Second-Order Coding Rates for Conditional Rate-Distortion

This paper characterizes the second-order coding rates for lossy source coding with side information available at both the encoder and the decoder. We first provide non-asymptotic bounds for this problem and then specialize the non-asymptotic bounds for three different scenarios: discrete memoryless sources, Gaussian sources, and Markov sources. We obtain the second-order coding rates for these settings. It is interesting to observe that the second-order coding rate for Gaussian source coding with Gaussian side information available at both the encoder and the decoder is the same as that for Gaussian source coding without side information. Furthermore, regardless of the variance of the side information, the dispersion is $1/2$ nats squared per source symbol.Comment: 20 pages, 2 figures, second-order coding rates, finite blocklength, network information theor

Elucidating glycosylation pattern of protein produced in mammalian cells

The glycosylation pathway is a highly branched network. Although only a relatively small number of enzymes are involved in the pathway, a multitude of intermediate and terminal glycans can be formed. Each intermediate glycan in the network can be the substrate of subsequent glycosylation steps. In each step, there can be multiple enzymes acting on a single glycan due to overlapping substrate specificity. These enzymes tend to compete with each other to divert the network flux toward a particular branch. Alternation of their relative ratios can result in different glycan profiles. In mammals, such enzymes are distributed in a tissue-specific manner to meet a variety of protein glycosylation requirements. How distinct expression patterns of these enzymes can affect the glycan structures of a protein is not well studied. Understanding the link between these expression patterns and the final glycan profile of a protein will be useful for glycoengineering. In this study, we develop a mathematical model that incorporates reaction rules for various Golgi-resident glycosylation enzymes. The kinetic information is obtained from in vitro enzyme kinetics research. Enzyme levels are estimated from their corresponding transcript levels in various mammalian tissues using public transcriptome data. Insights from this modeling effort will used to predict targets for glycoengineering of mammalian cells

Improved mitochondrial amino acid substitution models for metazoan evolutionary studies

Abstract Background Amino acid substitution models play an essential role in inferring phylogenies from mitochondrial protein data. However, only few empirical models have been estimated from restricted mitochondrial protein data of a hundred species. The existing models are unlikely to represent appropriately the amino acid substitutions from hundred thousands metazoan mitochondrial protein sequences. Results We selected 125,935 mitochondrial protein sequences from 34,448 species in the metazoan kingdom to estimate new amino acid substitution models targeting metazoa, vertebrates and invertebrate groups. The new models help to find significantly better likelihood phylogenies in comparison with the existing models. We noted remarkable distances from phylogenies with the existing models to the maximum likelihood phylogenies that indicate a considerable number of incorrect bipartitions in phylogenies with the existing models. Finally, we used the new models and mitochondrial protein data to certify that Testudines, Aves, and Crocodylia form one separated clade within amniotes. Conclusions We introduced new mitochondrial amino acid substitution models for metazoan mitochondrial proteins. The new models outperform the existing models in inferring phylogenies from metazoan mitochondrial protein data. We strongly recommend researchers to use the new models in analysing metazoan mitochondrial protein data

Shortest triplet clustering: reconstructing large phylogenies using representative sets

BACKGROUND: Understanding the evolutionary relationships among species based on their genetic information is one of the primary objectives in phylogenetic analysis. Reconstructing phylogenies for large data sets is still a challenging task in Bioinformatics. RESULTS: We propose a new distance-based clustering method, the shortest triplet clustering algorithm (STC), to reconstruct phylogenies. The main idea is the introduction of a natural definition of so-called k-representative sets. Based on k-representative sets, shortest triplets are reconstructed and serve as building blocks for the STC algorithm to agglomerate sequences for tree reconstruction in O(n(2)) time for n sequences. Simulations show that STC gives better topological accuracy than other tested methods that also build a first starting tree. STC appears as a very good method to start the tree reconstruction. However, all tested methods give similar results if balanced nearest neighbor interchange (BNNI) is applied as a post-processing step. BNNI leads to an improvement in all instances. The program is available at . CONCLUSION: The results demonstrate that the new approach efficiently reconstructs phylogenies for large data sets. We found that BNNI boosts the topological accuracy of all methods including STC, therefore, one should use BNNI as a post-processing step to get better topological accuracy

FLU, an amino acid substitution model for influenza proteins

Abstract Background The amino acid substitution model is the core component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference. Although several general amino acid substitution models have been estimated from large and diverse protein databases, they remain inappropriate for analyzing specific species, e.g., viruses. Emerging epidemics of influenza viruses raise the need for comprehensive studies of these dangerous viruses. We propose an influenza-specific amino acid substitution model to enhance the understanding of the evolution of influenza viruses. Results A maximum likelihood approach was applied to estimate an amino acid substitution model (FLU) from ~113, 000 influenza protein sequences, consisting of ~20 million residues. FLU outperforms 14 widely used models in constructing maximum likelihood phylogenetic trees for the majority of influenza protein alignments. On average, FLU gains ~42 log likelihood points with an alignment of 300 sites. Moreover, topologies of trees constructed using FLU and other models are frequently different. FLU does indeed have an impact on likelihood improvement as well as tree topologies. It was implemented in PhyML and can be downloaded from ftp://ftp.sanger.ac.uk/pub/1000genomes/lsq/FLU or included in PhyML 3.0 server at http://www.atgc-montpellier.fr/phyml/. Conclusions FLU should be useful for any influenza protein analysis system which requires an accurate description of amino acid substitutions.</p

The prospectus of family house reconstruction, Svoboda Square nr.55, City of Bohumin

Import 26/06/2013Bakalářská práce řeší studii rekonstrukce rodinného domu v Bohumíně, včetně změny užívání prvního nadzemního podlaží na nebytový prostor. Studie vychází ze schválené územně plánovací dokumentace a je zpracována formou dokumentace k územnímu řízení. Součástí návrhu je ekonomické zhodnocení z pohledu investičních nákladů potřebných k realizaci. Projektová dokumentace zahrnuje uspořádání dispozice objektu a napojení na technickou a dopravní infrastrukturu.The task of the bachelor thesis was to develop proposal for recontruction and change of use the family house to commercial ground floor in Bohumin in accordance with the territorial plan of the city. The proposal includes an economic evaluation in terms of capital costs required for construction. The solution follows the existing transport and technical infrastructure and solves internal layout of the rooms.Prezenční222 - Katedra městského inženýrstvídobř

Variation reduction in plasma etching via run-to-run process control and endpoint detection

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1997.Includes bibliographical references (leaves 89-91).by Minh Sy Le.M.S

Approximation techniques in network information theory

Ph.DDOCTOR OF PHILOSOPH

Fabrication and Mechanical Properties of Chitosan-Montmorillonite Nano-composite

Chitosan has found various applications in gastrointestinal stent, biomedical implants as well as an effective absorbent in waste water treatment. However, the material suffers from low strength and large shrinkage upon dehydration. The current project is aimed to develop a process to fabricate chitosan composites with the addition of functionalised montmorillonite nanoparticles and to examine the effect of ceramic content on the mechanical behavior of the composites. This paper describes the fabrication of chitosan with montmorrillonite composites and the mechanical testing of the samples and the mechanical behaviour of the composites, as well as the observations of the microstructure. The effects of composition and microstructure on the mechanical properties of the composite are investigated. The results indicate that the nanoparticles are dispersed uniformly in the matrix up to 40wt% using high speed homogeniser. The elastic modulus increases monotonically with the addition of nanoparticles, but the fracture strength drops due to the defects introduced by the nanoparticles.</jats:p