Physical Sciences and Mathematics Commons^™

Secondary Structure, A Missing Component Of Sequence- Based Minimotif Definitions, David P. Sargeant, Michael R. Gryk, Mark W. Maciejewsk, Vishal Thapar, Vamsi Kundeti, Sanguthevar Rajasekaran, Pedro Romero, Keith Dunker, Shun-Cheng Li, Tomonori Kaneko, Martin Schiller

Life Sciences Faculty Research

Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis …

Data Mining Of Pancreatic Cancer Protein Databases, Peter Revesz, Christopher Assi

CSE Conference and Workshop Papers

Data mining of protein databases poses special challenges because many protein databases are non- relational whereas most data mining and machine learning algorithms assume the input data to be a type of rela- tional database that is also representable as an ARFF file. We developed a method to restructure protein databases so that they become amenable for various data mining and machine learning tools. Our restructuring method en- abled us to apply both decision tree and support vector machine classifiers to a pancreatic protein database. The SVM classifier that used both GO term and PFAM families to characterize proteins gave …

Stretching A Surface Having A Layer Of Porous Medium In A Viscous Fluid, M. Sajid, Z. Abbas, N. Ali, T. Javed

Applications and Applied Mathematics: An International Journal (AAM)

The present analysis deals with the steady, incompressible flow of a viscous fluid over a stretching sheet having a layer of porous medium of uniform thickness. The two-dimensional flow equations are derived in a Cartesian coordinate system. The semi-infinite region filled with a viscous fluid is divided into two regions namely, a clear fluid region and a region having a uniform pores. Darcy's law has been used for the flow of fluid in the porous medium region. An exact similar solution of the problem is obtained. The obtained solution is constrained by a relation between the porosity parameter and the …

Solution Of Fuzzy System Of Linear Equations With Polynomial Parametric Form, Diptiranjan Behera, S. Chakraverty

Applications and Applied Mathematics: An International Journal (AAM)

This paper proposed two new and simple solution methods to solve a fuzzy system of linear equations having fuzzy coefficients and crisp variables using a polynomial parametric form of fuzzy numbers. Related theorems are stated and proved. The proposed methods are used to solve example problems. The results obtained are also compared with the known solutions and are found to be in good agreement.

Ultrafast Laser-Induced Damage And The Influence Of Spectral Effects, Jeremy R. Gulley

Faculty Articles

Numerous studies have investigated the prerequisite role of photoionization in ultrafast laser-induced damage (LID) of bulk dielectrics. This study examines the role of spectral width and instantaneous laser frequency in LID using a frequency dependent multiphoton ionization (MPI) model and numerical simulation of initially 800 nm laser pulses propagating through fused silica. Assuming a band gap of 9 eV, MPI by an 800 nm field is a six-photon process, but when the instantaneous wavelength is greater than 827 nm an additional photon is required for photoionization, reducing the probability of the event by many orders of magnitude. Simulation results suggest …

Single Top And Top Pair Production, Nikolaos Kidonakis

Faculty Articles

I present results for single-top and top-pair production at the LHC and the Tevatron. Higher-order two-loop corrections are used to achieve NNLL resummation, which is then used to derive NNLO soft-gluon corrections. Results are presented for total cross sections, top transverse momentum distributions, and top rapidity distributions. All results are in excellent agreement with data from the LHC and the Tevatron. I also clarify the differences between various methods in top-pair production and their relation to exact NNLO results.

Ghost Tiger Beetle (Cicindela Lepida): Species Conservation Assessment, Melissa J. Panella

Nebraska Game and Parks Commission: Publications

The primary goal in development of at-risk species conservation assessments is to compile biological and ecological information that may assist conservation practitioners in making decisions regarding the conservation of species of interest. The Nebraska Natural Legacy Project recognizes the ghost tiger beetle, a.k.a. white tiger beetle, (Cicindela lepida) as a Tier I at-risk species of high conservation priority. Some general management recommendations are made here regarding ghost tiger beetles; however, conservation practitioners will need to use professional judgment to make specific management decisions based on objectives, location, and a multitude of variables. This resource was designed to share available knowledge …

Progression Magazine, 2012-2013, Coastal Carolina University

Progression Magazine

Magazine of the College of Science at Coastal Carolina University.

