Digital Commons Network^™

Bayesian Modelling Of Nonlinear Poisson Regression With Artificial Neural Networks, Hansapani Rodrigo, Chris P. Tsokos

School of Mathematical & Statistical Sciences Faculty Publications

Modelling and prediction of count and rate responses have substantial usage in many fields, including health, finance, social, etc. Conventionally, linear Poisson regression models have been widely used to model these responses. However, the linearity assumption of the systematic component of linear Poisson regression models restricts their capability of handling complex data patterns. In this regard, it is important to develop nonlinear Poisson regression models to capture the inherent variability within the count data. In this study, we introduce a probabilistically driven nonlinear Poisson regression model with Bayesian artificial neural networks (ANN) to model count and rate data. This new …

Collection Weeding: Innovative Processes And Tools To Ease The Burden, Gregory M. Nelson, Michael C. Goates, David S. Pixton, Megan Frost, Dan Broadbent

Faculty Publications

Evaluating collections and ultimately removing content poses a variety of difficult issues, including choosing appropriate deselection criteria, communicating with stakeholders, providing accountability, and managing the overall timetable to finish projects on time. The Science and Engineering librarians at Brigham Young University evaluated their entire print collection of over 350,000 items within one year, significantly reducing the number of items kept on the open shelves and the physical collection footprint. Keys to accomplishing this project were extensive preparation, tracking progress and accountability facilitated by Google Sheets and an interactive GIS stacks map, and stakeholder feedback facilitated by a novel web-based tool. …

Genetic Evidence, Maoa, And State V. Yepez, Nita A. Farahany, Roderick T. Kennedy, Brandon L. Garrett

Faculty Scholarship

No abstract provided.

Richmond Law Magazine: Winter 2020, University Of Richmond

Richmond Law Magazine

To Right A Wrong

A Whistleblower and A Wiretap

A Homegrown Panel

Empowering Qualitative Research Methods In Education With Artificial Intelligence, Luca Longo

Conference papers

Artificial Intelligence is one of the fastest growing disciplines, disrupting many sectors. Originally mainly for computer scientists and engineers, it has been expanding its horizons and empowering many other disciplines contributing to the development of many novel applications in many sectors. These include medicine and health care, business and finance, psychology and neuroscience, physics and biology to mention a few. However, one of the disciplines in which artificial intelligence has not been fully explored and exploited yet is education. In this discipline, many research methods are employed by scholars, lecturers and practitioners to investigate the impact of different instructional approaches …

Ingenia, A Novel Program Impacting Sustainable Development Goals Locally Through Students’ Actions, C E Mora, Shannon M. Chance, Inês Direito, M D Morera, L Hernández-Zamora, B Williams

Research Outputs: 2025-Present

No abstract provided.

Modelling Mycorrhizal Fungi Dispersal By The Mycophagous Swamp Wallaby (Wallabia Bicolor) [Dataset], Melissa Danks, Natalie Simpson, Todd F. Elliot, C.E. Timothy Paine, Karl Vernes

Research Datasets

Despite the importance of mammal-fungal interactions, tools to estimate the mammal-assisted dispersal distances of fungi are lacking. Many mammals actively consume fungal fruiting bodies, the spores of which remain viable after passage through their digestive tract. Many of these fungi form symbiotic relationships with trees and provide an array of other key ecosystem functions. We present a flexible, general model to predict the distance a mycophagous mammal would disperse fungal spores. We modelled the probability of spore dispersal by combining animal movement data from GPS-telemetry with data on spore gut-retention time. We test this model using an exemplar generalist mycophagist, …

Human Impact Overrides Bioclimatic Drivers Of Red Fox Home Range Size Globally, Michael Main, Robert Davis, David Blake, Harriet Mills, Tim Doherty

Research Datasets

Aim Identifying the variables that influence animal home range size is important for understanding the biological requirements of individuals and their social interactions. Given their often broad distributions, carnivores are model organisms for studying range-wide determinants of home range size. Here we test predictions about environmental determinants of home range size for one of the world’s most widely distributed carnivores, the red fox (Vulpes vulpes).

Location Global

Methods We compiled a database of 70 mean home range estimates from 62 studies and four continents, which we analysed according to site-based temperature, precipitation, environmental productivity and human influence …

Hybrid Zone Barriers Comparative Data Set, David L. Field

Research Datasets

Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity …

Contemporary Epidemiology Of Rising Atrial Septal Defect Trends Across Usa 1991-2016: A Combined Ecological Geotemporospatial And Causal Inferential Study, Albert Stuart Reece

Research Datasets

Background: Cardiovascular anomalies are the largest group of congenital anomalies and the major cause of death in young children, with a range of data linking rising atrial septal defect incidence (ASDI) with prenatal cannabis exposure. Objectives / Hypotheses. Is cannabis associated with ASDI in USA? Is this relationship causal?

