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Full-Text Articles in Entire DC Network
Resource Assessment Report No. 05: West Coast Deep Sea Crustacean Resource 2024 Assessment, Emma-Jade Tuffley, Simon De Lestang
Resource Assessment Report No. 05: West Coast Deep Sea Crustacean Resource 2024 Assessment, Emma-Jade Tuffley, Simon De Lestang
Resource Assessment Reports
The West Coast Deep Sea Crustacean resource consists of crystal crab (snow) (Chaceon albus), champagne crab (spiny) (Hypothalassia acerba) and giant crab (Pseudocarcinus gigas). The resource is mainly accessed by the commercial West Coast Deep Sea Crustacean Managed Fishery (WCDSCMF), which primarily targets crystal crabs. The West Coast Rock Lobster Managed Fishery (WCRLMF) also retains a small amount of champagne crabs as byproduct of deep-water rock lobster fishing. The WCDSCMF is a pot-based fishery using baited pots operated in a long-line formation in shelf edge waters ( > 150 m in depth) off the West …
Resource Assessment Report No. 03: Gascoyne Demersal Scalefish Resource 2024 Assessment, Emily A. Fisher, Rachel Marks, Sybrand A. Hesp, Ainslie Denham, Gary Jackson, David V. Fairclough
Resource Assessment Report No. 03: Gascoyne Demersal Scalefish Resource 2024 Assessment, Emily A. Fisher, Rachel Marks, Sybrand A. Hesp, Ainslie Denham, Gary Jackson, David V. Fairclough
Resource Assessment Reports
The Gascoyne Demersal Scalefish Resource (GDSR) comprises over 80 species inhabiting inshore (20-250 m deep) and offshore ( > 250 m deep) waters in the Gascoyne Coast Bioregion (GCB; south of Onslow to north of Kalbarri). The GDSR is primarily targeted by commercial, charter and recreational boat-based line fishers. Snapper and Goldband Snapper are the indicator species selected for monitoring and assessing the status of the inshore suite of the GDSR, while Ruby Snapper and Greybanded Grouper are the indicators for the offshore suite.
Periodic assessments of GDSR indicator species demonstrated that historical fishing of Snapper led to stocks being below …
Resource Assessment Report No. 04: North Coast Demersal Scalefish Resource - Kimberley 2025 Assessment, Fabian Trinnie, Rubie Evans-Powell, Ainslie Denham, Sybrand A. Hesp, Corey Wakefield, Craig L. Skepper, Brett Crisafulli, Stephen J. Newman
Resource Assessment Report No. 04: North Coast Demersal Scalefish Resource - Kimberley 2025 Assessment, Fabian Trinnie, Rubie Evans-Powell, Ainslie Denham, Sybrand A. Hesp, Corey Wakefield, Craig L. Skepper, Brett Crisafulli, Stephen J. Newman
Resource Assessment Reports
The North Coast Demersal Scalefish Resource (NCDSR) comprises ecological suites of tropical demersal fish species that occur predominantly in inshore waters (20–250 m deep) and offshore waters ( > 250 m deep) of the North Coast Bioregion (NCB). More than 60 demersal species are landed by fisheries operating in the Kimberley and Pilbara regions of the NCB each year, including high-value snappers (Lutjanidae), groupers (Epinephelidae), and emperors (Lethrinidae). As outlined in the NCDSR Harvest Strategy (DPIRD, 2017), the Kimberley resource is currently monitored through annual reviews of total removals and catch rate trends of indicator species, as well as periodic (every …
Ibi-Dt: A Novel Approach Combining Individualized Bayesian Inference And Decision Tree For Identifying Cancer Drivers And Their Interactions, Md Asad Rahman, Gregory F. Cooper, Jinying Zhao, Xinghua Lu, Jinling Liu
Ibi-Dt: A Novel Approach Combining Individualized Bayesian Inference And Decision Tree For Identifying Cancer Drivers And Their Interactions, Md Asad Rahman, Gregory F. Cooper, Jinying Zhao, Xinghua Lu, Jinling Liu
Engineering Management and Systems Engineering Faculty Research & Creative Works
Cancer is mainly caused by a relatively small portion of somatic genome alterations (SGAs), called cancer drivers. Despite success in identifying a good number of cancer drivers, many more remain to be discovered to explain various cancers. Moreover, limited tools are available to identify potential interactions among cancer drivers for a better understanding of oncogenesis. To tackle these challenges, we have developed a novel approach called individualized Bayesian inference using a decision tree (IBI-DT). IBI-DT recognizes the genetic heterogeneity among cancer patients, where different individuals or patient subgroups of distinct genomic makeup may have different drivers. IBI-DT works by constructing …
Procedures For Rangeland Condition Assessment In The Pilbara And Southern Rangelands 2025, Department Of Primary Industries And Regional Development, Western Australia
Procedures For Rangeland Condition Assessment In The Pilbara And Southern Rangelands 2025, Department Of Primary Industries And Regional Development, Western Australia
Natural resources published reports
This report defines the procedures used in 2025 by DPIRD to complete rangeland condition assessment (RCA) in the Pilbara and southern rangelands region which has predominantly shrub-based pastures. For the rest of the pastoral estate, DPIRD uses the Procedures for RCA in the Kimberley which has grass pastures.
