Digital Commons Network^™

Drones For Large-Scale Wildlife Surveys: Raw Data To Support Manuscript - Hodgson Et Al, Amanda Hodgson

Research Datasets

We conducted trial ScanEagle drone surveys of dugongs in Shark Bay, Western Australia, covering the full extent of the drone’s range (~ 100 km), concurrently with observer surveys, with drone flying above or just behind the piloted aircraft. We aimed to test the assumption that drone imagery could provide comparable detection rates of dugongs to human observers when influenced by same environmental conditions. Data in "All data for analysis - Shark Bay Hodgson et al" include a summary of the sightings from both platforms per transect segment, including associated environmental covariates. Also included are details of each dugong group sighted …

Cellbrf: A Feature Selection Method For Single-Cell Clustering Using Cell Balance And Random Forest, Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang

Computer Science Faculty Publications

Motivation

Single-cell RNA sequencing (scRNA-seq) offers a powerful tool to dissect the complexity of biological tissues through cell sub-population identification in combination with clustering approaches. Feature selection is a critical step for improving the accuracy and interpretability of single-cell clustering. Existing feature selection methods underutilize the discriminatory potential of genes across distinct cell types. We hypothesize that incorporating such information could further boost the performance of single cell clustering. Results

We develop CellBRF, a feature selection method that considers genes’ relevance to cell types for single-cell clustering. The key idea is to identify genes that are most important for discriminating …

A Single-Cell Atlas Of Bovine Skeletal Muscle Reveals Mechanisms Regulating Intramuscular Adipogenesis And Fibrogenesis, Leshan Wang, Peidong Gao, Chaoyang Li, Qianglin Liu, Zeyang Yao, Yuxia Li, Xujia Zhang, Jiangwen Sun, Constantine Simintiras, Matthew Welborn, Kenneth Mcmillin, Stephanie Oprescu, Shihuan Kuang, Xing Fu

Computer Science Faculty Publications

Background

Intramuscular fat (IMF) and intramuscular connective tissue (IMC) are often seen in human myopathies and are central to beef quality. The mechanisms regulating their accumulation remain poorly understood. Here, we explored the possibility of using beef cattle as a novel model for mechanistic studies of intramuscular adipogenesis and fibrogenesis.

Methods

Skeletal muscle single-cell RNAseq was performed on three cattle breeds, including Wagyu (high IMF), Brahman (abundant IMC but scarce IMF), and Wagyu/Brahman cross. Sophisticated bioinformatics analyses, including clustering analysis, gene set enrichment analyses, gene regulatory network construction, RNA velocity, pseudotime analysis, and cell-cell communication analysis, were performed to elucidate …

Msdrp: A Deep Learning Model Based On Multisource Data For Predicting Drug Response, Haochen Zhao, Xiaoyu Zhang, Qichang Zhao, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Cancer heterogeneity drastically affects cancer therapeutic outcomes. Predicting drug response in vitro is expected to help formulate personalized therapy regimens. In recent years, several computational models based on machine learning and deep learning have been proposed to predict drug response in vitro. However, most of these methods capture drug features based on a single drug description (e.g. drug structure), without considering the relationships between drugs and biological entities (e.g. target, diseases, and side effects). Moreover, most of these methods collect features separately for drugs and cell lines but fail to consider the pairwise interactions between drugs and cell …

An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He

Computer Science Faculty Publications

More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental data sets have been used to test the approaches. There is limited understanding about potential factors, in data, that affect the performance of segmentation. We propose an approach to generate data sets with desired specifications in three potential factors - the protein sequence identity, structural contents, and data quality. The approach was implemented and has generated a test set and various training sets to study …

A Single-Cell Atlas Of Bovine Skeletal Muscle Reveals Mechanisms Regulating Intramuscular Adipogenesis And Fibrogenesis, Leshan Wang, Peidong Gao, Chaoyag Li, Qianglin Liu, Zeyang Yao, Yuxia Li, Xujia Zhang, Jiangwen Sun, Constantine Simintiras, Matthew Welborn, Kenneth Mcmillin, Stephanie Oprescu, Shihuan Kuang, Xing Fu

Computer Science Faculty Publications

Background: Intramuscular fat (IMF) and intramuscular connective tissue (IMC) are often seen in human myopathies and are central to beef quality. The mechanisms regulating their accumulation remain poorly understood. Here, we explored the possibility of using beef cattle as a novel model for mechanistic studies of intramuscular adipogenesis and fibrogenesis.

