Physical Sciences and Mathematics Commons^™

Uncovering And Characterizing Splice Variants Associated With Survival In Lung Cancer Patients, Sean West, Sushil Kumar, Surinder K. Batra, Hesham Ali, Dario Ghersi

Interdisciplinary Informatics Faculty Publications

Splice variants have been shown to play an important role in tumor initiation and progression and can serve as novel cancer biomarkers. However, the clinical importance of individual splice variants and the mechanisms by which they can perturb cellular functions are still poorly understood. To address these issues, we developed an efficient and robust computational method to: (1) identify splice variants that are associated with patient survival in a statistically significant manner; and (2) predict rewired protein-protein interactions that may result from altered patterns of expression of such variants. We applied our method to the lung adenocarcinoma dataset from TCGA …

Visualization, Feature Selection, Machine Learning: Identifying The Responsible Group For Extreme Acts Of Violence, Mahdi Hashemi, Margeret A. Hall

Interdisciplinary Informatics Faculty Publications

The toll of human casualties and psychological impacts on societies make any study on violent extremism worthwhile, let alone attempting to detect patterns among them. This paper is an effort to predict which violent extremist organization (VEO), among 14 currently active ones throughout the world, is responsible for a violent act based on 14 features, including its human and structural tolls, its target type and value, intelligence, and weapons utilized in the attack. Three main steps in our paper include: 1) the visualization of the violent acts through linear and non-linear dimensionality reduction techniques; 2) sequential forward feature selection based …

Two Critical Positions In Zinc Finger Domains Are Heavily Mutated In Three Human Cancer Types, Daniel Munro, Dario Ghersi, Mona Singh

Interdisciplinary Informatics Faculty Publications

A major goal of cancer genomics is to identify somatic mutations that play a role in tumor initiation or progression. Somatic mutations within transcription factors are of particular interest, as gene expression dysregulation is widespread in cancers. The substantial gene expression variation evident across tumors suggests that numerous regulatory factors are likely to be involved and that somatic mutations within them may not occur at high frequencies across patient cohorts, thereby complicating efforts to uncover which ones are cancerrelevant. Here we analyze somatic mutations within the largest family of human transcription factors, namely those that bind DNA via Cys2His2 zinc …

Patient Preferences For Authentication And Security: A Comparison Study Of Younger And Older Patients, Ann Fruhling, Devika Ramachandran, Tamara Bernard, Ryan Schuetzler, John R. Windle

Interdisciplinary Informatics Faculty Publications

We examine authentication and security preferences of younger versus older patients in the healthcare domain. Previous research has investigated users' perception of the acceptability of various forms of authentication in nonhealthcare domains, but not patients’ preferences. First, we developed an interactive prototype to test three authentication methods: passwords, pattern, and voice. Our results indicate that younger patients prefer passwords by a significant margin. Older patients indicated more mixed preferences. In addition, we evaluated the level of security patients desired for protection of health information compared to financial information. We found no difference based on age: both groups felt financial security …

Semantic Hierarchies For Extracting, Modeling, And Connecting Compliance Requirements In Information Security Control Standards, Matthew L. Hale, Rose F. Gamble

Interdisciplinary Informatics Faculty Publications

Companies and government organizations are increasingly compelled, if not required by law, to ensure that their information systems will comply with various federal and industry regulatory standards, such as the NIST Special Publication on Security Controls for Federal Information Systems (NIST SP-800-53), or the Common Criteria (ISO 15408-2). Such organizations operate business or mission critical systems where a lack of or lapse in security protections translates to serious confidentiality, integrity, and availability risks that, if exploited, could result in information disclosure, loss of money, or, at worst, loss of life. To mitigate these risks and ensure that their information systems …

Severity Of Acute Infectious Mononucleosis Correlates With Cross- Reactive Influenza Cd8 T-Cell Receptor Repertoires, Nuray Aslan, Levi B. Watkin, Anna Gil, Rabinarayan Mishra, Fransenio G. Clark, Raymond M. Welsh, Dario Ghersi, Katherine Luzuriaga, Liisa K. Selin

Interdisciplinary Informatics Faculty Publications

Fifty years after the discovery of Epstein-Barr virus (EBV), it remains unclear how primary infection with this virus leads to massive CD8 T-cell expansion and acute infectious mononucleosis (AIM) in young adults. AIM can vary greatly in severity, from a mild transient influenza-like illness to a prolonged severe syndrome. We questioned whether expansion of a unique HLA-A2.01-restricted, cross-reactive CD8 T-cell response between influenza virus A-M158 (IAV-M1) and EBV BMLF1280 (EBV-BM) could modulate the immune response to EBV and play a role in determining the severity of AIM in 32 college students. Only ex vivo total IAV-M1 and IAV-M1+EBV-BM cross-reactive tetramer+ …