RCA is the process DPIRD uses to make systematic, station-level assessment of rangeland. Rangeland condition considers both the condition of pastures (defined in the ‘Pasture condition guides for the Pilbara’ and ‘Pasture condition guides for the southern rangelands including the Gascoyne, Murchison and Goldfields-Nullarbor’) and soils as determined by erosion, using the …
Procedures For Rangeland Condition Assessment In The Kimberley 2025, Department Of Primary Industries And Regional Development, Western Australia
Procedures For Rangeland Condition Assessment In The Kimberley 2025, Department Of Primary Industries And Regional Development, Western Australia
Natural resources published reports
This report defines the procedures used in 2025 by DPIRD to complete rangeland condition assessment (RCA) in the Kimberley region which has grass-based pastures. For the rest of the pastoral estate, DPIRD uses the Procedures for RCA in the Pilbara and southern rangelands which have predominantly shrub pastures.
RCA is the process DPIRD uses to make systematic, station-level assessment of rangeland. Rangeland condition considers both the condition of pastures (as defined in the 'Pasture condition guide for the Kimberley') and soils as determined by erosion, using the erosion assessment method on pastoral lands in Western Australia. The methods have evolved …
Enhancing Preparedness: A Genetic Study Of Sar-Cov-2 And Other Microbial Public Health Threats In Wastewater From A College Town, Christian N. Hutchinson
Enhancing Preparedness: A Genetic Study Of Sar-Cov-2 And Other Microbial Public Health Threats In Wastewater From A College Town, Christian N. Hutchinson
Master's Theses
Problem
The SARS-CoV-2 (COVID-19) pandemic revealed both the systemic vulnerabilities of our healthcare system as well as the importance of timely, localized data for informing public health responses. Traditional testing approaches were essential but often failed to capture the full extent of viral spread, especially in those with mild or asymptomatic conditions that relied on at home testing. This underreporting hindered effective allocation of resources and made developing effective intervention strategies difficult. We also realized the potential for wastewater surveillance to be applied to tracking antimicrobial resistance gene markers. Taken together, this approach should have important implications for improving public …
Miscanthus × Giganteus Increases Soil Maximum Water Holding Capacity Compared To Maize, Jessica T. Nelson, Maoz Dor, Andy D. Vanloocke, Jacob E. Studt, Perla K. Schrock, Marshall D. Mcdaniel
Miscanthus × Giganteus Increases Soil Maximum Water Holding Capacity Compared To Maize, Jessica T. Nelson, Maoz Dor, Andy D. Vanloocke, Jacob E. Studt, Perla K. Schrock, Marshall D. Mcdaniel
School of Earth, Environmental, & Marine Sciences Faculty Publications
Soil ecosystem services, like the ability to store water, have been depleted after a century of conventional, annual cropping, and perennial crops offer a solution to this and other agricultural environmental issues. We assessed the impact of Miscanthus × giganteus (miscanthus), a perennial biomass crop, on soil water holding capacity and structure compared to continuous maize (Zea mays L.) at two sites in Iowa. After three growing seasons, we measured the following: (1) maximum water holding capacity (MWHC) with and without soil structure, and (2) total porosity and pore size distribution (PSD) via micro-computed tomography (microCT). Miscanthus increased MWHC …
