Life Sciences Commons^™

A Novel Synthetic Yeast For Enzymatic Biodigester Pretreatment, Tianyu Tan, Mark S. Aronson, Arren Liu, Jill H. Osterhus, Melissa Robins, Suraj Mohan, Erich Leazer, Bowman Clark, Alexa Petrucciani, Katherine Lowery, James Welch, Casey Martin, Helena Lysandrou, Michael E. Scharf, Jenna Rickus

The Summer Undergraduate Research Fellowship (SURF) Symposium

Lignin, a complex organic polymer, is a major roadblock to the efficiency of biofuel conversion as it both physically blocks carbohydrate substrates and poisons biomass degrading enzymes, even if broken down to monomer units. A pretreatment process is often applied to separate the lignin from biomass prior to biofuel conversion. However, contemporary methods of pretreatment require large amounts of energy, which may be economically uncompelling or unfeasible. Taking inspiration from several genes that have been isolated from termites and fungi which translate to enzymes that degrade lignin, we want to establish a novel “enzymatic pretreatment” system where microbes secrete these …

Captive Breeding Protocols And Their Impact On Genetic Diversity In White-Footed Mice (Peromyscus Leucopus): Implications For Threatened And Endangered Species, Maureen C. Lamb, Janna R. Willoughby, J. Andrew Dewoody

The Summer Undergraduate Research Fellowship (SURF) Symposium

Captive breeding protocols used in zoos often are aimed at increasing population sizes and retaining genetic diversity of endangered species. However, captive breeding causes genetic adaptation to captivity that can lead to an overall decrease in genetic diversity and reduce chances of a successful reintroduction to the wild. In this study, we assess how 3 different breeding protocols—random mating, preferential breeding of individuals with the lowest mean kinship scores, and selection for docility—affect the variability of mitochondrial DNA in white-footed mice (Peromyscus leucopus). We used mice that were captured from the wild but were mated for up to …

Susceptibility Of Parkinson’S Disease Following Mild Blast Traumatic Brain Injury, Glen Howel Galicia Acosta

Open Access Theses

Blast injury-induced neurotrauma (BINT) is steadily increasing in prevalence due to escalated terror activity and constitutes the signature injury associated with current military conflicts. BINT produces significant neurological deficiencies and there is a growing concern that the injury may produce long-term consequences that affect the resilience and the performance of soldiers. One of the potential consequences is an increased susceptibility to Parkinson's disease (PD). A vital goal aimed at curtailing the post-deployment long-term consequences of blast injury-induced neurotrauma is to further our knowledge of pathogenic mechanisms responsible for the escalation of post injury diseases. The purpose of this project is …

A Model Of How Different Biology Experts Explain Molecular And Cellular Mechanisms, Caleb M. Trujillo, Trevor R. Anderson, Nancy J. Pelaez

PIBERG Publications

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do explanations made by experts from different biology subdisciplines at a university support the validity of this model? Guided by the modeling framework of R. S. Justi and J. K. Gilbert, the validity of an initial model was tested by asking seven biologists to explain a molecular …

Characterizing Receptive Field Selectivity In Area V2, Corey M. Ziemba, Robbe Lt Goris, J Anthony Movshon, Eero P. Simoncelli

MODVIS Workshop

The computations performed by neurons in area V1 are reasonably well understood, but computation in subsequent areas such as V2 have been more difficult to characterize. When stimulated with visual stimuli traditionally used to investigate V1, such as sinusoidal gratings, V2 neurons exhibit similar selectivity (but with larger receptive fields, and weaker responses) relative to V1 neurons. However, we find that V2 responses to synthetic stimuli designed to produce naturalistic patterns of joint activity in a model V1 population are more vigorous than responses to control stimuli that lacked this naturalistic structure (Freeman, et. al. 2013). Armed with this signature …

‘Edge’ Integration Explains Contrast And Assimilation In A Gradient Lightness Illusion, Michael E. Rudd

