Digital Commons Network^™

Dna Analysis Using Grammatical Inference, Cory Cook

Master's Projects

An accurate language definition capable of distinguishing between coding and non-coding DNA has important applications and analytical significance to the field of computational biology. The method proposed here uses positive sample grammatical inference and statistical information to infer languages for coding DNA.

An algorithm is proposed for the searching of an optimal subset of input sequences for the inference of regular grammars by optimizing a relevant accuracy metric. The algorithm does not guarantee the finding of the optimal subset; however, testing shows improvement in accuracy and performance over the basis algorithm.

Testing shows that the accuracy of inferred languages for …

Image Spam Analysis, Annapurna Sowmya Annadatha

Master's Projects

Image spam is unsolicited bulk email, where the message is embedded in an image. This technique is used to evade text-based spam lters. In this research, we analyze and compare two novel approaches for detecting spam images. Our rst approach focuses on the extraction of a broad set of image features and selection of an optimal subset using a Support Vector Machine (SVM). Our second approach is based on Principal Component Analysis (PCA), where we determine eigenvectors for a set of spam images and compute scores by projecting images onto the resulting eigenspace. Both approaches provide high accuracy with low …

Job Satisfaction As Correlates Of Librarians’ Productivity In Public University Libraries In Nigeria, Japheth Abdulazeez Yaya Phd, Rosaline Oluremi Opeke Phd, Uluoma Doris Onuoha Phd

Library Philosophy and Practice (e-journal)

Job satisfaction of employees plays a crucial role in determining the general productivity of workers in any organization. The general opinion was that job satisfaction and productivity of librarians in public university libraries in Nigeria were low and a cause for concern. This study investigated the relationship between job satisfaction and productivity of librarians in Nigerian public universities. A correlational survey research design was adopted. The study population consisted of 1,254 librarians in public university libraries in Nigeria, from which 923 were selected using simple random sampling. The research instrument used was a self-developed questionnaire. The questionnaire validation was subjected …

Integration Of General Education Into The Senior Capstone Class In Engineering, Patricia Backer, Laura Sullivan-Green

Faculty Publications

Over the past few years, San Jose State University (SJSU) has mandated that all of the undergraduate degree programs including engineering degrees be set at 120 units. With the existing number of units for the BS engineering degrees, this mandatory requirement has led to new innovations in General Education (GE) at SJSU. We have created a two-course sequence to support the integration of upper division General Education into the engineering major. Advanced GE at SJSU is designed to help students become integrated thinkers who can see connections between and among a variety of concepts and ideas. In the College of …

The Role Of Bed Shear Stress In Sediment Sorting Patterns In A Reconstructed, Gravel Bed River, Samuel Emerson

Master's Theses

The role of bed shear stress in bed surface grain size sorting was investigated on a reconstructed reach of the Merced River in the Central Valley of California. Pebble count data were collected at the inside, middle, and outside of ten bends in April 2015 and compared to data from pebble counts conducted in previous years. Output from a previously developed 2D flow model (FaSTMECH) was compared to critical shear stresses calculated from median grain-size data. Comparison of pebble count results from 2002 through 2015 showed that there was no temporally consistent pattern of coarsening or fining along the study …

Effects Of Global Change On Algal Biomineralization And Benthic Community Interactions On California's Temperate Rocky Reefs, Emily Marie Donham

Master's Theses

Marine ecosystems are threatened by CO2-driven global change, such as ocean warming and acidification (OA). The primary objectives of this study were to: 1) assess the response of the coralline red alga, Calliarthron cheilosporioides, to global change; and 2) investigate the responses of California’s kelp forest communities to OA and sea urchin grazing. Results indicated that C. cheilosporioides growth and calcification were reduced under both increased temperatures and increased pCO2 despite increased photosynthetic rates in high pCO2 conditions. Mineralogy did not differ among treatments as a function of warming or acidification. Differences were observed in Mg incorporation into calcified walls …

