Life Sciences Commons^™

Developing An Unfolding-Incorporated Coarse-Grained Polymer Model For Fibrinogen To Study The Mechanical Behaviour, Vivek Sharma, Poulomi Sadhukhan

Northeast Journal of Complex Systems (NEJCS)

Fibrinogen is a protein found in blood that forms Fibrin polymer network to build a clot during wound healing process when there is a cut in the blood vessel. The fibrin fiber is highly stretchable and shows a complex mechanical properties. The fibrin monomer, Fibrinogen, has a very complex structure which is responsible for its unusual elastic behaviour. In this work, we focus on mechanism of unfolding of D-domain of Fibrinogen, and study its effect in the mechanical behaviour. We develop a coarse-grained (CG) bead-spring model for Fibrinogen which captures the unfolding of folded D-domains along with other necessary structural …

Reproduce Or Live Longer?: A Life History Analysis Of Black Bears In A Semiarid Environment, Brenden M. Orocu, Cambria Armstrong, Janene Auger, Hal L. Black, Randy T. Larsen, Brock R. Mcmillan, Mark C. Belk

Library/Life Sciences Undergraduate Poster Competition 2024

In population demographics, each population has an age stage vital rate (fecundity and survival) in its life history that has the greatest influence on the asymptotic population growth rate, λ.

American black bears (Ursus americanus) are found throughout North America. Other studies on population demographics have focused on populations in higher resource availability areas but none in semiarid environments where resource scarcity is a result of the variable climate.

Objective

Our objective was to determine if factors influencing population dynamics of black bears in semi-arid environments were similar to factors affecting population dynamics in mesic environments where …

Color Stability, Physical Properties And Antifungal Effects Of Zro2 Additions To Experimental Maxillofacial Silicones: Comparisons With Tio2, Mazen Alkahtany, Mark W. Beatty, Fahd Alsalleeh, Thomas M. Petro, Bobby Simetich, You Zhou, Dennis Feely, Grigoris Polyzois

School of Veterinary and Biomedical Sciences: Faculty Publications

(1) Background: Color changes, physical degradation, and fungal infections are challenges to the longevity of maxillofacial polydimethylsiloxane (PDMS) elastomers. This study aimed to evaluate color changes, physical properties, and antifungal properties of PDMS loaded with ZrO₂ and TiO₂ submicron- and nano-sized particles. (2) Methods: A 1% weight of 40 nm or 200 nm diameter ZrO₂ or TiO₂ nanoparticles was mixed into PDMS with 2% functional intrinsic yellow pigment and polymerized. Control materials contained 13% weight 200 nm silica. Samples were exposed to 3000 h of UVB radiation (200 μW/cm²) or darkness. Color parameters L*a*b* …

Effect Of Nodule Size And Stiffness On Phonation Threshold And Collision Pressures In A Synthetic Hemilaryngeal Vocal Fold Model, Mohsen Motie-Shirazi, Matías Zañartu, Sean D Peterson, Daryush D Mehta, Robert E Hillman, Byron D Erath

Faculty, Staff and Student Publications

Synthetic vocal fold (VF) replicas were used to explore the role of nodule size and stiffness on kinematic, aerodynamic, and acoustic measures of voiced speech production. Emphasis was placed on determining how changes in collision pressure may contribute to the development of phonotrauma. This was performed by adding spherical beads with different sizes and moduli of elasticity at the middle of the medial surface of synthetic silicone VF models, representing nodules of varying size and stiffness. The VF models were incorporated into a hemilaryngeal flow facility. For each case, self-sustained oscillations were investigated at the phonation threshold pressure. It was …

Distillers' Grains: Past, Present, And Future Economic Analyses, Daniel E. Gertner

Department of Agricultural Economics: Dissertations, Theses, and Student Research

This thesis is comprised of four chapters, each of which discusses or conducts economic research related to the distillers’ grains market. The first three chapters are meant to be standalone papers. Chapter four provides potential paths forward in distillers’ grains research based on the findings of the first three chapters and concludes the thesis.

