Engineering Commons^™

A Hybrid Mpi-Openmp Strategy To Speedup The Compression Of Big Next-Generation Sequencing Datasets, Sandino Vargas-Perez, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

DNA sequencing has moved into the realm of Big Data due to the rapid development of high-throughput, low cost Next-Generation Sequencing (NGS) technologies. Sequential data compression solutions that once were sufficient to efficiently store and distribute this information are now falling behind. In this paper we introduce phyNGSC, a hybrid MPI-OpenMP strategy to speedup the compression of big NGS data by combining the features of both distributed and shared memory architectures. Our algorithm balances work-load among processes and threads, alleviates memory latency by exploiting locality, and accelerates I/O by reducing excessive read/write operations and inter-node message exchange. To make the …

Women In Science 2017, Clark Science Center's Summer Research Fellows Program

SURF Abstracts (Women in Science)

Ever since its 1967 start, SURF has been a cornerstone of Smith’s science education. Women in Science 2017 summarizes research done by Smith College’s SURF Program participants during the summer of 2017. 151 students participated in SURF (144 hosted on campus and nearby eld sites), supervised by 58 faculty mentor-advisors drawn from the Clark Science Center and connected to its eighteen science, mathematics, and engineering departments and programs and associated centers and units. At summer’s end, SURF participants summarized their research experiences for this publication.

An Out-Of-Core Gpu Based Dimensionality Reduction Algorithm For Big Mass Spectrometry Data And Its Application In Bottom-Up Proteomics, Muaaz Awan, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

Modern high resolution Mass Spectrometry instruments can generate millions of spectra in a single systems biology experiment. Each spectrum consists of thousands of peaks but only a small number of peaks actively contribute to deduction of peptides. Therefore, pre-processing of MS data to detect noisy and non-useful peaks are an active area of research. Most of the sequential noise reducing algorithms are impractical to use as a pre-processing step due to high time-complexity. In this paper, we present a GPU based dimensionality-reduction algorithm, called G-MSR, for MS2 spectra. Our proposed algorithm uses novel data structures which optimize the memory and …

Gpu-Pcc: A Gpu Based Technique To Compute Pairwise Pearson’S Correlation Coefficients For Big Fmri Data, Taban Eslami, Muaaz Gul Awan, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

Functional Magnetic Resonance Imaging (fMRI) is a non-invasive brain imaging technique for studying the brain’s functional activities. Pearson’s Correlation Coefficient is an important measure for capturing dynamic behaviors and functional connectivity between brain components. One bottleneck in computing Correlation Coefficients is the time it takes to process big fMRI data. In this paper, we propose GPU-PCC, a GPU based algorithm based on vector dot product, which is able to compute pairwise Pearson’s Correlation Coefficients while performing computation once for each pair. Our method is able to compute Correlation Coefficients in an ordered fashion without the need to do post-processing reordering …

Resting State Functional Network Disruptions In A Kainic Acid Model Of Temporal Lobe Epilepsy., Ravnoor Singh Gill, Seyed M Mirsattari, L Stan Leung

Physiology and Pharmacology Publications

We studied the graph topological properties of brain networks derived from resting-state functional magnetic resonance imaging in a kainic acid induced model of temporal lobe epilepsy (TLE) in rats. Functional connectivity was determined by temporal correlation of the resting-state Blood Oxygen Level Dependent (BOLD) signals between two brain regions during 1.5% and 2% isoflurane, and analyzed as networks in epileptic and control rats. Graph theoretical analysis revealed a significant increase in functional connectivity between brain areas in epileptic than control rats, and the connected brain areas could be categorized as a limbic network and a default mode network (DMN). The …

An Investigation Of The Mechanism Of Traumatic Brain Injury Caused By Blast In The Open Field, Ke Feng

Wayne State University Dissertations

Blast-induced traumatic brain injury (bTBI) is a signature wound of modern warfare. The current incomplete understanding of its injury mechanism impedes the development of strategies for effective protection of bTBI. Despite a considerable amount of experimental animal studies focused on the evaluation of brain neurotrauma caused by blast exposure, there is very limited knowledge on the biomechanical responses of the gyrenecephalic brain subjected to primary free-field blast waves imposed in vivo, and the correlation analysis between the biomechanical responses and its injury outcomes. Such information is crucial to the development of injury criteria of bTBI.

