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The Scientist, Spring 2007, San Jose State University, College Of Science Jan 2007

The Scientist, Spring 2007, San Jose State University, College Of Science

The Scientist (College of Science)

No abstract provided.


India’S Emergence As A “Responsible” Nuclear Power, Karthika Sasikumar Jan 2007

India’S Emergence As A “Responsible” Nuclear Power, Karthika Sasikumar

Faculty Publications

In 2005, India and the United States announced a nuclear “deal” that would seek to clarify India’s ambiguous status in the nuclear order. The sole superpower appeared to be recognizing India’s status as a nuclear-armed state by opening up the possibility of nuclear cooperation. This announcement represented the fruit of many years of careful Indian diplomacy aimed at establishing its identity as a responsible possessor of nuclear weapons and forging a closer alliance with the US. This article provides a concise description of the provisions of the 2005 India-US nuclear agreement, and analyzes its global, regional, and domestic implications. While …


How Heel Oxygenation Changes Under Pressure, Vivian K. Wong, N. A. Stotts, H. W. Hopf, E. S. Froelicher, G. A. Dowling Jan 2007

How Heel Oxygenation Changes Under Pressure, Vivian K. Wong, N. A. Stotts, H. W. Hopf, E. S. Froelicher, G. A. Dowling

Faculty Publications

The mechanism of heel pressure ulcers after hip surgery is not entirely understood. The purpose of this one-group, prospective, repeated-measures design study was to examine how the external pressure of the bed surface affects heel skin oxygen tension in adults on the first 3 days after hip surgery. Transcutaneous oxygen sensors were placed on the plantar surface of each foot, close to the heels. Measures were taken on room air and with an oxygen challenge with the heels (1) suspended above the bed surface (preload), (2) on the bed surface for 15 minutes (loading), and (3) again suspended above the …


Left-Right Olfactory Asymmetry Results From Antagonistic Functions Of Voltage-Activated Calcium Channels And The Raw Repeat Protein Olrn-1 In C. Elegans, S L. Bauer Haung, Y Saheki, Miri Vanhoven, I Torayama, T Ishihara, I Katsura, A Van Der Linden, P Sengupta, C I. Bargmann Jan 2007

Left-Right Olfactory Asymmetry Results From Antagonistic Functions Of Voltage-Activated Calcium Channels And The Raw Repeat Protein Olrn-1 In C. Elegans, S L. Bauer Haung, Y Saheki, Miri Vanhoven, I Torayama, T Ishihara, I Katsura, A Van Der Linden, P Sengupta, C I. Bargmann

Faculty Publications, Biological Sciences

The left and right AWC olfactory neurons in Caenorhabditis elegans differ in their functions and in their expression of chemosensory receptor genes; in each animal, one AWC randomly takes on one identity, designated AWCOFF, and the contralateral AWC becomes AWCON. Signaling between AWC neurons induces left-right asymmetry through a gap junction network and a claudin-related protein, which inhibit a calcium-regulated MAP kinase pathway in the neuron that becomes AWCON. Results We show here that the asymmetry gene olrn-1 acts downstream of the gap junction and claudin genes to inhibit the calcium-MAP kinase pathway in AWCON. OLRN-1, a protein with potential …


Outsourcing In Biopharmaceutical Industry: India's Value Propositions, S. Dhar, Mahesh N. Rajan Jan 2007

Outsourcing In Biopharmaceutical Industry: India's Value Propositions, S. Dhar, Mahesh N. Rajan

Faculty Publications

In this paper we discuss the rationale behind biopharmaceutical outsourcing. We then discuss the benefits, challenges, current trends and market opportunities. From January 2005, India has agreed to comply with the product patent protection in accordance with the obligation under the TRIPS Agreement of the WTO. This has created new opportunities as well as challenges for the Indian biopharmaceutical companies. We analyze the value proposition of India as a suitable destination for outsourcing in biopharmaceutical industry in this new business environment. This research will help managers to understand the benefits of biopharmaceutical outsourcing along with its challenges under the current …


Finding Molecular Complexes Through Multiple Layer Clustering Of Protein Interaction Networks, Bill Andreopoulos, Aijun An, Xiangji Huang, Xiaogang Wang Jan 2007

Finding Molecular Complexes Through Multiple Layer Clustering Of Protein Interaction Networks, Bill Andreopoulos, Aijun An, Xiangji Huang, Xiaogang Wang

Faculty Publications, Computer Science

Clustering protein-protein interaction networks (PINs) helps to identify complexes that guide the cell machinery. Clustering algorithms often create a flat clustering, without considering the layered structure of PINs. We propose the MULIC clustering algorithm that produces layered clusters. We applied MULIC to five PINs. Clusters correlate with known MIPS protein complexes. For example, a cluster of 79 proteins overlaps with a known complex of 88 proteins. Proteins in top cluster layers tend to be more representative of complexes than proteins in bottom layers. Lab work on finding unknown complexes or determining drug effects can be guided by top layer proteins.


