A Declarative Semantics for CLP with Qualification and Proximity

Uncertainty in Logic Programming has been investigated during the last decades, dealing with various extensions of the classical LP paradigm and different applications. Existing proposals rely on different approaches, such as clause annotations based on uncertain truth values, qualification values as a generalization of uncertain truth values, and unification based on proximity relations. On the other hand, the CLP scheme has established itself as a powerful extension of LP that supports efficient computation over specialized domains while keeping a clean declarative semantics. In this paper we propose a new scheme SQCLP designed as an extension of CLP that supports qualification values and proximity relations. We show that several previous proposals can be viewed as particular cases of the new scheme, obtained by partial instantiation. We present a declarative semantics for SQCLP that is based on observables, providing fixpoint and proof-theoretical characterizations of least program models as well as an implementation-independent notion of goal solutions.Comment: 17 pages, 26th Int'l. Conference on Logic Programming (ICLP'10

A Transformation-based Implementation for CLP with Qualification and Proximity

Uncertainty in logic programming has been widely investigated in the last decades, leading to multiple extensions of the classical LP paradigm. However, few of these are designed as extensions of the well-established and powerful CLP scheme for Constraint Logic Programming. In a previous work we have proposed the SQCLP (proximity-based qualified constraint logic programming) scheme as a quite expressive extension of CLP with support for qualification values and proximity relations as generalizations of uncertainty values and similarity relations, respectively. In this paper we provide a transformation technique for transforming SQCLP programs and goals into semantically equivalent CLP programs and goals, and a practical Prolog-based implementation of some particularly useful instances of the SQCLP scheme. We also illustrate, by showing some simple-and working-examples, how the prototype can be effectively used as a tool for solving problems where qualification values and proximity relations play a key role. Intended use of SQCLP includes flexible information retrieval applications.Comment: 49 pages, 5 figures, 1 table, preliminary version of an article of the same title, published as Technical Report SIC-4-10, Universidad Complutense, Departamento de Sistemas Inform\'aticos y Computaci\'on, Madrid, Spai

INTEGRATING PHYLOGENOMICS AND CHROMOSOME MAPPING TO STUDY THE EVOLUTIONARY RELATIONSHIPS AMONG EUKARYOTES AND THE EVOLUTION OF THEIR GENOMES

Our knowledge about the evolution of eukaryotes and their genomes is very limited because it has largely been based on studies of plants, animals and fungi, which are not a significant representation of the diversity across the eukaryotic tree of life. Advances in sequencing technologies are helping to expand our knowledge by including underrepresented clades and revealing that eukaryotic genomes are much more complex and dynamic than originally thought. In response to the need to explore such levels of complexity in eukaryotic genomes and the earliest events of eukaryotic evolution, this dissertation focuses on the development of bioinformatic and phylogenomic tools to study karyotype evolution and answering deep evolutionary questions. The first chapter covers the development of a phylogenomic chromosome mapper, PhyloChromoMap, and its use to study karyotype evolution in the malaria parasite Plasmodium falciparum. In addition to providing a very flexible and powerful tool to map the phylogenetic history of genes across karyotypes, this chapter reveals very distinctive patterns of evolution between subtelomeric and internal regions of the chromosomes of P. falciparum. The second chapter focuses on the development of PhyloToL, a taxon- and gene-rich phylogenomic pipeline. This chapter presents examples of how to use PhyloToL for phylogenomic studies and studies of gene family evolution, and presents a series of benchmark studies comparing PhyloToL against other popular phylogenomic pipelines. Finally, the third chapter focuses on using PhyloToL to explore one of the most critical questions in field of evolution, the root of the eukaryotic tree of life. The results in this chapter suggest that the root should be placed between Opisthokonta and all other eukaryotes. Overall this dissertation contributes insights of the earliest events of evolution in eukaryotes and provides novel approaches to study this topic. The results of this dissertation are important for comparative biology as it allows to understand the timing and mode of evolution of eukaryotic features across the eukaryotic tree of lif

Performance of Alternative Diamond Interchange Forms: Volume 1—Research Report

Service interchanges connect freeways to arterial roads and are the backbone of the U.S. road network. Improving the operations of service interchanges is possible by applying one of several new solutions: diverging diamond, single point interchanges, and double or single roundabout diamonds. VISSIM was used to perform 13,500 experiments to simulate the traffic performance of the studied alternative interchanges during a typical day for a wide range of geometry and traffic scenarios. Five performance measures were investigated: daily-average delay, level of service of critical movement, daily-average number of stops, longest off-ramp queue, and longest crossing road queue. The obtained daily-average delays at the alternative interchanges were consistent with expectations. Roundabouts had the highest average delay while single-point interchanges had the lowest average delays. Roundabouts exhibited the lowest numbers of stops among all the alternatives in the low traffic range up to non-freeway 30,000 veh/day. Diverging diamonds tended to have the shortest and roundabouts tended to have the longest queues on their off-ramps. Overall, single-point interchanges had the shortest queues among all the alternatives. The study developed guidelines for early stage screening of alternative diamond. The guidelines exhibit performance measures for 25 traffic and geometric scenarios and a wide range of traffic volumes. The guidelines provide a fair comparison procedure for alternative diamond interchanges in the preliminary planning and conceptual design stages

