Quantitative comparison of performance analysis techniques for modular and generic network-on-chip

NoC-specific parameters feature a huge impact on performance and implementation costs of NoC. Hence, performance and cost evaluation of these parameter-dependent NoC is crucial in different design-stages but the requirements on performance analysis differ from stage to stage. In an early design-stage an analysis technique featuring reduced complexity and limited accuracy can be applied, whereas in subsequent design-stages more accurate techniques are required. <br><br> In this work several performance analysis techniques at different levels of abstraction are presented and quantitatively compared. These techniques include a static performance analysis using timing-models, a Colored Petri Net-based approach, VHDL- and SystemC-based simulators and an FPGA-based emulator. Conducting NoC-experiments with NoC-sizes from 9 to 36 functional units and various traffic patterns, characteristics of these experiments concerning accuracy, complexity and effort are derived. <br><br> The performance analysis techniques discussed here are quantitatively evaluated and finally assigned to the appropriate design-stages in an automated NoC-design-flow

Global Journalist: Prospects for George Bush’s second term and Middle East peace

In this November 4, 2004 episode of Global Journalist, Stuart Loory and political correspondents from around the world discuss foreign attitudes regarding the re-election of President George Bush. Also, Loory speaks with journalists in Japan and London about troop involvement in the Middle East

Characterization of bacterial operons consisting of two tubulins and a kinesin-like gene by the novel Two-Step Gene Walking method

Tubulins are still considered as typical proteins of Eukaryotes. However, more recently they have been found in the unusual bacteria Prosthecobacter (btubAB). In this study, the genomic organization of the btub-genes and their genomic environment were characterized by using the newly developed Two-Step Gene Walking method. In all investigated Prosthecobacters, btubAB are organized in a typical bacterial operon. Strikingly, all btub-operons comprise a third gene with similarities to kinesin light chain sequences. The genomic environments of the characterized btub-operons are always different. This supports the hypothesis that this group of genes represents an independent functional unit, which was acquired by Prosthecobacter via horizontal gene transfer. The newly developed Two-Step Gene Walking method is based on randomly primed polymerase chain reaction (PCR). It presents a simple workflow, which comprises only two major steps—a Walking-PCR with a single specific outward pointing primer (step 1) and the direct sequencing of its product using a nested specific primer (step 2). Two-Step Gene Walking proved to be highly efficient and was successfully used to characterize over 20 kb of sequence not only in pure culture but even in complex non-pure culture samples

Characterization and evolution of cell division and cell wall synthesis genes in the bacterial phyla Verrucomicrobia, Lentisphaerae, Chlamydiae and Planctomycetes and phylogenetic comparison with rRNA genes

In the past, studies on the relationships of the bacterial phyla Planctomycetes, Chlamydiae, Lentisphaerae, and Verrucomicrobia using different phylogenetic markers have been controversial. Investigations based on 16S rRNA sequence analyses suggested a relationship of the four phyla, showing the branching order Planctomycetes, Chlamydiae, Verrucomicrobia/Lentisphaerae. Phylogenetic analyses of 23S rRNA genes in this study also support a monophyletic grouping and their branching order—this grouping is significant for understanding cell division, since the major bacterial cell division protein FtsZ is absent from members of two of the phyla Chlamydiae and Planctomycetes. In Verrucomicrobia, knowledge about cell division is mainly restricted to the recent report of ftsZ in the closely related genera Prosthecobacter and Verrucomicrobium. In this study, genes of the conserved division and cell wall (dcw) cluster (ddl, ftsQ, ftsA, and ftsZ) were characterized in all verrucomicrobial subdivisions (1 to 4) with cultivable representatives (1 to 4). Sequence analyses and transcriptional analyses in Verrucomicrobia and genome data analyses in Lentisphaerae suggested that cell division is based on FtsZ in all verrucomicrobial subdivisions and possibly also in the sister phylum Lentisphaerae. Comprehensive sequence analyses of available genome data for representatives of Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes strongly indicate that their last common ancestor possessed a conserved, ancestral type of dcw gene cluster and an FtsZ-based cell division mechanism. This implies that Planctomycetes and Chlamydiae may have shifted independently to a non-FtsZ-based cell division mechanism after their separate branchings from their last common ancestor with Verrucomicrobia

Protein secretion and surface display in Gram-positive bacteria

The cell wall peptidoglycan of Gram-positive bacteria functions as a surface organelle for the transport and assembly of proteins that interact with the environment, in particular, the tissues of an infected host. Signal peptide-bearing precursor proteins are secreted across the plasma membrane of Gram-positive bacteria. Some precursors carry C-terminal sorting signals with unique sequence motifs that are cleaved by sortase enzymes and linked to the cell wall peptidoglycan of vegetative forms or spores. The sorting signals of pilin precursors are cleaved by pilus-specific sortases, which generate covalent bonds between proteins leading to the assembly of fimbrial structures. Other precursors harbour surface (S)-layer homology domains (SLH), which fold into a three-pronged spindle structure and bind secondary cell wall polysaccharides, thereby associating with the surface of specific Gram-positive microbes. Type VII secretion is a non-canonical secretion pathway for WXG100 family proteins in mycobacteria. Gram-positive bacteria also secrete WXG100 proteins and carry unique genes that either contribute to discrete steps in secretion or represent distinctive substrates for protein transport reactions