Analysis And Kinetics Of The Sequencing Batch Reactors, Udeme J. Ndon Jan 2007

Analysis And Kinetics Of The Sequencing Batch Reactors, Udeme J. Ndon

Faculty Publications

Fundamental analysis and kinetics of treatment reactors are major topics in environmental engineering literature. These fundamental topics in reactor processes are well known for the ideal batch reactor, the continuous stirred tank reactor, and the plug flow reactor. The sequencing batch reactors (SBRs) are relatively new in the field, but are widely used. Despite the wide application of sequencing batch reactors in the field, information is lacking on the fundamental analysis and kinetics, especially with comparison to the ideal batch reactor. This report presents analysis and kinetics of the sequencing batch reactors and compares the kinetics equations developed with those …


Feeding In Extreme Flows: Behavior Compensates For Mechanical Constraints In Barnacle Cirri, Luke P. Miller Jan 2007

Feeding In Extreme Flows: Behavior Compensates For Mechanical Constraints In Barnacle Cirri, Luke P. Miller

Faculty Publications, Biological Sciences

Plastic morphological changes in response to environmental cues can allow organisms to adapt to their local environment. Barnacle feeding legs (cirri) exhibit substantial plasticity in size and shape along wave exposure gradients on rocky shores, but only up to a certain limit in maximum water velocities. Above the limit, the morphology of the cirri becomes invariant. Behavioral observations of barnacles feeding at a wave-exposed shore indicate that the fast response time for feeding motions allows barnacles to avoid potentially damaging flows associated with breaking waves, while still allowing feeding between wave impacts. The ability of barnacles to avoid individual waves …


Corticosterone And Foraging Behaviour In A Pelagic Seabird, F Angelier, Scott A. Shaffer, H Weimerskirch, C Trouvé, O Chastel Jan 2007

Corticosterone And Foraging Behaviour In A Pelagic Seabird, F Angelier, Scott A. Shaffer, H Weimerskirch, C Trouvé, O Chastel

Faculty Publications, Biological Sciences

Because endocrine mechanisms are thought to mediate behavioral responses to changes in the environment, examining these mechanisms is essential for understanding how long-lived seabirds adjust their foraging decisions to contrasting environmental conditions in order to maximize their fitness. In this context, the hormone corticosterone (CORT) deserves specific attention because of its major connections with locomotor activities. We examined for the first time the relationships between individual CORT levels and measurements of foraging success and behavior using satellite tracking and blood sampling from wandering albatrosses (Diomedea exulans) before (pretrip CORT levels) and after (posttrip CORT levels) foraging trips during the incubation …


Hydrophobic, Organically-Modified Silica Gels Enhance The Structure Of Encapsulated Apomyoglobin, Daryl K. Eggers, V. A. Rocha Jan 2007

Hydrophobic, Organically-Modified Silica Gels Enhance The Structure Of Encapsulated Apomyoglobin, Daryl K. Eggers, V. A. Rocha

Faculty Publications, Chemistry

Insertion of hydrophobic groups in a silica matrix, by addition of propyl- or trifluoropropyltrimethoxysilane, leads to a surprising increase in the helical content of apomyoglobin following encapsulation by the sol–gel technique


Numerical Methods For The Stochastic Landau-Lifshitz Navier-Stokes Equations, Alejandro Garcia, J. B. Bell, S. Williams Jan 2007

Numerical Methods For The Stochastic Landau-Lifshitz Navier-Stokes Equations, Alejandro Garcia, J. B. Bell, S. Williams

Faculty Publications

The Landau-Lifshitz Navier-Stokes (LLNS) equations incorporate thermal fluctuations into macroscopic hydrodynamics by using stochastic fluxes. This paper examines explicit Eulerian discretizations of the full LLNS equations. Several computational fluid dynamics approaches are considered (including MacCormack’s two-step Lax-Wendroff scheme and the piecewise parabolic method) and are found to give good results for the variance of momentum fluctuations. However, neither of these schemes accurately reproduces the fluctuations in energy or density. We introduce a conservative centered scheme with a third-order Runge-Kutta temporal integrator that does accurately produce fluctuations in density, energy, and momentum. A variety of numerical tests, including the random walk …


Borders, Boundaries And Liminal Spaces Jan 2007

Borders, Boundaries And Liminal Spaces

SWITCH

The Borders, Boundaries & Liminal Spaces conference, hosted by Ars Virtua in Second Life and sponsored by CADRE, brought together theorists, scholars, and artists for a three-day discussion of how borders and identities shift in digital spaces. Set within the world of Second Life, the conference explored topics like architecture and archaeology, digital embodiment, posthuman performance, and gaming systems.


