Matching Items (418)
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Description
Sparsity has become an important modeling tool in areas such as genetics, signal and audio processing, medical image processing, etc. Via the penalization of l-1 norm based regularization, the structured sparse learning algorithms can produce highly accurate models while imposing various predefined structures on the data, such as feature groups

Sparsity has become an important modeling tool in areas such as genetics, signal and audio processing, medical image processing, etc. Via the penalization of l-1 norm based regularization, the structured sparse learning algorithms can produce highly accurate models while imposing various predefined structures on the data, such as feature groups or graphs. In this thesis, I first propose to solve a sparse learning model with a general group structure, where the predefined groups may overlap with each other. Then, I present three real world applications which can benefit from the group structured sparse learning technique. In the first application, I study the Alzheimer's Disease diagnosis problem using multi-modality neuroimaging data. In this dataset, not every subject has all data sources available, exhibiting an unique and challenging block-wise missing pattern. In the second application, I study the automatic annotation and retrieval of fruit-fly gene expression pattern images. Combined with the spatial information, sparse learning techniques can be used to construct effective representation of the expression images. In the third application, I present a new computational approach to annotate developmental stage for Drosophila embryos in the gene expression images. In addition, it provides a stage score that enables one to more finely annotate each embryo so that they are divided into early and late periods of development within standard stage demarcations. Stage scores help us to illuminate global gene activities and changes much better, and more refined stage annotations improve our ability to better interpret results when expression pattern matches are discovered between genes.
ContributorsYuan, Lei (Author) / Ye, Jieping (Thesis advisor) / Wang, Yalin (Committee member) / Xue, Guoliang (Committee member) / Kumar, Sudhir (Committee member) / Arizona State University (Publisher)
Created2013
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Description
The entire history of HIV-1 is hidden in its ten thousand bases, where information regarding its evolutionary traversal through the human population can only be unlocked with fine-scale sequence analysis. Measurable footprints of mutation and recombination have imparted upon us a wealth of knowledge, from multiple chimpanzee-to-human transmissions to patterns

The entire history of HIV-1 is hidden in its ten thousand bases, where information regarding its evolutionary traversal through the human population can only be unlocked with fine-scale sequence analysis. Measurable footprints of mutation and recombination have imparted upon us a wealth of knowledge, from multiple chimpanzee-to-human transmissions to patterns of neutralizing antibody and drug resistance. Extracting maximum understanding from such diverse data can only be accomplished by analyzing the viral population from many angles. This body of work explores two primary aspects of HIV sequence evolution, point mutation and recombination, through cross-sectional (inter-individual) and longitudinal (intra-individual) investigations, respectively. Cross-sectional Analysis: The role of Haiti in the subtype B pandemic has been hotly debated for years; while there have been many studies, up to this point, no one has incorporated the well-known mechanism of retroviral recombination into their biological model. Prior to the use of recombination detection, multiple analyses produced trees where subtype B appears to have first entered Haiti, followed by a jump into the rest of the world. The results presented here contest the Haiti-first theory of the pandemic and instead suggest simultaneous entries of subtype B into Haiti and the rest of the world. Longitudinal Analysis: Potential N-linked glycosylation sites (PNGS) are the most evolutionarily dynamic component of one of the most evolutionarily dynamic proteins known to date. While the number of mutations associated with the increase or decrease of PNGS frequency over time is high, there are a set of relatively stable sites that persist within and between longitudinally sampled individuals. Here, I identify the most conserved stable PNGSs and suggest their potential roles in host-virus interplay. In addition, I have identified, for the first time, what may be a gp-120-based environmental preference for N-linked glycosylation sites.
ContributorsHepp, Crystal Marie, 1981- (Author) / Rosenberg, Michael S. (Thesis advisor) / Hedrick, Philip (Committee member) / Escalante, Ananias (Committee member) / Kumar, Sudhir (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Studies of ancient pathogens are moving beyond simple confirmatory analysis of diseased bone; bioarchaeologists and ancient geneticists are posing nuanced questions and utilizing novel methods capable of confronting the debates surrounding pathogen origins and evolution, and the relationships between humans and disease in the past. This dissertation examines two ancient