Methods: Geospatiotemporal cohort study, 1991-2016. Census populations of adults, babies, congenital anomalies, income and ethnicity. Drug exposure data on cigarettes, alcohol abuse, past month cannabis use, analgesia abuse and cocaine taken from National Survey of Drug Use and Health (78.9% response rate). Cannabinoid concentrations from Drug Enforcement Agency. Inverse probability weighted …

A Genome-Wide Association Study Of Cocaine Use Disorder Accounting For Phenotypic Heterogeneity And Gene–Environment Interaction, Jiangwen Sun, Henry R. Kranzler, Joel Gelernter, Jinbo Bi

Computer Science Faculty Publications

Background: Phenotypic heterogeneity and complicated gene-environment interplay in etiology are among the primary factors that hinder the identification of genetic variants associated with cocaine use disorder. Methods: To detect novel genetic variants associated with cocaine use disorder, we derived disease traits with reduced phenotypic heterogeneity using cluster analysis of a study sample (n = 9965). We then used these traits in genome-wide association tests, performed separately for 2070 African Americans and 1570 European Americans, using a new mixed model that accounted for the moderating effects of 5 childhood environmental factors. We used an independent sample (918 African Americans, 1382 European …

Outlier Profiles Of Atomic Structures Derived From X-Ray Crystallography And From Cryo-Electron Microscopy, Lin Chen, Jing He, Angelo Facchiano

Computer Science Faculty Publications

Background: As more protein atomic structures are determined from cryo-electron microscopy (cryo-EM) density maps, validation of such structures is an important task. Methods: We applied a histogram-based outlier score (HBOS) to six sets of cryo-EM atomic structures and five sets of X-ray atomic structures, including one derived from X-ray data with better than 1.5 Å resolution. Cryo-EM data sets contain structures released by December 2016 and those released between 2017 and 2019, derived from resolution ranges 0–4 Å and 4–6 Å respectively. Results: The distribution of HBOS values in five sets of X-ray structures show that HBOS is sensitive distinguishing …

Granulosa Cell Proliferation Is Inhibited By Pge2 In The Primate Ovulatory Follicle, Patric S. Lundberg, Gil J. Moskowitz, Carmel Bellacose, Esra Demirel, Heidi A. Trau, Diane M. Duffy

Computer Science Faculty Publications

Prostaglandin E2 (PGE2) is a key paracrine mediator of ovulation. Few specific PGE2-regulated gene products have been identified, so we hypothesized that PGE2 may regulate the expression and/or activity of a network of proteins to promote ovulation. To test this concept, Ingenuity Pathway Analysis (IPA) was used to predict PGE2-regulated functionalities in the primate ovulatory follicle. Cynomolgus macaques underwent ovarian stimulation. Follicular granulosa cells were obtained before (0 h) or 36 h after an ovulatory dose of human chorionic gonadotropin (hCG), with ovulation anticipated 37-40 h after hCG. Granulosa cells were obtained from additional monkeys 36 h after treatment with …

Acknowledgement Entity Recognition In Cord-19 Papers, Jian Wu, Pei Wang, Xin Wei, Sarah Rajtmajer, C. Lee Giles, Christopher Griffin

Computer Science Faculty Publications

Acknowledgements are ubiquitous in scholarly papers. Existing acknowledgement entity recognition methods assume all named entities are acknowledged. Here, we examine the nuances between acknowledged and named entities by analyzing sentence structure. We develop an acknowledgement extraction system, AckExtract based on open-source text mining software and evaluate our method using manually labeled data. AckExtract uses the PDF of a scholarly paper as input and outputs acknowledgement entities. Results show an overall performance of F₁=0.92. We built a supplementary database by linking CORD-19 papers with acknowledgement entities extracted by AckExtract including persons and organizations and find that only up to …

Opening Books And The National Corpus Of Graduate Research, William A. Ingram, Edward A. Fox, Jian Wu

Computer Science Faculty Publications

Virginia Tech University Libraries, in collaboration with Virginia Tech Department of Computer Science and Old Dominion University Department of Computer Science, request $505,214 in grant funding for a 3-year project, the goal of which is to bring computational access to book-length documents, demonstrating that with Electronic Theses and Dissertations (ETDs). The project is motivated by the following library and community needs. (1) Despite huge volumes of book-length documents in digital libraries, there is a lack of models offering effective and efficient computational access to these long documents. (2) Nationwide open access services for ETDs generally function at the metadata level. …

Seagrass Losses Since Mid-20th Century Fuelled Co2 Emissions From Soil Carbon Stocks [Dataset], Cristian Salinas, Carlos M. Duarte, Paul S. Lavery, Pere Masque, Ariane Arias-Ortiz, Javier Leon, David Callaghan, Gary A. Kendrick, Oscar Serrano

Research Datasets

The database compiles published data (in Salinas et al. 2020) on biogeochemical characteristics (density, organic carbon, stable carbon isotopes, sediment grain size) of cores from Posidonia australis and sinuosa soil in Cockburn Sound, Western Australia.

