Physical Sciences and Mathematics Commons^™

Program Transformations For Information Personalization, Saverio Perugini

Saverio Perugini

Personalization constitutes the mechanisms and technologies necessary to customize information access to the end-user. It can be defined as the automatic adjustment of information content, structure, and presentation. The central thesis of this dissertation is that modeling interaction explicitly in a representation, and studying how partial information can be harnessed in it by program transformations to direct the flow of the interaction, can provide insight into, reveal opportunities for, and define a model for personalized interaction. To evaluate this thesis, a formal modeling methodology is developed for personalizing interactions with information systems, especially hierarchical hypermedia, based on program transformations. The …

A Generative Programming Approach To Interactive Information Retrieval: Insights And Experiences, Saverio Perugini, Naren Ramakrishnan

Saverio Perugini

We describe the application of generative programming to a problem in interactive information retrieval. The particular interactive information retrieval problem we study is the support for "out-of-turn interaction" with a website – how a user can communicate input to a website when the site is not soliciting such information on the current page, but will do so on a subsequent page. Our solution approach makes generous use of program transformations (partial evaluation, currying, and slicing) to delay the site’s current solicitation for input until after the user’s out-of-turn input is processed. We illustrate how studying out-of-turn interaction through a generative …

Realtime Query Expansion And Procedural Interfaces For Information Hierarchies, Saverio Perugini

Saverio Perugini

We demonstrate the use of two user interfaces for interacting with web hierarchies. One uses the dependencies underlying a hierarchy to perform real-time query expansion and, in this way, acts as an in situ feedback mechanism. The other enables the user to cascade the output from one interaction to the input of another, and so on, and, in this way, supports procedural information-seeking tasks without disrupting the flow of interaction.

Personalization By Program Slicing, Saverio Perugini, Naren Ramakrishnan

Saverio Perugini

Personalization involves customizing information access to the end-user. As any new area of computer science research it lacks formal models to guide the design of systems. In this paper, we present a modeling methodology, based on generative programming, for personalizing interactions with hierarchical websites. The methodology entails modeling a user’s interaction with a site in a program and applying program slicing to personalize the interaction. While preserving interactivity, this approach does not require the designer to anticipate all possible user interactions a priori and provide interfaces for each. Moreover, it provides a theoretical, systematic, and implementation-neutral way to design systems …

The Good, Bad And The Indifferent: Explorations In Recommender System Health, Benjamin J. Keller, Sun-Mi Kim, N. Srinivas Vemuri, Naren Ramakrishnan, Saverio Perugini

Saverio Perugini

Our work is based on the premise that analysis of the connections exploited by a recommender algorithm can provide insight into the algorithm that could be useful to predict its performance in a fielded system. We use the jumping connections model defined by Mirza et al. [6], which describes the recommendation process in terms of graphs. Here we discuss our work that has come out of trying to understand algorithm behavior in terms of these graphs. We start by describing a natural extension of the jumping connections model of Mirza et al., and then discuss observations that have come from …

Personalization By Website Transformation: Theory And Practice, Saverio Perugini

Saverio Perugini

We present an analysis of a progressive series of out-of-turn transformations on a hierarchical website to personalize a user’s interaction with the site. We formalize the transformation in graph-theoretic terms and describe a toolkit we built that enumerates all of the traversals enabled by every possible complete series of these transformations in any site and computes a variety of metrics while simulating each traversal therein to qualify the relationship between a site’s structure and the cumulative effect of support for the transformation in a site. We employed this toolkit in two websites. The results indicate that the transformation enables users …

Staging Transformations For Multimodal Web Interaction Management, Michael Narayan, Christopher Williams, Saverio Perugini, Naren Ramakrishnan

Saverio Perugini

Multimodal interfaces are becoming increasingly ubiquitous with the advent of mobile devices, accessibility considerations, and novel software technologies that combine diverse interaction media. In addition to improving access and delivery capabilities, such interfaces enable flexible and personalized dialogs with websites, much like a conversation between humans. In this paper, we present a software framework for multimodal web interaction management that supports mixed-initiative dialogs between users and websites. A mixed-initiative dialog is one where the user and the website take turns changing the flow of interaction. The framework supports the functional specification and realization of such dialogs using staging transformations – …

Developing Professional Skills In Stem Students: Data Information Literacy, Lisa Zilinski, Megan R. Sapp Nelson, Amy S. Van Epps

