Physical Sciences and Mathematics Commons^™

Structure Of Fully Hydrated Fluid Phase Lipid Bilayers With Monounsaturated Chains., Norbert Kucerka, Stephanie Tristram-Nagle, John Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

Quantitative structures are obtained at 30 degrees C for the fully hydrated fluid phases of palmitoyloleoylphosphatidylcholine (POPC), with a double bond on the sn-2 hydrocarbon chain, and for dierucoylphosphatidylcholine (di22:1PC), with a double bond on each hydrocarbon chain. The form factors F(qz) for both lipids are obtained using a combination of three methods. (1) Volumetric measurements provide F(0). (2) X-ray scattering from extruded unilamellar vesicles provides /F(qz)/ for low q(z). (3) Diffuse X-ray scattering from oriented stacks of bilayers provides /F(qz)/ for high q(z). Also, data using method (2) are added to our recent data for dioleoylphosphatidylcholine (DOPC) using methods …

Polymorphism In Myristoylpalmitoylphosphatidylcholine., Stephanie Tristram-Nagle, Yisrael Isaacson, Yulia Lyatskaya, Yufeng Liu, Kay Brummond, John Katsaras, John Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

This study focuses on the mixed-chain lipid myristoylpalmitoylphosphatidylcholine (MPPC) near full hydration. The lipid, synthesized according to the procedure of (Mason et al., 1981a, has a low degree of acyl chain migration. When MPPC is temperature-jumped (T-jumped) from the L alpha phase (T = 38 degrees C) to T = 20 degrees C or below, a subgel phase forms; this formation takes less than 1 h at a temperature below T = 12 degrees C. The subgel remains stable up to T = 29 degrees C. When MPPC is T-jumped from the L alpha phase to T = 24 degrees …

Polyunsaturated Docosahexaenoic Vs Docosapentaenoic Acid-Differences In Lipid Matrix Properties From The Loss Of One Double Bond., Nadukkudy Eldho, Scott Feller, Stephanie Tristram-Nagle, Ivan Polozov, Klaus Gawrisch

Prof. Stephanie Tristram-Nagle Ph.D.

Insufficient supply to the developing brain of docosahexaenoic acid (22:6n3, DHA), or its omega-3 fatty acid precursors, results in replacement of DHA with docosapentaenoic acid (22:5n6, DPA), an omega-6 fatty acid that is lacking a double bond near the chain's methyl end. We investigated membranes of 1-stearoyl(d(35))-2-docosahexaenoyl-sn-glycero-3-phosphocholine and 1-stearoyl(d(35))-2-docosapentaenoyl-sn-glycero-3-phosphocholine by solid-state NMR, X-ray diffraction, and molecular dynamics simulations to determine if the loss of this double bond alters membrane physical properties. The low order parameters of polyunsaturated chains and the NMR relaxation data indicate that both DHA and DPA undergo rapid conformational transitions with correlation times of the order of …

Characterization Of A Recently Purified Thermophilic Dnase From A Novel Thermophilic Fungus, Kyle Landry, Robert Levin

Kyle S Landry

Personalizing Software Development Practice Using Mastery-Based Coaching, Chris Boesch, Sandra Boesch

Chris BOESCH

The authors previously developed a system to facilitate the self-directed learning and practicing of software languages in Singapore. One of the goals of this self-directed learning was to enable the development of student mentors who would then be able to assist other students during classroom sessions. Building on this work, the authors extended the platform to support personalized coaching with the goals of further enabling and preparing students to mentor their peers. This paper covers the challenges, insights, and features that were developed in order to develop and deploy this mastery-based coaching feature.

Middle Paleozoic Sequence Stratigraphy And Paleontology Of The Cincinnati Arch: Part 2 Northern Kentucky And Se Indiana, Carlton Brett, Benjamin Dattilo, Patrick Mclaughlin, Thomas Schramm, James Thomka, Bradley Cramer

Benjamin F. Dattilo

No abstract provided.