Studies of ancient pathogens are moving beyond simple confirmatory analysis of diseased bone; bioarchaeologists and ancient geneticists are posing nuanced questions and utilizing novel methods capable of confronting the debates surrounding pathogen origins and evolution, and the relationships between humans and disease in the past. This dissertation examines two ancient human diseases through molecular and bioarchaeological lines of evidence, relying on techniques in paleogenetics and phylogenetics to detect, isolate, sequence and analyze ancient and modern pathogen DNA within an evolutionary framework. Specifically this research addresses outstanding issues regarding a) the evolution, origin and phylogenetic placement of the pathogen causing skeletal tuberculosis in New World prior to European contact, and b) the phylogeny and origins of the parasite causing the human leishmaniasis disease complex. An additional chapter presents a review of the major technological and theoretical advances in ancient pathogen genomics to frame the contributions of this work within a rapidly developing field. This overview emphasizes that understanding the evolution of human disease is critical to contextualizing relationships between humans and pathogens, and the epidemiological shifts observed both in the past and in the present era of (re)emerging infectious diseases. These questions continue to be at the forefront of not only pathogen research, but also

bioarchaeological and paleopathological scholarship.
ContributorsHarkins, Kelly M (Author) / Buikstra, Jane E. (Thesis advisor) / Stone, Anne C (Thesis advisor) / Knudson, Kelly (Committee member) / Kumar, Sudhir (Committee member) / Krause, Johannes (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Proteins are a fundamental unit in biology. Although proteins have been extensively studied, there is still much to investigate. The mechanism by which proteins fold into their native state, how evolution shapes structural dynamics, and the dynamic mechanisms of many diseases are not well understood. In this thesis, protein folding

Proteins are a fundamental unit in biology. Although proteins have been extensively studied, there is still much to investigate. The mechanism by which proteins fold into their native state, how evolution shapes structural dynamics, and the dynamic mechanisms of many diseases are not well understood. In this thesis, protein folding is explored using a multi-scale modeling method including (i) geometric constraint based simulations that efficiently search for native like topologies and (ii) reservoir replica exchange molecular dynamics, which identify the low free energy structures and refines these structures toward the native conformation. A test set of eight proteins and three ancestral steroid receptor proteins are folded to 2.7Å all-atom RMSD from their experimental crystal structures. Protein evolution and disease associated mutations (DAMs) are most commonly studied by in silico multiple sequence alignment methods. Here, however, the structural dynamics are incorporated to give insight into the evolution of three ancestral proteins and the mechanism of several diseases in human ferritin protein. The differences in conformational dynamics of these evolutionary related, functionally diverged ancestral steroid receptor proteins are investigated by obtaining the most collective motion through essential dynamics. Strikingly, this analysis shows that evolutionary diverged proteins of the same family do not share the same dynamic subspace. Rather, those sharing the same function are simultaneously clustered together and distant from those functionally diverged homologs. This dynamics analysis also identifies 77% of mutations (functional and permissive) necessary to evolve new function. In silico methods for prediction of DAMs rely on differences in evolution rate due to purifying selection and therefore the accuracy of DAM prediction decreases at fast and slow evolvable sites. Here, we investigate structural dynamics through computing the contribution of each residue to the biologically relevant fluctuations and from this define a metric: the dynamic stability index (DSI). Using DSI we study the mechanism for three diseases observed in the human ferritin protein. The T30I and R40G DAMs show a loss of dynamic stability at the C-terminus helix and nearby regulatory loop, agreeing with experimental results implicating the same regulatory loop as a cause in cataracts syndrome.
ContributorsGlembo, Tyler J (Author) / Ozkan, Sefika B (Thesis advisor) / Thorpe, Michael F (Committee member) / Ros, Robert (Committee member) / Kumar, Sudhir (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Multi-task learning (MTL) aims to improve the generalization performance (of the resulting classifiers) by learning multiple related tasks simultaneously. Specifically, MTL exploits the intrinsic task relatedness, based on which the informative domain knowledge from each task can be shared across multiple tasks and thus facilitate the individual task learning. It

