Digital Commons Network^™

High-Performance Reductive Strategies For Big Data From Lc-Ms/Ms Proteomics, Muaaz Gul Awan

Dissertations

Mass Spectrometry (MS)-based proteomics utilizes high performance liquid chromatography in tandem with high-throughput mass spectrometers. These experiments can produce MS data sets with astonishing speed and volume that can easily reach peta-scale level, creating storage and computational problems for large-scale systems biology studies. Each spectrum output by a mass spectrometer may consist of thousands of peaks, which must all be processed to deduce the corresponding peptide. However, only a small percentage of peaks in a spectrum are useful for further processing, as most of the peaks are either noise or are not useful. Our experiments have shown that 90 to …

Relative Importance Of Ions And Particles In Silver Nanoparticle Uptake And Accumulation In Keystone Estuarine Organisms; Prorocentrum Minimum And Crassostrea Virginica, Shelby Victoria Butz

Theses and Dissertations

In marine systems, silver is regarded as being one of the most toxic and readily accumulated metals, and is known to be taken up and accumulate within marine invertebrates, fish, phytoplankton and seaweeds. Reported open ocean concentrations of silver range from 0.1 – 2 ng L-1 while silver concentrations in coastal waters are typically 5 to 10 times higher than open ocean values (0.1 - 50 ng L-1). The determination of silver in marine and coastal waters presents several challenges including low concentrations and matrix complexity of seawater, which creates interferences and other challenges for many instrumental techniques creating a …

Structural Studies Of Dna Repeats Implicated In Cancer, Deondre Jordan , '19

Senior Theses, Projects, and Awards

DNA replication is an essential process for the survival of all organisms. Errors can occur during the process that leads to replication stress, which can promote genomic instability, a hallmark of cancer. The Brown lab conducted a genome wide study to identify sites and sequences linked to replication stress. Tandem DNA repeats comprised the sequences identified in this study. One particular DNA repeat (CAGAGG)ₙ stood out due to being highly associated with replication stress. Repeats such as (CAGAGG)ₙ are believed to fold into fold into intramolecular structures that physically block DNA polymerase during replication. Understanding the structures of these problematic …

Comparison Of Mini-Spectrophotometer And Conventional Spectrophotometers Efficiency For Determination Of Protein And Albumin, Natpasit Chaianantakul, Kanchaporn Wutthi, Nattanit Kamput, Tippawan Sungkapong, Nuttawan Pramanpol, Watcharapon Pummara

Asian Medical Journal and Alternative Medicine

Introduction: Since conventional spectrophotometer is typical large, complex, expensive, and not suitable of infield analysis, therefore a recent portable Mini-spectrophotometer with light emitting diode (LED) light source and microwell has been developed. This prototype has basic principle assay as a conventional spectrophotometer. However, there is no validation study for this prototype. Therefore, the objective of this study is to compare the efficiency of Mini-spectrophotometer and conventional spectrophotometers for detection of protein and albumin.

Method: The efficiency evaluation included Within-run, Between-run, and %Recovery. Comparison study was performed by comparing with Shimadzu and CECIL spectrophotometer.

Result: For protein determination, Within-run precision was …

Larry Prochaska, Professor Emeritus, Department Of Biochemistry And Molecular Biology, Wright State University, Dan Abrahamowicz, Larry Prochaska

Wright State University Retirees Association Oral History Project

On March 20, 2019, Dan Abrahamowicz interviewed Professor Emeritus Larry Prochaska about his 35-year career as Professor of Biochemistry and Molecular Biology at Wright State University . Prochaska discusses building a research laboratory, directing medical biochemistry, mentoring doctoral students, and advocating for diversity and faculty governance. The interview highlights his international teaching experience in Saudi Arabia, leadership in the American Heart Association, and reflections on university administration and the 2019 faculty strike.