The first chapter conducts a comprehensive literature review that categorizes and summarizes economic research on distillers’ grains products. This section shows how the physical market has moved beyond the current academic understanding of market products and structure. Existing research finds that traditional distillers’ grains products positively …

Simulation Of A Rat Muscle-Tendon Unit With Hill-Type Model Dynamics And The Study Of Viscoelasticity In A Collagen Molecule Via Molecular Dynamics, Veronica Siko

West Chester University Master’s Theses

The field of biological science has established that tendons transfer muscular forces to adjacent bones, but there is a dearth of information about the underlying physical principles of these interactions and how the property of viscoelasticity (displayed in tendons as a difference in mechanical response to stress with differing stretching rates) is encompassed in the collagen of tendons. This thesis details the results of concentric and eccentric contractions of the rat muscle-tendon unit (MTU) with and without viscoelasticity (concentric contraction requires active shortening of the muscle, while eccentric contraction requires active lengthening of the muscle) (Lovering & Brooks, 2014). Once …

The Effects Of Milk Phospholipids On Functional Properties Of Anhydrous Milk Fat And Oil Structured Gel Systems, Zachary Cooper

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Lecithin is an ingredient commonly used in foods composed of high concentration of phospholipids. Phospholipids are a type of fat that can mix with both water and oil. In the current food industry, most lecithins come from sunflower, egg, and soybean sources. An additional source of phospholipids can be the waste streams from the dairy industry, such as the whey protein and butter making processes, since these contain a high concentration of phospholipids. Dairy phospholipids have been isolated in the past, but their traits as a functional ingredient are still unknown. In addition, most isolated dairy phospholipids still contain protein, …

Piezoelastic Pvdf/Tpu Nanofibrous Composite Membrane: Fabrication And Characterization, Eman Elnabawy, Ahmed H. Hassanin, Nader Shehata, Anton Popelka, Remya Nair, Saifallah Yousef, Ishac Kandas

Biology Faculty Publications

Poly (vinylidene fluoride) nanofibers (PVDF NFs) have been extensively used in energy harvesting applications due to their promising piezoresponse characteristics. However, the mechanical properties of the generated fibers are still lacking. Therefore, we are presenting in this work a promising improvement in the elasticity properties of PVDF nanofibrous membrane through thermoplastic polyurethane (TPU) additives. Morphological, physical, and mechanical analyses were performed for membranes developed from different blend ratios. Then, the impact of added weight ratio of TPU on the piezoelectric response of the formed nanofibrous composite membranes was studied. The piezoelectric characteristics were studied through impulse loading testing where the …

How Do Ecological Resilience Metrics Relate To Community Stability And Collapse?, Caleb P. Roberts, Dirac L. Twidwell Jr, David G. Angeler, Craig R. Allen

Department of Agronomy and Horticulture: Faculty Publications

The concept of ecological resilience (the amount of disturbance a system can absorb before collapsing and reorganizing) holds potential for predicting community change and collapse—increasingly common issues in the Anthropocene. Yet neither the predictions nor metrics of resilience have received rigorous testing. The crossscale resilience model, a leading operationalization of resilience, proposes resilience can be quantified by the combination of diversity and redundancy of functions performed by species operating at different scales. Here, we use 48 years of sub-continental avian community data aggregated at multiple spatial scales to calculate resilience metrics derived from the cross-scale resilience model (i.e., cross-scale diversity, …

Heuristics From Statistics—Modeling The Behavior And Perception Of Non-Rigid Materials, Vivian C. Paulun, Roland W. Fleming

MODVIS Workshop

No abstract provided.

