Disocvering Ionic Liquid Resistant Genes, 2013 Joint BioEnergy Institute/ Lawerence Livermore National Laboratory
Disocvering Ionic Liquid Resistant Genes, Bree Person, Douglass Higgins, Michael Thelen
STAR Program Research Presentations
: Plant biomass is a rich source of sugars that can be converted to biofuels by engineered microbes. However, because the lignocellulose in biomass is insoluble in aqueous conditions and recalcitrant to enzymatic degradation, thermochemical treatment is required to break apart the lignin and cellulose polymers before sugars can be released. The most effective chemicals for doing this are known as ionic liquids, which are salts that are molten at temperatures below 100° C. Although these solvents have many unique properties that are ideal for solubilizing lignocellulose, they have been found to inhibit the growth of bacterial strains used to …
Floracultures: Conserving Perth's Botanical Heritage Through A Digital Repository, 2013 Edith Cowan University
Floracultures: Conserving Perth's Botanical Heritage Through A Digital Repository, John C. Ryan
Research outputs 2013
FloraCultures is a 2013 pilot project in development with Kings Park and Botanic Garden in Perth, Western Australia, and funded by Edith Cowan University’s Early Career Researcher grant scheme. The project aims to develop a model for documenting the plant-based cultural heritage of 30–50 indigenous species occurring in the Kings Park bushland. The FloraCultures initiative integrates archival and digital design techniques, creating a unique web portal of potential interest to a range of users -- from first-time tourists and amateur naturalists to heritage consultants and evironmental conservationists . The initiative reflects the belief that research into environmental heritage (defined broadly …
Protein Kinases: Structure Modeling, Inhibition, And Protein-Protein Interactions, 2013 University of Mississippi
Protein Kinases: Structure Modeling, Inhibition, And Protein-Protein Interactions, Khaled M. Elokely
Electronic Theses and Dissertations
Human protein kinases belong to a large and diverse enzyme family that contains more than 500 members. Deregulation of protein kinases is associated with many disorders, and this is why protein kinases are attractive targets for drug discovery. Due to the high conservation of the ATP binding pocket among this family, designing specific and/or selective inhibitors against certain member(s) is challenging. Several studies have been conducted on protein kinases to validate them as suitable drug targets. Although there are numerous target-validated protein kinases, the efforts to develop small molecule inhibitors have so far led to only a limited number of …
Determining A New Alignment Scoring Matrix For Disordered Proteins, 2013 Rochester Institute of Technology
Determining A New Alignment Scoring Matrix For Disordered Proteins, Adam Handen
Theses
Intrinsically disordered proteins (IDPs) are polypeptide sequences that do not form a rigid three dimensional structure when isolated in the cytosol of the cell. These sequences are very common in most genomes, and usually are involved in many protein-protein interactions. IDPs also play a key role in many diseases, including cancer and Huntington's disease. However, IDPs are difficult to study because of their amorphous shape, high mutation rate, and unique amino acid composition. These obstacles make homology studies especially difficult.