The Orientation Of Strophomenid Brachiopods On Soft Substrates, Roy Plotnick, Benjamin Dattilo, Daniel Piquard, Jennifer Bauer, Joshua Corrie

Benjamin F. Dattilo

Strophomenid brachiopods have long been interpreted as ‘‘snowshoe’’ strategists, with their flattened concavoconvex valves providing resistance to foundering in very soft sediments. There has been a sharp difference of opinion in whether the shells were oriented with their convex or their concave surface in contact with the sediment. This study, along with independent evidence from sedimentology, ichnology, and morphology, indicates that the strophomenids lived with their shells concave down (convex up). Experiments indicate the force required to push shells into soft cohesive muds is much greater for the convex up than for the convex down orientation. Forces also increase with …

Upper Ordovician Strata Of Southern Ohio-Indiana: Shales, Shell Beds, Storms, Sediment Starvation, And Cycles, Carlton Brett, Thomas Schramm, Benjamin Dattilo, Nathan Marshall

Benjamin F. Dattilo

The Cincinnatian Series (ca. 450 to 442 Ma) of the Cincinnati Arch features some of the most spectacular Ordovician fossils in the world. The rich faunas of bryozoans, brachiopods, molluscs, echinoderms, and trilobites are preserved as discrete shell-rich limestones, cyclically interbedded with sparsely fossiliferous shales and mudstones that may yield exceptionally preserved trilobites and crinoids. Similar successions of shell beds interbedded with mudstones are common components of Paleozoic successions. In such successions, the genesis of the highly concentrated shell beds is often attributed to storm-winnowing, but is this the whole story? This trip will offer an overview of the classic …

The Pitman Inequality For Exchangeable Random Vectors, J. Behboodian, Naveen Bansal, Gholamhossein Hamedani, Hans Volkmer

Naveen Bansal

In this short article the following inequality called the “Pitman inequality” is proved for the exchangeable random vector (X₁,X₂,…,X_n)(X1,X2,…,Xn) without the assumption of continuity and symmetry for each component X_iXi:

P(|1n∑i=1nXi|≤|∑i=1nαiXi|)≥12 ,

where allαi≥0 are special weights with∑i=1nαi=1.

A Comparative Analysis Of Decision Trees Vis-À-Vis Other Computational Data Mining Techniques In Automotive Insurance Fraud Detection, Adrian Gepp, Kuldeep Kumar, J Holton Wilson, Sukanto Bhattacharya

Kuldeep Kumar

No abstract provided.

Randomized Detection Of Extraneous Factors, Manfred Minimair

Manfred Minimair

A projection operator of a system of parametric polynomials is a polynomial in the coefficients of the system that vanishes if the system has a common root. The projection operator is a multiple of the resultant of the system, and the factors of the projection operator that are not contained in the resultant are called extraneous factors. The main contribution of this work is to provide a randomized algorithm to check whether a factor is extraneous, which is an important task in applications. A lower bound for the success probability is determined which can be set arbitrarily close to one. …

As-Trust: A Trust Quantification Scheme For Autonomous Systems In Bgp, Jian Chang, Krishna Venkatasubramanian, Andrew West, Sampath Kannan, Boon Thau Loo, Oleg Sokolsky, Insup Lee

Oleg Sokolsky

The Border Gateway Protocol (BGP) works by frequently exchanging updates that disseminate reachability information about IP prefixes (i.e., IP address blocks) between Autonomous Systems (ASes) on the Internet. The ideal operation of BGP relies on three major behavioral assumptions (BAs): (1) information contained in the update is legal and correct, (2) a route to a prefix is stable, and (3) the route adheres to the valley free routing policy. The current operation of BGP implicitly trusts all ASes to adhere to these assumptions. However, several documented violation of these assumptions attest to the fact that such an assumption of trust …

The Medical Device Dongle: An Open-Source Standards-Based Platform For Interoperable Medical Device Connectivity, Philip Asare, Danyang Cong, Santosh Vattam, Baekgyu Kim, Andrew King, Oleg Sokolsky, Insup Lee, Shan Lin, Margaret Mullen-Fortino

Oleg Sokolsky

Emerging medical applications require device coordination, increasing the need to connect devices in an interoperable manner. However, many of the existing health devices in use were not originally developed for network connectivity and those devices with networking capabilities either use proprietary protocols or implementations of standard protocols that are unavailable to the end user. The first set of devices are unsuitable for device coordination applications and the second set are unsuitable for research in medical device interoperability. We propose the Medical Device Dongle (MDD), a low-cost, open-source platform that addresses both issues.