On Metal Synthesis Of Some Substituted Rhenium And Manganese Complexes, Jaron Michael Thomas

Masters Theses & Specialist Projects

Heterocyclic organic and organometallic compounds (i.e. polypyrrole), and their derivatives, have been of great interest for conductive polymers due to their novel properties and environmental stability as compared to their non-aromatic analogs (i.e. polyacetylene). Our current interest focus upon the potential role of metal ligand bound pyridazines as the next generation of electronic devices that utilize the metal ligands bound to organics as the semiconducting material. Pyridazine is a 6-membered aromatic ring with two adjacent nitrogen atoms. These are promising candidates for a variety of materials and commercial applications; but they are difficult to get a metal ligand to fuse …

Ibinhunt: Binary Hunting With Inter-Procedural Control Flow, Jiang Ming, Meng Pan, Debin Gao

Research Collection School Of Computing and Information Systems

Techniques have been proposed to find the semantic differences between two binary programs when the source code is not available. Analyzing control flow, and in particular, intra-procedural control flow, has become an attractive technique in the latest binary diffing tools since it is more resistant to syntactic, but non-semantic, differences. However, this makes such techniques vulnerable to simple function obfuscation techniques (e.g., function inlining) attackers any malware writers could use. In this paper, we first show function obfuscation as an attack to such binary diffing techniques, and then propose iBinHunt which uses deep taint and automatic input generation to find …

Rounding Of A First-Order Quantum Phase Transition To A Strong-Coupling Critical Point, Fawaz Hrahsheh, Jose A. Hoyos, Thomas Vojta

Physics Faculty Research & Creative Works

We investigate the effects of quenched disorder on first-order quantum phase transitions on the example of the N-color quantum Ashkin-Teller model. By means of a strong-disorder renormalization group, we demonstrate that quenched disorder rounds the first-order quantum phase transition to a continuous one for both weak and strong coupling between the colors. In the strong-coupling case, we find a distinct type of infinite-randomness critical point characterized by additional internal degrees of freedom. We investigate its critical properties in detail and find stronger thermodynamic singularities than in the random transverse field Ising chain. We also discuss the implications for higher spatial …

Acoustic Scale From The Angular Power Spectra Of Sdss-Iii Dr8 Photometric Luminous Galaxies, Hee-Jong Seo, Shirley Ho, Martin White, Antonio J. Cuesta, Ashley J. Ross, Shun Saito, For Full List Of Authors, See Publisher's Website.

Physics Faculty Research & Creative Works

We measure the acoustic scale from the angular power spectra of the Sloan Digital Sky Survey III (SDSS-III) Data Release 8 imaging catalog that includes 872, 921 galaxies over ~10,000 deg² between 0.45 < z < 0.65. The extensive spectroscopic training set of the Baryon Oscillation Spectroscopic Survey luminous galaxies allows precise estimates of the true redshift distributions of galaxies in our imaging catalog. Utilizing the redshift distribution information, we build templates and fit to the power spectra of the data, which are measured in our companion paper, to derive the location of Baryon acoustic oscillations (BAOs) while marginalizing over many free parameters to exclude nearly all of the non-BAO signal. We derive the ratio of the angular diameter distance to the sound horizon scale D_A(z)/r_s = 9.212^+0.416_-0.404 at z = 0.54, and therefore DA (z) = 1411 ± 65 Mpc at z = 0.54; the result is fairly independent of assumptions on the underlying cosmology. Our measurement of angular diameter distance D_A(z) is 1.4σ higher than what is expected for the concordance ΛCDM, in accordance to the trend of other spectroscopic BAO measurements for …

