Liveness-Driven Random Program Generation

Randomly generated programs are popular for testing compilers and program analysis tools, with hundreds of bugs in real-world C compilers found by random testing. However, existing random program generators may generate large amounts of dead code (computations whose result is never used). This leaves relatively little code to exercise a target compiler's more complex optimizations. To address this shortcoming, we introduce liveness-driven random program generation. In this approach the random program is constructed bottom-up, guided by a simultaneous structural data-flow analysis to ensure that the generator never generates dead code. The algorithm is implemented as a plugin for the Frama-C framework. We evaluate it in comparison to Csmith, the standard random C program generator. Our tool generates programs that compile to more machine code with a more complex instruction mix.Comment: Pre-proceedings paper presented at the 27th International Symposium on Logic-Based Program Synthesis and Transformation (LOPSTR 2017), Namur, Belgium, 10-12 October 2017 (arXiv:1708.07854

Attribution of Atmospheric Sulfur Dioxide over the English Channel to Dimethylsulfide and Changing Ship Emissions

Atmospheric sulfur dioxide (SO2) was measured continuously from the Penlee Point Atmospheric Observatory(PPAO) near Plymouth, United Kingdom between May 2014 and November 2015. This coastal site is exposed to marine air across a wide wind sector. The predominant southwesterly winds carry relatively clean background Atlantic air. In contrast, air from the southeast is heavily influenced by exhaust plumes from ships in the English Channel as well as near the Plymouth Sound. New International Maritime Organization (IMO) regulation came into force in January 2015 to reduce sulfur emissions tenfold in Sulfur Emission Control Areas such as the English Channel. Our observations suggest a three-fold reduction from 2014 to 2015 in ship-emitted SO2 from that direction. Apparent fuel sulfur content calculated from coincidental SO2 and carbon dioxide (CO2) peaks from local ship plum es show a high level of compliance to the IMO regulation (> 95 %) in both years. Dimethylsulfide (DMS) is an important source of atmospheric SO2 even in this semi-polluted region. The relative contribution of DMS oxidation to the SO2 burden over the English Channel increased from ~ 1/3 in 2014 to ~ 1/2 in 2015 due to the reduction in ship sulfur emissions. Our diel analysis suggests that SO2 is removed from the marine atmospheric boundary layer in about half a day, with dry deposition to the ocean accounting for a quarter of the total loss

An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks

Tranilast increases vasodilator response to acetylcholine in rat mesenteric resistance arteries through increased EDHF participation

Background and Purpose: Tranilast, in addition to its capacity to inhibit mast cell degranulation, has other biological effects, including inhibition of reactive oxygen species, cytokines, leukotrienes and prostaglandin release. In the current study, we analyzed whether tranilast could alter endothelial function in rat mesenteric resistance arteries (MRA). Experimental Approach: Acetylcholine-induced relaxation was analyzed in MRA (untreated and 1-hour tranilast treatment) from 6 month-old Wistar rats. To assess the possible participation of endothelial nitric oxide or prostanoids, acetylcholineinduced relaxation was analyzed in the presence of L-NAME or indomethacin. The participation of endothelium-derived hyperpolarizing factor (EDHF) in acetylcholine-induced response was analyzed by preincubation with TRAM-34 plus apamin or by precontraction with a high K+ solution. Nitric oxide (NO) and superoxide anion levels were measured, as well as vasomotor responses to NO donor DEA-NO and to large conductance calcium-activated potassium channel opener NS1619. Key Results: Acetylcholine-induced relaxation was greater in tranilast-incubated MRA. Acetylcholine-induced vasodilation was decreased by L-NAME in a similar manner in both experimental groups. Indomethacin did not modify vasodilation. Preincubation with a high K+ solution or TRAM-34 plus apamin reduced the vasodilation to ACh more markedly in tranilastincubated segments. NO and superoxide anion production, and vasodilator responses to DEA-NO or NS1619 remained unmodified in the presence of tranilast. Conclusions and Implications: Tranilast increased the endothelium-dependent relaxation to acetylcholine in rat MRA. This effect is independent of the nitric oxide and cyclooxygenase pathways but involves EDHF, and is mediated by an increased role of small conductance calcium-activated K+ channelsThis study was supported by Ministerio de Ciencia e Innovación (SAF 2009-10374), Ministerio de Economía y Competitividad (SAF 2012-38530), and Fundación Mapfre. F.E. Xavier is recipient of research fellowship from Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brazil

