+publisher:"Penn State University" +contributor:("Reka Z Albert, Committee Member")

Penn State University

1. Schafer, Phillip Baker. Neuroscience-inspired computational systems for speech recognition under noisy conditions.

Degree: 2015, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/25082

► Humans routinely recognize speech in challenging acoustic environments with background music, engine sounds, competing talkers, and other acoustic noise. However, today's automatic speech recognition (ASR)… (more)

▼ Humans routinely recognize speech in challenging acoustic environments with background music, engine sounds, competing talkers, and other acoustic noise. However, today's automatic speech recognition (ASR) systems perform poorly in such environments. In this dissertation, I present novel methods for ASR designed to approach human-level performance by emulating the brain's processing of sounds. I exploit recent advances in auditory neuroscience to compute neuron-based representations of speech, and design novel methods for decoding these representations to produce word transcriptions. I begin by considering speech representations modeled on the spectrotemporal receptive fields of auditory neurons. These representations can be tuned to optimize a variety of objective functions, which characterize the response properties of a neural population. I propose an objective function that explicitly optimizes the noise invariance of the neural responses, and find that it gives improved performance on an ASR task in noise compared to other objectives. The method as a whole, however, fails to significantly close the performance gap with humans. I next consider speech representations that make use of spiking model neurons. The neurons in this method are feature detectors that selectively respond to spectrotemporal patterns within short time windows in speech. I consider a number of methods for training the response properties of the neurons. In particular, I present a method using linear support vector machines (SVMs) and show that this method produces spikes that are robust to additive noise. I compute the spectrotemporal receptive fields of the neurons for comparison with previous physiological results. To decode the spike-based speech representations, I propose two methods designed to work on isolated word recordings. The first method uses a classical ASR technique based on the hidden Markov model. The second method is a novel template-based recognition scheme that takes advantage of the neural representation's invariance in noise. The scheme centers on a speech similarity measure based on the longest common subsequence between spike sequences. The combined encoding and decoding scheme outperforms a benchmark system in extremely noisy acoustic conditions. Finally, I consider methods for decoding spike representations of continuous speech. To help guide the alignment of templates to words, I design a syllable detection scheme that robustly marks the locations of syllabic nuclei. The scheme combines SVM-based training with a peak selection algorithm designed to improve noise tolerance. By incorporating syllable information into the ASR system, I obtain strong recognition results in noisy conditions, although the performance in noiseless conditions is below the state of the art. The work presented here constitutes a novel approach to the problem of ASR that can be applied in the many challenging acoustic environments in which we use computer technologies today. The proposed spike-based processing… Advisors/Committee Members: Dezhe Jin, Dissertation Advisor/Co-Advisor, John Collins, Committee Member, Reka Z Albert, Committee Member, Patrick James Drew, Committee Member.

Subjects/Keywords: speech recognition; spike code; noise; neural representation

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APA (6^th Edition):

Schafer, P. B. (2015). Neuroscience-inspired computational systems for speech recognition under noisy conditions. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/25082

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Schafer, Phillip Baker. “Neuroscience-inspired computational systems for speech recognition under noisy conditions.” 2015. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/25082.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Schafer, Phillip Baker. “Neuroscience-inspired computational systems for speech recognition under noisy conditions.” 2015. Web. 06 Mar 2021.

Vancouver:

Schafer PB. Neuroscience-inspired computational systems for speech recognition under noisy conditions. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/25082.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Schafer PB. Neuroscience-inspired computational systems for speech recognition under noisy conditions. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/25082

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

2. Skocik, Michael Joseph. Bio-inspired and Neuromorphic Machine Vision System for Analyzing Three-dimensional Data.

Degree: 2016, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/28656

► This dissertation investigates neuron models, which are the basic units of computation in many bio-inspired data analysis systems; neural networks, which are used for abstract… (more)

Subjects/Keywords: Computer Aided Diagnosis; Computer Assisted Radiology; Alzheimer's; Mild Cognitive Impairment; Machine Learning; Machine Vision

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APA (6^th Edition):

Skocik, M. J. (2016). Bio-inspired and Neuromorphic Machine Vision System for Analyzing Three-dimensional Data. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/28656

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Skocik, Michael Joseph. “Bio-inspired and Neuromorphic Machine Vision System for Analyzing Three-dimensional Data.” 2016. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/28656.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Skocik, Michael Joseph. “Bio-inspired and Neuromorphic Machine Vision System for Analyzing Three-dimensional Data.” 2016. Web. 06 Mar 2021.

Vancouver:

Skocik MJ. Bio-inspired and Neuromorphic Machine Vision System for Analyzing Three-dimensional Data. [Internet] [Thesis]. Penn State University; 2016. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/28656.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Skocik MJ. Bio-inspired and Neuromorphic Machine Vision System for Analyzing Three-dimensional Data. [Thesis]. Penn State University; 2016. Available from: https://submit-etda.libraries.psu.edu/catalog/28656

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

3. Zhao, Kang. A multi-level analysis of information and supply flows in social and business networks.

Degree: 2012, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/14614

► Networks are ubiquitous in both the physical world and the cyberspace. They enable the flow of information, materials, services, etc. The common thread running through… (more)

Subjects/Keywords: Social networks; supply-chain networks; inter-organizational networks; information flow; influence; online health community.

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APA (6^th Edition):

Zhao, K. (2012). A multi-level analysis of information and supply flows in social and business networks. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/14614

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zhao, Kang. “A multi-level analysis of information and supply flows in social and business networks.” 2012. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/14614.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zhao, Kang. “A multi-level analysis of information and supply flows in social and business networks.” 2012. Web. 06 Mar 2021.

Vancouver:

Zhao K. A multi-level analysis of information and supply flows in social and business networks. [Internet] [Thesis]. Penn State University; 2012. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/14614.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zhao K. A multi-level analysis of information and supply flows in social and business networks. [Thesis]. Penn State University; 2012. Available from: https://submit-etda.libraries.psu.edu/catalog/14614

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

4. Miller, Aaron James. Characterization of Emergent Synaptic Topologies in Noisy Neural Networks.

Degree: 2012, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/14822

► Learned behaviors are one of the key contributors to an animal's ultimate survival. It is widely believed that the brain's microcircuitry undergoes structural changes when… (more)

▼ Learned behaviors are one of the key contributors to an animal's ultimate survival. It is widely believed that the brain's microcircuitry undergoes structural changes when a new behavior is learned. In particular, motor learning, during which an animal learns a sequence of muscular movements, often requires precisely-timed coordination between muscles and becomes very natural once ingrained. Experiments show that neurons in the motor cortex exhibit precisely-timed spike activity when performing a learned motor behavior, and constituent stereotypical elements of the behavior can last several hundred milliseconds. The subject of this manuscript concerns how organized synaptic structures that produce stereotypical spike sequences emerge from random, dynamical networks. After a brief introduction in Chapter 1, we begin Chapter 2 by introducing a spike-timing-dependent plasticity (STDP) rule that defines how the activity of the network drives changes in network topology. The rule is then applied to idealized networks of leaky integrate-and-fire neurons (LIF). These neurons are not subjected to the variability that typically characterize neurons \emph{in vivo}. In noiseless networks, synapses develop closed loops of strong connectivity that reproduce stereotypical, precisely-timed spike patterns from an initially random network. We demonstrate the characteristics of the asymptotic synaptic configuration are dependent on the statistics of the initial random network. The spike timings of the neurons simulated in Chapter 2 are generated exactly by a computationally economical, nonlinear mapping which is extended to LIF neurons injected with fluctuating current in Chapter 3. Development of an economical mapping that incorporates noise provides a practical solution to the long simulation times required to produce asymptotic synaptic topologies in networks with STDP in the presence of realistic neuronal variability. The mapping relies on generating numerical solutions to the dynamics of a LIF neuron subjected to Gaussian white noise (GWN). The system reduces to the Ornstein-Uhlenbeck first passage time problem, the solution of which we build into the mapping method of Chapter 2. We demonstrate that simulations using the stochastic mapping have reduced computation time compared to traditional Runge-Kutta methods by more than a factor of 150. In Chapter 4, we use the stochastic mapping to study the dynamics of emerging synaptic topologies in noisy networks. With the addition of membrane noise, networks with dynamical synapses can admit states in which the distribution of the synaptic weights is static under spontaneous activity, but the random connectivity between neurons is dynamical. The widely cited problem of instabilities in networks with STDP is avoided with the implementation of a synaptic decay and an activation threshold on each synapse. When such networks are presented with stimulus modeled by a focused excitatory current, chain-like networks can emerge with the addition of an axon-remodeling plasticity… Advisors/Committee Members: Dezhe Jin, Dissertation Advisor/Co-Advisor, Reka Z Albert, Committee Member, Alexay Kozhevnikov, Committee Member, Patrick James Drew, Committee Member.

Subjects/Keywords: learning; STDP; neural network; synaptic topology; synfire chain; event-driven simulation; emergent phenomena; complex network

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Miller, A. J. (2012). Characterization of Emergent Synaptic Topologies in Noisy Neural Networks. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/14822

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Miller, Aaron James. “Characterization of Emergent Synaptic Topologies in Noisy Neural Networks.” 2012. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/14822.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Miller, Aaron James. “Characterization of Emergent Synaptic Topologies in Noisy Neural Networks.” 2012. Web. 06 Mar 2021.

Vancouver:

Miller AJ. Characterization of Emergent Synaptic Topologies in Noisy Neural Networks. [Internet] [Thesis]. Penn State University; 2012. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/14822.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Miller AJ. Characterization of Emergent Synaptic Topologies in Noisy Neural Networks. [Thesis]. Penn State University; 2012. Available from: https://submit-etda.libraries.psu.edu/catalog/14822

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

5. Zesati, Natalie. Predicting Transcription Factor Binding Using Neural Structured Learning.

Degree: 2020, Penn State University

URL: https://etda.libraries.psu.edu/catalog/18406nkz5054

► Transcription Factors (TF) bind to sequence specific deoxyribonucleic acid (DNA) sites. Although a specific TF sequence is likely to exist in a multitude of locations… (more)

Subjects/Keywords: Neural Structured Learning; Convolution Neural Network; NSL; CNN; Transcription Factors

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zesati, N. (2020). Predicting Transcription Factor Binding Using Neural Structured Learning. (Thesis). Penn State University. Retrieved from https://etda.libraries.psu.edu/catalog/18406nkz5054

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zesati, Natalie. “Predicting Transcription Factor Binding Using Neural Structured Learning.” 2020. Thesis, Penn State University. Accessed March 06, 2021. https://etda.libraries.psu.edu/catalog/18406nkz5054.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zesati, Natalie. “Predicting Transcription Factor Binding Using Neural Structured Learning.” 2020. Web. 06 Mar 2021.