Snp Population Genetic Data For The Seagrass Halodule Uninervis From Pilbara Region, Western Australia, Kathryn Margaret Mcmahon, Richard Evans

Research Datasets

This dataset contains 80 SNP loci from 15 locations with 25-47 samples per locations. Each column contains data from two alleles. All genotyped samples are included. Prior to population genetic analysis clone mates were identified and removed.

Predictors Of Marine Genetic Structure In The Indo-Australian Archipelago, Kathryn M. Mcmahon, Udhi Eko Hernawan

Research Datasets

This is the dataset extracted from 101 publications on 99 marine species from eight taxonomic groups in the Indo Australian Archipelago. Data extracted includes measures of genetic structure and the potential predictors.

Conserving Critical Seagrass Habitat For Dugong. Dugong Seagrass Associations Summary Data., Kathryn M. Mcmahon, Paul Lavery, Nicole Said, Chris Cleguer, Amanda Hodgson

Research Datasets

This is the summary dataset of the dugong seagrass associations data containing dugong counts, benthic habitat cover, seagrass nutrient content, water temperature, water current speed, water depth and water transparency from three locations in the Pilbara over 3 time periods in 2018-2019.

Conserving Critical Seagrass Habitat For Dugong. Seagrass Network Monitoring Data Summary, Kathryn M. Mcmahon, Paul Lavery, Nicole Said

Research Datasets

This is the summary dataset of the seagrass monitoring data containing benthic habitat, seagrass meadow characteristics, seed density and environmental variables from three locations in the Pilbara over 3-4 time periods in 2018-2019.

Top 30 Cm Soil C Org Stocks, Isotopic C Org Signature (13dc) And Fine Sediment Content (Silt And Clay %) Estimated In Soil Cores Sampled In Seagrass Meadows Around Australia, Ines Mazarrasa, Paul Lavery, Carlos M. Duarte, Anna Lafratta, Catherine E. Lovelock, Peter I. Macreadie, Jimena Samper-Villarreal, Cristian Salinas, Christian Sanders, Stacey Trevathan-Tackett, Mary Young, Andy Steven, Oscar Serrano

Research Datasets

This database contains data on top 30 cm soil biogeochemical properties from soil cores (minimum length of 30 cm) sampled in seagrass (n=201 cores) and adjacent unvegetated patches (n=39) around Australia.

Average biogeochemical properties per core along with information about type of environment, biotic characteristics and environmental conditions.

In particular, the variables included in sheet 1 are:

Core ID (column A): core code

Location (column B): name of the region of the sampling site.

Latitude / Longitude (columns C, D): latitude and longitude

Bioregion (column E): classified the sampling sites according to their location in Temperate-Southern …

Chlorophyll Fluorescence Corrections From A Rapid-Profiling, Autonomous Wirewalker, Melanie Feen

Open Access Master's Theses

Stimulated chlorophyll fluorescence (ChlF) is a fairly simple measurement to collect, and is ubiquitous on most biogeochemical autonomous platforms. However, complex physiological phenomenon challenge the interpretation of the data. Nonphotochemical quenching (NPQ) markedly reduces the fluorescence during high light regimes, favoring dissipation of this energy as heat. This study evaluates previously developed NPQ correction methods, typically implemented on floats or gliders, for a fast profiling, autonomous, drifting Wirewalker deployed during the EXPORTS field campaign at Ocean Station Papa (OSP) in the Subpolar North Pacific Ocean. Through validating NPQ-corrected chlorophyll to absorption line height, which is not subject to the same …

Improving The Utilization Of Renewable Energies In Water Supply Systems Using Demand Side Management, Lukas Siemon

Open Access Master's Theses

The mitigation of global warming is one of the greatest challenges of the 21^st century. To reduce the emission of greenhouse gases, fossil fuels are being replaced with renewable energies. The increased share of solar and wind energy poses a complex challenge to the electricity grid due to the temporal variability in energy generation. Water supply is an energy intensive sector and entails a great potential to apply measures to synchronize the system’s energy demand to the renewable energy supply.