Lisa Zilinski

Undergraduate STEM students are increasingly expected to have some data use skills upon graduation, whether they pursue post-graduate education or move into industry. This project was an initial foray into the application of data information literacy competencies to training undergraduate students to identify markers of data and information quality. The data consumer training appeared within two courses to help students evaluate data objects, including databases and datasets available on the Internet. The application of the Data Credibility Checklist provides a foundation for developing data reuse competencies. Based upon the initial presentation of the content, it became obvious that students need …

Modeling The Progress And Retention Of International Students Using Markov Chains, Lucas Gagne

Lucas Gagne

Analyst A: Alternatives In Analysis Of The Utexas1 Surface Wave Dataset, Paul Michaels

Paul Michaels

In February of 2011 an earthquake event caused significant damage and loss of life in Christchurch, New Zealand. Such an event serves as motivation for improved foundation design and characterization of the shallow subsurface. In January of 2013, University of Texas engineers acquired surface wave data which has been made available to the ASCE GeoInstitute Geophysical Engineering Committee for a benchmark project. Participants were invited to process and interpret the common data set. This paper reports the results designated as those of "Analyst A". The active vibroseis and sledgehammer data were combined to produce a composite Rayleigh wave dispersion curve. …

Recent Advances In Quantum Chemical Predictions Of The Atmospheric Reactivity Of Criegee Intermediates, Keith Kuwata

Keith Kuwata

No abstract provided.

Motivation For Achievement And Attitudes Toward Mathematics Instruction In A Required Calculus Course At The Norwegian University Of Science And Technology, Donna Sundre, Carol Barry, Vidar Gynnild, Erin Tangen Ostgard

Donna L. Sundre

This study from the Norwegian University of Science and Technology (NTNU) examines students’ learning goals and attitudes toward mathematics in a first-year calculus course in undergraduate engineering education. Achievement motivation research using the Achievement Goal Questionnaire (AGQ) is advanced from current literature with two additions: (1) a course specific context using introductory college calculus students, and (2) participation of Norwegian students. Pre- and posttest measures of attitudes indicate that students do change learning goals over time, unfortunately opposite to the instructors’ aspirations. A significant increase in “Mastery Avoidance” and “Work Avoidance” was accompanied with a drop in “Mastery Approach” and …

Geochemistry Of The Great Valley Group: An Integrated Provenance Record, Kathleen Surpless

Kathleen D. Surpless

Sedimentary geochemistry of fine-grained strata of the Great Valley Group (GVG) in California documents a provenance signal that may better represent unstable, mafic minerals and volcanic clasts within sediment source regions than the provenance signal documented in the petrofacies and detrital zircon analysis of coarser sedimentary fractions. Geochemistry of the GVG provides an overall provenance framework within which to interpret sandstone petrofacies and detrital zircon age signatures. The geochemical signature for all Sacramento Valley samples records an overall continental arc source, with significant variation but no clear spatial or temporal trends, indicating that the geochemical provenance signal remained relatively consistent …

Does The Great Valley Group Contain Jurassic Strata? Reevaluation Of The Age And Early Evolution Of A Classic Forearc Basin, Kathleen D. Surpless, Stephan A. Graham, Jacob A. Covault, Joseph L. Wooden

Kathleen D. Surpless

The presence of Cretaceous detrital zircon in Upper Jurassic strata of the Great Valley Group may require revision of the lower Great Valley Group chronostratigraphy, with significant implications for the Late Jurassic–Cretaceous evolution of the continental margin. Samples (n = 7) collected from 100 km along strike in the purported Tithonian strata of the Great Valley Group contain 20 Cretaceous detrital zircon grains, based on sensitive high-resolution ion microprobe age determinations. These results suggest that Great Valley Group deposition was largely Cretaceous, creating a discrepancy between biostratigraphy based on Buchia zones and chronostratigraphy based on radiometric age dates. These …

Lithofacies Control In Detrital Zircon Provenance Studies: Insights From The Cretaceous Methow Basin, Southern Canadian Cordillera, Kathleen Surpless, J. Mahoney, Joseph Wooden, Michael Mcwilliams

Kathleen D. Surpless

High-frequency sampling for detrital zircon analysis can provide a detailed record of fine-scale basin evolution by revealing the temporal and spatial variability of detrital zircon ages within clastic sedimentary successions. This investigation employed detailed sampling of two sedimentary successions in the Methow/Methow-Tyaughton basin of the southern Canadian Cordillera to characterize the heterogeneity of detrital zircon signatures within single lithofacies and assess the applicability of detrital zircon analysis in distinguishing fine-scale provenance changes not apparent in lithologic analysis of the strata. The Methow/Methow-Tyaughton basin contains two distinct stratigraphic sequences of middle Albian to Santonian clastic sedimentary rocks: submarine-fan deposits of the …

