OSPRay - A CPU Ray Tracing Framework for Scientific Visualization.

Scientific data is continually increasing in complexity, variety and size, making efficient visualization and specifically rendering an ongoing challenge. Traditional rasterization-based visualization approaches encounter performance and quality limitations, particularly in HPC environments without dedicated rendering hardware. In this paper, we present OSPRay, a turn-key CPU ray tracing framework oriented towards production-use scientific visualization which can utilize varying SIMD widths and multiple device backends found across diverse HPC resources. This framework provides a high-quality, efficient CPU-based solution for typical visualization workloads, which has already been integrated into several prevalent visualization packages. We show that this system delivers the performance, high-level API simplicity, and modular device support needed to provide a compelling new rendering framework for implementing efficient scientific visualization workflows.

Changing views of the interconnections between the oceans and human health in Europe.

Early steps in the emergence of the discipline of "Oceans and Human Health" are charted in the USA and discussed in relation to past and present marine environment and human health research activities in Europe. Differences in terminology are considered, as well as differences in circumstances related to the various seas of Europe and the intensity of human coastal activity and impact. Opportunities to progress interdisciplinary research are described, and the value of horizon scanning for the early identification of emerging issues is highlighted. The challenges facing researchers and policymakers addressing oceans and human health issues are outlined and some suggestions offered regarding how further progress in research and training into both the risks and benefits of Oceans and Human Health might be made on both sides of the Atlantic.

Physically-Based Interactive Flow Visualization Based on Schlieren and Interferometry Experimental Techniques.

Understanding fluid flow is a difficult problem and of increasing importance as computational fluid dynamics (CFD) produces an abundance of simulation data. Experimental flow analysis has employed techniques such as shadowgraph, interferometry, and schlieren imaging for centuries, which allow empirical observation of inhomogeneous flows. Shadowgraphs provide an intuitive way of looking at small changes in flow dynamics through caustic effects while schlieren cutoffs introduce an intensity gradation for observing large scale directional changes in the flow. Interferometry tracks changes in phase-shift resulting in bands appearing. The combination of these shading effects provides an informative global analysis of overall fluid flow. Computational solutions for these methods have proven too complex until recently due to the fundamental physical interaction of light refracting through the flow field. In this paper, we introduce a novel method to simulate the refraction of light to generate synthetic shadowgraph, schlieren and interferometry images of time-varying scalar fields derived from computational fluid dynamics data. Our method computes physically accurate schlieren and shadowgraph images at interactive rates by utilizing a combination of GPGPU programming, acceleration methods, and data-dependent probabilistic schlieren cutoffs. Applications of our method to multifield data and custom application-dependent color filter creation are explored. Results comparing this method to previous schlieren approximations are finally presented.

Membrane recycling and calcium dynamics during settlement and adhesion of zoospores of the green alga Ulva linza.

Recruitment of individuals of the marine alga Ulva linza on to a suitable habitat involves the settlement of motile zoospores on to a substratum during which a preformed adhesive is secreted by vesicular exocytosis. The fluorescent styryl dye FM 1-43 and fluorescent Ca(2+) indicators were used to follow membrane cycling and changes in cytosolic Ca(2+) ([Ca(2+)](cyt)) associated with settlement. When swimming zoospores were exposed continuously to FM 1-43, the plasma membrane was preferentially labelled. During settlement, FM 1-43-labelled plasma membrane was rapidly internalized reflecting high membrane turnover. The internalized membrane was focused into a discrete region indicating targeting of membrane to an endosome-like compartment. Acetoxymethyl (AM)-ester derivatives were found to be unsuitable for monitoring [Ca(2+)](cyt) because the dyes were rapidly sequestered from the cytoplasm into sub-cellular compartments. [Ca(2+)](cyt) was, however, reliably measured using dextran-conjugated calcium indicators delivered into cells using a biolistic technique. Cells loaded with Oregon Green BAPTA-1 dextran (Invitrogen, Paisley, UK) showed diffuse cytosolic loading and reliably responded to imposed changes in [Ca(2+)](cyt). During settlement, zoospores exhibited both localized and diffuse increases in [Ca(2+)](cyt) implying a role for [Ca(2+)](cyt) in exocytosis of the adhesive.