As-Cred: Reputation And Alert Service For Inter-Domain Routing, Jian Chang, Krishna Venkatasubramanian, Andrew West, Sampath Kannan, Insup Lee, Boon Thau Loo, Oleg Sokolsky

Oleg Sokolsky

Being the backbone routing system of the Internet, the operational aspect of the inter-domain routing is highly complex. Building a trustworthy ecosystem for inter-domain routing requires the proper maintenance of trust relationships among tens of thousands of peer IP domains called Autonomous Systems (ASes). ASes today implicitly trust any routing information received from other ASes as part of the Border Gateway Protocol (BGP) updates. Such blind trust is problematic given the dramatic rise in the number of anomalous updates being disseminated, which pose grave security consequences for the inter-domain routing operation. In this paper, we present ASCRED, an AS reputation …

Link Spamming Wikipedia For Profit, Andrew West, Jian Chang, Krishna Venkatasubramanian, Oleg Sokolsky, Insup Lee

Oleg Sokolsky

Collaborative functionality is an increasingly prevalent web technology. To encourage participation, these systems usually have low barriers-to-entry and permissive privileges. Unsurprisingly, ill-intentioned users try to leverage these characteristics for nefarious purposes. In this work, a particular abuse is examined -- link spamming -- the addition of promotional or otherwise inappropriate hyperlinks.

Our analysis focuses on the "wiki" model and the collaborative encyclopedia, Wikipedia, in particular. A principal goal of spammers is to maximize *exposure*, the quantity of people who view a link. Creating and analyzing the first Wikipedia link spam corpus, we find that existing spam strategies perform quite poorly …

Implementation Of Standard Testbeds For Numerical Relativity, Maria Babiuc-Hamilton, Sascha Husa, Daniela Alic, Ian Hinder, Christiane Lechner, Erik Schnetter, Yosef Zlochower, Nils Dorband, Jeffrey Winicour, D. Pollney, B´Ela Szilagyi

Maria Babiuc-Hamilton

We discuss results that have been obtained from the implementation of the initial round of testbeds for numerical relativity which was proposed in the first paper of the Apples with Apples Alliance. We present benchmark results for various codes which provide templates for analyzing the testbeds and to draw conclusions about various features of the codes. This allows us to sharpen the initial test specifications, design a new test and add theoretical insight.

Some Mathematical Problems In Numerical Relativity, Maria Babiuc-Hamilton, B´Ela Szilagyi, Jeffrey Winicour

Maria Babiuc-Hamilton

The main goal of numerical relativity is the long time simulation of highly nonlinear spacetimes that cannot be treated by perturbation theory. This involves analytic, computational and physical issues. At present, the major impasses to achieving global simulations of physical usefulness are of an analytic/ computational nature. We present here some examples of how analytic insight can lend useful guidance for the improvement of numerical approaches.

Binary Black Hole Waveform Extraction At Null Infinity, Maria Babiuc-Hamilton, Jeffrey Winicour, Yosef Zlochower

Maria Babiuc-Hamilton

In this paper, we present a work in progress toward an efficient and economical computational module which interfaces between Cauchy and characteristic evolution codes. Our goal is to provide a standardized waveform extraction tool for the numerical relativity community which will allow CCE to be readily applied to a generic Cauchy code. The tool provides a means of unambiguous comparison between the waveforms generated by evolution codes based upon different formulations of the Einstein equations and different numerical approximation.

Gravitational Wave Extraction Based On Cauchy–Characteristic Extraction And Characteristic Evolution, Maria Babiuc-Hamilton, Yosef Zlochower, Béla Szilágyi, Ian Hawke

Maria Babiuc-Hamilton

We implement a code to find the gravitational news at future null infinity by using data from a Cauchy code as boundary data for a characteristic code. This technique of Cauchy–characteristic extraction (CCE) allows for the unambiguous extraction of gravitational waves from numerical simulations. We first test the technique on non-radiative spacetimes: Minkowski spacetime, perturbations of Minkowski spacetime and static black hole spacetimes in various gauges. We show the convergence and limitations of the algorithm and illustrate its success in cases where other wave extraction methods fail. We further apply our techniques to a standard radiative test case for wave …

