Reliability-aware multi-segmented bus architecture for photonic networks-on-chip

Network-on-chip (NoC) has emerged as an enabling platform for connecting hundreds of cores on a single chip, allowing for a structured, scalable system when compared to traditional on-chip buses. However, the multi-hop wireline paths in traditional NoCs result in high latency and energy dissipation causing an overall degradation in performance, especially for increasing system size. To alleviate this problem a few radically different interconnect technologies are envisioned. One such method of interconnecting different cores in NoCs is photonic interconnects. Photonic NoCs are on-chip communications networks in which information is transmitted in the form of optical signals. Photonic interconnection is one of the leading examples of emerging technology for on-chip interconnects. Existing innovative photonic NoC architectures have improved performance and reduced energy dissipation. Most architectures use Wavelength Division Multiplexing (WDM) on the photonic waveguides to increase the data bandwidth. However they have issues relating to reliability, such as waveguide losses and adjacent channel crosstalk. These phenomena could have a crippling effect on a system, and most current architectures do not address these effects. A newly proposed topology, known as the Multiple-Segmented Bus topology, or MSB, has shown promise for solving, or at least reducing, many of the problems plaguing the design of photonic networks using a modification of a folded torus to transmit different wavelength signals simultaneously. The MSB segments the waveguides into smaller parts to limit the waveguide losses. The formal performance evaluation of this proposed architecture has not been completed. This thesis will analyze the performance of such a network when implemented as a NoC in terms of data bandwidth, energy dissipation, latency, and reliability. By analyzing and comparing performance, energy dissipations, and reliability, the MSB-based photonic NoC (MSB-PNoC) can be compared to other state-of-the-art photonic NoCs to determine the feasibility of this topology for future network-on-chip designs

Redundancy and specialization among plant microRNAs : role of the MIR164 family in developmental robustness

In plants, members of microRNA (miRNA) families are often predicted to target the same or overlapping sets of genes. It has thus been hypothesized that these miRNAs may act in a functionally redundant manner. This hypothesis is tested here by studying the effects of elimination of all three members of the MIR164 family from Arabidopsis. It was found that a loss of miR164 activity leads to a severe disruption of shoot development, in contrast to the effect of mutation in any single MIR164 gene. This indicates that these miRNAs are indeed functionally redundant. Differences in the expression patterns of the individual MIR164 genes imply, however, that redundancy among them is not complete, and that these miRNAs show functional specialization. Furthermore, the results of molecular and genetic analyses of miR164-mediated target regulation indicate that miR164 miRNAs function to control the transcript levels, as well as the expression patterns, of their targets, suggesting that they might contribute to developmental robustness. For two of the miR164 targets, namely CUP-SHAPED COTYLEDON1 (CUC1) and CUC2, we provide evidence for their involvement in the regulation of growth and show that their derepression in miR164 loss-of-function mutants is likely to account for most of the mutant phenotype

X-ray Observations of the Compact Source in CTA 1

The point source RX J0007.0+7302, at the center of supernova remnant CTA 1, was studied using the X-Ray Multi-mirror Mission. The X-ray spectrum of the source is consistent with a neutron star interpretation, and is well described by a power law with the addition of a soft thermal component that may correspond to emission from hot polar cap regions or to cooling emission from a light element atmosphere over the entire star. There is evidence of extended emission on small spatial scales which may correspond to structure in the underlying synchrotron nebula. No pulsations are observed. Extrapolation of the nonthermal spectrum of RX J0007.0+7302 to gamma-ray energies yields a flux consistent with that of EGRET source 3EG J0010+7309, supporting the proposition that there is a gamma-ray emitting pulsar at the center of CTA 1. Observations of the outer regions of CTA 1 with the Advanced Satellite for Cosmology and Astrophysics confirm earlier detections of thermal emission from the remnant and show that the synchrotron nebula extends to the outermost reaches of the SNR.Comment: 5 pages, including 4 postscript figs.LaTex. Accepted for publication by Ap

The early extra petals1 Mutant Uncovers a Role for MicroRNA miR164c in Regulating Petal Number in Arabidopsis