This study focused on generating a new substitution matrix designed to aid in homology studies of IDPs. The matrix was …
Traffic Analytics Using Probabilistic Graphical Models Enhanced With Knowledge Bases, 2013 Wright State University - Main Campus
Traffic Analytics Using Probabilistic Graphical Models Enhanced With Knowledge Bases, Pramod Anantharam, Krishnaprasad Thirunarayan, Amit P. Sheth
Kno.e.sis Publications
Graphical models have been successfully used to deal with uncertainty, incompleteness, and dynamism within many domains. These models built from data often ignore preexisting declarative knowledge about the domain in the form of ontologies and Linked Open Data (LOD) that is increasingly available on the web. In this paper, we present an approach to leverage such 'top-down' domain knowledge to enhance 'bottom-up' building of graphical models. Specifically, we propose three operations on the graphical model structure to enrich it with nodes, edges, and edge directions. We illustrate the enrichment process using traffic data from 511.org and declarative knowledge from ConceptNet. …
Advancing Data Reuse In Phyloinformatics Using An Ontology-Driven Semantic Web Approach, 2013 Wright State University - Main Campus
Advancing Data Reuse In Phyloinformatics Using An Ontology-Driven Semantic Web Approach, Maryam Panahiazar, Amit P. Sheth, Ajith Harshana Ranabahu, Rutger Vos, Jim Leebens-Mack
Kno.e.sis Publications
Phylogenetic analyses can resolve historical relationships among genes, organisms or higher taxa. Understanding such relationships can elucidate a wide range of biological phenomena, including, for example, the importance of gene and genome duplications in the evolution of gene function, the role of adaptation as a driver of diversification, or the evolutionary consequences of biogeographic shifts. Phyloinformaticists are developing data standards, databases and communication protocols (e.g. Application Programming Interfaces, APIs) to extend the accessibility of gene trees, species trees, and the metadata necessary to interpret these trees, thus enabling researchers across the life sciences to reuse phylogenetic knowledge. Specifically, Semantic Web …
A Hybrid Approach To Finding Relevant Social Media Content For Complex Domain Specific Information Needs, 2013 Wright State University - Main Campus
A Hybrid Approach To Finding Relevant Social Media Content For Complex Domain Specific Information Needs, Delroy H. Cameron, Amit P. Sheth, Nishita Jaykumar, Gaurish Anand, Krishnaprasad Thirunarayan, Gary Alan Smith
Kno.e.sis Publications
While contemporary semantic search systems offer to improve classical keyword-based search, they are not always adequate for complex, domain specific information needs. Some complex search situations require knowledge of both ontological concepts as well as 'intelligible constructs' not typically modeled in ontologies. Intelligible constructs convey essential information, which may be important to the holistic information needs of information seekers. Such constructs may include notions of intensity, frequency, interval, dosage, emotion, sentiment, equivalence, synonymy, negation, parts-of-speech, etc. However, few search systems utilize both structured background knowledge (ontologies) and the aforementioned knowledge for query interpretation in domain specific searches. Instead, there is …
Where Does Neisseria Acquire Foreign Dna From: An Examination Of The Source Of Genomic And Pathogenic Islands And The Evolution Of The Neisseria Genus, 2013 Loyola University Chicago
Where Does Neisseria Acquire Foreign Dna From: An Examination Of The Source Of Genomic And Pathogenic Islands And The Evolution Of The Neisseria Genus, Catherine Putonti, Bogdan Nowicki, Michael Shaffer, Yuriy Fofanov, Stella Nowicki
Bioinformatics Faculty Publications
This journal is now called BMC Ecology and Evolution
Background
Pathogenicity islands (PAIs) or genomic islands (GEIs) are considered to be the result of a recent horizontal transfer. Detecting PAIs/GEIs as well as their putative source can provide insight into the organism’s pathogenicity within its host. Previously we introduced a tool called S-plot which provides a visual representation of the variation in compositional properties across and between genomic sequences. Utilizing S-plot and new functionality developed here, we examined 18 publicly availableNeisseria genomes, including strains of both pathogenic and non-pathogenic species, in order to identify regions of unusual compositional properties …
Twitris: Socially Influenced Browsing, 2013 Wright State University - Main Campus
Twitris: Socially Influenced Browsing, Ashutosh Sopan Jadhav, Wenbo Wang, Raghava Mutharaju, Pramod Anantharam, Vinh Nguyen, Amit P. Sheth, Karthik Gomadam, Meenakshi Nagarajan, Ajith Harshana Ranabahu
Kno.e.sis Publications
In this paper, we present Twitris, a semantic Web application that facilitates browsing for news and information, using social perceptions as the fulcrum. In doing so we address challenges in large scale crawling, processing of real time information, and preserving spatio-temporal-thematic properties central to observations pertaining to real time events. We extract metadata about events from Twitter and bring related news and Wikipedia articles to the user. In developing Twitris, we have used the DBPedia ontology.
Adaptive Semantic Annotation Of Entity And Concept Mentions In Text, 2013 Wright State University - Main Campus
Adaptive Semantic Annotation Of Entity And Concept Mentions In Text, Pablo N. Mendes
Kno.e.sis Publications
The recent years have seen an increase in interest for knowledge repositories that are useful across applications, in contrast to the creation of ad hoc or application-specific databases.