Vancouver:

Zesati N. Predicting Transcription Factor Binding Using Neural Structured Learning. [Internet] [Thesis]. Penn State University; 2020. [cited 2021 Mar 06]. Available from: https://etda.libraries.psu.edu/catalog/18406nkz5054.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zesati N. Predicting Transcription Factor Binding Using Neural Structured Learning. [Thesis]. Penn State University; 2020. Available from: https://etda.libraries.psu.edu/catalog/18406nkz5054

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

6. Saha, Rajib. Reconstruction and analysis of genome-scale metabolic models of photosynthetic organisms.

Degree: 2014, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/22798

► The scope and breadth of genome-scale metabolic reconstructions has continued to expand over the last decade. However, only a limited number of efforts exist on… (more)

▼ The scope and breadth of genome-scale metabolic reconstructions has continued to expand over the last decade. However, only a limited number of efforts exist on photosynthetic metabolism reconstruction. Cyanobacteria are an important group of photoautotrophic organisms that can synthesize valuable bio-products by harnessing solar energy. They are endowed with high photosynthetic efficiencies and diverse metabolic capabilities that confer the ability to convert solar energy into a variety of biofuels and their precursors. However, less well studied are the similarities and differences in metabolism of different species of cyanobacteria as they pertain to their suitability as microbial production chassis. Here we assemble, update and compare genome-scale models (iCyt773 and iSyn731) for two phylogenetically related cyanobacterial species, namely Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. Comparisons of model predictions against gene essentiality data reveal a specificity of 0.94 (94/100) and a sensitivity of 1 (19/19) for the Synechocystis iSyn731 model. The diurnal rhythm of Cyanothece 51142 metabolism is modeled by constructing separate (light/dark) biomass equations and introducing regulatory restrictions over light and dark phases. Specific metabolic pathway differences between the two cyanobacteria alluding to different bio-production potentials are reflected in both models. In addition to these cyanobacterial species we also develop a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). The metabolic model Zea mays i1563 contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct evidence for the participation of the reaction in maize was found. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). Recently, we develop a second-generation genome-scale metabolic model for the maize leaf to capture C4 carbon fixation by modeling the interactions between the bundle sheath and mesophyll cells. Condition-specific biomass descriptions are introduced that account for amino acids, fatty acids, soluble sugars, proteins, chlorophyll, lingo-cellulose, and nucleic acids as experimentally measured biomass constituents. Compartmentalization of the model is based on proteomic/transcriptomic data and literature evidence. With the incorporation of the information from MetaCrop and MaizeCyc databases, this updated model spans 5824 genes, 8484 reactions, and 8918 metabolites, an increase of approximately five times the size of the earlier iRS1563 model. Transcriptomic and proteomic data is also used to introduce regulatory constraints in the model to simulate the limited nitrogen condition and glutamine synthetase gln1-3 and… Advisors/Committee Members: Costas D Maranas, Dissertation Advisor/Co-Advisor, Costas D Maranas, Committee Chair/Co-Chair, Andrew Zydney, Committee Member, Howard M Salis, Committee Member, Reka Z Albert, Committee Member.

Subjects/Keywords: Genome-scale model; Cyanobacteria; Zea mays; Cyanothece sp. ATCC51142; Synechocystis sp. PCC6803

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Saha, R. (2014). Reconstruction and analysis of genome-scale metabolic models of photosynthetic organisms. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/22798

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Saha, Rajib. “Reconstruction and analysis of genome-scale metabolic models of photosynthetic organisms.” 2014. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/22798.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Saha, Rajib. “Reconstruction and analysis of genome-scale metabolic models of photosynthetic organisms.” 2014. Web. 06 Mar 2021.

Vancouver:

Saha R. Reconstruction and analysis of genome-scale metabolic models of photosynthetic organisms. [Internet] [Thesis]. Penn State University; 2014. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/22798.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Saha R. Reconstruction and analysis of genome-scale metabolic models of photosynthetic organisms. [Thesis]. Penn State University; 2014. Available from: https://submit-etda.libraries.psu.edu/catalog/22798

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

7. Evans, Garrett Nolan. Two Projects in Theoretical Neuroscience: A Convolution-based Metric for Neural Membrane Potentials and a Combinatorial Connectionist Semantic Network Method.

Degree: 2015, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/25060

► In this work, I present two projects that both contribute to the aim of discovering how intelligence manifests in the brain. The first project is… (more)

▼ In this work, I present two projects that both contribute to the aim of discovering how intelligence manifests in the brain. The first project is a method for analyzing recorded neural signals, which takes the form of a convolution-based metric on neural membrane potential recordings. Relying only on integral and algebraic operations, the metric compares the timing and number of spikes within recordings as well as the recordings’ subthreshold features: summarizing differences in these with a single “distance” between the recordings. Like van Rossum’s (2001) metric for spike trains, the metric is based on a convolution operation that it performs on the input data. The kernel used for the convolution is carefully chosen such that it produces a desirable frequency space response and, unlike van Rossum’s kernel, causes the metric to be first order both in differences between nearby spike times and in differences between same-time membrane potential values: an important trait. The second project is a combinatorial syntax method for connectionist semantic network encoding. Combinatorial syntax has been a point on which those who support a symbol- processing view of intelligent processing and those who favor a connectionist view have had difficulty seeing eye-to-eye. Symbol-processing theorists have persuasively argued that combinatorial syntax is necessary for certain intelligent mental operations, such as reason- ing by analogy. Connectionists have focused on the versatility and adaptability offered by self-organizing networks of simple processing units. With this project, I show that there is a way to reconcile the two perspectives and to ascribe a combinatorial syntax to a connectionist network. The critical principle is to interpret nodes, or units, in the connectionist network as bound integrations of the interpretations for nodes that they share links with. Nodes need not correspond exactly to neurons and may correspond instead to distributed sets, or assemblies, of neurons. Advisors/Committee Members: John C Collins, Dissertation Advisor/Co-Advisor, John C Collins, Committee Chair/Co-Chair, Reka Z Albert, Committee Member, Steven Schiff, Committee Member, Bradley Paul Wyble, Committee Member, Peter Cm Molenaar, Special Member.

Subjects/Keywords: distance measure; membrane potential; spike timing; subthreshold; connectionism; combinatorial syntax; semantic network

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APA (6^th Edition):

Evans, G. N. (2015). Two Projects in Theoretical Neuroscience: A Convolution-based Metric for Neural Membrane Potentials and a Combinatorial Connectionist Semantic Network Method. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/25060

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Evans, Garrett Nolan. “Two Projects in Theoretical Neuroscience: A Convolution-based Metric for Neural Membrane Potentials and a Combinatorial Connectionist Semantic Network Method.” 2015. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/25060.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Evans, Garrett Nolan. “Two Projects in Theoretical Neuroscience: A Convolution-based Metric for Neural Membrane Potentials and a Combinatorial Connectionist Semantic Network Method.” 2015. Web. 06 Mar 2021.

Vancouver:

Evans GN. Two Projects in Theoretical Neuroscience: A Convolution-based Metric for Neural Membrane Potentials and a Combinatorial Connectionist Semantic Network Method. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/25060.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Evans GN. Two Projects in Theoretical Neuroscience: A Convolution-based Metric for Neural Membrane Potentials and a Combinatorial Connectionist Semantic Network Method. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/25060

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

8. Barrows, Clayton Paul. Flexible Network Topologies and The Smart Grid in Electric Power Systems.

Degree: 2013, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/16420

► Recently, the demands placed on the electrical transmission system have increased disproportionally relative to the investments made in the system. As a result, the system… (more)

▼ Recently, the demands placed on the electrical transmission system have increased disproportionally relative to the investments made in the system. As a result, the system has become increasingly constrained, hindering the ability of the transmission system to facilitate competition among generators. New transmission can fix this problem, but is difficult to construct due to political, environment and financial concerns. Topological reconfigurations of the transmission system could improve the efficiency of power system operations and represents a particularly valuable application of the smart grid. However, in practice the topology reconfiguration problem is difficult to solve. Reconfiguration of the transmission network can be accomplished through topology optimization. The act of temporarily removing transmission lines from service, known as “transmission switching”, can relieve transmission congestion and enable the re-dispatch of lower cost generators. Optimal Transmission Switching (OTS) co-optimizes the generator dispatch and the network topology and has been shown to minimize costs when applied to test systems. When considering every line in the network as switchable, the problem scales such that 2#-lines distinct network topologies must be considered. Real systems often contain tens of thousands of transmission lines. The size and complexity of OTS has limited optimal solutions to small test systems and linearized DC power flow models. A Marginal Analysis of OTS investigates the predictors of the probability with which each transmission line is optimally switched and the contribution of each line to cost savings. The analysis leads to two conclusions. First, the majority of cost savings can be achieved through switching a small subset of lines. And second, the effects of transmission switching are relatively localized. These conclusions lead to the development of two strategies to reduce the computational complexity of the OTS problem. Network partitioning methods are used to iv generate sub-networks where the OTS problem can be solved in parallel and then aggregated to form a complete system solution. Additionally, a candidate switchable line screen based on the Line Outage Distribution Factors is presented to identify a superset of switchable lines. Thus far in the evolution of transmission topology and generation dispatch co-optimization problems, optimal solutions have been obtained using a linearized de-coupled power flow model. While this model is useful for many approximations, it fails to describe reactive power flows and voltage magnitudes; two critical parameters when considering the feasibility of a generation dispatch. However, topology optimization presents an intractable problem when implemented in the nonlinear and non-convex AC power flow model. The discrepancies between the AC and linearized DC power flow models have created speculation that the cost savings generated by optimizing transmission topology in the DC network may not translate into cost savings in the AC network. Using a method… Advisors/Committee Members: Seth Adam Blumsack, Dissertation Advisor/Co-Advisor, Reka Z Albert, Committee Member, Andrew Nathan Kleit, Committee Member, Luis Ayala, Committee Member, Paul Hines, Committee Member.

Subjects/Keywords: Power System Analysis; Optimization; Electricity Markets; Complex Network Science

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APA (6^th Edition):

Barrows, C. P. (2013). Flexible Network Topologies and The Smart Grid in Electric Power Systems. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/16420

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Barrows, Clayton Paul. “Flexible Network Topologies and The Smart Grid in Electric Power Systems.” 2013. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/16420.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Barrows, Clayton Paul. “Flexible Network Topologies and The Smart Grid in Electric Power Systems.” 2013. Web. 06 Mar 2021.

Vancouver:

Barrows CP. Flexible Network Topologies and The Smart Grid in Electric Power Systems. [Internet] [Thesis]. Penn State University; 2013. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/16420.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Barrows CP. Flexible Network Topologies and The Smart Grid in Electric Power Systems. [Thesis]. Penn State University; 2013. Available from: https://submit-etda.libraries.psu.edu/catalog/16420

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

9. Sawant, Neela Kamlakar. Statistical Modeling of Image Semantics from Imperfectly Labeled Data Sets.

Degree: 2013, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/18875

► Computer vision is an integral aspect of cognitive computing with diverse applications in medical diagnostics and health-care, communication, transportation, entertainment, and data management. It enables… (more)

▼ Computer vision is an integral aspect of cognitive computing with diverse applications in medical diagnostics and health-care, communication, transportation, entertainment, and data management. It enables actionable semantic-sensitive inferences by autonomously processing visual inputs in the form of images and videos in related problems of object recognition, object detection, scene analysis, image annotation, and automatic image tagging. Supervised learning is a common paradigm of semantic inference, i.e., learning the association between words and visual features, through a pre-selected labeled training data set. Collecting the labeled training data is a laborious process that is arguably the biggest bottleneck in scalable machine learning. To generalize the scope, it is imperative to devise self-learning machines to substitute human input in seeking quality training data, inferring the linguistic and semantic relationships between different concepts, and extending the scope to real-world applications. This dissertation offers new algorithms to extend the scope of image annotation with minimal manual supervision. The first major contribution is a mixture modeling technique to cluster noisy data. Using this technique, I developed the ARTEMIS system of training data selection from weakly-labeled images on social media sharing Websites. An ARTEMIS-trained annotation system has a similar performance to that trained using manually collected data. Secondly, I consider the issue of generating personalized annotations, essentially learning user-specific mappings from visual features to their semantic labels. A light-weight personalization model is developed using a transfer learning framework and the analysis of local social networks. Finally, I present a domain adaptation technique where training data from a labeled domain is leveraged to annotate images from an unlabeled target domain. This technique is used to recognize emotions from paintings using the recorded emotional response of human subjects on natural photographs. The research presented in this dissertation advances the technology to make sense of image semantics in challenging real-world scenarios by leveraging user-contributed data on photo sharing Websites. Advisors/Committee Members: James Z Wang, Dissertation Advisor/Co-Advisor, Jia Li, Dissertation Advisor/Co-Advisor, John Millar Carroll, Committee Member, C Lee Giles, Committee Member, Reka Z Albert, Committee Member.

