Modeling the peptide-T cell receptor interaction by the comparative molecular similarity indices analysis-soft independent modeling of class analogy technique

A set of 38 epitopes and 183 non-epitopes, which bind to alleles of the HLA-A3 supertype, was subjected to a combination of comparative molecular similarity indices analysis (CoMSIA) and soft independent modeling of class analogy (SIMCA). During the process of T cell recognition, T cell receptors (TCR) interact with the central section of the bound nonamer peptide; thus only positions 4−8 were considered in the study. The derived model distinguished 82% of the epitopes and 73% of the non-epitopes after cross-validation in five groups. The overall preference from the model is for polar amino acids with high electron density and the ability to form hydrogen bonds. These so-called “aggressive” amino acids are flanked by small-sized residues, which enable such residues to protrude from the binding cleft and take an active role in TCR-mediated T cell recognition. Combinations of “aggressive” and “passive” amino acids in the middle part of epitopes constitute a putative TCR binding motif

A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily

Epitope identification is the basis of modern vaccine design. The present paper studied the supermotif of the HLA-A3 superfamily, using comparative molecular similarity indices analysis (CoMSIA). Four alleles with high phenotype frequencies were used: A*1101, A*0301, A*3101 and A*6801. Five physicochemical properties—steric bulk, electrostatic potential, local hydro-phobicity, hydrogen-bond donor and acceptor abilities—were considered and ‘all fields’ models were produced for each of the alleles. The models have a moderate level of predictivity and there is a good correlation between the data. A revised HLA-A3 supermotif was defined based on the comparison of favoured and disfavoured properties for each position of the MHC bound peptide. The present study demonstrated that CoMSIA is an effective tool for studying peptide–MHC interactions.

Procedure of Formalization of the Indices of Banks’ Stable Functioning in Comparative Estimates of Their Development

The advisability of analyzing the banks liquidity and profitability as the key factor when building the comparative estimate of their functioning is considered. The procedure of formal description of the bank stable functioning indices is substantiated. Fuzzy interpretation of the bank management efficiency estimation is offered. The possibility to formalize the bank functioning estimates on the basis of the corresponding fuzzy set levels hierarchy is analyzed. The comparative estimate of different bank systems functioning is given.

Weighted Theorems on Fractional Integrals in the Generalized Hölder Spaces via Indices mω and Mω

Mathematics Subject Classification: 26A16, 26A33, 46E15.

The Wiener, Eccentric Connectivity and Zagreb Indices of the Hierarchical Product of Graphs

Let G1 = (V1, E1) and G2 = (V2, E2) be two graphs having a distinguished or root vertex, labeled 0. The hierarchical product G2 ⊓ G1 of G2 and G1 is a graph with vertex set V2 × V1. Two vertices y2y1 and x2x1 are adjacent if and only if y1x1 ∈ E1 and y2 = x2; or y2x2 ∈ E2 and y1 = x1 = 0. In this paper, the Wiener, eccentric connectivity and Zagreb indices of this new operation of graphs are computed. As an application, these topological indices for a class of alkanes are computed. ACM Computing Classification System (1998): G.2.2, G.2.3.

Distance-based accessibility indices

The paper attempts to develop a suitable accessibility index for networks where each link has a value such that a smaller number is preferred like distance, cost, or travel time. A measure called distance sum is characterized by three independent properties: anonymity, an appropriately chosen independence axiom, and dominance preservation, which requires that a node not far to any other is at least as accessible. We argue for the need of eliminating the independence property in certain applications. Therefore generalized distance sum, a family of accessibility indices, will be suggested. It is linear, considers the accessibility of vertices besides their distances and depends on a parameter in order to control its deviation from distance sum. Generalized distance sum is anonymous and satisfies dominance preservation if its parameter meets a sufficient condition. Two detailed examples demonstrate its ability to reflect the vulnerability of accessibility to link disruptions.

Repetitive DNA fragments as taxonomic markers for {\it Penaeus\/} sibling taxa (Decapoda: Dendrobranchiata: Penaeidae) from the southern terminus of the Florida peninsula, U.S.A.

