Learning a Static Analyzer from Data

To be practically useful, modern static analyzers must precisely model the effect of both, statements in the programming language as well as frameworks used by the program under analysis. While important, manually addressing these challenges is difficult for at least two reasons: (i) the effects on the overall analysis can be non-trivial, and (ii) as the size and complexity of modern libraries increase, so is the number of cases the analysis must handle. In this paper we present a new, automated approach for creating static analyzers: instead of manually providing the various inference rules of the analyzer, the key idea is to learn these rules from a dataset of programs. Our method consists of two ingredients: (i) a synthesis algorithm capable of learning a candidate analyzer from a given dataset, and (ii) a counter-example guided learning procedure which generates new programs beyond those in the initial dataset, critical for discovering corner cases and ensuring the learned analysis generalizes to unseen programs. We implemented and instantiated our approach to the task of learning JavaScript static analysis rules for a subset of points-to analysis and for allocation sites analysis. These are challenging yet important problems that have received significant research attention. We show that our approach is effective: our system automatically discovered practical and useful inference rules for many cases that are tricky to manually identify and are missed by state-of-the-art, manually tuned analyzers

Bioactive composites for bone tissue engineering

One of the major challenges of bone tissue engineering is the production of a suitable scaffold material. In this review the current composite materials options available are considered covering both the methods of both production and assessing the scaffolds. A range of production routes have been investigated ranging from the use of porogens to produce the porosity through to controlled deposition methods. The testing regimes have included mechanical testing of the materials produced through to in vivo testing of the scaffolds. While the ideal scaffold material has not yet been produced, progress is being made

Non-monotonic temperature dependent transport in graphene grown by Chemical Vapor Deposition

Temperature-dependent resistivity of graphene grown by chemical vapor deposition (CVD) is investigated. We observe in low mobility CVD graphene device a strong insulating behavior at low temperatures and a metallic behavior at high temperatures manifesting a non-monotonic in the temperature dependent resistivity.This feature is strongly affected by carrier density modulation. To understand this anomalous temperature dependence, we introduce thermal activation of charge carriers in electron-hole puddles induced by randomly distributed charged impurities. Observed temperature evolution of resistivity is then understood from the competition among thermal activation of charge carriers, temperature-dependent screening and phonon scattering effects. Our results imply that the transport property of transferred CVD-grown graphene is strongly influenced by the details of the environmentComment: 7 pages, 3 figure

Magnetic interactions in transition metal doped ZnO : An abinitio study

We calculate the nature of magnetic interactions in transition-metal doped ZnO using the local spin density approximation and LSDA+\textit{U} method of density functional theory. We investigate the following four cases: (i) single transition metal ion types (Cr, Mn, Fe, Co, Ni and Cu) substituted at Zn sites, (ii) substitutional magnetic transition metal ions combined with additional Cu and Li dopants, (iii) substitutional magnetic transition metal ions combined with oxygen vacancies and (iv) pairs of magnetic ion types (Co and Fe, Co and Mn, etc.). Extensive convergence tests indicate that the calculated magnetic ground state is unusually sensitive to the k-point mesh and energy cut-off, the details of the geometry optimizations and the choice of the exchange-correlation functional. We find that ferromagnetic coupling is sometimes favorable for single type substitutional transition metal ions within the local spin density approximation. However, the nature of magnetic interactions changes when correlations on the transition-metal ion are treated within the more realistic LSDA + \textit{U} method, often disfavoring the ferromagnetic state. The magnetic configuration is sensitive to the detailed arrangement of the ions and the amount of lattice relaxation, except in the case of oxygen vacancies when an antiferromagnetic state is always favored.Comment: 11 pages, 17 figure

Z_3 Strings and their Interactions

We construct Z_3 vortex solutions in a model in which SU(3) is spontaneously broken to Z_3. The model is truncated to one in which there are only two dimensionless free parameters and the interaction of vortices within this restricted set of models is studied numerically. We find that there is a curve in the two dimensional space of parameters for which the energy of two asymptotically separated vortices equals the energy of the vortices at vanishing separation. This suggests that the inter-vortex potential for Z_3 strings might be flat for these couplings, much like the case of U(1) strings in the Bogomolnyi limit. However, we argue that the intervortex potential is attractive at short distances and repulsive at large separations leading to the possibility of unstable bound states of Z_3 vortices.Comment: 8 pages; mainly corrected typos in table

Pathogenicity and Immune Response of Starry Flounder, Platichthys stellatus, Infected with Vibrio anguillarum

Vibrio anguillarum is the aetiological agent of vibriosis, a disease affecting many marine fish species. The occurrence of vibriosis in starry flounder, Platichthys stellatus, grown in an aquaculture farm has demonstrated the urgent need for information on pathogenic infection and immune response for efficient disease management. This is the first study to report Vibrio anguillarum isolation and infection in starry flounder. We evaluated immune responses, serum biochemical parameters, and cumulative mortality of the fish by experimentally challenging healthy fish. The expression levels of five immune genes (TNF, TNFR, IL-6, MHCII, and CXC) were measured by real-time quantitative PCR. The transcriptional levels of the genes encoding tumor necrosis factor (TNF), TNF receptor (TNFR), interleukin-6 (IL-6), the major histocompatibility complex (MHC-II), and a chemokine (CXC) in the head-kidney of V. anguillarum infected fish were significantly upregulated compared with control fish and biochemical indices including the alanine aminotransferase, total serum protein, and glucose levels of infected fish differed significantly from those of control. Additionally, Starry flounder infected with V. anguillarum at 1.67 × 106 and 1.67 × 108CFU/mL showed 53%, and 100% mortality, respectively. This study furthers our understanding of the immune and serum biochemical alterations, and mortality induced by bacterial infections, depending on pathogen concentration. This may advance strategies for control of V. anguillarum in cultured starry flounde

Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response

Dramatic rise of mutators has been found to accompany adaptation of bacteria in response to many kinds of stress. Two views on the evolutionary origin of this phenomenon emerged: the pleiotropic hypothesis positing that it is a byproduct of environmental stress or other specific stress response mechanisms and the second order selection which states that mutators hitchhike to fixation with unrelated beneficial alleles. Conventional population genetics models could not fully resolve this controversy because they are based on certain assumptions about fitness landscape. Here we address this problem using a microscopic multiscale model, which couples physically realistic molecular descriptions of proteins and their interactions with population genetics of carrier organisms without assuming any a priori fitness landscape. We found that both pleiotropy and second order selection play a crucial role at different stages of adaptation: the supply of mutators is provided through destabilization of error correction complexes or fluctuations of production levels of prototypic mismatch repair proteins (pleiotropic effects), while rise and fixation of mutators occur when there is a sufficient supply of beneficial mutations in replication-controlling genes. This general mechanism assures a robust and reliable adaptation of organisms to unforeseen challenges. This study highlights physical principles underlying physical biological mechanisms of stress response and adaptation

The C-Fern (Ceratopteris richardii) Genome: Insights Into Plant Genome Evolution With the First Partial Homosporous Fern Genome Assembly

Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes