Physical Sciences and Mathematics Commons^™

Coplanar Constant Mean Curvature Surfaces, Karsten Grosse-Brauckmann, Robert Kusner, John M. Sullivan

Robert Kusner

We consider constant mean curvature surfaces with finite topology, properly embedded in three-space in the sense of Alexandrov. Such surfaces with three ends and genus zero were constructed and completely classified by the authors. Here we extend the arguments to the case of an arbitrary number of ends, under the assumption that the asymptotic axes of the ends lie in a common plane: we construct and classify the entire family of these genus-zero, coplanar constant mean curvature surfaces.

Rapid Changes In Gene Expression Dynamics In Response To Superoxide Reveal Soxrs-Dependent And Independent Transcriptional Networks, Jeffrey L. Blanchard, Wei-Yun Wholey, Erin M. Conlon, Pablo J. Pomposiello

Erin M. Conlon

Background

SoxR and SoxS constitute an intracellular signal response system that rapidly detects changes in superoxide levels and modulates gene expression in E. coli. A time series microarray design was used to identify co-regulated SoxRS-dependent and independent genes modulated by superoxide minutes after exposure to stress.

Methodology/Principal Findings

soxS mRNA levels surged to near maximal levels within the first few minutes of exposure to paraquat, a superoxide-producing compound, followed by a rise in mRNA levels of known SoxS-regulated genes. Based on a new method for determining the biological significance of clustering results, a total of 138 genic regions, including several …

Brooks' Versus Linus' Law: An Empirical Test Of Open Source Projects, Charles M. Schweik, Robert English

National Center for Digital Government

Free/Libre and Open Source Software (FOSS) projects are Internet-based collaborations consisting of volunteers and paid professionals who come together to create computer software...

Reflections Of An Online Geographic Information Systems Course Based On Open Source Software, Charles M. Schweik, Maria Fernandez, Michael P. Hamel, Prakash Kashwan, Quentin Lewis, Alexander Stepanov

National Center for Digital Government

This SSCORE report summarizes our experience offering an online introductory course on Geographic Information Systems that utilizes available free/libre and open source software (FOSS). Two primary objectives were to (1) reach students in developing countries, and (2) to help move forward the development of an “open content” GIS curriculum as part of the “Open Source Geospatial Foundation” (OSGeo.org) educational effort. Course design, key software (QGIS, GRASS, PostGresql/PostGIS) and online delivery methods are described. Results and factors leading to a low course completion rate and discussed. Contributing factors include: (1) a for-credit versus no-credit decision; and (2) technical issues. Recommendations for …

Better Public Services For Growth And Jobs, Jane E. Fountain

National Center for Digital Government

No abstract provided.

Integrated Magnetic Bionanocomposites Through Nanoparticle-Mediated Assembly Of Ferritin, S Srivastava, B Samanta, Bj Jordan, R Hong, Q Xiao, Mt Tuominen, Vm Rotello

Vincent Rotello

Magnetic (FePt) and nonmagnetic (Au) nanoparticles were used to assemble ferritin into near-monodisperse bionanocomposites featuring regular interparticle spacing. The FePt/ferritin assemblies are integrated magnetic materials with ferritin providing added magnetic volume fraction to the magnetic nanocomposite. These assemblies differ from either of their constituent particles in terms of blocking temperature (TB), net magnetic moment, coercivity, and remnance.

Linking Lithology And Land Use To Sources Of Dissolved And Particulate Organic Matter In Headwaters Of A Temperate, Passive-Margin River System, Steven T. Petsch, B. E. Longwortha, P. A. Raymond, J. E. Bauerc

Steven T. Petsch

A number of rivers have been found to transport highly aged organic matter [OM]; however, the sources of this aged material remain a matter of debate. One potential source may be erosion and weathering of headwater lithologies rich in ancient sedimentary OM. In this study, waters, suspended particulates, streambed sediments, rocks and soils from fourteen small headwater watersheds of a mid-size, temperate, passive margin river were sampled and characterized by Δ14C, δ13C, and POC/TPN ratios to identify sources of particulate and dissolved OM delivered to the river mainstem. These headwater sites encompass a range in lithology (OM-rich shales, OM-lean carbonate/mudstone …

