Physical Sciences and Mathematics Commons^™

Sccad: Cluster Decomposition-Based Anomaly Detection For Rare Cell Identification In Single-Cell Expression Data, Yunpei Xu, Shaokai Wang, Qilong Feng, Jiazhi Xia, Yaohang Li, Hong-Dong Li, Jianxin Wang

Computer Science Faculty Publications

Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for characterizing cellular landscapes within complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological processes. Existing methods for identifying rare cell types often rely on one-time clustering using partial or global gene expression. However, these rare cell types may be overlooked during the clustering phase, posing challenges for their accurate identification. In this paper, we propose a Cluster decomposition-based Anomaly Detection method (scCAD), which iteratively decomposes clusters based on the most differential signals in each cluster to effectively separate …

Identifying New Cancer Genes Based On The Integration Of Annotated Gene Sets Via Hypergraph Neural Networks, Chao Deng, Hong-Dong Li, Li-Shen Zhang, Yiwei Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation

Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited.

Results

Here, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of …

A Comparison Of Adenosine Triphosphate With Other Metrics Of Microbial Biomass In A Gradient From The North Atlantic To The Chesapeake Bay, Alexander B. Bochdansky, Amber A. Beecher, Joshua R. Calderon, Alison N. Stouffer, Nyjaee N. Washington

OES Faculty Publications

A new, simplified protocol for determining particulate adenosine triphosphate (ATP) levels allows for the assessment of microbial biomass distribution in aquatic systems at a high temporal and spatial resolution. A comparison of ATP data with related variables, such as particulate carbon, nitrogen, chlorophyll, and turbidity in pelagic samples, yielded significant and strong correlations in a gradient from the tributaries of the Chesapeake Bay (sigma-t = 8) to the open North Atlantic (sigma-t = 29). Correlations varied between ATP and biomass depending on the microscopic method employed. Despite the much greater effort involved, biomass determined by microscopy correlated poorly with other …

Widespread Crab Burrows Enhance Greenhouse Gas Emissions From Coastal Blue Carbon Ecosystems, Kai Xiao, Yuchen Wu, Feng Pan, Yingrong Huang, Hebo Peng, Meiqing Lu, Yan Zhang, Hailong Li, Yan Zheng, Chunmiao Zheng, Yan Liu, Nengwan Chen, Leilei Xiao, Guangxuan Han, Yasong Li, Pei Xin, Ruili Li, Bochao Xu, Faming Wang, Joseph J. Tamborski, Alicia M. Wilson, Daniel M. Alongi, Isaac R. Santos

OES Faculty Publications

Fiddler crabs, as coastal ecosystem engineers, play a crucial role in enhancing biodiversity and accelerating the flow of material and energy. Here we show how widespread crab burrows modify the carbon sequestration capacity of different habitats across a large climatic gradient. The process of crab burrowing results in the reallocation of sediment organic carbon and humus. Crab burrows can increase more greenhouse gases emissions compared to the sediment matrix (CO2: by 17-30%; CH4: by 49-141%). Straightforward calculations indicate that these increased emissions could offset 35-134% of sediment carbon burial in these two ecosystems. This research highlights the complex interactions between …

Policy Recommendations For Tire Additive 6ppd And Its Derivative 6ppd-Q, Ashley E. King

Dissertations, Theses, and Masters Projects

Around 3.1 billion tires are produced around the world annually1. The antioxidant additive, 6PPD (i.e., N-(1,3-dimethylbutyl)-N’-phenyl-p-phenylenediamine) is widely employed in passenger and commercial vehicle tires at 0.4-2% by mass to impede tire degradation2. Antioxidants are intended to migrate to tire surfaces and form protective films to prevent rubber oxidation. 6PPD is designed to react with oxidant species like ozone, intentionally forming chemical transformation products that can then escape from the tire and into the environment. 6PPD-Q (i.e., 2-anilino-5-[(4-methylpentan-2-yl)amino]cyclohexa-2,5-diene-1,4-dione) is one such transformation product.

