Life Sciences Commons^™

History And Theory Of Near-Infrared Spectroscopic Analysis (Nirs), Arnold J. Eilert

IGC Proceedings (1993-2023)

The use of near infrared spectroscopy (NIRS) as an analytical technique has evolved greatly since it was first demonstrated to be a viable method of obtaining molecular compositional information from the “scanning” of a sample. Potential applications of the technology envisioned by early pioneers in the field have been realized or exceeded time after time, and it has now become a very broadly applied means of instrumental analysis. It is worth recalling the historical progression of the technology and the fact that the earliest applications were developed to meet the challenges of agricultural product analysis. In particular, forage analysis is …

Application Progress Of Supercritical Fluid Chromatography In Food Quality And Safety, Xing Qianqian

Food and Machinery

Modern supercritical fluid chromatography technology has better stability and robustness, which can be coupled with mass spectrometry. Supercritical fluid chromatography has the characteristics of high selectivity, high sensitivity and short consumption time, which is not only suitable for high-throughput analysis, but also the analysis of trace compounds in complex samples. Moreover, the application of supercritical fluid chromatography in food quality and safety and the future development direction of supercritical fluid chromatography were also discussed.

A Programmatic Geographic Information Systems Analysis Of Plant Hardiness Zones, Andrew Bowen

Electronic Theses and Dissertations

The Plant Hardiness Zone Map consists of thirteen geographical zones that describe whether a plant can survive based on average annual minimal temperatures. As climate change progresses, minimum temperatures in all regions are expected to change. This work programmatically evaluates predicted future climate projection data and converts it to United States Department of Agriculture-defined hardiness zones. Through the next 80 years, hardiness zones are projected to move poleward; in effect, colder zones will lose area and warmer zones will gain area globally. Some implications include changes in crop growing degree days, which could alter crop productivity, migration and settlement of …

Fitting Time Series Models To Fisheries Data To Ascertain Age, Kathleen S. Kirch, Norou Diawara, Cynthia M. Jones

OES Faculty Publications

The ability of government agencies to assign accurate ages of fish is important to fisheries management. Accurate ageing allows for most reliable age-based models to be used to support sustainability and maximize economic benefit. Assigning age relies on validating putative annual marks by evaluating accretional material laid down in patterns in fish ear bones, typically by marginal increment analysis. These patterns often take the shape of a sawtooth wave with an abrupt drop in accretion yearly to form an annual band and are typically validated qualitatively. Researchers have shown key interest in modeling marginal increments to verify the marks do, …

Global Phylogenomic Assessment Of Leptoseris And Agaricia Reveals Substantial Undescibed Diversity At Mesophotic Depths, J. C. Gijsbers, N. Englebert, K. E. Prata, M. Pichon, Z. Dinesen, R. Brunner, G. Eyal, F. L. González-Zapata, S. E. Kahng, K. R. W. Latijnhouwers, P. Muir, V. Z. Radice, J. A. Sánchez, M. J. A. Vermeij, O. Hoegh-Guldberg, S. J. Jacobs, P. Bongaerts

Biological Sciences Faculty Publications

Background: Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers.

Results: Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic …

Interactions Between Environmental Factors And The Mesozooplankton Community From The Romanian Black Sea Waters, Elena Bisinicu, George-Emanuel Harcota, Luminita Lazar

Turkish Journal of Zoology

The aim of the study was to trace the influence of several abiotic factors on the distribution of the mesozooplankton community from the Black Sea. Sampling was performed in cold and warm seasons of 2013-2020, from stations located on the three sectors of the Romanian Black Sea coast (northern-N, central-C, and southern-S). After determining the species composition, abundance, and biomass, the results were subjected to statistical analysis. A total of 25 taxa were identified, Copepoda representing the bulk of the community. The analysis of the main components explains, through the first two identified factors-temperature and salinity, the variation of environmental …

Flaws In The Methodologies For Organic Carbon Analysis In Seagrass Blue Carbon Soils, Oscar Serrano, Ines Mazarrasa, James W. Fourqurean, Eduard Serrano, Jeffrey Baldock, Jonathan Sanderman

Research outputs 2022 to 2026

The ability to accurately measure organic carbon (OC) in marine sediments or soils is overall taken for granted in scientific communities, yet this seemingly mundane task remains a methodological challenge when the soil matrix contains calcium carbonate (CaCO3), creating inaccuracies in Blue Carbon estimates. Here, we compared five common methods combining acidification, combustion, and wet oxidation pre-treatments for determination of OC in sediments and soils containing CaCO3 based on the analyses of artificial soil mixtures made of different OC and CaCO3 contents, and multiple soils from Australian seagrass cores. The results obtained showed that methods involving acidification pre-treatment entailed −17 …