U. S. Mushroom Import Demand Estimation With Source Differentiated Aids And Rotterdam Models, Jun Li

Department of Agricultural Economics: Dissertations, Theses, and Student Research

While technically considered as fungi, mushrooms are often classified as vegetables because they provide many of the nutritional attributes of produce as well as meat, beans, and grains. The U.S. is the largest consumer of mushrooms and the share of imports in total consumption of mushrooms has been rising and will likely continue to rise as U.S. consumers increasingly adopt healthier diets. While most of U.S. fresh mushroom imports are from Canada, China, Mexico and South Korea, most of U.S. canned mushroom imports are from China, India, Indonesia, and the Netherlands.

The contribution of this thesis is to provide the …

The Incredible Shrinking Dewlap: Signal Size, Skin Elasticity, And Mechanical Design In The Green Anole Lizard (Anolis Carolinensis), Simon P. Lailvaux, Jack Leifer, Bonnie K. Kircher, Michele A. Johnson

Biology Faculty Research

The expression of male secondary sexual traits can be dynamic, changing size, shape, color, or structure over the course of different seasons. However, the factors underlying such changes are poorly understood. In male Anolis carolinensis lizards, a morphological secondary sexual signal called the dewlap changes size seasonally within individuals. Here, we test the hypothesis that seasonal changes in male dewlap size are driven by increased use and extension of the dewlap in spring and summer, when males are breeding, relative to the winter and fall. We captured male green anole lizards prior to the onset of breeding and constrained the …

Three Essays On Food Demand, Land Use Intensity, And Food Crop Portfolio Choice Under Weather Risk, Aditya Raj Khanal

LSU Doctoral Dissertations

Food security and adaptation to climate change has been an important research and development agenda in most of the development organizations and in the national policy of developing countries. The most vulnerable population from climate change and food security problems are rural and agricultural households in the developing and low income countries. Weather and climatic factors and food security has a direct link with poverty because a large majority of poor live in rural areas and depend on agriculture for their livelihoods. The primary focus of this dissertation is to analyze consumption and production aspects of the rural agricultural households. …

Effects Of Nanosecond Pulse Electric Fields On Cellular Elasticity, Diganta Dutta, Anthony Asmar, Michael W. Stacey

Bioelectrics Publications

We investigated the effects of a single 60 nanosecond pulsed electric field (nsPEF) of low (15 kV/cm) and high (60 kV/cm) field strengths on cellular morphology and membrane elasticity in Jurkat cells using fluorescent microscopy and atomic force microscopy (AFM). We performed force displacement measurements on cells using AFM and calculated the Young's modulus for membrane elasticity. Differential effects were observed depending upon pulsing conditions. We found that a single nsPEF of low field strength did not induce any apparent cytoskeletal breakdown and had minor morphological changes. Interestingly, force measurements and calculation of Young's modulus showed a significant decrease in …

Elasticity Of Differentiated And Undifferentiated Human Neuroblastoma Cells Characterized By Atomic Force Microscopy, Shijia Zhao, Alexander B. Stamm, Jeong Soon Lee, Alexei Gruverman, Jung Yul Lim, Linxia Gu

Department of Mechanical and Materials Engineering: Faculty Publications

Human neuroblastoma (SH-SY5Y) cells, with its ability to differentiate into neurons, have been widely used as the in vitro cell culture model for neuroscience research, especially in studying the pathogenesis of Parkinson’s disease (PD) and developing therapeutic strategies. Cellular elasticity could potentially serve as a biomarker to quantitatively distinguish undifferentiated and differentiated SH-SY5Y cells. The goal of this work is to characterize the retinoic acid (RA) induced alternations of elastic properties of SH-SY5Y cells using atomic force microscopy (AFM). The elasticity was measured at multiple points of a single cell. Results have shown that the differentiation of SH-SY5Y cell led …

Changing Forest Water Yields In Response To Climate Warming: Results From Long-Term Experimental Watershed Sites Across North America, Irena F. Creed, Adam T. Spargo, Julia A. Jones, Jim M. Buttle, Mary B. Adams, Fred D. Beall, Eric G. Booth, John L. Campbell, Dave Clow, Kelly Elder, Mark B. Green, Nancy B. Grimm, Chelcy Miniat, Patricia Ramlal, Amartya Saha, Stephen Sebestyen, Dave Spittlehouse, Shannon Sterling, Mark W. Williams, Rita Wrinkler, Huaxia Yao