Intercolony Comparison Of Diets Of Western Gulls In Central California, Anne L. Cassell

Master's Theses

As human populations expand, they force free-ranging animals to adapt to an increasingly urban environment, resulting in changes in diets, reproductive success, and mortality. The diets of two western gull (Larus occidentalis) breeding populations in central California were compared. One colony, Año Nuevo Island (ANI), is 1 km from shore and within 30 km of a municipal landfill. The other colony, Southeast Farallon Island (SEFI), is located 45 km off the shore of San Francisco, CA. Given the proximity of ANI to the shore and the landfill, I predicted that gulls from ANI would have more garbage in their diets. …

Variation In Adrenal And Thyroid Hormones With Life-History Stage In Juvenile Northern Elephant Seals (Mirounga Angustirostris), Jennifer Jelincic

Master's Theses

Interpretation of stress responses in wildlife is inadequate due to the range of natural variation and potential confounds of individual and life-history variables. In marine mammals, endocrine response data are sparse and variable across species. Blood adrenal and thyroid hormones were measured in 144 chemically immobilized yearling elephant seals at Año Nuevo State Reserve to characterize variation between sexes and across semiannual haul-outs. There was no relationship between hormone concentration and time needed for collecting blood or diel pattern, suggesting that concentrations represented baseline values. Serum cortisol concentrations did not vary with gender or across fasts but increased dramatically during …

Effects Of Substrate Warming On Sessile Marine Invertebrate Communities In Monterey Bay, California, Stephen Loiacono

Master's Theses

Increasing average global sea temperatures are one of the most direct and alarming consequences of climate change, yet it is still unclear how sessile marine communities will respond in the near- and long-term. In addition, it is unclear if warming ocean temperatures will facilitate marine invasions or primarily benefit native species. To simulate the effects of increasing ocean temperatures on sessile communities, heated settlement plates (n=7) were used in an in situ field experiment to investigate how an increase in substrate temperature (2.5°C above ambient) would affect recruitment and community development as compared to unheated control plates (n=9). Experimental treatments …

Treatment Of Sk-Mel-28 Cells With R-Moj-Dm Upregulates Pro-Apoptotic Genes P53 And Tnf-B While Downregulating Oncogene C-Myc, Melissa Lombardo

Master's Theses

Cell death by apoptosis is the result of one or multiple signaling pathways that can be initiated inside or outside the cell for a variety of reasons. Integrins, expressing themselves on the cell surface, play a central role in some apoptotic pathways. Cancer cells have been known to bypass this function and upregulate survival factor genes in order to elude apoptosis and thrive in the body, thus creating an environment in which it is possible for them to grow and metastasize. Previously in Dr. Soto’s lab, a recombinant disintegrin mutant, r-Moj-DM, was shown to induce apoptosis in melanoma cell line …

Cultural Influences In Political Ideology: Conservatism And Vertical Individualism, Cyrus Sarrafpour

Master's Theses

After an extensive literature review on authoritarianism and right-wing ideology, Jost, Kruglanski, Glaser, and Sulloway (2003) developed a model of conservatism as motivated social cognition. The model asserts that feelings of uncertainty, fear, and threat stimulate existential, epistemic, and ideological social-cognitive motives, which in turn lead to political conservatism in the forms of resistance to change and endorsement of inequality. The model, however, generally bypassed the notion that situational factors, such as cultural values, might also be influential in the manifestation and shaping of conservative ideologies. This study included situational factors such as the role of a hierarchical cultural dimension …

Evaluation Of The Effects Of Walnut Extract On The Cell Division G2/M Cyclin-Cyclin B1 In Breast Cancer Cells, Savita Pinaki Shah

Master's Theses

Walnuts are rich in polyphenols and have potential for cancer prevention and treatment. Our lab has previously shown that a walnut extract (WE) is able to block the cell cycle at the S and G2 phases of cell division with a corresponding decrease in the amount of the cyclin B1 protein and induce cell death in human breast cancer cells (Le et al., 2014). The aim of the current research was to identify whether this effect on the expression of cyclin B1 was at the transcriptional or the translational level. A cycloheximide (CHX) chase revealed that a WE does not …