MODVIS Workshop

In the ‘phantom’ illusion (Galmonte, Soranzo, Rudd, & Agostini, submitted), either an incremental or a decremental target, when surrounded by a luminance gradient, can to be made to appear as an increment or a decrement, depending on the gradient width. For wide gradients, incremental targets appear as increments and decremental targets appear as decrements. For narrow gradients, the reverse is true. Here, I model these phenomena with a two-stage neural lightness theory (Rudd, 2013, 2014) in which local steps in log luminance are first encoded by oriented spatial filters operating on a log-transformed version of the image; then the filter …

Time-Lapse Statistics Of Cone Signals From Natural Scenes, David H. Foster, Kinjiro Amano, Sérgio M C Nascimento

MODVIS Workshop

In the natural world, the spectrum and geometry of the illumination from the sun and sky vary over the day. These geometric changes make it especially difficult to extract from the reflected light invariant signals for surface color perception. The aim of this study was to test the utility of certain combinations of retinal cone excitations, in particular, spatial cone-excitation ratios, known to be approximately invariant under non-geometric changes in illumination. Hyperspectral radiance images were acquired at roughly hourly intervals in four outdoor scenes in the Minho region of Portugal. Spatial resolution of the camera was 1344×1024 pixels. Peak-transmission wavelength …

The Bounded Log-Odds Model Of Frequency And Probability Distortion, Hang Zhang, Laurence T. Maloney

MODVIS Workshop

No abstract provided.

Putting Saliency In Its Place, John K. Tsotsos

MODVIS Workshop

The role of attention and the place within the visual processing stream where the concept of saliency has been situated is critically examined by considering the experimental evidence and performing tests that link experiment to computation.

Towards A Unified Computational Model Of Contextual Interactions Across Visual Modalities, David A. Mély, Thomas Serre

MODVIS Workshop

The perception of a stimulus is largely determined by its surrounding. Examples abound from color (Land and McCann, 1971), disparity (Westheimer, 1986) and motion induction (Anstis and Casco, 2006) to orientation tilt effects (O’Toole and Wenderoth, 1976). Some of these phenomena have been studied individually using monkey neurophysiology techniques. In these experiments, a center stimulus is typically used to probe a cell’s classical “center” receptive field (cRF), whose activity is then modulated by an annular “surround” (extra-cRF) stimulus. While this center-surround integration (CSI) has been well characterized, a theoretical framework which unifies these different phenomena across visual modalities is lacking. …

A Conceptual Framework Of Computations In Mid-Level Vision, Jonas Kubilius, Johan Wagemans, Hans P. Op De Beeck

MODVIS Workshop

The goal of visual processing is to extract information necessary for a variety of tasks, such as grasping objects, navigating in scenes, and recognizing them. While ultimately these tasks might be carried out by separate processing pathways, they nonetheless share a common root in the early and intermediate visual areas. What representations should these areas develop in order to facilitate all of these higher-level tasks? Several distinct ideas have received empirical support in the literature so far: (i) boundary feature detection, such as edge, corner, and curved segment extraction; (ii) second-order feature detection, such as the difference in orientation or …

Binocular 3d Motion Perception As Bayesian Inference, Martin Lages, Suzanne Heron

MODVIS Workshop

The human visual system encodes monocular motion and binocular disparity input before it is integrated into a single 3D percept. Here we propose a geometric-statistical model of human 3D motion perception that solves the aperture problem in 3D by assuming that (i) velocity constraints arise from inverse projection of local 2D velocity constraints in a binocular viewing geometry, (ii) noise from monocular motion and binocular disparity processing is independent, and (iii) slower motions are more likely to occur than faster ones. In two experiments we found that instantiation of this Bayesian model can explain perceived 3D line motion direction under …

A Binocular Model For Motion Integration In Mt Neurons, Pamela M. Baker, Wyeth Bair

MODVIS Workshop

Processing of visual motion by neurons in MT has long been an active area of study, however circuit models detailing the computations underlying binocular integration of motion signals remains elusive. Such models are important for studying the visual perception of motion in depth (MID), which involves both frontoparallel (FP) visual motion and binocular signal integration. Recent studies (Czuba et al. 2014, Sanada and DeAngelis 2014) have shown that many MT neurons are MID sensitive, contrary to the prevailing view (Maunsell and van Essen, 1983). These novel data are ideal for constraining models of binocular motion integration in MT. We have …