Subjects/Keywords: statistical modeling; image annotation; ARTEMIS; instance-weighting; mixture models; transfer learning; domain adaptation

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APA (6^th Edition):

Sawant, N. K. (2013). Statistical Modeling of Image Semantics from Imperfectly Labeled Data Sets. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/18875

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sawant, Neela Kamlakar. “Statistical Modeling of Image Semantics from Imperfectly Labeled Data Sets.” 2013. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/18875.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sawant, Neela Kamlakar. “Statistical Modeling of Image Semantics from Imperfectly Labeled Data Sets.” 2013. Web. 06 Mar 2021.

Vancouver:

Sawant NK. Statistical Modeling of Image Semantics from Imperfectly Labeled Data Sets. [Internet] [Thesis]. Penn State University; 2013. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/18875.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sawant NK. Statistical Modeling of Image Semantics from Imperfectly Labeled Data Sets. [Thesis]. Penn State University; 2013. Available from: https://submit-etda.libraries.psu.edu/catalog/18875

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

10. Shuster, Mitchell. DEVELOPMENT AND CHARACTERIZATION OF SMALL-MOLECULE-FUNCTIONALIZED CAPTURE SURFACES .

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/12423

► Self-assembly and nanofabrication techniques were combined with chemistry and neuroscience principles to produce small-molecule-functionalized surfaces capable of selective molecular recognition of large-molecule binding partners. To… (more)

▼ Self-assembly and nanofabrication techniques were combined with chemistry and neuroscience principles to produce small-molecule-functionalized surfaces capable of selective molecular recognition of large-molecule binding partners. To passivate biosensing substrates, self-assembled monolayers composed of oligo(ethylene glycol)alkanethiols (OEGs) were formed on gold substrates. To enable functionalization of monolayers with a dilute, non-phase-separated distribution of small-molecule probes, insertion-directed self assembly was used to intercalate OEGs with different terminal functional groups into existing monolayer matrices. Carbodiimide coupling chemistry was used to derivatize the dilute functional groups with small-molecule probes. Initially, a prototypical small-molecule neurotransmitter, serotonin, was used to produce small-molecule-functionalized substrates. Exploiting the knowledge gained from functionalizing surfaces with serotonin, a modified chemistry was used to attach the serotonin biological precursor, 5 hydroxytryptophan (5 HTP), to similarly prepared surfaces via its ectopic carboxyl group. 5 HTP surfaces were shown to be capable of selectively binding membrane-associated serotonin receptor proteins. In contrast, serotonin-functionalized surfaces fail to bind these receptors. Because native serotonin receptors bind serotonin in solution, these results suggest that all functional groups of serotonin are necessary for receptor recognition. To enhance the breadth of applications of such surfaces, the creation of chemically patterned surfaces was investigated. Both photolithographically assisted chemical patterning and microcontact insertion printing were used to create spatially controlled regions of inserted tether molecules. New probes, dopamine and biotin, were successfully used on these surfaces. Dopamine was functionalized in situ, while prefunctionalized biotinylated OEGs were used to create biotin-functionalized surfaces. Both types of surfaces were capable of capturing binding partners with high affinity for the small-molecule probes on the surfaces in single- and mixed-protein solutions. In addition to the biocapture properties of OEG monolayers, how insertion-directed self-assembly and chemical functionalization of OEGs compared to n alkanethiols were investigated. Differences in protonation and monomer/dimer ratios of the carboxy group of carboxy-terminated OEG vs n alkanethiol molecules on surfaces were found. Additionally, the fraction of insertion of OEGs into n-alkanethiolate monolayers under identical conditions was observed to vary based on the terminal functional groups of the OEG molecules. It was also found that single-component monolayers of OEGs were more amenable to chemical reaction than n alkanethiolate monolayers. Advisors/Committee Members: Paul S Weiss, Dissertation Advisor/Co-Advisor, Paul S Weiss, Committee Chair/Co-Chair, Anne M Andrews, Committee Member, Vincent Henry Crespi, Committee Chair/Co-Chair, Reka Z Albert, Committee Member, Jun Huang, Committee Member.

Subjects/Keywords: quartz crystal microgravimetry; infrared reflection absorption spectroscopy; oligo(ethylene glycol); small molecule functionalization; microcontact insertion printing; alkanethiol; self-assembled monolayer

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Shuster, M. (2011). DEVELOPMENT AND CHARACTERIZATION OF SMALL-MOLECULE-FUNCTIONALIZED CAPTURE SURFACES . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/12423

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Shuster, Mitchell. “DEVELOPMENT AND CHARACTERIZATION OF SMALL-MOLECULE-FUNCTIONALIZED CAPTURE SURFACES .” 2011. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/12423.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Shuster, Mitchell. “DEVELOPMENT AND CHARACTERIZATION OF SMALL-MOLECULE-FUNCTIONALIZED CAPTURE SURFACES .” 2011. Web. 06 Mar 2021.

Vancouver:

Shuster M. DEVELOPMENT AND CHARACTERIZATION OF SMALL-MOLECULE-FUNCTIONALIZED CAPTURE SURFACES . [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/12423.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Shuster M. DEVELOPMENT AND CHARACTERIZATION OF SMALL-MOLECULE-FUNCTIONALIZED CAPTURE SURFACES . [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/12423

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

11. Ranganathan, Sridhar. Using Computations to Analyze and Redesign Metabolism.

Degree: 2012, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/8855

► With the availability genome-wide datasets for various organisms, research in biology has moved towards a systems-level analysis that portrays a comprehensive picture of cellular physiology.… (more)

▼ With the availability genome-wide datasets for various organisms, research in biology has moved towards a systems-level analysis that portrays a comprehensive picture of cellular physiology. In the recent past, complete inventories of all the known genetic capabilities of microorganisms have been built into computational models. In this regard, we present studies aimed at making use of computational models of metabolism and developing computational algorithms that help in analyzing and redesigning the metabolism of microorganisms. We use procedures developed in this thesis as a predictive tool for exploring genetic manipulations that lead to the overproduction of value-added biochemicals. The key aims addressed in this work are - Aim 1: to assemble novel biosynthesis routes from a known substrate or starting metabolite to biofuel molecules, Aim 2: to develop computational / mathematical procedures that suggest genetic interventions in microorganisms that lead to the overproduction of value-added biochemicals. Throughout this work, we rely on systems biology, graph-theory and novel optimization approaches (i.e. bilevel optimization) to address problems related to Aims 1 and 2 in metabolic engineering. The potential of genetically engineering “user-friendly” microbes with non-native biosynthetic gene cascades has been identified as a promising method to produce biofuels during fermentation. To address this problem in Aim 1, we introduce a graph-based pathway prospecting approach that can help uncover all possible metabolic pathways to biofuel molecules such as 1-butanol. We derive computational predictions for these pathways by culling information from databases such as BRENDA, and KEGG. Subsequently under Aim 2, we introduce a novel computational strain redesign procedure called OptForce custom-made to predict genetic interventions (i.e. up-/down-regulations, knockouts, knock-ins) that guarantees a pre-specified yield for the target biofuel molecule. In addition to its capability of predicting multiple genetic interventions at a time, OptForce is also primed to incorporate experimental data (i.e. metabolic flux analysis data) within the procedure before starting the procedure for redesign. In this work, we demonstrate the validity of OptForce by comparing computational predictions with metabolic engineering experiments for overproducing various biochemicals such as succinate, 1-butanol (from the pathways identified under Aim 1), flavanones, fatty and amino acids in Escherichia coli. Advisors/Committee Members: Costas D Maranas, Dissertation Advisor/Co-Advisor, Costas D Maranas, Committee Chair/Co-Chair, Reka Z Albert, Committee Member, Eric Thomas Harvill, Committee Member, Howard M Salis, Committee Member, Cooduvalli S Shashikant, Committee Member.

Subjects/Keywords: Metabolic Engineering; Optimization

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ranganathan, S. (2012). Using Computations to Analyze and Redesign Metabolism. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/8855

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ranganathan, Sridhar. “Using Computations to Analyze and Redesign Metabolism.” 2012. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/8855.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ranganathan, Sridhar. “Using Computations to Analyze and Redesign Metabolism.” 2012. Web. 06 Mar 2021.

Vancouver:

Ranganathan S. Using Computations to Analyze and Redesign Metabolism. [Internet] [Thesis]. Penn State University; 2012. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/8855.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ranganathan S. Using Computations to Analyze and Redesign Metabolism. [Thesis]. Penn State University; 2012. Available from: https://submit-etda.libraries.psu.edu/catalog/8855

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

12. Kumar, Nitin. Ab Initio Molecular Dynamics Study of Water Dissociation and Proton Dynamics on Rutile and Cassiterite Surfaces.

Degree: 2012, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/13748

► Metal oxides have numerous applications in our everyday lives and in most of these applications their interaction with water is inevitable. Hence, it is important… (more)

▼ Metal oxides have numerous applications in our everyday lives and in most of these applications their interaction with water is inevitable. Hence, it is important to understand the interactions that occur at the water/metal oxide interfaces. In this dissertation, we have used ab initio molecular dynamics simulations to study these interactions. In particular, we will study the (110) surfaces of the commonly occurring natural polymorphs of titanium dioxide (TiO2) and tin dioxide (SnO2) known as rutile and cassiterite, respectively. A detailed analysis is presented for the structure of water above the rutile (110) surface. We find three distinct layers of water that are identified as L1, L2 and L3. The water molecules in L1 layer are covalently bonded with the metal atoms in the surface. The L2 layer is highly structured, which is in good agreement with the X-ray studies. The water molecules in this layer adsorb at two well-defined sites. The most prominent location is above and around the bridging oxygen. The other site is located above and between the two terminal oxygens from the L1 layer. The water molecules in the L3 layer do not show any specific adsorption preference. We show that the preferential adsorption sites, in L2 water layer, are produced by strong hydrogen bonds (H-bonds) between the surface and the water layer above the surface. The strength of these H-bonds is estimated from the broadening of the corresponding stretching mode of the vibrational band. The total vibrational spectrum from our ab initio simulations is in excellent agreement with those obtained from the inelastic neutron scattering experiments. We compare the proton jump processes in the hydration layer on both rutile (110) and cassiterite (110) surfaces. A set of five simulations is done, for both surfaces, to remove the effect of initial configuration on the simulation results. These simulations differ in the dissociation level of the adsorbed water molecules in the initial configurations. We find that all five simulations equilibrate to ~25% and ~60% water dissociation level on rutile and cassiterite, respectively. This dissociation level is dynamical and both surfaces exhibit proton jumping events for the whole time of the simulation and throughout the whole surface. The cassiterite surface has three times higher proton jumping events than rutile surface. The higher proton jump activity on cassiterite is produced by stronger H-bond between the surface and the water layer above the surface. We find that the stronger covalent and ionic interaction, due to the difference in the electronic structure, leads to stronger H-bond on cassiterite. In general, we find that the H-bonds are stronger on cassiterite than on rutile surface. Among these, the bridging oxygen atoms form the strongest H-bonds between the surface and the hydration layer. Thus, the cassiterite surface has the highest proton jump activity, around 10 times greater than the rutile surface. Another surface property that provides insight into the interaction of the water with… Advisors/Committee Members: Jorge Osvaldo Sofo, Dissertation Advisor/Co-Advisor, Jorge Osvaldo Sofo, Committee Chair/Co-Chair, Renee Denise Diehl, Committee Member, Reka Z Albert, Committee Member, Coray M Colina, Committee Member.

