Digital Commons Network^™

Finding Function In The Unknown, Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, Catherine Putonti

Bioinformatics Faculty Publications

Through high-throughput RNA sequencing (RNAseq), transcriptomes for a single cell, tissue, or organism(s) can be ascertained at a high resolution. While a number of bioinformatic tools have been developed for transcriptome analyses, significant challenges exist for studies of non-model organisms. Without a reference sequence available, raw reads must first be assembled de novo followed by the tedious task of BLAST searches and data mining for functional information. We have created a pipeline, PyRanger, to automate this process. The pipeline includes functionality to assess a single transcriptome and also facilitate comparative transcriptomic studies.

Values Guiding The Use Of Public Spaces And Presence Of Women, Shweta Singh

Women's Studies & Gender Studies: Faculty Publications and Other Works

This paper articulates the concept of space and gender using illustrations from the cultural iconography of Hindu Goddesses. The boundary and control of public and private spaces leading to differences in toleration of women within them is discussed. I apply the popular conception of values outlined within Ramayana and Mahabharata texts as they impacted Goddess Sita and Princess Draupadi. I have juxtaposed this against the cultural construction of Rani from the Bollywood cinema Queen. The paper contributes to a discussion and reflection on the values that guide women’s visibility and access in public and private spaces as a likely factor …

The Impact Of Large-Scale Asset Purchases On The S&P 500 Index, Long-Term Interest Rates And Unemployment, Anastasios G. Malliaris, Ramaprasad Bhar

School of Business: Faculty Publications and Other Works

After the bankruptcy of Lehman Brothers in September 2008 and the financial panic that ensued, the Federal Reserve moved rapidly to reduce the federal funds rate to .25%. It was quickly judged that additional measures were needed to stabilize the US economy. Beginning in December 2008, the Federal Reserve Bank initiated three rounds of unconventional monetary policies known as quantitative easing (QE). These policies were intended to reduce long-term interest rates when the short-term federal funds rates had reached the zero lower bound and could not become negative. It was argued that the lowering of longer-term interest rates would help …

When Traumatic Stressors Are Not Past, But Now: Psychosocial Treatment To Develop Resilience With Children And Youth Enduring Concurrent, Complex Trauma, Katherine Tyson Mccrea Professor, Deanna Guthrie, Jeffrey Bulanda

Social Work: School of Social Work Faculty Publications and Other Works

The article discusses a project called the Empowering Counseling Program (ECP) conducted in community schools using participatory action and consumer evaluation designs. It addressed the elements of treatment theories used by mental health providers such as values, assumptions and concepts. It cites findings that clients suffering from complex trauma in under-resourced communities, unavoidably traumatized concurrently with treatment do not benefit from treatment guidelines.

Spirituality In Professional Practice With Older Adults, Holly Nelson-Becker, Edward Canada, Mitsuko Nakashima

Social Work: School of Social Work Faculty Publications and Other Works

No abstract provided.

Towards Sustainable Digital Humanities Software, George K. Thiruvathukal, Shilpika Shilpika, Nicholas J. Hayward, Saulo Aguiar, Konstantin Läufer

Computer Science: Faculty Publications and Other Works

Our work in software quality for digital humanities was borne of an effort to address sustainable practices in scientific software development, where the speaker (Thiruvathukal) co-authored a position paper on the case for software engineering in scientific software development as part of an all-encompassing strategy to create more sustainable scientific software (an example of a well-known scientific software package is LINPACK). In this position paper, we addressed how “progress in scientific research is dependent on the quality and accessibility of software at all levels". This progress depends on embracing the best traditional--and emergent--practices in software engineering, especially agile practices that …

Cloudy With A Chance Of Sunshine, Or The Future Of Magazine Publishing, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

EIC George K. Thiruvathukal describes how the cloud can revolutionize printing and how the publishing world in particular can benefit.

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulos, Konstantin Laufer, George K. Thiruvathukal, Catherine Putonti

Bioinformatics Faculty Publications

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 …

"Thomas Mann, ‘Expressionism,’ And Ðeath In Venice” For “Death In Venice: Warrington Colescott And Thomas Mann”, David B. Dennis

History: Faculty Publications and Other Works

This was a public lecture in association with an excellent exhibition of works by one of America’s premier printmakers, on the theme of Mann’s work and German culture.