Multi-task learning (MTL) aims to improve the generalization performance (of the resulting classifiers) by learning multiple related tasks simultaneously. Specifically, MTL exploits the intrinsic task relatedness, based on which the informative domain knowledge from each task can be shared across multiple tasks and thus facilitate the individual task learning. It is particularly desirable to share the domain knowledge (among the tasks) when there are a number of related tasks but only limited training data is available for each task. Modeling the relationship of multiple tasks is critical to the generalization performance of the MTL algorithms. In this dissertation, I propose a series of MTL approaches which assume that multiple tasks are intrinsically related via a shared low-dimensional feature space. The proposed MTL approaches are developed to deal with different scenarios and settings; they are respectively formulated as mathematical optimization problems of minimizing the empirical loss regularized by different structures. For all proposed MTL formulations, I develop the associated optimization algorithms to find their globally optimal solution efficiently. I also conduct theoretical analysis for certain MTL approaches by deriving the globally optimal solution recovery condition and the performance bound. To demonstrate the practical performance, I apply the proposed MTL approaches on different real-world applications: (1) Automated annotation of the Drosophila gene expression pattern images; (2) Categorization of the Yahoo web pages. Our experimental results demonstrate the efficiency and effectiveness of the proposed algorithms.
ContributorsChen, Jianhui (Author) / Ye, Jieping (Thesis advisor) / Kumar, Sudhir (Committee member) / Liu, Huan (Committee member) / Xue, Guoliang (Committee member) / Arizona State University (Publisher)
Created2011
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Description
We propose a novel solution to prevent cancer by developing a prophylactic cancer. Several sources of antigens for cancer vaccines have been published. Among these, antigens that contain a frame-shift (FS) peptide or viral peptide are quite attractive for a variety of reasons. FS sequences, from either mistake in RNA

We propose a novel solution to prevent cancer by developing a prophylactic cancer. Several sources of antigens for cancer vaccines have been published. Among these, antigens that contain a frame-shift (FS) peptide or viral peptide are quite attractive for a variety of reasons. FS sequences, from either mistake in RNA processing or in genomic DNA, may lead to generation of neo-peptides that are foreign to the immune system. Viral peptides presumably would originate from exogenous but integrated viral nucleic acid sequences. Both are non-self, therefore lessen concerns about development of autoimmunity. I have developed a bioinformatical approach to identify these aberrant transcripts in the cancer transcriptome. Their suitability for use in a vaccine is evaluated by establishing their frequencies and predicting possible epitopes along with their population coverage according to the prevalence of major histocompatibility complex (MHC) types. Viral transcripts and transcripts with FS mutations from gene fusion, insertion/deletion at coding microsatellite DNA, and alternative splicing were identified in NCBI Expressed Sequence Tag (EST) database. 48 FS chimeric transcripts were validated in 50 breast cell lines and 68 primary breast tumor samples with their frequencies from 4% to 98% by RT-PCR and sequencing confirmation. These 48 FS peptides, if translated and presented, could be used to protect more than 90% of the population in Northern America based on the prediction of epitopes derived from them. Furthermore, we synthesized 150 peptides that correspond to FS and viral peptides that we predicted would exist in tumor patients and we tested over 200 different cancer patient sera. We found a number of serological reactive peptide sequences in cancer patients that had little to no reactivity in healthy controls; strong support for the strength of our bioinformatic approach. This study describes a process used to identify aberrant transcripts that lead to a new source of antigens that can be tested and used in a prophylactic cancer vaccine. The vast amount of transcriptome data of various cancers from the Cancer Genome Atlas (TCGA) project will enhance our ability to further select better cancer antigen candidates.
ContributorsLee, HoJoon (Author) / Johnston, Stephen A. (Thesis advisor) / Kumar, Sudhir (Committee member) / Miller, Laurence (Committee member) / Stafford, Phillip (Committee member) / Sykes, Kathryn (Committee member) / Arizona State University (Publisher)
Created2012
Description

Pay-for-performance (PFP) is a relatively new approach to agricultural conservation that attaches an incentive payment to quantified reductions in nutrient runoff from a participating farm. Similar to a payment for ecosystem services approach, PFP lends itself to providing incentives for the most beneficial practices at the field level. To date,

Pay-for-performance (PFP) is a relatively new approach to agricultural conservation that attaches an incentive payment to quantified reductions in nutrient runoff from a participating farm. Similar to a payment for ecosystem services approach, PFP lends itself to providing incentives for the most beneficial practices at the field level. To date, PFP conservation in the U.S. has only been applied in small pilot programs. Because monitoring conservation performance for each field enrolled in a program would be cost-prohibitive, field-level modeling can provide cost-effective estimates of anticipated improvements in nutrient runoff. We developed a PFP system that uses a unique application of one of the leading agricultural models, the USDA’s Soil and Water Assessment Tool, to evaluate the nutrient load reductions of potential farm practice changes based on field-level agronomic and management data. The initial phase of the project focused on simulating individual fields in the River Raisin watershed in southeastern Michigan. Here we present development of the modeling approach and results from the pilot year, 2015-2016. These results stress that (1) there is variability in practice effectiveness both within and between farms, and thus there is not one “best practice” for all farms, (2) conservation decisions are made most effectively at the scale of the farm field rather than the sub-watershed or watershed level, and (3) detailed, field-level management information is needed to accurately model and manage on-farm nutrient loadings.

