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Articles 1 - 16 of 16
Full-Text Articles in Life Sciences
Improving Adjacency List Storage Methods For Polypeptide Similarity Analysis, Arianna Swensen
Improving Adjacency List Storage Methods For Polypeptide Similarity Analysis, Arianna Swensen
Honors Theses
Protein design is a complex biomolecular and computational problem. Working on increasingly large protein folding problems requires an improvement in current analysis methods available. This work first discusses various methods of protein design, including de novo protein design, which is the primary focus of this thesis. Then, a new approach utilizing a B+ tree to effectively store and query a graph of keys and vertices is proposed in order to store the number of times two polypeptides are considered to be similar. This approach is found to have a reduction in time complexity from current mapping methods and thus provides …
Challenges Of Constructing Entrainment Map For Arbitrary Circadian Models, Yuxuan (Nelson) Wu
Challenges Of Constructing Entrainment Map For Arbitrary Circadian Models, Yuxuan (Nelson) Wu
Honors Theses
The entrainment map, developed by Dr.Diekman and Dr.Bose, is claimed to be a 1-dimensional map that produces a better prediction for phase-locking than methods than the phase response curve for circadian models. In his paper, he constructs the entrainment map for the two-dimensional circadian model, the Novak-Tyson model, and the other two higher-dimensional circadian models. For this thesis, we concentrate on exploring if it is viable to construct the entrainment map for other circadian models that are not included in his paper: the Becker-Weimann model and the Relogio model. In addition, we discuss the challenges of constructing the entrainment map …
Incorporating Demographic Structure And Variable Interaction Types Into Community Assembly Models, Akhil Reddy Alasandagutti, Nayan Chawla
Incorporating Demographic Structure And Variable Interaction Types Into Community Assembly Models, Akhil Reddy Alasandagutti, Nayan Chawla
Honors Theses
Theoretical studies of ecological food webs have allowed ecologists to remove the constraints of specific location and timescales from their study of ecological communities; food webs are generally complex and thus empirical study is difficult. Further, this theoretical approach allows ecologists to compare ecological processes and outcomes across any possible food web structures. However, these simulated communities are only as useful as the model from which they were constructed. Modifying existing considerations in these models, and generating new ones, are the jobs of theoretical ecologists that seek to achieve the shared goal of a majority of simulations: representation of real …
Meta-Analysis Of Biological Research Literature, Evan Suggs
Meta-Analysis Of Biological Research Literature, Evan Suggs
Honors Theses
Comparative studies have been powerful tools in generating a broad understanding about the evolution of animal social systems but they currently rely on the slow, manual process of reading thousands of abstracts and papers from research databases. A web application was created for researchers conducting a comparative survey, in order to speed up their research. This web application automates the retrieval of research papers and their selection process. Using previously obtained data sets on the orders Artiodacytla and Lagomorph, a machine learning application was created to classify the papers. These techniques and tools should greatly increase the speed at which …
Hinge Region In Dna Packaging Terminase Pul15 Of Herpes Simplex Virus: A Potential Allosteric Target For Antiviral Drugs, Lana Faisal Thaljeh
Hinge Region In Dna Packaging Terminase Pul15 Of Herpes Simplex Virus: A Potential Allosteric Target For Antiviral Drugs, Lana Faisal Thaljeh
Honors Theses
No abstract provided.