Sea Ice Feedback And Cenozoic Evolution Of Antarctic Climate And Ice Sheets, Robert M. Deconto, David Pollard, David Harwood

Robert M DeConto

The extent and thickness of Antarctic sea ice have important climatic effects on radiation balance, energy transfer between the atmosphere and ocean, and moisture availability. This paper explores the role of sea ice and related feedbacks in the Cenozoic evolution of Antarctic climate and ice sheets, using a numerical climate model with explicit, dynamical representations of sea ice and continental ice sheets. In a scenario of decreasing Cenozoic greenhouse gas concentrations, our model initiates continental glaciation before any significant sea ice forms around the continent. Once variable ice sheets are established, seasonal sea ice distribution is highly sensitive to orbital …

America Competes Act, United States

Ethics in Science and Engineering National Clearinghouse

The full text of the America COMPETES Act. See Sec. 7008. Postdoctoral Research Fellows, and Sec. 7009. Responsible Conduct of Research.

Increasing Social Capital For Disaster Response Through Social Networking Services (Sns) In Japanese Local Governments, Alexander Schellong

National Center for Digital Government

Researchers have argued that social networks within a community have positive effects on people’s behavior in the four stages of disaster. The Japanese government is testing Social Networking Service (SNS) at the municipal level with the intention to improve community building, democratic processes and disaster management. This paper presents results from two case studies of local SNS in Yatsushiro city, Kumamoto prefecture and Nagaoka city, Niigata prefecture. While the Yatsushiro’s solution seems to be sustainable, Nagaoka’s SNS is in decline. Both have to compete with popular SNS like Mixi and lack critical mass. Based on the reviewed literature I discuss …

Biomimetic Interactions Of Proteins With Functionalized Nanoparticies: A Thermodynamic Study, M De, Cc You, S Srivastava, Vm Rotello

Vincent Rotello

Gold nanoparticles (NPs) functionalized with L-amino acid-terminated monolayers provide an effective platform for the recognition of protein surfaces. Isothermal titration calorimetry (ITC) was used to quantify the binding thermodynamics of these functional NPs with alpha-chymotrypsin (ChT), histone, and cytochrome c (CytC). The enthalpy and entropy changes for the complex formation depend upon the nanoparticle structure and the surface characteristics of the proteins, e.g., distributions of charged and hydrophobic residues on the surface. Enthalpy-entropy compensation studies on these NP-protein systems indicate an excellent linear correlation between DeltaH and TDeltaS with a slope (alpha) of 1.07 and an intercept (TDeltaS0) of 35.2 …

A Liquid Xenon Ionization Chamber In An All-Fluoropolymer Vessel, F. Leport, Andrea Pocar, L. Bartoszek, R. Devoe, P. Fierlinger, B. Flatt, G. Gratta, M. Green, T. Koffas, M. Montero Diez, R. Neilson, K. O'Sullivan, S. Waldman, J. Wodin, D. Woisard, E. Baussan, M. Breidenbach, R. Conley, W. Fairbank Jr., J. Farine, C. Hall, K. Hall, D. Hallman, C. Hargrove, J. Hodgson, S. Jeng, D. S. Leonard, D. Mackay, Y. Martin, A. Odian, L. Ounalli, A. Piepke, C. Y. Prescott, P. C. Rowson, K. Skarpaas, D. Schenker, D. Sinclair, V. Stekhanov, V. Strickland, C. Virtue, J.-L. Vuilleumier, K. Wamba, P. Weber

Andrea Pocar

A novel technique has been developed to build vessels for liquid xenon ionization detectors entirely out of an ultra-clean fluoropolymer. One such detector was operated inside a welded, He leak tight, all-fluoropolymer chamber. The measured energy resolution for 570 keV gamma rays is σ/E=5.1% at a drift field of 1.5 kV/cm, in line with the best values obtained for ionization only detectors run in LXe using conventional, metal vessels.

