Physical Sciences and Mathematics Commons^™

Prediction Of Kinase-Substrate Associations Using The Functional Landscape Of Kinases And Phosphorylation Sites, Marzieh Ayati, Serhan Yılmaz, Filipa Blasco Tavares Pereira Lopes, Mark R. Chance, Mehmet Koyutürk

Computer Science Faculty Publications

Protein phosphorylation is a key post-translational modification that plays a central role in many cellular processes. With recent advances in biotechnology, thousands of phosphorylated sites can be identified and quantified in a given sample, enabling proteome-wide screening of cellular signaling. However, for most (> 90%) of the phosphorylation sites that are identified in these experiments, the kinase(s) that target these sites are unknown. To broadly utilize available structural, functional, evolutionary, and contextual information in predicting kinase-substrate associations (KSAs), we develop a network-based machine learning framework. Our framework integrates a multitude of data sources to characterize the landscape of functional relationships …

Adaptive Resolution Loss: An Efficient And Effective Loss For Time Series Self-Supervised Learning Framework, Kevin Garcia, Juan Manuel Perez, Yifeng Gao

Computer Science Faculty Publications

Time series data is a crucial form of information that has vast opportunities. With the widespread use of sensor networks, largescale time series data has become ubiquitous. One of the most prominent problems in time series data mining is representation learning. Recently, with the introduction of self-supervised learning frameworks (SSL), numerous amounts of research have focused on designing an effective SSL for time series data. One of the current state-of-the-art SSL frameworks in time series is called TS2Vec. TS2Vec specially designs a hierarchical contrastive learning framework that uses loss-based training, which performs outstandingly against benchmark testing. However, the computational cost …

An Intertwined Cauchy––Schwarz–Type Inequality Based On A Lagrange–Type Identity, Iosif Pinelis

Michigan Tech Publications

Based on an apparently new Lagrange-type identity, a Cauchy–Schwarz-type inequality is proved. The mentioned identity is obtained by using certain “macro” variables; it is hoped that such a method can be used to prove or produce other identities and inequalities.

Superheating Field In Superconductors With Nanostructured Surfaces, W. P. M. R. Pathirana, A. Gurevich

Physics Faculty Publications

We report calculations of a dc superheating field H_sh in superconductors with nanostructured surfaces. Numerical simulations of the Ginzburg-Landau (GL) equations were performed for a superconductor with an inhomogeneous impurity concentration, a thin superconducting layer on top of another superconductor, and superconductor-insulator-superconductor (S-I-S) multilayers.The superheating field was calculated taking into account the instability of the Meissner state with a nonzero wavelength along the surface, which is essential for realistic values of the GL parameter κ. Simulations were done for the materials parameters of Nb and Nb₃Sn at different values of κ and the mean free paths. We …

Further Investigation Of Lead Exposure As A Potential Threatening Process For A Scavenging Marsupial Species, D. J. Hutchinson, E. M. Jones, J. M. Pay, J. R. Clarke, Michael T. Lohr, J. O. Hampton

Research outputs 2022 to 2026

There is a growing recognition of the harmful effects of lead exposure on avian and mammalian scavengers. This can lead to both lethal and non-lethal effects which may negatively impact wildlife populations. Our objective was to assess medium-term lead exposure in wild Tasmanian devils (Sarcophilus harrisii). Frozen liver samples (n = 41), opportunistically collected in 2017–2022, were analysed using inductively coupled plasma mass spectrometry (ICP-MS) to determine liver lead concentrations. These results were then used to calculate the proportion of animals with elevated lead levels ( > 5 mg/kg dry weight) and examine the role of explanatory variables that may have …

Plastic Storage In River Sediments Across An Urbanization Gradient In The Ipswich Watershed In Massachusetts, Jackie L. Harris

Honors Theses and Capstones

The importance of plastic pollution research has become apparent as plastic pollution has increased exponentially since its introduction in the 1950s. Plastics mechanically break down into minuscule particles called microplastics, which are plastic particles with a size range of 0.1 micrometers (μm) to 5 millimeters (mm). Most of the research on microplastic pollution has centered around marine ecosystems rather than freshwater ecosystems. More freshwater microplastic research to date is emerging but is still nascent and sparse. Furthermore, the idea that rivers are merely conduits of microplastics to the ocean is even more limited and ignores microplastic loading and retention in …

Low Frequency Waves Due To He+ As Observed By The Ulysses Spacecraft, Anastasia V. Marchuk

