Engineering Commons^™

Why Latent Representations In Convolutional Neural Networks Fall Outside Visual Space, Katerina Malakhova

MODVIS Workshop

It is common to compare properties of visual information processing by artificial neural networks and the primate visual system.

Some remarkable similarities were observed in the responses of neurons in IT cortex and units in higher layers of CNNs. Here I show that latent representations formed by weights in convolutional layers do not necessarily reflect visual domain. Instead they are strongly dependent on a choice of training set and cost function.

The most striking example is when an individual unit, which is highly selective to some members of a category is, nevertheless, inhibited by visually similar objects of the same …

An Active Efficient Coding Model Of The Development Of Amblyopia, Samuel Eckmann, Lukas Klimmasch, Bertram Shi, Jochen Triesch

MODVIS Workshop

No abstract provided.

Functional Electrical Stimulation Of Peripheral Nerve Tissue Via Regenerative Sieve Microelectrodes, Matthew Reagan Macewan

McKelvey School of Engineering Graduate Student Theses & Dissertations

Functional electrical stimulation (FES) of peripheral nervous tissue offers a promising method for restoring motor function in patients suffering from complex neurological injuries. However, existing microelectrodes designed to stimulate peripheral nerve are unable to provide the type of stable, selective interface required to achieve near-physiologic control of peripheral motor axons and distal musculature. Regenerative sieve electrodes offer a unique alternative to such devices, achieving a highly stable, selective electrical interface with independent groups of regenerated nerve fibers integrated into the electrode. Yet, the capability of sieve electrodes to functionally recruit regenerated motor axons for the purpose of muscle activation remains …

The Santa Clara, 2018-05-10, Santa Clara University

The Santa Clara

No abstract provided.

The Role Of Criticality Of Gene Regulatory Networks On Emergent Properties Of Biological Systems, Hyobin Kim

Graduate Dissertations and Theses

The relationship between criticality of gene regulatory networks (GRNs) and dynamics of GRNs at a single cell level has been vigorously studied. However, the relationship between the criticality of GRNs and properties of multicellular organisms at a higher level has not been fully explored. Here we aim at revealing potential roles of the criticality of GRNs at a multicellular and hierarchical level, using a random Boolean network as a GRN. We perform three studies. Firstly, we propose a GRN-based morphogenetic model, and delve into the role of the criticality of GRNs in morphogenesis at a multicellular level. Secondly, we include …

Sustainable Agriculture: Integration Of Aquaponics At Punta Leona Hotel And Club In Costa Rica, Cailin Sierra Dyer, Paris Riley Smith

Senior Honors Projects, 2010-2019

Sustainable agriculture is becoming an increasingly important method of food production. As human populations continue to grow, attendant food demand has been increasingly met via agribusiness, including monoculture crop production and factory farming. As is well documented, the rise of agribusiness has led to resource degradation and declining stocks on which “sustainable agriculture” relies. This paper describes a local attempt to re-establish “sustainable agriculture” through the development of an aquaculture system that mimics a naturally occurring cycle that integrates fish and plants. The system was constructed over a three-week period in Punta Leona, Costa Rica. First, the ground was cleared …

Determinants Of Multi-Scale Patterning In Growth Plate Cartilage, Alek Erickson

Theses & Dissertations

ABSTRACT

Functional architectures of complex adaptive systems emerge by dynamic control over properties of individual components. During skeletal development, growth plate cartilage matches bone geometries to body plan requisites by spatiotemporally regulating chondrocyte actions. Bone growth potential is managed by the proximodistal patterning of chondrocyte populations into differentiation zones, while growth vectors are specified by the unique columnar arrangement of clonal groups. Chondrocyte organization at both tissue and cell levels is influenced by a cartilage-wide communication network that relies on zone-specific release and interpretation of paracrine signals. Despite genetic characterization of signaling interactions necessary for cartilage maturation, the regulatory mechanisms …

The Santa Clara, 2018-05-03, Santa Clara University

The Santa Clara

No abstract provided.