Am I Who I Say I Am? Unobtrusive Selfrepresentation And Personality Recognition On Facebook, Margeret A. Hall, Simon Caton

Interdisciplinary Informatics Faculty Publications

Across social media platforms users (sub)consciously represent themselves in a way which is appropriate for their intended audience. This has unknown impacts on studies with unobtrusive designs based on digital (social) platforms, and studies of contemporary social phenomena in online settings. A lack of appropriate methods to identify, control for, and mitigate the effects of self-representation, the propensity to express socially responding characteristics or self-censorship in digital settings, hinders the ability of researchers to confidently interpret and generalize their findings. This article proposes applying boosted regression modelling to fill this research gap. A case study of paid Amazon Mechanical Turk …

Enhancing Security Incident Response Follow-Up Efforts With Lightweight Agile Retrospectives, George Grispos, William Bradley Glisson, Tim Storer

Interdisciplinary Informatics Faculty Publications

Security incidents detected by organizations are escalating in both scale and complexity. As a result, security incident response has become a critical mechanism for organizations in an effort to minimize the damage from security incidents. The final phase within many security incident response approaches is the feedback/follow-up phase. It is within this phase that an organization is expected to use information collected during an investigation in order to learn from an incident, improve its security incident response process and positively impact the wider security environment. However, recent research and security incident reports argue that organizations find it difficult to learn …

Obesity-Induces Organ And Tissue Specific Tight Junction Restructuring And Barrier Deregulation By Claudin Switching, Rizwan Ahmad, Bilal Rah, Dhundy Bastola, Punita Dhawan, Amar B. Singh

Interdisciplinary Informatics Faculty Publications

Obesity increases susceptibility to multiple organ disorders, however, underlying mechanisms remain unclear. The subclinical inflammation assisted by obesity-induced gut permeability may underlie obesity-associated co-morbidities. Despite eminent clinical significance of the obesity led gut barrier abnormalities, its precise molecular regulation remains unclear. It is also unknown whether barrier deregulations, similar to the gut, characterize other vital organs in obese individuals. The claudin family of proteins is integral to the tight junction (TJ), the apical cell-cell adhesion and a key regulator of the epithelial barrier. Using comprehensive physiological and biochemical analysis of intestinal and renal tissues from high-fat diet fed mice, critical …

Phishing Suspiciousness In Older And Younger Adults: The Role Of Executive Functioning, Brandon E. Gavett, Rui Zhao, Samantha E. John, Cara A. Bussell, Jennifer R. Roberts, Chuan Yue

Interdisciplinary Informatics Faculty Publications

Phishing is the spoofing of Internet websites or emails aimed at tricking users into entering sensitive information, with such goals as financial or identity theft. The current study sought to determine whether age is associated with increased susceptibility to phishing and whether tests of executive functioning can predict phishing susceptibility. A total of 193 cognitively intact participants, 91 younger adults and 102 older adults, were primarily recruited through a Psychology department undergraduate subject pool and a gerontology research registry, respectively. The Executive Functions Module from the Neuropsychological Assessment Battery and the Iowa Gambling Task were the primary cognitive predictors of …

The Preferences For Creativity Scale (Pcs): Identifying The Underlying Constructs Of Creative Concept Selection, Christine A. Toh, Scarlett Miller

Interdisciplinary Informatics Faculty Publications

The current study was developed to investigate the factors that affect preferences for creativity during the engineering design process through the development of a psychometric scale, the Preferences for Creativity Scale (PCS). This study also explores the impact of student designer's scores on the PCS to their behavior during a creative concept selection activity.

