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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.

Orlowski First To Present In Expanded Academic Medicine Lecture Series, Kendra Carter

Browse All News

No abstract provided.

Assessing Foliar Ascorbate Content In A Rice Diversity Panel And In Selected Mapping Population Lines With Varying Levels Of Seedling Cold Tolerance, Sonia Elizabeth Castillo Gonzalez

Student Theses and Dissertations

Rice is economically, culturally, and socially important to many people in the world. Arkansas is the main rice producer in the USA. Climate change continues to increase the incidence of abiotic stresses such as cold, heat, drought, water excess, and soil salinity. These stresses pose a particular challenge to rice cultivation. Rice has lower yields under cold stress, particularly when plants are exposed to cold at the seedling and reproductive stages. Early spring plantings and field irrigation with underground cold water expose rice seedlings to cold stress. Previous studies in Arabidopsis thaliana have shown that lines engineered to have elevated …

A Model Microfluidics-Based System For The Human And Mouse Retina., Shawn Mishra, Ankush Thakur, Stephen Redenti, Maribel Vazquez

Publications and Research

The application of microfluidics technologies to the study of retinal function and response holds great promise for development of new and improved treatments for patients with degenerative retinal diseases. Restoration of vision via retinal transplantation therapy has been severely limited by the low numbers of motile cells observed post transplantation. Using modern soft lithographic techniques, we have developed the μRetina, a novel and convenient biomimetic microfluidics device capable of examing the migratory behavior of retinal lineage cells within biomimetic geometries of the human and mouse retina. Coupled computer simulations and experimental validations were used to characterize and confirm the formation …

Dean Of Engineering Receives Utah Governor’S Medal For Excellence | College Of Engineering, Usu College Of Engineering

College of Engineering News

Dec. 17, 2015 – Utah State University’s College of Engineering Dean Christine Hailey was among ten state leaders recognized this week by Utah Gov. Gary Herbert for outstanding service in academia, education and industry.

Hailey will receive the Governor’s Medal for Excellence at a special gala event on Jan. 13 at Rio Tinto Stadium along with fellow recipients including three other faculty members from USU.

Immunogenic Compositions Comprising Slcified Virus And Methods Of Use, Kenneth M. Stedman, James R. Laidler, Keith Bahjat

Technology Transfer - Patents

It is disclosed herein that viruses coated in silica retain infectivity and the capacity to induce an immune response in an infected host. In addition, silicified virus is remarkably resistant to desiccation. Provided herein are methods of inducing a virus-specific immune response in a subject by administering to the subject an effective amount of silicified virus or silicified virus particles. Methods of enhancing a virus-specific cell-mediated immune response (such as a T cell-mediated immune response) in a Subject by administering to the subject a silicified virus or silicified virus particles are also described herein. Further provided are immunogenic compositions comprising …

The Weekly Challenger, December 17, 2015, The Weekly Challenger, Et Al

Weekly Challenger Newspaper Collection

The December 17, 2015, issue of The Weekly Challenger.

Uncertainty Quantification Of Gas Production In The Barnett Shale Using Time Series Analysis, Kishan Ghanshyambhai Joshi

Engineering

Deterministic methods for evaluating uncertainty in production forecasts for unconventional shale plays are either unreliable or time intensive. This thesis presents an improved methodology for quantifying uncertainty in production forecasts using Logistic Growth Analysis (LGA) and time series modeling. The applicability of the proposed method is tested by history matching production data and providing uncertainty bounds for forecasts from eight Barnett Shale counties. The 80% confidence interval (CI) generated by this method successfully bracketed true production values for all the counties, even when approximately one-third of the data was used for history matching. In the methodology presented, the trend in …

Precipitation In The Alaska Central Arctic, Joel W. Homan

Engineering

Environmental change currently stimulates much of the interest in high-latitude hydrologic studies, as northern areas are expected to be strongly impacted by warming. This thesis consists of a comprehensive assessment of solid and liquid precipitation throughout the Alaska Central Arctic. The founding hypothesis are: (1) the spatial distribution of snow and warm season precipitation are linearly related to elevation, (2) annual precipitation inputs are dominated by warm season precipitation when potential moisture sources are ice free, and (3) moisture responsible for snow-producing storms is primarily advected through atmospheric circulation. To verify the validity of the hypothesis, the temporal variability and …

