Digital Commons Network^™

Breaking The Paradigm: Dr Insight Empowers Signature-Free, Enhanced Drug Repurposing, Jinyan Chan, Xuan Wang, Jacob A. Turner, Nicole E. Baldwin, Jinghua Gu

Faculty Publications

Motivation: Transcriptome-based computational drug repurposing has attracted considerable interest by bringing about faster and more cost-effective drug discovery. Nevertheless, key limitations of the current drug connectivity-mapping paradigm have been long overlooked, including the lack of effective means to determine optimal query gene signatures. Results: The novel approach Dr Insight implements a frame-breaking statistical model for the ‘hand-shake’ between disease and drug data. The genome-wide screening of concordantly expressed genes (CEGs) eliminates the need for subjective selection of query signatures, added to eliciting better proxy for potential disease-specific drug targets. Extensive comparisons on simulated and real cancer datasets have validated the …

A Limiting Process To Invert The Gauss-Radon Transform, Jeremy Becnel

Faculty Publications

In this work we extend the finite dimensional Radon transform [23] to the Gaussian measure. We develop an inversion formula for this GaussRadon transform by way of Fourier inversion formula. We then proceed to extend these results to the infinite dimensional setting.

Recovering A Random Variable From Conditional Expectations Using Reconstruction Algorithms For The Gauss Radon Transform, Jeremy Becnel, Daniel Riser-Espinoza

Faculty Publications

The Radon transform maps a function on n-dimensional Euclidean space onto its integral over a hyperplane. The fields of modern computerized tomography and medical imaging are fundamentally based on the Radon transform and the computer implementation of the inversion, or reconstruction, techniques of the Radon transform. In this work we use the Radon transform with a Gaussian measure to recover random variables from their conditional expectations. We derive reconstruction algorithms for random variables of unbounded support from samples of conditional expectations and discuss the error inherent in each algorithm.

Overview Of Big Data-Intensive Storage And Its Technologies For Cloud And Fog Computing, Richard S. Segall, Jeffrey S. Cook, Gao Niu

Faculty Publications

Computing systems are becoming increasingly data-intensive because of the explosion of data and the needs for processing the data, and subsequently storage management is critical to application performance in such data-intensive computing systems. However, if existing resource management frameworks in these systems lack the support for storage management, this would cause unpredictable performance degradation when applications are under input/output (I/O) contention. Storage management of data-intensive systems is a challenge. Big Data plays a most major role in storage systems for data-intensive computing. This article deals with these difficulties along with discussion of High Performance Computing (HPC) systems, background for storage …

Legal Sets, Jeremy N. Sheff

Faculty Publications

In this Article, I propose that the practices of legal reasoning and analysis are helpfully understood as being primarily concerned not with rules or propositions, but with sets. This Article develops a formal model of the role of sets in the practices of legal actors in a common-law system defined by a recursive relationship between cases and rules. In doing so, it demonstrates how conceiving of legal doctrines as a universe of discourse comprising (sometimes nested or overlapping) sets of cases can clarify the logical structure that governs marginal cases and help organize the available options for resolving such cases …

Ground State Phase Diagram Of The One-Dimensional Bose-Hubbard Model From Restricted Boltzmann Machines, Kristopher Mcbrian, Giuseppe Carleo, Ehsan Khatami

Faculty Publications

Motivated by recent advances in the representation of ground state wavefunctions of quantum many-body systems using restricted Boltzmann machines as variational ansatz, we utilize an open-source platform for constructing such ansatz called NetKet to explore the extent of applicability of restricted Boltzmann machines to bosonic lattice models. Within NetKet, we design and train these machines for the one-dimensional Bose-Hubbard model through a Monte Carlo sampling of the Fock space. We vary parameters such as the strength of the onsite repulsion, the chemical potential, the system size and the maximum site occupancy and use converged equations of state to identify phase …

Analyzing Documents With Tf-Idf, Matthew Lavin

Faculty Publications

No abstract provided.