Supplemental information mentioned in the article is attached as a separate document.

ContributorsMuenich, Rebecca (Author) / Kalcic, M. M. (Author) / Winsten, J. (Author) / Fisher, K. (Author) / Day, M. (Author) / O'Neil, G. (Author) / Wang, Y.-C. (Author) / Scavia, D. (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2017
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The emerging field of neuroprosthetics is focused on the development of new therapeutic interventions that will be able to restore some lost neural function by selective electrical stimulation or by harnessing activity recorded from populations of neurons. As more and more patients benefit from these approaches, the interest in neural

The emerging field of neuroprosthetics is focused on the development of new therapeutic interventions that will be able to restore some lost neural function by selective electrical stimulation or by harnessing activity recorded from populations of neurons. As more and more patients benefit from these approaches, the interest in neural interfaces has grown significantly and a new generation of penetrating microelectrode arrays are providing unprecedented access to the neurons of the central nervous system (CNS). These microelectrodes have active tip dimensions that are similar in size to neurons and because they penetrate the nervous system, they provide selective access to these cells (within a few microns). However, the very long-term viability of chronically implanted microelectrodes and the capability of recording the same spiking activity over long time periods still remain to be established and confirmed in human studies. Here we review the main responses to acute implantation of microelectrode arrays, and emphasize that it will become essential to control the neural tissue damage induced by these intracortical microelectrodes in order to achieve the high clinical potentials accompanying this technology.

ContributorsFernandez, Eduardo (Author) / Greger, Bradley (Author) / House, Paul A. (Author) / Aranda, Ignacio (Author) / Botella, Carlos (Author) / Albisua, Julio (Author) / Soto-Sanchez, Cristina (Author) / Alfaro, Arantxa (Author) / Normann, Richard A. (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2014-07-21
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Description

In this study, a low-cycle fatigue experiment was conducted on printed wiring boards (PWB). The Weibull regression model and computational Bayesian analysis method were applied to analyze failure time data and to identify important factors that influence the PWB lifetime. The analysis shows that both shape parameter and scale parameter

In this study, a low-cycle fatigue experiment was conducted on printed wiring boards (PWB). The Weibull regression model and computational Bayesian analysis method were applied to analyze failure time data and to identify important factors that influence the PWB lifetime. The analysis shows that both shape parameter and scale parameter of Weibull distribution are affected by the supplier factor and preconditioning methods Based on the energy equivalence approach, a 6-cycle reflow precondition can be replaced by a 5-cycle IST precondition, thus the total testing time can be greatly reduced. This conclusion was validated by the likelihood ratio test of two datasets collected under two different preconditioning methods Therefore, the Weibull regression modeling approach is an effective approach for accounting for the variation of experimental setting in the PWB lifetime prediction.

ContributorsPan, Rong (Author) / Xu, Xinyue (Author) / Juarez, Joseph (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2016-11-12
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Studies about the data quality of National Bridge Inventory (NBI) reveal missing, erroneous, and logically conflicting data. Existing data quality programs lack a focus on detecting the logical inconsistencies within NBI and between NBI and external data sources. For example, within NBI, the structural condition ratings of some bridges improve

Studies about the data quality of National Bridge Inventory (NBI) reveal missing, erroneous, and logically conflicting data. Existing data quality programs lack a focus on detecting the logical inconsistencies within NBI and between NBI and external data sources. For example, within NBI, the structural condition ratings of some bridges improve over a period while having no improvement activity or maintenance funds recorded in relevant attributes documented in NBI. An example of logical inconsistencies between NBI and external data sources is that some bridges are not located within 100 meters of any roads extracted from Google Map. Manual detection of such logical errors is tedious and error-prone. This paper proposes a systematical “hypothesis testing” approach for automatically detecting logical inconsistencies within NBI and between NBI and external data sources. Using this framework, the authors detected logical inconsistencies in the NBI data of two sample states for revealing suspicious data items in NBI. The results showed that about 1% of bridges were not located within 100 meters of any actual roads, and few bridges showed improvements in the structural evaluation without any reported maintenance records.

ContributorsDin, Zia Ud (Author) / Tang, Pingbo (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2016-05-20