty Publication Series

BACKGROUND:

SaTScan is a software program written to implement the scan statistic; it can be used to find clusters in space and/or time. It must often be run multiple times per day when doing disease surveillance. Running SaTScan frequently via its graphical user interface can be cumbersome, and the output can be difficult to visualize.

RESULTS:

The SaTScan Macro Accessory for Cartography (SMAC) package consists of four SAS macros and was designed as an easier way to run SaTScan multiple times and add graphical output. The package contains individual macros which allow the user to make the necessary input files …