Approximate Bayesian Computation For Probabilistic Decline Curve Analysis In Unconventional Reservoirs, Mohit Paryani

Engineering

Predicting the production rate and ultimate production of shale resource plays is critical in order to determine if development is economical. In the absence of production from the Shublik Shale, Alaska, Arps' decline model and other newly proposed decline models were used to analyze production data from oil producing wells in the Eagle Ford Shale, Texas. It was found that shales violated assumptions used in Arps' model for conventional hydrocarbon accumulations. Newly proposed models fit the past production data to varying degrees, with the Logistic Growth Analysis (LGA) and Power Law Exponential (PLE) models making the most conservative predictions and …

Understanding Reservoir Engineering Aspects Of Shale Gas Development On The Alaska North Slope, Anna Nyulund

Engineering

Horizontal drilling and multi-stage hydraulic fracturing made it possible to develop US shale resources. Shublik shale is one of such US shale resources - it is one of the largest source rocks for hydrocarbon accumulations located on the Alaska North Slope. This study used the workflow introduced by Mirzaei and Cipolla in 2012 to investigate the effects of fracturing fluid flowback; shale porosity; matrix, fracture and unpropped zone permeability; hydraulic fracture spacing; permeability anisotropy; non-Darcy flow; gas adsorption/desorption using the complex-fracture-network model, referred to as an Unconventional Fracture Model (UFM), and Voronoi grid on well performance in the Shublik shale …

Studies On Thermophysical Properties Of Nanofluids And Their Application In Ground Source Heat Pump, Jagannadha Reddy Satti

Engineering

The goals of this dissertation were to measure the thermal conductivity, specific heat, and density of different propylene glycol nanofluids; compare the results with existing correlations; and develop new correlations with the obtained data. A numerical study has been performed to study the benefits of nanofluids in cold climate ground source heat pumps. Nanofluids are dispersions of nanoparticles with average sizes of less than 100 nm in heat transfer fluids such as water, oil, ethylene glycol, and propylene glycol. In cold regions, the common heat transfer fluids used are ethylene glycol (EG) and propylene glycol (PG). In the present research, …

Three Dimensional Computational Fluid Dynamics Models Of Fugitive Dust Dispersion In High-Latitude Open-Pit Mines, Taraprasad Bhowmick

Engineering

The Arctic region contains vast mineral resources and mining of these resources is a major activity in several countries, including the United States. With the advancement of open-pit mining technology, the depth to which minerals can be profitably mined has increased, resulting in deeper pits than ever before. This increase in depth has several inherent challenges for mining operations. The ventilation of an open-pit mine is mostly dependent on natural airflow patterns. The dispersion behavior of the pollutants generated in a mine is also dependent on the atmospheric conditions. The control of fugitive dust in high-latitude open-pit mines is challenging …

Alternative Project Delivery In Rural Alaska: Experiences, Quality And Claims, Katrina L. Monta, Gerald S. Pehrson, Matthew N. Cryer

Engineering

The popularity of alternative project delivery systems has expanded beyond the private sector and into the public sector. Alaska embodies unique challenges that may present obstacles while using alternative project delivery systems. This analysis will provide an understanding of alternative project delivery systems in Alaska and how local experiences, quality and claims are affected. Alaska's unique characteristics present both challenges and opportunities for implementing alternative project delivery systems. This report begins with a discussion of experiences from several rural Alaska projects, and how alternative project delivery systems can be utilized. Some impacts that alternative project delivery systems have on quality …

Development And Economic Appraisal Of A Lightweight Zeolite Cement Blend For High Temperature - High Pressure Oil And Geothermal Wells, Jyotishka Misra

Engineering

With ever-increasing global energy demand, it is of vital importance that technology consistently meets industry requirements. As high temperature-high pressure reservoirs become more and more profitable, the energy industry can be expected to exploit them. Hence, a versatile cement system that can be used in such reservoirs would need to be capable of ensuring well integrity under such conditions. However, in order to overcome most of these challenges, cement systems are often too dense to pump into a formation without damaging it. Therefore, a lightweight cement is needed. One promising means of delivering a lightweight cement that meets these rigorous …

