Physical Sciences and Mathematics Commons^™

Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell

Faculty Publications

Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching to explore the effects of varying the gap open and gap extension penalties for three nuclear ribosomal data sets. Particular attention is given to optimal phylogeny scores for 200 alignments of a range of gap open and gap extension penalties and their respective …

Pharmacogenomics: Analyzing Snps In The Cyp2d6 Gene Using Amino Acid Properties, Wesley A. Beckstead, Mark J. Clement, Mark Ebbert, David Mcclellan, Timothy O'Connor

Faculty Publications

Each year people suffer from complications of adverse drug reactions, but with pharmacogenomics there is hope to prevent thousands of these people from suffering or dying needlessly. The CYP2D6 gene is responsible for metabolizing a large portion of these drugs. Because of the gene’s importance, various approaches have been taken to analyze CYP2D6 and single nucleotide polymorphisms (SNPs) throughout its sequence. This study introduces a novel method to analyze the effects of SNPs on encoded protein complexes by focusing on the biochemical properties of each nonsynonymous substitution using the program TreeSAAP. We apply this technique to SNPs found in the …

Non-Critical Waveguide Alignment For Vertically-Coupled Microring Using A Mode-Expanded Bus Architecture, Chyng Wen Tee, K. A. Williams, R. V. Penty, I. H. White

Research Collection Lee Kong Chian School Of Business

Vertically coupled microrings in an all-pass filter configuration are fabricated with a range of waveguide misalignments deliberately introduced into the lithography masks to demonstrate noncritical fabrication requirements. The microrings have a mode-expanded bus design which allows a greatly reduced variation in power coupling coefficient-only 6% for fabrication misalignments as high as 1 mum. This represents a five-fold improvement in fabrication tolerance when compared with conventional designs.

Iowa Academy Of Science: The New Bulletin, V02n4, Autumn 2006, Iowa Academy Of Science

New Bulletin

Inside This Issue:

--Executive Director Message

--Science Teaching Section Name Election

--Changes to IAS Sections

--Iowa Junior Academy of Science Supporting Student Inquiry

--ISTS President's Message

--Iowa Science Teachers Section Fall Conference

--In Memoriam: James A. Van Allen

Data Summary From The Tampa Bay Interagency Seagrass Monitoring Program Through Year 2005, Walt Avery, Roger Johansson

Reports

Results regarding seagrass species abundance, distribution, and zonation over time are presented for the 1997-2005 period in Hillsborough Bay (HB, Figures 17-27) and the 1998-2005 period for Old Tampa Bay (OTB, Figures 3-14), Middle Tampa Bay (MTB, Figures 29-41), Lower Tampa Bay, including Terra Ceia Bay (LTB, Figures 43-57), and Boca Ciega Bay (BCB, Figures 59-69). For each transect, results are presented in a graphic format illustrating annual species composition, abundance, and distribution. Seagrass abundance is presented as percent coverage within a square meter using the Braun Blanquet coverage class system.

The Grb 060218/Sn 2006aj Event In The Context Of Other Gamma-Ray Burst Supernovae, P. Ferreo, D. A. Kann, A. Zeh, S. Klose, E. Pian, E. Palazzi, N. Masetti, Dieter H. Hartmann, J. Sollerman, J. Deng, A V. Filippenko, J Greiner, M A. Hughes, P Mazzali, W Li, E Rol, R J. Smith, N R. Tanvir

Publications

The supernova SN 2006aj associated with GRB 060218 is the second-closest GRB-SN observed to date (z =0.033). We present Very Large Telescope, Liverpool Telescope, and Katzman Automatic Imaging Telescope multi-color photometry of SN 2006aj. This super-nova is found to be subluminous and rapidly evolving. Its early light curve includes an additional wavelength-dependent component, which can be interpreted as shock break-out. We compare the photometric evolution of multi-band light curves with the corresponding properties of the present sample of more than 10 GRB-SNe with precisely known redshifts. Using host-galaxy extinction measure-ments, we derive extinction-corrected GRB-SN luminosities and place SN 2006aj in …

Are Vultures Birds, And Do Snakes Have Venom, Because Of Macro- And Microscavenger Conflict?, John A. Shivik