Bacteriophages Isolated From Lake Michigan Demonstrate Broad Host-Range Across Several Bacterial Phyla, Kema Malki, Alex Kula, Katherine Bruder, Emily Sible, Thomas Hatzopoulos, Stephanie Steidel, Siobhan C. Watkins, Catherine Putonti

Biology: Faculty Publications and Other Works

BACKGROUND:

The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples.

FINDINGS:

Four phages were extracted from Lake Michigan …

Resource Sharing Begins At Home: Opportunities For Library Partnerships On A University Campus, Robert A. Seal

University Libraries: Faculty Publications and Other Works

Typical discussions of academic library resource sharing focus on activities between and among institutions: interlibrary loan, reciprocal borrowing, document delivery, group acquisitions, etc. But there is another equally important type of cooperation, i.e. working with other campus units to provide better service, more convenience, and enhanced resources for library users. Sometimes referred to as campus collaboration or convergence, this activity also advances institutional priorities, in particular that of student success. Library partners include information technology services, student development, writing centers, academic departments, and centers for teaching excellence, among others. This paper explores these relationships, their advantages and disadvantages, goals, the …

Generation Of A Novel Exactly Solvable Potential, Jonathan Bougie, Asim Gangopadhyaya, Jeffry V. Mallow, Emeritus, Constantin Rasinariu

Physics: Faculty Publications and Other Works

We report a new shape-invariant (SI) isospectral extension of the Morse potential. Previous investigations have shown that the list of “conventional” SI superpotentials that do not depend explicitly on Planck's constant ħ is complete. Additionally, a set of “extended” superpotentials has been identified, each containing a conventional superpotential as a kernel and additional ħ-dependent terms. We use the partial differential equations satisfied by all SI superpotentials to find a SI extension of Morse with novel properties. It has the same eigenenergies as Morse but different asymptotic limits, and does not conform to the standard generating structure for isospectral deformations.

The Merits Of Mentoring, Robert A. Seal

University Libraries: Faculty Publications and Other Works

No abstract provided.

Clinically Integrated Networks: A Cooperation Analysis, M. Therese Lysaught

Institute of Pastoral Studies: Faculty Publications and Other Works

This analysis outlines key aspects that may be included in the infrastructure of clinically integrated networks. The paper then provides a moral analysis of these aspects using the principle of moral cooperation. While CINs may differ from each other in the details of how they are organized, the analysis concludes that clinically integrated networks, as a model, should pose no new problems from the perspective of Catholic teaching and may, in fact, provide a new answer to the challenges of partnering

with non-Catholic health care providers.

Book Review: Transforming The Dead, Anne L. Grauer

Anthropology: Faculty Publications and Other Works

Hargrave, Schermer, Hedman, and Lillie have crafted a volume, Transforming the Dead: Culturally Modified Bone in the Prehistoric Midwest, that provides readers with a rich and nuanced understanding of human bone as object and symbol.

How Risky Are Your Lease Vs. Buy Decisions?, Thomas Zeller, Brian Stanko, Andrew D. Tressler

School of Business: Faculty Publications and Other Works

Adding risk analysis to your lease vs. buy analytics can make the decision process more involved, but it is worth the effort strategically. To accomplish this, you need to create a comparable analysis that estimates the risk in a lease vs. buy decision. With a few additional steps in the present value analytics, you can develop comparable information to capture the risk of one option over another and manage expectations.