Subjects/Keywords: rutile(110); interface; rutile water interface; proton jump; cassiterite water interface; water dissociation; ab initio

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kumar, N. (2012). Ab Initio Molecular Dynamics Study of Water Dissociation and Proton Dynamics on Rutile and Cassiterite Surfaces. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/13748

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Kumar, Nitin. “Ab Initio Molecular Dynamics Study of Water Dissociation and Proton Dynamics on Rutile and Cassiterite Surfaces.” 2012. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/13748.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Kumar, Nitin. “Ab Initio Molecular Dynamics Study of Water Dissociation and Proton Dynamics on Rutile and Cassiterite Surfaces.” 2012. Web. 06 Mar 2021.

Vancouver:

Kumar N. Ab Initio Molecular Dynamics Study of Water Dissociation and Proton Dynamics on Rutile and Cassiterite Surfaces. [Internet] [Thesis]. Penn State University; 2012. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/13748.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Kumar N. Ab Initio Molecular Dynamics Study of Water Dissociation and Proton Dynamics on Rutile and Cassiterite Surfaces. [Thesis]. Penn State University; 2012. Available from: https://submit-etda.libraries.psu.edu/catalog/13748

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

13. Cui, Liying. Mathematical theory of service composition and service networks .

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/11505

► This dissertation addresses the theoretical foundations of service composition and develops network based techniques, mathematical programming, and stochastic models for service composition. For the first… (more)

▼ This dissertation addresses the theoretical foundations of service composition and develops network based techniques, mathematical programming, and stochastic models for service composition. For the first time, a mathematical theory, which forms the foundation to define service science as a rigorous discipline is explored. The theorems of solution existence and convergence are generated. Mutuality/Duality theory of service space and concept space is established. The Concept Service (CS) network matrix is developed to study the network structure of service composition. The potential of CS network provides insights to identify important services and concepts. This information is used to connect the initial query with sub-components in CS network, thus reducing the computational time for the planning algorithms. A set of heuristic service composition algorithms is developed based on CS network matrix. Based on the mathematical theory established, three types of multi-criteria programming models are designed to find optimal service composition solutions for the offline-planning problem. The three types of mathematical programming models are: Multi Criteria Programming(MCP), Multi Criteria Goal Programming for Optimal composition(MCGPO) and Multi Criteria Goal Programming for Non-optimal composition(MCGPN). MCP model can generate an optimal solution if solutions satisfying all the customer’s functional and nonfunctional requirements exist. In addition, the MCGPO model allows to automatically select a trade-off among the objectives according to the customers’ preferences. MCGPN model is fast for generating satisficing solutions. Stochastic models are developed to compose service queries under uncertainty. In these models, nested compound work flow and service workload are considered. The algorithms directly utilize prior information of the potential of Concept Service (CS) network matrix to generate a transition matrix. This offers a fast and convenient approach for real time service composition to capture the uncertainty and dynamic phenomena. Finally, possible applications of service composition in product design, global manufacturing, supply chain and resource allocation are discussed. Advisors/Committee Members: Soundar Kumara, Dissertation Advisor/Co-Advisor, Soundar Kumara, Committee Chair/Co-Chair, Arunachalam Ravindran, Committee Member, Tao Yao, Committee Member, Hong Xu, Committee Member, Reka Z Albert, Committee Member, Dongwon Lee, Committee Member.

Subjects/Keywords: dynamic programming; service composition; complex networks; mathematical theory; concept service (CS) network matrix; goal programming; enterprise integration

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cui, L. (2011). Mathematical theory of service composition and service networks . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/11505

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Cui, Liying. “Mathematical theory of service composition and service networks .” 2011. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/11505.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Cui, Liying. “Mathematical theory of service composition and service networks .” 2011. Web. 06 Mar 2021.

Vancouver:

Cui L. Mathematical theory of service composition and service networks . [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/11505.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Cui L. Mathematical theory of service composition and service networks . [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/11505

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

14. Foley, Thomas Thomassen. Statistical Mechanics of Coarse-Graining.

Degree: 2017, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/14810ttf110

► The systems scientists study are becoming increasingly complex while the data collected grows in both magnitude and dimension. This relentless advancement necessitates the utilization of… (more)

▼ The systems scientists study are becoming increasingly complex while the data collected grows in both magnitude and dimension. This relentless advancement necessitates the utilization of models, especially simplifying models, to make efficient use of the data. Of course, models have long served as essential tools in science, but the utility of simplifying, or coarse-grained, models is greater than ever before (even outside the sciences) owing to this explosion in data. However, their tremendous potential is hindered by outstanding challenges concerning their optimal construction and appropriate use. Among other challenges, it is generally unclear what effect the simplifications used – which gives the coarse-grained model many of its desirable features – have upon the model's ability to describe the phenomena of interest. As one specific example, coarse-grained modeling typically relies upon physical intuition to inform the choice of representation for the system under consideration, which has become untenable as researchers model more complex systems. In this thesis, I present progress on the fundamentals of modeling, in the equilibrium statistical mechanics setting, by focusing on the basic questions that arise when constructing coarse-grained models. Particular attention is given to the role of the representation (or mapping) in determining the behavior of the coarsened system, which may be the least well understood step in model construction. This work carefully considers the statistical mechanics of the coarse-graining procedure as applied to the simple Gaussian network model (GNM), a linear mass-and-spring system that can also be viewed as a complex network, for which an exact renormalization is derived. I present an exact thermodynamic decomposition of the potential of mean force (PMF), which is the the central object in coarse-grained models. The consequences of this decomposition into entropic and energetic terms (a free energy) are illustrated by considering the variation with resolution of these terms for the coarsening of the GNM. This work provides a clarifying and concrete exposition of some long-held notions among model builders, in addition to suggesting some candidate principles for optimal model construction. Based upon this foundational work, I develop a statistical mechanics framework for studying the relationship between model representation and quality. Utilizing Monte Carlo simulations and free energy reweighting, I present the picture of a `model-scape', in analogy to free energy landscape, which is composed of: representations, which serve as `coordinates'; models, which serve as `configurations'; and weights, which are induced by varying combinations of energy functions and artificial temperatures. Employing the full statistical mechanics machinery and drawing heavily on analogy to physical systems, I explore and characterize this space, thus revealing the properties of this space. Two of our findings concerning the role of representation in… Advisors/Committee Members: William George Noid, Dissertation Advisor/Co-Advisor, Jorge Osvaldo Sofo, Committee Chair/Co-Chair, Reka Z Albert, Committee Member, Lu Bai, Committee Member, Lu Bai, Outside Member.

Subjects/Keywords: Coarse-graining; Modeling; Renormalization; Statistical Mechanics; Gaussian Network Model; Complex Networks; Community Detection; Model Selection; Phase Transitions

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Foley, T. T. (2017). Statistical Mechanics of Coarse-Graining. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/14810ttf110

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Foley, Thomas Thomassen. “Statistical Mechanics of Coarse-Graining.” 2017. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/14810ttf110.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Foley, Thomas Thomassen. “Statistical Mechanics of Coarse-Graining.” 2017. Web. 06 Mar 2021.

Vancouver:

Foley TT. Statistical Mechanics of Coarse-Graining. [Internet] [Thesis]. Penn State University; 2017. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/14810ttf110.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Foley TT. Statistical Mechanics of Coarse-Graining. [Thesis]. Penn State University; 2017. Available from: https://submit-etda.libraries.psu.edu/catalog/14810ttf110

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

15. Zomorrodi, Ali Reza. Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities.

Degree: 2012, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/15389

► Genome-scale metabolic reconstructions are increasingly becoming available for a wide range of microorganisms. Given the inherent complexity of these reconstructions on one hand and their… (more)

▼ Genome-scale metabolic reconstructions are increasingly becoming available for a wide range of microorganisms. Given the inherent complexity of these reconstructions on one hand and their growing influence on biological, biotechnological and biomedical research on the other hand, it is timely to develop new analysis and modeling tools to improve their predictive ability, elucidate and quantify the full range of metabolic capabilities of the underlying microbial system, and provide guidance for metabolic engineering efforts. The central theme of this dissertation is the development and deployment of efficient mathematical modeling approaches, and in particular optimization-based algorithms, for the curation, analysis and redesign of metabolic networks of single and multi-species microbial systems. First, an efficient optimization-based procedure, namely SL Finder, is introduced for the targeted enumeration of multi-gene (and by extension multi-reaction) synthetic lethals using genome-scale metabolic models. The complete identification of all double and triple gene and reaction synthetic lethals as well as some quadruple and higher order ones using the iAF1260 metabolic model of E. coli uncovered complex patterns of network robustness and gene/reaction utilization and interdependence thereby providing a bird’s-eye-view of the avenues available for redirecting metabolism. Subsequently, a systematic optimization-based protocol is presented for the curation of metabolic models using multi-gene deletion (i.e., synthetic lethal) experiments. By using the existing and developed curation procedures, 90 distinct modifications for the iMM904 metabolic model of S. cerevisiae along with several regulatory constraints were identified and vetted using literature sources. Incorporation of the suggested modifications led to substantial improvements in the prediction accuracy of the iMM904 model for essentiality and synthetic lethality data. Next, a comprehensive flux balance analysis (FBA) framework, called OptCom, is introduced for the metabolic modeling and analysis of microbial communities. In contrast to earlier FBA approaches that are based on optimization problems with a single objective function, OptCom relies on a multi-level and multi-objective optimization formulation to properly describe trade-offs between individual vs. community level fitness criteria. The applicability of OptCom is demonstrated by modeling three different microbial communities of varying complexities to uncover the inter-species interactions, identify the optimality levels of growth for the species involved, and examine the possibility of adding a new member to an existing microbial community. In next part, the OptForce procedure is employed as a computational strain design tool to identify the minimal set of metabolic interventions leading to overproduction of L-serine in E. coli. The suggested interventions include not only straightforward upregulation of the terminal pathway but also non-intuitive manipulations distant from the target product.… Advisors/Committee Members: Costas D Maranas, Dissertation Advisor/Co-Advisor, Costas D Maranas, Committee Chair/Co-Chair, Ali Borhan, Committee Member, Howard M Salis, Committee Member, Reka Z Albert, Committee Member.