Honors Theses and Capstones

We surveyed magnetic field data from the Ulysses spacecraft and found examples of magnetic waves with characteristics that point to excitation by newborn pickup He+. With interstellar neutrals as the likely source for the pickup ions, we have modeled the ion production rates and used them to produce wave excitation rates that we compare to the background turbulence rates. The source ions are thought to be always present, but the waves are seen when growth rates are comparable to or exceed the turbulence rates. With the exception of the fast latitude scans, and unlike the waves excited by newborn interstellar …

General-Purpose Planning Algorithms In Partially-Observable Stochastic Games, Bryan Mckenney

Honors Theses and Capstones

Partially observable stochastic games (POSGs) are difficult domains to plan in because they feature multiple agents with potentially opposing goals, parts of the world are hidden from the agents, and some actions have random outcomes. It is infeasible to solve a large POSG optimally. While it may be tempting to design a specialized algorithm for finding suboptimal solutions to a particular POSG, general-purpose planning algorithms can work just as well, but with less complexity and domain knowledge required. I explore this idea in two different POSGs: Navy Defense and Duelyst.

In Navy Defense, I show that a specialized algorithm framework, …

A Cross-Domain Trust Model Of Smart City Iot Based On Self-Certification, Yao Wang, Yubo Wang, Zhenhu Ning, Sadaqat Ur Rehman, Muhammad Waqas

Research outputs 2022 to 2026

Smart city refers to the information system with Internet of things and cloud computing as the core technology and government management and industrial development as the core content, forming a large-scale, heterogeneous and dynamic distributed Internet of things environment between different Internet of things. There is a wide demand for cooperation between equipment and management institutions in the smart city. Therefore, it is necessary to establish a trust mechanism to promote cooperation, and based on this, prevent data disorder caused by the interaction between honest terminals and malicious terminals. However, most of the existing research on trust mechanism is divorced …

Camdec: Advancing Axis P1435-Le Video Camera Security Using Honeypot-Based Deception, Leslie F. Sikos, Craig Valli, Alexander E. Grojek, David J. Holmes, Samuel G. Wakeling, Warren Z. Cabral, Nickson M. Karie

Research outputs 2022 to 2026

The explosion of online video streaming in recent years resulted in advanced services both in terms of efficiency and convenience. However, Internet-connected video cameras are prone to exploitation, leading to information security issues and data privacy concerns. The proliferation of video-capable Internet of Things devices and cloud-managed surveillance systems further extend these security issues and concerns. In this paper, a novel approach is proposed for video camera deception via honeypots, offering increased security measures compared to what is available on conventional Internet-enabled video cameras.

Cybersecurity Knowledge Graphs, Leslie Sikos

Research outputs 2022 to 2026

Cybersecurity knowledge graphs, which represent cyber-knowledge with a graph-based data model, provide holistic approaches for processing massive volumes of complex cybersecurity data derived from diverse sources. They can assist security analysts to obtain cyberthreat intelligence, achieve a high level of cyber-situational awareness, discover new cyber-knowledge, visualize networks, data flow, and attack paths, and understand data correlations by aggregating and fusing data. This paper reviews the most prominent graph-based data models used in this domain, along with knowledge organization systems that define concepts and properties utilized in formal cyber-knowledge representation for both background knowledge and specific expert knowledge about an actual …

Normal Redefined: Exploring Decontextualization Of Lorises (Nycticebus & Xanthonycticebus Spp.) On Social Media Platforms, Luke F. Quarles, Kim Feddema, Marco Campera, K. A.I. Nekaris

Research outputs 2022 to 2026

Introduction: Decontextualization is a concept from psychology whereby new words are learned outside of the context of the here-and-now. Decontextualized language is used for discussing abstract concepts and is crucial to the development of academic language. When it comes to images, a dearth of context can lead to a lack of clarity, such as the use of ambiguous decontextualized images in environmental communication, leading to the promotion of greenwashing. Here we refer to decontextualization as the removal of wildlife from their wild ecological context. Images and videos of globally threatened species are increasingly popular on social media. Showing such taxa …

A Review Of Multi-Factor Authentication In The Internet Of Healthcare Things, Tance Suleski, Mohiuddin Ahmed, Wencheng Yang, Eugene Wang