This study aims to evaluate …

Biomechanics Of Concussion: The Importance Of Neck Tension, Ron Jadischke

Wayne State University Dissertations

Linear and angular velocity and acceleration of the head are typically correlated to concussion. Despite improvements in helmet performance to reduce accelerations, a corresponding reduction in the incidence of concussion has not occurred (National Football League [NFL] 1996 – present).

There is compelling research that forces on and deformation to the brain stem are related to concussion. The brain stem is the center of control for respiration, blood pressure and heart rate and is the root of most cranial nerves. Injury to the brain stem is consistent with most symptoms of concussion reported in the National Football League and the …

Development Of A Finite Element Pelvis And Lower Extremity Model With Growth Plates For Pediatric Pedestrian Protection, Ming Shen

Wayne State University Dissertations

Finite element (FE) model is a useful tool frequently used for investigating the injury mechanisms and designing protection countermeasures. At present, no 10 years old (YO) pedestrian FE model has been developed from appropriate anthropometries and validated against limitedly available impact response data. A 10 YO child FE pelvis and lower extremities (PLEX) model was established to fill the gap of lacking such models in this age group. The baseline model was validated against available pediatric postmortem human subjects (PMHS) test data and additional scaled adult data, then the PLEX model was integrated to build a whole-body FE model representing …

Field-Observed Angles Of Repose For Stored Grain In The United States, Rumela Bhadra, Mark E. Casada, Sidney A. Thompson, Josephine M. Boac, Ronaldo G. Maghirang, Michael D. Montross, Aaron P. Turner, Samuel G. Mcneill

Biosystems and Agricultural Engineering Faculty Publications

Bulk grain angle of repose (AoR) is a key parameter for inventorying grain, predicting flow characteristics, and designing bins and grain handling systems. The AoR is defined for two cases, piling (dynamic) or emptying (static), and usually varies with grain type. The objective of this study was to measure piling angles of repose for corn, sorghum, barley, soybeans, oats, and hard red winter (HRW) wheat in steel and concrete bins in the United States. Angles were measured in 182 bins and 7 outdoor piles. The piling AoR for corn ranged from 15.7° to 30.2° (median of 20.4° and standard deviation …

Application Of Hyperspectral Imaging And Acoustic Emission Techniques For Apple Quality Prediction, Nader Ekramirad, Ahmed Rady, Akinbode A. Adedeji, Reza Alimardani

Biosystems and Agricultural Engineering Faculty Publications

There is a growing demand for developing effective non-destructive quality assessment methods with quick response, high accuracy, and low cost for fresh fruits. In this study, hyperspectral reflectance imaging (400 to 1000 nm) and acoustic emission (AE) tests were applied to ‘GoldRush‘ apples (total number, n = 180) to predict fruit firmness, total soluble solids (TSS), and surface color parameters (L*, a*, b*) during an eight-week storage period. Partial least squares (PLS) regression, least squares support vector machine (LS-SVM), and multivariate linear regression (MLR) methods were used to establish models to predict the quality attributes of the apples. The results …

Ammonia And Carbon Dioxide Emissions Of Three Laying-Hen Housing Systems As Affected By Manure Accumulation Time, Timothy A. Shepherd, Hongwei Xin, John P. Stinn, Morgan D. Hayes, Yang Zhao, Hong Li

Biosystems and Agricultural Engineering Faculty Publications

Laying-hen housing design and management are the most significant factors affecting the generation and release of gaseous ammonia to the atmosphere. Transitioning the hen housing type from traditional high-rise (where manure is stored within the house for about one year) to modern manure-belt style (where manure is removed every 1 to 4 d and placed into long-term storage) has significantly improved in-barn air quality and reduced farm-level ammonia emissions. As a direct result of the advantages, 100% of new construction for U.S. egg production incorporates manure-belt systems that regularly remove manure from the houses. However, manure-belt system designs (e.g., active …

Development And Evaluation Of A Low-Cost Probe-Type Instrument To Measure The Equilibrium Moisture Content Of Grain, Paul R. Armstrong, Samuel G. Mcneill, Naomi Manu, Augustine Bosomtwe, James K. Danso, Enoch Osekre, George Opit

Biosystems and Agricultural Engineering Faculty Publications

Storage of grain in bags is common in Africa, Asia, and many other less developed countries making a bag probing method well-suited for moisture content (MC) measurement. A low-cost meter was developed under a USAID project to reduce post-harvest loss (PHL). The meter, referred to as the PHL meter, measures the MC of maize and other grains based on relative humidity (RH) and temperature (T) measurements obtained by a small digital sensor located in the tip of a tubular probe that can be inserted into bags of grain or other grain bulks. Measurements are used by equilibrium moisture content (EMC) …

