A Component-Based Simplex Architecture for High-Assurance Cyber-Physical Systems

We present Component-Based Simplex Architecture (CBSA), a new framework for assuring the runtime safety of component-based cyber-physical systems (CPSs). CBSA integrates Assume-Guarantee (A-G) reasoning with the core principles of the Simplex control architecture to allow component-based CPSs to run advanced, uncertified controllers while still providing runtime assurance that A-G contracts and global properties are satisfied. In CBSA, multiple Simplex instances, which can be composed in a nested, serial or parallel manner, coordinate to assure system-wide properties. Combining A-G reasoning and the Simplex architecture is a challenging problem that yields significant benefits. By utilizing A-G contracts, we are able to compositionally determine the switching logic for CBSAs, thereby alleviating the state explosion encountered by other approaches. Another benefit is that we can use A-G proof rules to decompose the proof of system-wide safety assurance into sub-proofs corresponding to the component-based structure of the system architecture. We also introduce the notion of coordinated switching between Simplex instances, a key component of our compositional approach to reasoning about CBSA switching logic. We illustrate our framework with a component-based control system for a ground rover. We formally prove that the CBSA for this system guarantees energy safety (the rover never runs out of power), and collision freedom (the rover never collides with a stationary obstacle). We also consider a CBSA for the rover that guarantees mission completion: all target destinations visited within a prescribed amount of time.Comment: Extended version of a paper to be presented at ACSD 2017, 12 pages, 3 figures, 1 appendi

Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1.

UnlabelledDespite evidence for the prevalence of horizontal gene transfer of respiratory genes, little is known about how pathways functionally integrate within new hosts. One example of a mobile respiratory metabolism is bacterial chlorate reduction, which is frequently encoded on composite transposons. This implies that the essential components of the metabolism are encoded on these mobile elements. To test this, we heterologously expressed genes for chlorate reduction from Shewanella algae ACDC in the non-chlorate-reducing Shewanella oneidensis MR-1. The construct that ultimately endowed robust growth on chlorate included cld, a cytochrome c gene, clrABDC, and two genes of unknown function. Although strain MR-1 was unable to grow on chlorate after initial insertion of these genes into the chromosome, 11 derived strains capable of chlorate respiration were obtained through adaptive evolution. Genome resequencing indicated that all of the evolved chlorate-reducing strains replicated a large genomic region containing chlorate reduction genes. Contraction in copy number and loss of the ability to reduce chlorate were also observed, indicating that this phenomenon was extremely dynamic. Although most strains contained more than six copies of the replicated region, a single strain with less duplication also grew rapidly. This strain contained three additional mutations that we hypothesized compensated for the low copy number. We remade the mutations combinatorially in the unevolved strain and determined that a single nucleotide polymorphism (SNP) upstream of cld enabled growth on chlorate and was epistatic to a second base pair change in the NarP binding sequence between narQP and nrfA that enhanced growth.ImportanceThe ability of chlorate reduction composite transposons to form functional metabolisms after transfer to a new host is an important part of their propagation. To study this phenomenon, we engineered Shewanella oneidensis MR-1 into a chlorate reducer. We defined a set of genes sufficient to endow growth on chlorate from a plasmid, but found that chromosomal insertion of these genes was nonfunctional. Evolution of this inoperative strain into a chlorate reducer showed that tandem duplication was a dominant mechanism of activation. While copy number changes are a relatively rapid way of increasing gene dosage, replicating almost 1 megabase of extra DNA is costly. Mutations that alleviate the need for high copy number are expected to arise and eventually predominate, and we identified a single nucleotide polymorphism (SNP) that relieved the copy number requirement. This study uses both rational and evolutionary approaches to gain insight into the evolution of a fascinating respiratory metabolism

A Dust Twin of Cas A: Cool Dust and 21-micron Silicate Dust Feature in the Supernova Remnant G54.1+0.3

We present infrared (IR) and submillimeter observations of the Crab-like supernova remnant (SNR) G54.1+0.3 including 350 micron (SHARC-II), 870 micron (LABOCA), 70, 100, 160, 250, 350, 500 micron (Herschel) and 3-40 micron (Spitzer). We detect dust features at 9, 11 and 21 micron and a long wavelength continuum dust component. The 21 micron dust coincides with [Ar II] ejecta emission, and the feature is remarkably similar to that in Cas A. The IRAC 8 micron image including Ar ejecta is distributed in a shell-like morphology which is coincident with dust features, suggesting that dust has formed in the ejecta. We create a cold dust map that shows excess emission in the northwestern shell. We fit the spectral energy distribution of the SNR using the continuous distributions of ellipsoidal (CDE) grain model of pre-solar grain SiO2 that reproduces the 21 and 9 micron dust features and discuss grains of SiC and PAH that may be responsible for the 10-13 micron dust features. To reproduce the long-wavelength continuum, we explore models consisting of different grains including Mg2SiO4, MgSiO3, Al2O3, FeS, carbon, and Fe3O4. We tested a model with a temperature-dependent silicate absorption coefficient. We detect cold dust (27-44 K) in the remnant, making this the fourth such SNR with freshly-formed dust. The total dust mass in the SNR ranges from 0.08-0.9 Msun depending on the grain composition, which is comparable to predicted masses from theoretical models. Our estimated dust masses are consistent with the idea that SNe are a significant source of dust in the early Universe.Comment: MNRAS: accepted on June 28, 2018 and published on July 4, 201