Nitrogen And Weed Management In Transplanted Tomato In The Nigerian Forest-Savanna Transition Zone, J. A. Adigun, O. S. Daramola, O. R. Adeyemi, P. M. Olorunmaiye, O. A. Osipitan

Haskell Agricultural Laboratory (Northeast Research and Extension Center)

Weed infestation and inherent low soil fertility are among primary reasons for low yields of tomato in Nigeria. Field trials were carried out during the wet season of 2015 and 2016 to evaluate yield response of tomato to nitrogen (N) application and weed control methods in the forest-savanna transition zone of Abeokuta, Nigeria. Positive relationship exists between growth of weed species and increase in N application. Across the years of study, increase in N up to 90 kg/ha increased weed density by 11–25%, however, the increased N gave the transplanted tomato competitive advantage and thus enhanced weed smothering. Pre-transplant application …

Effect Of Silk-Based Hydrogel Topography On Intestinal Epithelial Cell Morphology And Wound Healing In Vitro, Marisa E. Boch

University Scholar Projects

Recent advances in the field of biomaterials have suggested that cells cultured on substrates resembling the native tissue mechanical properties, matrix and growth factor composition, and topography can adopt phenotypes that more closely resemble the in vivo tissue compared to cells cultured on non-mimetic constructs. Understanding the effect of culture substrate on in vitro tissue formation is important for bioengineering applications that include mechanistic studies of healthy tissue function and development of disease models. In this work, Caco-2 adenocarcinoma cells were seeded on flat and crypt-like topographies of 3D-printed cytocompatible hydrogels derived from silk fibroin protein. Silk hydrogels were selected …

State Dependent Function And Dynamics In Cerebral Cortical Networks, Leila Fakhraei

Graduate Theses and Dissertations

Cerebral cortex exhibits vigorous ongoing, internal neural activity even with no sensory input is present or the animal is minimally engaged in a task or behavior. This internal ongoing activity is not static; the ‘cortical state’ varies ranging from synchronous and highly correlated activity to asynchronous and weakly correlated neural activity. The main goal of the work presented here is to understand how changes in cortical states effect several aspects of cortical function and dynamics.

To meet this goal, we did three separate projects. First, we compared the predictability of neuronal network dynamics across cortical states in somatosensory cortex of …

A Survey Of Three-Dimensional Sound And Its Applications, Andrew Topping

Capstone Projects and Master's Theses

This research project seeks to develop a foundation of knowledge about three-dimensional sound (3-D sound) and its utilization across various media. Topics covered include the techniques by which 3-D sound is accomplished, its departures from the standard paradigm of stereophonic audio, the range of creative and engineering considerations within 3-D contexts and examinations of existing 3-D audio applications.

Longitudinal Tracking Of Physiological State With Electromyographic Signals., Robert Warren Stallard

Electronic Theses and Dissertations

Electrophysiological measurements have been used in recent history to classify instantaneous physiological configurations, e.g., hand gestures. This work investigates the feasibility of working with changes in physiological configurations over time (i.e., longitudinally) using a variety of algorithms from the machine learning domain. We demonstrate a high degree of classification accuracy for a binary classification problem derived from electromyography measurements before and after a 35-day bedrest. The problem difficulty is increased with a more dynamic experiment testing for changes in astronaut sensorimotor performance by taking electromyography and force plate measurements before, during, and after a jump from a small platform. A …

Nutrient Limitation Of Algal Growth In Fishery Lakes, Madeline Ludwig

Biological and Agricultural Engineering Undergraduate Honors Theses

This study investigated the effect of nutrient addition on algal growth in three United States Forest Service lakes for fishery management in Arkansas. In fishery managed lakes, fertilization works by manipulating algae growth, a basal food resource in lakes, to promote the growth of the fish population. For the nutrient addition experiments, water was collected from each lake in cubitainers and spiked with nutrients; the treatments included the control, nitrogen (+N), phosphorus (+P), and nitrogen and phosphorus (+N +P). When algal growth was visually observed, a water sample was collected from each cubitainer and analyzed for chlorophyll-α. The results showed …

Optimizing Genetic Manipulation Of Methanogens Through Faster Cloning Techniques, Merrisa Jennings

Biological and Agricultural Engineering Undergraduate Honors Theses

Methanogenesis is the biological production of methane. Only anaerobic archaea known as methanogens are capable of such a metabolic feat. They have strict living conditions and substrate sources which determine their rate of metabolism. This is of particular importance from a greenhouse gas reduction perspective or biogas capturing perspective. One of the best ways to optimize methanogen methane production is via genetic manipulation. The current procedures are timely though, therefore a faster cloning processes should be developed. The objective of this study was to optimize a premade genetic transformation kit known as the Gibson Kit. The Gibson Kit was supposed …

Chloride Salt Inhibition On Lipid Production In Wastewater-Grown Algae For Biofuel Production, Will Richardson

