Physical Sciences and Mathematics Commons^™

Hash-Map-Eradicator: Filtering Non-Target Sequences From Next Generation Sequencing Reads, Jonathon Brenner, Catherine Putonti

Bioinformatics Faculty Publications

Contemporary DNA sequencing technologies are continuously increasing throughput at ever decreasing costs. Moreover, due to recent advances in sequencing technology new platforms are emerging. As such computational challenges persist. The average read length possible has taken a giant leap forward with the PacBio and Nanopore solutions. Regardless of the platform used, impurities within the DNA preparation of the sample - be it from unintentional contaminants or pervasive symbiots - remains an issue. We have developed a new tool, HAsh-MaP-ERadicator (HAMPER), for the detection and removal of non-target, contaminating DNA sequences. Integrating hash-based and mapping-based strategies, HAMPER is both memory and …

The Next Generation Of Computational Science And Engineering, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

Editor-in-Chief message.

Scientific Software Communities [Guest Editor Introduction], Andy Terrel, Michael Tobis, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

Guest editor introduction

Network And Device Forensic Analysis Of Android Social-Messaging Applications, Daniel Walnycky, Ibrahim Baggili, Andrew Marrington, Jason Moore, Frank Breitinger

All Works

In this research we forensically acquire and analyze the device-stored data and network traffic of 20 popular instant messaging applications for Android. We were able to reconstruct some or the entire message content from 16 of the 20 applications tested, which reflects poorly on the security and privacy measures employed by these applications but may be construed positively for evidence collection purposes by digital forensic practitioners. This work shows which features of these instant messaging applications leave evidentiary traces allowing for suspect data to be reconstructed or partially reconstructed, and whether network forensics or device forensics permits the reconstruction of …

Computational Development Of Selective Nnos Inhibitors: Binding Modes And Pharmacokinetic Considerations, Adam Curtin, Gemma K. Kinsella, John Stephens

Articles

Abstract: Neuronal nitric oxide synthase (nNOS) produces the key signalling mediator nitric oxide, (NO). This gaseous, free radical molecule modulates a vast array of biological processes, from vascular pressure to immune responses and neurological signalling cascades. Overproduction of NO has been implicated in conditions including Alzheimer’s disease, Parkinson’s disease and schizophrenia. Inhibition of nNOS therefore offers a potential therapeutic approach for treatment of these conditions. This endeavour is made more complex by the fact that there are two other isoforms of nitric oxide synthase (NOS), endothelial NOS (eNOS) and inducible NOS (iNOS). The selectivity of nNOS inhibitors is therefore a …

Distributed Computing And Artificial Intelligence, 12th International Conference, Sigeru Omatu, Qutaibah M. Malluhi, Sara Rodríguez González, Grzegorz Bocewicz, Edgardo Bucciarelli, Gianfranco Giulioni, Farkhund Iqbal

All Works

No abstract provided.

E-Mail Authorship Attribution Using Customized Associative Classification, Michael R. Schmid, Farkhund Iqbal, Benjamin C.M. Fung

All Works

E-mail communication is often abused for conducting social engineering attacks including spamming, phishing, identity theft and for distributing malware. This is largely attributed to the problem of anonymity inherent in the standard electronic mail protocol. In the literature, authorship attribution is studied as a text categorization problem where the writing styles of individuals are modeled based on their previously written sample documents. The developed model is employed to identify the most plausible writer of the text. Unfortunately, most existing studies focus solely on improving predictive accuracy and not on the inherent value of the evidence collected. In this study, we …

A Service Oriented Broker-Based Approach For Dynamic Resource Discovery In Virtual Networks, Sleiman Rabah, May El Barachi, Nadjia Kara, Rachida Dssouli, Joey Paquet

All Works

© 2015, Rabah et al.; licensee Springer. In the past few years, the concept of network virtualization has received significant attention from industry and research fora. This concept applies virtualization to networking infrastructures by enabling the dynamic creation of several co-existing logical network instances (or virtual networks) over a shared physical network infrastructure (or substrate network). Due to the potential it offers in terms of diversifying existing networks and ensuring the co-existence of heterogeneous network architectures on top of shared substrates, network virtualization is often considered as an enabler of a polymorphic Internet and a cornerstone of the future Internet …

Enhancing Social Science Research In The Uae: An Open Source Software Solution University Of Sharjah (Uos) Case Study, Manar Abu Talib, Muhammed Abuodeh, Adhraa Almansoori, Arwa Alnauimi