Background: MicroRNAs (miRNAs) are small 20–25 nucleotide non-protein-coding RNAs that negatively regulate expression of genes in many organisms, ranging from plants to humans. The MIR164 family of miRNAs in Arabidopsis consists of three members that share sequence complementarity to transcripts of NAC family transcription factors, including CUP-SHAPED COTYLEDON1 (CUC1) and CUC2. CUC1 and CUC2 are redundantly required for the formation of boundaries between organ primordia. The analysis of transgenic plants that either overexpress miR164a or miR164b or express a miRNA-resistant version of CUC1 or CUC2 has shown that miRNA regulation of CUC1 and CUC2 is necessary for normal flower development. A loss-of-function allele of MIR164b did not result in a mutant phenotype, possibly because of functional redundancy among the three members of the MIR164 family. Results: In this study, we describe the characterization of the early extra petals1 (eep1) Arabidopsis mutant, whose predominant phenotype is the formation of extra petals in early-arising flowers. We demonstrate that eep1 is a loss-of-function allele of MIR164c, one of three known members of the MIR164 family. Our analyses of miR164c function and eep1 mir164b double mutants reveal that miR164c controls petal number in a nonredundant manner by regulating the transcript accumulation of the transcription factors CUC1 and CUC2. Conclusions: The data presented in this study indicate that closely related miRNA family members that are predicted to target the same set of genes can have different functions during development, possibly because of nonoverlapping expression patterns

Patterns of Auxin Transport and Gene Expression during Primordium Development Revealed by Live Imaging of the Arabidopsis Inflorescence Meristem

Background: Plants produce leaf and flower primordia from a specialized tissue called the shoot apical meristem (SAM). Genetic studies have identified a large number of genes that affect various aspects of primordium development including positioning, growth, and differentiation. So far, however, a detailed understanding of the spatio-temporal sequence of events leading to primordium development has not been established. Results: We use confocal imaging of green fluorescent protein (GFP) reporter genes in living plants to monitor the expression patterns of multiple proteins and genes involved in flower primordial developmental processes. By monitoring the expression and polarity of PINFORMED1 (PIN1), the auxin efflux facilitator, and the expression of the auxin-responsive reporter DR5, we reveal stereotypical PIN1 polarity changes which, together with auxin induction experiments, suggest that cycles of auxin build-up and depletion accompany, and may direct, different stages of primordium development. Imaging of multiple GFP-protein fusions shows that these dynamics also correlate with the specification of primordial boundary domains, organ polarity axes, and the sites of floral meristem initiation. Conclusions: These results provide new insight into auxin transport dynamics during primordial positioning and suggest a role for auxin transport in influencing primordial cell type

Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype

Histopathology, clinical chemistry, hematology and gene expression data were collected from the rat liver and blood after treatment with eight known hepatotoxins

Human neural crest cells display molecular and phenotypic hallmarks of stem cells

The fields of both developmental and stem cell biology explore how functionally distinct cell types arise from a self-renewing founder population. Multipotent, proliferative human neural crest cells (hNCC) develop toward the end of the first month of pregnancy. It is assumed that most differentiate after migrating throughout the organism, although in animal models neural crest stem cells reportedly persist in postnatal tissues. Molecular pathways leading over time from an invasive mesenchyme to differentiated progeny such as the dorsal root ganglion, the maxillary bone or the adrenal medulla are altered in many congenital diseases. To identify additional components of such pathways, we derived and maintained self-renewing hNCC lines from pharyngulas. We show that, unlike their animal counterparts, hNCC are able to self-renew ex vivo under feeder-free conditions. While cross species comparisons showed extensive overlap between human, mouse and avian NCC transcriptomes, some molecular cascades are only active in the human cells, correlating with phenotypic differences. Furthermore, we found that the global hNCC molecular profile is highly similar to that of pluripotent embryonic stem cells when compared with other stem cell populations or hNCC derivatives. The pluripotency markers NANOG, POU5F1 and SOX2 are also expressed by hNCC, and a small subset of transcripts can unambiguously identify hNCC among other cell types. The hNCC molecular profile is thus both unique and globally characteristic of uncommitted stem cells

A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds

This work was financially supported by ETH Zürich, University of Minnesota, the Swiss National Science Foundation (grant nos. 31003A_149512 and 200021–159713), Wellcome Trust (094476/Z/10/Z), ERC (NCB-TNT 339367), and BBSRC (BB/R018189/1).The peptide bond, the defining feature of proteins, governs peptide chemistry by abolishing nucleophilicity of the nitrogen. This and the planarity of the peptide bond arise from the delocalization of the lone pair of electrons on the nitrogen atom into the adjacent carbonyl. While chemical methylation of an amide bond uses a strong base to generate the imidate, OphA, the precursor protein of the fungal peptide macrocycle omphalotin A, self-hypermethylates amides at pH 7 using S-adenosyl methionine (SAM) as cofactor. The structure of OphA reveals a complex catenane-like arrangement in which the peptide substrate is clamped with its amide nitrogen aligned for nucleophilic attack on the methyl group of SAM. Biochemical data and computational modeling suggest a base-catalyzed reaction with the protein stabilizing the reaction intermediate. Backbone N-methylation of peptides enhances their protease resistance and membrane permeability, a property that holds promise for applications to medicinal chemistry.Publisher PDFPeer reviewe