These knowledge repositories figure as a central provider of unambiguous identifiers and semantic relationships between entities. As such, these shared entity descriptions serve as a common vocabulary to exchange and organize information in different formats and for different purposes. Therefore, there has been remarkable interest in systems that are able to automatically tag textual documents with identifiers from shared knowledge repositories so that the content in those documents is described in a …
Gulf-Wide Decreases In The Size Of Large Coastal Sharks Documented By Generations Of Fishermen, 2013 University of South Alabama
Gulf-Wide Decreases In The Size Of Large Coastal Sharks Documented By Generations Of Fishermen, Sean P. Powers, F. Joel Frodrie, Steven B. Scyphers, J. Marcus Drymon, Robert L. Shipp, Gregory W. Stunz
University Faculty and Staff Publications
Large sharks are top predators in most coastal and marine ecosystems throughout the world, and evidence of their reduced prominence in marine ecosystems has been a serious concern for fisheries and ecosystem management. Unfortunately, quantitative data to document the extent, timing, and consequences of changes in shark populations are scarce, thwarting examination of long-term (decadal, century) trends, and reconstructions based on incomplete data sets have been the subject of debate. Absence of quantitative descriptors of past ecological conditions is a generic problem facing many fields of science but is particularly troublesome for fisheries scientists who must develop specific targets for …
Automatic Elucidation Of Gpi Molecular Structures With Grid Computing Technology, 2013 University of Texas at El Paso
Automatic Elucidation Of Gpi Molecular Structures With Grid Computing Technology, Juan Clemente Aguilar Bonavides
Open Access Theses & Dissertations
Glycosylphosphatidylinositol (GPI)-anchored proteins are involved in many biological processes and are of medical importance. The identification and analysis of the entire collection of free and protein-linked GPIs within an organism (i.e., GPIomics) requires highly sensitive instruments. At present, liquid chromatography-tandem mass spectrometry (LC-MS/MS or -MSn) is the most efficient laboratory technique for these tasks. As a typical MSn experiment produces hundreds of thousands of spectra, the data analysis creates a major bottleneck in high-throughput GPIomic projects. Yet, no computational tool for characterizing the chemical structures of GPI is available to date. We propose a library-search algorithm to …
Natural Resources Biometrics, 2013 SUNY College of Environmental Science and Forestry
Natural Resources Biometrics, Diane Kiernan
Open Educational Resources
Natural Resources Biometrics is a peer reviewed open textbook that begins with a review of descriptive statistics, estimation, and hypothesis testing. The following chapters cover one- and two-way analysis of variance (ANOVA), including multiple comparison methods and interaction assessment, with a strong emphasis on application and interpretation. Simple and multiple linear regressions in a natural resource setting are covered in the next chapters, focusing on correlation, model fitting, residual analysis, and confidence and prediction intervals. The final chapters cover growth and yield models, volume and biomass equations, site index curves, competition indices, importance values, and measures of species diversity, association, …
Seqnls: Nuclear Localization Signal Prediction Based On Frequent Pattern Mining And Linear Motif Scoring, 2013 University of South Carolina - Columbia
Seqnls: Nuclear Localization Signal Prediction Based On Frequent Pattern Mining And Linear Motif Scoring, J.-R. Lin, Jianjun Hu
Faculty Publications
Nuclear localization signals (NLSs) are stretches of residues in proteins mediating their importing into the nucleus. NLSs are known to have diverse patterns, of which only a limited number are covered by currently known NLS motifs. Here we propose a sequential pattern mining algorithm SeqNLS to effectively identify potential NLS patterns without being constrained by the limitation of current knowledge of NLSs. The extracted frequent sequential patterns are used to predict NLS candidates which are then filtered by a linear motif-scoring scheme based on predicted sequence disorder and by the relatively local conservation (IRLC) based masking.
