Analysis of a Cone-Based Distributed Topology Control Algorithm for Wireless Multi-hop Networks

The topology of a wireless multi-hop network can be controlled by varying the transmission power at each node. In this paper, we give a detailed analysis of a cone-based distributed topology control algorithm. This algorithm, introduced in [16], does not assume that nodes have GPS information available; rather it depends only on directional information. Roughly speaking, the basic idea of the algorithm is that a node $u$ transmits with the minimum power $p_{u,\alpha}$ required to ensure that in every cone of degree $\alpha$ around $u$, there is some node that $u$ can reach with power $p_{u,\alpha}$. We show that taking $\alpha = 5\pi/6$ is a necessary and sufficient condition to guarantee that network connectivity is preserved. More precisely, if there is a path from $s$ to $t$ when every node communicates at maximum power, then, if $\alpha <= 5\pi/6$, there is still a path in the smallest symmetric graph $G_\alpha$ containing all edges $(u,v)$ such that $u$ can communicate with $v$ using power $p_{u,\alpha}$. On the other hand, if $\alpha > 5\pi/6$, connectivity is not necessarily preserved. We also propose a set of optimizations that further reduce power consumption and prove that they retain network connectivity. Dynamic reconfiguration in the presence of failures and mobility is also discussed. Simulation results are presented to demonstrate the effectiveness of the algorithm and the optimizations.Comment: 10 page

Tamm states and nonlinear surface modes in photonic crystals

We predict the existence of surface gap modes, known as Tamm states for electronic systems, in truncated photonic crystals formed by two types of dielectric rods. We investigate the energy threshold, dispersion, and modal symmetries of the surface modes, and also demonstrate the existence and tunability of nonlinear Tamm states in binary photonic crystals with nonlinear response.Comment: 11 pages, 3 figures, submitted to Optics Communication

Lack of Association of Rare Functional Variants in TSC1/TSC2 Genes with Autism Spectrum Disorder

Background: Autism spectrum disorder (ASD) is reported in 30 to 60% of patients with tuberous sclerosis complex (TSC) but shared genetic mechanisms that exist between TSC-associated ASD and idiopathic ASD have yet to be determined. Through the small G-protein Rheb, the TSC proteins, hamartin and tuberin, negatively regulate mammalian target of rapamycin complex 1 (mTORC1) signaling. It is well established that mTORC1 plays a pivotal role in neuronal translation and connectivity, so dysregulation of mTORC1 signaling could be a common feature in many ASDs. Pam, an E3 ubiquitin ligase, binds to TSC proteins and regulates mTORC1 signaling in the CNS, and the FBXO45-Pam ubiquitin ligase complex plays an essential role in neurodevelopment by regulating synapse formation and growth. Since mounting evidence has established autism as a disorder of the synapses, we tested whether rare genetic variants in TSC1, TSC2, MYCBP2, RHEB and FBXO45, genes that regulate mTORC1 signaling and/or play a role in synapse development and function, contribute to the pathogenesis of idiopathic ASD. Methods: Exons and splice junctions of TSC1, TSC2, MYCBP2, RHEB and FBXO45 were resequenced for 300 ASD trios from the Simons Simplex Collection (SSC) using a pooled PCR amplification and next-generation sequencing strategy, targeted to the discovery of deleterious coding variation. These detected, potentially functional, variants were confirmed by Sanger sequencing of the individual samples comprising the pools in which they were identified. Results: We identified a total of 23 missense variants in MYCBP2, TSC1 and TSC2. These variants exhibited a near equal distribution between the proband and parental pools, with no statistical excess in ASD cases (P > 0.05). All proband variants were inherited. No putative deleterious variants were confirmed in RHEB and FBXO45. Three intronic variants, identified as potential splice defects in MYCBP2 did not show aberrant splicing upon RNA assay. Overall, we did not find an over-representation of ASD causal variants in the genes studied to support them as contributors to autism susceptibility. Conclusions: We did not observe an enrichment of rare functional variants in TSC1 and TSC2 genes in our sample set of 300 trios