After release and disbursement in the environment, 6PPD-Q is bioavailable to aquatic animals and mammals and acute …

Reducing Short-Chain Pfas Levels In California Water Supplies, Manu Prabandham

Pomona Senior Theses

This thesis proposes twelve specific policies based on precedents set by prior regulation of persistent organic pollutants (such as PCBs), the costs and benefits of short-chain PFAS, technologies available to remove and destroy short-chain PFAS, and the roles and limitations of California’s regulatory institutions. The twelve policies are chosen to be politically and financially feasible, effective at removing short-chain PFAS from water supplies, and equitable towards lower-income and minority Californians, who suffer the most from the consequences of PFAS and other environmental pollutants. The new definitions, education campaigns, studies, taxes, bans, standards, testing, and filtration systems proposed are intended to …

Assessing Carbon Sequestration Of Mixed Hardwood Forests Through Optimizing Harvesting Strategies And Biomass Utilization For Biochar, Bibek Aryal

Graduate Theses, Dissertations, and Problem Reports

This study investigated the long-term carbon stock of central Appalachian mixed hardwood forests under several harvesting strategies. The strategies were optimized to maximize both long-term carbon sequestration and timber supply during harvest using Mixed-Integer Linear Programming (MILP) models. Clear-cut (CC), Partial cut (PC), and mixed harvesting methods to unharvested conditions over 190 years were studied. Initially, harvested forests showed lower sequestration rates than unharvested forests but eventually surpassed them, with CC showing the highest rates over time. Younger forests, particularly those aged 85 to 130 years, exhibited peak carbon sequestration rates. Regarding carbon stock, the unharvested scenario initially had the …

A Few Lessons From Venezuela: Introducing A New Path Of Appropriate Farming And Appropriate Renewable Energy, Victor Christianto, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

In development economics literatures, there is a known term for developing countries which tend to mismanage natural resources, that term is called natural resources curse. And two examples which have been discussed quite often is Venezuela and Norway. Here we also discuss other countries as well, including Argentina and a few lessons for Indonesia in choosing the next course of development path, especially with appropriate farming and appropriate renewable energy.

Implementing Unmanned Aerial Vehicles To Collect Human Gait Data At Distance And Altitude For Identification And Re-Identification, Donn E. Bartram

Graduate Theses, Dissertations, and Problem Reports

Gait patterns are a class of biometric information pertaining to the way a person moves and poses. Gait information is unique to each person and can be used to identify and reidentify people. Historically, this task has been achieved through the use of multiple ground-based imaging sensors. However, as Unmanned Aerial Vehicles (UAVs) advance, they present the opportunity to evolve the process of persons identification and re-identification. Collecting human gait data using UAVs at distances ranging from 20m to 500m and altitudes ranging from 0m to 120m is a challenging task. The current biometric data collection methods, primarily designed for …

Measuring And Modeling Riparian Wetland Saturated Hydraulic Conductivity, Nutrient Concentrations And Shallow Groundwater Dynamics In An Appalachian Mixed Land Use Catchment, Bidisha Faruque Abesh

Graduate Theses, Dissertations, and Problem Reports

The paucity of research on accurate predictions of saturated hydraulic conductivity (Ksat), spatiotemporal analysis of nutrient concentrations relative to water source types (stream and shallow groundwater (SGW)), water flow directions, and land use in riparian wetlands of Appalachian mixed land use catchments underscored the need for this study. Additionally, the lack of SGW flow simulations and stream-SGW interactions using three-dimensional (3D) numerical models (i.e., MODFLOW) in these riparian wetlands further highlighted the research gap. Observed data including soil properties, Ksat, surface water (SW) and SGW levels, and nutrient concentrations, including nitrate (NO3-N), nitrite (NO2-N), ammonium (NH4-N), orthophosphate (PO43-P), total nitrogen …

Late Holocene Fire History Reconstruction Of Beaver Lake In The Northwest Lowlands Of The Olympic Peninsula, Grace Mckenney

All Master's Theses

Fire is an essential component of the landscapes and forests of the Pacific Northwest, including the temperate rainforests of the Olympic Peninsula. Previous fire history reconstructions from the peninsula show that fire return intervals varied throughout the postglacial period, primarily in response to climatic changes and corresponding shifts in vegetation. However, much less is known about the fire history of the low-elevation forests of the Olympic Peninsula and the role of cultural fire regimes in these environments. The purpose of this study was to reconstruct the paleoenvironmental history of a low-elevation study site, Beaver Lake, located in the northwestern part …