Evaluating Ventilation Rates Based On New Heat And Moisture Production Data For Swine Production, Yanxi Lu, Morgan D. Hayes, John P. Stinn, Tami M. Brown-Brandl, Hongwei Xin

Biosystems and Agricultural Engineering Faculty Publications

Heat and moisture production (HMP) rates of animals are used for calculation of ventilation rate (VR) in animal housing. New swine HMP data revealed considerable differences from previously reported data. This project determined new design VRs and evaluated differences from previously recommended VRs. The swine production stages evaluated included gestation, farrowing, nursery, growing, and finishing. The ranges of ambient temperature and ambient relative humidity (RH) evaluated for VR were -25°C to 15°C in 10°C increments and 15% to 75% in 15% increments, respectively. Indoor set points for temperature and RH were, respectively, 15°C, 20°C, 25°C and 60%, 70%, 80% for …

Effects Of Biochar Treatment Of Municipal Biosolids And Horse Manure On Quality Of Runoff From Fescue Plots, Rachel Williams, Dwayne R. Edwards

Biosystems and Agricultural Engineering Faculty Publications

Land-applied horse manure and municipal biosolids can increase nutrient and bacteria concentrations in runoff. Biochar has been demonstrated to have beneficial impacts on nutrient retention and runoff quality when used to treat other land-applied organic soil amendments (e.g., poultry manure). The objective of this study was to evaluate the effects of biochar addition to horse manure and municipal biosolids on runoff concentrations of nutrients and fecal coliforms. Biochar was added at 5% to 8% (wet basis) to horse manure and biosolids that were applied to 2.4 m x 6.1 m fescue plots followed by application of simulated rainfall (102 mm …

3d Bioprinting Of Stem Cells And Polymer/Bioactive Glass Composite Scaffolds For Bone Tissue Engineering, Caroline Murphy, Krishna Kolan, Wenbin Li, Julie A. Semon, D. E. Day, Ming-Chuan Leu

Biological Sciences Faculty Research & Creative Works

A major limitation of using synthetic scaffolds in tissue engineering applications is insufficient angiogenesis in scaffold interior. Bioactive borate glasses have been shown to promote angiogenesis. There is a need to investigate the biofabrication of polymer composites by incorporating borate glass to increase the angiogenic capacity of the fabri-cated scaffolds. In this study, we investigated the bioprinting of human adipose stem cells (ASCs) with a polycaprolac-tone (PCL)/bioactive borate glass composite. Borate glass at the concentration of 10 to 50 weight %, was added to a mixture of PCL and organic solvent to make an extrudable paste. ASCs suspended in Matrigel …

Journal Of The Arkansas Academy Of Science- Volume 71 2017, Academy Editors

Journal of the Arkansas Academy of Science

No abstract provided.

Using Remote Sensing To Estimate Crop Water Use To Improve Irrigation Water Management, Arturo Reyes-Gonzalez

Electronic Theses and Dissertations

Irrigation water is scarce. Hence, accurate estimation of crop water use is necessary for proper irrigation managements and water conservation. Satellite-based remote sensing is a tool that can estimate crop water use efficiently. Several models have been developed to estimate crop water requirement or actual evapotranspiration (ETa) using remote sensing. One of them is the Mapping EvapoTranspiration at High Resolution using Internalized Calibration (METRIC) model. This model has been compared with other methods for ET estimations including weighing lysimeters, pan evaporation, Bowen Ratio Energy Balance System (BREBS), Eddy Covariance (EC), and sap flow. However, comparison of METRIC model outputs to …

Electrotransfer Of Plasmid Dna Radiosensitizes B16f10 Tumors Through Activation Of Immune Response, Monika Savarin, Urska Kamensek, Maja Cemazar, Richard Heller, Gregor Sersa

Bioelectrics Publications

Background. Tumor irradiation combined with adjuvant treatments, either vascular targeted or immunomodulatory, is under intense investigation. Gene electrotransfer of therapeutic genes is one of these approaches. The aim of this study was to determine, whether gene electrotransfer of plasmid encoding shRNA for silencing endoglin, with vascular targeted effectiveness, can radiosensitize melanoma B16F10 tumors.