In The Wild Residual Data Research And Privacy, William Bradley Glisson, Tim Storer, Andrew Blyth, George Grispos, Matt Campbell

Interdisciplinary Informatics Faculty Publications

As the world becomes increasingly dependent on technology, researchers in both industry and academia endeavor to understand how technology is used, the impact it has on everyday life, the artifact life-cycle and overall integrations of digital information. In doing so, researchers are increasingly gathering ‘real- world’ or ‘in-the-wild’ residual data, obtained from a variety of sources, without the explicit consent of the original owners. This data gathering raises significant concerns regarding privacy, ethics and legislation, as well as practical considerations concerning investigator training, data storage, overall security and data disposal. This research surveys recent studies of residual data gathered in-the-wild …

Identifying Enriched Drug Fragments As Possible Candidates For Metabolic Engineering, Sunandini Sharma, Kritika Karri, Ishwor Thapa, Dhundy Bastola, Dario Ghersi

Interdisciplinary Informatics Faculty Publications

Background: Fragment-based approaches have now become an important component of the drug discovery process. At the same time, pharmaceutical chemists are more often turning to the natural world and its extremely large and diverse collection of natural compounds to discover new leads that can potentially be turned into drugs. In this study we introduce and discuss a computational pipeline to automatically extract statistically overrepresented chemical fragments in therapeutic classes, and search for similar fragments in a large database of natural products. By systematically identifying enriched fragments in therapeutic groups, we are able to extract and focus on few fragments …

Building Towards Precision Medicine: Empowering Medical Professionals For The Next Revolution, Scott Mcgrath, Dario Ghersi

Interdisciplinary Informatics Faculty Publications

A new paradigm in disease classification, diagnosis and treatment is rapidly approaching. Known as precision medicine, this new healthcare model incorporates and integrates genetic information, microbiome data, and information on patients’ environment and lifestyle to better identify and classify disease processes, and to provide custom-tailored therapeutic solutions. In spite of its promises, precision medicine faces several challenges that need to be overcome to successfully implement this new healthcare model. In this paper we identify four main areas that require attention: data, tools and systems, regulations, and people. While there are important ongoing efforts for addressing the first three areas, we …

The Impact Of Virtual Dissection On Engineering Student Learning And Self-Efficacy, Christine A. Toh, Connor Disco, Scarlett Miller

Interdisciplinary Informatics Faculty Publications

Product dissection activities are widely practiced in engineering education and recent efforts have sought to develop and utilize virtual dissection tools, little data exists on how these tools impact the learning process. Therefore, this study investigates the impact of virtual dissection on student learning and self-efficacy to understand the effects of virtual dissection tools for enhancing engineering instruction.

Identifying Aging-Related Genes In Mouse Hippocampus Using Gateway Nodes, Kathryn Dempsey Cooper, Hesham Ali

Interdisciplinary Informatics Faculty Publications

Background: High-throughput studies continue to produce volumes of metadata representing valuable sources of information to better guide biological research. With a stronger focus on data generation, analysis models that can readily identify actual signals have not received the same level of attention. This is due in part to high levels of noise and data heterogeneity, along with a lack of sophisticated algorithms for mining useful information. Networks have emerged as a powerful tool for modeling high-throughput data because they are capable of representing not only individual biological elements but also different types of relationships en masse. Moreover, well-established graph …

A Study Of Product Dissection’S Impact On Engineering Creativity, Christine A. Toh, Scarlett Miller

Interdisciplinary Informatics Faculty Publications

Designers typically interact with products during the early stages of design to gain an understanding of the solution space. However, few studies have been conducted to understand how these practices affect idea generation which thereby limits our understanding of the utility of these methods. Therefore, the current study was conducted to understand designer-product interactions in order to develop recommendations for their use during the design process.

A Parallel Template For Implementing Filters For Biological Correlation Networks, Kathryn Dempsey Cooper, Vladimir Ufimtsev, Sanjukta Bhowmick, Hesham Ali

Interdisciplinary Informatics Faculty Publications

High throughput biological experiments are critical for their role in systems biology – the ability to survey the state of cellular mechanisms on the broad scale opens possibilities for the scientific researcher to understand how multiple components come together, and what goes wrong in disease states. However, the data returned from these experiments is massive and heterogeneous, and requires intuitive and clever computational algorithms for analysis. The correlation network model has been proposed as a tool for modeling and analysis of this high throughput data; structures within the model identified by graph theory have been found to represent key players …

Calm Before The Storm: The Challenges Of Cloud Computing In Digital Forensics, George Grispos, Tim Storer, William Bradley Glisson

Interdisciplinary Informatics Faculty Publications

Cloud computing is a rapidly evolving information technology (IT) phenomenon. Rather than procure, deploy and manage a physical IT infrastructure to host their software applications, organizations are increasingly deploying their infrastructure into remote, virtualized environments, often hosted and managed by third parties. This development has significant implications for digital forensic investigators, equipment vendors, law enforcement, as well as corporate compliance and audit departments (among others). Much of digital forensic practice assumes careful control and management of IT assets (particularly data storage) during the conduct of an investigation. This paper summarises the key aspects of cloud computing and analyses how established …