Strontium potently inhibits mineralisation in bone-forming primary rat osteoblast cultures and reduces numbers of osteoclasts in mouse marrow cultures

The basic mechanisms by which strontium ranelate acts on bone are still unclear. We show that an important action of strontium salts is to block calcification in cultures of osteoblasts, the bone-forming cells. These results suggest that strontium treatment could have previously overlooked effects on bone

Exact exchange-correlation potential of a ionic Hubbard model with a free surface

We use Lanczos exact diagonalization to compute the exact exchange-correlation (xc) potential of a Hubbard chain with large binding energy ("the bulk") followed by a chain with zero binding energy ("the vacuum"). Several results of density functional theory in the continuum (sometimes controversial) are verified in the lattice. In particular we show explicitly that the fundamental gap is given by the gap in the Kohn-Sham spectrum plus a contribution due to the jump of the xc-potential when a particle is added. The presence of a staggered potential and a nearest-neighbor interaction V allows to simulate a ionic solid. We show that in the ionic regime in the small hopping amplitude limit the xc-contribution to the gap equals V, while in the Mott regime it is determined by the Hubbard U interaction. In addition we show that correlations generates a new potential barrier at the surface

RNAi-Based Functional Genomics Identifies New Virulence Determinants in Mucormycosis

Mucorales are an emerging group of human pathogens that are responsible for the lethal disease mucormycosis. Unfortunately, functional studies on the genetic factors behind the virulence of these organisms are hampered by their limited genetic tractability, since they are reluctant to classical genetic tools like transposable elements or gene mapping. Here, we describe an RNAi-based functional genomic platform that allows the identification of new virulence factors through a forward genetic approach firstly described in Mucorales. This platform contains a whole-genome collection of Mucor circinelloides silenced transformants that presented a broad assortment of phenotypes related to the main physiological processes in fungi, including virulence, hyphae morphology, mycelial and yeast growth, carotenogenesis and asexual sporulation. Selection of transformants with reduced virulence allowed the identification of mcplD, which encodes a Phospholipase D, and mcmyo5, encoding a probably essential cargo transporter of the Myosin V family, as required for a fully virulent phenotype of M. circinelloides. Knock-out mutants for those genes showed reduced virulence in both Galleria mellonella and Mus musculus models, probably due to a delayed germination and polarized growth within macrophages. This study provides a robust approach to study virulence in Mucorales and as a proof of concept identified new virulence determinants in M. circinelloides that could represent promising targets for future antifungal therapies

Air–sea exchange of acetone, acetaldehyde, DMS and isoprene at a UK coastal site

Volatile organic compounds (VOCs) are ubiquitous in the atmosphere and are important for atmospheric chemistry. Large uncertainties remain in the role of the ocean in the atmospheric VOC budget because of poorly constrained marine sources and sinks. There are very few direct measurements of air–sea VOC fluxes near the coast, where natural marine emissions could influence coastal air quality (i.e. ozone, aerosols) and terrestrial gaseous emissions could be taken up by the coastal seas. To address this, we present air–sea flux measurements of acetone, acetaldehyde and dimethylsulfide (DMS) at the coastal Penlee Point Atmospheric Observatory (PPAO) in the south-west UK during the spring (April–May 2018). Fluxes of these gases were measured simultaneously by eddy covariance (EC) using a proton-transfer-reaction quadrupole mass spectrometer. Comparisons are made between two wind sectors representative of different air–water exchange regimes: the open-water sector facing the North Atlantic Ocean and the terrestrially influenced Plymouth Sound fed by two estuaries. Mean EC (± 1 standard error) fluxes of acetone, acetaldehyde and DMS from the open-water wind sector were −8.0 ± 0.8, −1.6 ± 1.4 and 4.7 ± 0.6 µmol m−2 d−1 respectively (“−” sign indicates net air-to-sea deposition). These measurements are generally comparable (same order of magnitude) to previous measurements in the eastern North Atlantic Ocean at the same latitude. In comparison, the Plymouth Sound wind sector showed respective fluxes of −12.9 ± 1.4, −4.5 ± 1.7 and 1.8 ± 0.8 µmol m−2 d −1. The greater deposition fluxes of acetone and acetaldehyde within the Plymouth Sound were likely to a large degree driven by higher atmospheric concentrations from the terrestrial wind sector. The reduced DMS emission from the Plymouth Sound was caused by a combination of lower wind speed and likely lower dissolved concentrations as a result of the estuarine influence (i.e. dilution). In addition, we measured the near-surface seawater concentrations of acetone, acetaldehyde, DMS and isoprene from a marine station 6 km offshore. Comparisons are made between EC fluxes from the open-water and bulk air–sea VOC fluxes calculated using air and water concentrations with a two-layer (TL) model of gas transfer. The calculated TL fluxes agree with the EC measurements with respect to the directions and magnitudes of fluxes, implying that any recently proposed surface emissions of acetone and acetaldehyde would be within the propagated uncertainty of 2.6 µmol m−2 d −1. The computed transfer velocities of DMS, acetone and acetaldehyde from the EC fluxes and air and water concentrations are largely consistent with previous transfer velocity estimates from the open ocean. This suggests that wind, rather than bottom-driven turbulence and current velocity, is the main driver for gas exchange within the open-water sector at PPAO (depth of ∼ 20 m)