Subjects/Keywords: Metabolic networks; Flux balance analysis; Metabolic Enginnering; Optimization; Systems biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zomorrodi, A. R. (2012). Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/15389

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zomorrodi, Ali Reza. “Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities.” 2012. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/15389.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zomorrodi, Ali Reza. “Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities.” 2012. Web. 06 Mar 2021.

Vancouver:

Zomorrodi AR. Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities. [Internet] [Thesis]. Penn State University; 2012. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/15389.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zomorrodi AR. Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities. [Thesis]. Penn State University; 2012. Available from: https://submit-etda.libraries.psu.edu/catalog/15389

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

16. Kumar, Sushant. Molecular principles of folding upon binding processes in disordered proteins: a computational case study .

Degree: 2013, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/19811

► Proteins are dynamic biomolecules which undergo structural fluctuations to adopt multiple conformations while performing important biological functions, such as catalysis and cell regulation. A wide… (more)

▼ Proteins are dynamic biomolecules which undergo structural fluctuations to adopt multiple conformations while performing important biological functions, such as catalysis and cell regulation. A wide range of debilitating human diseases including Alzheimer’s, Huntington’s, and Parkinson’s disease arise from improper conformational transition of proteins. These protein conformational disorders (PCD), results from misfolding and protein aggregation. Intrinsically disordered proteins are special class of proteins that are frequently implicated in misfolding events due to lack of a well defined structure. These proteins demonstrate remarkable structural plasticity by coupling their folding to binding of appropriate ligands. In this coupled folding-binding process, protein domains that are disordered in solution adopt well defined three dimensional structures upon binding a ligand. In this work, we employed native topology based Go-type models to investigate the coupled folding-binding mechanism for the disordered C-terminal domain of phosphatase protein(FCP1) to bind the ordered Rap74 subunit of transcription factor protein (TFIIF). The interaction between these two proteins is considered vital for the regulation of DNA transcription. Our analyses reveal the mechanism and dynamics of the two proteins as they approach and bind each other. The simulations predict that the disordered FCP1 adopts partially folded structure prior to binding and complete its folding upon binding Rap74. Our results also elucidate the impact of residual structure, binding and folding cooperativity, and non-native interactions along with long-ranged electrostatics. The primary aim of this work was to obtain better mechanistic understanding of various physical factors in influencing the coupled folding and binding events commonly observed among disordered proteins. Advisors/Committee Members: William George Noid, Dissertation Advisor/Co-Advisor, William George Noid, Committee Chair/Co-Chair, Arthur Mallay Lesk, Committee Member, Michael Axtell, Committee Member, Reka Z Albert, Committee Member.

Subjects/Keywords: IDPs; Coupled folding-binding; FCP1-Rap74; Structure-based model; Coarse-grained simulations

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kumar, S. (2013). Molecular principles of folding upon binding processes in disordered proteins: a computational case study . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/19811

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Kumar, Sushant. “Molecular principles of folding upon binding processes in disordered proteins: a computational case study .” 2013. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/19811.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Kumar, Sushant. “Molecular principles of folding upon binding processes in disordered proteins: a computational case study .” 2013. Web. 06 Mar 2021.

Vancouver:

Kumar S. Molecular principles of folding upon binding processes in disordered proteins: a computational case study . [Internet] [Thesis]. Penn State University; 2013. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/19811.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Kumar S. Molecular principles of folding upon binding processes in disordered proteins: a computational case study . [Thesis]. Penn State University; 2013. Available from: https://submit-etda.libraries.psu.edu/catalog/19811

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

17. Veeraraghavan, Narayanan. CATALYTIC AND STRUCTURAL ROLES OF NUCLEOBASES AND METAL IONS IN SMALL RIBOZYMES: NEW INSIGHTS FROM CALCULATIONS AND COMPARISON TO EXPERIMENTS .

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/11987

► The hepatitis delta virus (HDV) ribozyme is a small self-cleaving RNA with a compact tertiary structure and buried active site that functions to cleave an… (more)

▼ The hepatitis delta virus (HDV) ribozyme is a small self-cleaving RNA with a compact tertiary structure and buried active site that functions to cleave an internal phosphodiester bond and linearize concatemers during the rolling-circle genome replication of the virus. Crystal structures of the ribozyme have been solved in both precleaved and product forms and reveal an intricate network of interactions that conspire to catalyze bond cleavage. In addition, extensive biochemical studies have been performed to work out a mechanism for bond cleavage in which C75 and a magnesium ion catalyze the reaction by general acid-base chemistry. Some questions that have remained unclear in this and other ribozymes is the nature of long-distance communication between peripheral regions of the RNA and the buried active site, the roles of metal ions within and near the active site, and the structural effects of varying pH and its consequent impact on catalysis. We performed molecular dynamics simulations and non-linear Poisson Boltzmann electrostatic calculations on the HDV ribozyme in the precleaved and product forms and assessed the above probing questions. Overall, these studies indicate that small functional RNAs have the potential to communicate interactions over long distances, and that wild-type RNAs may have evolved ways to prevent such interactions from interfering with catalysis. We identified a rare reverse G•U wobble close to the active site and show that this motif in conjunction with surrounding phosphates forms an anionic pocket in the active site. This anionic pocket likely serves to bind metal ions and to help shift the pKa of the catalytic nucleobase, C75. Thus, the reverse G•U wobble motif serves to organize two catalytic elements, a metal ion and catalytic nucleobase, within the active site of the HDV ribozyme. We further identified two types of Mg2+ ions associated with the ribozyme, chelated and diffuse, at the reverse and standard G•U wobbles, respectively, which appear to contribute to catalysis and stability, respectively. These two metal ion sites exhibit relatively independent behavior. Protonation of C75 was observed to locally organize the active site in a manner that facilitates the catalytic mechanism, in which C75+ acts as a general acid and Mg2+ as a Lewis acid. The simulations also indicated that the overall structure and thermal motions of the ribozyme are not significantly influenced by the catalytic Mg2+ interaction or C75 protonation. This is suggestive of a reaction pathway of the ribozyme dominated by small local motions at the active site rather than large-scale global conformational changes. These results are consistent with a wealth of experimental data and pave the way for a greater understanding of structure-function relationships and the role of metal ions in RNA. Advisors/Committee Members: Prof Sharon Hammes Schiffer, Dissertation Advisor/Co-Advisor, Philip C. Bevilacqua, Committee Chair/Co-Chair, Sharon Hammes Schiffer, Committee Chair/Co-Chair, William George Noid, Committee Member, Andrey S Krasilnikov, Committee Member, Reka Z Albert, Committee Member.

Subjects/Keywords: NLPB; reverse GU wobble; wobble; ribozyme; RNA; molecular dynamics; HDV

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Veeraraghavan, N. (2011). CATALYTIC AND STRUCTURAL ROLES OF NUCLEOBASES AND METAL IONS IN SMALL RIBOZYMES: NEW INSIGHTS FROM CALCULATIONS AND COMPARISON TO EXPERIMENTS . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/11987

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Veeraraghavan, Narayanan. “CATALYTIC AND STRUCTURAL ROLES OF NUCLEOBASES AND METAL IONS IN SMALL RIBOZYMES: NEW INSIGHTS FROM CALCULATIONS AND COMPARISON TO EXPERIMENTS .” 2011. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/11987.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Veeraraghavan, Narayanan. “CATALYTIC AND STRUCTURAL ROLES OF NUCLEOBASES AND METAL IONS IN SMALL RIBOZYMES: NEW INSIGHTS FROM CALCULATIONS AND COMPARISON TO EXPERIMENTS .” 2011. Web. 06 Mar 2021.

Vancouver:

Veeraraghavan N. CATALYTIC AND STRUCTURAL ROLES OF NUCLEOBASES AND METAL IONS IN SMALL RIBOZYMES: NEW INSIGHTS FROM CALCULATIONS AND COMPARISON TO EXPERIMENTS . [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/11987.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Veeraraghavan N. CATALYTIC AND STRUCTURAL ROLES OF NUCLEOBASES AND METAL IONS IN SMALL RIBOZYMES: NEW INSIGHTS FROM CALCULATIONS AND COMPARISON TO EXPERIMENTS . [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/11987

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

18. Chen, Ke. GRANULAR MATERIALS UNDER VIBRATION AND THERMAL CYCLES .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/8811

► We report flow rate measurement of granular materials from a lab size silo with and without sinusoidal vibration, and the flows from a jammed container… (more)

▼ We report flow rate measurement of granular materials from a lab size silo with and without sinusoidal vibration, and the flows from a jammed container under mechanical shocks. We also report the investigation of fragility in granular materials using controlled cyclic temperature variation, or thermal cycling that induces microscopic changes in the size of the grains and the container. When placed under sinusoidal vibration, the flow rate or flux from an unjammed container decreases with the peak velocity of the vibration, and becomes a constant at the highest peak velocities. The flux under vibration follows a 5/2 power scaling rule to corrected orifice diameter, the same scaling rule that is also observed in the absence of vibration. Under vibration, granular flux is no greater than the flux without vibration. Density dilution of granular packs under vibration is likely the cause for such reduced flux, and can be described by a model based on energy balance at the vibrating boundary. The eventual saturation of flux at the highest peak velocities signifies a possible transition from granular fluid to granular gas, as the density decreases and inter-grain interaction changes. Brief flows can be initiated from a jammed container using mechanical impacts. The number of grains flowing out of the container as well as the duration of these flows follows an almost exponential decay distribution. The probability that a flow can be initiated by an impact increases with impact intensity and ratio the diameters of the orifice and the grain. The possible container size and filling depth dependence are also discussed. For the thermal cycling measurement, data show that the packing fraction of granular samples increases under thermal cycles regardless of the relative thermal expansions of the grains or the container. A heavy intruder, when passing a density threshold, sinks in a granular pile under thermal cycles. The results show that the bulk property of granular materials can be impacted by microscopic changes orders or magnitudes less, and without the input of mechanical energy. We believe both the packing fraction relaxation and the intruder displacement in thermally cycled granular systems demonstrate the fragility of disordered granular media, which can be defined as the “inability to elastically support some infinitesimal loads”. Advisors/Committee Members: Peter E Schiffer, Committee Chair/Co-Chair, Julian Decatur Maynard Jr., Committee Member, Reka Z Albert, Committee Member.

Subjects/Keywords: thermal cycles; Granular flow; vibration

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Chen, K. (2008). GRANULAR MATERIALS UNDER VIBRATION AND THERMAL CYCLES . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/8811

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chen, Ke. “GRANULAR MATERIALS UNDER VIBRATION AND THERMAL CYCLES .” 2008. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/8811.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chen, Ke. “GRANULAR MATERIALS UNDER VIBRATION AND THERMAL CYCLES .” 2008. Web. 06 Mar 2021.