Examining The Challenges And Practices Of Our Russian Partners In The Institution Of Teacher Librarianship, Lucy Santos Green, M. P. Johnston

Faculty Publications

Examining international teacher librarianship enables school library researchers and practitioners to continue uncovering the institutional factors that impact school librarianship; further strengthening the case for cross-cultural partnerships. In 2015, researchers conducted an institutional ethnography confirmatory study of school librarianship in Moscow, Russia. Emergent themes culled from previous research and confirmed in this new study were: collaboration, literacy, instruction, technology integration, and the learning environment. Confirmation of these themes in Russian school librarianship indicates teacher librarians around the world struggle with strikingly similar challenges despite varied contexts and socioeconomic situations.

A Knowledge Lens: Humans In Action, Darin S. Freeburg

Faculty Publications

Every member of a social system sees that system in a particular way. This essay outlines a

new way of seeing the uniquely human characteristics in these systems, with particular attention to what happens when this view is taken. Termed the Knowledge Lens, this view embraces complexity, sees the potential of innovation through conversation, and understands the barriers limiting the traditionally assumed powers of data, information, and knowledge. This lens is approached within the context of ensuring that graduates of a Knowledge School are equipped with the tools and understanding necessary to facilitate positive change and increase human agency--both in …

Using Science To Build Better Learners: One School's Successful Efforts To Raise Its Bar Passage Rates In An Era Of Decline, Louis N. Schulze Jr.

Faculty Publications

What measures can law schools take to improve student performance and bar passage? The answer is not what you think.

Recent developments in the science of learning show that most law students learn wrong. In fact, ineffective methods of learning pervade all levels of education. We now know that widely accepted learning and study strategies that were once considered gospel are actually deeply flawed. Yet we still embrace and propagate those myths.

Meanwhile, bar passage rates and law student performance are plummeting. Everyone in legal education is asking “what can we do?” But, “what can we do?” is the wrong …

Toward A Performative Understanding Of Politeness, C. Kyle Rudick, Danielle E. Mcgeough

Faculty Publications

In this article, we argue that critical communication scholars have largely overlooked the study of politeness as a constitutive component of identity, culture, and power. We offer a critical-performative framework for critical scholars interested in studying politeness as a political, discursive, and embodied act. To develop this agenda, we first outline Brown and Levinson’s postpositivist theory of politeness. We then review three challenges to their use of intentionality, Grice’s cooperative principle, and Goffman’s concept of face. These challenges are located in interactional, traditional critical, and discursive understandings of politeness (respectively). Next, we show how a performative understanding of politeness both …

Y2O3 Optical Constants Between 5 Nm And 50 Nm, Joseph B. Muhlestein, Benjamin D. Smith, Margaret Miles, Stephanie M. Thomas, Anthony Willey, David D. Allred, R. Steven Turley

Faculty Publications

We report optical constants of e-beam evaporated yttrium oxide Y₂O₃ thin films as determined from angle-dependent reflectance measurements at wavelengths from 5 to 50 nm. Samples were measured using synchrotron radiation at the Advanced Light Source. The experimental reflectance data were fit to obtain values for the index of refraction and thin film roughness. We compare our computed constants with those of previous researchers and those computed using the independent atom approximation from the CXRO website. We found that the index of refraction near 36 nm is much lower than previous data from Tomiki as reported by …

Laser-Induced Plasma Analysis For Surrogate Nuclear Debris, Michael B. Shattan, John Auxier, A. C. Stowe, Christian G. Parigger

Faculty Publications

This work identifies analytical lines in laser-induced plasma for chemical analyses of major elements found in surrogate nuclear debris. These lines are evaluated for interferences and signal strength to insure they would be useful to measure relative concentrations. Compact, portable instruments are employed and can be included as part of a mobile nuclear forensics laboratory for field screening of nuclear debris and contamination. The average plasma temperature is measured using the well-established Boltzmann plot technique, and plasma's average electron density is determined using empirical formulae based on Stark broadening of the H-alpha line. These measurements suggest existence of partial local …

Expectations And Challenges Of Non-Native University Writers At The Outset Of Discipline-Specific Study, K. James Hartshorn, Norman W. Evans