Research outputs 2022 to 2026

Objective: This review paper aims to evaluate existing solutions in healthcare authentication and provides an insight into the technologies incorporated in Internet of Healthcare Things (IoHT) and multi-factor authentication (MFA) applications for next-generation authentication practices. Our review has two objectives: (a) Review MFA based on the challenges, impact and solutions discussed in the literature; and (b) define the security requirements of the IoHT as an approach to adapting MFA solutions in a healthcare context. Methods: To review the existing literature, we indexed articles from the IEEE Xplore, ACM Digital Library, ScienceDirect, and SpringerLink databases. The search was refined to combinations …

Leveraging Machine Learning To Analyze Sentiment From Covid-19 Tweets: A Global Perspective, Md Mahbubar Rahman, Nafiz Imtiaz Khan, Iqbal H. Sarker, Mohiuddin Ahmed, Muhammad Nazrul Islam

Research outputs 2022 to 2026

Since the advent of the worldwide COVID-19 pandemic, analyzing public sentiment has become one of the major concerns for policy and decision-makers. While the priority is to curb the spread of the virus, mass population (user) sentiment analysis is equally important. Though sentiment analysis using different state-of-the-art technologies has been focused on during the COVID-19 pandemic, the reasons behind the variations in public sentiment are yet to be explored. Moreover, how user sentiment varies due to the COVID-19 pandemic from a cross-country perspective has been less focused on. Therefore, the objectives of this study are: to identify the most effective …

The Discovery And Characterization Of Novel Potent 5-Substituted 3, 3’, 4’, 7-Tetramethoxyflavonoid Dna Triplex Specific Binding Ligands, Vanessa Marie Rangel

University of the Pacific Theses and Dissertations

Chemotherapy works by killing fast dividing cells. Unfortunately, these drugs are not specific to cancer tissue and can damage normal cells. Chemotherapy is like taking poison and hoping it kills the cancer cells before it kills you. As an alternative, many researchers have investigated the use of antigene therapy to selectively target cancer causing genes to avoid off target effects. Although promising, the theory is limited by the stability of the triplex structure. Here, we report the discovery of potent triplex binding ligands derived from the natural product quercetin. Chemical derivatives of 5-substituted 3, 3’, 4’, 7-tetramethoxyquercetin derivatives were characterized …

Remote Ambient Aerosols Found In The Southern Great Plains And Eastern North Atlantic: A Comprehensive Analysis Of Optical Behavior And Aerosol-Cloud Interaction, Daniel J. Bonanno

University of the Pacific Theses and Dissertations

The data presented in this thesis showcases the investigation of various aerosol types and the role they play in the hydrological system and global climate models. Long-range transport aerosols, including atmospheric soot, mineral dust, and ammonium sulfate, in addition to near-site sources such as secondary organic aerosols (SOAs), sea spray, aliphatic hydrocarbons, and other organics, are prioritized in the analysis of two separate remote field studies. Each of these campaigns revealed the juxtaposition between dry summer months and wet winter months, and the connection between seasonal variability and sample collection. Two spectromicroscopic techniques were used to elucidate chemical composition, morphology …

Chemically Mediated Algal-Bacterial Interactions: Promotion & Inhibition, Kara Talbott

University of the Pacific Theses and Dissertations

Algae-bacteria interactions range from mutualistic, Chlamydomonas reinhardtii (green algae) provides carbonate complexes for surface associated bacteria (SAB) and the bacteria in turn provide B-12 for the algae, to pathogenic, the presence of certain bacteria increases the incidence of bleaching in the algae. Algal natural products have been found to display the following activities: anti-fouling, anti-bacterial, anti-cancer, and anti-feedant. Separately, it has been well documented in the literature that algae mediate their SAB, also known as their microbiome, using natural products to attract and inhibit different bacterial strains. My graduate work builds on these findings; our hypothesis is that the algal-bacterial …

Design And Development Of Hybrid Spectrum Access Technique For Cr-Iot Network, Sandeep Singh

Mesopotamian Journal of Computer Science

The radio spectrum is an underutilized natural resource with significant untapped potential. The rapid proliferation of Internet of Things (IoT) devices is driving a dramatic increase in radio spectrum demand. These devices can utilize cognitive radio (CR) technology to access the bandwidth left unused by licensed spectrum users, also known as primary users (PUs), to meet end users spectrum requirements efficiently. However, because PUs are given priority, CR-enabled Internet of Things (CR-IoT) devices, also known as secondary users (SU), must frequently communicate with one another in an opportunistic manner or under stringent power constraints. This can complicate CR-IoT device communication, …

Machine Learning Application On Employee ‎Promotion, Muhannad Ilwani, Ghalia Nassreddine, Joumana Younis