Performance of Alternative Diamond Interchange Forms: Volume 2—Guidelines for Selecting Alternative Diamond Interchanges

Service interchanges connect freeways to arterial roads and are the backbone of the U.S. road network. Improving the operations of service interchanges is possible by applying one of several new solutions: diverging diamond, single point interchanges, and double or single roundabout diamonds. VISSIM was used to perform 13,500 experiments to simulate the traffic performance of the studied alternative interchanges during a typical day for a wide range of geometry and traffic scenarios. Five performance measures were investigated: daily-average delay, level of service of critical movement, daily-average number of stops, longest off-ramp queue, and longest crossing road queue. The obtained daily-average delays at the alternative interchanges were consistent with expectations. Roundabouts had the highest average delay while single-point interchanges had the lowest average delays. Roundabouts exhibited the lowest numbers of stops among all the alternatives in the low traffic range up to non-freeway 30,000 veh/day. Diverging diamonds tended to have the shortest and roundabouts tended to have the longest queues on their off-ramps. Overall, single-point interchanges had the shortest queues among all the alternatives. The study developed guidelines for early stage screening of alternative diamond. The guidelines exhibit performance measures for 25 traffic and geometric scenarios and a wide range of traffic volumes. The guidelines provide a fair comparison procedure for alternative diamond interchanges in the preliminary planning and conceptual design stages

Performance Measure That Indicates Geometry Sufficiency of State Highways: Volume I—Project Scoring and Network Screening

The Indiana Department of Transportation (INDOT) selects projects for implementation by taking into account several criteria related to cross-section, alignment and safety to evaluate various geometry improvements to be carried out as a part of projects. The existing practice uses an intuitive point allocation method to score these individual categories. The current study proposes a methodology to evaluate these projects considering the safety and mobility impacts of the improvements which lie in the scope of each project. This methodology is also used to screen roads based on existing geometry deficiencies with respect to a desirable design standard. The road screening process and the project evaluation process form two steps that support the asset management process. The road screening process helps in filtering road segments based on geometry deficiencies and identifies the least adequate road segments. Projects may be further developed with estimated improvements to be carried out on such segments using detailed information regarding these improvements. As part of the study, we have also investigated feasible ways of extracting additional elements from available datasets to support asset management in Indiana. We have looked into available data sources for their suitability. We have combined the use of orthophotos, LiDAR point clouds, digital elevation and surface models to identify remote sensing methods that are capable of extracting the required features efficiently. We propose a framework for determining the paved surface, average grade, embankment slopes, extracting the obstructions near the traveled way like trees and man-made structures

Obesity Induces Hypothalamic Endoplasmic Reticulum Stress and Impairs Proopiomelanocortin (POMC) Post-translational Processing

It was shown previously that abnormal prohormone processing or inactive proconverting enzymes that are responsible for this processing cause profound obesity. Our laboratory demonstrated earlier that in the diet-induced obesity (DIO) state, the appetite-suppressing neuropeptide -melanocyte-stimulating hormone ( -MSH) is reduced, yet the mRNA of its precursor protein proopiomelanocortin (POMC) remained unaltered. It was also shown that the DIO condition promotes the development of endoplasmic reticulum (ER) stress and leptin resistance. In the current study, using an in vivo model combined with in vitro experiments, we demonstrate that obesity-induced ER stress obstructs the post-translational processing of POMC by decreasing proconverting enzyme 2, which catalyzes the conversion of adrenocorticotropin to -MSH, thereby decreasing -MSH peptide production. This novel mechanism of ER stress affecting POMC processing in DIO highlights the importance of ER stress in regulating central energy balance in obesity.Fil: Cakir, Isin. Brown University; Estados UnidosFil: Cyr, Nicole E.. Brown University; Estados UnidosFil: Perello, Mario. Brown University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Litvinov, Bogdan Patedakis. Brown University; Estados UnidosFil: Romero, Amparo. Brown University; Estados UnidosFil: Stuart, Ronald C.. Brown University; Estados UnidosFil: Nillni, Eduardo A.. Brown University; Estados Unido