Protein Residue-Residue Contact Prediction Using Stacked Denoising Autoencoders, Joseph Bailey Luttrell Iv
Protein Residue-Residue Contact Prediction Using Stacked Denoising Autoencoders, Joseph Bailey Luttrell Iv
Honors Theses
Protein residue-residue contact prediction is one of many areas of bioinformatics research that aims to assist researchers in the discovery of structural features of proteins. Predicting the existence of such structural features can provide a starting point for studying the tertiary structures of proteins. This has the potential to be useful in applications such as drug design where tertiary structure predictions may play an important role in approximating the interactions between drugs and their targets without expending the monetary resources necessary for preliminary experimentation. Here, four different methods involving deep learning, support vector machines (SVMs), and direct coupling analysis were …
The Effects Of Early Confidence Interval Training On User Efficacy In A P300 Brain-Computer Interface Spelling Task, Adam Starkman
The Effects Of Early Confidence Interval Training On User Efficacy In A P300 Brain-Computer Interface Spelling Task, Adam Starkman
Honors Theses
Brain-computer interface (BCI) technology can provide communication for individuals suffering from degenerative neuromuscular disorders. The present study sought to demonstrate improved BCI performance in healthy individuals using confidence interval training with a P300 BCI spelling program. In this BCI interface, electroencephalographic (EEG) activity was recorded as participants attended to a specific target character within a matrix of flashing letters and numbers presented on a computer screen. The BCI uses the P300 Event Related Potential to select the intended character. In a prior patient case, use of a confidence measure that rejected questionable selections improved that user’s spelling efficiency. The present …
Foundations And Interpretations Of Quantum Mechanics, Cory Johnson
Foundations And Interpretations Of Quantum Mechanics, Cory Johnson
Honors Theses
The first famous thought experiment of Einstein gives rise to his theories of relativity, the bedrock of modern astrophysics and cosmology. His second famous thought experiment begins the investigation into the foundations of quantum mechanics. It leads to a paradox, inspiring various 'no-go' theorems proven by Bell, Kochen, and Specker. Physicists and philosophers worldwide become increasingly dissatisfied with the probabilistic complementarity interpretation (Born-Bohr) and eventually offer their own accounts of the theory. By the end of the 20th century two alternative approaches stand out as the best candidates: Both the hidden variables interpretation (de Broglie-Bohm) and the many worlds interpretation …
Effects Of Context Of Natural And Artifactual Objects On Categorization, Linsey Walker
Effects Of Context Of Natural And Artifactual Objects On Categorization, Linsey Walker
Honors Theses
Categorization of animals and vehicles in different contexts was investigated in three experiments using event related potentials (ERPs). The presence of a background and congruency of the background in relation to the object were both manipulated in order to determine the effects of context on visual processing. In Experiment 1, adults were presented with images of animals and vehicles in two conditions: situated in a congruent context (e.g. an animal in a field) and in the absence of a context (an animal in a white homogeneous background). In experiment 2, adults were presented with images of animals and vehicles in …
World Bank -Cpa Conflict: The Struggle To Define Human Rights And Development In The Philippines, Adam B. Robbins
World Bank -Cpa Conflict: The Struggle To Define Human Rights And Development In The Philippines, Adam B. Robbins
Honors Theses
This thesis analyzes the interactions between the World Bank (hereafter, the Bank) and the Cordillera Peoples Alliance (CPA), an indigenous and environmental advocacy group based in the Cordillera region of Luzon, in the Philippines. Using data gathered through both text-based and participatory research methods, I analyze the discursive relationship and violent confrontations between the two organizations. Conflicting development and human rights values cause the majority of these conflicts. I focus on how each organization enacts development and human rights, and how this leads to conflict. Ultimately, I intend for this thesis to offer practical guidance for the reader involved in …
Sedimentological And Plant Taphonomic Evaluation Of The Early Middle Devonian Trout Valley Formation, Jonathan Allen
Sedimentological And Plant Taphonomic Evaluation Of The Early Middle Devonian Trout Valley Formation, Jonathan Allen
Honors Theses