Array-Based Sensing Of Proteins Using Conjugated Polymers, Or Miranda, Cc You, R Phillips, Ib Kim, Ps Ghosh, Uhf Bunz, Vm Rotello

Vincent Rotello

A sensor array comprising six functionalized poly(p-phenyleneethynylene) polymers was constructed and used to detect and identify protein analytes. The presence of proteins alters the fluorescence properties of the polymers, generating a distinct fluorescence response pattern for a given protein. Linear discriminant analyses accurately differentiate the patterns of 17 proteins at nano- to micromolar concentrations. An identification accuracy of 97% was obtained on the basis of the tests with 68 unknown protein samples from the training set.

Salinity Constraints On Subsurface Archaeal Diversity And Methanogenesis In Sedimentary Rock Rich In Organic Matter, Steven T. Petsch, P. Waldron, A. M. Martini, K. Nüsslein

Steven T. Petsch

The diversity of microorganisms active within sedimentary rocks provides important controls on the geochemistry of many subsurface environments. In particular, biodegradation of organic matter in sedimentary rocks contributes to the biogeochemical cycling of carbon and other elements and strongly impacts the recovery and quality of fossil fuel resources. In this study, archaeal diversity was investigated along a salinity gradient spanning 8 to 3,490 mM Cl− in a subsurface shale rich in CH4 derived from biodegradation of sedimentary hydrocarbons. Shale pore waters collected from wells in the main CH4-producing zone lacked electron acceptors such as O2, NO3−, Fe3+, or SO42−. Acetate …

Mesophase Separation And Probe Dynamics In Protein–Polyelectrolyte Coacervates, A. Basak Kayitmazer, Himadri B. Bohidar, Kevin W. Mattison, Arijit Bose, Jayashri Sarkar, Akihito Hashidzume, Paul S. Russo, Werner Jaeger, Paul Dubin

Paul Dubin

Protein–polyelectrolyte coacervates are self-assembling macroscopically monophasic biomacromolecular fluids whose unique properties arise from transient heterogeneities. The structures of coacervates formed at different conditions of pH and ionic strength from poly(dimethyldiallylammonium chloride) and bovine serum albumin (BSA), were probed using fluorescence recovery after photobleaching. Measurements of self-diffusion in coacervates were carried out using fluorescein-tagged BSA, and similarly tagged Ficoll, a non-interacting branched polysaccharide with the same size as BSA. The results are best explained by temporal and spatial heterogeneities, also inferred from static light scattering and cryo-TEM, which indicate heterogeneous scattering centers of several hundred nm. Taken together with previous dynamic …

Open-Source Collaboration In The Public Sector: The Need For Leadership And Value, Michael P. Hamel

National Center for Digital Government

From executive summary: The “open-source” movement in information technology is largely based on the innovative licensing schemes that encourage collaboration and sharing and promise reduced cost of ownership, customizable software and the ability to extract data in a usable format. Government organizations are becoming increasingly intolerant of the forced migrations (upgrades) and closed data standards (or incompatible data standards) that typically come with the use of proprietary software. To combat the problems of interoperability and cost, governments around the globe are beginning to consider, and in some cases, even require the use of open-source software (Hahn, 2002; Wong, 2004).

Implications Of D0- ¯D0 Mixing For New Physics, Eugene Golowich, Joanne Hewett, Sandip Pakvasa, Alexey A. Petrov

Eugene Golowich

We provide a comprehensive, up-to-date analysis of possible New Physics contributions to the mass difference ∆M_D in D^0- D ̅^0 mixing. We consider the most general low energy effective Hamiltonian and include leading order QCD running of effective operators. We then explore an extensive list of possible New Physics models that can generate these operators, which we organize as including Extra Fermions, Extra Gauge Bosons, Extra Scalars, Extra Space Dimensions and Extra Symmetries. For each model we place restrictions on the allowed parameter space using the recent evidence for observation of D meson mixing. In many scenarios, we find strong …