Sympatric populations of P. brasiliensis and P. duorarum from Biscayne Bay, Florida, revealed species-specific satellite DNA organizational patterns with the restriction endonuclease EcoRI. The species-specific satellite DNA patterns can be explained as resulting from differential amplification/deletion events having altered monomer arrays after the divergence of these two species. Two discontinuous populations of P. duorarum (Biscayne Bay and Dry Tortugas) were found to exhibit distinct EcoRI satellite fragment patterns; BamHI repetitive fragments specific to the Dry Tortugas P. duorarum population were also detected. In addition, the evolutionary conservation of the Penaeus (Farfantepenaeus) satellites was investigated. The putative conservation of sequences related to one cloned P. duorarum satellite monomer unit suggests that the FTR satellite DNA family may not only be of use as a genome tag to distinguish between sibling and cryptic Penaeus species but may also serve as a probe to better understand decapod crustacean genome organization and evolution. ^

The Influence of Phosphorus on Periphyton Mats from the Everglades and Three Tropical Karstic Wetlands

The distinctive karstic, freshwater wetlands of the northern Caribbean and Central American region support the prolific growth of calcite-rich periphyton mats. Aside from the Everglades, very little research has been conducted in these karstic wetlands, which are increasingly threatened by eutrophication. This study sought to (i) test the hypothesis that water depth and periphyton total phosphorus (TP) content are both drivers of periphyton biomass in karstic wetland habitats in Belize, Mexico and Jamaica, (ii) provide a taxonomic inventory of the periphytic diatom species in these wetlands and (iii) examine the relationship between periphyton mat TP concentration and diatom assemblage at Everglades and Caribbean locations. ^ Periphyton biomass, nutrient and diatom assemblage data were generated from periphyton mat samples collected from shallow, marl-based wetlands in Belize, Mexico and Jamaica. These data were compared to a larger dataset collected from comparable sites within Everglades National Park. A diatom taxonomic inventory was conducted on the Caribbean samples and a combination of ordination and weighted-averaging modeling techniques were used to compare relationships between periphyton TP concentration, periphyton biomass and diatom assemblage composition among the locations. ^ Within the Everglades, periphyton biomass showed a negative correlation with water depth and mat TP, while periphyton mat percent organic content was positively correlated with these two variables. These patterns were also exhibited within the Belize, Mexico and Jamaica locations, suggesting that water depth and periphyton TP content are both drivers of periphyton biomass in karstic wetland systems within the northern Caribbean region. ^ A total of 146 diatom species representing 39 genera were recorded from the three Caribbean locations, including a distinct core group of species that may be endemic to this habitat type. Weighted averaging models were produced that effectively predicted mat TP concentration from diatom assemblages for both Everglades (R2=0.56) and Caribbean (R2=0.85) locations. There were, however, significant differences among Everglades and Caribbean locations with respect to species TP optima and indicator species. This suggests that although diatoms are effective indicators of water quality in these wetlands, differences in species response to water quality changes can reduce the predictive power of these indices when applied across systems. ^

A multi-method approach for the assessment of composite indices and rankings

There is growing popularity in the use of composite indices and rankings for cross-organizational benchmarking. However, little attention has been paid to alternative methods and procedures for the computation of these indices and how the use of such methods may impact the resulting indices and rankings. This dissertation developed an approach for assessing composite indices and rankings based on the integration of a number of methods for aggregation, data transformation and attribute weighting involved in their computation. The integrated model developed is based on the simulation of composite indices using methods and procedures proposed in the area of multi-criteria decision making (MCDM) and knowledge discovery in databases (KDD). The approach developed in this dissertation was automated through an IT artifact that was designed, developed and evaluated based on the framework and guidelines of the design science paradigm of information systems research. This artifact dynamically generates multiple versions of indices and rankings by considering different methodological scenarios according to user specified parameters. The computerized implementation was done in Visual Basic for Excel 2007. Using different performance measures, the artifact produces a number of excel outputs for the comparison and assessment of the indices and rankings. In order to evaluate the efficacy of the artifact and its underlying approach, a full empirical analysis was conducted using the World Bank's Doing Business database for the year 2010, which includes ten sub-indices (each corresponding to different areas of the business environment and regulation) for 183 countries. The output results, which were obtained using 115 methodological scenarios for the assessment of this index and its ten sub-indices, indicated that the variability of the component indicators considered in each case influenced the sensitivity of the rankings to the methodological choices. Overall, the results of our multi-method assessment were consistent with the World Bank rankings except in cases where the indices involved cost indicators measured in per capita income which yielded more sensitive results. Low income level countries exhibited more sensitivity in their rankings and less agreement between the benchmark rankings and our multi-method based rankings than higher income country groups.