KnowTox: pipeline and case study for confident prediction of potential toxic effects of compounds in early phases of development

Risk assessment of newly synthesised chemicals is a prerequisite for regulatory approval. In this context, in silico methods have great potential to reduce time, cost, and ultimately animal testing as they make use of the ever-growing amount of available toxicity data. Here, KnowTox is presented, a novel pipeline that combines three different in silico toxicology approaches to allow for confident prediction of potentially toxic effects of query compounds, i.e. machine learning models for 88 endpoints, alerts for 919 toxic substructures, and computational support for read-across. It is mainly based on the ToxCast dataset, containing after preprocessing a sparse matrix of 7912 compounds tested against 985 endpoints. When applying machine learning models, applicability and reliability of predictions for new chemicals are of utmost importance. Therefore, first, the conformal prediction technique was deployed, comprising an additional calibration step and per definition creating internally valid predictors at a given significance level. Second, to further improve validity and information efficiency, two adaptations are suggested, exemplified at the androgen receptor antagonism endpoint. An absolute increase in validity of 23% on the in-house dataset of 534 compounds could be achieved by introducing KNNRegressor normalisation. This increase in validity comes at the cost of efficiency, which could again be improved by 20% for the initial ToxCast model by balancing the dataset during model training. Finally, the value of the developed pipeline for risk assessment is discussed using two in-house triazole molecules. Compared to a single toxicity prediction method, complementing the outputs of different approaches can have a higher impact on guiding toxicity testing and de-selecting most likely harmful development-candidate compounds early in the development process

Changes in global and thalamic brain connectivity in LSD-induced altered states of consciousness are attributable to the 5-HT2A receptor

Background:Lysergic acid diethylamide (LSD) has agonist activity at various serotonin (5-HT) and dopamine receptors. Despite the therapeutic and scientific interest in LSD, specific receptor contributions to its neurobiological effects remain unknown. Methods: We therefore conducted a double-blind, randomized, counterbalanced, cross-over study (ClinicalTrials.gov, NCT02451072) during which 24 healthy human participants received either (i) placebo+placebo, (ii) placebo+LSD (100 µg po), or (iii) Ketanserin, a selective 5-HT receptor antagonist,+LSD. We quantified resting-state functional connectivity via a data-driven global brain connectivity method and compared it to cortical gene expression maps. Findings: LSD reduced associative, but concurrently increased sensory-somatomotor brain-wide and thalamic connectivity. Ketanserin fully blocked the subjective and neural LSD effects. Whole-brain spatial patterns of LSD effects matched 5-HT receptor cortical gene expression in humans. Conclusion: Together, these results strongly implicate the 5-HT receptor in LSD's neuropharmacology. This study therefore pinpoints the critical role of 5-HT in LSD's mechanism, which informs its neurobiology and guides rational development of psychedelic-based therapeutics. Funding: Swiss National Science Foundation (SNSF, P2ZHP1_161626, KHP), the Swiss Neuromatrix Foundation (2015 - 0103, FXV), the Usona Institute (2015 - 2056, FXV), the NIH (R01MH112746, JDM; DP5OD012109, AA; R01MH108590, AA), the NIAA ( P50AA012870-16, AA & JHK), the NARSAD Independent Investigator Grant (AA), the Yale CTSA grant (UL1TR000142 Pilot Award, AA), and the Slovenian Research Agency (ARRS J7-6829 & ARRS J7-8275, GR)

Hybrid renewable energy systems: the value of storage as a function of PV-wind variability

As shares of variable renewable energy (VRE) on the electric grid increase, sources of grid flexibility will become increasingly important for maintaining the reliability and affordability of electricity supply. Lithium-ion battery energy storage has been identified as an important and cost-effective source of flexibility, both by itself and when coupled with VRE technologies like solar photovoltaics (PV) and wind. In this study, we explored the current and future value of utility-scale hybrid energy systems comprising PV, wind, and lithium-ion battery technologies (PV-wind-battery systems). Using a price-taker model with simulated hourly energy and capacity prices, we simulated the revenue-maximizing dispatch of a range of PV-wind-battery configurations across Texas, from the present through 2050. Holding PV capacity and point-of-interconnection capacity constant, we modeled configurations with varying wind-to-PV capacity ratios and battery-to-PV capacity ratios. We found that coupling PV, wind, and battery technologies allows for more effective utilization of interconnection capacity by increasing capacity factors to 60%–80%+ and capacity credits to close to 100%, depending on battery capacity. We also compared the energy and capacity values of PV-wind and PV-wind-battery systems to the corresponding stability coefficient metric, which describes the location-and configuration-specific complementarity of PV and wind resources. Our results show that the stability coefficient effectively predicts the configuration-location combinations in which a smaller battery component can provide comparable economic performance in a PV-wind-battery system (compared to a PV-battery system). These PV-wind-battery hybrids can help integrate more VRE by providing smoother, more predictable generation and greater flexibility