Methods: Skeletal muscle single-cell RNAseq was performed on three cattle breeds, including Wagyu (high IMF), Brahman (abundant IMC but scarce IMF), and Wagyu/Brahman cross. Sophisticated bioinformatics analyses, including clustering analysis, gene set enrichment analyses, gene regulatory network construction, RNA velocity, pseudotime analysis, and cell-cell communication analysis, were performed to elucidate …

Unttangling Irregular Actin Cytoskeleton Architectures In Tomograms Of The Cell With Struwwel Tracer, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers

Computer Science Faculty Publications

In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellular architectures in which a long-range cytoskeleton network extends throughout the cell bodies and protrusions. The irregular organization of the actin network, as well as cryo-electron-tomography-specific noise, missing wedge artifacts, and map dimensions call for a specialized implementation that is both robust and efficient. Our proposed solution, Struwwel Tracer, accumulates densities along paths of a specific length in various directions, starting from locally determined seed points. The highest-density paths originating …

Response Of Some Mango-Infesting Fruit Flies To Aqueous Solutions Of The Basil Plant Ocimum Tenuiflorum L, Saliou Niassy, Samira Abuelgasim Mohamed, Xavier Cheseto, Evanson Rigan Omuse, John Bwire Ochola, Fathiya Mbarak Khamis, Boubacar Badji, Sheppard Ndlela, Levi Ombura, Noelah Leah Okun, David Mfuti Kupesa, Thomas Dubois, Yeneneh Taye Belayneh, Sevgan Subramanian, Sunday Ekesi

All Peer-Reviewed Publications

Introduction: Horticulture is an important sub-sector for many African countries. Tephritid fruit flies continue to cause serious direct and indirect damage to the sub-sector. The male annihilation technique (MAT) using methyl eugenol (ME) is among the most revered techniques in fruit fly management. However, ME-based lures are only available to some farmers in Africa. Several basils of the genus Ocimum produce ME. Methods: In laboratory experiments, we used a dual choice olfactometer to assess the attraction of adult oriental fruit fly Bactrocera dorsalis to intact plants, 100 µL commercial methyl eugenol (ME) (positive control), 10 mg/mL of O. tenuiflorum aqueous …

Gender Equality In Ocean Science For Sustainable Development : Analysis Of Ocean Science Institutions In Kenya, Renis Auma Ojwala

World Maritime University Ph.D. Dissertations

Gender inequality poses a serious problem for national and international developmental programmes such as the United Nations Decade of Ocean Science for Sustainable Development (the Ocean Decade) and appears in both developed and developing countries. The fundamental aim of the Ocean Decade is to improve ocean health worldwide through generating knowledge, supporting innovations, discovering creative ideas and developing solutions to achieve equitable and sustainable development under the changing environmental, social and climate conditions. The paucity of women in ocean management has been documented as a major hindrance to ocean sustainability and a top challenge to diversity in workplaces because of …

Assessing The Need For Harmonized Marine Debris Monitoring And Equity To Support Participation In The Global Plastics Treaty Negotiations By Caribbean Sids, Kristal Ambrose

World Maritime University Ph.D. Dissertations

This research addresses the challenge of marine plastic pollution with particular reference to Caribbean Small Island Developing States (SIDS). Marine plastic pollution is of particular significance to these states since they suffer from a disproportionate incidence of plastic pollution on their coasts. In line with the region's need to protect its marine environment and subsequently its economy from the grave impacts of plastic pollution, this work assesses marine debris monitoring within Caribbean SIDS, and the barriers faced and considerations needed for unified monitoring efforts that support policy development. Additionally, the research examines microplastics on the beaches of Caribbean SIDS, and …

Combatting The Marine Litter Crisis In The Windward Islands : Examining Source-To-Sea Pathways And Fostering Multi-Scale Solutions, Roxanne Elizabeth Donna Graham

World Maritime University Ph.D. Dissertations

This research investigates the intricate and all-pervasive challenge of combatting marine litter in small island developing states (SIDS), specifically in the Wider Caribbean Region (WCR) with a focus on the understudied Windward Islands located in the south-east of the Caribbean. Notably, this research is a ground- breaking and innovative effort in several respects, marking the first time a study of such magnitude and depth has been conducted and published for the WCR and the Windward Islands in particular. This pioneering work thus not only fills a significant gap in the existing literature but also sets a benchmark for future studies …

The Problem Of Abandoned, Lost, And Otherwise Discarded Fishing Gear In Eastern Caribbean Small-Scale Fisheries : Understanding The Challenges, Defining Solutions, Tricia Lovell

World Maritime University Ph.D. Dissertations

/="/">Abandoned, lost, and otherwise discarded fishing gear (ALDFG—also termed derelict fishing gear) is a complex and significant global challenge for which strong, robust, and holistic governance is required. ALDFG is considered the most dangerous form of marine debris, as it is designed to capture marine organisms and can do so long after it has become derelict. While there has been an increasing body of work in academic literature on the scale, impact, and management of ALDFG, significant knowledge gaps still exist about how this challenge is affecting the small-scale fisheries of the Eastern Caribbean. This research has been designed …

2023-2024 Faculty Handbook, Morehead State University. Faculty Senate.