Optimization Of Quechers And High Performance Liquid Chromatography-Fluorescence Detection Conditions To Assess The Impact Of Preparation Procedures On Eu Priority Pahs In Coffee Samples And Their Pahs Consumption Risk, Ying-Chun Wan, Zwe-Lin Kong, Yu-Hsuan Chao, Chia-Fang Teng, Deng-Jye Yang

Journal of Food and Drug Analysis

The good performance conditions for determination of EU priority PAHs in coffee samples were established to evaluate the effects of roasting degree on the PAHs in coffee beans and the brewing methods on the PAHs transfer from coffee beans to their brews. The consumption risk of the PAHs in coffee products was also assessed. The PAHs levels of the roasted coffee beans were in the order: 923.65 ng/g (dark roast) > 132.20 ng/g (medium roast) > 69.28 ng/g (light roast). Compared with general brewing with the drip bag (PAHs content, 0.30–0.62 ng/mL in coffee brews), the coffee machine brewing (set at 4 …

Safe - A Tool For Assessing The Sustainability Of Agricultural Systems: An Illustration, X. Sauvenier, C. Bielders, M. Hermy, E. Mathijs, B. Muys, J. Valckx, N. Van Cauwenbergh, M. Vanclooster, E. Wauters, A. Peeters

IGC Proceedings (1993-2023)

SAFE (Framework for Assessing Sustainability levels) is a tool for evaluating the sustainability of agricultural systems and uses a hierarchical framework populated with indicators objectively selected by multicriteria evaluation. Indicators are measured at field, farm and landscape scales and progressively integrated into a global sustainability index (SI). SAFE is illustrated below with results on a field scale from a farm site.

People-Powered Research And Experiential Learning: Unravelling Hidden Biodiversity, Melanie Pivarski, Matt Von Konrat, Tom Campbell, Numerous Other Co-Authors

Biology Faculty Publications

Globally, thousands of institutions house nearly three billion scientific collections offering unparallelled resources that contribute to both science and society. For herbaria alone - facilities housing dried plant collections - there are over 3,000 herbaria worldwide with an estimated 350 million specimens that have been collected over the past four centuries. Digitisation has greatly enhanced the use of herbarium data in scientific research, impacting diverse research areas, including biodiversity informatics, global climate change, analyses using next-generation sequencing technologies and many others. Despite the entrance of herbaria into a new era with enhanced scientific, educational and societal relevance, museum specimens remain …

Significance Of Autumn And Winter Food Consumption For Reproduction By Southern Beaufort Sea Polar Bears, Ursus Maritimus, Blaine D. Griffen, John P. Whiteman, Sariah Pullan

Biological Sciences Faculty Publications

Polar bears (Ursus maritimus) in the southern Beaufort Sea experience long annual periods when preferred seal prey are scarce or are unavailable. Consumption of bowhead whale (Balaena mysticetus) carcasses from native Alaskan subsistence hunting is increasingly common for onshore polar bears, yet the energetic consequences of this consumption remain unclear. We use data on bears captured repeatedly over periods that encompassed autumn and winter, combined with calculations, to show that adult female bears likely consume an average of at least 4 seal equivalents during both autumn and winter periods and that considerable variation in energy intake …

Identification Of A Rickettsial Endosymbiont In A Soft Tick Ornithodoros Turicata Americanus, Lichao Liu, Daniel E. Sonenshine, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Bacterial endosymbionts are abundantly found in both hard and soft ticks. Occidentia massiliensis, a rickettsial endosymbiont, was first identified in the soft tick Ornithodoros sonrai collected from Senegal and later was identified in a hard tick Africaniella transversale. In this study, we noted the presence of Occidentia species, designated as Occidentia-like species, in a soft tick O. turicata americanus. Sequencing and phylogenetic analyses of the two genetic markers, 16S rRNA and groEL confirmed the presence of Occidentia-like species in O. turicata americanus ticks. The Occidentia-like species was noted to be present in all developmental stages …

The Decline Of Lake Superior's Woodland Caribou: A Historical Gis Analysis, Jordan W. Kelley

Dissertations, Master's Theses and Master's Reports

Lake Superior’s woodland caribou have been declining since the early 1800s. This thesis asks: why? We hypothesize that as settlers expanded into the region, industrial development in woodland caribou habitat reduced woodland caribou persistence. Using an Historical Geospatial Information System (HGIS) analysis, we find that historical mining and railroad infrastructure are associated with woodland caribou extirpation, while wetlands and protected areas are associated with caribou persistence. We also conducted a stakeholder synthesis of the region to help understand diverse perspectives within and between advocacy coalitions that take different positions on the most effective caribou restoration policies. Beliefs on recovery options …

Energetic Potential Of Co‐Fermented Substrate Of Plant And Animal Biomass, Lubomir Gonda

IGC Proceedings (1993-2023)

No abstract provided.