Evaluation of resuscitation skills in new residents before and after pediatric advanced life support course.

OBJECTIVE: Acquisition of resuscitation skills taught in advanced resuscitation courses has not been evaluated. We sought to determine the interobserver reliability of a resuscitation performance skills checklist to assess resident performance of bag mask ventilation, intubation, defibrillation, and intraosseous vascular access, and to measure skill acquisition by entering residents after a pediatric advanced life support (PALS) course. DESIGN: The resuscitation skills of all 39 pediatric R1's in 2 university-based training programs were assessed immediately before and after completion of a PALS course just before starting residency. Independent observers scored and timed resident performance of bag mask ventilation, endotracheal intubation, intraosseous access, and defibrillation. Scores before and after the PALS course were compared. Four independent observers scored 4 residents' videotaped skills performance. Observers' scores for each resident were compared. RESULTS: Successful performance improved for bag mask ventilation from 62% to 97% after the PALS course; for successful endotracheal intubation, from 64% to 90%; for successful intraosseous needle placement, from 54% to 92%; and for successful defibrillation, from 77% to 97%. Interobserver reliability was high for continuous and noncontinuous variables. CONCLUSIONS: New residents demonstrated significant acquisition of pediatric resuscitation skills immediately after completion of the PALS course. The skills performance checklist has excellent interobserver reliability and is a useful tool for evaluation of other training venues.

Calcium uptake by plant cells--channels and pumps acting in concert.

How do plant cells accomplish a net uptake of Ca(2+) but keep the membrane potential under control? Consideration of the voltage dependence of the depolarization-activated calcium channel and hyperpolarization-activated calcium channel types, and two other major transporters in the plasma membrane, the H(+)-ATPase and I(K,out), suggests that one channel is well suited for both nutritive and signalling Ca(2+) uptake whereas the other could be limited to a signalling function.

Cell cycle-dependent control of polarised development by a cyclin-dependent kinase-like protein in the Fucus zygote.

Although iterative development can be uncoupled from morphogenesis in plant organs, the relationship between the cell cycle and developmental events is not well established in embryos. Zygotes of fucoid algae, including Fucus and Pelvetia are particularly well suited for studying the interaction(s) between cell cycle progression and the early morphogenetic events, as the establishment of polarity and its morphogenetic expression, i.e. germination, and the first cell cycle are concomitant. We have previously demonstrated that, in Fucus zygotes, various aspects of cell cycle progression are tightly controlled by cyclin-dependent kinase (CDK)-like proteins, including two PSTAIRE CDK-like proteins, p34 and p32, which are synthesised after fertilisation. We show that specific inhibition of CDK-like proteins, either with purine derivatives such as olomoucine and amino-purvalanol or by microinjection of the CDK inhibitor p21(cip1), prevents germination and cell division. Whereas direct inhibition of DNA replication by aphidicolin did not affect polarised development, olomoucine, which has previously been shown to prevent entry in S phase, and other purine derivatives also inhibited photopolarisation. Early microinjection of a monoclonal anti-PSTAIRE antibody also prevented germination and cell division. Only p34 had affinity for amino-purvalanol, suggesting that among PSTAIRE CDKs, this protein is the main target of purine derivatives. Models to account for the simultaneous control of early cell cycle progression and polarisation are proposed.

Choosing sides: establishment of polarity in zygotes of fucoid algae.

The acquisition and expression of polarity during early embryogenesis underlies developmental pattern. In many multicellular organisms an initial asymmetric division of the zygote is critical to the determination of different cell fates of the early embryonic cells. Zygotes of the marine fucoid algae are initially apolar and become polarized in response to external cues. This results in an initial asymmetric division of the zygote. Subsequent divisions occur in a highly ordered spatial and temporal pattern. A combination of cell biological and biochemical studies is providing new details, and some controversies concerning the mechanisms by which zygotic polarity is acquired and amplified. Here, we discuss some of the more recent studies that are allowing improved understanding of polarization in this system.

Intracellular signalling: sphingosine-1-phosphate branches out.