Faculty Senate Records

Morehead State University Faculty Handbook for 2023-2024.

Hydrogen Deuterium Exchange And Other Mass Spectrometry-Based Approaches For Epitope Mapping, Prashant N Jethva, Michael L Gross

2020-Current year OA Pubs

Antigen-antibody interactions are a fundamental subset of protein-protein interactions responsible for the "survival of the fittest". Determining the interacting interface of the antigen, called an epitope, and that on the antibody, called a paratope, is crucial to antibody development. Because each antigen presents multiple epitopes (unique footprints), sophisticated approaches are required to determine the target region for a given antibody. Although X-ray crystallography, Cryo-EM, and nuclear magnetic resonance can provide atomic details of an epitope, they are often laborious, poor in throughput, and insensitive. Mass spectrometry-based approaches offer rapid turnaround, intermediate structural resolution, and virtually no size limit for the …

Island Meltdown: Demise Of The Abrolhos Painted Button-Quail Turnix Varius Scintillans In The Face Of Multiple Threats, Ryan Carter

Theses: Doctorates and Masters

Island avifauna suffer high rates of extinction and decline. The major threats to island birds centre around the ecological impacts of invasive predators, competitors, and grazers. The Abrolhos Painted Button-quail (Turnix varius scintillans) is a subspecies that has been determined to be the 5th most likely taxon to become extinct in Australia. T. v. scintillans historically inhabited three islands in the Houtman Abrolhos archipelago off the mid-west coast of Australia. This study aimed to 1) confirm the status of T. v. scintillans on North Island and determine the main causes of decline, 2) model habitat variables with detections from camera …

Plant-Herbivore Interactions In A Changing Climate And Implications For Seagrass Resilience, Caitlyn M. O'Dea

Theses: Doctorates and Masters

Climate change is affecting herbivore distributions and abundance, resulting in intensified grazing pressure on foundation species such as seagrasses. This, coupled with other, rapid changes in estuarine ecosystems, may threaten the resilience of seagrass. While the overall resilience of seagrasses is generally well-studied, the timeframes of recovery have received comparatively little attention, particularly in temperate estuaries. This study investigated the recovery time of two colonising seagrasses (Halophila ovalis and Ruppia megacarpa) following various intensities of simulated grazing in two southwestern Australian estuaries. Simulated grazing treatments (25%, 50%, 75%, and 100% removal from 1 m2 plots) were applied in field experiments …

How Public Libraries In Western Australia Support The Language And Literacy Learning Of Children From Birth To Age Three Years, Jennifer Ruth Campbell-Hicks

Theses: Doctorates and Masters

Early language and literacy skills develop rapidly during the first three years of children’s lives. Successful development of these skills is based on dynamic interactions and supportive relationships within children’s families and communities. However, nearly a quarter of Australia’s children do not receive the necessary support or proactive interactions, and therefore start their schooling at age four or five with inadequate language and literacy skills. Reducing early difficulties is beneficial since evidence indicates that children who struggle at the start of their education rarely catch up.

Children and their families may be supported with language and literacy learning by engaging …

Mass Spectrometry-Based Proteomic Analysis To Characterise Barley Breeding Lines, Mahya Bahmani

Theses: Doctorates and Masters

Barley is a key ingredient in the malting and brewing industry, and it is the fourth most important crop being cultivated worldwide. The protein content of the barley grain is one of the main components determining the quality and nutritive value of the food and beverages prepared from barley. Mass spectrometry-based proteomic analysis is a valuable tool that can guide and inform plant breeding strategies and crop improvement programs. Understanding the proteome changes in barley grain under different growing locations, the impact of different environmental conditions and its relationship with malting characteristics have the potential to inform breeding programs to …

A Designed Two-Body Hinged Raft Wave Energy Converter: From Experimental Study To Annual Power Prediction For The Emec Site Using Wec-Sim, Siya Jin, Daming Wang, Martyn Hann, Keri Collins, Daniel Conley, Deborah Greaves