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Climate warming is projected to affect forest water yields but the effects are expected to vary. We investigated how forest type and age affect water yield resilience to climate warming. To answer this question, we examined the variability in historical water yields at long-term experimental catchments across Canada and the United States over 5-year cool and warm periods. Using the theoretical framework of the Budyko curve, we calculated the effects of climate warming on the annual partitioning of precipitation (P) into evapotranspiration (ET) and water yield. Deviation (d) was defined as a catchment’s change in actual ET divided by P …

Modeling Black Bear Population Dynamics In A Human-Dominated Stochastic Environment, David L. Lewis, Stewart W. Breck, Kenneth R. Wilson, Colleen T. Webb

United States Department of Agriculture Wildlife Services: Staff Publications

Many large carnivore populations exist in human-influenced stochastic environments where availability of natural food sources vary annually and anthropogenic food sources can supplement energetic demands, but at a potential demographic cost due to human–wildlife conflict and subsequent conflict management. Understanding how these competing factors influence a population is complex and difficult to study, but here we demonstrate the utility of using a stochastic projection matrix model and perturbation analysis to gain insight into this problem. We modeled a black bear population subjected to stochastic failures of fruiting and masting species, but with access to garbage in urban environments.We parameratized our …

Microfluidic-Assisted Atomic Force Microscopy For The Mechanical Characterization Of Soft Biological Materials, Aaron Peter Mosier

Legacy Theses & Dissertations (2009 - 2024)

Viable methods for bacterial biofilm remediation require a fundamental understanding of biofilm mechanical properties and their dependence on dynamic environmental conditions. Mechanical test data, quantifying elasticity or adhesion, may be used to perform physical modeling of biofilm behavior, thus enabling the development of novel remediation strategies. To achieve real-time, dynamic measurements of these properties, a novel analysis platform consisting of a microfluidic flowcell device has been designed and fabricated for in situ analysis using atomic force microscopy (AFM) and confocal laser scanning microscopy (CLSM). The flowcell consists of microfluidic channels for biofilm establishment that are then converted into an open …

Elastic Deformations Of The Rotary Double Motor Of Single F(O)F(1)-Atp Synthases Detected In Real Time By Förster Resonance Energy Transfer., Stefan Ernst, Monika G Düser, Nawid Zarrabi, Stanley D Dunn, Michael Börsch

Biochemistry Publications

Elastic conformational changes of the protein backbone are essential for catalytic activities of enzymes. To follow relative movements within the protein, Förster-type resonance energy transfer (FRET) between two specifically attached fluorophores can be applied. FRET provides a precise ruler between 3 and 8nm with subnanometer resolution. Corresponding submillisecond time resolution is sufficient to identify conformational changes in FRET time trajectories. Analyzing single enzymes circumvents the need for synchronization of various conformations. F(O)F(1)-ATP synthase is a rotary double motor which catalyzes the synthesis of adenosine triphosphate (ATP). A proton-driven 10-stepped rotary F(O) motor in the Escherichia coli enzyme is connected to …

Temporal Aggregation And Treatment Of Zero Dependent Variables In The Estimation Of Food Demand Using Cross-Sectional Data, Kristyn Leffler

All Theses

This study analyzes U.S. consumers' demand for eight food commodity groups: Cereal and Bakery goods, Meat and Eggs, Dairy, Fruits and Vegetables, Nonalcoholic Beverages, Fats and Oils, Sugar and Sweets, and Miscellaneous goods. The estimation of the demand system of equations is carried out using the EASI demand model of Lewbel and Pendakur (2009) and five years of data (2002-2006) from the Nielsen Homescan program. Two different levels of temporal aggregation, monthly and the average month within a year, referred to as 'annual' were considered. Using the monthly data, I evaluated the performance of two econometric methods to account for …

