Computing lower and upper expectations under epistemic independence

This paper investigates the computation of lower/upper expectations that must cohere with a collection of probabilistic assessments and a collection of judgements of epistemic independence. New algorithms, based on multilinear programming, are presented, both for independence among events and among random variables. Separation properties of graphical models are also investigated.

A new sensory organ in "primitive" molluscs (Polyplacophora Lepidopleurida), and its context in the nervous system of chitons

Introduction: Chitons (Polyplacophora) are molluscs considered to have a simple nervous system without cephalisation. The position of the class within Mollusca is the topic of extensive debate and neuroanatomical characters can provide new sources of phylogenetic data as well as insights into the fundamental biology of the organisms. We report a new discrete anterior sensory structure in chitons, occurring throughout Lepidopleurida, the order of living chitons that retains plesiomorphic characteristics.

Results: The novel "Schwabe organ" is clearly visible on living animals as a pair of streaks of brown or purplish pigment on the roof of the pallial cavity, lateral to or partly covered by the mouth lappets. We describe the histology and ultrastructure of the anterior nervous system, including the Schwabe organ, in two lepidopleuran chitons using light and electron microscopy. The oesophageal nerve ring is greatly enlarged and displays ganglionic structure, with the neuropil surrounded by neural somata. The Schwabe organ is innervated by the lateral nerve cord, and dense bundles of nerve fibres running through the Schwabe organ epithelium are frequently surrounded by the pigment granules which characterise the organ. Basal cells projecting to the epithelial surface and cells bearing a large number of ciliary structures may be indicative of sensory function. The Schwabe organ is present in all genera within Lepidopleurida (and absent throughout Chitonida) and represents a novel anatomical synapomorphy of the clade.

Conclusions: The Schwabe organ is a pigmented sensory organ, found on the ventral surface of deep-sea and shallow water chitons; although its anatomy is well understood, its function remains unknown. The anterior commissure of the chiton oesophagial nerve ring can be considered a brain. Our thorough review of the chiton central nervous system, and particularly the sensory organs of the pallial cavity, provides a context to interpret neuroanatomical homology and assess this new sense organ.

Evidence of plasma polarization shift of Ti He-alpha resonance line in high density laser produced plasmas

A spectroscopic study of the He-alpha (1s(2) S-1(0) - 1s2p P-1(1)) line emission (4749.73 eV) from high density plasma was conducted. The plasma was produced by irradiating Ti targets with intense (I approximate to 1x10(19) W/cm(2)), 400nm wavelength high contrast, short (45fs) p-polarized laser pulses at an angle of 45 degrees. A line shift up to 3.4 +/- 1.0 eV (1.9 +/- 0.55 m angstrom) was observed in the He-alpha line. The line width of the resonance line at FWHM was measured to be 12.1 +/- 0.6 eV (6.7 +/- 0.35 m angstrom). For comparison, we looked into the emission of the same spectral line from plasma produced by irradiating the same target with laser pulses of reduced intensities (approximate to 10(17) W/cm(2)): we observed a spectral shift of only 1.8 +/- 1.0 eV (0.9 +/- 0.55m angstrom) and the line-width measures up to 5.8 +/- 0.25 eV (2.7 +/- 0.35 m angstrom). These data provide evidence of plasma polarization shift of the Ti He-alpha line.

Transport of laser accelerated proton beams and isochoric heating of matter

The acceleration of intense proton and ion beams by ultra-intense lasers has matured to a point where applications in basic research and technology are being developed. Crucial for harvesting the unmatched beam parameters driven by the relativistic electron sheath is the precise control of the beam. We report on recent experiments using the PHELIX laser at GSI, the VULCAN laser at RAL and the TRIDENT laser at LANL to control and use laser accelerated proton beams for applications in high energy density research. We demonstrate efficient collimation of the proton beam using high field pulsed solenoid magnets, a prerequisite to capture and transport the beam for applications. Furthermore we report on two campaigns to use intense, short proton bunches to isochorically heat solid targets up to the warm dense matter state. The temporal profile of the proton beam allows for rapid heating of the target, much faster than the hydrodynamic response time thereby creating a strongly coupled plasma at solid density. The target parameters are then probed by X-ray Thomson scattering (XRTS) to reveal the density and temperature of the heated volume. This combination of two powerful techniques developed during the past few years allows for the generation and investigation of macroscopic samples of matter in states present in giant planets or the interior of the earth.

XUV Emission from Autoionizing Hole States Induced by Intense XUV-FEL at Intensities up to 10(17) W/cm(2)

Aluminium targets were irradiated with 92 eV radiation from FLASH Free Electron Laser at DESY at intensities up to 10(17)W/cm(2) by focussing the beam on target down to a spot size of similar to 1 mu m by means of a parabolic mirror. High resolution XUV spectroscopy was used to identify aluminium emission from complex hole-states. Simulations carried out with the MARIA code show that the emission characterizes the electron heating in the transition phase solid-atomic. The analysis allows constructing a simple model of electron heating via Auger electrons.