A Five Parameter Statistical Distribution With Application To Real Data, Abdullahi Yusuf, Sania Qureshi

Journal of Statistics Applications & Probability

A five parameter lifetime statistical model is proposed in this research. The model is called the Kumuraswamy (KW) exponentiated linear exponential distribution. We derive some statistical properties such as quantile functions, median, moments, entropy, order statistics and many more. The estimation of the model parameters is provided by means of the maximum likelihood(MLEs) approach and the observed information matrix is also presented. Moreover, we perform simulation analysis in order to analyze the effectiveness of the parameters estimation. A set of real data is used to demonstrate the efficiency and effectiveness of the model proposed model with the well-known lifetime models.

Dynamic Molecular Changes During The First Week Of Human Life Follow A Robust Developmental Trajectory., Amy H. Lee, Casey P. Shannon, Nelly Amenyogbe, Tue B. Bennike, Joann Diray-Arce, Olubukola T. Idoko, Erin E. Gill, Rym Ben-Othman, William S. Pomat, Simon D. Van Haren, Kim-Anh Lê Cao, Momoudou Cox, Alansana Darboe, Reza Falsafi, Davide Ferrari, Daniel J. Harbeson, Daniel He, Cai Bing, Samuel J. Hinshaw, Jorjoh Ndure, Jainaba Njie-Jobe, Matthew A. Pettengill, Peter C. Richmond, Rebecca Ford, Gerard Saleu, Geraldine Masiria, John Paul Matlam, Wendy Kirarock, Elishia Roberts, Mehrnoush Malek, Guzmán Sanchez-Schmitz, Amrit Singh, Asimenia Angelidou, Kinga K. Smolen, Diana Vo, Ken Kraft, Kerry Mcenaney, Sofia Vignolo, Arnaud Marchant, Ryan R. Brinkman, Al Ozonoff, Robert E.W. Hancock, Anita H.J. Van Den Biggelaar, Hanno Steen, Scott J. Tebbutt, Beate Kampmann, Ofer Levy, Tobias R. Kollmann

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Systems biology can unravel complex biology but has not been extensively applied to human newborns, a group highly vulnerable to a wide range of diseases. We optimized methods to extract transcriptomic, proteomic, metabolomic, cytokine/chemokine, and single cell immune phenotyping data fromblood, a volume readily obtained from newborns. Indexing to baseline and applying innovative integrative computational methods reveals dramatic changes along a remarkably stable developmental trajectory over the first week of life. This is most evident in changes of interferon and complement pathways, as well as neutrophil-associated signaling. Validated across two independent cohorts of newborns from West Africa and Australasia, a …

White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated With Wound Healing And The Maintenance Of Genome Stability, Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Minghui Wang, Qi Sun, Paulina D. Pavinski Bitar, Vincent P. Richards, Aleksey S. Komissarov, Mike Rayko, Sergey Kliver, Bryce J. Stanhope, Chuck Winkler, Stephen James O'Brien, Agostinho Antunes, Salvador Jorgensen, Mahmood S. Shivji

Biology Faculty Articles

The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability …

The Ralph Mueller Health Galleries: Uncovering The Lost History Of Unl’S Morrill Hall, Eleanor Schmidt

Honors Program: Senior Projects (Public)

The Birth Series sculptures portrayed human development from fertilization through birth and were created by Robert Latou Dickinson, an obstetrician-gynecologist, and Abram Belskie, an artist. The sculptures were commission by the Maternity Center Association and were exhibited in 1939, at the Word’s Fair in New York City. Extremely popular at the fair, the sculptures were displayed all over the world, were used as educational models, and were the subject of the Birth Atlas.

In 1952, a set made their way to Morrill Hall as part of the Great Plain’s first health exhibit where they would remain on display for …

Streaming Feature Grouping And Selection (Sfgs) For Big Data Classification, Noura Helal Hamad Al Nuaimi

Dissertations

Real-time data has always been an essential element for organizations when the quickness of data delivery is critical to their businesses. Today, organizations understand the importance of real-time data analysis to maintain benefits from their generated data. Real-time data analysis is also known as real-time analytics, streaming analytics, real-time streaming analytics, and event processing. Stream processing is the key to getting results in real-time. It allows us to process the data stream in real-time as it arrives. The concept of streaming data means the data are generated dynamically, and the full stream is unknown or even infinite. This data becomes …