A Critical Evaluation Of Computational Mechanisms Of Binocular Disparity Processing, Junkyung Kim, David A. Mély, Thomas Serre

MODVIS Workshop

The past decades of research in visual neuroscience have generated a large and disparate body of literature on the computation of binocular disparity in the primary visual cortex. Models have been proposed to describe specific phenomena, yet we lack a theoretical framework which is grounded in neurophysiology and also explains the effectiveness of disparity computation. Here, we examine neural circuits that are thought to play an important role in the computation of binocular disparity. Starting with the binocular energy model (Ohzawa et al. 1990), we consider plausible extensions which include suppressive mechanisms from units tuned to different phase disparities (Tanabe …

Modeling Shape Representation In Area V4, Wyeth Bair, Dina Popovkina, Abhishek De, Anitha Pasupathy

MODVIS Workshop

Our model builds on a convolutional-style neural network with hierarchical stages representing processing steps in the ventral visual pathway. It was designed to capture the translation-invariance and shape-selectivity of neurons in area V4. The model uses biologically plausible linear filters at the front end, normalization and sigmoidal nonlinear activation functions. The max() function is used to generate translation invariance.

A Recurrent Multilayer Model With Hebbian Learning And Intrinsic Plasticity Leads To Invariant Object Recognition And Biologically Plausible Receptive Fields, Michael Teichmann, Fred H. Hamker

MODVIS Workshop

Much effort has been spent to develop biologically plausible models for different aspects of the processing in the visual cortex. However, most of these models are not investigated with respect to the functionality of the neural code for the purpose of object recognition comparable to the framework of deep learning in the machine learning community.
We developed a model of V1 and V2 based on anatomical evidence of the layered architecture, using excitatory and inhibitory neurons where the connectivity to each neuron is learned in parallel. We address learning by three different mechanisms of plasticity: intrinsic plasticity, Hebbian learning with …

A Computational Model To Account For Dynamics Of Spatial Updating Of Remembered Visual Targets Across Slow And Rapid Eye Movements, Yalda Mohsenzadeh, J. Douglas Crawford

MODVIS Workshop

Despite the ever-changing visual scene on the retina between eye movements, our perception of the visual world is constant and unified. It is generally believed that this space constancy is due to the brain’s ability of spatial updating. Although many efforts have been made to discover the mechanism underlying spatial updating across eye movements, still there are many unanswered questions about the neuronal mechanism of this phenomenon.

We developed a state space model for updating gaze-centered spatial information. To explore spatial updating, we considered two kinds of eye movements, saccade and smooth pursuit. The inputs to our proposed model are: …

A Model Of Repetitive Microsaccades, Coupled With Pre-Microsaccadic Changes In Vision, Is Sufficient To Account For Both Attentional Capture And Inhibition Of Return In Posner Cueing, Ziad M. Hafed, Xiaoguang Tian

MODVIS Workshop

When a cue is presented at a location, orienting efficacy towards that location is improved relative to other locations (“attentional capture”), but only briefly; a mere few hundred milliseconds later, orienting incurs large costs. These costs have been classically termed “inhibition of return” (IOR), alluding to voluntary, cognitive strategies avoiding perseverance at one location. However, despite this popular hypothesis, the origins of both attentional capture and IOR remain elusive. Here we show that both of these phenomena can be accounted for by a single concept of oculomotor rhythmicity, and one that involves the entire gamut of saccadic activity including microsaccades. …

Object Recognition And Visual Search With A Physiologically Grounded Model Of Visual Attention, Frederik Beuth, Fred H. Hamker

MODVIS Workshop

Visual attention models can explain a rich set of physiological data (Reynolds & Heeger, 2009, Neuron), but can rarely link these findings to real-world tasks. Here, we would like to narrow this gap with a novel, physiologically grounded model of visual attention by demonstrating its objects recognition abilities in noisy scenes.