A Sedimentological Analysis Of The Siliciclastic Fraction In Pliocene Core Sediments From Bowers Ridge, Bering Sea (Iodp Exp 323), Melinda Tanner

Master's Theses

The analysis and interpretation of sediment cores constitutes an important data record that can be used to evaluate paleoclimatic conditions and changes over time. The causes for the cooling trend that began in the Eocene, and its intensification with the onset of North Hemisphere Glaciation (NHG), remain under debate. Using sediment core samples from Site U1341 in the Bering Sea, the principal goal of this thesis was to examine the record at 1.9-4.2 Ma, using sedimentologic tools to interpret the siliciclastic fraction and ascertain whether and which portion is due to ice-related input. Previous research estimates the onset to begin …

34th Annual African American Commencement, 2016, San Jose State University, Associated Students

African American Commencement

34th Annual African American Commencement

"Black Grad: Cultivating Black Excellence." The 2016 African American Commencement ceremony was held on Friday, May 27, 2016 in the Student Union Ballroom at San Jose State University.

Multiple Sequence Alignment With Pro Le Hidden Markov Models, Shubhangi Rakhonde

Master's Projects

The human genome consists of various patterns and sequences that are of biolog- ical signi cance. Capturing these patterns can help us in resolving various mysteries related to the genome, like how genomes evolve, how diseases occur due to genetic mutation, how viruses mutate to cause new disease and what is the cure for these diseases. All these applications are covered in the study of bioinformatics.

One of the very common tasks in bioinformatics involves simultaneous alignment of a number of biological sequences. In bioinformatics, this is widely known as Mul- tiple Sequence Alignment. Multiple sequence alignments help in grouping …

Spartan Daily, May 12, 2016, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2016

Volume 146, Issue 42

Spartan Daily, May 11, 2016, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2016

Volume 146, Issue 41

Applications Of Forensic Evidence In Criminal Cases, Emily Wheeler

Themis: Research Journal of Justice Studies and Forensic Science

In 2003, Massachusetts governor Mitt Romney proposed a plan for an infallible death penalty that required irrefutable scientific evidence, effectively removing any doubt regarding potential innocence in death penalty cases. Forensic science encompasses many scientific disciplines including natural sciences and pattern analysis, but not all such areas experience equal amounts of general acceptance or influence in criminal cases. While DNA analysis and fingerprint identification using the Integrated Automated Fingerprint Identification System (IAFIS) are both widely accepted forensic applications, recent events expose concerns regarding the authenticity of other disciplines such as hair and bite mark comparison. Before policymakers address the issue …

Spartan Daily, May 10, 2016, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2016

Volume 146, Issue 40

The Effects Of Epigenetics On Stress Response, Kevin Suddarth

Themis: Research Journal of Justice Studies and Forensic Science

Despite the vast amount of resources at the disposal of humanity today, the intricacies of human biology are often a mystery. The chemical and biological products of the human genome have been well studied and documented, but many of the chemical and neurological pathways are missing quite a few details. The human stress response is one of the most primal and valuable functions of this code that developed as a self- preservation mechanism (Hans, 1975) to naturally increase the odds of procreation. However, this function is prone to overload, particularly in individuals with certain epigenetic traits instilled by early life …

Not Yet Legal And In Prison?, Araseli Saldivar

Themis: Research Journal of Justice Studies and Forensic Science

The United States is the only industrialized country that

sentences individuals to spend the remainder of their lives in

prison for a crime they committed before the age of eighteen.