Cophosk: A Method For Comprehensive Kinase Substrate Annotation Using Co-Phosphorylation Analysis, Marzieh Ayati, Danica D. Wiredja, Daniela M. Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance

Faculty Scholarship

We present CoPhosK to predict kinase-substrate associations for phosphopeptide substrates detected by mass spectrometry (MS). The tool utilizes a Naïve Bayes framework with priors of known kinase-substrate associations (KSAs) to generate its predictions. Through the mining of MS data for the collective dynamic signatures of the kinases’ substrates revealed by correlation analysis of phosphopeptide intensity data, the tool infers KSAs in the data for the considerable body of substrates lacking such annotations. We benchmarked the tool against existing approaches for predicting KSAs that rely on static information (e.g. sequences, structures and interactions) using publically available MS data, including breast, colon, …

Cophosk: A Method For Comprehensive Kinase Substrate Annotation Using Co-Phosphorylation Analysis, Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance

Computer Science Faculty Publications

We present CoPhosK to predict kinase-substrate associations for phosphopeptide substrates detected by mass spectrometry (MS). The tool utilizes a Naïve Bayes framework with priors of known kinase-substrate associations (KSAs) to generate its predictions. Through the mining of MS data for the collective dynamic signatures of the kinases’ substrates revealed by correlation analysis of phosphopeptide intensity data, the tool infers KSAs in the data for the considerable body of substrates lacking such annotations. We benchmarked the tool against existing approaches for predicting KSAs that rely on static information (e.g. sequences, structures and interactions) using publically available MS data, including breast, colon, …

Benefit And Risk Of Utilizing Antimicrobials In Animal Husbandry Development, Yu Yang, Fang Liangxing, Zhou Yufeng, Sun Jian, Liao Xiaoping, Liu Yahong

Bulletin of Chinese Academy of Sciences (Chinese Version)

For decades, antimicrobials have played a key role in helping and protecting the sound development of animal husbandry. Undoubtedly, for intensive farming, antibiotics will still be one of the essential strategies for preventing and treating the bacterial infectious disease in a very long time. Nevertheless, due to the widely use of antimicrobials, the resistant bacteria and antimicrobial resistance have emerged, which become a severe challenge threatening the whole public for returning to the "pre-antibiotic era". For comprehensively understanding of this issue, here this study focuses on the pros and cons of using antibiotics in livestock, global experience in balancing the …

Spring Water Of An Alpine Karst Aquifer Is Dominated By A Taxonomically Stable But Discharge-Responsive Bacterial Community, Domenico Savio, Philipp Stadler, Georg H. Reischer, Katalin Demeter, Rita B. Linke, Alfred P. Blaschke, Robert L. Mach, Alexander K. T. Kirschner, Hermann Stadler, Andreas H. Farnleitner

KIP Articles

No abstract provided.

Demographic Analyses Of The Data Limited Silky Shark Population In The Indian Ocean Using A Two-Sex Stochastic Matrix Framework, Wen-Pei Tsai, Yen-Jun Wang, Atsuko Yamaguchi

Journal of Marine Science and Technology–Taiwan

The silky shark, Carcharhinus falciformis, is a common bycatch species of tuna and swordfish longline fishing in the Indian Ocean. The high value of its fins makes it one of the most heavily fished shark species in the world. Concern over declining populations and the uncertainty surrounding its population dynamics has increased the urgency of developing appropriate methods to assess its stock status. This study developed a two-sex stage-based structured matrix model with Monte Carlo simulations to examine silky shark demography and population dynamics. The simulations indicate that, without mortality from fishing, the stock will increase slightly (sex combined mean …

Spring Water Of An Alpine Karst Aquifer Is Dominated By A Taxonomically Stable But Discharge-Responsive Bacterial Community, Domenico Savio, Philipp Stadler, Georg H. Reischer, Katalin Demeter, Rita B. Linke, Alfred P. Blaschke, Robert L. Mach, Alexander K. T. Kirschner, Hermann Stadler, Andreas H. Farnleitner