Mathematical Modeling Of Microscale Biology In Polyelectrolyte Brushes, William J. Ceely

CGU Theses & Dissertations

Biological macromolecules including nucleic acids, proteins, and glycosaminoglycans are typically anionic and can span domains of up to hundreds of nanometers and even micron length scales. The structures exist in crowded environments that are dominated by multivalent electrostatic interactions that can be modeled using mean-field continuum approaches that represent underlying molecular nanoscale biophysics. In this thesis, we develop such models for polyelectrolyte brushes using both steady state modified Poisson-Boltzmann models and transient modified Poisson-Nernst-Planck models that incorporate important ion-specific (Hofmeister) effects. The transient model enables observation of the relative physical effects as an initial non-equilibrium state relaxes to the steady …

Incorporating Effects-Based Approaches Into Environmental Impact Assessment To Improve Post-Development Monitoring, Carolyn J M Brown

Theses and Dissertations (Comprehensive)

Over the last 50 years, improvements in design of industrial facilities have significantly reduced environmental impacts. But impacts still occur and monitoring programs are the main mechanism to inform when modification/implementation of mitigation is needed. Informed decisions require adequate baseline (pre-development) data to predict impacts based on the development’s design and to understand when the post-development environment has changed. An adaptive monitoring plan provides an effective way to evaluate monitoring results and allow for proactive responses to environmental change before impacts become difficult or challenging to reverse. Unfortunately, baseline data gathered during an environmental impact assessment (EIA) is often inadequate …

The Perspective Of Cash Flow Risks On Earnings Measurement, Daisuke Suzuki, Junpei Yamada, Shoji Kamimura

ASEAN Journal on Science and Technology for Development

The essence of earnings in financial statements is significantly influenced by changes in the economic environment. The main objective of this paper is to elucidate a universal principle capable of explaining any types of earnings measurements. To achieve this, we examine the factors influencing earnings by modeling them from a cash flow perspective. Consequently, this paper directs the attention away from stocks and flows, placing emphasis on the risks inherent in income and expenditure in the context of earnings measurements. It highlights the crucial role of these risks in earnings. Additionally, we illustrate that adjusting these risk tolerances enables the …

Social Media Marketing Audiences And Adaptive Behavior In Brunei: Sem Analysis Using Smartpls, Shahid Anjum, Asmah Ahmad, Jefri Basiuni, Najeeba Tazeen

ASEAN Journal on Science and Technology for Development

The social media and Internet technology penetrations and usage are quite high in Brunei Darussalam. The use of social media marketing among micro, small, and relatively medium businesses to promote their products has also grown as businesses desire to engage and build relationships with customers through social media. This has generated an interest in studying the adaption of social media marketing campaigns among customers, which indirectly determines the effectiveness of social media marketing itself, as well as in studying the facilitation factors for such an adaption. Technology Acceptance Model (TAM) has been used extensively because of its simplicity and usefulness. …

Does The Foreign Direct Investment In Emerging Asian Countries Get ‘Greased’ Or ‘Sanded’ By Corruption? Evidence From Gets Model, Rainah Ginsad, Imbarine Bujang, Abdul Aziz Karia, Emelia Girau, Siti Rahayu Beli

ASEAN Journal on Science and Technology for Development

Inflows of foreign direct investment (FDI) considerably boost industrialization and economic growth in emerging economies. Corruption, human capital, and the economic environment are just a few factors mentioned in the literature as influencing FDI inflow. The impact of corruption on FDI, whether FDI is greased or sanded by corruption, has received greater interest in recent empirical study. This study analysed the impact of the Corruption Perception Index (CPI) on foreign direct investment (FDI) in selected Asian emerging economies. Utilising annual panel data covering 22 selected Asian emerging economies, this study uses the General-to-specific (GETS) model to analyse the impact. The …

The Contribution Of Outcome Expectation In Water Saving Among Malaysians For Sustainable Living Standard, Ganesh. R, Vxynette Fiorna, Ammar Abdulaziz Al-Talib, Haslinda. A, Elango Natarajan