Testing Numerical Evolution With The Shifted Gauge Wave, Maria Babiuc-Hamilton, Jeffrey Winicour, B´Ela Szilágyi

Maria Babiuc-Hamilton

Computational methods are essential to provide waveforms from coalescing black holes, which are expected to produce strong signals for the gravitational wave observatories being developed. Although partial simulations of the coalescence have been reported, scientifically useful waveforms have so far not been delivered. The goal of the AppleswithApples (AwA) Alliance is to design, coordinate and document standardized code tests for comparing numerical relativity codes. The first round of AwA tests has now been completed and the results are being analyzed. These initial tests are based upon the periodic boundary conditions designed to isolate performance of the main evolution code. Here …

Finite Difference Schemes For Second Order Systems Describing Black Holes, Mohammad Motamed, Maria Babiuc-Hamilton, B. Szilágyi, H-O. Kreiss, J. Winicour

Maria Babiuc-Hamilton

In the harmonic description of general relativity, the principal part of Einstein’s equations reduces to 10 curved space wave equations for the components of the space-time metric. We present theorems regarding the stability of several evolution-boundary algorithms for such equations when treated in second order differential form. The theorems apply to a model black hole space-time consisting of a spacelike inner boundary excising the singularity, a timelike outer boundary and a horizon in between. These algorithms are implemented as stable, convergent numerical codes and their performance is compared in a 2-dimensional excision problem.

Transport Properties Of The La1−Xcaxmno3 (0.5 ≤ X < 1), H. Zhou, R. Zheng, G. Li, S. Feng, Xiaojuan Fan, X. Lia

Xiaojuan Fan

The transport properties of the La1−xCaxMnO3 (0.5 ≤ x < 1) system in magnetic fields up to 14 T were studied. We found that the relationship between the charge ordering temperature TCO and Mn4+ content nMn4+ obeys the formula TCO/Tmax = 1−a(nMn4+ −n0)2, here n0 and a are constants and Tmax is the maximum of TCO. For x = 0.65, TCO arrives at the maximum value of 249.5 K in zero magnetic field, while the charge ordered (CO) state is most stable around x = 0.75. For x = 0.5 when H < 6 T the resistivity displays Mott’s variable-range hopping (VRH) behavior, when 6 < H < 12 T it is suggested that two kinds of conduction mechanism, i.e., VRH and magnetic polarons, coexist in the material, and when H > 12 T the resistivity shows metallic-like behavior and the transport mechanism is attributed to coexistence of magnetic polarons and free carriers. For x = 0.95, the conduction mechanism accords with the coexistence of VRH and magnetic polarons.

The Jahn–Teller Effect And Electron–Phonon Interaction In La0.25ca0.75mn1−Xcrxo3, H. Zhou, G. Li, H. Chen, R. Zheng, Xiaojuan Fan, X. Li

Xiaojuan Fan

The ultrasonic (longitudinal and transverse) velocities and the transport and magnetic properties of polycrystalline La0.25Ca0.75Mn1-xCrxO3 (x = 0, 0.03, 0.05, and 0.07) have been studied systematically. It was found that with increasing Cr content, the resistivity increases, the charge-ordering transition temperature TCO shifts to low temperature, and the magnetic moment of the system is strengthened. From the temperature dependence of the ultrasonic velocities, one can establish that the Jahn-Teller energy and phonon exchange constant decrease with increasing Cr content.

From Question Context To Answer Credibility: Modeling Semantic Structures For Question Answering Using Statistical Methods, Protima Banerjee, Hyoil Han

Hyoil Han

Within a Question Answering (QA) framework, Question Context plays a vital role. We define Question Context to be background knowledge that can be used to represent the user’s information need more completely than the terms in the query alone. This paper proposes a novel approach that uses statistical language modeling techniques to develop a semantic Question Context which we then incorporate into the Information Retrieval (IR) stage of QA. Our approach proposes an Aspect-Based Relevance Language Model as basis of the Question Context Model. This model proposes that the sparse vocabulary of a query can be supplemented with semantic information …

A Computationally Efficient System For High-Performance Multi-Document Summarization, Sean Sovine, Hyoil Han

Hyoil Han

We propose and develop a simple and efficient algorithm for generating extractive multi-document summaries and show that this algorithm exhibits state-of-the-art or near state-of-the-art performance on two Document Understanding Conference datasets and two Text Analysis Conference datasets. Our results show that algorithms using simple features and computationally efficient methods are competitive with much more complex methods for multi-document summarization (MDS). Given these findings, we believe that our summarization algorithm can be used as a baseline in future MDS evaluations. Further, evidence shows that our system is near the upper limit of performance for extractive MDS.