The Trout Valley Formation of Emsian-Eifelian age, outcropped in Baxter State Park, Maine, consists offluvial and coastal deposits preserving early land plants. Massive, crudely bedded conglomerate represents deposits of proximal braided channels on an alluvial fan complex. Lithic sandstone bodies in channel-form geometries represent deposits of river channels draining the Acadian highlands whereas associated siltstones represent overbank deposits, intertidal flats, and tidal channels. Localized lenticular quartz arenites represent nearshore shelf bar deposits that were storm influenced. The majority of plant assemblages preserved mainly in siltstone lithologies are allochthonous and parautochthonous, with only one autochthonous assemblage identified in the sequence. Plant …
Communicator-In-Chief: Presidential Use Of Television Past, Present, And Future, Jenna Wasson
Communicator-In-Chief: Presidential Use Of Television Past, Present, And Future, Jenna Wasson
Honors Theses
This thesis seeks to determine how television has changed as a communication medium for presidents over the past half century. An evaluation of the evolving ways presidents use television to communicate with and to build support from the American people has been conducted. Presidential communication strategies have been identified by drawing primarily from primary sources written by presidents and White House staff. Television technology and the television audience have changed over the years. Presidents have taken a more pro-active, aggressive role in their efforts to harness television for their own purposes. Why have these changes occurred? What impact have these …
Method For Identification Of Origins Of Replication And Genes Regulated By Dnaa In Bacteria, Olga G. Troyanskaya
Method For Identification Of Origins Of Replication And Genes Regulated By Dnaa In Bacteria, Olga G. Troyanskaya
Honors Theses
The study is focused on developing computer programs to identify origin of DNA replication based on analysis of total bacterial genomes, scoring regions for number of DnaA binding sites, AT content, DNA adenine methylase boxes, and integration host factors binding sites. The programs were tested on cyanobacterium Synechocystis, and several potential origins were identified. However, no one definite region could be located. Currently, software is being developed to analyze common motifs around the origins of all bacteria with known origins. Genes whose transcription could be regulated by DnaA were identified by searching for DnaA boxes preceding promoter regions.
Celluloid Blackness : Race, Modernity, And The Conflicted Roots Of American Cinema (1915-1939), Lincoln Farr
Celluloid Blackness : Race, Modernity, And The Conflicted Roots Of American Cinema (1915-1939), Lincoln Farr
Honors Theses
Introduction: "The Problem of the Twentieth Century" In a full page interview in the New York Times on May 29, 1912, the Swiss psychiatrist Dr. Carl G. Jung told the American people, "It seems to me that you are about to discover yourselves. You have discovered everything else-all the land of this continent; all the resources, all the hidden things of nature."Jung used the interview to address the American people, at a moment which he somehow recognized as crucial in the development of human civilization. America, the "tragic" country which he struggled to comprehend, would soon become the harbinger of …
Transitions In Masculinity And Hemingway's Developed "Code", Daniel Polk
Transitions In Masculinity And Hemingway's Developed "Code", Daniel Polk
Honors Theses
The "Hemingway Code" is much more than two words that fit nicely together for a scholar's usage; the words signify a much deeper championing of masculinity, almost a haunting presence. For Ernest Hemingway living life every day, every moment with its fullest masculine fervor, became an obsession, a never-ending quest to be at one with the attitude of never complaining, never crying out, panicking, thinking too much, or regretting. To live a manly life in a series of tactical victories, performed with steadfast ritualistic mannerisms, is to embody masculinity, and therefore the "Hemingway Code."
Rise To Power Of Senator Joseph R. Mccarthy: Reflections Of The Cold War Mccarthy Era In American Film, Scott Lainer
Rise To Power Of Senator Joseph R. Mccarthy: Reflections Of The Cold War Mccarthy Era In American Film, Scott Lainer
Honors Theses
The common bond between much of the film industry and Joseph McCarthy was insecurity and the drive for national approval. If one grasps the specific characteristics of McCarthy the man, and the methods of these politically "inspired" movies, we can to better place the period into context and acknowledge the fact that, if the citizenry is not aware, and is again caught by an ever-building wave of trickle down sentiment, the 1950s might not prove to be an isolated period in American history. Insecurity was not a fifties novelty. It still exists, and could potentially escalate anti-Communist policy and sentiment …