Opportunities And Impacts For Recreational Fishing From The Westport Development: Final Report, Matt Navarro, Michael Burton, Abbie Rogers, Joanna Pearce, Julian Clifton, Milena Kim, Clara Obregón
Opportunities And Impacts For Recreational Fishing From The Westport Development: Final Report, Matt Navarro, Michael Burton, Abbie Rogers, Joanna Pearce, Julian Clifton, Milena Kim, Clara Obregón
Reports accepted as research outputs
Executive summary: This project employs a mixed methods approach to evaluate the significance of Cockburn Sound for recreational fishers, examine the potential effects of the proposed port development on recreational fishing experiences, and understand fishers' preferences for initiatives to improve recreational fishing in Cockburn Sound. Initial qualitative interviews with six local recreational fishing stakeholders were conducted to establish an early understanding of the primary issues and contextual factors with respect to opportunities and impacts of the proposed Westport development. These were followed by on-site surveys at boat ramps and shore access points across Cockburn Sound and the surrounding region. In …
Fisheries Science Update - West Coast Demersal Scalefish Resource - September 2025, Department Of Primary Industries And Regional Development, Western Australia
Fisheries Science Update - West Coast Demersal Scalefish Resource - September 2025, Department Of Primary Industries And Regional Development, Western Australia
Fisheries Science Updates
The Department of Primary Industries and Regional Development (DPIRD) monitors the status of Western Australia’s demersal scalefish resources by undertaking regular stock assessments on indicator species.
This summary provides key outcomes of the 2025 assessment of the West Coast Demersal Scalefish Resource (Resource Assessment Report No. 2).
Fisheries Science Update - Gascoyne Demersal Scalefish Resource - September 2025, Department Of Primary Industries And Regional Development, Western Australia
Fisheries Science Update - Gascoyne Demersal Scalefish Resource - September 2025, Department Of Primary Industries And Regional Development, Western Australia
Fisheries Science Updates
The Department of Primary Industries and Regional Development (DPIRD) monitors the status of Western Australia’s demersal scalefish resources by undertaking periodic stock assessments on key indicator species.
This summary provides key outcomes of the 2024 Gascoyne Demersal Scalefish Resource Stock Assessment (Resource Assessment Report No. 3).
Origin And Maintenance Of The Andean Bird Fauna, Elkin A. Tenorio
Origin And Maintenance Of The Andean Bird Fauna, Elkin A. Tenorio
Dissertations, Theses, and Capstone Projects
The origin and maintenance of the tropical montane diversity have been evaluated over multiple decades using various techniques and perspectives. Despite major progress in understanding phylogenetic relationships, diversification patterns, distributional data, and general ecology in the Andean biota, large gaps in our understanding remain, particularly in the synthesis across scales. To fill these gaps, I aimed to explore patterns and processes that underlie species diversification in birds of the tropical Andes of South America by combining different approaches using phenotypic, phylogenetic, and genomic data in multiple temporal and spatial scales.