A Flexible LDPC/Turbo Decoder Architecture

Low-density parity-check (LDPC) codes and convolutional Turbo codes are two of the most powerful error correcting codes that are widely used in modern communication systems. In a multi-mode baseband receiver, both LDPC and Turbo decoders may be required. However, the different decoding approaches for LDPC and Turbo codes usually lead to different hardware architectures. In this paper we propose a unified message passing algorithm for LDPC and Turbo codes and introduce a flexible soft-input soft-output (SISO) module to handle LDPC/Turbo decoding. We employ the trellis-based maximum a posteriori (MAP) algorithm as a bridge between LDPC and Turbo codes decoding. We view the LDPC code as a concatenation of n super-codes where each super-code has a simpler trellis structure so that the MAP algorithm can be easily applied to it. We propose a flexible functional unit (FFU) for MAP processing of LDPC and Turbo codes with a low hardware overhead (about 15% area and timing overhead). Based on the FFU, we propose an area-efficient flexible SISO decoder architecture to support LDPC/Turbo codes decoding. Multiple such SISO modules can be embedded into a parallel decoder for higher decoding throughput. As a case study, a flexible LDPC/Turbo decoder has been synthesized on a TSMC 90 nm CMOS technology with a core area of 3.2 mm2. The decoder can support IEEE 802.16e LDPC codes, IEEE 802.11n LDPC codes, and 3GPP LTE Turbo codes. Running at 500 MHz clock frequency, the decoder can sustain up to 600 Mbps LDPC decoding or 450 Mbps Turbo decoding.NokiaNokia Siemens Networks (NSN)XilinxTexas InstrumentsNational Science Foundatio

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids.Fil: Klumper, Uli. Technical University of Denmark; DinamarcaFil: Riber, Leise. Universidad de Copenhagen; DinamarcaFil: Dechesne, Arnaud. Technical University of Denmark; DinamarcaFil: Sannazzaro, Analía Inés. Universidad de Copenhagen; DinamarcaFil: Hansen, Lars H.. Universidad de Copenhagen; Dinamarca. Aarhus University. Roskilde; DinamarcaFil: Sørensen, Søren. Universidad de Copenhagen; DinamarcaFil: Smets, Barth F. Technical University of Denmark; Dinamarc

The Transcriptome of the Intraerythrocytic Developmental Cycle of Plasmodium falciparum

Plasmodium falciparum is the causative agent of the most burdensome form of human malaria, affecting 200–300 million individuals per year worldwide. The recently sequenced genome of P. falciparum revealed over 5,400 genes, of which 60% encode proteins of unknown function. Insights into the biochemical function and regulation of these genes will provide the foundation for future drug and vaccine development efforts toward eradication of this disease. By analyzing the complete asexual intraerythrocytic developmental cycle (IDC) transcriptome of the HB3 strain of P. falciparum, we demonstrate that at least 60% of the genome is transcriptionally active during this stage. Our data demonstrate that this parasite has evolved an extremely specialized mode of transcriptional regulation that produces a continuous cascade of gene expression, beginning with genes corresponding to general cellular processes, such as protein synthesis, and ending with Plasmodium-specific functionalities, such as genes involved in erythrocyte invasion. The data reveal that genes contiguous along the chromosomes are rarely coregulated, while transcription from the plastid genome is highly coregulated and likely polycistronic. Comparative genomic hybridization between HB3 and the reference genome strain (3D7) was used to distinguish between genes not expressed during the IDC and genes not detected because of possible sequence variations. Genomic differences between these strains were found almost exclusively in the highly antigenic subtelomeric regions of chromosomes. The simple cascade of gene regulation that directs the asexual development of P. falciparum is unprecedented in eukaryotic biology. The transcriptome of the IDC resembles a “just-in-time” manufacturing process whereby induction of any given gene occurs once per cycle and only at a time when it is required. These data provide to our knowledge the first comprehensive view of the timing of transcription throughout the intraerythrocytic development of P. falciparum and provide a resource for the identification of new chemotherapeutic and vaccine candidates