Measurement of The Dynamic Response of Compressed Hydrogen by Inelastic X-Ray Scattering

Measurement of the dynamic properties of hydrogen and helium under extreme pressures is a key to understanding the physics of planetary interiors. The inelastic scattering signal from statically compressed hydrogen inside diamond anvil cells at 2.8 GPa and 6.4 GPa was measured at the Diamond Light Source synchrotron facility in the UK. The first direct measurement of the local field correction to the Coulomb interactions in degenerate plasmas was obtained from spectral shifts in the scattering data and compared to predictions by the Utsumi-Ichimaru theory for degenerate electron liquids.

Enhancing design space exploration by extending CPU/GPU specifications onto FPGAs

The design cycle for complex special-purpose computing systems is extremely costly and time-consuming. It involves a multiparametric design space exploration for optimization, followed by design verification. Designers of special purpose VLSI implementations often need to explore parameters, such as optimal bitwidth and data representation, through time-consuming Monte Carlo simulations. A prominent example of this simulation-based exploration process is the design of decoders for error correcting systems, such as the Low-Density Parity-Check (LDPC) codes adopted by modern communication standards, which involves thousands of Monte Carlo runs for each design point. Currently, high-performance computing offers a wide set of acceleration options that range from multicore CPUs to Graphics Processing Units (GPUs) and Field Programmable Gate Arrays (FPGAs). The exploitation of diverse target architectures is typically associated with developing multiple code versions, often using distinct programming paradigms. In this context, we evaluate the concept of retargeting a single OpenCL program to multiple platforms, thereby significantly reducing design time. A single OpenCL-based parallel kernel is used without modifications or code tuning on multicore CPUs, GPUs, and FPGAs. We use SOpenCL (Silicon to OpenCL), a tool that automatically converts OpenCL kernels to RTL in order to introduce FPGAs as a potential platform to efficiently execute simulations coded in OpenCL. We use LDPC decoding simulations as a case study. Experimental results were obtained by testing a variety of regular and irregular LDPC codes that range from short/medium (e.g., 8,000 bit) to long length (e.g., 64,800 bit) DVB-S2 codes. We observe that, depending on the design parameters to be simulated, on the dimension and phase of the design, the GPU or FPGA may suit different purposes more conveniently, thus providing different acceleration factors over conventional multicore CPUs.

X-ray Polarization Spectroscopy from Ultra-Intense Interactions

Detailed knowledge of fast electron energy transport following the interaction of ultrashort intense laser pulses is a key subject for fast ignition. This is a problem relevant to many areas of laser-plasma physics with particular importance to fast ignition and X-ray secondary source development, necessary for the development of large-scale facilities such as HiPER and ELI. Operating two orthogonal crystal spectrometers set at Bragg angles close to 45 degrees determines the X-ray s- and p-polarization ratio. From this ratio, it is possible to infer the velocity distribution function of the fast electron beam within the dense plasma. We report on results of polarization measurements at high density for sulphur and nickel buried layer targets in the high intensity range of 10(19) - 10(21) Wcm(-2). We observe at 45 degrees the Ly-alpha doublet using two sets of orthogonal highly-orientated pyrolytic graphite (HOPG) crystals set in 1(st) order for sulphur and 3(rd) order for nickel.

Age- and Sex-Specific Causal Effects of Adiposity on Cardiovascular Risk Factors

Observational studies have reported different effects of adiposity on cardiovascular risk factors across age and sex. Since cardiovascular risk factors are enriched in obese individuals, it has not been easy to dissect the effects of adiposity from those of other risk factors. We used a Mendelian randomization approach, applying a set of 32 genetic markers to estimate the causal effect of adiposity on blood pressure, glycemic indices, circulating lipid levels, and markers of inflammation and liver disease in up to 67,553 individuals. All analyses were stratified by age (cutoff 55 years of age) and sex. The genetic score was associated with BMI in both nonstratified analysis (P = 2.8 × 10(-107)) and stratified analyses (all P < 3.3 × 10(-30)). We found evidence of a causal effect of adiposity on blood pressure, fasting levels of insulin, C-reactive protein, interleukin-6, HDL cholesterol, and triglycerides in a nonstratified analysis and in the <55-year stratum. Further, we found evidence of a smaller causal effect on total cholesterol (P for difference = 0.015) in the ≥55-year stratum than in the <55-year stratum, a finding that could be explained by biology, survival bias, or differential medication. In conclusion, this study extends previous knowledge of the effects of adiposity by providing sex- and age-specific causal estimates on cardiovascular risk factors.