In this study, the potential of implementing demand side management into the water supply system operation is assessed with …

Analysis Of Missing Data In Marine Dissolved Oxygen Time Series Using Dynamic Linear Models, Shajratul Alam

Open Access Master's Theses

The marine ecosystems cannot survive without dissolved oxygen (DO). Low oxygen events (hypoxia) in the ocean cause stress on the benthic community and, hampers their growth rate initiating mortality. To monitor the concentration of oxygen, different water quality monitoring sites have been established across the globe. The Narragansett Bay fixed-site water quality monitoring network (NBFWQMN) is a facility that regularly measures oxygen level as well as other important water parameters (temperature, salinity, pH level, and Chlorophyll) at different locations of Narragansett Bay (NB). Missing observation is a common phenomenon for this times-series dataset and, can occur for various reasons. In …

Applications To Collect And Analyze Or Destroy Energetics And Chemical Warfare Agents, Victoria Stubbs

Open Access Master's Theses

Terrorism is an ever-present threat in our society. In the last decade alone, terrorists killed an average of 21,000 people each year [1]. In 2018, there were 289 bombings in the US, and bomb threats increased by 32% since the year prior [2]. Before that, there was an average of 205 criminal bombings in the US between 2004 and 2005 [3]. All of this is not including the 2,996 lives lost when 4 planes struck the Pentagon, the Twin Towers, and a field in Pennsylvania, leaving long term physical and mental wounds on those who were affected by it [4]. …

Trophic Niche Overlap Of Atlantic Cod And Black Sea Bass In Relation To Warming Southern New England Waters, Nina Santos

Open Access Master's Theses

In southern New England (SNE), a new ecological interaction is occurring as temperate black sea bass abundance increases in the home range of the iconic Atlantic cod as a result of climate-induced ocean warming. In this study, we examined the diet and trophic dynamics of both SNE Atlantic cod and black sea bass using a multi-tracer approach of stomach content analysis as well as bulk and compound-specific amino acid isotope analyses. We reveal a highly selective diet (0.01-0.43 Levin’s index) with decapod crustaceans occurring in 82-89% of stomachs and making up 72-79% of the total wet weight for both species, …

Taxonomic Profiling Of Metagenomic Reads Using Deep Learning, Cecile Cres

Open Access Master's Theses

The field of metagenomics studies microbes from environmental samples in a process generating millions of short DNA sequences called reads. The final outcome is to discover the diversity as well as the function of complex microbial communities using computational tools. The general idea adopted by most taxonomic classifiers, which aim to assign taxonomic groups to individual reads, is to compare the target DNA sequences to a reference database and identify the taxon of the best match. This method has many disadvantages including the necessity for large computing resources in order to process large sequence databases. The current project aims to …

Remote Sensing Of Phytoplankton Size Classes On The Northeast U.S. Continental Shelf, Kyle J. Turner

Open Access Master's Theses

The size structure of phytoplankton communities influences important ecological and biogeochemical processes, including the transfer of energy through marine food webs. A variety of algorithms have been developed to estimate phytoplankton size classes (PSCs) from satellite ocean color data. However, many of these algorithms were developed for application to the open ocean, and their performance in more productive, optically complex continental shelf systems has not been fully evaluated. In this study, several existing PSC algorithms were applied in the Northeast U.S. continental shelf (NES) and assessed by comparison to in situ PSC estimates derived from a regional HPLC pigment data …

Control System For Low-Cost Miniature Isopycnal Floats (Minions)' Targeting Distributed Observations Of The Oceanic Biological Carbon Pump, Jackson Sugar

Open Access Master's Theses

The flux and attenuation of Particulate Organic Carbon (POC) export through the mid-water column has been a subject of oceanographic research for decades. The methods to sample sinking particles have remained largely unchanged, and interpretation of the data is challenged by uncertainty and sparse measurements. This need prompted our efforts to develop a standalone sensor platform for subsurface timelapse photography of accumulated particles as a proxy for carbon export, combined with simultaneous measurements of dissolved oxygen, temperature and pressure. The use of a flexible Linux single board computer with power cycling enabled the float to be; low power (for long …

Training, Equipping, And Deploying Teenagers For Preaching With A Prophetic Emphasis At The Plantation Seventh-Day Adventist Church, Iosif Salajan

Doctor of Ministry Projects

Problem

Teenagers were not integrated in the preaching ministry of the Plantation Seventh-day Adventist Church. Their involvement in the worship service revealed challenges in publicly expressing their faith and spiritual experience. The absence of training, equipping, and deploying teenagers for preaching ministry contributed to their low retention and their lack of representation in the leadership of the church.

Method

Between August 2018 and May 2019, under the coordination of the researcher, preaching mentors offered teenage mentees from the Plantation Seventh-day Adventist Church a complete learning cycle called sermonic process. It started with producing the sermon, continued with practicing the sermon …