Euclidean network information theory

Thesis (Ph. D.)--Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2013.Cataloged from PDF version of thesis.Includes bibliographical references (pages 121-123).Many network information theory problems face the similar difficulty of single letterization. We argue that this is due to the lack of a geometric structure on the space of probability distributions. In this thesis, we develop such a structure by assuming that the distributions of interest are all close to each other. Under this assumption, the Kullback-Leibler (K-L) divergence is reduced to the squared Euclidean metric in an Euclidean space. In addition, we construct the notion of coordinate and inner product, which will facilitate solving communication problems. We will present the application of this approach to the point-to-point channels, general broadcast channels (BC), multiple access channels (MAC) with common sources, interference channels, and multi-hop layered communication networks without or with feedback. It can be shown that with this approach, information theory problems, such as the single-letterization, can be reduced to some linear algebra problems. Solving these linear algebra problems, we will show that for the general broadcast channels, transmitting the common message to receivers can be formulated as the trade-off between linear systems. We also provide an example to visualize this trade-off in a geometric way. For the MAC with common sources, we observe a coherent combining gain due to the cooperation between transmitters, and this gain can be obtained quantitively by applying our technique. In addition, the developments of the broadcast channels and multiple access channels suggest a trade-off relation between generating common messages for multiple users and transmitting them as the common sources to exploit the coherent combining gain, when optimizing the throughputs of communication networks. To study the structure of this trade-off and understand its role in optimizing the network throughput, we construct a deterministic model by our local approach that captures the critical channel parameters and well models the network. With this deterministic model, for multi-hop layered networks, we analyze the optimal network throughputs, and illustrate what kinds of common messages should be generated to achieve the optimal throughputs. Our results provide the insight of how users in a network should cooperate with each other to transmit information efficiently.by Shao-Lun Huang.Ph.D

The design of binary shaping filter of binary code

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.Includes bibliographical references (p. 35).In information theory, in order to maximize the total throughput, it is required that the codebook has an empirical distribution that maximizes the mutual information over the channel. In coding theory, however, most codes we can generate have Bernoulli (1/2) distribution. In this thesis, we present a new coding scheme to efficiently generate binary codes with different distributions. Our main approach is to first encode the information bits by a linear code C, and then quantized the codeword to the closest codeword in another linear code C,. The quantization error is then treated as the encoded codeword in our coding scheme. We discuss the practicality and advantage of such codes and give a design example.by Shao-Lun Huang.S.M

Transgenic zebrafish eggs containing hepcidin as a novel feed supplement enhances fish immunity against pathogen infection

Penyakit yang diinduksi patogen menyebabkan kerugian stok yang signifikan dalam akuakultur. Sebagian besar penyakit ikan disebabkan oleh bakteri patogen. Antibiotik umumnya diterapkan untuk mengobati penyakit dalam budidaya, namun penggunaan antibiotik untuk hewan air mungkin tidak hanya menyebabkan masalah pencemaran lingkungan tetapi juga dapat mempengaruhi kesehatan manusia karena residu obat dan perkembangan strain patogen yang resisten. Peptida antimikroba (AMP) adalah komponen penting dari host pertahanan. AMP dapat merusak atau mengganggu membran sel dari patogen dan mengatur respon imun terhadap infeksi patogen. Hepcidin adalah peptida bioaktif kecil dengan peran ganda sebagai antimikroba peptida (AMP) dan sebagai pengatur hormon utama besi homeostatis. Dalam penelitian ini, ekspresi plasmid di mana gen hepcidin yang menyatu dengan EGFP didorong oleh spesifik oosit ikan zebra Promotor ZP3 dan digunakan untuk membentuk ikan zebra transgenik Tg (Zp3:hepc). Ekspresi protein hepc-EGFP rekombinan dalam telur yang dibuahi F2 dikonfirmasi oleh RT-PCR dan Western blot. Hasil yang ditampilkan dewasa ikan zebra yang diberi makan dengan telur yang dibuahi yang mengekspresikan hepc selama 3 bulan dipamerkan tingkat ekspresi gen respon imun yang lebih tinggi seperti IL-1β, IL-6, IL-10, IL-15, TNF-α, COX-2, NF-ĸB, C3b, dan TLR-4α dibandingkan dengan mereka dalam kelompok kontrol menyarankan telur yang dibuahi yang mengekspresikan hepc digunakan sebagai suplementasi diet dapat meningkatkan kekebalan terhadap infeksi penyakit

