HLA-E coding and 3' untranslated region variability determined by next-generation sequencing in two West-African population samples

HLA-E is a non-classical Human Leucocyte Antigen class I gene with immunomodulatory properties. Whereas HLA-E expression usually occurs at low levels, it is widely distributed amongst human tissues, has the ability to bind self and non-self antigens and to interact with NK cells and T lymphocytes, being important for immunosurveillance and also for fighting against infections. HLA-E is usually the most conserved locus among all class I genes. However, most of the previous studies evaluating HLA-E variability sequenced only a few exons or genotyped known polymorphisms. Here we report a strategy to evaluate HLA-E variability by next-generation sequencing (NGS) that might be used to other HLA loci and present the HLA-E haplotype diversity considering the segment encoding the entire HLA-E mRNA (including 5'UTR, introns and the 3'UTR) in two African population samples, Susu from Guinea-Conakry and Lobi from Burkina Faso. Our results indicate that (a) the HLA-E gene is indeed conserved, encoding mainly two different protein molecules; (b) Africans do present several unknown HLA-E alleles presenting synonymous mutations; (c) the HLA-E 3'UTR is quite polymorphic and (d) haplotypes in the HLA-E 3'UTR are in close association with HLA-E coding alleles. NGS has proved to be an important tool on data generation for future studies evaluating variability in non-classical MHC genes.

A New Cryptographic Scheme for Securing Dynamic Conferences in Data Networks

Dynamic conferencing refers to a scenario wherein any subset of users in a universe of users form a conference for sharing confidential information among themselves. The key distribution (KD) problem in dynamic conferencing is to compute a shared secret key for such a dynamically formed conference. In literature, the KD schemes for dynamic conferencing either are computationally unscalable or require communication among users, which is undesirable. The extended symmetric polynomial based dynamic conferencing scheme (ESPDCS) is one such KD scheme which has a high computational complexity that is universe size dependent. In this paper we present an enhancement to the ESPDCS scheme to develop a KD scheme called universe-independent SPDCS (UI-SPDCS) such that its complexity is independent of the universe size. However, the UI-SPDCS scheme does not scale with the conference size. We propose a relatively scalable KD scheme termed as DH-SPDCS that uses the UI-SPDCS scheme and the tree-based group Diffie- Hellman (TGDH) key exchange protocol. The proposed DH-SPDCS scheme provides a configurable trade-off between computation and communication complexity of the scheme.

A Novel Cost-Efficient On-Line Intermediate Waveband-Switching Scheme in WDM Mesh Networks

Waveband switching (WBS) is an important technique to save switching and transmission cost in wavelength -division multiplexed (WDM) optical networks. A cost-efficient WBS scheme would enable network carriers to increase the network throughput (revenue) while achieving significant cost savings. We identify the critical factors that determine the WBS network throughput and switching cost and propose a novel intermediate waveband switching (IT-WBS) algorithm, called the minimizing-weighted-cost (MWC) algorithm. The MWC algorithm defines a cost for each candidate route of a call. By selecting the route with the smallest weighted cost, MWC balances between minimizing the call blocking probability and minimizing the network switching cost. Our simulations show that MWC outperforms other wavelength/waveband switching algorithms and can enhance the network throughput at a reduced cost.

KeyRev: An Efficient Key Revocation Scheme for Wireless Sensor Networks

Key management is a core mechanism to ensure the security of applications and network services in wireless sensor networks. It includes two aspects: key distribution and key revocation. Key distribution has been extensively studied in the context of sensor networks. However, key revocation has received relatively little attention. Existing key revocation schemes can be divided into two categories: centralized key revocation scheme and distributed key revocation scheme. In this paper, we first summarize the current key revocation schemes for sensor networks. Then, we propose an efficient centralized key revocation scheme, KeyRev, for wireless sensor networks. Unlike most proposed key revocation schemes focusing on removing the compromised keys, we propose to use key updating techniques to obsolesce the keys owned by the compromised sensor nodes and thus remove the nodes from the network. Our analyses show that the KeyRev scheme is secure inspite of not removing the pre-distributed key materials at compromised sensor nodes. Simulation results also indicate that the KeyRev scheme is scalable and performs very well in wireless sensor networks.

