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A Database For The Study Of Marine Mammal Behavior: Gap Analysis, Data Standardization, And Future Directions, Scott A. Shaffer, D P. Costa Jan 2006

A Database For The Study Of Marine Mammal Behavior: Gap Analysis, Data Standardization, And Future Directions, Scott A. Shaffer, D P. Costa

Faculty Publications, Biological Sciences

A relational database that contained published information on the diving behavior and/or movement patterns of marine mammals was compiled to facilitate a modeling effort of the Effects of Sound on the Marine Environment (ESME) program. A total of 448 references from reports, books, and peer-reviewed journal articles were obtained. The metadata describing each animal studied, location of the study, and equipment used were entered into the database as well as empirical data describing the diving behavior and movement patterns of each animal. In total, the database contained 1815 entries from 51 different marine mammal species or subspecies. The majority of …

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Interpolation Of Tracking Data In A Fluid Environment, Y Tremblay, Scott A. Shaffer, S L. Fowler, C E. Kuhn, B I. Mcdonald, M J. Weise, C -A Bost, H Weimerskirch, D E. Crocker, M E. Goebel, D P. Costa Jan 2006

Interpolation Of Tracking Data In A Fluid Environment, Y Tremblay, Scott A. Shaffer, S L. Fowler, C E. Kuhn, B I. Mcdonald, M J. Weise, C -A Bost, H Weimerskirch, D E. Crocker, M E. Goebel, D P. Costa

Faculty Publications, Biological Sciences

Interpolation of geolocation or Argos tracking data is a necessity for habitat use analyses of marine vertebrates. In a fluid marine environment, characterized by curvilinear structures, linearly interpolated track data are not realistic. Based on these two facts, we interpolated tracking data from albatrosses, penguins, boobies, sea lions, fur seals and elephant seals using six mathematical algorithms. Given their popularity in mathematical computing, we chose Bézier, hermite and cubic splines, in addition to a commonly used linear algorithm to interpolate data. Performance of interpolation methods was compared with different temporal resolutions representative of the less-precise geolocation and the more-precise Argos …

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Estimating Hydrodynamic Quantities In The Presence Of Microscopic Fluctuations, Alejandro Garcia Jan 2006

Estimating Hydrodynamic Quantities In The Presence Of Microscopic Fluctuations, Alejandro Garcia

Faculty Publications

This paper discusses the evaluation of hydrodynamic variables in the presence of spontaneous fluctuations, such as in molecular simulations of fluid flows. The principal point is that hydrodynamic variables such as fluid velocity and temperature must be defined in terms of mechanical variables such as momentum and energy density). Because these relations are nonlinear and because fluctuations of mechanical variables are correlated, care must be taken to avoid introducing a bias when evaluating means, variances, and correlations of hydrodynamic variables. The unbiased estimates are formulated; some alternative, incorrect approaches are presented as cautionary warnings. The expressions are verified by numerical …

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Conservation Genetics Of Wild Born Bonobos (Pan Paniscus) Using Mitochondrial Dna, Amy E. Fontarensky Jan 2006

Conservation Genetics Of Wild Born Bonobos (Pan Paniscus) Using Mitochondrial Dna, Amy E. Fontarensky

Master's Theses

No abstract provided.

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Front Matter: Pacific Rim Jan 2006

Front Matter: Pacific Rim

SWITCH

Front matter for Issue 21 of SWITCH. This issue focuses on the Pacific Rim, a shared georgraphic and cultural space, and one of the four chosen themes for the ZeroOne/ ISEA 2006 Festival and Symposium.

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Towards New Bodies And New Biologies: Life As Code, Body As Protocol, Carlos Castellanos Jan 2006

Towards New Bodies And New Biologies: Life As Code, Body As Protocol, Carlos Castellanos

SWITCH

This article explores how advancement in technology has given rise to new ideas about the relationship between the human body and technology. The author examines bioart and interactive art practices to assess how bodies are shaped and controlled by information systems and, in return, how biological systems might influence technology.

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Biogeographical Genetic Variation Of The Dungeness Crab (Cancer Magister), Corinne H. Lardy Jan 2006

Biogeographical Genetic Variation Of The Dungeness Crab (Cancer Magister), Corinne H. Lardy

Master's Theses

No abstract provided.