Detrital Zircon Provenance Analysis Of The Great Valley Group, California: Evolution Of An Arc-Forearc System, Kathleen Surpless, Stephan Graham, Joseph Wooden, Michael Mcwilliams

Kathleen D. Surpless

The improved resolution of sediment provenance from detrital zircon analysis of Great Valley stratigraphy enables recognition of previously undocumented arc magmatism and the evolution of regional drainage systems within the Cretaceous arc-forearc system related to uplift, magmatism, and structure in the arc. Great Valley detrital zircon age data confirm previous studies that indicate that the locus of the sediment source in the southern Sierra Nevada arc migrated east with the active volcanic front and suggest rapid rates of uplift and unroofing of the southern arc. Sacramento Valley detrital zircon age data indicate a more complex history of drainage in the …

Provenance Of The Pythian Cave Conglomerate, Northern California: Implications For Mid-Cretaceous Paleogeography Of The U.S. Cordillera, Kathleen D. Surpless, Gregory Alan Augsburger

Kathleen D. Surpless

Provenance analysis of middle Cretaceous sedimentary rocks can help distinguish between disparate tectonic models of Cretaceous Cordilleran paleogeography by establishing links between sediment and source, as well as between currently separated basins. This study combines new detrital zircon age data and compositional data with existing provenance data for the Pythian Cave conglomerate, an informally-named unit deposited unconformably on the eastern Klamath Mountains, to test possible correlations between the Pythian Cave conglomerate and similar-age deposits in the Hornbrook Formation and the Great Valley Group. These provenance results indicate that restoring Late Cretaceous clockwise rotation of the Blue Mountains adds a significant …

Understanding A Critical Basinal Link In Cretaceous Cordilleran Paleogeography: Detailed Provenance Of The Hornbrook Formation, Oregon And California, Kathleen Surpless, Emily Beverly

Kathleen D. Surpless

The Hornbrook Formation is a Cretaceous overlap assemblage that rests unconformably on accreted terranes and plutons of the Klamath Mountains in southern Oregon and northern California. The combined results of sandstone petrography, detrital zircon U-Pb age and Hf isotopic systematics, and whole-rock Nd analysis document an abrupt change in sediment sources for the Hornbrook Formation during the Late Cretaceous. The lower members of the Hornbrook Formation record provenance in the Klamath Mountains and the Sierran Foothills belt that is characterized by detrital zircon age distributions with large Jurassic and Early Cretaceous peaks (170-130 Ma) and positive zircon Hf and whole-rock …

Evolution And Stratigraphic Architecture Of Marine Slope Gully Complexes: Monterey Formation (Miocene), Gaviota Beach, California, Kathleen Surpless, Richard Ward, Stephan Graham

Kathleen D. Surpless

Three small headlands in the sea cliffs west of Gaviota Beach, California, are the remnant fill of three discrete submarine gullies incised into the late Miocene submarine slope environment. These promontories provide excellent, three-dimensional exposure of the gully fill in outcrop, permitting documentation of their complex internal stratigraphic architecture. Detailed study of these exposures elucidates the sedimentologic processes that occur in the filling of slope gullies, guides interpretation of the acoustic records of otherwise unsampled modern gully systems on continental slopes, and provides insight into the heterogeneity that may characterize slope gully petroleum reservoirs. We develop a comprehensive facies scheme …

East-Derived Strata In The Methow Basin Record Rapid Mid-Cretaceous Uplift Of The Southern Coast Mountains Batholith, Kathleen Surpless, Zachary Sickmann, Trevor Koplitz

Kathleen D. Surpless

The Jurassic–Cretaceous Methow basin of northern Washington State and southern British Columbia forms an overlap sequence linking several small tectonostratigraphic terranes. Sandstone petrography, sandstone and mudrock geochemistry, and detrital zircon U–Pb age and Hf analysis of mid-Cretaceous, east-derived Methow strata together document a remarkably uniform provenance signature that suggests proximal, abundant, and unchanging sediment sources throughout deposition. The eastern belt of the Coast Mountains batholith, intruded into Stikine and related inboard terranes of the Intermontane superterrane, along with Jurassic and Cretaceous plutons of the westernmost Okanogan Range, provide the best match to the provenance signature of east-derived sediment in the …