In the first chapter, I examined the macroevolutionary patterns of …
Non-Linear Heart Rate Variability: Investigating Cardiac Complexity Of Psychopathic Traits, Khaya A. Roach
Non-Linear Heart Rate Variability: Investigating Cardiac Complexity Of Psychopathic Traits, Khaya A. Roach
Dissertations, Theses, and Capstone Projects
Psychopathy is a complex personality disorder characterized by distinct emotional and interpersonal deficits, and affects approximately 25% of the prison population and 4.5% of nonincarcerated populations. The manifestation of psychopathy can be understood through two distinct variants, each demonstrating unique etiological pathways and clinical presentations. Primary psychopathy is characterized by core interpersonal and affective deficits, including shallow emotions and manipulativeness, while demonstrating reduced autonomic responsivity and lower anxiety levels. Secondary psychopathy presents with higher levels of impulsivity, anxiety, and emotional dysregulation, showing stronger associations with various psychopathologies. Treatment outcomes also vary between the variants, with primary psychopaths typically showing poor …
Comprehensive Review Of In Vitro Approaches For Environmental Heavy Metal Exposure, Manas Warke, Madeline English, Camila Padilla, Lexie Gasco, Wendy Leisner, Rupali Datta, Smitha Rao
Comprehensive Review Of In Vitro Approaches For Environmental Heavy Metal Exposure, Manas Warke, Madeline English, Camila Padilla, Lexie Gasco, Wendy Leisner, Rupali Datta, Smitha Rao
Michigan Tech Publications
Heavy metals are ubiquitous environmental pollutants, contaminating air, soil, and water via the erosion of natural deposits, as well as originating from anthropogenic sources, such as agriculture, industries, transportation, and landfills. The increasing utilization of heavy metals over the years, combined with the persistent nature of metals in the environment poses a direct threat to human and environment health. Although regulatory limits have been established for toxic metals, assessing the associated health risks using real-life exposure scenarios remains challenging. In this review, we summarize the development and use of in vitro models based two- and three-dimensional cell culture systems, focusing …
Maize Yield Stability Under Organic And Conventional Farming Systems In Sub-Humid Agro-Ecozones Of Central Kenya, Milka Kiboi, David Bautze, Felix Matheri, Amritbir Riar, Andreas Fliessbach
Maize Yield Stability Under Organic And Conventional Farming Systems In Sub-Humid Agro-Ecozones Of Central Kenya, Milka Kiboi, David Bautze, Felix Matheri, Amritbir Riar, Andreas Fliessbach
All Peer-Reviewed Publications
Maize (Zea mays L.) is the main staple crop and is important to the food security and livelihoods of people globally. We evaluated the effects of organic and conventional farming systems on maize grain yield and temporal yield stability under different external input levels in a long-term experiment (2007–2022) at two sites in Kenya. We implemented four farming systems: organic high (Org-High), conventional high (Conv-High), organic low (Org-Low), and conventional low (Conv-Low) in a randomized complete block design. Growth indicators for maize, height, stem diameter, and grain yield were higher in high input systems, but grain yield stability was not. …
Tetrigidae Of Ethiopia: First Species Delimitation Via Dna Barcoding And Description Of Three New Species †, Tarekegn Fite, Hendrik Devriese, Dustin Kulanek, Josip Skejo, Niko Kasalo, Manaye Misganaw, Tadele Tefera, Jandouwe Villinger, Martin Husemann
Tetrigidae Of Ethiopia: First Species Delimitation Via Dna Barcoding And Description Of Three New Species †, Tarekegn Fite, Hendrik Devriese, Dustin Kulanek, Josip Skejo, Niko Kasalo, Manaye Misganaw, Tadele Tefera, Jandouwe Villinger, Martin Husemann
All Peer-Reviewed Publications
Tetrigidae is a caeliferan family of Orthoptera constituting a diverse and relatively ancient lineage of small Orthopterans, which has its greatest diversity in tropical and subtropical areas. However, to date, few studies have been conducted on the identification and description of Tetrigidae species in Ethiopia, and even fewer molecular data are available. Hence, we performed the first species delimitation study via DNA barcoding of species belonging to the genera Paratettix, Leptacrydium, Dasyleurotettix, and Morphopoides from Ethiopia. We provide 35 new sequences of the COI gene belonging to six species of these genera. We show that Ethiopian Tetrigidae can be successfully …
Fisheries Science Update - Pilbara Demersal Scalefish Resource - September 2025, Department Of Primary Industries And Regional Development, Western Australia
Fisheries Science Update - Pilbara Demersal Scalefish Resource - September 2025, Department Of Primary Industries And Regional Development, Western Australia
Fisheries Science Updates
The Department of Primary Industries and Regional Development (DPIRD) monitors the status of Western Australia’s demersal scalefish resources by undertaking periodic stock assessments on key indicator species.
This summary provides key outcomes of the 2024 assessment of the Pilbara Demersal Scalefish Resource (Fisheries Research Report No. 338).