All Works

© 2015 The Manar Abu Talib, Muhammed AbuOdeh, Adhraa Almansoori and Arwa AlNauimi. Researchers, practitioners and social scientists all agree on the enormous importance of social science research in advancing human knowledge and informing public policy makers. The National Research Foundation, along with other organizations in the UAE, is leading the initiative to integrate the efforts of social research institutions in order to support the decision making process in the UAE. As indicated by a number of social researchers during the last forum held on May 29-30, 2012, at the Emirates Center for Strategic Studies and Research, Abu Dhabi, UAE, …

Factors Influencing Digital Forensic Investigations: Empirical Evaluation Of 12 Years Of Dubai Police Cases, Ibtesam Alawadhi, Janet Read, Andrew Marrington, Virginia Franqueira

All Works

In Digital Forensics, the number of person-hours spent on investigation is a key factor which needs to be kept to a minimum whilst also paying close attention to the authenticity of the evidence. The literature describes challenges behind increasing person-hours and identifies several factors which contribute to this phenomenon. This paper reviews these factors and demonstrates that they do not wholly account for increases in investigation time. Using real case records from the Dubai Police, an extensive study explains the contribution of other factors to the increase in person-hours. We conclude this work by emphasizing on several factors affecting the …

The Contribution Of Non-Thermal And Advanced Oxidation Technologies Towards Dissipation Of Pesticide Residues, N. Misra

Articles

Background

The use of pesticides has stabilised the food production to a great extent and their usage cannot be avoided anymore. Nevertheless, common food processing operations always allowed dissipating pesticide residues in foods to some extent. Within the food science community and the food processing sector, non-thermal food technologies are being researched and commercialised at a great pace over the past three decades.

Scope and Approach

In this review we provide a critical analysis of the literature pertinent to the fate of pesticide residues during non-thermal processing of solid and liquid foods. We also identify the opportunities for further development …

Controlling Microbial Multicellular Behaviors With Saccharide Derivatives, Nischal Singh

Dissertations - ALL

Microbial multicellular behaviors like biofilm formation and swarming motility are known to increase their tolerance against antimicrobials. From microbial standpoint, nonmicrobicidal agents that do not impede growth are tolerable and therefore, there is a lower propensity to develop resistance against such agents as compared to microbicidal ones (antibiotics). This study describes a new antibiofilm approach of using nonmicrobicidal saccharide derivatives for controlling the multicellular behaviors of gram-negative bacteria, Pseudomonas aeruginosa and fungus, Candida albicans.

Pseudomonas aeruginosa is known to secrete rhamnolipids, a class of biosurfactants that plays an important role in maintaining the architecture of its biofilm and promoting its …

Development Of Improved Methodologies Toward The Formation Of C-C And C-N Bonds, Ijaz Ahmed

Dissertations - ALL

Organometallic chemistry provides valuable tools for the formation of carbon-carbon and carbon-heteroatom bonds that would otherwise require multiple steps and resources to achieve through conventional methods. Studies toward the regioselective and stereoselective formation these types of bonds using different organometallic methods will be presented. Three focal areas have been studied: C-N bond formation, C-H borylation, and silylvinylation of alkynes.

In Chapter 1, palladium-catalyzed amidation has been used to effectively form C-N bonds toward the synthesis of valuable imidazo[4,5-b]pyridines and imidazo[4,5-c]pyridines. The reaction conditions are tolerable for a variety of N-substituted-3-amino-2-chloropyridines. All current routes to expand the substrate scope in regards …

Change Point Detection And Estimation In Sequences Of Dependent Random Variables, Benjamin Cortese

Dissertations - ALL

Two change point detection and estimation procedures for sequences of dependent binary random variables are proposed and their asymptotic properties are explored. The two procedures are a dependent cumulative sum statistic (DCUSUM) and a dependent likelihood ratio test (LRT) statistic, which are generalizations of the independent CUSUM and LRT statistics.