In-situ measurements of the optical absorption of dioxythiophene-based conjugated polymers

Conjugated polymers can be reversibly doped by electrochemical means. This doping introduces new sub-bandgap optical absorption bands in the polymer while decreasing the bandgap absorption. To study this behavior, we have prepared an electrochemical cell allowing measurements of the optical properties of the polymer. The cell consists of a thin polymer film deposited on gold-coated Mylar behind which is another polymer that serves as a counterelectrode. An infrared transparent window protects the upper polymer from ambient air. By adding a gel electrolyte and making electrical connections to the polymer-on-gold films, one may study electrochromism in a wide spectral range. As the cell voltage (the potential difference between the two electrodes) changes, the doping level of the conjugated polymer films is changed reversibly. Our experiments address electrochromism in poly(3,4-ethylene-dioxy-thiophene) (PEDOT) and poly(3,4-dimethyl-propylene-dioxy-thiophene) (PProDOT-Me$_2$). This closed electrochemical cell allows the study of the doping induced sub-bandgap features (polaronic and bipolaronic modes) in these easily oxidized and highly redox switchable polymers. We also study the changes in cell spectra as a function of polymer thickness and investigate strategies to obtain cleaner spectra, minimizing the contributions of water and gel electrolyte features

Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.

BackgroundDesulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations.ResultsThe functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells.ConclusionsEven though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion

Immunocompetent murine models for the study of glioblastoma immunotherapy.

Glioblastoma remains a lethal diagnosis with a 5-year survival rate of less than 10%. (NEJM 352:987-96, 2005) Although immunotherapy-based approaches are capable of inducing detectable immune responses against tumor-specific antigens, improvements in clinical outcomes are modest, in no small part due to tumor-induced immunosuppressive mechanisms that promote immune escape and immuno-resistance. Immunotherapeutic strategies aimed at bolstering the immune response while neutralizing immunosuppression will play a critical role in improving treatment outcomes for glioblastoma patients. In vivo murine models of glioma provide an invaluable resource to achieving that end, and their use is an essential part of the preclinical workup for novel therapeutics that need to be tested in animal models prior to testing experimental therapies in patients. In this article, we review five contemporary immunocompetent mouse models, GL261 (C57BL/6), GL26 (C57BL/6) CT-2A (C57BL/6), SMA-560 (VM/Dk), and 4C8 (B6D2F1), each of which offer a suitable platform for testing novel immunotherapeutic approaches

Integrated spatial multiplexing of heralded single photon sources

The non-deterministic nature of photon sources is a key limitation for single photon quantum processors. Spatial multiplexing overcomes this by enhancing the heralded single photon yield without enhancing the output noise. Here the intrinsic statistical limit of an individual source is surpassed by spatially multiplexing two monolithic silicon correlated photon pair sources, demonstrating a 62.4% increase in the heralded single photon output without an increase in unwanted multi-pair generation. We further demonstrate the scalability of this scheme by multiplexing photons generated in two waveguides pumped via an integrated coupler with a 63.1% increase in the heralded photon rate. This demonstration paves the way for a scalable architecture for multiplexing many photon sources in a compact integrated platform and achieving efficient two photon interference, required at the core of optical quantum computing and quantum communication protocols.Comment: 10 pages, 3 figures, comments welcom

Constituting monetary conservatives via the 'savings habit': New Labour and the British housing market bubble

The ongoing world credit crunch might well kill off the most recent bubble dynamics in the British housing market by driving prices systematically downwards from their 2007 peak. Nonetheless, the experience of that bubble still warrants analytical attention. The Labour Government might not have been responsible for consciously creating it, but it has certainly grasped the opportunities the bubble has provided in an attempt to enforce a process of agential change at the heart of the British economy. The key issue in this respect is the way in which the Government has challenged the legitimacy of passive welfare receipts in favour of establishing a welfare system based on incorporating the individual into an active asset-holding society. The housing market has taken on new political significance as a means for individuals first to acquire assets and then to accumulate wealth on the back of asset ownership. The ensuing integration of the housing market into an increasingly reconfigured welfare system has permeated into the politics of everyday life. It has been consistent with individuals remaking their political subjectivities in line with preferences for the type of conservative monetary policies that typically keep house price bubbles inflated

Genomic innovation for crop improvement

Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genomes and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access the large and complex genomes of crops and their wild relatives. These have helped to identify a wide spectrum of genetic variation and permitted the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems