Life Sciences Commons^™

Simulation Modeling Within Workflow Technology, John A. Miller, Amit P. Sheth, Krzysztof J. Kochut, Xuzhong Wang, Arun Murugan

Kno.e.sis Publications

This paper presents an approach for integrating simulation modeling and analysis capabilities within the workflow management system (WFMS) being developed in the Large Scale Distributed Information Systems (LSDIS) Lab at the University of Georgia. Simulation modeling can be used for studying the efficiency of workflow designs as well as studying the general performance and reliability of WFMSs. We also discuss the importance of using sophisticated monitoring and animation capabilities, and the use of workflow management technology to advance simulation technology itself. Finally, we demonstrate a sample simulation where tasks and task managers are simulated.

On The Equivalence Of Upward And Downward Inheritance Reasoners, Krishnaprasad Thirunarayan

Kno.e.sis Publications

In this paper, we analyze systematically the downward (property flow) and the upward (individual flow) views of inheritance for different categories of inheritance networks. We observe that both these views assign the same meaning to tree-structured hierarchies, and explain the divergence in the interpretation of more general networks in terms of their expressive power. This simple analysis sheds light on the inherent nature of nonmonotonic inheritance and can form the basis for the design of efficient algorithms for certain classes of queries. In addition, we describe the notion of preferential inheritance to specify additional conflict resolution information that can be …

Power Systems Marginal Cost Curve And Its Applications, Shaojun Wang, S. M. Shahidehpour, Nian-De Xiang

Kno.e.sis Publications

This paper presents a forward recursive procedure to calculate the expected system marginal cost curve (EMC). The EMC formulation allows for multi-state and multi-block dispatch of generating units and is used to determine the optimal energy of pumped-storage units. A new approach is developed to compute the first and second derivatives of the expected generation energy of a thermal unit with respect to the capacity of all thermal units in the system. The salient feature of the proposed approach is that it applies to hydro-thermal systems with multiple limited-energy hydro units.

Predicting Conserved Water-Mediated Interactions In Protein Active Sites, Michael L. Raymer, Sridhar Venkataraman, William F. Punch, Erik D. Goodman, Brenda Kuhn

Kno.e.sis Publications

No abstract provided.

A Meta-Interpreter For Circuit-Extraction, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The design of a VLSI circuit consists of a description of the circuit in terms of its components and subcomponents, at various levels of detail. To verify that the layout of a VLSI circuit conforms to its design, one needs to work backwards from the lowest-level description of the circuit and recognize the higher-level components it constitutes. This paper is concerned with the application of logic programming techniques in the formal verification of the structural correctness of the VLSI circuit layouts. In particular, we review Michael Dukes' Generalized Extraction System (1990) that compiles design descriptions into a set of extraction …

Nonrecursive Incremental Evaluation Of Datalog Queries, Guozhu Dong, Jianwen Su, Rodney Topor

Kno.e.sis Publications

We consider the problem of repeatedly evaluating the same (computationally expensive) query to a database that is being updated between successive query requests. In this situation, it should be possible to use the difference between successive database states and the answer to the query in one state to reduce the cost of evaluating the query in the next state. We use nonrecursive Datalog (which are unions of conjunctive queries) to compute the differences, and call this process “incremental query evaluation using conjunctive queries”. After formalizing the notion of incremental query evaluation using conjunctive queries, we give an algorithm that constructs, …

The "Infoharness" Information Integration Platform, Leon Shklar, Satish Thatte, Howard Marcus, Amit P. Sheth

Kno.e.sis Publications

The "InfoHarness" information integration platform, tools, and services being developed at Bellcore are aimed at providing integrated and rapid access to huge amounts of heterogeneous information independent of the type, representation, and location of information. InfoHarness provides advanced search and browsing capabilities without imposing the burden of restructuring, reformatting or relocating information on information suppliers or creators. This is achieved through object-oriented encapsulation of information and the associated meta-information (e.g., type, location, access rights, owner, creation date, etc.). The meta-information extraction methods ensure rapid and largely automatic creation of information repositories. A gateway that supports access to InfoHarness repositories from …

Effects Of Natural Sequence Variation On Recognition By Monoclonal Antibodies Neutralize Simian Immunodeficiency Virus Infectivity, Weon Sang Choi, Catherine Collignon, Clotilde Thiriart, Dawn P. Wooley, E. J. Scott, Karen A. Kent, Ronald C. Desrosiers

Neuroscience, Cell Biology & Physiology Faculty Publications

The determinants of immune recognition by five monoclonal antibodies (KK5, KK9, KK17, Senv7.1, and Senv101.1) that neutralize simian immunodeficiency virus infectivity were analyzed. These five neutralizing monoclonal antibodies were generated to native SIVmac251 envelope glycoprotein expressed by a vaccinia virus recombinant vector. All five recognize conformational or discontinuous epitopes and require native antigen for optimal recognition. These monoclonal antibodies also recognize SIVmac239 gp120, but they do not recognize gp120 of two natural variants of SIVmac239, 1-12 and 8-22, which evolved during the course of persistent infection in vivo (D.P.W. Burns and R.C. Desrosiers, J. Virol. 65:1843-1854, 1991). Recombinant viruses which …

Benthic-Pelagic Links: Responses Of Benthos To Water-Column Nutrient Enrichment, S. C. Blumenshine, Yvonne Vadeboncoeur, D. M. Lodge, K. L. Cottingham, S. E. Knight

Biological Sciences Faculty Publications

Although the responses of pelagic algae and invertebrates to gradients of nutrient enrichment are well known, less is known about the responses of benthos to such gradients or how benthic and pelagic responses may interact. We performed a 9-wk experiment in 2000-L mesocosms in the field to test for the effect of water-column nutrient enrichment on phytoplankton, algae on sediments (epipelon) and hard surfaces (plastic strips), as well as pelagic and benthic primary consumers. The experimental design consisted of 4 nutrient enrichment rates (0, 0.5, 1.0 and 2.0 μg P L^-1 d^-1, together with N to yield …

High Rates Of Frameshift Mutations Within Homo-Oligomeric Runs During A Single Cycle Of Retroviral Replication, Dawn P. Wooley, H. M. Temin

Neuroscience, Cell Biology & Physiology Faculty Publications

Homo-oligomeric runs were inserted into a spleen necrosis virus-based retrovirus vector to determine the nature and rate of mutations within runs of 10 to 12 identical nucleotides during a single replication cycle. Clones of helper cells containing integrated copies of retroviral vectors were used to produce virus for infection of target (nonhelper) cells. Proviral sequences from target cell clones were compared with proviral sequences from helper cell clones to study mutations that occurred during a single cycle of replication. In addition to the internal region spanning the homo-oligomeric inserts, a naturally occurring run of 10 T's in the long terminal …

Longitudinal Dynamics Of Seston Concentration And Composition In A Lake Outlet Stream, Yvonne Vadeboncoeur

Biological Sciences Faculty Publications

Concentrations of suspended particulate organic carbon (POC), dissolved organic carbon, bacteria, and chlorophyll a were measured in a lake outlet in western Montana, USA. Seven sites within the first 3 km downstream from the lake were sampled over 14 mo. Downstream change in concentration of each variable was tested for fit to a power function (C=aD^b). Downstream changes in POC, bacteria, and chlorophyll a, sometimes fit a power function, and the value of the exponent b was positively correlated with discharge. At low discharge, a downstream decline in lake algae was accompanied by an increase in stream algae. …

Using Tickets To Enforce The Serializability Of Multidatabase Transactions, Dimitrios Georgakopoulos, Marek Rusinkiewicz, Amit P. Sheth

Kno.e.sis Publications

To enforce global serializability in a multidatabase environment the multidatabase transaction manager must take into account the indirect (transitive) conflicts between multidatabase transactions caused by local transactions. Such conflicts are difficult to resolve because the behavior or even the existence of local transactions is not known to the multidatabase system. To overcome these difficulties, we propose to incorporate additional data manipulation operations in the subtransactions of each multidatabase transaction. We show that if these operations create direct conflicts between subtransactions at each participating local database system, indirect conflicts can be resolved even if the multidatabase system is not aware of …