ASEAN Journal on Science and Technology for Development

Saving water is an essential component of a higher level of living for each individual in any Nation. The current and next generation will be greatly impacted by attitudes and emotional aspects of social cognitive behaviour. This empirical investigation was carried out in Malaysia. To determine their attitude and behaviour, a convenience sampling method was applied to a sample size of 265 individuals. It was discovered that outcome expectancy significantly improves water saving. Observed self-efficacy, personal elements, and environmental elements all impacted the outcome expectancy. The model evaluation showed that the adjusted R2 was 0.78, or about 78% of the …

Assessing The Organic Acids-Solubilized Collagen Derived From The Skin Of Unicornfish (Naso Reticulatus Randall, 2011) On Physicochemical And Structural Characteristics: Toward Alternative Source For Industrial Applications, Dayang Fazrianie Harianto, Abdul Aziz Jaziri, Rossita Shapawi, Ruzaidi Azli Mohd Mokhtar, Wan Norhana Md. Noordin, Masmunira Rambli, Nurul Huda

ASEAN Journal on Science and Technology for Development

Converting skin by-product of unicornfish (Naso reticulatus Randall, 2011) into a valuable commodity like collagen is a good strategy to explore alternative sources for land-based animals. Additionally, marine fish collagens are preferable due to their safer and great properties. This project aimed to compare extractability of collagens prepared with three organic acids (i.e., acetic, lactic and citric acids), and their characteristics were also discussed. Collagen extracted with citric acid (CSCUS) (7.10%) had a significantly higher yield (p

Kinetic Modelling During Soaking Of Dried Long Grain Paddy Mr297, Jhauharotul Muchlisyiyah, Rosnah Shamsudin, Roseliza Kadir Basha, Radhiah Shukri, Syahmeer How, Masmunira Rambli

ASEAN Journal on Science and Technology for Development

This study aimed to assess the soaking behaviour of MR 297 dried paddy under two conditions: room temperature and hot water soaking at 60°C. The experiment involved soaking dried MR297 paddy samples in water for 0.5 to 8 hours at room temperature and 0.5 to 5 hours for soaking at 60°C. The water absorption of MR 297 behaved differently at two different soaking conditions. The kinetic behaviour of the soaking process was also simulated using established 25 predictive models and incorporating 5 novel models presented in this work. The comparison of all prediction models involved using three statistical measures: the …

Food Labelling Practices Of Local Products In Brunei Darussalam, Asrarul A. Noraidi, Zikri Zulkifli, Aida M. Basri, Ernina Rani, Beston F. Nore

ASEAN Journal on Science and Technology for Development

Food labelling is an essential feature for food product marketing and is mainly regulated by national food authority. Food package labelling provides information on product composition, usage instructions, shelf-life safety, storage conditions, and nutritional profile. The purpose of this study is to review the scope of the current food labelling system used in local food products. We surveyed 3 different food categories: 1) processed meat products, 2) bread, and 3) snacks, and examined the nutritional labelling criteria with respect to the carbohydrates, protein, and particularly sodium (salt) content. A broad market survey was carried out across Brunei and Muara district, …

Protein Content Analysis On Brunei Delicacies: Kelupis Sulang And Sulang Fruit, Siti Nadia Saifullzan, Jhoorhanah A. Halim, Mas M. Rambli, Aida M. Basri

ASEAN Journal on Science and Technology for Development

Traditional Bruneian delicacy which are often reserved for special occasions; called the kelupis Sulang made from glutinous rice, coconut milk, and the flesh of the Brunei Sulang fruit’s protein content were studied. The protein content of both kelupis and the sulang fruit were examined using both qualitative and protein concentration analyses. The analysis was performed using the Xanthoproteic test, Ninhydrin test, Sulphur Reduction test, and the Biuret test. The readings were obtained from the UV-Visible Spectrophotometry and revealed an average protein concentration of 21 mg/ml in aqueous extracts of kelupis sulang and 26.8 mg/ml in aqueous suspension of kelupis sulang …

Nanocellulose Synthesized From Sugarcane Bagasse (S. Officinarum) Via Alkaline-Mechanical Process And Its Characterization, Wafiqah Daim, Hiroshi Uyama, Syazana Abdullah Lim