Faculty Publications

Little is known about how best to prepare non-native students matriculated at universities in the United States to succeed in discipline-specific writing. Whilesome studies have suggested differences in the types and volumes of writing across disciplines, such studies have compared very few disciplines simultaneously and have not always examined the disciplines most commonly studied by international students. Thus, this study seeks to fill an important gap in the literature by examining the perspectives of university professors regarding their expectations and purposes for student writing as well as their observations about the greatest writing challenges their students face within five of …

Increasing English Learners’ Positive Emotional Response To Learning Through Dance, Grant Eckstein, Elizabeth Hanks

Faculty Publications

This study investigates dance as an English Second Language (ESL) curriculum enhancement. The curriculum utilizes kinesthetic learning, which is a method seldom incorporated in formal academic classrooms (Pourhosein Gilakjani, 2011) despite evidence suggesting that it benefits all students, including those without kinesthetic learning preferences (Schumann, 1997). Supporters believe that the benefits of incorporating movement in the classroom include increased student enjoyment, motivation, and confidence in learning. However, these beliefs are merely anecdotal at present. This study analyzes quantitative questionnaires and qualitative feedback from 26 students who participated in a 4-week long Dance ESL curriculum to determine whether dance-based learning can …

Theory Of Experiential Career Exploration Technology (Tecet): Increasing Cybersecurity Career Interest Through Playable Case Studies, Justin Scott Giboney, Derek L. Hansen, Tanner Johnson, Desiree Winters, Jason K. Mcdonald, Jonathan Balzotti, Elizabeth Bonsignore

Faculty Publications

There is a large demand to fill cybersecurity jobs. To alleviate this need, it is important to generate interest in cybersecurity as a career. One way to do this is through job shadowing and internships. Using design science principles, we have built and tested a playable case study (PCS) where participants can act out a virtual internship and learn relevant cybersecurity skills. We ran a study with students in introductory university courses where they played through a simulated internship at a penetration testing company called CyberMatics. In the study we showed that a PCS format helps students 1) better understand …

The Free-Market Family And Children’S Caretaking, Maxine Eichner

Faculty Publications

No abstract provided.

Lenders' Roles And Responsibilities In Sovereign Debt Markets, Susan Block-Lieb, W. Mark C. Weidemaier

Faculty Publications

Academic and policy debates about the multi-trillion-dollar sovereign debt markets presume these markets are unique. The reason is that sovereigns differ from other borrowers. To the extent observers look elsewhere for guidance, they turn to corporate debt as a comparison. For example, official actors have repeatedly intervened in sovereign debt markets by prodding market participants to draft loan contracts that simulate aspects of corporate bankruptcy. We argue that the conventional view of sovereign debt—though useful to a point—has substantially and unjustifiably limited the academic and policy agenda. Rather than dwell on the unique characteristics of sovereign borrowers, we examine the …

Clarifying The Interpretation Of Carbon Use Efficiency In Soil Through Methods Comparison, Kevin M. Geyer, Paul Dijkstra, Robert Sinsabaugh, Serita D. Frey

Faculty Publications

Accurate estimates of microbial carbon use efficiency (CUE) are required to predict how global change will impact microbially-mediated ecosystem functions such as organic matter decomposition. Multiple approaches are currently used to quantify CUE but the extent to which estimates reflect methodological variability is unknown. This limits our ability to apply or cross-compare published CUE values. Here we evaluated the performance of five methods in a single soil under standard conditions. The microbial response to three substrate amendment rates (0.0, 0.05, and 2.0 mg glucose-C g−1 soil) was examined using: 13C and 18O isotope tracing approaches which estimate CUE based on …

How Bitcoin Functions As Property Law, Eric D. Chason

Faculty Publications

Bitcoin replicates many of the formal aspects of real estate transactions. Bitcoin transactions have features that closely resemble grantor names, grantee names, legal descriptions, and signatures found in real property deeds. While these “Bitcoin deeds” may be interesting, they are not profound. Bitcoin goes beyond creating simple digital deeds, however, and replicates important institutional aspects of real estate transactions, in particular recordation and title assurance. Deeds to real property are recorded in a central repository (e.g., the public records office), which the parties (and the public) can search to determine title. When one grantor executes more than one deed covering …