“Educational Regionalization” And The Gated Global: The Construction Of The Caribbean Educational Policy Space, Tavis D. Jules

Education: School of Education Faculty Publications and Other Works

This article draws on “regime theory,” particularly on the concepts of cooperation, compatibility of interests, and proclivity to compromise, to examine the rise of the Caribbean Educational Policy Space (CEPS). In making this argument, with the aid of a content analysis of 26 educational policies from the 15 member states of the Caribbean Community (CARICOM), this article first locates the different policy mechanism of external effects, or policy tools, within the regional policy environment that governs and regulates education at the national level to explain how these policy tools and mechanisms have given rise to a very distinctive form of …

Escalation In International Conflict Management: A Foreign Policy Perspective, Molly M. Melin

Political Science: Faculty Publications and Other Works

Efforts to resolve interstate disputes are often characterized by repeated engagement and evolving strategies. What explains a state’s decision to continue conflict resolution efforts but escalate their management strategy? Drawing from foreign policy literature, I argue third parties escalate policies both in response to past failures, shifting conflict dynamics, and their relationship with the disputants. Analysis of management efforts from 1946 to 2001 reveals that the changing nature of the conflict, policy failures and relationships between the third party and disputants are integral to understanding the management decision process, but the effects of these factors depend on the management history.

Future Orientation As A Protective Factor For African American Adolescents Exposed To Community Violence, Suzanna So, Noni K. Gaylord-Harden, Dexter R. Voisin, Darrick Scott

Psychology: Faculty Publications and Other Works

For African American youth disproportionately exposed to community violence and the associated risk of externalizing behaviors, developmental assets that reduce the risk for externalizing behaviors and enhance adaptive coping should be explored. In a sample of 572 African American adolescents (M_age = 15.85; SD = 1.42), the current study explored whether future orientation or gender buffered the impact of community violence exposure on externalizing behaviors. The current study also examined the interaction between future orientation, gender, and violence-specific coping strategies to determine their association with externalizing behaviors. Future orientation moderated the relationship between violence exposure and delinquent, but …

"The Nazi War On Weimar 'Asphalt Culture'" For "Dissonance: Music And Globalization Since Edison's Phonograph", David B. Dennis

History: Faculty Publications and Other Works

No abstract provided.

Injury In Aged Animals Robustly Activates Quiescent Olfactory Neural Stem Cells, Jessica H. Brann, Deandra Ellis, Benson Ku, Eleonora Spinazzi, Stuart Firestein

Biology: Faculty Publications and Other Works

While the capacity of the olfactory epithelium (OE) to generate sensory neurons continues into middle age in mice, it is presumed that this regenerative potential is present throughout all developmental stages. However, little experimental evidence exists to support the idea that this regenerative capacity remains in late adulthood, and questions about the functionality of neurons born at these late stages remain unanswered. Here, we extend our previous work in the VNO to investigate basal rates of proliferation in the OE, as well as after olfactory bulbectomy, a commonly used surgical lesion. In addition, we show that the neural stem cell …

A Gene-Based Association Method For Mapping Traits Using Reference Transcriptome Data, Eric R. Gamazon, Heather Wheeler, Kaanan P. Shah, Sahar V. Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, Gtex Consortium, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im

Bioinformatics Faculty Publications

Genome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation affects phenotype. The approach estimates the component of gene expression determined by an individual’s genetic profile and correlates ‘imputed’ gene expression with the phenotype under investigation to identify genes involved in the etiology of the phenotype. Genetically regulated gene expression is estimated using whole-genome tissue-dependent prediction models trained with reference transcriptome data sets. PrediXcan enjoys …

Leaving The Gang: A Review And Thoughts On Future Research, Dena C. Carson, J. Michael Vecchio

Criminal Justice & Criminology: Faculty Publications & Other Works

Researchers have examined aspects of gangs and their members for almost a century. This work, however, focuses primarily on youth prior to joining as well as during gang involvement. While comparatively less is known about the leaving processes, work in this area has been increasing in recent years. This chapter will discuss the growing body of research on the processes associated with leaving the gang. Specifically, it will review difficulties associated with defining gang desistance, theoretical perspectives on desistance, variations in motives, methods, and consequences of leaving, barriers to desistance, as well as make recommendations for policy and future research.

An Analytical Method For Detecting Toxic Metal Cations Using Cyclotriveratrylene Derivative Capped Gold Nanoparticles, Zachary R. Osner, Richard C. Holz, Daniel P. Becker Ph.D.