Using Deep Learning For Children Brain Image Analysis, Rafael Toche Pizano

Computer Science and Computer Engineering Undergraduate Honors Theses

Analyzing the correlation between brain volumetric/morphometry features and cognition/behavior in children is important in the field of pediatrics as identifying such relationships can help identify children who may be at risk for illnesses. Understanding these relationships can not only help identify children who may be at risk of illnesses, but it can also help evaluate strategies that promote brain development in children. Currently, one way to do this is to use traditional statistical methods such as a correlation analysis, but such an approach does not make it easy to generalize and predict how brain volumetric/morphometry will impact cognition/behavior. One of …

Genetics Of Pediatric Musculoskeletal Disorders, Lilian Antunes

Arts & Sciences Electronic Theses and Dissertations

Pediatric musculoskeletal disorders are an extremely broad category of diseases that are often inherited. While individually rare, collectively these disorders are common, affecting around 3% of live births in the US. Despite the mounting clinical and molecular evidence for a genetic etiology, the cause for many patients with pediatric musculoskeletal disorders remain largely unknown. Major challenges in rare pediatric diseases include recruiting large numbers of patients and determining the significance and functional impacts of variants associated with disease within individuals or families. Whole exome sequencing (WES) is a powerful tool to identify coding variants that are associated with rare pediatric …

Establecimiento De 2.500 M2 De Frijol (Phaseolus Vulgaris) Como Una Alternativa Comercial En El Municipio De El Tarra Y Municipios Cercanos De Norte De Santander, Robinson Meza Rincon

Ingeniería Agronómica

El siguiente trabajo tiene como finalidad proporcionar alternativas de apoyo familiar a través de la implementación, producción y comercialización de frijol (Phaseolus vulgaris), variedad zaragoza rosado en 2.500 m2 y contribuir así a la economía del municipio de El Tarra. De igual forma, la metodología para el desarrollo del proyecto se describe paso a paso, desde el establecimiento, producción hasta la comercialización del cultivo obteniendo resultados no favorables para la comercialización de este producto debido a un problema fitosanitario. Por otro lado, se realizó componente investigación cuyo objetivo fue realizar un análisis de crecimiento de la variedad puyita del cultivo …

El Cultivo De Fríjol (Phaseolus Vulgaris L) Como Un Modelo De Producción Agrícola En La Vereda Mercadillo Del Municipio De Guavatá, José Norvey Mateus García

Ingeniería Agronómica

La progresiva necesidad en la elaboración de alimentos a escala mundial, demanda mayor eficiencia en la creación de excelentes alternativas técnicas especializadas en la producción de cultivos, para colocarlas a disposición de pequeños, medianos y grandes productores de este sector (Escoto, 2013). El proyecto productivo del cultivo de fríjol (P. vulgaris L.) desde el componente agronómico se fundamentó en integrar una estrategia productiva para terrenos con pendientes predominantes, como alternativa transitoria en los lugares donde se realiza renovación de cultivos, principalmente en café (Coffea arabica ), minimizando costos directos en contraste con un aumento de utilidad recaudada. Desde el componente …

Comparison Of Computational Fluid Dynamics-Based Simulations And Visualized Seed Trajectories In Different Seed Tubes, Arzu Yazgi, Vedat Demi̇r, Adnan Deği̇rmenci̇oğlu

Turkish Journal of Agriculture and Forestry

The objective of this study was to compare computational fluid dynamics (CFD)-based simulations and visualized seed trajectories in different seed tubes that can provide seed incorporation into the soil with enhanced seed spacing. The other objective was to determine the relation between the seed trajectories and peripheral speed of the vacuum disk. In order to meet the first objective, 2 different seeds (corn and cotton) and artificial spherical material (∅10 mm) were tested under laboratory conditions. The seeds and artificial material were released by free fall into the semitransparent seed tubes (seed tubes A and B) from different release points, …

Geographic Classification Of U.S. Washington State Wines Using Elemental And Water Isotope Composition, Shirley Orellana, Anne M. Johansen, Carey A. Gazis