ASEAN Journal on Science and Technology for Development

Nanocellulose is one of many promising materials that have garnered the attention of researchers and industries. In this study, sugarcane bagasse (S. officinarum) was used to synthesize cellulose nanofiber (SB-CNF) via an alkaline-mechanical process. A comprehensive characterization of SB-CNF was conducted to explore its morphology via scanning electron microscopy (SEM) and dynamic force microscopy (DFM), assess its functional groups using Fourier transform infrared spectroscopy (FT-IR), analyze its thermal properties through thermogravimetric analysis (TGA), and lastly, evaluate light absorbance and transmittance using a UV-VIS spectrophotometer. Our findings revealed that SB-CNF resulted in a highly intertwined nanofiber structure within a nano-scale dimension. …

Innovative Approaches And Challenges In Brunei's Agricultural Management, Nuramalina Manshor, Ulaganathan Subramanian

ASEAN Journal on Science and Technology for Development

The management and development in agriculture attract agricultural economic science for the pricing, business, farm policy, and financial knowledge. It conjointly draws on plant and animal sciences for soil, seed and fertilizer information, weed control, insect management, and rationing and breeding; agricultural engineering knowledge for farmhouses, vehicles, irrigation, field drying, drainage, and management of erosions; and data on human behavior in Science and Social Science.

Entrepreneurship Education In The Lens Of The Senior High School Students, Calvin J. Caliat, Nehmar J. Dalhadi, Kathleen M. Ishmael

ASEAN Journal on Science and Technology for Development

This study uncovers the perspective on the entrepreneurship education of senior high school students on the university campus. This paper is employed a descriptive research design using a survey ques-tionnaire for the respondents. The survey found that respondents are willing to engage in business be-tween one to 10 years after college. The willingness is due to the encouragement from their parents, independent decision-making, building self-confidence and knowledge, and chasing their dreams. However, there are two significant factors that hinder this, including a need for more business investment and experience. The principal attitudes of an entrepreneur include self-control and creativity. Gaining …

Spf 50: Safe And Prosperous Futures Preparing For The Mid-Century Climate Reality, Michele Romolini, Mary Hillemeier, Dustin Herrmann, Miriam Bar-Zemer

Center for Urban Resilience Reports

The Safe and Prosperous Futures Project, SPF 50, is the third and final phase of a multi-year project led by TreePeople entitled Cooler and Healthier: Reducing Heat-Health Risk Using Urban Forestry & Stakeholder Engagement. The overall project aim is to address heat exposure by 1) developing a model analysis and processes to assess heatrelated mortality and morbidity, 2) creating strategies to address heat effects by canopy increase and albedo changes in the built environment, and 3) conducting stakeholder engagement to develop culturally relevant climate adaptation responses. Earlier phases of the project resulted in the publications RX for Hot Cities 2 …

Weather Information For Garden City, 2023, Anthony Zukoff

Kansas Agricultural Experiment Station Research Reports

Summary of 2023 weather for research conducted at the research locations included in the 2024 Western Kansas Agricultural Research report.

Weather Information For Tribune, Ks 2023, Amanda Burnett

Kansas Agricultural Experiment Station Research Reports

Summary of 2023 weather for research conducted at the research locations included in the 2024 Western Kansas Agricultural Research report.

East Central Kansas Experiment Field: Field Station Weather Reports: 2023 Growing Season, Eric Adee

Kansas Agricultural Experiment Station Research Reports

This report includes the annual summary of precipitation and temperatures from 2023 at the research locations represented in the 2024 Field Research Report and further details about the east central Kansas location.

Southeast Kansas Climate Summary For 2023, Matthew Sittel

Kansas Agricultural Experiment Station Research Reports

Temperature and rainfall are important factors influencing agricultural performance. This report summarizes weather conditions in southeast Kansas. Comparisons to long-term records are used to indicate deviations from historical averages. Overall, in 2023 the southeast region had below average precipitation and above normal temperatures.

Alfred Russel Wallace Notes 29. Extraterrestrial Entertainment: Are We Being Monitored By Alien Beings?, Charles H. Smith

Faculty/Staff Personal Papers

Alfred Russel Wallace (1823−1913) was an early advocate for the rational assessment of likelihood of extraterrestrial life. Current efforts to evaluate the situation have ranged from the heavily self-indulgent to the more objective, and it is still often difficult to decide just how much of the information we are receiving on the subject is dependable. An attempt is made here to cut through the haze and reduce the matter to elementals.