Impact of smoking and smoking cessation on cardiovascular events and mortality among older adults: meta-analysis of individual participant data from prospective cohort studies of the CHANCES consortium

OBJECTIVE: To investigate the impact of smoking and smoking cessation on cardiovascular mortality, acute coronary events, and stroke events in people aged 60 and older, and to calculate and report risk advancement periods for cardiovascular mortality in addition to traditional epidemiological relative risk measures.

DESIGN: Individual participant meta-analysis using data from 25 cohorts participating in the CHANCES consortium. Data were harmonised, analysed separately employing Cox proportional hazard regression models, and combined by meta-analysis.

RESULTS: Overall, 503,905 participants aged 60 and older were included in this study, of whom 37,952 died from cardiovascular disease. Random effects meta-analysis of the association of smoking status with cardiovascular mortality yielded a summary hazard ratio of 2.07 (95% CI 1.82 to 2.36) for current smokers and 1.37 (1.25 to 1.49) for former smokers compared with never smokers. Corresponding summary estimates for risk advancement periods were 5.50 years (4.25 to 6.75) for current smokers and 2.16 years (1.38 to 2.39) for former smokers. The excess risk in smokers increased with cigarette consumption in a dose-response manner, and decreased continuously with time since smoking cessation in former smokers. Relative risk estimates for acute coronary events and for stroke events were somewhat lower than for cardiovascular mortality, but patterns were similar.

CONCLUSIONS: Our study corroborates and expands evidence from previous studies in showing that smoking is a strong independent risk factor of cardiovascular events and mortality even at older age, advancing cardiovascular mortality by more than five years, and demonstrating that smoking cessation in these age groups is still beneficial in reducing the excess risk.

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.

LIAD-fs: A novel method for studies of ultrafast processes in gas phase neutral biomolecules

A new experimental technique for femtosecond (fs) pulse studies of gas phase biomolecules is reported. Using Laser-Induced Acoustic Desorption (LIAD) to produce a plume of neutral molecules, a time-delayed fs pulse is employed for ionisation/fragmentation, with subsequent products extracted and mass analysed electrostatically. By varying critical laser pulse parameters, this technique can be used to implement control over molecular fragmentation for a range of small biomolecules, with specific studies of amino acids demonstrated.

The TARANIS laser : A multi-terawatt system for laser plasma physics

The Terawatt Apparatus for Relativistic And Non-linear Interdisciplinary Science (TARANIS), installed in the Centre for Plasma Physics at the Queen's University Belfast, supports a wide ranging science program, including laser-driven particle acceleration, X-ray lasers and high energy density physics experiments. We present (1) an overview of the laser facility, (2) results of preliminary investigations on proton acceleration, laser action at 13.9 nm and Kα sources and (3) speculation on future experiments using these extreme sources.

The vascular targeting agent combretastatin-A4 and a novel cis-Restricted {beta}-Lactam Analogue, CA-432, induce apoptosis in human chronic myeloid leukemia cells and ex vivo patient samples including those displaying multidrug resistance

Combretastatin-A4 (CA-4) is a natural derivative of the African willow tree Combretum caffrum. CA-4 is one of the most potent antimitotic components of natural origin, but it is, however, intrinsically unstable. A novel series of CA-4 analogs incorporating a 3,4-diaryl-2-azetidinone (β-lactam) ring were designed and synthesized with the objective to prevent cis -trans isomerization and improve the intrinsic stability without altering the biological activity of CA-4. Evaluation of selected β-lactam CA-4 analogs demonstrated potent antitubulin, antiproliferative, and antimitotic effects in human leukemia cells. A lead β-lactam analog, CA-432, displayed comparable antiproliferative activities with CA-4. CA-432 induced rapid apoptosis in HL-60 acute myeloid leukemia cells, which was accompanied by depolymerization of the microtubular network, poly(ADP-ribose) polymerase cleavage, caspase-3 activation, and Bcl-2 cleavage. A prolonged G(2)M cell cycle arrest accompanied by a sustained phosphorylation of mitotic spindle checkpoint protein, BubR1, and the antiapoptotic proteins Bcl-2 and Bcl-x(L) preceded apoptotic events in K562 chronic myeloid leukemia (CML) cells. Molecular docking studies in conjunction with comprehensive cell line data rule out CA-4 and β-lactam derivatives as P-glycoprotein substrates. Furthermore, both CA-4 and CA-432 induced significantly more apoptosis compared with imatinib mesylate in ex vivo samples from patients with CML, including those positive for the T315I mutation displaying resistance to imatinib mesylate and dasatinib. In summary, synthetic intrinsically stable analogs of CA-4 that display significant clinical potential as antileukemic agents have been designed and synthesized.