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Genetic Analysis Of Oncorhynchus Mykiss In South San Francisco Bay Tributaries, Adam Hurst Gemar Jan 2006

Genetic Analysis Of Oncorhynchus Mykiss In South San Francisco Bay Tributaries, Adam Hurst Gemar

Master's Theses

No abstract provided.

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Generating Stable Constructs Of Beta-2 Adrenergic Receptor By Truncation, Meera Kumar Jan 2006

Generating Stable Constructs Of Beta-2 Adrenergic Receptor By Truncation, Meera Kumar

Master's Theses

No abstract provided.

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Microscopy Of The Turtle Utricle And Its Innervation, Heeral C. Kothari Jan 2006

Microscopy Of The Turtle Utricle And Its Innervation, Heeral C. Kothari

Master's Theses

No abstract provided.

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Habitat Partitioning In Two Sympatric Species Of Chipmunk, Warner Mountains, Ca, Mary Helen Poffenroth Jan 2006

Habitat Partitioning In Two Sympatric Species Of Chipmunk, Warner Mountains, Ca, Mary Helen Poffenroth

Master's Theses

No abstract provided.

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Genetic Characterization Of Four Populations In Two Subspecies Of Spotted Owl, Tonja Y. Chi Jan 2006

Genetic Characterization Of Four Populations In Two Subspecies Of Spotted Owl, Tonja Y. Chi

Master's Theses

No abstract provided.

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Genotyping A Second Growth Coast Redwood Forest : A High Throughput Methodology, Charles Steven Glavas Jan 2006

Genotyping A Second Growth Coast Redwood Forest : A High Throughput Methodology, Charles Steven Glavas

Master's Theses

No abstract provided.

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Factors Affecting Stickhouse Site Selection In Neotoma Fuscipes Using Gis, Jenna Catherine Patton Jan 2006

Factors Affecting Stickhouse Site Selection In Neotoma Fuscipes Using Gis, Jenna Catherine Patton

Master's Theses

No abstract provided.

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A Low-Noise, Low-Power Circuit For Impedance Measurement Of Biological Processes, Daniella Schefer Jan 2006

A Low-Noise, Low-Power Circuit For Impedance Measurement Of Biological Processes, Daniella Schefer

Master's Theses

No abstract provided.

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Molecular Methods For Estimating Soil Microbial Diversity In Salt Marshes, Jyoti Vyas Jan 2006

Molecular Methods For Estimating Soil Microbial Diversity In Salt Marshes, Jyoti Vyas

Master's Theses

No abstract provided.

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Landbird Diversity And Abundance In Native Monterey Pine Forests, Nellie Thorngate Jan 2006

Landbird Diversity And Abundance In Native Monterey Pine Forests, Nellie Thorngate

Master's Theses

No abstract provided.

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Morphological Variation In Clark's Nutcracker (Nucifraga Columbiana), Karen Viotto Jan 2006

Morphological Variation In Clark's Nutcracker (Nucifraga Columbiana), Karen Viotto

Master's Theses

No abstract provided.

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Analysis And Detection Of Metamorphic Computer Viruses, Wing Wong Jan 2006

Analysis And Detection Of Metamorphic Computer Viruses, Wing Wong

Master's Projects

Virus writers and anti-virus researches generally agree that metamorphism is the way to generate undetectable viruses. Several virus writers have released virus creation kits and claimed that they possess the ability to automatically produce morphed virus variants that look substantially different from one another. To see how effective these code morphing engines are, and how much difference exists between variants of a same virus, we measured the similarity between virus variants generated by four virus generators downloaded from the Internet. Our result shows that the effectiveness of these generators varies widely. While the best generator, NGVCK, is able to create …

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Study Of Rna Secondary Structure Prediction Algorithms, Lisa Yu Jan 2006

Study Of Rna Secondary Structure Prediction Algorithms, Lisa Yu

Master's Projects

Dynamic programming algorithms such as Nussinov algorithm and Zuker algorithm define criteria to search the most stable RNA secondary structures. Stochastic Context-Free Grammar (SCFG) predicts the most possible RNA secondary structure using context-free grammar and a defined set of probabilities for each grammar rule. These algorithms form the base of using computer programs to predict RNA secondary structures without pseudoknots. In this report, we review these RNA secondary structure prediction algorithms and present our own software implementations of these algorithms. The Nussinov algorithm is easy to understand. But our results show that the Nussinov algorithm is overly simplified and can …

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Visualization Of Secondary Rna Structure Prediction Algorithms, Brandon Hunter Jan 2006

Visualization Of Secondary Rna Structure Prediction Algorithms, Brandon Hunter

Master's Projects

This chapter introduces the secondary structure prediction problem. It describes what the secondary structure prediction problem is and why it is important. Based on the importance of the algorithm it is essential to have a clear means to visually represent the problem. Therefore, this chapter details the high level goals of the visualization. It details how the visualization will visually represent the problem through several simultaneous representations. These visual representations will be tied together in order to increase the understanding of the algorithm.