To base the model on physiological data, we used a recently developed microcircuit model of visual attention (Beuth & Hamker, in revision, Vision Res) which explains a large set of attention experiments, e.g. biased competition, modulation of contrast response functions, tuning curves, and surround suppression. Objects are represented by …

Modeling Visual Features To Recognize Biological Motion: A Developmental Approach, Giulio Sandini, Nicoletta Noceti, Alessia Vignolo, Alessandra Sciutti, Francesco Rea, Alessandro Verri, Francesca Odone

MODVIS Workshop

In this work we deal with the problem of designing and developing computational vision models – comparable to the early stages of the human development – using coarse low-level information.

More specifically, we consider a binary classification setting to characterize biological movements with respect to non-biological dynamic events. To this purpose, our model builds on top of the optical flow estimation, and abstract the representation to simulate the limited amount of visual information available at birth. We take inspiration from known biological motion regularities explained by the Two-Thirds Power Law, and design a motion representation that includes different low-level features, …

Optimizing The Neural Response To Electrical Stimulation And Exploring New Applications Of Neurostimulation, Kurt Yuqin Qing

Open Access Dissertations

Electrical stimulation has been successful in treating patients who suffer from neurologic and neuropsychiatric disorders that are resistant to standard treatments. For deep brain stimulation (DBS), its official approved use has been limited to mainly motor disorders, such as Parkinson's disease and essential tremor. Alcohol use disorder, and addictive disorders in general, is a prevalent condition that is difficult to treat long-term. To determine whether DBS can reduce alcohol drinking in animals, voluntary alcohol consumption of alcohol-preferring rats before, during, and after stimulation of the nucleus accumbens shell were compared. Intake levels in the low stimulus intensity group (n=3, 100&mgr;A …

The Effect Of Macromolecular Crowding On The Structure Of The Protein Complex Superoxide Dismutase, Ajith Rathnaweera Rajapaksha Mudalige

Open Access Dissertations

Biological environments contain between 7 - 40% macromolecules by volume. This reduces the available volume for macromolecules and elevates the osmotic pressure relative to pure water. Consequently, biological macromolecules in their native environments tend to adopt more compact and dehydrated conformations than those in vitro. This effect is referred to as macromolecular crowding and constitutes an important physical difference between native biological environments and the simple solutions in which biomolecules are usually studied.^ We used small angle scattering (SAS) to measure the effects of macromolecular crowding on the size of a protein complex, superoxide dismutase (SOD). Crowding was induced using …

Effects Of Temperature And Pollinator Availability On Plant Reproductive Success In The Indiana Spring Ephemeral Community, Asya Robertshaw

Open Access Dissertations

Temperature is a key driver of phenology in both plants and insects, and even small changes in temperature can impact the reproductive success of insect-pollinated plants by influencing access to pollinator services. While it is well-established that temperature variation directly impacts the flowering phenology of many plant species, the mechanisms by which it ultimately influences seed production via the pollinator community are not well understood. Climate change has the potential to disrupt the temporal synchrony between plants and their primary pollinators, especially if the two rely on different seasonal cues for the timing of their life history events. If the …

Genetic, Agronomic And Compositional Characterization Of Brown Midrib Sweet Sorghum Lignocellulosic Biomass For Ethanol Production, Luis A. Rivera Burgos

Open Access Dissertations

Sorghum is a promising bioenergy crop due to its unique phenotypic and genotypic attributes. Quality (low lignin and high stem sugar concentration) and quantity (biomass yield, plant height, plant maturity, etc.) biomass traits are key contributors to ethanol yield and production. In this study, a 236 sorghum recombinant inbred line (RIL) population was subjected to genetic, agronomic and compositional characterization for ethanol yield and production. We found that the sweet mutation enhances biomass quantity traits in the RILs which translates to higher ethanol production and biomass quality which improves ethanol yield. The variance components showed from moderate to high heritability …

The Pathological Role Of Acrolein In Experimental Autoimmune Encephalomyelitis And Multiple Sclerosis, Melissa A. Tully