A Role For Huntingtin In Dynein/Dynactin-Mediated Vesicle Trafficking, Jennifer Ross, Juliane P. Caviston, Sheila M. Antony, Mariko Tokito, Erika L.F Holzbaur

Jennifer Ross

Cytoplasmic dynein is a multisubunit microtubule motor complex that, together with its activator, dynactin, drives vesicular cargo toward the minus ends of microtubules. Huntingtin (Htt) is a vesicle-associated protein found in both neuronal and nonneuronal cells that is thought to be involved in vesicular transport. In this study, we demonstrate through yeast two-hybrid and affinity chromatography assays that Htt and dynein intermediate chain interact directly; endogenous Htt and dynein coimmunoprecipitate from mouse brain cytosol. Htt RNAi in HeLa cells results in Golgi disruption, similar to the effects of compromising dynein/dynactin function. In vitro studies reveal that Htt and dynein are …

Exterminator: Automatically Correcting Memory Errors With High Probability, Gene Novark

Computer Science Department Faculty Publication Series

Programs written in C and C++ are susceptible to memory errors, including buffer overflows and dangling pointers. These errors, which can lead to crashes, erroneous execution, and security vulnerabilities, are notoriously costly to repair. Tracking down their location in the source code is difficult, even when the full memory state of the program is available. Once the errors are finally found, fixing them remains challenging: even for critical security-sensitive bugs, the average time between initial reports and the issuance of a patch is nearly one month. We present Exterminator, a system that automatically corrects heap-based memory errors without programmer intervention. …

On The Parameterization Dependence Of The Energy Momentum Tensor And The Metric, N. E. J. Bjerrum-Bohr, John Donoghue, Barry R. Holstein

John Donoghue

We use results by Kirilin to show that in general relativity the nonleading terms in the energy-momentum tensor of a particle depends on the parameterization of the gravitational field. While the classical metric that is calculated from this source, used to define the leading long-distance corrections to the metric, also has a parameteriztion dependence, it can be removed by a coordinate change. Thus the classical observables are parameterization independent. The quantum effects that emerge within the same calculation of the metric also depend on the parameterization and a full quantum calculation requires the inclusion of further diagrams. However, within a …

Utilizing A Multi-Technique, Multi-Taxa Approach To Monitoring Wildlife Passageways On The Bennington Bypass In Southern Vermont, Mark A. Bellis, Scott D. Jackson, Curtis R. Griffin, Paige S. Warren, Alan O. Thompson

Scott D. Jackson

Roadways affect wildlife habitat disproportionate to the area of land they occupy while impacting wildlife directly through direct loss of habitat, road mortality and disruption of movement. Roadways indirectly impact wildlife by isolating populations and disrupting gene flow and metapopulation dynamics. A variety of strategies have been used with mixed success to mitigate the impacts of transportation systems on wildlife. Underpasses are commonly used to facilitate movement of wildlife across roadways in Europe, Australia, Canada and the U.S. Through 2005, 460 terrestrial and 300 aquatic crossing structures have been identified throughout the United States but only a small portion of …

Peptide Ligation Catalyzed By Functionalized Gold Nanoparticles, Y Fillon, A Verma, P Ghosh, D Ernenwein, Vm Rotello, J Chmielewski

Vincent Rotello

Trimethylammonium functionalized gold nanoparticles are demonstrated as templates for the assembly of peptide fragments and their subsequently promoted ligation. This system displays the use of organically tailored nanoparticles as effective supramolecular reagents for catalyzing bond-forming reactions and may also serve as a model for prebiotic conditions where charged surfaces may have promoted the polymerization of the early biopolymers.

Probing The Solvent-Induced Tautomerism Of A Redox-Active Ureidopyrimidinone, Am Alexander, M Bria, G Brunklaus, S Caldwell, G Cooke, Jf Garety, Sg Hewage, Y Hocquel, N Mcdonald, G Rabani, G Rosair, Bo Smith, Hw Spiess, Vm Rotello, P Woisel

Vincent Rotello

Trimethylammonium functionalized gold nanoparticles are demonstrated as templates for the assembly of peptide fragments and their subsequently promoted ligation. This system displays the use of organically tailored nanoparticles as effective supramolecular reagents for catalyzing bond-forming reactions and may also serve as a model for prebiotic conditions where charged surfaces may have promoted the polymerization of the early biopolymers.