Biological and Agricultural Engineering Undergraduate Honors Theses

Algae are increasingly being recognized as useful organisms for many applications in today’s world. Their ability to remove nitrogen, phosphorus, and trace metals from water while adding oxygen to water makes them an attractive tertiary treatment technology in municipal wastewater treatment facilities. At the same time, algae produce lipids and carbohydrates that are useful for biofuel production, and they are not a human food crop unlike many biofuel feedstocks. In this study the effect of increased chloride concentrations in wastewater was assessed on the ability of two species of algae, Chlorella vulgaris and Scenedesmus dimorphus, to function as a …

Characterization And Analysis Of Ultrathin Cigs Films And Solar Cells Deposited By 3-Stage Process, Grace Rajan, Krishna Aryal, Shankar Karki, Puruswottam Aryal, Robert W. Collins, Sylvain Marsillac

Electrical & Computer Engineering Faculty Publications

In view of the large-scale utilization of Cu(In,Ga)Se₂ (CIGS) solar cells for photovoltaic application, it is of interest not only to enhance the conversion efficiency but also to reduce the thickness of the CIGS absorber layer in order to reduce the cost and improve the solar cell manufacturing throughput. In situ and real-time spectroscopic ellipsometry (RTSE) has been used conjointly with ex situ characterizations to understand the properties of ultrathin CIGS films. This enables monitoring the growth process, analyzing the optical properties of the CIGS films during deposition, and extracting composition, film thickness, grain size, and surface roughness which …

Effect Of Silk-Based Hydrogel Topography On Intestinal Epithelial Cell Morphology And Wound Healing In Vitro, Marisa E. Boch

Honors Scholar Theses

Recent advances in the field of biomaterials have suggested that cells cultured on substrates resembling the native tissue mechanical properties, matrix and growth factor composition, and topography can adopt phenotypes that more closely resemble the in vivo tissue compared to cells cultured on non-mimetic constructs. Understanding the effect of culture substrate on in vitro tissue formation is important for bioengineering applications that include mechanistic studies of healthy tissue function and development of disease models. In this work, Caco-2 adenocarcinoma cells were seeded on flat and crypt-like topographies of 3D-printed cytocompatible hydrogels derived from silk fibroin protein. Silk hydrogels were selected …

Mitochondrial Mrna Translation Is Required For Maintenance Of Oxidative Capacity, David Lee

Graduate Theses and Dissertations

Oxidative metabolism is required to produce adequate energy to sustain human life. A primary example of deteriorating oxidative capacity is seen in the cardiac musculature during chronic heart failure. This suggests that by improving oxidative potential, chronic heart disease could be mitigated and one approach to accomplish this may be through targeting the mt-mRNA translation system. Purpose: This investigation’s purpose was to characterize disruptions in mt-mRNA translation machinery in multiple forms of cardiomyopathy and to determine if mitochondrial mRNA translation initiation factor (mtIF2) is necessary to maintain oxidative capacity in cardiomyocytes. Methods Using a combination of animal and cell culture …

Characterization Of Bacteriorhodopsin And Halorhodopsin Reconstituted In Lipid Bilayer Membranes, Joel Domkam Kamwa

Graduate Theses and Dissertations

Motivated to produce electricity with photon activated ion pumps, the main purpose of this work was to characterize the photosynthetic membrane proteins bacteriorhodopsin (proton pump) and halorhodopsin (chloride pump). The proteins were re-suspended in lipid bilayers. For this work, an experimental set-up was built which included: chambers for lipid bilayer formation and characterization, lasers for ion pump activation, and an AxoPatch electrophysiology system for small photocurrent measurement. Lipid bilayer membranes were formed using mostly folding method: folding two monolayers together. The membranes were characterized by their resistance, capacitance, and generated photocurrent. Photocurrent was generated upon illumination of lipid-protein membranes with …

Advancing The Understanding Of Environmental Transformations, Bioavailability And Effects Of Nanomaterials, An International Us Environmental Protection Agency—Uk Environmental Nanoscience Initiative Joint Program, Mitch M. Lasat, Kian Fan Chung, Jamie Lead, Steve Mcgrath, Richard J. Owen, Sophie Rocks, Jason M. Unrine, Junfeng Zhang

Plant and Soil Sciences Faculty Publications

Nanotechnology has significant economic, health, and environmental benefits, including renewable energy and innovative environmental solutions. Manufactured nanoparticles have been incorporated into new materials and products because of their novel or enhanced properties. These very same properties also have prompted concerns about the potential environmental and human health hazard and risk posed by the manufactured nanomaterials. Appropriate risk management responses require the development of models capable of predicting the environmental and human health effects of the nanomaterials. Development of predictive models has been hampered by a lack of information concerning the environmental fate, behavior and effects of manufactured nanoparticles. The United …