Derivation of lake mixing and stratification indices from high-resolution lake buoy data

Lake Analyzer is a numerical code coupled with supporting visualization tools for determining indices of mixing and stratification that are critical to the biogeochemical cycles of lakes and reservoirs. Stability indices, including Lake Number, Wedderburn Number, Schmidt Stability, and thermocline depth are calculated according to established literature definitions and returned to the user in a time series format. The program was created for the analysis of high-frequency data collected from instrumented lake buoys, in support of the emerging field of aquatic sensor network science. Available outputs for the Lake Analyzer program are: water temperature (error-checked and/or down-sampled), wind speed (error-checked and/or down-sampled), metalimnion extent (top and bottom), thermocline depth, friction velocity, Lake Number, Wedderburn Number, Schmidt Stability, mode-1 vertical seiche period, and Brunt-Väisälä buoyancy frequency. Secondary outputs for several of these indices delineate the parent thermocline depth (seasonal thermocline) from the shallower secondary or diurnal thermocline. Lake Analyzer provides a program suite and best practices for the comparison of mixing and stratification indices in lakes across gradients of climate, hydro-physiography, and time, and enables a more detailed understanding of the resulting biogeochemical transformations at different spatial and temporal scales.

Better primer design for metagenomics applications by increasing taxonomic distinguishability

Current methods of understanding microbiome composition and structure rely on accurately estimating the number of distinct species and their relative abundance. Most of these methods require an efficient PCR whose forward and reverse primers bind well to the same, large number of identifiable species, and produce amplicons that are unique. It is therefore not surprising that currently used universal primers designed many years ago are not as efficient and fail to bind to recently cataloged species. We propose an automated general method of designing PCR primer pairs that abide by primer design rules and uses current sequence database as input. Since the method is automated, primers can be designed for targeted microbial species or updated as species are added or deleted from the database. In silico experiments and laboratory experiments confirm the efficacy of the newly designed primers for metagenomics applications.

Molecular Evidence for Taxonomic Relationships of the Endangered Species Jacquemontia Reclinata (Convolvulaceae)

Jacquemontia reclinata House (Convolvulaceae) is a federally-listed endangered species endemic to coastal strand habitat of southeastern Florida, from Palm Beach to Miami-Dade counties. Although J. reclinata is currently defined as a species, its taxonomic distinctness has never been analyzed using phylogenetic evidence. In order to assess the evolutionary distinctness of J. reclinata and identify its closest relatives, internal transcribed spacer (ITS) regions within nuclear ribosomal DNA were sequenced, and the sequence data was used to reconstruct a phylogeny of Jacquemontia. The study included the three putative relatives of J. reclinata and all other species within Jacquemontia known to occur in the Greater Antilles and Bahamas, except for three species. Results concur with previous morphological studies, which suggest that J. reclinata is closely related to J. cayensis Britton, J. curtisii Peter, and J. havanensis Urban. These three species and J. reclinata form an unresolved clade. Therefore, it is not certain which of these Caribbean species is sister to J. reclinata. The lack of resolution within the clade that includes J. reclinata implies that the taxa within the clade are evolutionarily similar. Future taxonomic studies of J. reclinata should focus in resolving relationships within the Jacquemontia reclinata clade.