Two Rotary Motors In F-Atp Synthase Are Elastically Coupled By A Flexible Rotor And A Stiff Stator Stalk., André Wächter, Yumin Bi, Stanley D Dunn, Brian D Cain, Hendrik Sielaff, Frank Wintermann, Siegfried Engelbrecht, Wolfgang Junge

Biochemistry Publications

ATP is synthesized by ATP synthase (F(O)F(1)-ATPase). Its rotary electromotor (F(O)) translocates protons (in some organisms sodium cations) and generates torque to drive the rotary chemical generator (F(1)). Elastic power transmission between F(O) and F(1) is essential for smoothing the cooperation of these stepping motors, thereby increasing their kinetic efficiency. A particularly compliant elastic domain is located on the central rotor (c(10-15)/ε/γ), right between the two sites of torque generation and consumption. The hinge on the active lever on subunit β adds further compliance. It is under contention whether or not the peripheral stalk (and the "stator" as a whole) …

Environmentally Sensitive Life-Cycle Traits Have Low Elasticity: Implications For Theory And Practice, Valery E. Forbes, Mette Olsen, Annemette Palmqvist, Peter Calow

Valery Forbes Publications

The relationships between population growth rate and the life-cycle traits contributing to it are nonlinear and variable. This has made it difficult for ecologists to consistently predict changes in population dynamics from observations on changes in life-cycle traits. We show that traits having a high sensitivity to chemical toxicants tend to have a low elasticity, meaning that changes in them have a relatively low impact on population growth rate, compared to other life-cycle traits. This makes evolutionary sense in that there should be selection against variability in population growth rate. In particular, we found that fecundity was generally more sensitive …

Effects Of The Polycyclic Musk Hhcb On Individual- And Population-Level Endpoints In Potamopyrgus Antipodarum, Signe Pedersen, Henriette Selck, Daniel Salvito, Valery E. Forbes

Valery Forbes Publications

Although the polycyclic musk 1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexamethylcyclopenta[γ]-2-benzopyran (HHCB) is frequently detected in aquatic sediments, very little is known about its effects on sediment-feeding organisms. Effects of sediment-associated HHCB on growth, feeding rate, survival and reproduction in the gastropod Potamopyrgus antipodarum were measured in the laboratory. Snails were exposed to six nominal HHCB concentrations: 0, 0.1, 1, 10, 30 and 100 μg g−1 dry weight (dw) sediment. Adult survival and growth were not affected by HHCB. However, juvenile growth and survival, reproduction, time to first reproduction and adult feeding rate were more sensitive endpoints and declined with increasing HHCB concentration. Individual-level endpoints for …

Nonylphenol Stimulates Fecundity But Not Population Growth Rate (Λ) Of Folsomia Candida, T. H. Widarto, P. H. Krogh, Valery E. Forbes

Valery Forbes Publications

The toxicity of nonylphenol (NP) to springtails was pronounced at 40 mg/kg dry weight soil, at which no animals survived. Body length and fecundity were the individual life-history traits significantly stimulated by sublethal concentrations of NP during a 64-day experiment. However, the effects of NP on these traits did not result in a statistically significant increase in population growth rate (λ). Decomposition analysis indicated that fecundity was the main contributor to the (non-significant) changes observed in λ. However, since the elasticity of fecundity was very low, large changes in fecundity resulted in a minimal effect on λ. Juvenile survival had …

Robust Population Management Under Uncertainty For Structured Population Models, A. Deines, E. Peterson, Derek Boeckner, J. Boyle, A. Keighley, J. Kogut, J. Lubben, Richard Rebarber, R. Ryan, Brigitte Tenhumberg, S. Townley, Andrew J. Tyre