A Microbial Infected In Vitro Wound Model Treated Through Microdialysis, Gina T. Giannini Jan 2007

A Microbial Infected In Vitro Wound Model Treated Through Microdialysis, Gina T. Giannini

Master's Theses

No abstract provided.


Afferent Innervation Of The Toadfish Utricle (Opsanus Tau), Alireza Ehsanian Mofrad Jan 2007

Afferent Innervation Of The Toadfish Utricle (Opsanus Tau), Alireza Ehsanian Mofrad

Master's Theses

No abstract provided.


Design And Analysis Of Ultra Wide Band Cmos Lna, Janmejay Adhyaru Jan 2007

Design And Analysis Of Ultra Wide Band Cmos Lna, Janmejay Adhyaru

Master's Theses

No abstract provided.


Using Phone Call Reports To Assess The Relative Abundance Of Urban Mesopredators, Christine Alyssa Klinkowski Jan 2007

Using Phone Call Reports To Assess The Relative Abundance Of Urban Mesopredators, Christine Alyssa Klinkowski

Master's Theses

No abstract provided.


Emotional And Domain Concept Enhancements To Alicebot, Alvin Cho Jan 2007

Emotional And Domain Concept Enhancements To Alicebot, Alvin Cho

Master's Projects

Extensive research and development have been done in the area of human simulation and artificial intelligence and their related fields, such as common sense knowledge bases, chatterbots, natural language parsing, semantic analysis, synthetic actors, and cognitive sciences. This paper takes part in that extensive research by focusing on the improvement of human simulation in chatterbots, specifically in Alicebot, a prominent non-emotional pattern-matching chatbot. An emotion and personality model is added to Alicebot so that it can make decisions based on its emotions and personality. Alicebot is also augmented with the ability to determine what it likes or does not like …


Pairwise Alignment Of Metamorphic Computer Viruses, Scott Mcghee Jan 2007

Pairwise Alignment Of Metamorphic Computer Viruses, Scott Mcghee

Master's Projects

Computer viruses and other forms of malware pose a threat to virtually any software system (with only a few exceptions). A computer virus is a piece of software which takes advantage of known weaknesses in a software system, and usually has the ability to deliver a malicious payload. A common technique that virus writers use to avoid detection is to enable the virus to change itself by having some kind of self-modifying code. This kind of virus is commonly known as a metamorphic virus, and can be particularly difficult to detect [17]. Existing virus detection software is continually being improved …


Operon Prediction With Bayesian Classifiers, Natalia Khuri Jan 2007

Operon Prediction With Bayesian Classifiers, Natalia Khuri

Master's Projects

In this work, we present an approach to predicting transcription units based on Bayesian classifiers. The predictor uses publicly available data to train the classifier, such as genome sequence data from Genbank, expression values from microarray experiments, and a collection of experimentally verified transcription units. We have studied the importance of each of the data source on the performance of the predictor by developing three classifier models and evaluating their outcomes. The predictor was trained and validated on the E. coli genome, but can be extended to other organisms. Using the full Bayesian classifier, we were able to correctly identify …


Prediction Of Alternative Splice Sites In Human Genes, Douglas Simmons Jan 2007

Prediction Of Alternative Splice Sites In Human Genes, Douglas Simmons

Master's Projects

This thesis addresses the problem of predicting alternative splice sites in human genes. The most common way to identify alternative splice sites are the use of expressed sequence tags and microarray data. Since genes only produce alternative proteins under certain conditions, these methods are limited to detecting only alternative splice sites in genes whose alternative protein forms are expressed under the tested conditions. I have introduced three multiclass support vector machines that predict upstream and downstream alternative 3’ splice sites, upstream and downstream alternative 5’ splice sites, and the 3’ splice site of skipped and cryptic exons. On a test …


Biogeography And The Cambrian Radiation Of Arachnomorph Arthropods, Jonathan R. Hendricks, Bruce S. Lieberman Jan 2007

Biogeography And The Cambrian Radiation Of Arachnomorph Arthropods, Jonathan R. Hendricks, Bruce S. Lieberman