Optimizing The Use Of A Liquid Handling Robot To Conduct A High Throughput Forward Chemical Genetics Screen Of Arabidopsis Thaliana, B. Kirtley Amos, Victoria G. Pook, Seth Debolt

Horticulture Faculty Publications

Chemical genetics is increasingly being employed to decode traits in plants that may be recalcitrant to traditional genetics due to gene redundancy or lethality. However, the probability of a synthetic small molecule being bioactive is low; therefore, thousands of molecules must be tested in order to find those of interest. Liquid handling robotics systems are designed to handle large numbers of samples, increasing the speed with which a chemical library can be screened in addition to minimizing/standardizing error. To achieve a high-throughput forward chemical genetics screen of a library of 50,000 small molecules on Arabidopsis thaliana (Arabidopsis), protocols using a …

The Santa Clara, 2018-04-26, Santa Clara University

The Santa Clara

No abstract provided.

Transcriptomics To Develop Biochemical Network Models In Cyanobacteria, Bridget E. Hegarty, Jordan Peccia, Ratanachat Racharaks

Yale Day of Data

Through targeted genetic manipulations guided by network modeling, we will create a flexible, cyanobacteria-based platform for the production of biofuel-precursors and valuable chemical products. To build gene-metabolite predictive models, we have characterized Synecococcus elongatus sp. UTEX 2973’s (henceforth, UTEX 2973) gene expression and metabolite production under a number of environmental conditions.

Evaluation Of A Novel Finite Element Model Of Active Contraction In The Heart, Xiaoyan Zhang, Zhan-Qiu Liu, Kenneth S. Campbell, Jonathan F. Wenk

Mechanical Engineering Faculty Publications

Finite element (FE) modeling is becoming a widely used approach for the investigation of global heart function. In the present study, a novel model of cellular-level systolic contraction, which includes both length- and velocity-dependence, was implemented into a 3D non-linear FE code. To validate this new FE implementation, an optimization procedure was used to determine the contractile parameters, associated with sarcomeric function, by comparing FE-predicted pressure and strain to experimental measures collected with magnetic resonance imaging and catheterization in the ventricles of five healthy rats. The pressure-volume relationship generated by the FE models matched well with the experimental data. Additionally, …

The Santa Clara, 2018-04-19, Santa Clara University

The Santa Clara

No abstract provided.

2018 - The Twenty-Third Annual Symposium Of Student Scholars

Symposium of Student Scholars Program Books

The full program book from the Twenty-third Annual Symposium of Student Scholars, held on April 19, 2018. Includes abstracts from the presentations and posters.

1918 - Geology And Oil Prospects Of Salinas Valley-Parkfield Area, California; Walter A. English

Miscellaneous Documents and Reports

A 1981 report on an investigation undertaken partly to procure data for the classification of public lands located in the Salinas Valley-Parkfield area of California withdrawn from entry pending classification, and partly to determine areas in which the geologic conditions were favorable for oil prospecting so as to prevent useless expenditures in drilling dry holes in unfavorable areas. The work on which the report was based was done during the field seasons of 1915 and 1916.

Swosu Research And Scholarly Activity Fair 2018, Lisa Appeddu, Cj Smith

SWOSU Research and Scholarly Activity Fair Programs

On behalf of the members of the Southwestern Oklahoma State University (SWOSU) University Research and Scholarly Activity Committee (USRAC) - Welcome to the Twenty-Fifth SWOSU Research and Scholarly Activity Fair! There are 130 poster presentations and 10 oral presentations involving 293 student researchers, writers, presenters, artists, collaborators, and faculty sponsors encompassing activities from the SWOSU College of Pharmacy; SWOSU School of Nursing & Allied Health Sciences; and SWOSU Departments of Art, Communication, & Theatre; Biological Sciences; Business & Computer Science; Chemistry and Physics; Education; Engineering Technology; Language & Literature; Music; Psychology; and Social Sciences. This also includes guest presenters from …

1920 - California's Greatest Opportunity - Reclaiming An Empire--The Valley Of California, Col. R. B. Marshall

Miscellaneous Documents and Reports

Col. Marshall proposed a state-wide engineering project that would provide irrigation water to 12,000,000 acres of land in the Sacramento, San Joaquin, Santa Clara, Livermore and Concord valleys, as well as water for Los Angeles, San Francisco and Bay cities. The water would come from the Sacramento and San Joaquin rivers. He envisioned an increase in the State valuation of $6,000,000,000. Additionally hydro-electric current generation would furnish all the power necessary for construction as well as supply more power than would be needed for use on electric railroads, in municipal lighting, for manufacturing, and for domestic use in homes, and …