Loss Of Dnmt3b Function Upregulates The Tumor Modifier Ment And Accelerates Mouse Lymphomagenesis, Ryan A. Hlady, Slavomira Novakova, Jana Opavska, David Klinkebiel, Staci L. Peters, Juraj Bies, Jay Hannah, Javeed Iqbal, Kristi M. Anderson, Hollie M. Siebler, Lynette M. Smith, Timothy C. Greiner, Dhundy Bastola, Shantaram Joshi, Oksana Lockridge, Melanie A. Simpson, Dean W. Felsher, Kay-Uwe Wagner, Wing C. Chan, Judith K. Christman, Rene Opavsky

Interdisciplinary Informatics Faculty Publications

DNA methyltransferase 3B (Dnmt3b) belongs to a family of enzymes responsible for methylation of cytosine residues in mammals. DNA methylation contributes to the epigenetic control of gene transcription and is deregulated in virtually all human tumors. To better understand the generation of cancer-specific methylation patterns, we genetically inactivated Dnmt3b in a mouse model of MYC-induced lymphomagenesis. Ablation of Dnmt3b function using a conditional knockout in T cells accelerated lymphomagenesis by increasing cellular proliferation, which suggests that Dnmt3b functions as a tumor suppressor. Global methylation profiling revealed numerous gene promoters as potential targets of Dnmt3b activity, the majority of which were …

An Evaluation Of The Usability Of A Computerized Decision Support System For Nursing Homes, M. Fossum, M. Ehnfors, Ann L. Fruhling, A. Ehrenberg

Interdisciplinary Informatics Faculty Publications

Background: Computerized decision support systems (CDSSs) have the potential to significantly improve the quality of nursing care of older people by enhancing the decision making of nursing personnel. Despite this potential, health care organizations have been slow to incorporate CDSSs into nursing home practices.

Objective: This study describes facilitators and barriers that impact the ability of nursing personnel to effectively use a clinical CDSS for planning and treating pressure ulcers (PUs) and malnutrition and for following the suggested risk assessment guidelines for the care of nursing home residents.

Methods: We employed a qualitative descriptive design using varied …

A Parallel Graph Sampling Algorithm For Analyzing Gene Correlation Networks, Kathryn Dempsey Cooper, Kanimathi Duraisamy, Hesham Ali, Sanjukta Bhowmick

Interdisciplinary Informatics Faculty Publications

Effcient analysis of complex networks is often a challenging task due to its large size and the noise inherent in the system. One popular method of overcoming this problem is through graph sampling, that is extracting a representative subgraph from the larger network. The accuracy of the sample is validated by comparing the combinatorial properties of the subgraph and the original network. However, there has been little study in comparing networks based on the applications that they represent. Furthermore, sampling methods are generally applied agnostically, without mapping to the requirements of the underlying analysis. In this paper,we introduce a parallel …

A Comparison Of Forensic Evidence Recovery: Techniques For A Windows Mobile Smart Phone, George Grispos, Tim Storer, William Bradley Glisson

Interdisciplinary Informatics Faculty Publications

Acquisition, decoding and presentation of information from mobile devices is complex and challenging. Device memory is usually integrated into the device, making isolation prior to recovery difficult. In addition, manufacturers have adopted a variety of file systems and formats complicating decoding and presentation.

A variety of tools and methods have been developed (both commercially and in the open source community) to assist mobile forensics investigators. However, it is unclear to what extent these tools can present a complete view of the information held on a mobile device, or the extent the results produced by different tools are consistent.

This paper …

Leveraging Human Genomic Information To Identify Nonhuman Primate Sequences For Expression Array Development, Eliot R. Spindel, Mark Pauley, Yibing Jia, Courtney Gravett, Shaun L. Thompson, Nicholas F. Boyle, Sergio R. Ojeda, Robert B. Norgren Jr.

Interdisciplinary Informatics Faculty Publications

Background: Nonhuman primates (NHPs) are essential for biomedical research due to their similarities to humans. The utility of NHPs will be greatly increased by the application of genomicsbased approaches such as gene expression profiling. Sequence information from the 3' end of genes is the key resource needed to create oligonucleotide expression arrays.

Results: We have developed the algorithms and procedures necessary to quickly acquire sequence information from the 3' end of nonhuman primate orthologs of human genes. To accomplish this, we identified terminal exons of over 15,000 human genes by aligning mRNA sequences with genomic sequence. We found …