Faculty Publications

Biogeographic patterns in primarily Cambrian arachnomorph taxa are investigated using a recently constructed phylogenetic hypothesis in order to explore the biogeographic context of the Cambrian radiation. A modified version of Brooks Parsimony Analysis is employed to elucidate patterns of vicariance and geodispersal in taxa from six regions (Laurentia, Baltica, Siberia, Australia, Africa and China). Well resolved vicariance and geodispersal trees are very similar and reconstruct Laurentia and China as sister areas. This close area relationship between Laurentia and China provides extensive evidence for congruent vicariance and range expansion in Cambrian arachnomorphs, while data from trilobites do not show this pattern. …


Learning 2.0 At Sjsu And Sjpl, Susan L. Kendall Jan 2007

Learning 2.0 At Sjsu And Sjpl, Susan L. Kendall

Faculty and Staff Publications

No abstract provided.


Interdisciplinary Research At The University Of Illinois At Chicago: A Campus-Wide Survey Of Climate, Obstacles And Opportunities, Dennis Rosenbaum, Amie Schuck, Mark Mattaini, Ericka Adams Jan 2007

Interdisciplinary Research At The University Of Illinois At Chicago: A Campus-Wide Survey Of Climate, Obstacles And Opportunities, Dennis Rosenbaum, Amie Schuck, Mark Mattaini, Ericka Adams

Faculty Publications

In recent years, the administration, faculty and research professionals at the University of Illinois at Chicago have shown considerable interest in facilitating interdisciplinary research on campus. Beginning in 2006, the Office of the Provost and the Office of the Vice Chancellor for Research provided seed funding for the creation of several interdisciplinary research (IDR) centers on campus to encourage interdisciplinary and transdisciplinary scholarship and education. This study is a product of one of those centers – the UIC Interdisciplinary Center for Research on Violence. The study was undertaken with three primary objectives: (1) to assess the IDR climate and level …


A Conversation With Michael Joaquin Grey, Thomas Asmuth Jan 2007

A Conversation With Michael Joaquin Grey, Thomas Asmuth

SWITCH

In this interview, Michael Joaquin Grey discusses his work at the intersection of art, science, and pedagogy, including the art/science movement of the 1970’s and its counterpart around the year 2000. With a background in both genetics and sculpture, he’s interested in how complex systems like biology, computers, or culture grow and connect. Grey also talks about inventing ZOOB, a building toy that helps kids understand how living systems work. Throughout the conversation, he reflects on why artists don’t always need big institutions to do meaningful research and how early learning and play can shape how we think about the …


Effects Of Fire On Rare Ericameria Fasciculata (Asteraceae), Jon Detka Jan 2007

Effects Of Fire On Rare Ericameria Fasciculata (Asteraceae), Jon Detka

Master's Theses

No abstract provided.


Distribution And Abundance Of Forensically Important Flies In Santa Clara County, Adrienne Leane Brundage Jan 2007

Distribution And Abundance Of Forensically Important Flies In Santa Clara County, Adrienne Leane Brundage

Master's Theses

No abstract provided.


Molecular Detection And Genotyping Of Human Respiratory Viruses, Ishmeet Kalra Jan 2007

Molecular Detection And Genotyping Of Human Respiratory Viruses, Ishmeet Kalra

Master's Theses

No abstract provided.


Cattle Grazing Impacts On Vegetation Adjacent To Ponds In Santa Clara County, Ca, Dawn Elizabeth Lippe Jan 2007

Cattle Grazing Impacts On Vegetation Adjacent To Ponds In Santa Clara County, Ca, Dawn Elizabeth Lippe

Master's Theses

No abstract provided.


Provision Of Library And Information Services To The Visually Challenged Students In University Of Ghana, Legon, Efua Mansa Ayiah Mrs Jan 2007

Provision Of Library And Information Services To The Visually Challenged Students In University Of Ghana, Legon, Efua Mansa Ayiah Mrs

Library Philosophy and Practice (e-journal)

Visually Challenged students (VCS) in University of Ghana, Legon face various constraints in accessing library and information services. The study was based on Ranganathan’s five principles of librarianship. Literature was reviewed on provision and access to library and information services. The researcher adopted case study, since the sample size was small they were all included in the study. Descriptive data analysis technique was used to analyze data. Tables and graphs were used to display information. Findings of the study indicated that there is no program for VCS, they were aware of technological developments in information communication technologies (ICT), access to …


Spartan Daily, December 6, 2006, San Jose State University, School Of Journalism And Mass Communications Dec 2006

Spartan Daily, December 6, 2006, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily (School of Journalism and Mass Communications)

Volume 127, Issue 55