Chemistry: Faculty Publications and Other Works

Cyclotriveratrylene-oxime (CTV-oxime) derivatives that terminate with a dithiolate linker were synthesized enabling the supramolecular scaffold to adhere to gold nanoparticles (AuNPs) with the bowl-shaped cavity of the CTV scaffold exposed for utilization in host–guest chemistry. Exposure of these CTV functionalized AuNPs to varying concentrations of di- and trivalent metal cations resulted in the formation of large CTV-AuNP polymeric clusters and an accompanying a shift in the plasmon resonance. These interactions between the CTV-AuNPs and the metal cations in solution provides proof-of-concept that supramolecular functionalized AuNPs can be used as a simple and straightforward, on-site detection system for toxic metal cations …

Tradition, Innovation, And The Value Of The Liberal Arts, Paul Jay

English: Faculty Publications and Other Works

My main message about defending the humanities and liberal arts is that divided we lose. Divided we lose. What's great about our disciplines, collectively, is the way in which they preserve and value the past, but in a context in which that past is subject to reflective and constructive critique, so that the ways in which we think about what constitutes the human keeps changing, and the collection of texts, ideas, historical events, material realities, and cultural forms we discuss with our students keeps expanding as well. The liberal arts are living arts. They are about both the perpetuation and …

Swipe Left: A Theology Of Tinder And Digital Dating, Michael Murphy

Theology: Faculty Publications and Other Works

The juggernaut of digital culture, which really has hatched the biggest cultural metamorphosis since Gutenberg’s printing press, affects every aspect of late modern life in fundamental ways—ways, moreover, that are often obscured from our perception. After all, the hardest chains to break, the saying goes, are the ones you can’t see.

Software Metrics And Dashboard, Shilpika Shilpika, George K. Thiruvathukal, Saulo Aguiar, Konstantin Läufer, Nicholas J. Hayward

Computer Science: Faculty Publications and Other Works

Software metrics are a critical tool which provide continuous insight to products and processes and help build reliable software in mission critical environments. Using software metrics we can perform calculations that help assess the effectiveness of the underlying software or process. The two types of metrics relevant to our work is complexity metrics and in-process metrics. Complexity metrics tend to focus on intrinsic code properties like code complexity. In-process metrics focus on a higher-level view of software quality, measuring information that can provide insight into the underlying software development process.

Our aim is to develop and evaluate a metrics dashboard …

Sustainable Social Work: An Environmental Justice Framework For Social Work Education, Samantha Teixeira, Amy Krings

Social Work: School of Social Work Faculty Publications and Other Works

Environmental degradation is not experienced by all populations equally; hazardous and toxic waste sites, resource contamination (e.g., exposure to pesticides), air pollution, and numerous other forms of environmental degradation disproportionately affect low income and minority communities. The communities most affected by environmental injustices are often the same communities where social workers are entrenched in service provision at the individual, family, and community level. In this article, we use a global social work paradigm to describe practical ways in which environmental justice content can be infused in the training and education of social workers across contexts in order to prepare professionals …

The Comparative Impacts Of Social Justice Educational Methods On Political Participation, Civic Engagement, And Multicultural Activism, Amy Krings, Elizabeth A. Austic, Lorraine M. Gutierrez, Kaleigh E. Dirksen

Social Work: School of Social Work Faculty Publications and Other Works

This cross-sectional, repeated measures, quasi-experimental study evaluates changes in college stu- dents’ commitment toward, and confidence in, political participation, civic engagement, and multi- cultural activism. Our sample (n = 653) consisted of college students in a Midwestern university who participated in one of three social justice education course types (service learning, intergroup dialogue, or lecture-based diversity classes) or in an “introduction to psychology” course (the non-intervention group). After completion of a social justice education course, students reported an increase in politi- cal participation and multicultural activism, whereas students enrolled in the non-intervention group reported no changes in these measures. Service …

Gower And The Peasants’ Revolt, Ian Cornelius

English: Faculty Publications and Other Works

This essay examines the moral and political thought of John Gower's poem on the English Rising of 1381, situating it within three contrastive fields: Gower’s moral project, his Virgilian intertext, and the practices of moral community employed by the rebels of 1381.