An Efficient Scheduling Scheme For On-Demand Lightpath Reservations In Reconfigurable WDM Optical Networks

We propose an efficient scheduling scheme that optimizes advance-reserved lightpath services in reconfigurable WDM networks. A re-optimization approach is devised to reallocate network resources for dynamic service demands while keeping determined schedule unchanged.

Applications of Linear Programming to Coding Theory

Maximum-likelihood decoding is often the optimal decoding rule one can use, but it is very costly to implement in a general setting. Much effort has therefore been dedicated to find efficient decoding algorithms that either achieve or approximate the error-correcting performance of the maximum-likelihood decoder. This dissertation examines two approaches to this problem. In 2003 Feldman and his collaborators defined the linear programming decoder, which operates by solving a linear programming relaxation of the maximum-likelihood decoding problem. As with many modern decoding algorithms, is possible for the linear programming decoder to output vectors that do not correspond to codewords; such vectors are known as pseudocodewords. In this work, we completely classify the set of linear programming pseudocodewords for the family of cycle codes. For the case of the binary symmetric channel, another approximation of maximum-likelihood decoding was introduced by Omura in 1972. This decoder employs an iterative algorithm whose behavior closely mimics that of the simplex algorithm. We generalize Omura's decoder to operate on any binary-input memoryless channel, thus obtaining a soft-decision decoding algorithm. Further, we prove that the probability of the generalized algorithm returning the maximum-likelihood codeword approaches 1 as the number of iterations goes to infinity.

Challenges of Students’ Industrial Work Experience Scheme (SIWES) in Library and Information Science in the ICT Environment

The ICT revolution has permeated every profession and all areas of human endeavour. Professions such as law, medicine , engineering, and library and information science are adjusting to the ICT environment through re-tooling, retraining, and curriculum revision. The purpose of this study is to explore the impact of ICT on the student industrial work experience scheme (SIWES) of library and information science students. It traces the historical development of the scheme, the ICT development trends in LIS, and the challenges this development brings to SIWES. Strategies to absorb this shock created by ICT are offered.

Constrained least square pre-distortion scheme for multiuser ultra-wideband

The study proposes a constrained least square (CLS) pre-distortion scheme for multiple-input single-output (MISO) multiple access ultra-wideband (UWB) systems. In such a scheme, a simple objective function is defined, which can be efficiently solved by a gradient-based algorithm. For the performance evaluation, scenarios CM1 and CM3 of the IEEE 802.15.3a channel model are considered. Results show that the CLS algorithm has a fast convergence and a good trade-off between intersymbol interference (ISI) and multiple access interference (MAI) reduction and signal-to-noise ratio (SNR) preservation, performing better than time-reversal (TR) pre-distortion.

New Isomers in the Full Seniority Scheme of Neutron-Rich Lead Isotopes: The Role of Effective Three-Body Forces

The neutron-rich lead isotopes, up to Pb-216, have been studied for the first time, exploiting the fragmentation of a primary uranium beam at the FRS-RISING setup at GSI. The observed isomeric states exhibit electromagnetic transition strengths which deviate from state-of-the-art shell-model calculations. It is shown that their complete description demands the introduction of effective three-body interactions and two-body transition operators in the conventional neutron valence space beyond Pb-208.

Unique Alterations of an Ultraconserved Non-Coding Element in the 3 ' UTR of ZIC2 in Holoprosencephaly

Coding region alterations of ZIC2 are the second most common type of mutation in holoprosencephaly (HPE). Here we use several complementary bioinformatic approaches to identify ultraconserved cis-regulatory sequences potentially driving the expression of human ZIC2. We demonstrate that an 804 bp element in the 3' untranslated region (3'UTR) is highly conserved across the evolutionary history of vertebrates from fish to humans. Furthermore, we show that while genetic variation of this element is unexpectedly common among holoprosencephaly subjects (6/528 or >1%), it is not present in control individuals. Two of six proband-unique variants are de novo, supporting their pathogenic involvement in HPE outcomes. These findings support a general recommendation that the identification and analysis of key ultraconserved elements should be incorporated into the genetic risk assessment of holoprosencephaly cases.