KIP Articles

Alpine karst aquifers are important groundwater resources for the provision of drinking water all around the world. Yet, due to difficult accessibility and long-standing methodological limitations, the microbiology of these systems has long been understudied. The aim of the present study was to investigate the structure and dynamics of bacterial communities in spring water of an alpine limestone karst aquifer (LKAS2) under different hydrological conditions (base vs. event flow). The study was based on high-throughput 16S rRNA gene amplicon sequencing, study design and sample selection were guided by hydrology and pollution microbiology data. Spanning more than 27 months, our analyses …

The Rider (2019-02-04), Victor G. Ramirez

The Rider Archives

Vol.4 No.18

Bed Bugs (Cimex Lectularius L.) Exhibit Limited Ability To Develop Heat Resistance, Aaron R. Ashbrook, Michael E. Scharf, Gary W. Bennett, Ameya D. Gondhalekar

Faculty Publications

The global population growth of the bed bug, Cimex lectularius (L.), is attributed to their cryptic behavior, diverse insecticide resistance mechanisms, and lack of public awareness. Bed bug control can be challenging and typically requires chemical and non-chemical treatments. One common non-chemical method for bed bug management is thermal remediation. However, in certain instances, bed bugs are known to survive heat treatments. Bed bugs may be present after a heat treatment due to (i) abiotic factors associated with the inability to achieve lethal temperatures in harborage areas for a sufficient time period, (ii) re-infestation from insects that escaped to cooler …

Anty 418.01: Evolution And Genetic Variation In Human Populations, Meradeth H. Snow

University of Montana Course Syllabi

No abstract provided.

Prediction Of Ice-Free Conditions For A Perennially Ice-Covered Antarctic Lake, M. K. Obryk, P. T. Doran, J. C. Priscu

Faculty Publications

©2019. American Geophysical Union. All Rights Reserved. Although perennially ice-covered Antarctic lakes have experienced variable ice thicknesses over the past several decades, future ice thickness trends and associated aquatic biological responses under projected global warming remain unknown. Heat stored in the water column in chemically stratified Antarctic lakes that have middepth temperature maxima can significantly influence the ice thickness trends via upward heat flux to the ice/water interface. We modeled the ice thickness of the west lobe of Lake Bonney, Antarctica, based on possible future climate scenarios utilizing a 1D thermodynamic model that accounts for surface radiative fluxes as well …

Carbapenem-Resistant Enterobacteriaceae Infections: A Review Of Epidemiology And Treatment Options, Julie Harting

The University of Louisville Journal of Respiratory Infections

No abstract provided.

Deep Learning Based Medical Image Analysis With Limited Data, Jiaxing Tan

Dissertations, Theses, and Capstone Projects

Deep Learning Methods have shown its great effort in the area of Computer Vision. However, when solving the problems of medical imaging, deep learning’s power is confined by limited data available. We present a series of novel methodologies for solving medical imaging analysis problems with limited Computed tomography (CT) scans available. Our method, based on deep learning, with different strategies, including using Generative Adversar- ial Networks, two-stage training, infusing the expert knowledge, voting based or converting to other space, solves the data set limitation issue for the cur- rent medical imaging problems, specifically cancer detection and diagnosis, and shows very …

Composition Of The Survival Motor Neuron (Smn) Complex In Drosophila Melanogaster, A. Gregory Matera, Amanda C. Raimer, Casey A. Schmidt, Jo A. Kelly, Gaith N. Droby, David Baillat, Sara Ten Have, Angus I. Lamond, Eric J. Wagner, Kelsey M. Gray

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Spinal Muscular Atrophy (SMA) is caused by homozygous mutations in the human survival motor neuron 1 (SMN1) gene. SMN protein has a well-characterized role in the biogenesis of small nuclear ribonucleoproteins (snRNPs), core components of the spliceosome. SMN is part of an oligomeric complex with core binding partners, collectively called Gemins. Biochemical and cell biological studies demonstrate that certain Gemins are required for proper snRNP assembly and transport. However, the precise functions of most Gemins are unknown. To gain a deeper understanding of the SMN complex in the context of metazoan evolution, we investigated its composition in Drosophila …