Laser-Induced Electron Diffraction For Probing Rare Gas Atoms, Junliang Xu, Cosmin I. Blaga, Anthony D. Dichiara, Emily Sistrunk, Kaikai Zhang, Zhangjin Chen, Anh-Thu Le, Toru Morishita, C. D. Lin, Pierre Agostini, Louis F. Dimauro

Physics Faculty Research & Creative Works

Recently, using midinfrared laser-induced electron diffraction (LIED), snapshots of a vibrating diatomic molecule on a femtosecond time scale have been captured [C.I. Blaga et al., Nature (London) 483, 194 (2012)]. In this Letter, a comprehensive treatment for the atomic LIED response is reported, a critical step in generalizing this imaging method. Electron-ion differential cross sections (DCSs) of rare gas atoms are extracted from measured angular-resolved, high-energy electron momentum distributions generated by intense midinfrared lasers. Following strong-field ionization, the high-energy electrons result from elastic rescattering of a field-driven wave packet with the parent ion. For recollision energies [greater or equal] 100eV, …

Issue 2

The Synapse: Intercollegiate science magazine

No abstract provided.

The X-Ray View Of Ob Star Wind Structure And Dynamics, David H. Cohen

Physics & Astronomy Faculty Works

High-resolution X-ray grating spectroscopy enables us to measure the kinematics and spatial distribution of the shock-heated wind plasma in O and early B stars, testing the predictions of the embedded wind shock scenario of massive star X-ray production. By fitting models to the resolved, Doppler broadened X-ray emission line profiles measured by the Chandra X-ray Observatory's grating spectrometer, we find an onset radius of X-ray production of roughly Ro = 1.5 R★ for the O supergiants, ζ Pup and HD 93129A. From the profile fitting we also find that the terminal velocity of the X-ray emitting plasma is consistent with …

Density And Diversity Of Penaeid Shrimp And Fish Species In Near-Shore Seagrass Beds Of Northern Biscayne Bay, Florida (Usa), Robin Cascioli

HCNSO Student Theses and Dissertations

Seagrass beds serve critical functions in coastal Florida ecosystems. The beds serve as nursery habitat for many juvenile reef fish species and provide protection for many types of benthic organisms found in Biscayne Bay. They help stabilize sediment that would otherwise increase turbidity around coral reefs, filter the water of contaminants, and help support an entire food web. Three species of seagrass were found at the study sites in northern Biscayne Bay: Thalassia testudinum, Halodule wrightii, and Syringodium filiforme. This study focused on understanding the organism habitat interaction by determining the species diversity, seasonal densities, and the …

The Measure And Instruction Of Scale In Introductory Chemistry, Karrie Linn Gerlach

Theses and Dissertations

As a student, it is fundamental to comprehend how small an atom or molecule is in order to truly understand how the world works. The American Association for the Advancement of Science (AAAS) has determined that scale is a critical theme that pervades through all areas of science and is critical to a deep understanding. This project determined that students, which are more proficient with scale and moving between the macroscopic and particle worlds, were better performers in chemistry classes. Interviews were used to determine what the students understood and what common misconceptions were present. These lead to the development …

Complexity And Uncertainty In Human And Ecological Risk Assessment, Matthew Jordan Dellinger

Theses and Dissertations

Multiple interacting stressors in the environment present increasingly complex risks to human health. Too often, however, the data required for traditional risk assessment are either lacking or unavailable at the necessary spatial or temporal scale. In addition, assessment practices and management policies need to move away from single factor approaches in order to accommodate the reality of complex chemical mixtures and environmental stressors. Recent literature suggests that a paradigm shift is under way. This points to a need for the development of new techniques both for rapid data collection and flexible risk assessment strategies that can adapt to make use …

Force-Feedback High-Speed Atomic Force Microscope For Studying Large Biological Systems, Byung I. Kim, Ryan Boehm

Physics Faculty Publications and Presentations

We designed and developed a high-speed atomic force microscope (HSAFM) utilizing a force-feedback scheme for imaging large biological samples. The system collects three simultaneous images: a deflection image, a topographic image, and a force image. We demonstrated that this force-feedback HSAFM is capable of acquiring large topographic images of Escherichia coli biofilms at approximately one frame per second in air. We discuss how the self-actuating cantilever and the piezo tube follow those larger biological topographic features during the HSAFM imaging process.