United States Department of Agriculture Wildlife Services: Staff Publications

I outline models that describe vertebrate and microbial competition for carrion resources and help explain the resultant morphologies observed in extant vertebrate scavengers. Odors from microbial decomposition signal the presence of a carcass to vertebrate scavengers. Therefore, microbes must consume carcasses rapidly or evolve toxic defenses to protect themselves and their resource from their vertebrate competitors. Similarly, macroscavengers must evolve traits that allow rapid detection of carcasses or develop chemical defenses against microbial toxins. My modeling suggests that the most efficient macroscavenger adaptations increase the probability of carcass detection, which explains why highly vagile species, such as vultures, are the …

Investigating The Feasibility Of A Passive Tracking Index For Monitoring Wildlife In The Lower Omo Valley, Ethiopia, Richard M. Engeman, Paul Evangilista

United States Department of Agriculture Wildlife Services: Staff Publications

In many places in Africa, constraints in human, financial and physical resources are common problems that limit the effectiveness of wildlife researchers and managers. In an attempt to identify a useful tool for monitoring African wildlife populations, we tested a passive tracking index (PTI) methodology on a unique wildlife resource area in the Lower Omo Valley, Ethiopia. The methodology had previously proved valuable for monitoring a wide variety of wildlife species, including ungulates and carnivores in North America and Australia. Two ungulates (lesser kudu and dikdik), a carnivore (hyena), a primate (baboon), and a ground foraging bird (guineafowl) were simultaneously …

Water Supplies For Horticulture In The Lower Great Southern, D J. Mcfarlane Dr, Ruhi Ferdowsian, Arjen Ryder

Bulletins 4000 -

No abstract provided.

A Process For Producing Ice Coverage Marine Information Objects (Mios) In Iho S-57 Format, George Dias, David F. Coleman, Ahmed El-Rabbany, Benson Agi, Lee Alexander

Center for Coastal and Ocean Mapping

While global warming may be opening up more Arctic waters in the summer, ice still infests key shipping lanes in the northern hemisphere during the winter months. To safely navigate these areas, mariners rely on daily ice coverage charts produced by national governmental agencies. Ice charts are primarily issued in paper format or as a fax. However, there is increased interest to ice coverage information on vessel navigation systems such as an Electronic Chart and Display Information Systems (ECDIS). However, to do so, the ice information must be provided as a separate layer of information to the Electronic Navigational Chart …

Protcom: Searchable Database Of Protein Complexes Enhanced With Domain-Domain Structures, Petras Kundrotas, Emil Alexov

Publications

The database of protein complexes (PROTCOM) is a compilation of known 3D structures of protein–protein complexes enriched with artificially created domain–domain structures using the available entries in the Protein Data Bank. The domain–domain structures are generated by parsing single chain structures into loosely connected domains and are important features of the database. The database (http://www.ces.clemson.edu/compbio/protcom) could be used for benchmarking purposes of the docking and other algorithms for predicting 3D structures of protein–protein complexes. The database can be utilized as a template database in the homology or threading methods for modeling the 3D structures of unknown protein–protein complexes. …

Steganalysis Embedding Percentage Determination With Learning Vector Quantization, Benjamin M. Rodriguez, Gilbert L. Peterson, Kenneth W. Bauer, Sos S. Agaian

Faculty Publications

Steganography (stego) is used primarily when the very existence of a communication signal is to be kept covert. Detecting the presence of stego is a very difficult problem which is made even more difficult when the embedding technique is not known. This article presents an investigation of the process and necessary considerations inherent in the development of a new method applied for the detection of hidden data within digital images. We demonstrate the effectiveness of learning vector quantization (LVQ) as a clustering technique which assists in discerning clean or non-stego images from anomalous or stego images. This comparison is conducted …

Membrane Systems With Limited Parallelism, Bianca Daniela Popa

Doctoral Dissertations

Membrane computing is an emerging research field that belongs to the more general area of molecular computing, which deals with computational models inspired from bio-molecular processes. Membrane computing aims at defining models, called membrane systems or P systems, which abstract the functioning and structure of the cell. A membrane system consists of a hierarchical arrangement of membranes delimiting regions, which represent various compartments of a cell, and with each region containing bio-chemical elements of various types and having associated evolution rules, which represent bio-chemical processes taking place inside the cell.