Semantics-Based Information Brokering: A Step Towards Realizing The Infocosm, Vipul Kashyap, Amit P. Sheth

Kno.e.sis Publications

The rapid advances in computer and communication technologies, and their merger, is leading to a global information market place. It will consist of federations of very large number of information systems that will cooperate to varying extents to support the users' information needs. We propose an architecture which may facilitate meeting these needs. It consists of three main components: information providers, information brokers and information consumers. We also propose an approach to information brokering. We discuss two of it's tasks: information resource discovery, which identities relevant information sources for a given query, and query processing, which involves the generation of …

Specifying And Enforcing Intertask Dependencies, Paul Attie, Munindar Singh, Amit P. Sheth, Marek Rusinkiewicz

Kno.e.sis Publications

Extensions of the traditional atomic transaction model are needed to support the development of multi-system applications or workflows that access heterogeneous databases and legacy application systems. Most extended transaction models use conditions involving events or dependencies between transactions. Intertask dependencies can serve as a uniform framework for defining extended transaction models. In this paper we introduce event attributes needed to determine whether a dependency is enforceable and to properly schedule events in extended transaction models. Using these attributes and a formalization of a dependency into the temporal logic CTL, we can automatically synthesize an automaton that captures the computations that …

A Framework For Controlling Cooperative Agents, Kuo-Chu Lee, William H. Mansfield, Amit P. Sheth

Kno.e.sis Publications

Presents an overview of the ITX (Interacting Transaction) system, which supports complex interactions among cooperating agents in the presence of user interventions that change application objectives and system failures. The system's components and its unique fixed-point criterion for feedback control of iterative interactions are described. An example of a simplified multimedia teleconferencing application is discussed to illustrate the features of the ITX system.

Simian Immunodeficiency Virus Mutants Resistant To Serum Neutralization Arise During Persistent Infection Of Rhesus Monkeys, Dawn P. Wooley, Catherine Collignon, Ronald C. Desrosiers

Neuroscience, Cell Biology & Physiology Faculty Publications

We previously described the pattern of sequence variation in gp120 following persistent infection of rhesus monkeys with the pathogenic simian immunodeficiency virus SIVmac239 molecular clone (D.P.W. Burns and R.C. Desrosiers, J. Virol. 65:1843, 1991). Sequence changes were confined largely to five variable regions (V1 to V5), four of which correspond to human immunodeficiency virus type 1 (HIV-1) gp120 variable regions. Remarkably, 182 of 186 nucleotide substitutions that were documented in these variable regions resulted in amino acid changes. This is an extremely nonrandom pattern, which suggests selective pressure driving amino acid changes in discrete variable domains. In the present study, …

So Far (Schematically) Yet So Near (Semantically), Amit P. Sheth, Vipul Kashyap

Kno.e.sis Publications

In a multidatabase system, schematic conflicts between two objects are usually of interest only when the objects have some semantic affinity. In this paper we try to reconcile the two perspectives. We first define the concept of semantic proximity and provide a semantic taxonomy. We then enumerate and classify the schematic and data conflicts. We discuss possible semantic similarities between two objects that have various types of schematic and data conflicts. Issues of uncertain information and inconsistent information are also addressed.

On Transactional Workflows, Amit P. Sheth, Marek Rusinkiewicz

Kno.e.sis Publications

The basic transaction model has evolved over time to incorporate more complex transactions structures and to take the advantage of semantics of higher-level operations that cannot be seen at the level of page reads and writes. Well known examples of such extended transaction models include nested and multi-level transactions. A number of relaxed transaction models have been defined in the last several years that permit a controlled relaxation of the transaction isolation and atomicity to better match the requirements of various database applications. Correctness criteria other than global serializability have also been proposed. Several examples of extended/relaxed transaction models are …