A Consensus Guide To Preclinical Indirect Calorimetry Experiments, Alexander S Banks, David B Allison, Thierry Alquier, Ansarullah, Steven N Austad, Johan Auwerx, Julio E Ayala, Joseph A Baur, Stefania Carobbio, Gary A Churchill, Morten Dall, Rafael De Cabo, Jose Donato, Nathalia R V Dragano, Carol F Elias, Anthony W Ferrante, Brian N Finck, Jose E Galgani, Zachary Gerhart-Hines, Laurie J Goodyear, Justin L Grobe, Rana K Gupta, Kirk M Habegger, Sean M Hartig, Andrea L Hevener, Steven B Heymsfield, Corey D Holman, Martin Hrabě De Angelis, David E James, Lawrence Kazak, Jae Bum Kim, Martin Klingenspor, Xingxing Kong, Sander Kooijman, Louise Lantier, K C Kent Lloyd, James C Lo, Irfan J Lodhi, Paul S Maclean, Owen P Mcguinness, Gema Medina-Gómez, Raghavendra G Mirmira, Christopher D Morrison, Gregory J Morton, Timo D Müller, Yoshihiro Ogawa, David Pajuelo-Reguera, Matthew J Potthoff, Nathan Qi, Marc L Reitman, Patrick C N Rensen, Jan Rozman, Jennifer M Rutkowsky, Kei Sakamoto, Philipp E Scherer, Gary J Schwartz, Radislav Sedlacek, Mohammed Selloum, Saame Raza Shaikh, Shuai Chen, Gerald I Shulman, Vojtěch Škop, Alexander A Soukas, John R Speakman, Bruce M Spiegelman, Gregory R Steinberg, Katrin J Svensson, John P Thyfault, Tony Tiganis, Paul M Titchenell, Nigel Turner, Licio A Velloso, Antonio Vidal-Puig, Christopher S Ward, Ashley S Williams, Christian Wolfrum, Allison W Xu, Ying Xu, Juleen R Zierath, International Indirect Calorimetry Consensus Committee (Iiccc)
A Consensus Guide To Preclinical Indirect Calorimetry Experiments, Alexander S Banks, David B Allison, Thierry Alquier, Ansarullah, Steven N Austad, Johan Auwerx, Julio E Ayala, Joseph A Baur, Stefania Carobbio, Gary A Churchill, Morten Dall, Rafael De Cabo, Jose Donato, Nathalia R V Dragano, Carol F Elias, Anthony W Ferrante, Brian N Finck, Jose E Galgani, Zachary Gerhart-Hines, Laurie J Goodyear, Justin L Grobe, Rana K Gupta, Kirk M Habegger, Sean M Hartig, Andrea L Hevener, Steven B Heymsfield, Corey D Holman, Martin Hrabě De Angelis, David E James, Lawrence Kazak, Jae Bum Kim, Martin Klingenspor, Xingxing Kong, Sander Kooijman, Louise Lantier, K C Kent Lloyd, James C Lo, Irfan J Lodhi, Paul S Maclean, Owen P Mcguinness, Gema Medina-Gómez, Raghavendra G Mirmira, Christopher D Morrison, Gregory J Morton, Timo D Müller, Yoshihiro Ogawa, David Pajuelo-Reguera, Matthew J Potthoff, Nathan Qi, Marc L Reitman, Patrick C N Rensen, Jan Rozman, Jennifer M Rutkowsky, Kei Sakamoto, Philipp E Scherer, Gary J Schwartz, Radislav Sedlacek, Mohammed Selloum, Saame Raza Shaikh, Shuai Chen, Gerald I Shulman, Vojtěch Škop, Alexander A Soukas, John R Speakman, Bruce M Spiegelman, Gregory R Steinberg, Katrin J Svensson, John P Thyfault, Tony Tiganis, Paul M Titchenell, Nigel Turner, Licio A Velloso, Antonio Vidal-Puig, Christopher S Ward, Ashley S Williams, Christian Wolfrum, Allison W Xu, Ying Xu, Juleen R Zierath, International Indirect Calorimetry Consensus Committee (Iiccc)
Children’s Nutrition Research Center Staff Publications
Understanding the complex factors influencing mammalian metabolism and body weight homeostasis is a long-standing challenge requiring knowledge of energy intake, absorption and expenditure. Using measurements of respiratory gas exchange, indirect calorimetry can provide non-invasive estimates of whole-body energy expenditure. However, inconsistent measurement units and flawed data normalization methods have slowed progress in this field. This guide aims to establish consensus standards to unify indirect calorimetry experiments and their analysis for more consistent, meaningful and reproducible results. By establishing community-driven standards, we hope to facilitate data comparison across research datasets. This advance will allow the creation of an in-depth, machine-readable data …
Resource Assessment Report No. 02: West Coast Demersal Scalefish Resource 2025 Assessment, Emily A. Fisher, David V. Fairclough, Elaine Lek, Jeremy Briggs, Sybrand Alex Hesp, Ainslie Denham
Resource Assessment Report No. 02: West Coast Demersal Scalefish Resource 2025 Assessment, Emily A. Fisher, David V. Fairclough, Elaine Lek, Jeremy Briggs, Sybrand Alex Hesp, Ainslie Denham
Resource Assessment Reports
The West Coast Demersal Scalefish Resource (WCDSR) comprises over 100 species inhabiting inshore (20-250 m deep) and offshore ( > 250 m deep) waters of the West Coast Bioregion (WCB; north of Kalbarri to east of Augusta). The WCDSR is primarily targeted by commercial, charter and recreational boat-based line fishers, including the commercial West Coast Demersal Scalefish (Interim) Managed Fishery (WCDSIMF). Indicator species selected for monitoring and assessing the status of the inshore suite of the WCDSR include Snapper, WA Dhufish and Baldchin Groper, while indicators for the offshore suite include Hapuku, Bass Groper and Blue-eye Trevalla.
