Strong Secrecy for Multiple Access Channels

We show strongly secret achievable rate regions for two different wiretap multiple-access channel coding problems. In the first problem, each encoder has a private message and both together have a common message to transmit. The encoders have entropy-limited access to common randomness. If no common randomness is available, then the achievable region derived here does not allow for the secret transmission of a common message. The second coding problem assumes that the encoders do not have a common message nor access to common randomness. However, they may have a conferencing link over which they may iteratively exchange rate-limited information. This can be used to form a common message and common randomness to reduce the second coding problem to the first one. We give the example of a channel where the achievable region equals zero without conferencing or common randomness and where conferencing establishes the possibility of secret message transmission. Both coding problems describe practically relevant networks which need to be secured against eavesdropping attacks.Comment: 55 page

Single-Cell Gene Expression Variation as A Cell-Type Specific Trait: A Study of Mammalian Gene Expression Using Single-Cell RNA Sequencing

In this dissertation, we used single-cell RNA sequencing data from five mammalian tissues to characterize patterns of gene expression across single cells, transcriptome-wide and in a cell-type-specific manner (Part 1). Additionally, we characterized single-cell RNA sequencing methods as a resource for experimental design and data analysis (Part 2). Part 1: Differentiation of metazoan cells requires execution of different gene expression programs but recent single cell transcriptome profiling has revealed considerable variation within cells of seemingly identical phenotype. This brings into question the relationship between transcriptome states and cell phenotypes. We used high quality single cell RNA sequencing for 107 single cells from five mammalian tissues, along with 30 control samples, to characterize transcriptome heterogeneity across single cells. We developed methods to filter genes for reliable quantification and to calibrate biological variation. We found evidence that ubiquitous expression across cells may be indicative of critical gene function and that, for a subset of genes, biological variability within each cell type may be regulated in order to perform dynamic functions. We also found evidence that single-cell variability of mouse pyramidal neurons was correlated with that in rats consistent with the hypothesis that levels of variation may be conserved. Part 2: Many researchers are interested in single-cell RNA sequencing for use in identification and classification of cell types, finding rare cells, and studying single-cell expression variation; however, experimental and analytic methods for single-cell RNA sequencing are young and there is little guidance available for planning experiments and interpreting results. We characterized single-cell RNA sequencing measurements in terms of sensitivity, precision and accuracy through analysis of data generated in a collaborative control project, where known reference RNA was diluted to single-cell levels and amplified using one of three single-cell RNA sequencing protocols. All methods perform comparably overall, but individual methods demonstrate unique strengths and biases. Measurement reliability increased with expression level for all methods and we conservatively estimated measurements to be quantitative at an expression level of ~5-10 molecules

Transfer RNA-derived small RNAs in the cancer transcriptome

The cellular lifetime includes stages such as differentiation, proliferation, division, senescence and apoptosis.These stages are driven by a strictly ordered process of transcription dynamics. Molecular disruption to RNA polymerase assembly, chromatin remodelling and transcription factor binding through to RNA editing, splicing, post-transcriptional regulation and ribosome scanning can result in significant costs arising from genome instability. Cancer development is one example of when such disruption takes place. RNA silencing is a term used to describe the effects of post-transcriptional gene silencing mediated by a diverse set of small RNA molecules. Small RNAs are crucial for regulating gene expression and microguarding genome integrity.RNA silencing studies predominantly focus on small RNAs such as microRNAs, short-interfering RNAs and piwi-interacting RNAs. We describe an emerging renewal of inter-est in a‘larger’small RNA, the transfer RNA (tRNA).Precisely generated tRNA-derived small RNAs, named tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been reported to be abundant with dysregulation associated with cancer. Transfection of tiRNAs inhibits protein translation by displacing eukaryotic initiation factors from messenger RNA (mRNA) and inaugurating stress granule formation.Knockdown of an overexpressed tRF inhibits cancer cell proliferation. Recovery of lacking tRFs prevents cancer metastasis. The dual oncogenic and tumour-suppressive role is typical of functional small RNAs. We review recent reports on tiRNA and tRF discovery and biogenesis, identification and analysis from next-generation sequencing data and a mechanistic animal study to demonstrate their physiological role in cancer biology. We propose tRNA-derived small RNA-mediated RNA silencing is an innate defence mechanism to prevent oncogenic translation. We expect that cancer cells are percipient to their ablated control of transcription and attempt to prevent loss of genome control through RNA silencing