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Dna Damage Responses In Progeroid Syndromes Arise From Defective Maturation Of Prelamin A, Michael Sinensky, Y. Liu, A. Rusinol, Y. Wang, Y. Zou Jan 2006

Dna Damage Responses In Progeroid Syndromes Arise From Defective Maturation Of Prelamin A, Michael Sinensky, Y. Liu, A. Rusinol, Y. Wang, Y. Zou

Faculty Publications, Biological Sciences

The genetic diseases Hutchinson-Gilford progeria syndrome (HGPS) and restrictive dermopathy (RD) arise from accumulation of farnesylated prelamin A because of defects in the lamin A maturation pathway. Both of these diseases exhibit symptoms that can be viewed as accelerated aging. The mechanism by which accumulation of farnesylated prelamin A leads to these accelerated aging phenotypes is not understood. Here we present evidence that in HGPS and RD fibroblasts, DNA damage checkpoints are persistently activated because of the compromise in genomic integrity. Inactivation of checkpoint kinases Ataxia-telangiectasia-mutated (ATM) and ATR (ATM- and Rad3-related) in these patient cells can partially overcome their …

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Farnesylated Lamins, Progeroid Syndromes And Farnesyl Transferase Inhibitors, Michael Sinensky, A. E. Rusinol Jan 2006

Farnesylated Lamins, Progeroid Syndromes And Farnesyl Transferase Inhibitors, Michael Sinensky, A. E. Rusinol

Faculty Publications, Biological Sciences

Three mammalian nuclear lamin proteins, lamin B1, lamin B2 and the lamin A precursor, prelamin A, undergo canonical farnesylation and processing at CAAX motifs. In the case of prelamin A, there is an additional farnesylation-dependent endoproteolysis, which is defective in two congenital diseases: Hutchinson-Gilford progeria (HGPS) and restrictive dermopathy (RD). These two diseases arise respectively from defects in the prelamin A substrate and the enzyme (ZmpSte24) that processes it. Recent work has shed light on the roles of the lamin proteins and the enzymes involved in their farnesylation-dependent maturation. Other experimental work, including mouse model studies, have examined the possibility …

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Here Be Dragons!: Bio-Art Beyond The Edge Of Everything., Anne Farren, Andrew Hutchison Jan 2006

Here Be Dragons!: Bio-Art Beyond The Edge Of Everything., Anne Farren, Andrew Hutchison

SWITCH

This article explores how Perth, Western Australia has become an important center when it comes to bio-art.

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Spartan Daily, December 8, 2005, San Jose State University, School Of Journalism And Mass Communications Dec 2005

Spartan Daily, December 8, 2005, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily (School of Journalism and Mass Communications)

Volume 125, Issue 57

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Spartan Daily, December 5, 2005, San Jose State University, School Of Journalism And Mass Communications Dec 2005

Spartan Daily, December 5, 2005, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily (School of Journalism and Mass Communications)

Volume 125, Issue 54

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Spartan Daily, December 1, 2005, San Jose State University, School Of Journalism And Mass Communications Dec 2005

Spartan Daily, December 1, 2005, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily (School of Journalism and Mass Communications)

Volume 125, Issue 53

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Information Outlook, December 2005, Special Libraries Association Dec 2005

Information Outlook, December 2005, Special Libraries Association

Information Outlook, 2005

Volume 9, Issue 12

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Transvergence In Art History, Ami Davis Dec 2005

Transvergence In Art History, Ami Davis

SWITCH

SWITCH Issue 20 explores the theme of “Transvergence” in preparation for the ISEA2006 Symposium, hosted in San Jose as part of the ZeroOne Festival. This issue brings together ideas from artists, scientists, educators, and others to examine hybrid cultural experiences that transcend disciplines.

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Spartan Daily, November 30, 2005, San Jose State University, School Of Journalism And Mass Communications Nov 2005

Spartan Daily, November 30, 2005, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily (School of Journalism and Mass Communications)

Volume 125, Issue 52

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