This work is a continuation of the investigations aiming to …

Gravitational Diffraction Radiation, Vitor Cardoso, Marco Cavaglia, Mario Pimenta

Physics Faculty Research & Creative Works

We show that if the visible universe is a membrane embedded in a higher-dimensional space, particles in uniform motion radiate gravitational waves because of spacetime lumpiness. This phenomenon is analogous to the electromagnetic diffraction radiation of a charge moving near to a metallic grating. In the gravitational case, the role of the metallic grating is played by the inhomogeneities of the extra-dimensional space, such as a hidden brane. We derive a general formula for gravitational diffraction radiation and apply it to a higher-dimensional scenario with flat compact extra dimensions. Gravitational diffraction radiation may carry away a significant portion of the …

The Jabal Qarah Caves Of The Hofuf Area, Northeastern Saudi Arabia: A Geological Investigation, Nazrul I. Khandaker, Mahbub Hussain, Fadhel Al-Khalifah

Publications and Research

The Jabal Al Qarah Caves, located approximately 13 km east of Al Hofuf, Eastern Province of Saudi Arabia, are an intricate cave system developed in the calcareous sandstone, marl and clay of the Upper Miocene to Lower Pliocene Hofuf Formation. Physiographically, the hill of Jabal Al Qarah is an outlier mesa that is located at the eastern edge of the Shedgum Plateau, the southern extension of the As Summan Plateau, and the larger Syrian Plateau to the north. Based on cave morphology and interpreted evolutionary histoty, the Jabal Al Qarah caves appear to be significantly different from other limestone caves …

สรุปกิจกรรม & สถานการณ์สิ่งแวดล้อม

Thai Environment

No abstract provided.

สัมภาษณ์พิเศษ : คุณไกรสีห์ กรรณสูต (ผู้ว่าการการไฟฟ้าฝ่ายผลิตแห่งประเทศไทย)

Thai Environment

No abstract provided.

สัมภาษณ์พิเศษ : คุณวิทิต ฮาวชานนท์ (ผู้ว่าการการประปานครหลวง)

Thai Environment

No abstract provided.

การยกระดับคุณภาพน้ำประปา ด้วยกระบวนการนาโนฟิลเตรชันเมมเบรน, ธนากร เมธาธรรม, ชวลิต รัตนธรรมสกุล

Thai Environment

No abstract provided.

เทคนิคการประหยัดพลังงานในอาคารและสำนักงาน, วิสาขา ภู่จินดา

Thai Environment

No abstract provided.

พลังงานจากพืชยุทธศาสตร์พลังงานของชาติตามแนวพระราชดำรัส, ธีรพล คังคะเกตุ

Thai Environment

No abstract provided.

เทคนิคในการฟื้นฟูดิน, พิสมัย ชัยรัตน์อุทัย

Thai Environment

No abstract provided.

การจัดการของเสียบรรจุภัณฑ์ในต่างประเทศ : กรณีศึกษาและบทวิเคราะห์, นพภาพร พานิช, ดารารัตน์ อานันทนะสุวงศ์, อุดมศักดิ์ ศีลประชาวงศ์

Thai Environment

No abstract provided.

ก๊าซชีวภาพ กับ การอนุรักษ์สิ่งแวดล้อม, สถานเทคโนโลยีก๊าซชีวภาพ, จังหวัดเชียงใหม่

Thai Environment

No abstract provided.

เครื่องมือเพื่อการบริหารจัดการทรัพยากรธรรมชาติและสิ่งแวดล้อมสำหรับประเทศไทย, ทวีวงศ์ ศรีบุรี