Proterozoic Metamorphism Of The Tobacco Root Mountains, Montana, John Cheney, John Brady, Kara Tierney, Kathleen Surpless, Heidi Mohlman, Jessica Frisch, Christine Hatch, Michael Steiner, Sarah Carmichael, Robin Fisher, Carrie Tuit, Kurt Steffen, Pamela Cady, Josh Lowell, Leandra Archuleta, Jillian Hirst, Karl Wegmann, Brian Monteleone

Kathleen D. Surpless

Textures and mineral assemblages of metamorphic rocks of the Tobacco Root Mountains are consistent with metamorphism of all rocks during the Big Sky orogeny (1.77 Ga) at relatively high pressure (P >1.0 GPa) followed by differential reequilibration on a clockwise P-T path at lower pressures (0.6–0.8 GPa). The highest pressures are documented by coarse-grained kyanite and orthopyroxene in aluminous orthoamphibolites, which require P ≥ 1.0 GPa. Other higher-pressure mineral assemblages of note include kyanite + orthoamphibole and kyanite + K-feldspar. Abundant textural evidence for partial melting in pelitic and basaltic rocks includes leucosomes, very large (several cm across) porphyroblasts of …

Inhibitors Of Nα-Acetyl-L-Ornithine Deacetylase: Synthesis, Characterization And Analysis Of Their Inhibitory Potency, J. Hlavacek, J. Picha, V. Vanek, J. Jiracek, J. Slaninova, V. Fucik, M. Budesinsky, Danuta Gillner, Richard Holz

Richard C. Holz

A series of N α-acyl (alkyl)- and N α-alkoxycarbonyl-derivatives of l- and d-ornithine were prepared, characterized, and analyzed for their potency toward the bacterial enzyme N α-acetyl-l-ornithine deacetylase (ArgE). ArgE catalyzes the conversion of N α-acetyl-l-ornithine to l-ornithine in the fifth step of the biosynthetic pathway for arginine, a necessary step for bacterial growth. Most of the compounds tested provided IC50 values in the μM range toward ArgE, indicating that they are moderately strong inhibitors. N α-chloroacetyl-l-ornithine (1g) was the best inhibitor tested toward ArgE providing an IC50 value of 85 μM while N α-trifluoroacetyl-l-ornithine (1f), N α-ethoxycarbonyl-l-ornithine (2b), and …

The Dape-Encoded N-Succinyl-L,L-Diaminopimelic Acid Desuccinylase From Haemophilus Influenzae Contains Two Active-Site Histidine Residues, Danuta M. Gillner, David L. Bienvenue, Boguslaw P. Nocek, Andzrej Joachimiak, Vincentos Zachary, Brian Bennett, Richard C. Holz

Richard C. Holz

The catalytic and structural properties of the H67A and H349A dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) from Haemophilus influenzae were investigated. On the basis of sequence alignment with the carboxypeptidase from Pseudomonas sp. strain RS-16, both H67 and H349 were predicted to be Zn(II) ligands. The H67A DapE enzyme exhibited a decreased catalytic efficiency (180-fold) compared with wild-type (WT) DapE towards N-succinyldiaminopimelic acid. No catalytic activity was observed for H349A under the experimental conditions used. The electronic paramagnetic resonance (EPR) and electronic absorption data indicate that the Co(II) ion bound to H349A-DapE is analogous to that of WT DapE after the …

Mutation Of H63 And Its Catalytic Affect On The Methionine Aminopeptidase From Escherichia Coli, Sanghamitra Mitra, Brian Bennett, Richard C. Holz

Richard C. Holz

In order to gain insight into the mechanistic role of a flexible exterior loop near the active site, made up of Y62, H63, G64, and Y65, that has been proposed to play an important role in substrate binding and recognition in the methionyl aminopeptidase from Escherichia coli (EcMetAP-I), the H63A enzyme was prepared. Mutation of H63 to alanine does not affect the ability of the enzyme to bind divalent metal ions. The specific activity of H63A EcMetAP-I was determined using four different substrates of varying lengths, namely, l-Met-p-NA, MAS, MGMM and MSSHRWDW. For the smallest/shortest substrate (l-Met-p-NA) the specific activity …

Identification Of An Active Site-Bound Nitrile Hydratase Intermediate Through Single Turnover Stopped-Flow Spectroscopy, Natalie Gumataotao, Misty L. Kuhn, Natalia Hajnas, Richard C. Holz