Materials and methods. The murine melanoma Bl6F10 tumors, growing on the back of C57BI/6 mice, were treated by triple gene electrotransfer and irradiation. The antitumor effect was evaluated by determination of tumor growth delay and proportion of tumor free mice. Furthermore, histological analysis of tumors (necrosis, apoptosis, …

Transient Alt Activation Protects Human Primary Cells From Chromosome Instability Induced By Low Chronic Oxidative Stress, Elisa Coluzzi, Rossella Buonsante, Stefano Leone, Anthony J. Asmar, Kelley L. Miller, Daniela Cimini, Antonella Sgura

Bioelectrics Publications

Cells are often subjected to the effect of reactive oxygen species (ROS) as a result of both intracellular metabolism and exposure to exogenous factors. ROS-dependent oxidative stress can induce 8-oxodG within the GGG triplet found in the G-rich human telomeric sequence (TTAGGG), making telomeres highly susceptible to ROS-induced oxidative damage. Telomeres are nucleoprotein complexes that protect the ends of linear chromosomes and their dysfunction is believed to affect a wide range of cellular and/or organismal processes. Acute oxidative stress was shown to affect telomere integrity, but how prolonged low level oxidative stress, which may be more physiologically relevant, affects telomeres …

Nanosecond Pulsed Electric Field Induced Changes In Cell Surface Charge Density, Diganta Dutta, Xavier-Lewis Palmer, Anthony Asmar, Michael Stacey, Shizhi Qian

Bioelectrics Publications

This study reports that the surface charge density changes in Jurkat cells with the application of single 60 nanosecond pulse electric fields, using atomic force microscopy. Using an atomic force microscope tip and Jurkat cells on silica in a 0.01 M KCl ionic concentration, we were able to measure the interfacial forces, while also predicting surface charge densities of both Jurkat cell and silica surfaces. The most important finding is that the pulsing conditions varyingly reduced the cells' surface charge density. This offers a novel way in which to examine cellular effects of pulsed electric fields that may lead to …

Kentucky Water Resources Research Institute Annual Technical Report Fy 2016, Kentucky Water Resources Research Institute, University Of Kentucky

KWRRI Annual Technical Reports (USGS’s 104b Grant Program)

The 2016 Annual Technical Report for Kentucky consolidates reporting requirements for the Section 104(b) base grant award into a single document that includes: 1) a synopsis of each student research enhancement project that was conducted during the period, 2) citations for related publications, reports, and presentations, 3) a description of information transfer activities, 4) a summary of student support during the period, and 5) notable awards and achievements.

No funds were requested for general program administration activities. However, travel funds were provided to support the participation of the director and associate director in the annual meeting of the National Institutes …

Modulating The Innate Immune Response To Electrospun Scaffolds And Polymer Degradative Byproducts, Daniel Abebayehu

Theses and Dissertations

Implanted biomaterials often induce inflammation that frequently leads to the foreign body response, fibrosis, and the failure of the implant. Thus, it is important to evaluate how cells interact with materials to promote a more regenerative response. It is critical to determine how to modulate the response of tissue resident innate immune cells, as they are among the first cells to interact with implanted materials. Among tissue resident innate immune cells are mast cells, which are inflammatory sentinels that degranulate and orchestrate the fate of other cell populations, such as monocytes/macrophages and lymphocytes. Mast cells have also been reported to …

Pretreatment, Enzymatic Hydrolysis, And Fermentation To Ethanol Using A Lignocellulosic Feedstock And Subsequent Recovery Of A Value Added Co-Product: Pure Crystalline Cellulose, Ryan J. Bouza

Electronic Theses and Dissertations

As more demand for alternatives to petroleum and the industrial world’s love of cars increase, cellulosic ethanol will become more important. The ethanol can, of course, be used in the transportation fuel sector, but there is also a potential for co-products to be developed out of the cellulose to ethanol process. Some of these co-products have the potential to replace current petrol products. These co-products may provide the extra revenue generation needed for further investment and development of this industry. This would not only provide better energy independence, but in the United States, it would better satisfy the cellulosic ethanol …

Understanding The Impact Of Extrusion Processing On Rheological, Textural And Functional Properties Of High-Protein, High-Fiber Extrudates, Poonam Singha

Electronic Theses and Dissertations

Extrusion processing is a technology widely used to make ready-to-eat snack and breakfast cereal products. Expanded products mainly consists of high levels of starch resulting in optimal texture and consumer acceptance. However, these products are usually low in nutritional value. One of the many alternatives are to combine legumes and cereals to improve the protein quality of the product. Another possibility is to enhance the nutritional value by incorporating fruits and vegetables. Fruits and vegetables are consistently under-consumed by the American population and incorporation into extruded products may help increase the intake of important nutrients, such as dietary fiber. The …