Thai Environment

เครื่องมือเพื่อการบริหารจัดการทรัพยากรธรรมชาติและสิ่งแวดล้อมที่กำลังใช้และมีการพัฒนาเพิ่มเติมและ เป็นที่ยอมรับของประเทศต่างๆ โดยเฉพาะประเทศที่พัฒนาแล้ว คือ ระบบการวิเคราะห์ผลกระทบสิ่งแวดล้อม (Environmental Impact Assessment, EIA) และระบบการประเมินสิ่งแวดล้อมระดับยุทธศาสตร์ (Strategic Environmental Assessment, SEA) สำหรับประเทศไทย ระบบการวิเคราะห์ผลกระทบสิ่งแวดล้อมมีการนำมาใช้และอยู่ในกฎหมาย คือ พระราชบัญญัติส่งเสริมและรักษาคุณภาพสิ่งแวดล้อมแห่งชาติ พ.ศ. 2535 แต่ระบบการประเมินสิ่งแวดล้อมระดับ ยุทธศาสตร์ ยังไม่มีการนำมาใช้อย่างเป็นทางการ ซึ่งหน่วยราชการที่เกี่ยวข้องกำลังดำเนินการจัดทำและเตรียมคู่มือ และขั้นตอนในการดำเนินการอยู่ ซึ่งเมื่อเสร็จเรียบร้อย การประเมินสิ่งแวดล้อมระดับยุทธศาสตร์จะเป็นเครื่องมือใน ระดับที่กว้างกว่าระดับของระบบการวิเคราะห์ผลกระทบสิ่งแวดล้อมที่มีอยู่ในปัจจุบัน ซึ่งจะพิจารณาเฉพาะในส่วน ของโครงการหรือกิจกรรมเป็นหลัก รวมทั้งระบบการประเมินสิ่งแวดล้อมระดับยุทธศาสตร์จะสามารถช่วยในการตัดสิน ใจการดําเนินโครงการอย่างถูกต้อง เพราะต้องพิจารณาตั้งแต่ระดับนโยบาย (Policy) การวางแผน (Plan) และการ วางแผนงาน (Program) ก่อนการตัดสินใจดําเนินโครงการ (Project)

Natural Document Clustering By Clique Percolation In Random Graphs, Wei Gao, Kam-Fai Wong

Research Collection School Of Computing and Information Systems

Document clustering techniques mostly depend on models that impose explicit and/or implicit priori assumptions as to the number, size, disjunction characteristics of clusters, and/or the probability distribution of clustered data. As a result, the clustering effects tend to be unnatural and stray away more or less from the intrinsic grouping nature among the documents in a corpus. We propose a novel graph-theoretic technique called Clique Percolation Clustering (CPC). It models clustering as a process of enumerating adjacent maximal cliques in a random graph that unveils inherent structure of the underlying data, in which we unleash the commonly practiced constraints in …

Fast Tracking Of Near-Duplicate Keyframes In Broadcast Domain With Transitivity Propagation, Chong-Wah Ngo, Wan-Lei Zhao, Yu-Gang Jiang

Research Collection School Of Computing and Information Systems

The identification of near-duplicate keyframe (NDK) pairs is a useful task for a variety of applications such as news story threading and content-based video search. In this paper, we propose a novel approach for the discovery and tracking of NDK pairs and threads in the broadcast domain. The detection of NDKs in a large data set is a challenging task due to the fact that when the data set increases linearly, the computational cost increases in a quadratic speed, and so does the number of false alarms. This paper explores the symmetric and transitive nature of near-duplicate for the effective …

Large Grain Size Stochastic Optimization Alignment, Hyrum Carroll, Mark J. Clement, Perry Ridge, Dan Sneddon, Quinn O. Snell

Faculty Publications

DNA sequence alignment is a critical step in identifying homology between organisms. The most widely used alignment program, ClustalW, is known to suffer from the local minima problem, where suboptimal guide trees produce incorrect gap insertions. The optimization alignment approach, has been shown to be effective in combining alignment and phylogenetic search in order to avoid the problems associated with poor guide trees. The optimization alignment algorithm operates at a small grain size, aligning each tree found, wasting time producing multiple sequence alignments for suboptimal trees. This research develops and analyzes a large grain size algorithm for optimization alignment that …

Simulating The Maximum Domain Wall Speed In A Magnetic Nanowire, Andrew Kunz

Physics Faculty Research and Publications

The dynamics of domain wall motion in permalloy nanowires have been simulated utilizing the Landau-Lifshitz-Gilbert (LLG) equation of motion. The simulation results are presented in terms of the domain wall speed for ranges of the Gilbert damping parameter alpha and nanowire width. The maximum domain wall speed is independent of alpha. The speed of the domain wall can be increased by increasing the nanowire width, but this lowers the critical field. For applied fields below the critical field, the wall moves uniformly along the wire and the speed of the wall increases with increases in the driving field. This behavior …

New Physics Professor Returns To Alma Mater, Bjorn Karlman

Lake Union Herald

No abstract provided.