Designing Transit Networks For Equity And Accessibility, Kelly L. Bertolaccini

Doctoral Dissertations

The equitable provision of public transportation services is a major concern for transit planners and service providers around the world. However, very few tools are available to planners seeking to incorporate equity concerns into their transit network designs. This research proposes innovative models for directly incorporating equity into the stop sequencing and stop grouping components of the Transit Network Design Problem (TNDP) and develops a solution method, a genetic algorithm, for solving these models. First, a single route model is developed to test the effects of designing routes according to different definitions of equity. This research explores nine possible inequity …

Using Twitter To Analyze Stock Market And Assist Stock And Options Trading, Yuexin Mao

Doctoral Dissertations

Twitter has rapidly gained popularity since its creation in March 2006. Stock is a popular topic in Twitter. Many traders, investors, financial analysts and news agencies post tweets about various stocks on a daily basis. These tweets reflect their collective wisdom, and may provide important insights on the stock market. In this dissertation work, we investigate using the tweets concerning Standard & Poor 500 (S&P 500) stocks to analyze the stock markets and assist stock and option trading.

The first part of the dissertation focuses on understanding the correlation between Twitter data and stock trading volume, and predicting stock trading …

X-Ray Fluorescence Spectrometry Using Synchrotron Radiation With Applications In Unmanned Aircraft Environmental Sensing, Sean Richard Barberie

Chemistry and Biochemistry

In this thesis I present an analytical optimization of the Synchrotron Radiation X-Ray Fluorescence (SR-XRF) technique for applications in unmanned aircraft aerosol studies. In environmental and atmospheric science, there is a pressing need for aerosol measurements at various altitudes in the atmosphere and spanning large regions. This need is currently either ignored, or met to a limited degree by studies that employ manned aircraft. There is, however, a great deal of opportunity to improve and expand on these studies using the emerging technology of unmanned aircraft systems. A newly developed aerosol sampler makes this opportunity a near-reality by its ability …

After The Prestige: A Postmodern Analysis Of Penn And Teller, Liz Miller, Joseph Zompetti

Faculty Publications - Communications

By mocking the magic community and revealing the secret behind some of their tricks, Penn and Teller perform a kind of parodic and post-modern “anti-magic.” Penn and Teller display an artful use of rhetoric; in exposing the secrets and shortcomings of conjuring, they are revolutionizing the way people think about both the art of magic and the magic community. Individuals such as Penn and Teller may use parody to subvert the hegemonic interpretations. However, we also know that it is difficult to bring down a system while operating within that system. Thus, this article explores the way Penn and Teller …

Visual Artists Experiencing Nature: Examining Human-Environment Relationships, Amy Lynn Wiita

Anthropology

Anthropology has a long history collaborating with artists to understand their artwork. However, little research exists in the discipline that focuses on artists as a group, their creative process, and what may influence that process. In particular, how artists use nature and place has not been studied; instead, anthropology has generally considered nature and place as merely a backdrop for culture rather than for its impact on cultural expression. Identification of diverse aspects of the interdependence of ecological and social systems can inform our understanding of how people address issues of environmental concern. Managers, scientists, creative people, and others working …

Investigation Of Strongly Ducted Infrasonic Dispersion Using A Vertical Eigenfunction Expansion Of The Helmholtz Equation In A Modal Broad Band Acoustic Propagation Code, Robert Alexander Edon

Physics

This study investigates an infrasound propagation model created by the National Center for Physical Acoustics (NCPA) which is applied to atmospheric data with a strong temperature inversion in the lower atmosphere. This temperature inversion is believed to be the primary cause of a dispersed infrasonic signal recorded by an infrasound sensor array located on the Southern California coast in August, 2012. The received signal is characterized by initial low frequency content followed by a high frequency content tail. It is shown the NCPA model is hindered by limited atmospheric data and no ground truth for the source function which generated …

Development And Preliminary Evaluation Of A Spray Deposition Sensing System For Improving Pesticide Application, Melissa A. Kesterson, Joe D. Luck, Michael P. Sama