Vancouver:

Chen K. GRANULAR MATERIALS UNDER VIBRATION AND THERMAL CYCLES . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/8811.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chen K. GRANULAR MATERIALS UNDER VIBRATION AND THERMAL CYCLES . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/8811

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

19. Burgard, Anthony P. OPTIMIZATION-BASED FRAMEWORKS FOR THE ANALYSIS AND REDESIGN OF METABOLIC NETWORKS.

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/6410

► The central theme of this thesis is the development of computational tools for the analysis and redesign of metabolic networks. The key questions that are… (more)

▼ The central theme of this thesis is the development of computational tools for the analysis and redesign of metabolic networks. The key questions that are addressed in this work are: how can one (i) select the optimal set(s) of functions to recombine into microbial strains to enhance their maximum theoretical production capabilities, (2) identify the smallest set of reactions capable of supporting minimal metabolism under various conditions, (3) test whether hypothesized intracellular objectives are consistent with experimental measurements, (4) shape the connectivity of a metabolic network in such a way that a targeted biochemical becomes an obligatory byproduct of cell growth, and (5) elucidate the topological and structural features of metabolic reconstructions at the genome-scale. In the first part of this thesis, a computational protocol is introduced and applied to select the optimal foreign reactions from a genomic database encompassing multiple species for increasing the maximum theoretical yields of the twenty amino acids in Escherichia coli. Here it was found that the production capabilities of seven amino acids could be enhanced by the addition of only one or two foreign functionalities. Next, the minimal reaction network framework revealed that 224 or 229 metabolic reactions are required to support E. coli growth on glucose or acetate, respectively, while a cell cultured on a rich optimally engineered medium could theoretically support growth with as few as 122 metabolic reactions. Thus the minimal reaction sets were revealed to be highly dependent on the imposed uptake environment and the growth requirements. In the following section, the ObjFind procedure is applied to two sets of experimental E. coli flux data (i.e., anaerobic and aerobic growth) revealing that a common metabolic objective, biomass production, is the most explanatory. The OptKnock framework is then introduced for pinpointing reactions in a metabolic network for removal to force growth-coupled biochemical production. Computational results for the overproduction of lactic acid, succinic acid, and 1,3-propanediol are consistent with both intuitive and non-intuitive knockout strategies published in the literature. Lastly, the flux coupling finder procedure is applied to three genome-scale metabolic models enabling the exhaustive identification of various types of reaction coupling. Advisors/Committee Members: Costas D Maranas, Committee Chair/Co-Chair, Andrew Zydney, Committee Member, Darrell Velegol, Committee Member, Reka Z Albert, Committee Member.

Subjects/Keywords: metabolic network; stoichiometric modeling; microbial strain design

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Burgard, A. P. (2008). OPTIMIZATION-BASED FRAMEWORKS FOR THE ANALYSIS AND REDESIGN OF METABOLIC NETWORKS. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/6410

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Burgard, Anthony P. “OPTIMIZATION-BASED FRAMEWORKS FOR THE ANALYSIS AND REDESIGN OF METABOLIC NETWORKS.” 2008. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/6410.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Burgard, Anthony P. “OPTIMIZATION-BASED FRAMEWORKS FOR THE ANALYSIS AND REDESIGN OF METABOLIC NETWORKS.” 2008. Web. 06 Mar 2021.

Vancouver:

Burgard AP. OPTIMIZATION-BASED FRAMEWORKS FOR THE ANALYSIS AND REDESIGN OF METABOLIC NETWORKS. [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/6410.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Burgard AP. OPTIMIZATION-BASED FRAMEWORKS FOR THE ANALYSIS AND REDESIGN OF METABOLIC NETWORKS. [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/6410

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

20. Pomeroy, Laura Warlow. Ecology and Evolution of the Paramyxoviridae .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/8545

► Classical epidemiological theory uses compartmental susceptible-infected-removed (SIR) models to quantitatively explore epidemics caused by acute, immunizing viruses that sweep through local populations. While the basic… (more)

▼ Classical epidemiological theory uses compartmental susceptible-infected-removed (SIR) models to quantitatively explore epidemics caused by acute, immunizing viruses that sweep through local populations. While the basic theory explains viral-host dynamics in some systems, added model complexity creates a more accurate context for other systems. As a case study, I investigate the system of phocine distemper virus (PDV), a morbillivirus, in harbor seals (Phoca vitulina) in the North Sea. Using this dataset, I extend the classical theory by incorporating host age or stage heterogeneities, geographical heterogeneities, and host movement heterogeneities. First, I investigated age or stage heterogeneities in transmission among the harbor seals in the Dutch 2002 PDV epidemic by creating three models to see which best fit the data. The model with the highest degree of heterogeneity best fit the host stage-structure (p=0.0004). I also estimated the “who acquires infection from whom” (WAIFW) matrix from detailed incidence data and confirmed with an R0 calculation using next-generation formalism. Next, I addressed geographic heterogeneity in the host population by addressing error inherent in the PDV incidence data in the entire North Sea with a Bayesian framework to estimate the initial population of susceptible individuals (S0), the rate of pathogen transmission (â), and the time series of infected individuals with imperfect binomial reporting to the biweekly incidence time series and used this information to create distance and gravity based models to discriminate how different geographic locations are coupled by infected host movement. Results show that the distance model has a better fit to the seal stranding data, indicating that the distance between harbor seal haulouts drives the spatial spread of PDV. Lastly, I looked at the epidemiological and evolutionary dynamics of the viral family Paramyxoviridae by investigating serially-sampled genomes of measles virus, mumps virus, and canine distemper virus. Using a Bayesian coalescent approach, we estimate viral substitution rates, the time to common ancestry and elements of their demographic history. Strikingly, the mean Time to the Most Recent Common Ancestor (TMRCA) was both similar and very recent among the viruses studied, ranging from only 58 to 91 years (1908 to 1943). Advisors/Committee Members: Ottar N Bjornstad, Committee Chair/Co-Chair, Reka Z Albert, Committee Member, Bryan Grenfell, Committee Member, Edward C Holmes, Committee Member, Peter John Hudson, Committee Member.

Subjects/Keywords: SIR models; harbor seals; wildlife diseases; phocine distemper virus; Paramyxoviruses; coalescent methods

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Pomeroy, L. W. (2008). Ecology and Evolution of the Paramyxoviridae . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/8545

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Pomeroy, Laura Warlow. “Ecology and Evolution of the Paramyxoviridae .” 2008. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/8545.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Pomeroy, Laura Warlow. “Ecology and Evolution of the Paramyxoviridae .” 2008. Web. 06 Mar 2021.

Vancouver:

Pomeroy LW. Ecology and Evolution of the Paramyxoviridae . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/8545.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Pomeroy LW. Ecology and Evolution of the Paramyxoviridae . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/8545

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

21. Nelson, Martha Irene. The Genomic Evolution of Human Influenza A Virus .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/8617

► The genetic diversity and evolutionary plasticity of the influenza A virus poses a continual, yet unpredictable threat to public health. The notorious 1918 pandemic of… (more)

▼ The genetic diversity and evolutionary plasticity of the influenza A virus poses a continual, yet unpredictable threat to public health. The notorious 1918 pandemic of ‘Spanish flu’ was associated with 20-50 million deaths worldwide and is considered one of the most devastating single disease outbreaks in history. Despite intensive year-round sequencing and antigenic characterization of global influenza A viruses, major aspects of influenza A virus evolution and epidemiology remain poorly understood. In particular, the dominant model of influenza A virus evolution by long-term ‘antigenic drift’, while clearly of great importance for viral escape of host antibodies, inadequately explains important epidemic dynamics. Significantly, neither the distinct winter seasonality of the influenza A virus, nor the sudden emergence of major antigenic variants are fully accounted for on the basis of antigenic drift alone. Through phylogenetic analysis of whole-genome influenza viruses sampled intensively over multiple discrete spatial-temporal scales, the studies in this thesis reveal evolutionary dynamics that have been previously obscured by spatially limited sampling and sequencing of the HA1 domain in isolation. Most notably, although strong immune selection periodically limits genetic diversity through antigenic drift, multiple diverse viral lineages typically co-circulate globally and are introduced into a given locality during an epidemic. This genetic diversity co-circulates over the course of an epidemic, allowing for frequent genomic ‘reassortment’ and greatly complicating patterns of spatial-temporal dissemination. The process of reassortment is capable of situating antigenic novelty within a more compatible viral genome, rapidly producing influenza viruses of greater overall fitness that occasionally are associated with major epidemics. In addition, extensive global migration results in complex global networks between viral populations from different geo-climatic regions, and these networks appear to be critical for the continual survival of the virus and ‘re-seeding’ of local epidemics. Further understanding of this intricate global ecology is central to understanding the evolution of the influenza A virus, and will require surveillance to be substantially increased in important under-sampled regions such as South-East Asia. Advisors/Committee Members: Andrew George Stephenson, Committee Chair/Co-Chair, Edward C Holmes, Committee Member, Reka Z Albert, Committee Member, Kateryna Dmytrivna Makova, Committee Member.

Subjects/Keywords: influenza virus; phylogenetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Nelson, M. I. (2008). The Genomic Evolution of Human Influenza A Virus . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/8617

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Nelson, Martha Irene. “The Genomic Evolution of Human Influenza A Virus .” 2008. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/8617.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Nelson, Martha Irene. “The Genomic Evolution of Human Influenza A Virus .” 2008. Web. 06 Mar 2021.

Vancouver:

Nelson MI. The Genomic Evolution of Human Influenza A Virus . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/8617.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Nelson MI. The Genomic Evolution of Human Influenza A Virus . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/8617

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

22. Zhao, Zhixin. FUNCTIONAL PROTEOMICS OF ARABIDOPSIS THALIANA GUARD CELLS UNCOVERS NEW STOMATAL SIGNALING PATHWAYS .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/9238

► The guard cell is a specialized cell type, located in the epidermes of higher plants. The guard cell has been used as a model system… (more)

▼ The guard cell is a specialized cell type, located in the epidermes of higher plants. The guard cell has been used as a model system in plant cell biology for decades. Here, I isolated a total of 3x108 guard cell protoplasts from 22,000 Arabidopsis plants and identified 1,764 unique proteins using three complementary proteomic methods: protein spot identification from broad and narrow pH range 2D gels, and 2D LC-MALDI MudPIT. Proteomic study suggested that myrosinase 1 (TGG1) is the most abundant protein in guard cells. TGG1 catalyzes the production of toxic isothiocyanates from glucosinolates, and the glucosinolate-myrosinase system is well known as a defense system against biotic invaders. Phenotypic analysis showed that tgg1 mutants were hyposensitive to abscisic acid (ABA)-inhibition of guard cell inward K+ channels and stomatal opening, revealing that the glucosinolate-myrosinase system is also central to abiotic stress responses. TopGO analysis of the identified guard cell proteome revealed that proteins involved in energy production were enriched in the GC proteome. I further characterized mutants lacking the glycolytic enzyme iPGM (2,3-biphosphoglycerate-independent phosphoglycerate mutase). ipgm mutants showed defects in stomatal movements, growth, and pollen production in our study. Our study demonstrates that proteomic studies can make powerful contributions to the identification of novel signaling pathways. In addition to the guard cell proteomic study, I also compared the proteomic patterns of Col and gpa1-4 guard cells with and without ABA treatment using iTARQ technology. The gpa1-4 mutant, lacking the heterotrimeric G protein alpha subunit, shows hyposensitivity to ABA inhibition of inward K+ channels and ABA inhibition of stomatal opening. This iTRAQ study showed that two and six proteins were significantly regulated by ABA in protein abundance in Col and gpa1-4 guard cells respectively, while the abundance of 18 proteins in guard cells was affected by mutation of GPA1. Novel signaling models were proposed on the basis of the iTRAQ results. To study the correlation of the transcriptome and proteome in guard cells, we also pursued microarray experiments. Comparison of transcriptome to proteome revealed that the correlation between mRNA and protein levels is poor in Arabidopsis guard cells, suggesting that the protein abundance in guard cells is not primarily regulated at the transcriptional level. Advisors/Committee Members: Sarah Mary Assmann, Committee Chair/Co-Chair, Hong Ma, Committee Member, Ming Tien, Committee Member, Reka Z Albert, Committee Member, Jiaxuan Li, Committee Member.