Abduction In Annotated Logic Programming, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The author investigates techniques to make the logic programming paradigm more expressive for knowledge representation, while simultaneously retaining the computational advantages of efficiency and simplicity. He extends the annotated language of K. Thirunarayan and K. Kifer (1989) in various directions to obtain an enriched representation language. In particular, rule bodies are permitted to be a conjunction of literals, and the rules to be recursive. A class of annotated logic programs called the stratified programs is identified which can be given a unique supported minimal Herbrand model as their meaning. Abductive reasoning is integrated into this annotated logic framework. The notion …

Using Flexible Transactions To Support Multisystem Telecommunication Applications, Mansoor Ansari, Linda Ness, Marek Rusinkiewicz, Amit P. Sheth

Kno.e.sis Publications

Service order provisioning is an important telecommunication application that automates the process of providing telephone services in response to the customer requests. It is an example of a multi-system application that requires access to multiple, independently developed application systems and their databases. In this paper, we describe the design and implementation of a prototype system1 that supports the execution of the Flexible Transactions and its use to develop the service order provisioning application. We argue that such approach may be used to support the development of multi-system, flow-through processing applications in a systematic and organized manner. Its advantages include fast …

Algorithms For Structural Schema Integration, James Geller, Ashish Mehra, Yehoshua Perl, Erich Neuhold, Amit P. Sheth

Kno.e.sis Publications

Current view and schema integration methodologies are driven by semantic considerations, and allow integration of objects only if that is valid from semantic and structural viewpoints. We had introduced a new integration technique called structural integration. It permits integration of objects that have structural similarities, even if they differ semantically. This technique uses the object-oriented Dual Model which separates the representation of structure and semantics.

In this paper we introduce algorithms for structural integration. We apply these algorithms to integrate two views of a large university database schema which had significant structural similarities but differed semantically.

Executing Multidatabase Transactions, Mansoor Ansari, Marek Rusinkiewicz, Linda Ness, Amit P. Sheth

Kno.e.sis Publications

In a multidatabase environment, the traditional transaction model has been found to be too restrictive. Therefore, several extended transaction models have been proposed in which some of the requirements of transaction, such as isolation or atomicity, are optional. The authors describe one of such extensions, the flexible transaction model and discuss the scheduling of transactions involving multiple autonomous database systems managed by heterogeneous DBMS.

The scheduling algorithm for flexible transactions is implemented using L.0, a logically parallel language which provides a framework for concisely specifying the multidatabase transactions and for scheduling them. The key aspects of a flexible transaction specification, …

Specifying Interdatabase Dependencies In A Multidatabase Environment, Marek Rusinkiewicz, Amit P. Sheth, George Karabatis

Kno.e.sis Publications

The problem of interdatabase dependencies and the effect they have on applications updating interdependent data are addressed. A model that allows specifications of constraints among multiple databases in a declarative fashion is proposed. The separation of the constraints from the application programs facilitates the maintenance of data constraints and allows flexibility in their implementation. It allows investigation of various mechanisms for enforcing the constraints, independently of the application programs. By grouping the constraints together, it is possible to check their completeness and discover possible contradictions among them. The concepts of polytransactions, which use interdatabase dependencies to generate a series of …

On The Relationship Between Parsimonious Covering And Boolean Minimization, Venu Dasigi, Krishnaprasad Thirunarayan

Kno.e.sis Publications

Minimization of Boolean switching functions is a basic problem in the design of logic circuits. The designer first comes up with a switching function expressed in terms of several binary input variables that satisfies the desired functionality, and then attempts to minimize the function as a sum of products or product of sums. It turns out that a sum of products form of a switching function that has no redundancy is a union of prime implicants of the function.