A Demonstration Study Of Drainage Water Management In Eastern South Dakota, Ashik Sahani

Electronic Theses and Dissertations

Subsurface drainage is a common water management practice for improving crop production in poorly drained soils; however, the practice is associated with several environmental concerns such as nutrient losses to downstream surface waters. These environmental concerns from subsurface drainage have prompted interest in drainage water management strategies such as controlled drainage. This study assessed the agronomic and environmental impacts of drainage water management in eastern South Dakota by using two demonstration plots for controlled and conventional drainage. Drain flow, nitrate and dissolved phosphorous concentration in drain water, shallow groundwater, crop yield, residual soil nitrate, soil moisture and temperature, soil penetration …

The Synthetic Biology Of N2-Fixing Cyanobacteria For Photosynthetic Terpenoid Production, Charles T. Halfmann

Electronic Theses and Dissertations

In the last few decades, concerns over global climate change, energy security, and environmental pollution have been rising. To overcome these challenges, the concept of “-n^th generation” biofuels has emerged as a strategy to convert solar radiation into fuels and bulk industrial chemicals for societal use, while decreasing our consumption of nonrenewable energy sources. Nitrogen-fixing cyanobacteria hold a distinct advantage in biofuel production over plants, given their ability to convert sunlight, air (CO₂ and N₂), and mineralized water to energy-dense carbon molecules, as well as fix atmospheric nitrogen gas into ammonia for metabolism. Engineered cyanobacteria with …

Profiling Resistance To P450-Activated Food Carcinogens Using Toxicogenomic Approaches In Budding Yeast, Nicholas Stjohn

Legacy Theses & Dissertations (2009 - 2024)

The human response to environmental carcinogens, some of which require metabolic activation, is highly variable. Factors such as environment, lifestyle, and genetics all influence the rates of exposure to and ultimate bioactivation of these compounds. Genetic factors include mutations to cell-cycle regulation, cell proliferation, and DNA repair genes; however, epidemiological studies may lack significance due to inadequate patient numbers. We used budding yeast as a model organism to determine genetic susceptibility to food-associated carcinogens, including aflatoxin (AFB1) and heterocyclic aromatic amines (HAAs). Budding yeast does not contain P450s that activate these compounds, so expression vectors were induced that contain human …

Novel Approaches To Mitigating Bacterial Biofilm Formation And Intercellular Communication, Stephen Kasper

Legacy Theses & Dissertations (2009 - 2024)

Long thought of as solitary single-cell organisms, it is now widely accepted that bacteria can act and cooperate as social organisms. Phenomena such as biofilm formation and quorum sensing (QS) are two intimately intertwined cooperative behaviors that significantly contribute to the pathogenesis of many bacteria. Biofilms are surface associated communities of bacteria encased in a secreted extracellular matrix, which provides several advantages over an individualized lifestyle, such as increased protection from antimicrobial agents as well as enhanced opportunity for the exchange of genetic material. Bacterial QS is a system of population-based communication through the production, sensing, and response to chemical …

Multifunctional Nanomaterials Utilizing Hybridization Chain Reaction For Molecular Diagnostics And Bioanalytical Applications, Md Muhit Rana

Legacy Theses & Dissertations (2009 - 2024)

DNA nanotechnology has shown great promise in molecular diagnostic, bioanalytical and biomedical applications. The great challenge of detecting target analytes, biomarkers and small molecules, in molecular diagnostics is low yield sensitivity. To address this challenge, different nanomaterials have been used for a long time and to date there is no such cost-effective bioanalytical technique which can detect these target biomarkers (DNA, RNA, circulating DNA/miRNA) or environmental heavy metal ions (Hg2+ and Ag+) in a cost-effective and efficient manner.

Detecting And Analyzing Trna Modification Systems And Homologs Using In Silico And Colorectal Cancer Models, Khadijah Onanuga

Legacy Theses & Dissertations (2009 - 2024)

tRNA modifications can be considered epitranscriptomic signaling components that regulate translation and play integral roles in stress response pathways. As such, tRNA modification enzymes have roles in cancer etiology and potential utility as biomarkers of pathological states. For my thesis project I have used computational and wet bench approaches to study tRNA modification systems. Chapter two of my thesis deals with tRNA modification detection, as current methods are costly, time consuming, and require RNA fragmentation. I present a single-molecule-based approach for RNA modification detection, which involves in slico studies using a 5-layered graphene nanopore. Our simulations using a 1.5 nm …