A realistic pattern of fermion masses from a five-dimensional SO(10) model

We provide a unified description of fermion masses and mixing angles in the framework of a supersymmetric grand unified SO(10) model with anarchic Yukawa couplings of order unity. The space-time is five dimensional and the extra flat spatial dimension is compactified on the orbifold $S^1/(Z_2 \times Z_2')$, leading to Pati-Salam gauge symmetry on the boundary where Yukawa interactions are localised. The gauge symmetry breaking is completed by means of a rather economic scalar sector, avoiding the doublet-triplet splitting problem. The matter fields live in the bulk and their massless modes get exponential profiles, which naturally explain the mass hierarchy of the different fermion generations. Quarks and leptons properties are naturally reproduced by a mechanism, first proposed by Kitano and Li, that lifts the SO(10) degeneracy of bulk masses in terms of a single parameter. The model provides a realistic pattern of fermion masses and mixing angles for large values of $\tan\beta$. It favours normally ordered neutrino mass spectrum with the lightest neutrino mass below 0.01 eV and no preference for leptonic CP violating phases. The right handed neutrino mass spectrum is very hierarchical and does not allow for thermal leptogenesis. We analyse several variants of the basic framework and find that the results concerning the fermion spectrum are remarkably stable.Comment: 30 pages, 7 figures, 4 table

On the automatic construction of indistinguishable operations

An increasingly important design constraint for software running on ubiquitous computing devices is security, particularly against physical methods such as side-channel attack. One well studied methodology for defending against such attacks is the concept of indistinguishable functions which leak no information about program control flow since all execution paths are computationally identical. However, constructing such functions by hand becomes laborious and error prone as their complexity increases. We investigate techniques for automating this process and find that effective solutions can be constructed with only minor amounts of computational effort.Fundação para a Ciência e Tecnologia - SFRH/BPD/20528/2004

Neutrino Mass and μ→e+γ\mu \rightarrow e + \gamma from a Mini-Seesaw

The recently proposed "mini-seesaw mechanism" combines naturally suppressed Dirac and Majorana masses to achieve light Standard Model neutrinos via a low-scale seesaw. A key feature of this approach is the presence of multiple light (order GeV) sterile-neutrinos that mix with the Standard Model. In this work we study the bounds on these light sterile-neutrinos from processes like \mu ---> e + \gamma, invisible Z-decays, and neutrinoless double beta-decay. We show that viable parameter space exists and that, interestingly, key observables can lie just below current experimental sensitivities. In particular, a motivated region of parameter space predicts a value of BR(\mu ---> e + \gamma) within the range to be probed by MEG.Comment: 1+26 pages, 7 figures. v2 JHEP version (typo's fixed, minor change to presentation, results unchanged

Stacked Search for Gravitational Waves from the 2006 SGR 1900+14 Storm

We present the results of a LIGO search for short-duration gravitational waves (GWs) associated with the 2006 March 29 SGR 1900+14 storm. A new search method is used, "stacking'' the GW data around the times of individual soft-gamma bursts in the storm to enhance sensitivity for models in which multiple bursts are accompanied by GW emission. We assume that variation in the time difference between burst electromagnetic emission and potential burst GW emission is small relative to the GW signal duration, and we time-align GW excess power time-frequency tilings containing individual burst triggers to their corresponding electromagnetic emissions. We use two GW emission models in our search: a fluence-weighted model and a flat (unweighted) model for the most electromagnetically energetic bursts. We find no evidence of GWs associated with either model. Model-dependent GW strain, isotropic GW emission energy E_GW, and \gamma = E_GW / E_EM upper limits are estimated using a variety of assumed waveforms. The stacking method allows us to set the most stringent model-dependent limits on transient GW strain published to date. We find E_GW upper limit estimates (at a nominal distance of 10 kpc) of between 2x10^45 erg and 6x10^50 erg depending on waveform type. These limits are an order of magnitude lower than upper limits published previously for this storm and overlap with the range of electromagnetic energies emitted in SGR giant flares.Comment: 7 pages, 3 figure

Neutrinoless double-beta decay and seesaw mechanism

From the standard seesaw mechanism of neutrino mass generation, which is based on the assumption that the lepton number is violated at a large (~10exp(+15) GeV) scale, follows that the neutrinoless double-beta decay is ruled by the Majorana neutrino mass mechanism. Within this notion, for the inverted neutrino-mass hierarchy we derive allowed ranges of half-lives of the neutrinoless double-beta decay for nuclei of experimental interest with different sets of nuclear matrix elements. The present-day results of the calculation of the neutrinoless double-beta decay nuclear matrix elements are briefly discussed. We argue that if neutrinoless double-beta decay will be observed in future experiments sensitive to the effective Majorana mass in the inverted mass hierarchy region, a comparison of the derived ranges with measured half-lives will allow us to probe the standard seesaw mechanism assuming that future cosmological data will establish the sum of neutrino masses to be about 0.2 eV.Comment: Some changes in sections I, II, IV, and V; two new figures; additional reference

Sensitivity to Gravitational Waves from Compact Binary Coalescences Achieved during LIGO's Fifth and Virgo's First Science Run

We summarize the sensitivity achieved by the LIGO and Virgo gravitational wave detectors for compact binary coalescence (CBC) searches during LIGO's fifth science run and Virgo's first science run. We present noise spectral density curves for each of the four detectors that operated during these science runs which are representative of the typical performance achieved by the detectors for CBC searches. These spectra are intended for release to the public as a summary of detector performance for CBC searches during these science runs.Comment: 12 pages, 5 figure