Subjects/Keywords: PROTEOMICS; CORRELATION BETWEEN TRANSCRIPTOME AND PROTEOME; GUARD CELL

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zhao, Z. (2008). FUNCTIONAL PROTEOMICS OF ARABIDOPSIS THALIANA GUARD CELLS UNCOVERS NEW STOMATAL SIGNALING PATHWAYS . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/9238

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zhao, Zhixin. “FUNCTIONAL PROTEOMICS OF ARABIDOPSIS THALIANA GUARD CELLS UNCOVERS NEW STOMATAL SIGNALING PATHWAYS .” 2008. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/9238.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zhao, Zhixin. “FUNCTIONAL PROTEOMICS OF ARABIDOPSIS THALIANA GUARD CELLS UNCOVERS NEW STOMATAL SIGNALING PATHWAYS .” 2008. Web. 06 Mar 2021.

Vancouver:

Zhao Z. FUNCTIONAL PROTEOMICS OF ARABIDOPSIS THALIANA GUARD CELLS UNCOVERS NEW STOMATAL SIGNALING PATHWAYS . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/9238.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zhao Z. FUNCTIONAL PROTEOMICS OF ARABIDOPSIS THALIANA GUARD CELLS UNCOVERS NEW STOMATAL SIGNALING PATHWAYS . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/9238

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

23. Carrino, Christopher N. A Study of Repeat Collaboration in Social Affiliation Networks.

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/7370

► In recent years complex systems have often been analyzed from an abstract perspective using nodes that represent system entities and edges that represent the relationships… (more)

▼ In recent years complex systems have often been analyzed from an abstract perspective using nodes that represent system entities and edges that represent the relationships among entities. The system itself is represented by the collection of nodes and entities, referred to as a network. This perspective forms the basis of a new field of study known as network science, and has been used to analyze complex systems across many diverse disciplines including sociology, biology, linguistics and engineering. One of the most critical questions that network scientists seek to answer is “Which processes determine the network’s topology of nodes and edges?” The purpose of this thesis is to extend the field of network science by providing an analysis of one such process that has yet to be analyzed in detail - the process of repeat collaboration. Repeat collaboration is a special case of collaboration where, in the case of a social network, people (nodes) choose to work with each other (edges) on more than one occasion. The amount of repeat collaboration that occurs among the participants in a social network varies across different networks and different social contexts. To fully understand this process, patterns of repeat collaboration are analyzed in this thesis across five different social contexts: corporate boards of directors, coauthors, creative artists, entertainment actors and casual acquaintances. Repeat collaboration is shown to significantly influence the formation of the topology of social networks of multiple types and to influence the performance of algorithms on these networks as well. The goals of this analysis of repeat collaboration are to: 1) develop metrics of repeat collaboration from various perspectives within a social affiliation network; 2) identify and explain patterns of repeat collaboration within various social contexts; 3) utilize these metrics and patterns to extrapolate knowledge from any given affiliation network topology about the participants and events that inhabit the network. Advisors/Committee Members: Soundar Rajan Tirupatikumara, Committee Chair/Co-Chair, Reka Z Albert, Committee Member, Leah C Newman, Committee Member, Tao Yao, Committee Member.

Subjects/Keywords: social network analysis; repeat collaboration; link prediction; link analysis; affiliation network; centrality; similarity; network data mining; pareto clique

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Carrino, C. N. (2008). A Study of Repeat Collaboration in Social Affiliation Networks. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/7370

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Carrino, Christopher N. “A Study of Repeat Collaboration in Social Affiliation Networks.” 2008. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/7370.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Carrino, Christopher N. “A Study of Repeat Collaboration in Social Affiliation Networks.” 2008. Web. 06 Mar 2021.

Vancouver:

Carrino CN. A Study of Repeat Collaboration in Social Affiliation Networks. [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/7370.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Carrino CN. A Study of Repeat Collaboration in Social Affiliation Networks. [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/7370

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

24. Dasika, Madhukar S. SYSTEMS ENGINEERING BASED APPROACHES FOR BIOLOGICAL NETWORK INFERENCE, ANALYSIS AND REDESIGN .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/7631

► Nature has created a wide range of diversity in the form of microorganisms with sometimes less than 200 genes to highly complex biological entities… (more)

▼ Nature has created a wide range of diversity in the form of microorganisms with sometimes less than 200 genes to highly complex biological entities such as humans. All these biological systems are driven by an underlying complex cascade of biochemical reactions. These reactions are often represented as “networks”; these networks come in different flavors such as Metabolic, Signaling and Gene Regulatory. It is now clear that development of systematic procedures to analyze biological networks will lead to advances in biotechnology and therapeutics. To this end, in this thesis we develop computational approaches which can serve as powerful tools in various stages of biological research and discovery. Specifically, this thesis is composed of four parts that address inference, topological analysis and redesign of biological networks. While complementary these approaches are not necessarily interlinked. The first part of this thesis focuses on development of a mathematical programming based framework to extract the underlying layer of complex component interaction networks using high-throughput biological data. Specifically, a mixed-integer linear programming based modeling and solution framework for inferring time delay in gene regulatory networks is developed. Solution of the model with real microarray data indicates that (i) The model predicts considerable number of interactions with a non zero value of time delay suggesting that time delay is prominent in gene regulation and (ii) Predicts a network that is more sparse and less sensitive to random fluctuations in gene expression, when time delay is accounted for. Subsequently, optimization based frameworks are introduced for elucidating the input-output structure and redesigning large-scale cell signaling networks for pinpointing targeted disruptions leading to the silencing of undesirable outputs in the context of therapeutic interventions. The Min-Input framework is used to exhaustively identify all input-output connections implied by the signaling network structure. Results reveal that there exists two distinct types of outputs in the signaling network that either can be elicited by many different input combinations (i.e., degenerate) or are highly specific requiring dedicated inputs. The Min-Interference framework is next used to precisely pinpoint key disruptions that negate undesirable outputs while leaving unaffected necessary ones. In addition to identifying disruptions of terminal steps, we also identify complex disruption combinations in upstream pathways that indirectly negate the targeted output by propagating their action through the signaling cascades. Next, we focus our attention to the development of computational tools construct and validate biological networks. Specifically, a discrete event based mechanistic simulation platform DEMSIM was developed for testing and validating putative regulatory interactions. The proposed framework models the main processes in gene expression, which are transcription, translation and decay… Advisors/Committee Members: Costas D Maranas, Committee Chair/Co-Chair, Reka Z Albert, Committee Member, Patrick C Cirino, Committee Member, Antonios Armaou, Committee Member.

Subjects/Keywords: gene regulatory networks; signaling networks; Optimization; synthetic biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dasika, M. S. (2008). SYSTEMS ENGINEERING BASED APPROACHES FOR BIOLOGICAL NETWORK INFERENCE, ANALYSIS AND REDESIGN . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/7631

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Dasika, Madhukar S. “SYSTEMS ENGINEERING BASED APPROACHES FOR BIOLOGICAL NETWORK INFERENCE, ANALYSIS AND REDESIGN .” 2008. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/7631.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Dasika, Madhukar S. “SYSTEMS ENGINEERING BASED APPROACHES FOR BIOLOGICAL NETWORK INFERENCE, ANALYSIS AND REDESIGN .” 2008. Web. 06 Mar 2021.

Vancouver:

Dasika MS. SYSTEMS ENGINEERING BASED APPROACHES FOR BIOLOGICAL NETWORK INFERENCE, ANALYSIS AND REDESIGN . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/7631.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Dasika MS. SYSTEMS ENGINEERING BASED APPROACHES FOR BIOLOGICAL NETWORK INFERENCE, ANALYSIS AND REDESIGN . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/7631

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

25. Wolfe, Daniel N. Interactions Between Endemic Bordetella Species and Host Immunity .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/7990

► Bordetella pertussis and Bordetella parapertussis are bacterial pathogens that cause whooping cough, a disease that is re-emerging in vaccinated populations. The diseases caused by these… (more)

▼ Bordetella pertussis and Bordetella parapertussis are bacterial pathogens that cause whooping cough, a disease that is re-emerging in vaccinated populations. The diseases caused by these bacteria are clinically indistinguishable, but pertussis toxin, which is only expressed by B. pertussis, has a variety of effects on the host immune response and hinders the clearance of B. pertussis from the respiratory tract. This led us to investigate the host factors that overcome the effects of pertussis toxin. In a mouse model of infection, Tumor Necrosis Factor-á was required to limit leukocyte accumulation and survive during infection by B. pertussis, but not a pertussis toxin-deficient strain of B. pertussis. Interferon-ã combatted the effects of pertussis toxin by contributing to the recruitment of leukocytes and the antibody-mediated clearance of B. pertussis. Interestingly, B. parapertussis does not express pertussis toxin but causes the same disease in the same host. We sought to elucidate the host factors that protect against B. parapertussis infection and how this bacterium may evade host immunity. Antibodies, T cells, and neutrophils were crucial to the elimination of B. parapertussis from the respiratory tract. However, B. parapertussis did not stimulate an early Toll-like receptor-4-mediated recruitment of leukocytes to the site of infection, resulting in the evasion of rapid clearance. Interferon-ã overcame the lack of Toll-like receptor-4 stimulation by contributing to the inflammatory response, but Interferon-ã production was inhibited by Interleukin-10, facilitating the persistence of the infection. Ultimately, both B. pertussis and B. parapertussis infections induce protective immunity. Since ecological theory predicts that two closely related immunizing pathogens can not coexist in the same host population, we assessed the cross reactivity of immunity to these pathogens. Immunity induced by B. parapertussis protected against both species while immunity induced by B. pertussis only protected against B. pertussis. O antigen enabled B. parapertussis to avoid cross immunity and may be a key protective antigen. These studies contribute to the understanding of interactions between the bordetellae and host immunity and will guide any future vaccine design against B. parapertussis. Advisors/Committee Members: Eric Thomas Harvill, Committee Chair/Co-Chair, Avery August, Committee Member, Reka Z Albert, Committee Member, Biao He, Committee Member, Mary J Kennett, Committee Member.

Subjects/Keywords: infectious disease; bacteria; parapertussis; Bordetella; whooping cough

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Wolfe, D. N. (2008). Interactions Between Endemic Bordetella Species and Host Immunity . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/7990

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Wolfe, Daniel N. “Interactions Between Endemic Bordetella Species and Host Immunity .” 2008. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/7990.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Wolfe, Daniel N. “Interactions Between Endemic Bordetella Species and Host Immunity .” 2008. Web. 06 Mar 2021.