School of Engineering, Computing and Mathematics

The present study aims at providing more data and insights for the hinged type WEC, especially focusing on the two-body hinged raft WECs. Two WECs are considered: a well-studied generic hinged raft WEC (G-HRWEC) and a 1:25 scale designed hinged raft WEC (D-HRWEC). The open-source tool WEC-Sim is employed in numerical studies. Referring to the published numerical data for G-HRWEC, corrections are proposed to the WEC-Sim model which are shown to realise the ability of WEC-Sim to model the two-body hinged WEC. For the 1:25 scale D-HRWEC, the physical results show that the relative hinge motion between the rafts is …

Size Distribution, Elemental Composition And Morphology Of Nanoparticles Separated From Respirable Coal Mine Dust, Shoeleh Assemi, Lei Pan, Xuming Wang, Titilayo Akinseye, Jan D. Miller

Michigan Tech Publications, Part 1

Nanoparticles, defined as particles with one dimension below 100 nm, contribute little to the total mass concentration in respirable coal mine dust (RCMD) toxicological studies, but they could have a considerable part in the adverse health effects by RCMD inhalation. It has been shown that inhaled nanoparticles can penetrate deep into the lung and could plausibly contribute to acute and chronic pulmonary diseases by triggering oxidative stress formation and inducing inflammation. RCMD nanoparticles from samples collected in an underground mine in the United States were analyzed by a particle separation technique, field-flow fractionation (FFF), for size, morphology, and elemental composition. …

Modelling The Transmission Dynamics Of African Animal Trypanosomiasis; A Case Study Of Shimba Hills, Kwale County, Kenya, Gladys Jerono Rotich

All Master’s Theses

African Animal Trypanosomiasis (AAT) is caused by parasites of the species Trypanosoma vivax, Trypanosoma congolense, and Trypanosoma rhodesiense. Of 48 sub-Saharan African nations, 36 have endemic cases of AAT. The disease is prevalent in savannah and woodland areas. It poses a major threat to livestock production and health in agro-pastoralist communities, many of which are located along the boundaries of wildlife reserves. Most epidemiological studies on AAT around Shimba Hills National Reserve (SHNR) have focused on the vectors (tsetse fly) and the host (cattle). No studies have been done to show how efficiently a trypanosome can be transmitted from tsetse …

Liquid Waste Treatment For Sustainable Tapioca Industry: A Comparison Between Biogas And Liquid Sugar, Lilik Sulistyowati, Novi Andareswari, Rifqi Rahmat Hidayatullah, Nurul Amri Komarudin, Yuni Yolanda

ASEAN Journal on Science and Technology for Development

There have been many studies examining the processing of tapioca wastewater. However, most studies have only researched at a laboratory scale without considering whether the treatment is appropriate. The study's purpose is to compare the processing technology of biogas and liquid sugar using technical, environmental, social, and cost-benefit analysis criteria to determine the appropriate technology to be applied. Literature study, observation, and interviews were used to determine the characteristics of each criterion. Cost-benefit analysis is calculated using the R/C Ratio. Furthermore, priority determination is carried out using the Exponential Comparison Method (MPE) using assessments from environmental and industrial experts on …

Neighbor-Anchoring Adversarial Graph Neural Networks, Zemin Liu, Yuan Fang, Yong Liu, Vincent W. Zheng

Research Collection School Of Computing and Information Systems

Graph neural networks (GNNs) have witnessed widespread adoption due to their ability to learn superior representations for graph data. While GNNs exhibit strong discriminative power, they often fall short of learning the underlying node distribution for increased robustness. To deal with this, inspired by generative adversarial networks (GANs), we investigate the problem of adversarial learning on graph neural networks, and propose a novel framework named NAGNN (i.e., Neighbor-anchoring Adversarial Graph Neural Networks) for graph representation learning, which trains not only a discriminator but also a generator that compete with each other. In particular, we propose a novel neighbor-anchoring strategy, where …

Taurus: Towards A Unified Force Representation And Universal Solver For Graph Layout, Mingliang Xue, Zhi Wang, Fahai Zhong, Yong Wang, Mingliang Xu, Oliver Deussen, Yunhai Wang

Research Collection School Of Computing and Information Systems

Over the past few decades, a large number of graph layout techniques have been proposed for visualizing graphs from various domains. In this paper, we present a general framework, Taurus, for unifying popular techniques such as the spring-electrical model, stress model, and maxent-stress model. It is based on a unified force representation, which formulates most existing techniques as a combination of quotient-based forces that combine power functions of graph-theoretical and Euclidean distances. This representation enables us to compare the strengths and weaknesses of existing techniques, while facilitating the development of new methods. Based on this, we propose a new balanced …

Deconstructing Motherhood And Fatherhood: An Exploration Of Same-Sex Parents’ Experiences And Construction Of Their Parenting Roles, Jenine M. Giles