Ethics Across The Curriculum Modules For Eac Toolkit Workshops, William J. Frey, Jose A. Cruz-Cruz

Ethics in Science and Engineering National Clearinghouse

This collection of modules has been designed to show how the Ethics Across the Curriculum Toolkit project provides for the preparation and pairing of student and instructor modules. These modules have been brought together and paired to aid in Toolkit demonstrations designed for faculty developement workshops in ethics across the curriculum.

Abstract by author.

Soft Spheres Make More Mesophases, Mattew A. Glaser, Gregory M. Granson, Randall D. Kamien, A. Kosmrlj, Christian Santangelo, P. Ziherl

Christian Santangelo

We use both mean-field methods and numerical simulation to study the phase diagram of classical particles interacting with a hard core and repulsive, soft shoulder. Despite the purely repulsive and isotropic interaction, this system displays a remarkable array of aggregate phases arising from the competition between the hard-core and soft-shoulder length scales, including fluid and crystalline phases with micellar, lamellar, and inverse micellar morphology. In the limit of large shoulder width to core size, we argue that this phase diagram has a number of universal features, and classify the set of repulsive shoulders that lead to aggregation at high density. …

Coarse-Graining Schemes And A Posteriori Error Estimates For Stochastic Lattice Systems, Ma Katsoulakis, P Plechac, L Rey-Bellet, Dk Tsagkarogiannis

Luc Rey-Bellet

The primary objective of this work is to develop coarse-graining schemes for stochastic many-body microscopic models and quantify their effectiveness in terms of a priori and a posteriori error analysis. In this paper we focus on stochastic lattice systems of interacting particles at equilibrium. The proposed algorithms are derived from an initial coarse-grained approximation that is directly computable by Monte Carlo simulations, and the corresponding numerical error is calculated using the specific relative entropy between the exact and approximate coarse-grained equilibrium measures. Subsequently we carry out a cluster expansion around this first – and often inadequate – approximation and obtain …

Ethics Bowl Competition As Capstone Activity For Practical And Professional Ethics Classes, William J. Frey, Jose A. Cruz-Cruz

Ethics in Science and Engineering National Clearinghouse

In Connexions, a course is both a course (what is offered in a school curriculum) and a collection of modules. This course as a collection of modules has been designed to pull together the modules published in Connexions by this author for the purpose of showing different aspects of the Ethics Bowl competition and how it can be used in a university course on practical and professional ethics. The Ethics Bowl concept comes from Robert Ladenson of the Illinois Institute of Technology. Through the Association of Practical and Professional Ethics, the Ethics Bowl competition has been carried out nationally for …

Dynamic Reorganization Of Eg5 In The Mammalian Spindle Throughout Mitosis Requires Dynein And Tpx2, Jennifer Ross, C. Fagerstrom, G. Yang, E. S. Collins, N. Ma, N. P. Ferenz, S. Balchand, P. Wadsworth, J. Titus, M. Qiu, A. Gabel

Jennifer Ross

Kinesin-5 is an essential mitotic motor. However, how its spatial-temporal distribution is regulated in mitosis remains poorly understood. We expressed localization and affinity purification-tagged Eg5 from a mouse bacterial artificial chromosome (this construct was called mEg5) and found its distribution to be tightly regulated throughout mitosis. Fluorescence recovery after photobleaching analysis showed rapid Eg5 turnover throughout mitosis, which cannot be accounted for by microtubule turnover. Total internal reflection fluorescence microscopy and high-resolution, single-particle tracking revealed that mEg5 punctae on both astral and midzone microtubules rapidly bind and unbind. mEg5 punctae on midzone microtubules moved transiently both toward and away from …

Using Case Studies In Teaching Research Ethics, Kenneth D. Pimple

Ethics in Science and Engineering National Clearinghouse

No abstract provided.

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

Erin M. Conlon

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 …