Student Published Works

Wine fraud leaves wineries vulnerable to damage in reputation and potential lost revenue. To reduce this risk for wines from Washington State (WA), USA, advanced analytical instrumentation and statistical methods were employed to geographically classify 133 wines from 4 major wine producing regions, including 70 wines from WA. Analyses of 37 elements and 2 water isotopes were performed with Triple Quadrupole Inductively Coupled Plasma Mass Spectrometry and Cavity Ring-Down Spectroscopy, respectively. Linear discriminant analysis resulted in 96.2% discrimination, achieved with 11 parameters (Mn, Zn, Pb, Ni, As, D/H, La, Ce, Si, Zr and Sr) that were linearly combined into 3 …

Transition State Analysis Of The Reaction Catalyzed By The Phosphotriesterase From Sphingiobium Sp. Tcm1, Andrew N. Bigley, Dao Feng Xiang, Tamari Narindoshvili, Charlie W. Burgert, Alvan C. Hengge, Frank M. Raushel

Chemistry and Biochemistry Faculty Publications

Organophosphorus flame retardants are stable toxic compounds used in nearly all durable plastic products and are considered major emerging pollutants. The phosphotriesterase from Sphingobium sp. TCM1 (Sb-PTE) is one of the few enzymes known to be able to hydrolyze organophosphorus flame retardants such as triphenyl phosphate and tris(2-chloroethyl) phosphate. The effectiveness of Sb-PTE for the hydrolysis of these organophosphates appears to arise from its ability to hydrolyze unactivated alkyl and phenolic esters from the central phosphorus core. How Sb-PTE is able to catalyze the hydrolysis of the unactivated substituents is not known. To interrogate the catalytic …

Portable X-Ray Fluorescence Spectroscopy For Rapid And Cost-Effective Determination Of Elemental Composition Of Ground Forage, Yadav Sapkota, Louis M. Mcdonald, Thomas C. Griggs, Thomas J. Basden, Brandon Lee Drake

Faculty & Staff Scholarship

The recent development of portable X-ray fluorescence spectrometers (PXRF) has created new avenues for rapid plant elemental concentration determination at reduced cost while avoiding hazardous chemicals. A few studies have indicated the potential use of PXRF for homogenous plant tissue analysis. However, there is a lack of information for analysis of heterogeneous plant samples like livestock forage, which consists of a mixture of several species and plant parts, each varying in elemental concentration. Our objective was to evaluate PXRF for forage analysis, specifically the effect of forage particle size and scan time on important elements including P, K, Ca, and …

Unintended Consequences Of Dna Analysis Delays In North Carolina, Pamela Cook Woodard

Walden Dissertations and Doctoral Studies

The processing of DNA recovered from felony crime scenes often causes delays in trials of up to 3 years, calling into question defendants' rights to a speedy trial. Using Lewin's force field analysis as the theoretical framework, the purpose of this quantitative, comparative study was to compare the processing and reporting of results related to DNA testing in 4 states. Survey data were collected from state bar members (n=137), members of a professional law organization (n=149), and members of a state DNA laboratory (n=20). The purpose of this quantitative, comparative study was to determine whether these variables (interagency communications, staff …

Serological Proteomic Screening And Evaluation Of A Recombinant Egg Antigen For The Diagnosis Of Low-Intensity Schistosoma Mansoni Infections In Endemic Area In Brazil, Vanessa Silva-Moraes, Lisa Marie Shollenberger, William Castro-Borges, Ana Lucia Teles Rabello, Donald A. Harn, Lia Carolina Soares Medeiros, Wander De Jesus Jeremias, Liliane Maria Vidal Siqueira, Caroline Stephane Salviano Pereira, Maria Luysa Camargos Pedrosa, Nathalie Bonatti Franco Almeida, Aureo Almeida, Jose Roberto Lambertucci, Nidia Francisca De Figueiredo Carneiro, Paulo Marcos Zech Coelho, Refaella Fortini Queiroz Grenfell

Biological Sciences Faculty Publications

Background

Despite decades of use of control programs, schistosomiasis remains a global public health problem. To further reduce prevalence and intensity of infection, or to achieve the goal of elimination in low-endemic areas, there needs to be better diagnostic tools to detect low-intensity infections in low-endemic areas in Brazil. The rationale for development of new diagnostic tools is that the current standard test Kato-Katz (KK) is not sensitive enough to detect low-intensity infections in low-endemic areas. In order to develop new diagnostic tools, we employed a proteomics approach to identify biomarkers associated with schistosome-specific immune responses in hopes of developing …