Updated Manuscript Submission Guidelines For The Prairie Naturalist, Christopher N. Jacques, Troy W. Grovenburg, Jonathan A. Jenks

The Prairie Naturalist

These guidelines present updated policies and procedures for submitting scientific manuscripts for consideration for publication in The Prairie Naturalist (PNAT). These guidelines incorporate substantial changes that have occurred following a change in Editorial staff during January 2009, and update the online “Suggestions for Contributors” guidelines provided on the PNAT website (http://www.sdstate.edu/nrm/organizations/gpnss/tpn/index.cfm); these instructions supersede all previous guidelines.

Tables and appendices are included for common word expressions with superfluous wording (Table 1), examples of correct format and style guidelines for tables accompanying manuscripts (Table 2, Appendix A), guidance in properly preparing Research notes (Appendix B) and citing literature (Appendix …

Fish Assemblage Structure In Black Hills, South Dakota Streams, Luke D. Schultz, Sarah J. Lewis, Katie Nicole Bertrand

The Prairie Naturalist

Understanding factors structuring fish assemblages in a particular area is valuable to both sport fishery management and native species conservation. Fish assemblages in the Black Hills are unique to South Dakota because they contain economically valuable introduced salmonids as well as native species of conservation need. Our objective was to examine the relationship between fish assemblages and geomorphic and reach-scale habitat features across multiple stream reaches in the Black Hills. Canonical correspondence analysis, a direct gradient ordination analysis, indicated that factors operating at multiple spatial scales interacted to structure fish assemblages. There also was indication of segregation between native species …

Terrestrial And Semi-Aquatic Vertebrates In Diets Of Largemouth Bass In Central Nebraska, Seth A. Lundgren, Keith Geluso, Casey W. Schoenebeck

The Prairie Naturalist

Largemouth bass (Micropterus salmoides) are opportunistic predators often feeding in littoral areas during crepuscular periods (Snow 1971). Adult largemouth bass primarily are piscivorous, whereas juveniles generally consume zooplankton, insects, and small fish (Zweiacker and Summerfelt 1974, Carlander 1977, Post 2003). Age-0 largemouth bass generally consume zooplankton and macroinvertebrates (Keast and Webb 1966, Keast 1985, Phillips et al. 1995, Post 2003) and shift to piscivory at 50-70 mm in length (Phillips et al. 1995, Olson 1996, Post 2003). Few studies have documented detailed accounts of other vertebrates besides fish in diets of largemouth bass, which include amphibians (Hodgson and …

Interior Least Tern Powerline Collision On The Lower Platte River, Lauren R. Dinan, Joel G. Jorgensen, Mary Bomberger Brown

The Prairie Naturalist

Collisions with electrical powerlines are a well-known documented cause of avian mortality (Avian Power Line Interaction Committee [APLIC] 1994, Savereno et al. 1996). Mortality caused by collisions with powerlines can be an important concern for many bird species, but is a serious conservation problem for threatened and endangered species because any mortality can have biological and legal ramifications (Janss 2000). Loss of individuals, particularly breeding adults, from an already small population may impede a species’ recovery by reducing reproduction and recruitment into the breeding population. The death of an individual from a threatened or endangered species as a result of …

Walleye Trophic Position Before And After A Gizzard Shad Extirpation, Bethany J. Bethke, Justin A. Vandehey, Mark J. Fincel, Brian D.S. Graeb, Mark T. Porath

The Prairie Naturalist

Walleye (Sander vitreus) are an ecologically and recreationally important sport fish species. Reduced growth and condition in walleye can occur when prey availability is limited. In two Nebraska reservoirs, walleye consumed gizzard shad (Dorosoma cepedianum) as their primary prey until a winterkill extirpated the gizzard shad in 2001. Because of the winterkill, walleye in the two reservoirs had to change to alternative prey items. Our objective was to determine if stable isotope analysis on archived walleye scales can be used to detect a known food web shift in two reservoir food webs. We quantified the changes …