The justice system established the sentencing of juveniles to life

in prison without the possibility of parole to deter juvenile

delinquency. Life without parole was regarded as an appropriate

punishment following the rise of juvenile crime during the 1980s

and 1990s. However, as psychological differences between

juveniles and adults became more prominent, society began to

regard life without the possibility of parole as a cruel and

unusual punishment. Although some …

A Prison Of Education: The School-To-Prison Pipeline In Low-Income Schools, Adam Le

Themis: Research Journal of Justice Studies and Forensic Science

This paper examines the relationship between prisons and education in American culture, comparing public schools in California cities to wealthier private schools. The essay critiques the American dream’s notions of social stratification and success of the individual in racialized areas. The first section compares funding disparities between education and prison and argues that while funding is an integral part of the inner-city’s problem, the curriculum itself is ineffective. The second section takes a closer look at differences in the curricula and educational settings of an inner-city school and a private school. It offers ethnic studies in secondary education as a …

Beyond Dna: Epigenetics And Proteomics In Forensic Science, Diane F. Eilerts

Themis: Research Journal of Justice Studies and Forensic Science

The use of genetic evidence in criminal cases is well established and has improved the public opinion and credibility of forensic science. However, several shortcomings associated with current genetic profiling techniques exist. Scientific research aimed at increasing the overall knowledge and understanding of biological factors will lead to the development of methods capable of improving the discriminating power of DNA evidence, overcoming limitations associated with DNA evidence, or complementing current methods of DNA profiling. Increased research in the fields of epigenetics and proteomics are particularly promising and relevant to forensic science. Research suggests that epigenetic biomarkers can be used to …

Spartan Daily, May 5, 2016, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2016

Volume 146, Issue 39

Ron Pinkham Interview, Ron Pinkham

San Jose Experiences of American Indians in the Urban Relocation Project

No abstract provided.

Sjsu Erfa Board Minutes, May 2, 2016, San Jose State University, Emeritus And Retired Faculty Association

SJSU ERFA Minutes

SJSU ERFA Executive Board Minutes

May 2, 2016

How Code Enforcement Mitigates Hoarding In The Community, Jason Gibilisco

Master's Projects

No abstract provided.

Undiagnosed Depression In The Elderly And Healthcare Education, Nancy J. Wynn-Grundy

Doctoral Projects

This descriptive study examined undiagnosed depression in the elderly and how it affects the elderly from retaining healthcare education. It is estimated by 2029, 20% of the United States population will be age 65 and older (Colby & Ortman, 2014). Depression in the elderly who have chronic diseases, is estimated to be undiagnosed up to 40% (Chaoyang et al., 2009). A hallmark symptom of depression is the inability to concentrate. It is unknown if undiagnosed depression will affect the older adult from retaining pertinent healthcare education. The 30 point Geriatric Depression Scale (GDS) was administered to a class of elderly …

Teaching And Evaluation Of Suicidal Assessment, Five-Step Evaluation And Triage (Safe-T) In The Emergency Department, Evangeline Rico

Doctoral Projects

Suicide remains to be a global and a national problem, and it continues to be one of the leading causes of death in the United States (U.S.) The Emergency Department (ED), being the gateway to the hospital can provide a great opportunity to assess each patient for suicidal ideation, and evaluate if patients present with risk factors for suicide. The competency of the ED staff plays a critical role in early recognition of patients who are at risk, and in implementing a plan of care for those with positive screens. However, researchers showed that knowledge deficit and lack of education …

The Impact Of Intensive Case Management On Hospice Utilization, Debra Lowry Hummel

Doctoral Projects

Objective: The purpose of this study is to examine if patients enrolled in multi-disciplinary intensive case management program (ImPACT) alter the patient’s end-of-life path or setting of death.

Methods: The quality improvement project is a quantitative retrospective study that compared patients receiving standard primary care vs intensive case management (ImPACT) during 2/2013-1/2014. It is a secondary analysis of a larger study of a quality improvement evaluation that took place at the Veterans Administration facility in Palo Alto, Ca.

Results: Among the 82 patients who died, 19 were enrolled in ImPACT for approximately 249 days compared to 63 who received standard …