Recent studies indicate that sphingosine-1-phosphate - known to be an important signalling molecule in animal cells - is involved in Ca(2+)-dependent signalling in yeast and higher plants, raising the likelihood that it is a universal signalling molecule with a diverse range of functions in eukaryotes.

Cell cycle in the fucus zygote parallels a somatic cell cycle but displays a unique translational regulation of cyclin-dependent kinases.

In eukaryotic cells, the basic machinery of cell cycle control is highly conserved. In particular, many cellular events during cell cycle progression are controlled by cyclin-dependent kinases (CDKs). The cell cycle in animal early embryos, however, differs substantially from that of somatic cells or yeasts. For example, cell cycle checkpoints that ensure that the sequence of cell cycle events is correct have been described in somatic cells and yeasts but are largely absent in embryonic cells. Furthermore, the regulation of CDKs is substantially different in the embryonic and somatic cells. In this study, we address the nature of the first cell cycle in the brown alga Fucus, which is evolutionarily distant from the model systems classically used for cell cycle studies in embryos. This cycle consists of well-defined G1, S, G2, and M phases. The purine derivative olomoucine inhibited CDKs activity in vivo and in vitro and induced different cell cycle arrests, including at the G1/S transition, suggesting that, as in somatic cells, CDKs tightly control cell cycle progression. The cell cycle of Fucus zygotes presented the other main features of a somatic cell cycle, such as a functional spindle assembly checkpoint that targets CDKs and the regulation of the early synthesis of two PSTAIRE CDKs, p32 and p34, and the associated histone H1 kinase activity as well as the regulation of CDKs by tyrosine phosphorylation. Surprisingly, the synthesis after fertilization of p32 and p34 was translationally regulated, a regulation not described previously for CDKs. Finally, our results suggest that the activation of mitotic CDKs relies on an autocatalytic amplification mechanism.

Cellular calcium imaging: so, what's new?

The ability to uncover the fine details of intracellular Ca(2+) signals has improved remarkably in recent years, largely as a result of developments in methods for reporting Ca(2+), coupled with great improvements in measurement instrumentation. The cell biologist wishing to image intracellular Ca(2+) has a range of options to consider. These include the use of photoproteins, commercially available fluorescent indicators or the new generation of fluorescent protein Ca(2+) probes. Molecular biology and biophysics are now joining forces to bring major advances in the art of deciphering the complexity of spatiotemporal Ca(2+) signals.

Elemental propagation of calcium signals in response-specific patterns determined by environmental stimulus strength.

Plant cells can respond qualitatively and quantitatively to a wide range of environmental signals. Ca(2+) is used as an intracellular signal for volume regulation in response to external osmotic changes. We show here that the spatiotemporal patterns of hypo-osmotically induced Ca(2+) signals vary dramatically with stimulus strength in embryonic cells of the marine alga Fucus. Biphasic or multiphasic Ca(2+) signals reflect Ca(2+) elevations in distinct cellular domains. These propagate via elemental Ca(2+) release in nuclear or peripheral regions that are rich in endoplasmic reticulum. Cell volume regulation specifically requires Ca(2+) elevation in apical peripheral regions, whereas an altered cell division rate occurs only in response to stimuli that cause Ca(2+) elevation in nuclear regions.

Inhibition of the establishment of zygotic polarity by protein tyrosine kinase inhibitors leads to an alteration of embryo pattern in Fucus.