The WCDSR is more …
Uinta Basin Snow Shadow: Impact Of Snow-Depth Variation On Winter Ozone Formation, Michael J. Davies, John R. Lawson, Trevor O’Neil, Seth N. Lyman, Karlee Zager, Tristan D. Coxson
Uinta Basin Snow Shadow: Impact Of Snow-Depth Variation On Winter Ozone Formation, Michael J. Davies, John R. Lawson, Trevor O’Neil, Seth N. Lyman, Karlee Zager, Tristan D. Coxson
Bingham Research Center
After heavy snowfall in the Uinta Basin, Utah, elevated surface ozone occurs if a cold-air pool persists and traps emissions from oil and gas industry operations. Sunlight and actinic flux from a high-albedo snowpack drive ozone buildup via photolysis. Snow coverage is paramount in initiating the cold pool and driving ozone generation. Its depth is critical for predicting ozone concentrations. The Basin’s location leeward of the Wasatch Mountains provides conditions for a precipitation shadow, where sinking air suppresses snowfall. We analyzed multiple years of ground-based snow depth measurements, surface ozone data, and meteorological observations; we found that ozone levels track …
Optimizing Hip And Knee Assistance For Walking And Sit-To-Stand Transitions: An Intrinsic Muscle Mechanics Based Predictive Approach, Neethan Ratnakumar
Optimizing Hip And Knee Assistance For Walking And Sit-To-Stand Transitions: An Intrinsic Muscle Mechanics Based Predictive Approach, Neethan Ratnakumar
Dissertations
As the global population ages, the demand for wearable assistive technologies continues to rise, driven by their potential to enhance mobility and independence in older adults. Effectively designed controllers for lower-limb exoskeletons to assist sit-to-stand (STS) and walking are crucial for delivering efficient, safe, and comfortable assistance during daily activities. Traditionally, controller optimization involves biomechanical modeling and user-specific customization. Musculoskeletal simulations play a central role in this process by providing insights into human-exoskeleton interaction dynamics, thereby informing and refining control strategies.