Biosystems and Agricultural Engineering Faculty Publications

An electronic, resistance-based sensor array and data acquisition system was developed to measure spray deposition from hydraulic nozzles. The sensor surface consisted of several parallel tin plated copper traces of varying widths with varying gap widths. The system contained an embedded microprocessor to monitor output voltage corresponding to spray deposition every second. In addition, a wireless module was used to transmit the voltage values to a remote laptop. Tests were conducted in two stages to evaluate the performance of the sensor array in an attempt to quantify the spray deposition. Initial tests utilized manual droplet placement on the sensor surface …

From The Library Stacks, Brian Young

University of Mississippi News

Electronic kits available for use to all library users

A "Case" Study On Developing Science Communication And Outreach Skills Of University Graduate Student Researchers In Alaska, Molly E. Tedesche, Laura Conner, Jennifer Danielson

Research Posters

Well rounded scientific researchers are not only experts in their field, but can also communicate their work to a multitude of various audiences, including the general public and undergraduate university students. Training in these areas should ideally start during graduate school, but many programs are not preparing students to effectively communicate their work. Here, we present results from the NSF-funded CASE (Changing Alaska Science Education) program, which was funded by NSF under the auspices of the GK-12 program. CASE placed science graduate students (fellows) in K-12 classrooms to teach alongside of K-12 teachers with the goal of enhancing communication and …

Wsu Board Of Trustees Meeting Minutes, December 17-18, 2015

Board of Trustees Minutes

Minutes from the Wright State University Board of Trustees Meeting held on December 17-18, 2015.

Geomorphic And Geologic Controls Of Geohazards Induced By Nepal’S 2015 Gorkha Earthquake, J. S. Kargel, G. J. Leonard, D. H. Shugar, U. K. Haritashya, A. Bevington, E. J. Fielding, K. Fujita, M. Geertsema, E. S. Miles, J. Steiner, E. Anderson, S. Bajracharya, G. W. Bawden, D. F. Breashears, A. Byers, B. Collins, M. R. Dhital, A. Donnellan, T. L. Evans, M. L. Geai, M. T. Glasscoe, D. Green, D. R. Gurung, R. Heijenk, A. Hilborn, K. Hudnut, C. Huyck, W. W. Immerzeel, Jiang Liming, R. Jibson, A. Kääb, N. R. Khanal, D. Kirschbaum, P. D. A. Kraaijenbrink, D. Lamsal, Liu Shiyin, Lv Mingyang, D. Mckinney, N. K. Nahirnick, Nan Zhuotong, S. Ojha, J. Olsenholler, T. H. Painter, M. Pleasants, K. C. Pratima, Q. I. Yuan, B. H. Raup, D. Regmi, D. R. Rounce, A. Sakai, Shangguan Donghui, J. M. Shea, A. B. Shrestha, A. Shukla, D. Stumm, M. Van Der Kooij, K. Voss, Wang Xin, Brandon J. Weihs, D. Wolfe, Wu Lizong, Yao Xiaojun, M. R. Yoder, N. Young

Geography and Geology Faculty Publications

INTRODUCTION

RATIONALE

Tailgating With The Dean' Was A Top Draw, Edwin Smith

University of Mississippi News

Engineering tent attracted, served record number of patrons during 2015 home football games

Crull Calling The Shots, Edwin Smith

University of Mississippi News

Civil engineering alumna is senior engineer at U.S. Army Engineering and Support Center

Dawn Of A New Era, Edwin Smith

University of Mississippi News

School of Engineering's first female department chair taking CIS to another level

The Ecological Importance Of Brachiopods Versus Bivalves In The Paleozoic: Taphonomy, Biomass, And Energy Use, Shannon (Shin-Nan) Hsieh

Master's Theses

Brachiopods have commonly been considered more important than bivalves in Paleozoic ecosystems due to their greater global diversity and greater abundance in many fossil assemblages. New sampling-standardized diversity curves verify that brachiopods were more diverse than bivalves at the global level in the Paleozoic; they declined in the Permian-Triassic extinction, largely recovered, then faded away later in the Mesozoic. However, the subordinate ecological status of bivalves within local Paleozoic ecosystems has been challenged on two fronts. First, bivalve abundance may be underestimated due to preferential dissolution of aragonitic shells. Second, bivalve contribution to ecosystem function may be underestimated by abundance …