Mesopotamian Journal of Computer Science

Any company's most valuable asset, its workforce, is its employees. As a result, the company's primary goal should be to develop an excellent strategy for supporting and investing in its employees and staff by providing the best training and development. Employee Promotion denotes the advancement of an employee's rank. It raises the salary, position, duties, and benefits. It is a part of the job that propels employees to the highest commitment and loyalty to their organizations. Employee morale and loyalty are two critical components of any successful business. Employee promotion is the key to improving employee performance and engagement. It …

Clustering Algorithms And Comparisons In Vehicular Ad Hoc Networks, Radhakrishna Karne, Sreeja Tk

Mesopotamian Journal of Computer Science

Vehicular Ad hoc Network (VANET) is a new era in the transmission of dynamic information across communities. Intelligent Transportation Systems is only one of the many applications for VANET (ITS). The topology of VANET is extremely dynamic, and connections are irregular. These features cause information transmission in the VANET to be unreliable. Vehicle clustering is a successful strategy to increase the network's scalability and connection dependability. Characteristics of the VANET have an impact on clustering performance as well. An extensive explanation of VANET clustering algorithms is given in this article. A complete evaluation of clustering in VANETs is provided based …

Artificial Neural Networks: An Overview, Roheen Qamar, Baqar Ali Zardari

Mesopotamian Journal of Computer Science

Neural networks, also known as artificial neural networks (ANNs) or artificially generated neural networks (SNNs) are a subset of machine learning that provide the foundation of deep learning techniques. Their name and form are inspired by the human brain, and they replicate the way real neurons communicate with one another. Artificial neural networks (ANNs) are massively parallel systems comprised of a huge number of interconnected basic processors. This paper discuss about the artificial neural network and its basic types. This article explains the ANN and its basic outlines the fundamental neuron and the artificial computer model. It describes network structures …

Preface : Fruit And Vegetable Waste Utilization And Sustainability, Sachin A. Mandavgane, Ipsita Chakravarty, Amit Jaiswal

Books/Book Chapters

Fruits and vegetables are an important source of nutrition and a key element of a healthy balanced diet. Several organizations such as the World Health Organization (WHO), Food and Agriculture Organization of United Nations (FAO), and Food Health England suggest consuming more than 400 g of fruits and vegetables per day (roughly five portions per day) to improve overall health and reduce the risk of certain cardiovascular diseases and cancer; subsequently, consumption and production of fruits and vegetables are on the rise. The increased consumption/production of fruits and vegetables has resulted in huge quantities of waste (approximately 42% of the …

Investigation Of Oleic Acid As A Dispersant For Hydroxyapatite Powders For Use In Ceramic Filled Photo-Curable Resins For Stereolithography, Brendan Kennedy, Eamonn De Barra, Stuart Hampshire, Maura Kelleher

Articles

Stereolithography allows production of porous hydroxyapatite scaffolds for bone regeneration but is limited by the challenging rheology of ceramic filled resins. Oleic acid, a natural fatty acid, was applied in concentrations of 0.0–0.3 wt% to improve the rheological properties of HAp resins for the fabrication of solid cylinders and scaffolds by digital light processing (DLP) printing in a wiperless system. Bonding by chemisorption was confirmed by FTIR analysis. The powders were then incorporated into a photo-curable resin of 1–6 hexanediol diacrylate at 18–30 vol%. The shear viscosity and sedimentation rates of photocurable resins containing HAp powder decreased with increasing concentration …

Pro-Environmental Diversification Of Pasture-Based Dairy And Beef Production In Ireland, The United Kingdom And New Zealand: A Scoping Review Of Impacts And Challenges, Maria Markiewicz-Keszycka, Aileen Carter, Donal O'Brien, Maeve Henchion, Simon Mooney, Paul Hynds

Articles

Grass-fed dairy and beef products are valued by consumers for their unique nutrient profile, enhanced animal welfare and lower environmental footprint compared to conventional produce derived from animals reared indoors on higher volumes of concentrate feeds (O'Callaghan et al., Reference O'Callaghan, Vázquez-Fresno, Serra-Cayuela, Dong, Mandal, Hennessy, McAuliffe, Dillon, Wishart, Stanton and Ross2018; Moscovici Joubran et al., Reference Moscovici Joubran, Pierce, Garvey, Shalloo and O'Callaghan2021). For the current study, pasture-based production of dairy and beef is defined as a system within which cattle graze freely outdoors on green pasture for ≥6 months per year, using grazed grass as the primary feed …