This work presents a simulation-driven approach for developing exoskeleton controllers for walking and STS using two distinct methods: optimal …
Development And Implementation Of Novel Mass Spectrometric Methods For Metabolism Studies In Drug Discoveries, Huifang Yao
Development And Implementation Of Novel Mass Spectrometric Methods For Metabolism Studies In Drug Discoveries, Huifang Yao
Dissertations
The field of drug discovery has evolved significantly over the past few decades, with a growing emphasis on understanding the metabolic pathways and biotransformation processes that influence the pharmacokinetics and pharmacodynamics of drug candidates. Novel mass spectrometric methods have emerged as powerful tools in this domain, facilitating the comprehensive analysis of metabolic profiles and enabling the identification of metabolites with implications for safety, efficacy, and overall drug development. However, challenges remain in quantifying metabolic flux—an essential aspect of understanding drug action—particularly due to the limitations of traditional isotope kinetic assays, which often involve lengthy sample preparation and the use of …
Braingenebot: A Framework For Variant Prioritization And Generative Pretrained Transformer-Informed Interpretation Across Polygenic Risk Score Studies, Gang Qu, Nitesh Enduru, Xinyi Liu, Xiaoqian Jiang, Zhongming Zhao
Braingenebot: A Framework For Variant Prioritization And Generative Pretrained Transformer-Informed Interpretation Across Polygenic Risk Score Studies, Gang Qu, Nitesh Enduru, Xinyi Liu, Xiaoqian Jiang, Zhongming Zhao
Faculty, Staff and Student Publications
Polygenic risk scores (PRS) are widely used to assess genetic susceptibility in Alzheimer's disease (AD) research. However, the rapid expansion of PRS studies has led to dataset-specific biases-stemming from factors like population makeup, genotyping methods, and analysis pipelines-that result in inconsistent variant prioritization and limit generalizability and reproducibility. To address these challenges, we propose a transductive learning framework that integrates multiple PRS datasets for more robust risk variant prioritization, incorporating genome-wide association study (GWAS) priority scores as biologically informed priors. Additionally, we introduce BrainGeneBot, an AI-driven tool leveraging generative pretrained transformers with retrieval-augmented generation technology to streamline genomic analyses in …
Low-Cost Cutaneous Protoporphyrin Ix (Ppix) Detection (Cpd) Device For Follow-Up Monitoring Of Patients After Photodynamic Therapy, Md Asaduzzaman Rasel
Low-Cost Cutaneous Protoporphyrin Ix (Ppix) Detection (Cpd) Device For Follow-Up Monitoring Of Patients After Photodynamic Therapy, Md Asaduzzaman Rasel
Graduate Masters Theses
Background: Photodynamic Therapy (PDT) utilizes specific wavelengths of light to activate photosensitizing chemical compounds, known as photosensitizers, which induce the generation of cytotoxic reactive oxygen species (ROS) for the targeted destruction of cancer cells. Among various photosensitizers for PDT, Protoporphyrin IX (PpIX) is widely employed in oncology and dermatology due to its natural in situ generation via the metabolic conversion of 5- aminolevulinic acid (ALA), a non-phototoxic prodrug. Systemic administration of ALA after 3-6 hr drug delay leads to peak PpIX accumulation in tissues, facilitating therapeutic and diagnostic applications. However, PpIX can persist in the skin for 24–48 hours post-treatment, …
Design And Development Of A Standalone Digital Holographic Microscope Employing Phase-Driven Reconstruction And Classification For Biomedical Imaging And Optical Diagnostics, Charlotte Kyeremah
Design And Development Of A Standalone Digital Holographic Microscope Employing Phase-Driven Reconstruction And Classification For Biomedical Imaging And Optical Diagnostics, Charlotte Kyeremah
Graduate Doctoral Dissertations
Access to advanced biomedical imaging technologies remains a significant challenge in resource-limited settings, especially for early disease detection and monitoring of diseases such as malaria, HIV, and other blood-borne diseases. Although point-of-care (POC) devices have gained popularity in global health, many rely on antibody-based tests, lateral flow strips, or optical readouts that often lack quantitative capabilities, sensitivity to early infections, or versatility in different diagnostic targets. In addition, these systems are typically dependent on disposable reagents or manual interpretation, which limits their effectiveness in remote areas. Digital Holographic Microscopy (DHM) presents a promising alternative as a label-free imaging method capable …
Access To Information On Toddler Family Development Program And Family Participation In Child Growth And Development, Dita Dhammayanti, Demsa Simbolon, Lissa Ervina, Yusran Fauzi
Access To Information On Toddler Family Development Program And Family Participation In Child Growth And Development, Dita Dhammayanti, Demsa Simbolon, Lissa Ervina, Yusran Fauzi
Kesmas