School of Biological Sciences: Faculty Publications

Structured population models are increasingly used in decision making, but typically have many entries that are unknown or highly uncertain. We present an approach for the systematic analysis of the effect of uncertainties on long-term population growth or decay. Many decisions for threatened and endangered species are made with poor or no information. We can still make decisions under these circumstances in a manner that is highly defensible, even without making assumptions about the distribution of uncertainty, or limiting ourselves to discussions of single, infinitesimally small changes in the parameters. Suppose that the model (determined by the data) for the …

An Application Of Linear Approximation Of Almost Ideal Demand System: Data From Erzurum Central District, Fahri̇ Yavuz, Mustafa Baydemi̇r

Turkish Journal of Agriculture and Forestry

In this study, a food demand analysis of Erzurum central district was conducted. This study differs from previous ones by the use of current data and a new model. Various elasticities computed in this study might be used in the analysis of food consumption policies. The cross-sectional and time series data used were collected by surveying 30 families once every three months from July 1995 to April 1997. Data from a total of 240 families were used to divide the families into high and low income groups. A demand analysis was done using LA/AIDS for five food groups (cereal, vegetable, …

Demographic Viability Of Populations Of Silene Regis In Midwestern Prairies: Relationships With Fire Management, Genetic Variation, Geographic Location, Population Size And Isolation, Eric S. Menges, Rebecca W. Dolan

Scholarship and Professional Work - LAS

1. We studied the demographic viability of populations of a long-lived iteroparous prairie perennial, Silene regia, in relation to management regimes, population sizes, geographical region (Ohio and Indiana vs. Missouri and Arkansas), degree of isolation and amount of genetic variation. Demographic data were collected from 16 populations for up to 7 years.

2. This species has high survivorship, slow growth, frequent flowering and episodic seedling recruitment. Matrix projection methods were used to summarize population performance with and without recruitment. Median finite rates of increase by population varied from 0.57 to 1.82 and from 0.44 to 0.99, respectively.

3. Populations with the highest rates …

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Stress Corrosion And Stress Induced Surface Morphology Of Epitaxial Films, Michael Grinfeld

Scanning Microscopy

In addition to several new predictions, the general theory of thermodynamic stability of heterogeneous systems with rearrangement has allowed us to understand the roots of several experimental and theoretical results of the past. One of them is an outstanding paper of Asaro and Tiller on stress corrosion cracking by surface diffusion published two decades ago. We compare results of Asaro and Tiller with conclusions of thermodynamic theory of solids with rearrangement and develop some Asaro-Tiller results in the directions dictated by the needs of thin films technology and experiment. A surface diffusion model in a prestressed elastic solid is studied …

A New Atomic Force Microscopy Technique For The Measurement Of The Elastic Properties Of Biological Materials, W. Xu, P. J. Mulhern, B. L. Blackford, M. H. Jericho, I. Templeton

Scanning Microscopy

We developed a new technique to measure elastic properties by using the atomic force microscope (AFM) tip to press samples into grooves etched in a GaAs substrate.

We measured the Young's modulus of β-chitin fibres with cross-sections less than 40 nm X 20 nm to be 1-2 X 10¹¹ N/m². In the isotropic approximation, the Young's modulus of the S-layer sheath of the archaeobacterium Methanospirillum hungatei was 1-3 X 10¹⁰ N/m². By testing the sheath to breaking strength we estimated the bacterium can sustain an internal pressure as high as 100-200 atmospheres (1-2 x …

Coherent Strain And Clustering In Ge/Si Heteroepitaxy, Jeff Drucker

Scanning Microscopy

The Ge/Si heteroepitaxial system grows in the Stranski-Krastanov (layer + island) growth mode with an equilibrium intermediate layer thickness of 3 monolayers. Initially, coherent (dislocation free) islands form above the intermediate layer. These coherent islands relieve part of their lattice mismatch by elastic deformation of the layer + island + substrate system. After cluster growth, these islands may reach a critical radius above which it becomes energetically favorable for strain relief through the introduction of misfit dislocations. Particle size distributions generated from digitally acquired secondary electron images of Ge/Si(100) films grown in situ in an ultra-high scanning transmission electron microscope …