Richard C. Holz

Stopped-flow kinetic data were obtained for the iron-type nitrile hydratase from Rhodococcus equi TG328-2 (ReNHase) using methacrylonitrile as the substrate. Multiple turnover experiments suggest a three-step kinetic model that allows for the reversible binding of substrate, the presence of an intermediate, and the formation of product. Microscopic rate constants determined from these data are in good agreement with steady state data confirming that the stopped-flow method used was appropriate for the reaction. Single turnover stopped-flow experiments were used to identify catalytic intermediates. These data were globally fit confirming a three-step kinetic model. Independent absorption spectra acquired between 0.005 …

Immobilization Of The Aminopeptidase From Aeromonas Proteolytica On Mg2+/Al3+ Layered Double Hydroxide Particles, Steven Frey, Stephanie Guilmet, Richard Egan, Alyssa Bennett, Sarah Soltau, Richard Holz

Richard C. Holz

A novel biomaterial formed by the immobilization of the Aminopeptidase from Aeromonas proteolytica (AAP) on synthetic Mg2+ and Al3+ ion-containing layered double hydroxide (LDH) particles was prepared. Immobilization of AAP on the LDH particles in a buffered, aqueous mixture is rapid such that the maximum loading capacity, 1 × 10−9 moles of AAP/mg LDH, is achieved in a few minutes. X-ray powder diffraction of LDH samples before and after treatment with AAP indicates that the enzyme does not intercalate between the layers of LDH, but instead binds to the surface. Treatment of AAP/LDH with various amounts of salt in a …

Analyzing The Binding Of Co(Ii)-Specific Inhibitors To The Methionyl Aminopeptidases From Escherichia Coli And Pyrococcus Furiosus, Sanghamitra Mitra, George Sheppard, Jieyi Wang, Brian Bennett, Richard Holz

Richard C. Holz

Methionine aminopeptidases (MetAPs) represent a unique class of protease that is capable of the hydrolytic removal of an N-terminal methionine residue from nascent polypeptide chains. MetAPs are physiologically important enzymes; hence, there is considerable interest in developing inhibitors that can be used as antiangiogenic and antimicrobial agents. A detailed kinetic and spectroscopic study has been performed to probe the binding of a triazole-based inhibitor and a bestatin-based inhibitor to both Mn(II)- and Co(II)-loaded type-I (Escherichia coli) and type-II (Pyrococcus furiosus) MetAPs. Both inhibitors were found to be moderate competitive inhibitors. The triazole-type inhibitor was found to …

Direct Patterning Of Silanized-Biomolecules On Semiconductor Surfaces, Dorjderem Nyamjav, Richard Holz

Richard C. Holz

A novel approach to pattern silanized-biomolecules directly onto glass (SiO_x) substrates via Dip-Pen nanolithography (DPN) and microcontact printing (μCP) is presented. Subsequent hybridization reactions of DPN patterned silanized-DNA with its complementary strands provide “proof-of-concept” that the patterned oligonucleotides maintain their biological activities. The fabrication strategy does not require premodification of substrates and offers a cheap and robust way to immobilize molecules on electronically important semiconductor surfaces.

Direct Patterning Of A Cyclotriveratrylene Derivative For Directed Self-Assembly Of C60, Zachary Osner, Dorjderem Nyamjav, Richard Holz, Daniel Becker

Richard C. Holz

A novel apex-modified cyclotriveratrylene (CTV) derivative with an attached thiolane-containing lipoic acid linker was directly patterned onto gold substrates via dip-pen nanolithography (DPN). The addition of a dithiolane-containing linker to the apex of CTV provides a molecule that can adhere to a gold surface with its bowl-shaped cavity directed away from the surface, thereby providing a surface-bound CTV host that can be used for the directed assembly of guest molecules. Subsequent exposure of these CTV microarrays to C60 in toluene resulted in the directed assembly of predesigned, spatially controlled, high-density microarrays of C60. The molecular recognition capabilities of this CTV …

Structural Basis For Catalysis By The Mono- And Dimetalated Forms Of The Dape-Encoded N-Succinyl-L,L-Diaminopimelic Acid Desuccinylase, Boguslaw Nocek, Danuta Gillner, Yao Fan, Richard Holz, Andzrej Joachimiak

Richard C. Holz

Biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. The dapE operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent potential targets for novel antibacterials. The dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts N-succinyl-l,l-diaminopimelic acid to l,l-diaminopimelic acid and succinate. Deletion of the dapE gene is lethal to Helicobacter pylori and Mycobacterium smegmatis, indicating that DapE's are essential for cell growth and proliferation. Since there are no similar pathways in humans, inhibitors …