Theses: Doctorates and Masters

Dominant discourses regarding motherhood and fatherhood are entrenched in Australian culture and are often implied during public discussions of families with same-sex parents. Using a post structuralist approach, this project aimed to identify how parents in same-sex relationships experience and construct their parenting roles through combinations of dominant and alternative discourses of families, motherhood, and fatherhood. Following ethics approval, participants were recruited primarily through communication with Australian LGBTQIA+ community organisations and publications. Twenty-nine respondents each participated in one one-on-one semi-structured interview, which was audio- and video-recorded with their consent. The participants were eighteen years of age or older, in a …

Investigation And Development Of Titanium Nitride Solid-State Potentiometric Ph Sensor, Shimrith Paul Shylendra

Theses: Doctorates and Masters

The measurement of pH value is crucial parameter in various fields like, drinking water monitoring, food preparation, biomedical and environmental applications. The most common device for pH sensing is the conventional pH glass electrode. While glass electrodes have several advantages, such as Nernstian sensitivity, superior ion selectivity, excellent stability, and extensive operating range, they have several key disadvantages. pH glass electrodes need to be stored in buffer solutions, they are fragile and have limited size and shape, making them impractical for some applications, such as being potentially used as miniature pH sensors for capsule endoscopy and ambulatory esophageal pH monitoring. …

Comparison Of Methods For Metabolite Extraction From Rat Polycystic Kidney Tissue For Gas Chromatography-Mass Spectrometry-Based Metabolomics, Matthew Oosthuizen

Theses: Doctorates and Masters

This study included a series of experiments focussed on comparing extraction protocols for metabolomics-based analysis of Lewis rat polycystic kidney (LPK) tissue samples and healthy Lewis rat tissue samples. Firstly, the optimal sample loading (mass of tissue) was investigated. Based on previous studies, the appropriate mass to test was approximately 5 mg. Three different volumes of tissue extract equivalent to 1, 2.5 and 5mg of pooled healthy kidney tissue and pooled polycystic kidney tissue were trialled to see how they differed in terms of the number of reproducible, uniquely identified peaks captured after metabolite extraction, derivatisation and gas chromatography-mass spectrometry …

An Examination Of Kinanthropometric And Physical Injury Risk Factors In Elite Australian Football, Callum J. Mccaskie

Theses: Doctorates and Masters

Kinanthropometric assessment is an integral part of understanding an athlete’s physical profile and readiness for competition. This typically includes a variety of different assessments which serve to quantify body shape, proportion, and composition in a bid to understand human physiology. Common assessments include stature, body mass, limb ratios, body circumferences, body mass index, skinfold testing, body composition testing, and musculoskeletal morphological evaluations. Specifically, kinanthropometric evaluations have involved the characterisation of athletes according to sport, sex, competition level and playing position. While this has provided researchers and practitioners with greater insight into athletic phenotypes, more purposeful kinanthropometric assessments which focus on …

Ph-Responsive Polymeric Nanostructures For Cancer Theranostics, Devadass Jessy Mercy, Karthick Harini, Swaminathan Madhumitha, Chinnadurai Anitha, Jayakumar Iswariya, Koyeli Girigoswami, Agnishwar Girigoswami

Journal of Metals, Materials and Minerals

Responsive polymeric nanostructures are being designed to improve the efficiency of existing treatment techniques by delivering therapeutics in precise locations. The properties of the particles can be altered to act as a probe for imaging applications also. Hence, an effective theranostic agent can be tailor-made to meet the requirements. The pH variability has aroused considerable interest in nano-responsive-stimulus production since the mild acidic condition is a hallmark of the tumor microenvironment. The cargo sealed inside the carrier will be released either by swelling or disassembly of the carrier as they meet a pH drop. The modification strategy for the synthesis …

Paper-Based Colorimetric Sensor For Mercury Ion Detection Using Smartphone Digital Imaging, Pakorn Preechaburana, Somsak Sangnuy, Supaluck Amloy

Journal of Metals, Materials and Minerals

In this research, we have developed a colorimetric paper-based sensing platform for the determination of mercury ion (Hg2+) using gold nanoparticles (AuNPs). To evaluate the selectivity in the response to a special target, urea is used as recognizing ligands on AuNPs for selective sensing Hg2+. Colorimetric readings in the presence of various environmentally relevant metal ions, such as Na+, K+, Zn2+, Pb2+, and Hg2+, were also studied. The results show that amongst all the tested metal ions, the SPR peaks are located at 525 nm except in the case of the present of Hg2+, in which is red shifted to …