Early growth response gene-2 (Egr-2) regulates the development of B and T cells

The study was supported by Arthritis Research UK. Copyright @ 2011 Li et al.BACKGROUND: Understanding of how transcription factors are involved in lymphocyte development still remains a challenge. It has been shown that Egr-2 deficiency results in impaired NKT cell development and defective positive selection of T cells. Here we investigated the development of T, B and NKT cells in Egr-2 transgenic mice and the roles in the regulation of distinct stages of B and T cell development. METHODS AND FINDINGS: The expression of Egr1, 2 and 3 were analysed at different stages of T and B cell development by RT-PCT and results showed that the expression was strictly regulated at different stages. Forced expression of Egr-2 in CD2+ lymphocytes resulted in a severe reduction of CD4+CD8+ (DP) cells in thymus and pro-B cells in bone marrow, which was associated with reduced expression of Notch1 in ISP thymocytes and Pax5 in pro-B cells, suggesting that retraction of Egr-2 at the ISP and pro-B cell stages is important for the activation of lineage differentiation programs. In contrast to reduction of DP and pro-B cells, Egr-2 enhanced the maturation of DP cells into single positive (SP) T and NKT cells in thymus, and immature B cells into mature B cells in bone marrow. CONCLUSIONS: Our results demonstrate that Egr-2 expressed in restricted stages of lymphocyte development plays a dynamic, but similar role for the development of T, NKT and B cells.This article is provided by the Brunel Open Access publishing fund

A formally verified compiler back-end

This article describes the development and formal verification (proof of semantic preservation) of a compiler back-end from Cminor (a simple imperative intermediate language) to PowerPC assembly code, using the Coq proof assistant both for programming the compiler and for proving its correctness. Such a verified compiler is useful in the context of formal methods applied to the certification of critical software: the verification of the compiler guarantees that the safety properties proved on the source code hold for the executable compiled code as well

Sample size calculation for microarray experiments with blocked one-way design

<p>Abstract</p> <p>Background</p> <p>One of the main objectives of microarray analysis is to identify differentially expressed genes for different types of cells or treatments. Many statistical methods have been proposed to assess the treatment effects in microarray experiments.</p> <p>Results</p> <p>In this paper, we consider discovery of the genes that are differentially expressed among <it>K </it>(> 2) treatments when each set of <it>K </it>arrays consists of a block. In this case, the array data among <it>K </it>treatments tend to be correlated because of block effect. We propose to use the blocked one-way ANOVA <it>F</it>-statistic to test if each gene is differentially expressed among <it>K </it>treatments. The marginal p-values are calculated using a permutation method accounting for the block effect, adjusting for the multiplicity of the testing procedure by controlling the false discovery rate (FDR). We propose a sample size calculation method for microarray experiments with a blocked one-way design. With FDR level and effect sizes of genes specified, our formula provides a sample size for a given number of true discoveries.</p> <p>Conclusion</p> <p>The calculated sample size is shown via simulations to provide an accurate number of true discoveries while controlling the FDR at the desired level.</p

Preface for the IJSME Special Issue: Metacognition for Science and Mathematics Learning in Technology-Infused Learning Environments

The final publication is available at Springer via http://dx.doi.org/10.1007/s10763-016-9727-9

Asteroseismology and Interferometry

Asteroseismology provides us with a unique opportunity to improve our understanding of stellar structure and evolution. Recent developments, including the first systematic studies of solar-like pulsators, have boosted the impact of this field of research within Astrophysics and have led to a significant increase in the size of the research community. In the present paper we start by reviewing the basic observational and theoretical properties of classical and solar-like pulsators and present results from some of the most recent and outstanding studies of these stars. We centre our review on those classes of pulsators for which interferometric studies are expected to provide a significant input. We discuss current limitations to asteroseismic studies, including difficulties in mode identification and in the accurate determination of global parameters of pulsating stars, and, after a brief review of those aspects of interferometry that are most relevant in this context, anticipate how interferometric observations may contribute to overcome these limitations. Moreover, we present results of recent pilot studies of pulsating stars involving both asteroseismic and interferometric constraints and look into the future, summarizing ongoing efforts concerning the development of future instruments and satellite missions which are expected to have an impact in this field of research.Comment: Version as published in The Astronomy and Astrophysics Review, Volume 14, Issue 3-4, pp. 217-36

Search for CP violation in D+→K−K+π+D^{+} \to K^{-}K^{+}\pi^{+} decays

A model-independent search for direct CP violation in the Cabibbo suppressed decay $D^+ \to K^- K^+\pi^+$ in a sample of approximately 370,000 decays is carried out. The data were collected by the LHCb experiment in 2010 and correspond to an integrated luminosity of 35 pb$^{-1}$. The normalized Dalitz plot distributions for $D^+$ and $D^-$ are compared using four different binning schemes that are sensitive to different manifestations of CP violation. No evidence for CP asymmetry is found.Comment: 13 pages, 8 figures, submitted to Phys. Rev.

Measurement of charged particle multiplicities in pppp collisions at s=7{\sqrt{s} =7}TeV in the forward region

The charged particle production in proton-proton collisions is studied with the LHCb detector at a centre-of-mass energy of ${\sqrt{s} =7}$TeV in different intervals of pseudorapidity $\eta$. The charged particles are reconstructed close to the interaction region in the vertex detector, which provides high reconstruction efficiency in the $\eta$ ranges $-2.5<\eta<-2.0$ and $2.0<\eta<4.5$. The data were taken with a minimum bias trigger, only requiring one or more reconstructed tracks in the vertex detector. By selecting an event sample with at least one track with a transverse momentum greater than 1 GeV/c a hard QCD subsample is investigated. Several event generators are compared with the data; none are able to describe fully the multiplicity distributions or the charged particle density distribution as a function of $\eta$. In general, the models underestimate the charged particle production