Open Access Dissertations

Multiple sclerosis (MS) is an autoimmune demyelinating neuropathy that affects nearly 2.5 million people worldwide. Despite substantial efforts, few treatments are currently available largely due to limited knowledge of pathogenic mechanisms underlying the disease. The immune-inflammatory nature of the pathology has prompted investigation of the role of oxidative stress in disease development and progression; however targeting reactive oxygen species for neutralization has had marginal success therapeutically, suggesting that an alternate oxidative stress-related target would prove beneficial. Recently, our lab has implicated acrolein, a highly reactive aldehyde that is both a byproduct and catalyst of lipid peroxidation, as a potential therapeutic …

The Role Of Entomology In Environmental And Science Education: Comparing Outreach Methods For Their Impact On Student And Teacher Content Knowledge And Motivation, Faith J. Weeks

Open Access Dissertations

Outreach programming can be an important way for local students and teachers to be exposed to new fields while enhancing classroom learning. University-based outreach programs are offered throughout the country, including most entomology departments as few individuals learn about insects in school and these programs can be excellent sources of entomological education, as well as models to teach environmental and science education. Each department utilizes different instructional delivery methods for teaching about insects, which may impact the way in which students and teachers understand the insect concepts presented. To determine the impact of using entomology to enhance science and environmental …

Paralogous Genes In Arabidopsis Thaliana Contribute To Diversified Phenylpropanoid Metabolism, Li Yi

Open Access Dissertations

Significant evidence supports the idea that gene duplication drives the evolution of new gene function. Besides being silenced, duplicated genes can either neofunctionalize or subfunctionalize under selective pressure or neutral drift. Understanding the trajectory of how each gene is fixed and presumably provides added fitness remains difficult. Plant specialized metabolism provides an attractive platform to study the fixation of genes post duplication and how this process leads to the chemical diversity seen today. Specialized metabolites by definition are thought to be dispensable under normal growth conditions. Thus deleterious mutations occurring in paralogous genes that otherwise would be selected against in …

Modeling, Empirics And Policy Implications Of Firm Heterogeneity In International Trade, Zeynep Akgul

Open Access Dissertations

Computable General Equilibrium (CGE) models are essential computational tools for trade policy analysis. While traditional CGE models based on the Armington assumption of national product differentiation have been successfully applied to various policy scenarios, they also have significant limitations in explaining the firm-level information prevalent in the recent international trade literature. The pioneering work of Melitz (2003) has provided a firm heterogeneity theory that can help address the shortcomings of Armington-based CGE models by introducing additional productivity mechanisms and extensive margin effects. Incorporation of firm heterogeneity in mainstream CGE models offers great potential to improve computational policy analysis. Even though …

Analysis Of Chd Remodelers During Development: A Tale In Two Organisms, Brett Bishop

Open Access Dissertations

The correct development of different organisms requires the precise timing of genes important for development transitions. Organisms have recruited ATP-dependent chromatin remodelers to ensure the correct timing of gene expression during developmental transitions. Here I show how different CHD ATP-dependent chromatin remodelers regulate developmental transitions of different organisms. I show that PICKLE not only promotes H3K27me3 during development to repress developmental genes but also is targeted to these genes. The association of PICKLE to these genes suggests that both repression and H3K27me3 levels is a direct action of PICKLE on these loci. Using zebrafish as a model system, I show …

Undercover Predators: Vegetation Mediates Foraging, Trophic Cascades, And Biological Control By Omnivorous Weed Seed Predators, Carmen K Blubaugh

Open Access Dissertations

Weed pressure is the most costly challenge that vegetable growers face, requiring more labor investment than other production inputs. Vertebrate and invertebrate seed predators destroy a large percentage of weed propagules on the soil surface, and their ecosystem services may ease labor requirements for farmers in herbicide-free systems. Cover provided by living vegetation is an important predictor of seed predator activity, and my dissertation takes a comprehensive approach to understanding the behavior, predator, and environment-mediated mechanisms by which cover impacts weed seed predation in crop environments. ^ First, I performed a meta-analysis of 27 studies to quantitatively evaluate what is …