The experiment results on …
Hybrid Plasmonic Biosensor For Simultaneous Measurement Of Both Thickness And Refractive Index, 2013 Technological University Dublin
Hybrid Plasmonic Biosensor For Simultaneous Measurement Of Both Thickness And Refractive Index, Youqiao Ma, Gerald Farrell, Yuliya Semenova, Hau Ping Chan, Qiang Wu
Articles
A novel hybrid plasmonic biosensor using a sub-wavelength reflection metal grating is proposed and analyzed. The simulation results show that the hybrid plasmonic-cavity (HPCM) are wavelength dependent on both the refractive index (RI) and thickness of the surrounding analyte layer, with a sensitivity of 448 nm/RIU (refractive index unit) and 75 nm/um, respectively. However wavelength related to the cavity resonant mode (CRM) related is only sensitive to the environmental refractive index changes. In principle it is possible to determine both RI and thickness of the coating layer simultaneously.
An Investigation Of Alternative Oxidase Presence, Expression, And Regulation In The Moss Physcomitrella Patens, 2013 Wilfrid Laurier University
An Investigation Of Alternative Oxidase Presence, Expression, And Regulation In The Moss Physcomitrella Patens, Karina I. Neimanis
Theses and Dissertations (Comprehensive)
Alternative oxidase (AOX) is an inner mitochondrial membrane protein that introduces a branch point at ubiquinone within the respiratory electron transport system (ETS). The AOX protein bypasses two sites of proton translocation within the ETS and as a result the yield of ATP per oxygen consumed is significantly reduced. Although AOX appears to be energetically wasteful, recent studies have revealed that AOX has a wide taxonomic distribution. AOX multigene families, transcripts, protein levels, and enzymatic activity have been most thoroughly characterized in many angiosperm (flowering) plants. Given the data available for angiosperm AOXs, evidence of non-angiosperm AOXs in the primary …
Hydraphiles: A Rigorously Studied Class Of Synthetic Channel Compounds With In Vivo Activity, 2013 University of Missouri–St. Louis
Hydraphiles: A Rigorously Studied Class Of Synthetic Channel Compounds With In Vivo Activity, Saeedeh Negin, Bryan Smith, Alexandra Unger, W. Leevy, George Gokel
Chemistry & Biochemistry Faculty Works
No abstract provided.
A Bayesian Decision Theoretic Approach To Directional Multiple Hypotheses Problems, 2012 Marquette University
A Bayesian Decision Theoretic Approach To Directional Multiple Hypotheses Problems, Naveen Bansal
Naveen Bansal
No abstract provided.
Phylotastic! Making Tree-Of-Life Knowledge Accessible, Reusable And Convenient, 2012 National Institute of Standards and Technology
Phylotastic! Making Tree-Of-Life Knowledge Accessible, Reusable And Convenient, Arlin Stoltzfus, Hilmar Lapp, Helena Deus, Brian Sidlauskas, Christian M. Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O. Webb, Luke J. Harmon, Megan Pirrung, Brian O'Meara, Matthew W. Pennell, Siavash Mirarab, Michael S. Rosenburg, James P. Balhoff, Holly M. Bik, Tracy A. Heath, Peter E. Midford, Joseph W. Brown, Emily Jane Mctavish, Jeet Sukumaran, Mark Westneat, Michael E. Alfaro, Aaron Steele, Greg Jordan
Tracy Heath
The Computation Of Cyclic Peptide With Prolin-Prolin Bond As Fusion Inhibitor Of Denv Envelope Protein Through Molecular Docking And Molecular Dynamics Simulation, 2012 University of Indonesia
The Computation Of Cyclic Peptide With Prolin-Prolin Bond As Fusion Inhibitor Of Denv Envelope Protein Through Molecular Docking And Molecular Dynamics Simulation, Arli A. Parikesit, Hilyatuz Zahroh, Andreas S. Nugroho, Amalia Hapsari, Usman Sumo F. Tambunan
Arli A Parikesit
A disease that caused by dengue virus (DENV) has become the major health problem of the world. Nowadays, no effective treatment is available to overcome the disease due to the level of dengue virus pathogeneses. A novel treatment method such as antiviral drug is highly necessary for coping with the dengue disease. Envelope protein is one of the non-structural proteins of DENV, which engaged in the viral fusion process. It penetrates into the host cell to transfer its genetic material into the targeted cell followed by replication and establishment of new virus. Thus, the envelope protein can be utilized as …