Microarray Data Analysis And Classification Of Cancers, Grant Gates

Williams Honors College, Honors Research Projects

When it comes to cancer, there is no standardized approach for identifying new cancer classes nor is there a standardized approach for assigning cancer tumors to existing classes. These two ideas are known as class discovery and class prediction. For a cancer patient to receive proper treatment, it is important that the type of cancer be accurately identified. For my Senior Honors Project, I would like to use this opportunity to research a topic in bioinformatics. Bioinformatics incorporates a few different subjects into one including biology, computer science and statistics. An intricate method for class discovery and class prediction is …

The Coexistence Of Heart Murmurs And Arrhythmias In An Equine Hospital Population ? A Retrospective Study, Ali̇ Cesur Onmaz, Vehbi̇ Güneş, Alexandra Pavaloiu, René Van Den Hoven

Turkish Journal of Veterinary & Animal Sciences

This study was performed to characterize the coexistence of valvar insufficiencies of the mitral, tricuspid, aortic, and pulmonary valves and their possible association with atrial fibrillation in an equine clinic population. During an 11-year period, 348 horses had been examined for cardiac arrhythmias and suspected defects of the cardiac valves at the Vetmeduni Vienna, Austria. The study population included 256 male and 92 female horses. A subpopulation of 197 (57%) horses was identified with at least one valvular disorder. In these horses, mitral valve regurgitation (MR) was reported in 124 animals (63%), aortic valve regurgitation (AR) in 101 (51%), tricuspid …

Chemical Analysis Of Aerosol Particle Surfaces, Hillary Woolf

Fall Student Research Symposium 2018

Aerosol particles are thought to impact climate properties. The ability to probe aerosols to understand their chemical properties has been difficult due to a lack of appropriate analytical techniques. Here we present interface-specific SHS techniques to allow for in situ analysis of aerosol particles. Transportation of aerosols from their collection site to the laboratory disturbs their chemical and physical properties thus making it difficult to take accurate measurements of aerosol particles. We show that using a CCD detector is a more effective option for producing more sensitive results and can greatly reduce sampling time and could possibly detect measurements from …

Evaluating The Performance Of Gene-Based Tests Of Genetic Association When Testing For Association Between Methylation And Change In Triglyceride Levels At Gaw20, Jason Vander Woude, Jordan Huisman, Lucas Vander Berg, Jenna Veenstra, Abbey Bos, Anya Kalsbeek, Karissa Koster, Nathan Ryder, Nathan L. Tintle

Faculty Work Comprehensive List

Although methylation data continues to rise in popularity, much is still unknown about how to best analyze methylation data in genome-wide analysis contexts. Given continuing interest in gene-based tests for next-generation sequencing data, we evaluated the performance of novel gene-based test statistics on simulated data from GAW20. Our analysis suggests that most of the gene-based tests are detecting real signals and maintaining the Type I error rate. The minimum pvalue and threshold-based tests performed well compared to single-marker tests in many cases, especially when the number of variants was relatively large with few true causal variants in the set.

Turning The Ship: A New Direction For Managing Wood Waste In The Salish Sea Of Washington State, Russ Mcmillan, Chance Asher, John Evered, Celina Abercrombie

Salish Sea Ecosystem Conference

Wood waste has been a major driver in numerous large scale, nearshore cleanups in Washington State Its presence has contributed substantially to both the extent and volume of sediment requiring cleanup which is costly and time consuming. Success in dealing with wood waste must start with controlling sources and a reassessment of how timber-related uses of our waters are conducted. Recognizing its ecological impacts and the financial burden of cleanup prompts the change from practices that release wood waste to state waters. While it is tough to change from traditional use of waters for transport and storage of logs or …

Analytical Approaches To Improve Accuracy In Solving The Protein Topology Problem, Kamal Al Nasr, Feras Yousef, Ruba Jebril, Christopher Jones

Computer Science Faculty Research

To take advantage of recent advances in genomics and proteomics it is critical that the three-dimensional physical structure of biological macromolecules be determined. Cryo-Electron Microscopy (cryo-EM) is a promising and improving method for obtaining this data, however resolution is often not sufficient to directly determine the atomic scale structure. Despite this, information for secondary structure locations is detectable. De novo modeling is a computational approach to modeling these macromolecular structures based on cryo-EM derived data. During de novo modeling a mapping between detected secondary structures and the underlying amino acid sequence must be identified. DP-TOSS (Dynamic Programming for determining the …