The Incentive And Benefits To Publish Research, Christopher N. Jacques

The Prairie Naturalist

In the northern Great Plains, December is a month marked by the end of the year and a period of much-needed rest and relaxation during the start of the winter season. Landscapes will soon be blanketed with snow and local floral and faunal species have adapted to the ensuing winter months ahead. Winter is a season that reminds you who you live in the Plains states, and as such, should expect bitter cold temperatures, strong winds, and blowing and drifting snow. However, December is a great time to enjoy the outdoors across the Great Plains, a time to reflect on …

Avian Diversity And Habitat Use On Wetland Reserve Program Lands In The Lower Missouri River Valley, Eric C. Hopps

The Prairie Naturalist

A primary objective of the Wetland Reserve Program (WRP) is to provide habitat for migratory birds throughout all seasons of the year. Comprehensive avian assessments are lacking and limit our ability to evaluate the benefits of the WRP to continental bird populations. I investigated avian species occurrence on WRP lands within the Lower Missouri River Valley (LMRV), Nebraska, USA, from March 2010 to February 2011. Ten WRP habitat types are described based on plant community assemblages and observed hydrological regimes. Estimates of avian species richness were greatest in lowland forest (n = 115), lowland woodland (n = 83) and upland …

A Treeboost Model For Software Effort Estimation Based On Use Case Points, Luiz Fernando Capretz, Ali Bou Nassif

Electrical and Computer Engineering Publications

Software effort prediction is an important task in the software development life cycle. Many models including regression models, machine learning models, algorithmic models, expert judgment and estimation by analogy have been widely used to estimate software effort and cost. In this work, a Treeboost (Stochastic Gradient Boosting) model is put forward to predict software effort based on the Use Case Point method. The inputs of the model include software size in use case points, productivity and complexity. A multiple linear regression model was created and the Treeboost model was evaluated against the multiple linear regression model, as well as the …

Height And Light: Optical Profilometry Characterization For Conservation Of Abraded Plastics, Sarah Lavin

Intersections Fall 2020

This project aims to understand how surface polishing affects different materials in the context of art conservation. These materials include both those used in the creation and preservation of art objects, and those used to house and display them in a museum. Conservators at SBE Conservation and Cooper Hewitt have been working on two series of art objects, Still Life #46 and Still Life #54 by Tom Wesselman, for the past 6 years. The two sculptures are identical with the difference being that those from the Still Life #46 series were backlit while the others were not. Working with conservators …

Plant Community Composition And Structure Monitoring For Scotts Bluff National Monument, 2012 Annual Report, Isabel W. Ashton, Michael Prowatzke, Stephen K. Wilson

United States National Park Service: Publications

Executive Summary

the last remnants of native mixed-grass prairie in the region. The Northern Great Plains Inventory & Monitoring Network (NGPN) surveyed 8 long-term monitoring plots in Scotts Bluff National Monument in 2012 as part of an effort to better understand the condition of plant communities in the park. We measured plant diversity and cover, estimated tree and shrub density, looked for the presence of exotic species that are of concern to park management, and evaluated the amount of human and natural disturbance at all plots. This effort was the second year in a multiple-year venture to document the current …

Are Twitter Users Equal In Predicting Elections? A Study Of User Groups In Predicting 2012 U.S. Republican Primaries, Lu Chen, Wenbo Wang, Amit P. Sheth

Kno.e.sis Publications

Existing studies on predicting election results are under the assumption that all the users should be treated equally. However, recent work [14] shows that social media users from different groups (e.g., “silent majority” vs. “vocal minority”) have significant differences in the generated content and tweeting behavior. The effect of these differences on predicting election results has not been exploited yet. In this paper, we study the spectrum of Twitter users who participate in the on-line discussion of 2012 U.S. Republican Presidential Primaries, and examine the predictive power of different user groups (e.g., highly engaged users vs. lowly engaged users, right-leaning …