Of Piketty And Perpetuities: Dynastic Wealth In The Twenty-First Century (And Beyond), Eric Kades

Faculty Publications

For the first time since independence, in a nation founded in large part on the rejection of a fixed nobility determined by birth and perpetuated by inheritance, America is paving the way for the creation of dynastic family wealth. Abolition of the Rule Against Perpetuities in over half the states along with sharp reductions in, and likely elimination of, the federal estate tax mean that there soon will be no obstacles to creating large pools of dynastic wealth insuring lavish incomes to heirs for generations without end. The timing of these legal changes could hardly be worse. Marshaling innovative economic …

Carbon In The Deep Biosphere: Forms, Fates, And Biogeochemical Cycling, Susan Q. Lang, Magdalena R. Osburn, Andrew D. Steen

Faculty Publications

Building on the synthesis of carbon reservoirs in Earth's subsurface, this chapter focuses on the forms, cycling, and fate of the carbon supporting microbial life in the terrestrial and marine subsurface. As the subsurface is estimated to host a vast reservoir of life on Earth, identifying the carbon compounds that life uses for energy and growth is key to understanding ecosystem functioning in the past and at present, and also for extrapolating these findings to the search for life in the universe. This chapter highlights advances in quantifying small carbon compounds, measuring rates of carbon turnover, and the fate of …

Make Summer Great Again -- Do The Research Experience For Teachers (Ret) Program, Dan Broadbent

Faculty Publications

What is the RET Program?

• “Research Experience for Teachers”
• It is a National Science Foundation (NSF) program that…
• “supports the active involvement of K-12 teachers and community college faculty in research in order to bring knowledge and innovation into their classrooms.”
• So, research universities apply for a grant from the NSF and then set it up.
• Usually paired with REU

Comparison Of Wind Farm Layout Optimization Results Using A Simple Wake Model And Gradient-Based Optimization To Large-Eddy Simulations, Jared J. Thomas, Jennifer Annoni, Paul Fleming, Andrew Ning

Faculty Publications

The models used during wind farm layout optimization use simplifying assumptions that can alter the design space. Some characteristics of the simple models may negatively influence the resulting layouts. In this paper, we perform wind farm layout optimization using a simple wake model and compare the resulting improvements to large-eddy simulation (LES) results to confirm that the layout was actually improved. We begin by describing the models used, including changes specific for use with gradient-based optimization. We then compare our models’ output to previously published model and LES results. Using the models described, we performed gradient-based wind farm layout optimization …

Combined Trajectory, Propulsion, And Battery Mass Optimization For Solar-Regenerative High-Altitude Long Endurance Unmanned Aircraft, Nathaniel S. Gates, Kevin R. Moore, Andrew Ning, John D. Hedengren

Faculty Publications

Combined optimization of propulsion system design, flight trajectory planning and battery mass optimization for solar-regenerative high-altitude long endurance (SRHALE) aircraft through a sequential iterative approach yields an increase of 20.2% in the end-of-day energy available on the winter solstice at 35 deg N latitude, resulting in an increase in flight time of 2.36 hours. The optimized flight path is obtained by using nonlinear model predictive control to solve flight and energy system dynamics over a 24 hour period with a 15 second time resolution. The optimization objective is to maximize the total energy in the system while flying a station-keeping …

Redmond (2002) Revisited: Have Standardized Behavioral Rating Scales Gotten Better At Accommodating For Overlapping Symptoms With Language Impairment?, Kirsten M. Hannig, Sean M. Redmond, Amy Wilder

Faculty Publications

Seventeen years ago, Redmond ¹ reviewed five standardized behavioral rating scales and identified several aspects of their design that made them prone to mischaracterize language impairments as socioemotional behavioral disorders. The purpose of this report is to provide an update and extension of the original audit. We consulted test manuals to evaluate: (1) representation of children with language impairments in their standardization samples; (2) presence of language, or academic items within their inventories; (3) accommodations for administering the measure to children with language impairments; and (4) procedures for identifying inordinately punitive ratings. Overlapping language and academic symptoms continued to be …