Vancouver:

Wolfe DN. Interactions Between Endemic Bordetella Species and Host Immunity . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/7990.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Wolfe DN. Interactions Between Endemic Bordetella Species and Host Immunity . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/7990

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

26. JEONG, JIEUN. Algorithms for classification and prediction of protein structure and function.

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/8094

► The subject of this thesis is predicting the function of a protein. Many aspects of protein function are determined by its shape, or the structure.… (more)

Subjects/Keywords: protein structure; protein folds; hairpin loops; folding rules; approximation algorithms; gene regulatory network

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

JEONG, J. (2008). Algorithms for classification and prediction of protein structure and function. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/8094

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

JEONG, JIEUN. “Algorithms for classification and prediction of protein structure and function.” 2008. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/8094.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

JEONG, JIEUN. “Algorithms for classification and prediction of protein structure and function.” 2008. Web. 06 Mar 2021.

Vancouver:

JEONG J. Algorithms for classification and prediction of protein structure and function. [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/8094.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

JEONG J. Algorithms for classification and prediction of protein structure and function. [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/8094

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

27. Mallapragada, Girish. Being Open in a Closed World: Essays on Innovation in Open Source Networks .

Degree: 2008, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/7928

► My thesis consists of a brief introduction, two essays, and a brief conclusion. The two essays that form the core of my thesis investigate innovation… (more)

▼ My thesis consists of a brief introduction, two essays, and a brief conclusion. The two essays that form the core of my thesis investigate innovation coordination in the open source community model of product development. For this purpose, a social network approach is used to understand the effects of network structure that arises due to relationships between open source projects and developers. In the first essay we build on the notion of the criticality of social networks for the new product development process. We rely on organizational founding literature to suggest that the network structure at the inception of a new product development project would have a lingering effect on the time to development of the new product. We test this assertion in the context of open source software development projects, where the open source community has emerged as a viable alternative to traditional firm-based software development initiatives. The open source community builds products through online collaboration, products whose source code is in the public domain. In this open source environment, we conceptualize a product development process consisting of two stages: (1) some projects transition from ideas to some development activity and (2) for the projects that make the transition at the first stage, some projects mature into ‘marketable’ products. Specifically, we hypothesize how network structure that surrounds a project at inception will play a role in determining which projects will stay inactive as against being active (stage 1), and influence the time to market for that the projects that become active (stage 2). We test the hypotheses with data from 817 new open source projects from SourceForge.net, the largest forum of open source projects on the Internet. Results from simulated maximum likelihood estimation of a Type II Tobit model specification provide support for the hypotheses that network structure at inception of a project impacts whether the project becomes active and the time to first release of the project. In the second essay we address issues relating to the participation of large firms in the open source software development community. The network structure that exists among open source projects is changing continuously due to the nature of collaboration in such communities. As the value and quality of resources available to the open source projects depends on the network configurations that surround the projects, it becomes important to understand what impacts these changes and what the consequences will be. Relying on social capital theory, we develop a model in which projects change their network connections by constantly evaluating the utility they derive from their current location in the network structure. We hypothesize that two important network characteristics namely, embeddedness and structural holes affect the network change process. We test the hypotheses with data from 43 open source projects that are being sponsored by a large firm on SourceForge.net, the largest forum of… Advisors/Committee Members: Gary L Lilien, Committee Chair/Co-Chair, Rajdeep Grewal, Committee Chair/Co-Chair, William T Ross, Committee Member, John C Liechty, Committee Member, Reka Z Albert, Committee Member.

Subjects/Keywords: new product development; innovation; collaboration; social networks; open source

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Mallapragada, G. (2008). Being Open in a Closed World: Essays on Innovation in Open Source Networks . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/7928

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Mallapragada, Girish. “Being Open in a Closed World: Essays on Innovation in Open Source Networks .” 2008. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/7928.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Mallapragada, Girish. “Being Open in a Closed World: Essays on Innovation in Open Source Networks .” 2008. Web. 06 Mar 2021.

Vancouver:

Mallapragada G. Being Open in a Closed World: Essays on Innovation in Open Source Networks . [Internet] [Thesis]. Penn State University; 2008. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/7928.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Mallapragada G. Being Open in a Closed World: Essays on Innovation in Open Source Networks . [Thesis]. Penn State University; 2008. Available from: https://submit-etda.libraries.psu.edu/catalog/7928

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

28. De Keyser, Joshua Gordon. ALTERNATIVE SPLICING OF THE HUMAN CONSTITUTIVE ANDROSTANE RECEPTOR GENE CREATES RECEPTORS WITH UNIQUE FUNCTION AND LIGAND SPECIFICITY .

Degree: 2009, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/9350

► The human constitutive androstane receptor (CAR) regulates the expression of genes involved in xenobiotic metabolism in the liver. The CAR gene utilizes multiple alternative splicing… (more)

▼ The human constitutive androstane receptor (CAR) regulates the expression of genes involved in xenobiotic metabolism in the liver. The CAR gene utilizes multiple alternative splicing events during pre-mRNA processing, thereby increasing the CAR transcriptome. The work presented in this dissertation focuses on the functional analysis of a prominent human CAR variant, CAR2 that possesses a 4- amino acid insertion in the ligand binding domain. Previous investigations led us to hypothesize that the CAR2 variant is a ligand-activated receptor and possesses a unique ligand binding profile giving rise to novel biological function. We now demonstrate that CAR2 constitutes approximately one-third and one-half of the total CAR transcriptome in human hepatocytes and small intestine, respectively. Further, we identify the common plasticizers, di(2-ethylhexyl) phthalate (DEHP) and di-isononyl phthalate (DiNP) as highly potent and uniquely selective agonists of CAR2. Results from reporter transactivation assays reveal that DEHP and DiNP activate CAR2 at low nanomolar concentrations. In addition, comparative genomic analysis show that the typical mouse, rat and marmoset models of toxicity can not accurately profile potential human toxicity due to these species inability to generate a CAR2-like transcript. It is also demonstrated that CAR2 possesses an altered ligand pocket that allows for the highly potent and specific activation of the variant by DEHP and DiNP. Further studies show that CAR1 and CAR3 share similar ligand activation profiles; whereas CAR2 responds to most CAR1 and CAR3 ligands as well as a unique subset of chemicals. Finally, it is now shown that meclizine, a human CAR1 inverse-agonist, is a specific agonist of CAR2. A meclizine derived pharmacophore was utilized in a ligand-based virtual screening and identified two novel CAR2 agonists from the NCI chemical database. The results of this dissertation will aid in the development of better models of human CAR activation, give a more complete understanding of the interaction of CAR with xenobiotics, yield novel insight into potential mechanisms of phthalate toxicity and provide the foundation for future studies into the physiologic functions of alternatively spliced variants of CAR. Advisors/Committee Members: Curtis John Omiecinski, Dissertation Advisor/Co-Advisor, Curtis John Omiecinski, Committee Chair/Co-Chair, Reka Z Albert, Committee Member, Adam Bleier Glick, Committee Member, John Patrick Vanden Heuvel, Committee Member.

Subjects/Keywords: phthalates; alternative splicing; constitutive androstane receptor; drug and xenobiotic metabolism; meclizine; nuclear receptors; gene induction

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

De Keyser, J. G. (2009). ALTERNATIVE SPLICING OF THE HUMAN CONSTITUTIVE ANDROSTANE RECEPTOR GENE CREATES RECEPTORS WITH UNIQUE FUNCTION AND LIGAND SPECIFICITY . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/9350

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

De Keyser, Joshua Gordon. “ALTERNATIVE SPLICING OF THE HUMAN CONSTITUTIVE ANDROSTANE RECEPTOR GENE CREATES RECEPTORS WITH UNIQUE FUNCTION AND LIGAND SPECIFICITY .” 2009. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/9350.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

De Keyser, Joshua Gordon. “ALTERNATIVE SPLICING OF THE HUMAN CONSTITUTIVE ANDROSTANE RECEPTOR GENE CREATES RECEPTORS WITH UNIQUE FUNCTION AND LIGAND SPECIFICITY .” 2009. Web. 06 Mar 2021.

Vancouver:

De Keyser JG. ALTERNATIVE SPLICING OF THE HUMAN CONSTITUTIVE ANDROSTANE RECEPTOR GENE CREATES RECEPTORS WITH UNIQUE FUNCTION AND LIGAND SPECIFICITY . [Internet] [Thesis]. Penn State University; 2009. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/9350.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

De Keyser JG. ALTERNATIVE SPLICING OF THE HUMAN CONSTITUTIVE ANDROSTANE RECEPTOR GENE CREATES RECEPTORS WITH UNIQUE FUNCTION AND LIGAND SPECIFICITY . [Thesis]. Penn State University; 2009. Available from: https://submit-etda.libraries.psu.edu/catalog/9350

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

29. Chung, Wen-Yu. Uncovering hidden genomic features using computational approaches.

Degree: 2009, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/9398

► Modern genetic studies are heavily dependent on analyses of whole genome sequences that have only become available in the past decade. Technologies such as microarrays… (more)

Subjects/Keywords: Computational Biology; Bioinformatics; Systems Biology; Molecular Evolution

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Chung, W. (2009). Uncovering hidden genomic features using computational approaches. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/9398

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chung, Wen-Yu. “Uncovering hidden genomic features using computational approaches.” 2009. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/9398.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chung, Wen-Yu. “Uncovering hidden genomic features using computational approaches.” 2009. Web. 06 Mar 2021.

Vancouver:

Chung W. Uncovering hidden genomic features using computational approaches. [Internet] [Thesis]. Penn State University; 2009. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/9398.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chung W. Uncovering hidden genomic features using computational approaches. [Thesis]. Penn State University; 2009. Available from: https://submit-etda.libraries.psu.edu/catalog/9398

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

30. Ko, Kyung Dae. QUANTITATIVE FUNCTIONAL MEASUREMENT OF A PROTEIN USING PHYLOGENETIC PROFILES .

Degree: 2009, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/9452

► In principle, the amino acid sequence of a protein contains structural, functional, and evolutionary characteristics. Investigating these characteristics using computational methods provides a powerful resource.… (more)

Subjects/Keywords: the function of protein; proteomics; bioinformatics; RNA binding protein

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ko, K. D. (2009). QUANTITATIVE FUNCTIONAL MEASUREMENT OF A PROTEIN USING PHYLOGENETIC PROFILES . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/9452

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ko, Kyung Dae. “QUANTITATIVE FUNCTIONAL MEASUREMENT OF A PROTEIN USING PHYLOGENETIC PROFILES .” 2009. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/9452.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ko, Kyung Dae. “QUANTITATIVE FUNCTIONAL MEASUREMENT OF A PROTEIN USING PHYLOGENETIC PROFILES .” 2009. Web. 06 Mar 2021.

Vancouver:

Ko KD. QUANTITATIVE FUNCTIONAL MEASUREMENT OF A PROTEIN USING PHYLOGENETIC PROFILES . [Internet] [Thesis]. Penn State University; 2009. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/9452.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ko KD. QUANTITATIVE FUNCTIONAL MEASUREMENT OF A PROTEIN USING PHYLOGENETIC PROFILES . [Thesis]. Penn State University; 2009. Available from: https://submit-etda.libraries.psu.edu/catalog/9452

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Open Access Theses and Dissertations