The comprehension of the Toddler Family Development (TFD) Program among families in Indonesia remains limited, likely due to insufficient access to information and low participation rates. Limited participation can negatively affect a family’s ability to support optimal child growth and development. This study examined the relationship between access to information on the TFD Program and family participation in child growth and development. Using secondary data from the 2019 Program Performance and Accountability Survey in Indonesia, the cross-sectional analysis included 21,497 respondents. The results revealed an association between access to information on the TFD Program and family participation in child growth …
Expression Graph Network Framework For Biomarker Discovery, Yang Liu, Jason Huse, Kasthuri Kannan
Expression Graph Network Framework For Biomarker Discovery, Yang Liu, Jason Huse, Kasthuri Kannan
Faculty, Staff and Student Publications
Biomarker discovery for complex diseases, such as cancer, hinges on uncovering molecular signatures that capture intricate, interconnected relationships within biological data-a challenge that traditional statistical and machine learning methods often fail to meet due to the complexity of high-dimensional gene expression profiles. To overcome this, we introduce the expression graph network framework (EGNF). This cutting-edge graph-based approach integrates graph neural networks with network-based feature engineering to enhance the predictive identification of biomarkers. EGNF constructs biologically informed networks by combining gene expression data and clinical attributes within a graph database, utilizing hierarchical clustering to generate dynamic, patient-specific representations of molecular interactions. …
Auprc: A Metric For Evaluating The Performance Of In-Silico Perturbation Methods In Identifying Differentially Expressed Genes, Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P Long
Auprc: A Metric For Evaluating The Performance Of In-Silico Perturbation Methods In Identifying Differentially Expressed Genes, Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P Long
Faculty, Staff and Student Publications
In silico perturbation models, computational methods that can predict cellular responses to perturbations, present an opportunity to reduce the need for costly and time-intensive in vitro experiments. Many recently proposed models predict high-dimensional cellular responses, such as gene or protein expression to perturbations such as gene knockout or drugs. However, evaluating in silico performance has largely relied on metrics such as $R^{2}$, which assess overall prediction accuracy but fail to capture biologically significant outcomes like the identification of differentially expressed (DE) genes. In this study, we present a novel evaluation framework that introduces the AUPRC metric to assess the precision …
Reconstruction Of Water Storage Variability In The Aral Sea Region, Nikita Murzintcev, Sahibjamal Nietullaeva, Timur Berdimbetov, Buddhi Pushpawela, Asiya Tureniyazova, Sherly Shelton, Bakbergen Aytmuratov, Khusen Gafforov, Kanat Parakhatov, Alimjan Erdashov, Abdul-Aziz Makhamatdinov, Timur Allamuratov
Reconstruction Of Water Storage Variability In The Aral Sea Region, Nikita Murzintcev, Sahibjamal Nietullaeva, Timur Berdimbetov, Buddhi Pushpawela, Asiya Tureniyazova, Sherly Shelton, Bakbergen Aytmuratov, Khusen Gafforov, Kanat Parakhatov, Alimjan Erdashov, Abdul-Aziz Makhamatdinov, Timur Allamuratov
Plants, Soils and Climate Student Research
The Gravity Recovery and Climate Experiment (GRACE) mission, operational from 2002 to 2017, provided critical measurements of Earth's gravity field anomalies which have been extensively used to study groundwater and terrestrial water storage (TWS) dynamics. In this research, we utilize GRACE data to identify, model, and analyze potential climate parameters contributing to the reconstruction of TWS variability in the Aral Sea Basin region (ASB). We assess the impact of climate change and anthropogenic nature management on TWS change using a quantitative method. Our analysis reveals a significant decline in the TWS at a rate of 0.44 cm year-1 during …
Impact Of Temperature On Larval Mortality And Performance Of The Acorn Barnacle Chthamalus Fissus In San Diego, Ca, Alberto Rivera
Impact Of Temperature On Larval Mortality And Performance Of The Acorn Barnacle Chthamalus Fissus In San Diego, Ca, Alberto Rivera
Theses
Rising ocean temperatures and increasingly frequent marine heatwaves threaten the physiological performance and survival of marine larvae. This study quantifies the thermal tolerance, respiration, and swimming behavior of Chthamalus fissus cyprid larvae to establish a baseline for understanding their vulnerability under future climate scenarios. Larvae were collected from the Scripps Pier in La Jolla, CA and exposed to a range of temperatures (12–50°C, dependent on the experiment) to assess oxygen consumption, mortality, and swimming speeds. Oxygen consumption rates increased significantly with temperature, peaking at 30°C, with cyprids exposed to temperatures above 26°C showing significantly higher respiration rates than those below …