Fucoid algae, including the genus Fucus and Pelvetia, are recognized as model systems to study early embryogenesis in plants. In particular the zygotes of these fucoid algae are highly suitable experimental systems for investigating the establishment of polarity and its requirement for later embryogenesis. However, the transduction pathways involved in the initiation of polarization are still poorly understood, and the link between the early polarization processes and embryo long-term patterning has never been experimentally demonstrated. We, therefore, have investigated the putative role of protein phosphorylation in the regulation of early embryogenesis, using a combined pharmacological and biochemical approach. Among the various protein kinase inhibitors tested, a subset of well-known PTK inhibitors, including genistein, prevented germination but had no effect on growth of germinated zygotes and embryos. Inhibition of germination appeared to be a direct consequence of prevention of polarization since genistein and other PTK inhibitors specifically inhibited axis formation in a light-independent manner. Genistein inhibited cellular events associated with polarization such as polarized secretion of cell wall sulfated compounds. Anchorage of F-actin at the rhizoid pole was also inhibited and F-actin redistributed in response to a new light vector. Zygotes inhibited in the polarization process over the period of axis formation recovered from the treatment and displayed differentiated cellular structures after a few days. However, they exhibited a deeply disorganized pattern, suggesting that the early polarization process is essential for normal patterning of the embryo. Western blot analysis of protein phosphorylation showed that the patterns of protein phosphorylation changed during development and were disturbed by treatments with genistein. This drug also inhibited in vitro autophosphorylation. The nature of the genistein-sensitive kinases required for polarization and long-term patterning is discussed in light of these data.

Extracellular carbonic anhydrase facilitates carbon dioxide availability for photosynthesis in the marine dinoflagellate prorocentrum micans

This study investigated inorganic carbon accumulation in relation to photosynthesis in the marine dinoflagellate Prorocentrum micans. Measurement of the internal inorganic carbon pool showed a 10-fold accumulation in relation to external dissolved inorganic carbon (DIC). Dextran-bound sulfonamide (DBS), which inhibited extracellular carbonic anhydrase, caused more than 95% inhibition of DIC accumulation and photosynthesis. We used real-time imaging of living cells with confocal laser scanning microscopy and a fluorescent pH indicator dye to measure transient pH changes in relation to inorganic carbon availability. When steady-state photosynthesizing cells were DIC limited, the chloroplast pH decreased from 8.3 to 6.9 and cytosolic pH decreased from 7.7 to 7.1. Re-addition of HCO3- led to a rapid re-establishment of the steady-state pH values abolished by DBS. The addition of DBS to photosynthesizing cells under steady-state conditions resulted in a transient increase in intracellular pH, with photosynthesis maintained for 6 s, the amount of time needed for depletion of the intracellular inorganic carbon pool. These results demonstrate the key role of extracellular carbonic anhydrase in facilitating the availability of CO2 at the exofacial surface of the plasma membrane necessary to maintain the photosynthetic rate. The need for a CO2-concentrating mechanism at ambient CO2 concentrations may reflect the difference in the specificity factor of ribulose-1,5 bisphosphate carboxylase/oxygenase in dinoflagellates compared with other algal phyla.

Performance of advanced resuscitation skills by pediatric housestaff.

OBJECTIVE: To describe pediatric housestaff resuscitation experience and their ability to perform key resuscitation skills. DESIGN: Cohort study of 63 pediatric residents in a university-based training program. PARTICIPANTS AND METHODS: Investigators observed, scored, and timed resident performance on 4 key resuscitation skills. Cognitive ability was tested with 4 written scenarios. Housestaff provided self-reports of the number of months since their last American Heart Association Pediatric Advanced Life Support course, number of mock and actual codes attended, number of times skills were performed, and self-confidence with respect to resuscitation. RESULTS: A total of 45 pediatric residents (71%) participated. Median cognitive score was 5 (range, 1-5). Of all residents, 44 (97%) successfully bag mask-ventilated the mannequin; 24 (53%) and 36 (80%) used the correct bag and mask size, respectively. Thirty-nine residents (87%) placed a tube in the mannequin trachea, 12 (27%) checked that suction was working prior to intubation, and 30 (67%) chose the correct endotracheal tube size. Forty residents (89%) discharged the defibrillator, and 25 (56%) and 32 (71%) correctly chose asynchronous mode and infant paddles, respectively. Thirty-eight residents (84%) inserted an intraosseous line; 35 (78%) had correct placement. Median times for successful skill completion were 83 seconds for bag mask ventilation, 136 seconds for intubation, 149 seconds for defibrillation, and 68 seconds for intraosseous line placement. CONCLUSION: Pediatric housestaff previously trained in pediatric advanced life support were generally able to reach the end point of 4 key resuscitation skills but less frequently performed the specific subcomponents of each skill. This poor performance and the prolonged time to skill completion suggest the need for greater attention to detail during training.