Little Race Or Gender Bias In An Experiment Of Initial Review Of Nih R01 Grant Proposals, Patrick S. Forscher, William T.L. Cox, Markus Brauer, Patricia G. Devine

Psychological Science Faculty Publications and Presentations

Many granting agencies allow reviewers to know the identity of a proposal’s Principal Investigator (PI), which opens the possibility that reviewers discriminate on the basis of PI race and gender. We investigated this experimentally with 48 NIH R01 grant proposals, representing a broad spectrum of NIH-funded science. We modified PI names to create separate White male, White female, Black male, and Black female versions of each proposal, and 412 scientists each submitted initial reviews for three proposals. We find little to no race or gender bias in initial R01 evaluations, and additionally find that any bias that might have been …

Illumination Pattern Design With Deep Learning For Single-Shot Fourier Ptychographic Microscopy, Yi Fei Cheng , '21, Megan Strachan , '21, Zachary Weiss , '20, Moniher Deb , '19, Dawn M. Carone, Vidya Ganapati

Biology Faculty Works

Fourier ptychographic microscopy allows for the collection of images with a high space-bandwidth product at the cost of temporal resolution. In Fourier ptychographic microscopy, the light source of a conventional widefield microscope is replaced with a light-emitting diode (LED) matrix, and multiple images are collected with different LED illumination patterns. From these images, a higher-resolution image can be computationally reconstructed without sacrificing field-of-view. We use deep learning to achieve single-shot imaging without sacrificing the space-bandwidth product, reducing the acquisition time in Fourier ptychographic microscopy by a factor of 69. In our deep learning approach, a training dataset of high-resolution images …

Assessing Relative Sensitivity Of Marine And Freshwater Bivalves Following Exposure To Copper: Application Of Classical And Novel Genotoxicological Biomarkers, Awadhesh N. Jha, Emily L. Vernon

School of Biological and Marine Sciences

No abstract provided.

Psychology: The Science Of Human Potential, Jeffrey Levy

Psychology (OER)

No abstract provided.

Mrub_3020, A Paralog Of Mrub_1489, Is Orthologous To E. Coli Casc (Locus Tag B2761), Alfred Dei-Ampeh, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological functions of two genes: mrub_3020 and mrub_1489. We make two hypotheses in this investigation: a) mrub_3020 is orthologous to the gene b2761 in E. coli K12 MG1655 (a.k.a. casC); b) mrub_1489 is a paralog of mrub_3020. We also predict that the two genes encode unique proteins: mrub_3020 with DNA coordinates 3060491…3063190 encodes a CRISPR – associated helicase (Cas3) that supports the Cascade complex of the CRISPR – Cas adaptive immune system …

Biodiversity And Conservation Study Of The St. Norbert Abbey, De Pere, Wisconsin - 2018 Annual Report, Nick Moran, Mya Mcdaniel, Adam L. Brandt

Student Creative and Scholarly Works

Long term biological studies are rare but incredibly valuable for examining natural phenomena. Data collected over many years or decades allows for analyses of trends that would never be apparent in a single season. The research presented here is the completion of the second annual field season of a long term study to analyze biodiversity trends at the St. Norbert Abbey. Using visual searches, live trapping, and trail cameras, the biodiversity and abundance of species were examined. Special emphasis was placed on small mammals, though other groups were observed and documented. The goals of this project are to (1) collect …

Comparative Analysis Of Four Dna Preparation Kits For Quercus Falcata, Palustris, And Rubra Dna Extractions And Subsequent Dna Sequencing, Devin Cummins, Timothy D. Trott

Research in Biology

In 2011, of the 8.7 million species of lif suspected to populate the globe only 1.2 million had been catalogued and it was estimated that 1,200 years would pass before the remainder were processed, allowing the possibility that some species would go extinct before they were even discovered (Mora, Tittensor, Adl, Simpson, & Worm, 2011). DNA barcoding may provide an answer to this problem. According to Hebert and Gregory, “DNA barcoding will accelerate the pace of species discovery by allowing taxonomists to rapidly sort specimens... by highlighting divergent taxa that may represent new species… and by making species identifications more …