Domain Rearrangement And Denaturation In Ebola Virus Protein Vp40, Rudramani Pokhrel, Pornthep Sompornpisut, Prem Chapagain, Brian Olson, Bernard Gertsman, Ras B. Pandey

Faculty Publications

The VP40 protein plays a critical role in coordinating the virion assembly, budding, and replication of the Ebola virus. Efforts have been made in recent years to understand various aspects of VP40 structure, dynamics, and function such as assembly of the protein and its roles in virus replication and penetration of the protein into the plasma membrane. A major conformational transformation is necessary for VP40 to form some of its oligomeric structures and to perform various functions. This conformational change from a compact structure with the N-terminal domain (NTD) and C-terminal domain (CTD) closely associated involves a dissociation or springing-out …

Study Of The Reactions E+E-→Π+Π-Π0Π0Π0 And Π+Π-Π0Π0Η At Center-Of-Mass Energies From Threshold To 4.35 Gev Using Initial-State Radiation, J. P. Lees, V. Poireau, V. Tisserand, E. Grauges, A. Palano, G. Eigen, D. N. Brown, Yu G. Kolomensky, M. Fritsch, H. Koch, T. Schroeder, C. Hearty, T. S. Mattison, J. A. Mckenna, R. Y. So, V. E. Blinov, A. R. Buzykaev, V. P. Druzhinin, V. B. Golubev, E. A. Kozyrev, Milind Purohit, Jeffrey Wilson, Et. Al.

Faculty Publications

We study the processes e⁺e⁻ → π⁺π⁻π⁰π⁰π⁰nγ in which an energetic photon is radiated from the initial state. The data are collected with the BABAR detector at SLAC. About 14 000 and 4700 events, respectively, are selected from a data sample corresponding to an integrated luminosity of 469 fb⁻¹. The invariant mass of the hadronic final state defines the effective e⁺e⁻ center-of-mass energy. From the mass spectra, the first precise measurement of the e⁺e⁻ → π⁺π^{− …}

Fundamental Limits On The Capacities Of Bipartite Quantum Interactions, Stefan Bäuml, Siddhartha Das, Mark M. Wilde

Faculty Publications

Bipartite quantum interactions have applications in a number of different areas of quantum physics, reaching from fundamental areas such as quantum thermodynamics and the theory of quantum measurements to other applications such as quantum computers, quantum key distribution, and other information processing protocols. A particular aspect of the study of bipartite interactions is concerned with the entanglement that can be created from such interactions. In this Letter, we present our work on two basic building blocks of bipartite quantum protocols, namely, the generation of maximally entangled states and secret key via bipartite quantum interactions. In particular, we provide a nontrivial, …

Measurement Of The Branching Fraction And Time-Dependent Cp Asymmetry For B0→J/Ψπ0 Decays, B. Pal, A.J. Schwartz, H. Aihara, S. Al Said, D. M. Asner, H. Atmacan, V. Aulchenko, T. Aushev, R. Ayad, I. Badhrees, S. Bahinipati, V. Bansal, P. Behera, C. Beleño, B. Bhuyan, T. Bilka, J. Biswal, A. Bozek, M. Bračko, L. Cao, Milind Purohit, Et. Al.

Faculty Publications

We measure the branching fraction and time-dependent CP-violating asymmetry for B0 → J=ψπ0 decays using a data sample of 711 fb⁻¹ collected on the ϒ(4S) resonance by the Belle experiment running at the KEKB e⁺e⁻ collider. The branching fraction is measured to be B(B⁰ → J/_ψπ⁰) ¼ [1.62 ± 0.11(stat) ± 0.06(syst) × 10⁻⁵, which is the most precise measurement to date. The measured CP asymmetry parameters are S =−0.59 ±0.19(stat) 0.03(syst) and A = −0.15 ± 0.14(stat) ^+0.04 _−0.03 (syst). The mixing-induced CP asymmetry (S) differs …