Language Modeling Approaches To Information Retrieval, Protima Banerjee, Hyoil Han

Hyoil Han

This article surveys recent research in the area of language modeling (sometimes called statistical language modeling) approaches to information retrieval. Language modeling is a formal probabilistic retrieval framework with roots in speech recognition and natural language processing. The underlying assumption of language modeling is that human language generation is a random process; the goal is to model that process via a generative statistical model. In this article, we discuss current research in the application of language modeling to information retrieval, the role of semantics in the language modeling framework, cluster-based language models, use of language modeling for XML retrieval and …

An Integrated Systems Approach To Deconstructing Glycosylation, L. Mahal, John Rakus, Kanoelani Pilobello, P. Agrawal

John F. Rakus

Glycosylation involves the post-translational addition of carbohydrates to protein molecules and is an intricate and indispensable biochemical process. Study of this complicated network of interactions is hindered by the lack of a coding template analogous to the genetic code, and by the vast structural complexity inherent to carbohydrate polymers. We use lectins (non-enzymatic carbohydrate-binding proteins of non-immunological origin) as microarray probes to identify carbohydrate features expressed on cellular surfaces. Specifically, we utilized lectin microarray technology to investigate the differences in carbohydrates expressed by the cell lines of the Nation Cancer Institute’s NCI-60 panel. Our investigation identified tissue-specific expression differences in …

Crystal Structure And Functional Assignment Of Yfau, A Metal Ion Dependent Class Ii Aldolase From Escherichia Coli K12, Dean Rea, Rebecca Hovington, John Rakus, John Gerlt, Vilmos Fu¨Lo¨P, Timothy Bugg, David Roper

John F. Rakus

One of the major challenges in the postgenomic era is the functional assignment of proteins using sequence- and structure-based predictive methods coupled with experimental validation. We have used these approaches to investigate the structure and function of theEscherichia coli K-12 protein YfaU, annotated as a putative 4-hydroxy-2-ketoheptane-1,7-dioate aldolase (HpcH) in the sequence databases. HpcH is the final enzyme in the degradation pathway of the aromatic compound homoprotocatechuate. We have determined the crystal structure of apo-YfaU and the Mg2+−pyruvate product complex. Despite greater sequence and structural similarity to HpcH, genomic context suggests YfaU is instead a 2-keto-3-deoxy sugar aldolase like the …

Will Fault Localization Work For These Failures? An Automated Approach To Predict Effectiveness Of Fault Localization Tools, Tien-Duy B. Le, David Lo

David LO

Debugging is a crucial yet expensive activity to improve the reliability of software systems. To reduce debugging cost, various fault localization tools have been proposed. A spectrum-based fault localization tool often outputs an ordered list of program elements sorted based on their likelihood to be the root cause of a set of failures (i.e., their suspiciousness scores). Despite the many studies on fault localization, unfortunately, however, for many bugs, the root causes are often low in the ordered list. This potentially causes developers to distrust fault localization tools. Recently, Parnin and Orso highlight in their user study that many debuggers …

Drone: Predicting Priority Of Reported Bugs By Multi-Factor Analysis, Yuan Tian, David Lo, Chengnian Sun

David LO

Bugs are prevalent. To improve software quality, developers often allow users to report bugs that they found using a bug tracking system such as Bugzilla. Users would specify among other things, a description of the bug, the component that is affected by the bug, and the severity of the bug. Based on this information, bug triagers would then assign a priority level to the reported bug. As resources are limited, bug reports would be investigated based on their priority levels. This priority assignment process however is a manual one. Could we do better? In this paper, we propose an automated …