A one step Markov dependence is assumed between consecutive variables in the sequence, and the performance of the DCUSUM and dependent LRT are shown to have substantially better size and power performance than their independent counterparts. In most cases, a comparison of the dependent procedures via simulation shows that the …

Modulation And Interactions Of Charged Biomimetic Membranes With Bivalent Ions, Adolphe Kazadi Badiambile

Dissertations - ALL

The biological membrane of an eukaryotic cell is a two-dimensional structure of mostly phospholipids with embedded proteins. This two-dimensional structure plays many key roles in the life of a cell. Transmembrane proteins, for example, play the role of a gate for different ions (such as Ca2+). Also found are peripheral proteins that are used as enzymes for different purposes in the inner leaflet of the plasma membrane. Phospholipids, in particular play three key roles. Firstly, some members of this group are used to store energy. Secondly, the hydrophobic and hydrophilic properties inherent to phospholipids enable them to be used as …

Mechanics, Shape, And Programmability In Soft Matter Systems: From Fluid Membranes To Spring And Droplet Networks, Tao Zhang

Dissertations - ALL

This thesis analyzes three different soft matter systems---membranes, polymers, and droplets---to answer questions about shape, mechanics, and programmability.

For membranes, my collaborators and I have developed a theoretical model of endocytosis in yeast. Endocytosis is the process by which a cell membrane deforms to surround extracellular material to draw it into the cell. Endocytosis in yeast involves clathrin, actin, and Bar proteins. Our model breaks up the process into three stages: (i) initiation, where clathrin interacts with the cell membrane via adaptor proteins, (ii) elongation, where the membrane is then further deformed by polymerizing actin filaments, followed by (iii) pinch-off. …

Geometry Dependence Of The Sign Problem In Quantum Monte Carlo Simulations, V. Iglovikov, Ehsan Khatami, R. Scalettar

Faculty Publications

The sign problem is the fundamental limitation to quantum Monte Carlo simulations of the statistical mechanics of interacting fermions. Determinant quantum Monte Carlo (DQMC) is one of the leading methods to study lattice fermions, such as the Hubbard Hamiltonian, which describe strongly correlated phenomena including magnetism, metal-insulator transitions, and possibly exotic superconductivity. Here, we provide a comprehensive dataset on the geometry dependence of the DQMC sign problem for different densities, interaction strengths, temperatures, and spatial lattice sizes. We supplement these data with several observations concerning general trends in the data, including the dependence on spatial volume and how this can …

Finite-Temperature Superconducting Correlations Of The Hubbard Model, Ehsan Khatami, Richard Scalettar, Rajiv Singh

Faculty Publications

We utilize numerical linked-cluster expansions (NLCEs) and the determinantal quantum Monte Carlo algorithm to study pairing correlations in the square-lattice Hubbard model. To benchmark the NLCE, we first locate the finite-temperature phase transition of the attractive model to a superconducting state away from half filling. We then explore the superconducting properties of the repulsive model for the d-wave and extended s-wave pairing symmetries. The pairing structure factor shows a strong tendency to d-wave pairing and peaks at an interaction strength comparable to the bandwidth. The extended s-wave structure factor and correlation length are larger at higher temperatures but clearly saturate …

Spectroscopic Confirmation Of The Existence Of Large, Diffuse Galaxies In The Coma Cluster, Pieter Van Dokkum, Aaron Romanowsky, Roberto Abraham, Jean Brodie, Charlie Conroy, Marla Geha, Allison Merritt, Alexa Villaume, Jielai Zhang

Faculty Publications

No abstract provided.

The Scientist, 2015, San Jose State University, College Of Science

The Scientist (College of Science)

No abstract provided.

The Door At The End Of The Hall Or Why There Is Life On Earth, And Why We Should Have Seen It Coming, Kirk Pearson

The Synapse: Intercollegiate science magazine

No abstract provided.

Increasing Lightning: How Man-Made Airborne Particles Are Effecting Extreme Weather Events Over The Amazon Basin, Natalie Pierson

The Synapse: Intercollegiate science magazine

No abstract provided.

Gmos, Nate Bohm-Levine

The Synapse: Intercollegiate science magazine

No abstract provided.

Socializing With Scientists, Gabe Hitchcock

The Synapse: Intercollegiate science magazine

No abstract provided.

Against The Grain, Dayna Gallagher, Jenn Feigin

The Synapse: Intercollegiate science magazine

No abstract provided.

The Brain Before The Bench, Lena Lane

The Synapse: Intercollegiate science magazine

No abstract provided.

Scientific Psychology: Why The Doubt?, Kevin Ng

The Synapse: Intercollegiate science magazine

No abstract provided.

Our Curiosity Intensifies, Jacob Turner

The Synapse: Intercollegiate science magazine

No abstract provided.

The Evolution Of Tattoos: Revolutionizing One Of Humanity’S Oldest Art Forms, Marisa Atkins

The Synapse: Intercollegiate science magazine

No abstract provided.

References & Acknowledgements

The Synapse: Intercollegiate science magazine

No abstract provided.