Identical sequence patterns in the ends of exons and introns of human protein-coding genes

Intron splicing is one of the most important steps involved in the maturation process of a pre-mRNA. Although the sequence profiles around the splice sites have been studied extensively, the levels of sequence identity between the exonic sequences preceding the donor sites and the intronic sequences preceding the acceptor sites has not been examined as thoroughly. In this study we investigated identity patterns between the last 15 nucleotides of the exonic sequence preceding the 5' splice site and the intronic sequence preceding the 3' splice site in a set of human protein-coding genes that do not exhibit intron retention. We found that almost 60% of consecutive exons and introns in human protein-coding genes share at least two identical nucleotides at their 3' ends and, on average, the sequence identity length is 2.47 nucleotides. Based on our findings we conclude that the 3' ends of exons and introns tend to have longer identical sequences within a gene than when being taken from different genes. Our results hold even if the pairs are non-consecutive in the transcription order. (C) 2012 Elsevier Ltd. All rights reserved.

A scheme for synchronizing clocks connected by a packet communication network

Consider a communication system in which a transmitter equipment sends fixed-size packets of data at a uniform rate to a receiver equipment. Consider also that these equipments are connected by a packet-switched network, which introduces a random delay to each packet. Here we propose an adaptive clock recovery scheme able of synchronizing the frequencies and the phases of these devices, within specified limits of precision. This scheme for achieving frequency and phase synchronization is based on measurements of the packet arrival times at the receiver, which are used to control the dynamics of a digital phase-locked loop. The scheme performance is evaluated via numerical simulations performed by using realistic parameter values. (C) 2011 Elsevier By. All rights reserved.

Simulation results and applications of an advection bounded scheme to practical flows

This paper reports experiments on the use of a recently introduced advection bounded upwinding scheme, namely TOPUS (Computers & Fluids 57 (2012) 208-224), for flows of practical interest. The numerical results are compared against analytical, numerical and experimental data and show good agreement with them. It is concluded that the TOPUS scheme is a competent, powerful and generic scheme for complex flow phenomena.

A continuously differentiable upwinding scheme for the simulation of fluid flow problems

This paper deals with the numerical solution of complex fluid dynamics problems using a new bounded high resolution upwind scheme (called SDPUS-C1 henceforth), for convection term discretization. The scheme is based on TVD and CBC stability criteria and is implemented in the context of the finite volume/difference methodologies, either into the CLAWPACK software package for compressible flows or in the Freeflow simulation system for incompressible viscous flows. The performance of the proposed upwind non-oscillatory scheme is demonstrated by solving two-dimensional compressible flow problems, such as shock wave propagation and two-dimensional/axisymmetric incompressible moving free surface flows. The numerical results demonstrate that this new cell-interface reconstruction technique works very well in several practical applications. (C) 2012 Elsevier Inc. All rights reserved.

Expression of Mitochondrial Non-coding RNAs (ncRNAs) Is Modulated by High Risk Human Papillomavirus (HPV) Oncogenes

The study of RNA and DNA oncogenic viruses has proved invaluable in the discovery of key cellular pathways that are rendered dysfunctional during cancer progression. An example is high risk human papillomavirus (HPV), the etiological agent of cervical cancer. The role of HPV oncogenes in cellular immortalization and transformation has been extensively investigated. We reported the differential expression of a family of human mitochondrial non-coding RNAs (ncRNAs) between normal and cancer cells. Normal cells express a sense mitochondrial ncRNA (SncmtRNA) that seems to be required for cell proliferation and two antisense transcripts (ASncmtRNAs). In contrast, the ASncmtRNAs are down-regulated in cancer cells. To shed some light on the mechanisms that trigger down-regulation of the ASncmtRNAs, we studied human keratinocytes (HFK) immortalized with HPV. Here we show that immortalization of HFK with HPV-16 or 18 causes down-regulation of the ASncmtRNAs and induces the expression of a new sense transcript named SncmtRNA-2. Transduction of HFK with both E6 and E7 is sufficient to induce expression of SncmtRNA-2. Moreover, E2 oncogene is involved in down-regulation of the ASncmtRNAs. Knockdown of E2 in immortalized cells reestablishes in a reversible manner the expression of the ASncmtRNAs, suggesting that endogenous cellular factors(s) could play functions analogous to E2 during non-HPV-induced oncogenesis.