Selection And Characterization Of Bacteriocinogenic Lactic Acid Bacteria From The Intestine Of Gilthead Seabream (Sparus Aurata) And Whiting Fish (Merlangius Merlangus): Promising Strains For Aquaculture Probiotic And Food Bio-Preservation, Sarah Cheriet, Sana Lenglitz, Amel Romdhani, Paul Hynds, Mohamed Salah Abbassi, Taofik Ghrairi

Articles

This study sought to evaluate the probiotic properties and the food preservation ability of lactic acid bacteria isolates collected from the intestines of wild marine fishes (gilthead seabream (Sparus aurata) (n = 60) and whiting fish (Merlangius merlangus) (n = 40)) from the Mediterranean sea in the area of Mostaganem city, Algeria. Forty-two isolates were identified as: Enterococcus durans (n = 19), Enterococcus faecium (n = 15), Enterococcus faecalis (n = 4), Lactococcus lactis subp. lactis (n = 3), and Lactobacillus plantarum (n = 1). All isolates showed inhibition to at least one indicator strain, especially against Listeria monocytogenes, Staphylococcus …

Color-Changing Reflection Hologram For Quality Assurance Of Therapeutic Ultrasound Systems, Tatsiana Mikulchyk, John Walsh, Jacinta Browne, Izabela Naydenova, Dervil Cody

Articles

The acoustic output of clinical therapeutic ultrasound equipment requires regular quality assurance (QA) testing to ensure the safety and efficacy of the treatment and that any potentially harmful deviations from the expected output power density are detected as soon as possible. A hologram, consisting of a reflection grating fabricated in an acrylate photopolymer film, has been developed to produce an immediate, visible, and permanent change in the color of the reconstructed hologram from red to green in response to incident ultrasound energy. The influence of the therapeutic ultrasound insonation parameters (exposure time, ultrasound power density, and proximity to the point …

The Development Of Optomechanical Sensors—Integrating Diffractive Optical Structures For Enhanced Sensitivity, Faolan Radford Mcgovern, Aleksandra Hernik, Catherine M. Grogan, George Amarandei, Izabela Naydenova

Conference Papers

The term optomechanical sensors describes devices based on coupling the optical and mechanical sensing principles. The presence of a target analyte leads to a mechanical change, which, in turn, determines an alteration in the light propagation. Having higher sensitivity in comparison with the individual technologies upon which they are based, the optomechanical devices are used in biosensing, humidity, temperature, and gases detection. This perspective focuses on a particular class, namely on devices based on diffractive optical structures (DOS). Many configurations have been developed, including cantilever- and MEMS-type devices, fiber Bragg grating sensors, and cavity optomechanical sensing devices. These state-of-the-art sensors …

The Proof Is In The Pudding – Using Perceived Stress To Measure Short-Term Impact In Initiatives To Enhance Gender Balance In Computing Education, Alina Berry, Sarah Jane Delany

Academic Posters Collection

The problem of gender imbalance in computing higher education has forced academics and professionals to implement a wide range of initiatives. Many initiatives use recruitment or retention numbers as their most obvious evidence of impact. This type of evidence of impact is, however, more resource heavy to obtain, as well as often requires a longitudinal approach. There are many shorter term initiatives that use other ways to measure their success.

First, this poster presents with a review of existing evaluation measures in interventions to recruit and retain women in computing education across the board. Three main groups of evaluation come …

Evaluation Of Gender-Based Differences In Primary School Maths Education: The Potential Of Digital Games, Maíra Amaral

Academic Posters Collection

Digital Game-Based Learning is shown to be a more effective instructional method than traditional instruction, however less effective than other technology-supported instruction according to Byun and Joung (2018). Regarding gender aspects, according to findings by Mclaren and colleagues in 2022, girls may learn more mathematics from digital learning games than boys. In their study, even reporting greater behavioural and cognitive engagement, boys did not learn more with the game than girls.

Using Machine Learning For Web Accessibility, Tlamelo Makati

Academic Posters Collection

This research will explore the potential of machine learning to enhance web accessibility. Web accessibility is typically defined in terms of Web Accessibility Guidelines (WCAG), which states that everyone should be able to perceive, operate, understand and interpret the web regardless of disability or use of assistive technology. We would like to consult digital accessibility experts through interviews and focus groups to understand the web accessibility auditing and remediation processes in detail, with a focus on web navigation. An important goal of this work is to establish development processes where all stakeholders can leverage machine-learning tools to produce more accessible …