In this paper we would like to explicate some of the relationships of the boolean minimization problem to a formalization of …

Strain-Specific Neutralizing Determinant In The Transmembrane Protein Of Simian Immunodeficiency Virus, Toshiaki Kodama, Dawn P. Wooley, Daniel P. Silva, Fulvia Dimarzo Veronese, Ronald C. Desrosiers

Neuroscience, Cell Biology & Physiology Faculty Publications

Monoclonal antibody SF8/5E11, which recognizes the transmembrane protein (TMP) of simian immunodeficiency virus of macaque monkeys (SIVmac), displayed strict strain specificity. It reacted with cloned and uncloned SIVmac251 but not with cloned SIVmac142 and SIVmac239 on immunoblots. This monoclonal antibody neutralized infection by cloned, cell-free SIVmac251 and inhibited formation of syncytia by cloned SIVmac251-infected cells; these activities were specific to cloned SIVmac251 and did not occur with the other viruses. Site-specific mutagenesis was used to show that TMP amino acids 106 to 110 (Asp-Trp-Asn-Asn-Asp) determined the strain specificity of the monoclonal antibody. This strain-specific neutralizing determinant is located within a …

The Architecture Of Braid: A System For Bridging Al/Db Systems, Amit P. Sheth, Anthony B. O'Hare

Kno.e.sis Publications

We describe the design of BrAID (a Bridge between Artificial Intelligence and Database Management Systems), an experimental system for the efficient integration of logic based Artificial Intelligence (Al) and database (DB) technologies. Features provided by BrAID include (a) access to conventional DBMSs, (b) support for multiple inferencing strategies, (c) a powerful caching subsystem that manages views and employs subsumption to facilitate the reuse of previously cached data, (d) lazy or eager evaluation of queries submitted by the AI system, and (e) the generation of advice by the AI system to aid in cache management and query execution planning. To discuss …

Selection Of Genetic Variants Of Simian Immunodeficiency Virus In Persistently Infected Rhesus Monkeys, Dawn P. Wooley, Ronald C. Desrosiers

Neuroscience, Cell Biology & Physiology Faculty Publications

Genetic and antigenic variation may be one means by which lentiviruses that cause AIDS avoid elimination by host immune responses. Genetic variation in the envelope gene (env) was studied by comparing the nucleotide sequences of 27 clones obtained from two rhesus monkeys infected with molecularly cloned simian immunodeficiency virus. All 27 clones differed from each other and differed from the input clone in the gp120 (SU) portion of the envelope gene. Nucleotide substitutions were shown to accumulate with time at an average rate of 8.5 per 1,000 per year in SU. Surprisingly, the majority of nucleotide substitutions (81%) resulted in …

On Serializability Of Multidatabase Transactions Through Forced Local Conflict, Dimitrios Georgakopoulos, Marek Rusinkiewicz, Amit P. Sheth

Kno.e.sis Publications

The main difficulty in enforcing global serializability in a multidatabase environment lies in resolving indirect transitive conflicts between multidatabase transactions. Indirect conflicts introduced by local transactions are difficult to resolve because the behavior or even the existence of local transactions is not known to the multidatabase system. To overcome these problems, we propose to incorporate additional data manipulation operations in the subtransactions of each multidatabase transaction. We show that if these operations create direct conflicts between subtransactions at each participating local database system, indirect conflicts can be resolved even if the multidatabase system is not aware of their existence. Based …

Management Of Interdependent Data: Specifying Dependency And Consistency Requirements, Amit P. Sheth, Marek Rusinkiewicz

Kno.e.sis Publications

Multiple databases that serve the needs of various application systems are considered. One of the significant problems in managing these databases is to maintain the related data items consistent to the required degree. This problem is frequently referred to as `redundant data management'. Since the term `redundancy' tends to imply that the data is unwanted or superfluous, the authors use the more general term `management of interdependent data'. Some preliminary ideas in this area are discussed. The problem of managing interdependent data is characterized, and some important types of interdatabase dependency are identified.

Attribute Relationships: An Impediment In Automating Schema Integration, Amit P. Sheth, Sunit K. Gala

Kno.e.sis Publications

Success in schema integration depends on understanding the semantics of schema components (e.g., entity sets, relationship sets, attributes), and the ability to capture and reason about these semantics. An important objective of our work on schema integration is to automate the reasoning as much as possible, and when not possible, depend on the human input and guidance. A key results of comparing the semantics associated with schema objects is that of determining attribute relationship. Once attribute relationships are determined, the task of object class(e.g., entity sets and relationship sets) integration becomes simpler and can e automated to a great extent. …