The 'At-risk mental state' for psychosis in adolescents : clinical presentation, transition and remission.

Despite increased efforts over the last decade to prospectively identify individuals at ultra-high risk of developing a psychotic illness, limited attention has been specifically directed towards adolescent populations (<18 years). In order to evaluate how those under 18 fulfilling the operationalised criteria for an At-Risk Mental State (ARMS) present and fare over time, we conducted an observational study. Participants (N = 30) generally reported a high degree of functional disability and frequent and distressing perceptual disturbance, mainly in the form of auditory hallucinations. Seventy percent (21/30) were found to fulfil the criteria for a co-morbid ICD-10 listed mental health disorder, with mood (affective; 13/30) disorders being most prevalent. Overall transition rates to psychosis were low at 24 months follow-up (2/28; 7.1 %) whilst many participants demonstrated a significant reduction in psychotic-like symptoms. The generalisation of these findings may be limited due to the small sample size and require replication in a larger sample

Structure of the hDmc1-ssDNA filament reveals the principles of its architecture

In eukaryotes, meiotic recombination is a major source of genetic diversity, but its defects in humans lead to abnormalities such as Down's, Klinefelter's and other syndromes. Human Dmc1 (hDmc1), a RecA/Rad51 homologue, is a recombinase that plays a crucial role in faithful chromosome segregation during meiosis. The initial step of homologous recombination occurs when hDmc1 forms a filament on single-stranded (ss) DNA. However the structure of this presynaptic complex filament for hDmc1 remains unknown. To compare hDmc1-ssDNA complexes to those known for the RecA/Rad51 family we have obtained electron microscopy (EM) structures of hDmc1-ssDNA nucleoprotein filaments using single particle approach. The EM maps were analysed by docking crystal structures of Dmc1, Rad51, RadA, RecA and DNA. To fully characterise hDmc1-DNA complexes we have analysed their organisation in the presence of Ca2+, Mg2+, ATP, AMP-PNP, ssDNA and dsDNA. The 3D EM structures of the hDmc1-ssDNA filaments allowed us to elucidate the principles of their internal architecture. Similar to the RecA/Rad51 family, hDmc1 forms helical filaments on ssDNA in two states: extended (active) and compressed (inactive). However, in contrast to the RecA/Rad51 family, and the recently reported structure of hDmc1-double stranded (ds) DNA nucleoprotein filaments, the extended (active) state of the hDmc1 filament formed on ssDNA has nine protomers per helical turn, instead of the conventional six, resulting in one protomer covering two nucleotides instead of three. The control reconstruction of the hDmc1-dsDNA filament revealed 6.4 protein subunits per helical turn indicating that the filament organisation varies depending on the DNA templates. Our structural analysis has also revealed that the N-terminal domain of hDmc1 accomplishes its important role in complex formation through domain swapping between adjacent protomers, thus providing a mechanistic basis for coordinated action of hDmc1 protomers during meiotic recombination