07291 Abstracts Collection -- Scientific Visualization

From 15.07. to 20.07.07, the Dagstuhl Seminar 07291 ``Scientific Visualization\u27\u27 was held in the International Conference and Research Center (IBFI),Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Fatal Disseminated Cryptococcus gattii Infection in New Mexico

We report a case of fatal disseminated infection with Cryptococcus gattii in a patient from New Mexico. The patient had no history of recent travel to known C. gattii-endemic areas. Multilocus sequence typing revealed that the isolate belonged to the major molecular type VGIII. Virulence studies in a mouse pulmonary model of infection demonstrated that the strain was less virulent than other C. gattii strains. This represents the first documented case of C. gattii likely acquired in New Mexico

Plant fitness assessment for wild relatives of insect resistant crops

Risk assessments of new insect-resistant crops will need to estimate the potential for increased weediness of wild crop relatives as a consequence of gene flow. When field experiments are precluded by containment concerns, simulation experiments can identify hazards or measure expected differences between GMOs and parental plants. To measure plant fitness consequences of wild plant protection from Bt-susceptible herbivores, we used topical sprays of bacterial Bacillus thuringiensis larvacide (Bt) on Brassica rapa. Spontaneous crosses between B. rapa and Bt cole crops cannot be precluded, especially if adoption of Bt varieties leads to high exposure. We compared survivorship and seed output of B. rapa that were either protected from or exposed to Bt-susceptible Lepidoptera in the various conditions where hybrids are likely to occur: cultivated (disked) soil, uncultivated agricultural field margins, and nearby non-crop habitats (meadows and ruderal areas). The relative effect of herbivore protection varied among years, habitats, and populations of seedlings. In 2003–2004, Bt sprays did not result in lower herbivory on B. rapa, and plant fitness was not increased. However, in 2004–2006 B. rapa seedlings protected from Bt-susceptible herbivores lived 25% longer, on average, than those that were exposed to these herbivores. In addition, an average B. rapa seedling sprayed with Bt throughout its lifetime was twice as likely to produce siliques and had 251% of the seed output of a seedling exposed to herbivores. The fitness advantage of Bt-based plant protection was apparent in 2004–2005 in half the plants that experienced higher herbivory, and for 2005–2006, was more pronounced in agricultural habitats than in meadows with established, perennial vegetation and less disturbance. Positive effects of Bt-based plant protection and greater fitness in disturbed habitats suggest that crop-wild gene flow may benefit weed populations, and that field tests with herbivore exclusion/addition experiments are feasible alternatives when molecular containment of transgenes restricts field experiments with insect resistant crop-wild hybrids

crops: Predicting effects of escaped transgenes on the fitness of wild plants and their herbivores

One prominent concern about genetically modified crops is the possibility of environmental impacts from the movement of fitness-enhancing traits to wild plant populations. Decisions to deregulate Bt crops in the USA have relied strongly on arguments that these crops will not interbreed with wild relatives in the permitted growing regions. Limited attention therefore has been directed to analyses of the consequences of gene flow. To provide a transparent evaluation process for risks associated with insecticidal transgene escape, we crafted a series of questions designed to guide this aspect of the risk assessment. We then explored the current knowledge base available for answering such risk-related questions for three Bt crops (cotton, rapeseed, and rice). First, we generated a list of wild relatives of these crops. A definitive list of potential transgene recipients is not yet possible for some crops. Sufficient data are not available for some crops to eliminate certain related plant species from consideration of fertile hybrid formation, thus making lists for these crops subject to speculation. Second, we queried the HOSTS database (UK) to obtain a worldwide listing of lepidopteran species that feed on these crops and their wild relatives, and to determine the host range of the larvae. To our knowledge, this list of 502 lepidopteran species is the first such list published for these crops and wild crop relatives. Third, we used a data set maintained by the Canadian Forest Service to assess Bt toxin susceptibility for these lepidopterans. Only 3% of those species have been tested for susceptibility; and the literature suggests that generalizations about susceptibility among taxa are difficult due to the variability within families. Fourth, we consulted the literature to interpret what is known about the ability of lepidopterans to regulate plant fitness or invasiveness. We could not eliminate the possibility of ecological release due to plant resistance against lepidopterans. In fact, there is strong experimental evidence that lepidopteran herbivores do limit the distribution and/or abundances of at least some wild plant species. Neither could we eliminate the possibility that non-target lepidopterans might have important functions in the ecosystem as pollinators or alternate hosts to natural enemies of pest species. This study suggests that crucial data are lacking for the development of a credible scientific basis to confirm or deny environmental risks associated with the escape of Bt transgene constructs to wild relatives. Given the absence of information on the identity, level of susceptibility, and ecological roles of lepidopterans exploiting specific wild relatives of Bt crops, we suggest that new efforts be directed to assessing possible consequences of lepidopteran mortality on resistant wild relatives

07291 Summary -- Scientific Visualization

Scientific visualization (SV) is concerned with the use of computer-generated images to aid the understanding, analysis and manipulation of data. Since its beginning in the early 90\u27s, the techniques of SV have aided scientists, engineers, medical practitioners, and others in the study of a wide variety of data sets including, for example, high performance computing simulations, measured data from scanners (CAT, MR, confocal microscopy), internet traffic, and financial records. One of the important themes being nurtured under the aegis of Scientific Visualization is the utilization of the broad bandwidth of the human sensory system in steering and interpreting complex processes and simulations involving voluminous data sets across diverse scientific disciplines. Since vision dominates our sensory input, strong efforts have been made to bring the mathematical abstraction and modeling to our eyes through the mediation of computer graphics. This interplay between various application areas and their specific problem solving visualization techniques was emphasized in the proposed seminar

Development of Bipotent Cardiac/Skeletal Myogenic Progenitors from MESP1+ Mesoderm

The branchiomeric skeletal muscles co-evolved with new chambers of the heart to enable predatory feeding in chordates. These co-evolved tissues develop from a common population in anterior splanchnic mesoderm, referred to as cardiopharyngeal mesoderm (CPM). The regulation and development of CPM are poorly understood. We describe an embryonic stem cell-based system in which MESP1 drives a PDGFRA+ population with dual cardiac and skeletal muscle differentiation potential, and gene expression resembling CPM. Using this system, we investigate the regulation of these bipotent progenitors, and find that cardiac specification is governed by an antagonistic TGFβ-BMP axis, while skeletal muscle specification is enhanced by Rho kinase inhibition. We define transcriptional signatures of the first committed CPM-derived cardiac and skeletal myogenic progenitors, and discover surface markers to distinguish cardiac (PODXL+) from the skeletal muscle (CDH4+) CPM derivatives. These tools open an accessible window on this developmentally and evolutionarily important population

A critical literature review of focused electron beam induced deposition

An extensive review is given of the results from literature on electron beam induced deposition. Electron beam induced deposition is a complex process, where many and often mutually dependent factors are involved. The process has been studied by many over many years in many different experimental setups, so it is not surprising that there is a great variety of experimental results. To come to a better understanding of the process, it is important to see to which extent the experimental results are consistent with each other and with the existing model. All results from literature were categorized by sorting the data according to the specific parameter that was varied (current density, acceleration voltage, scan patterns, etc.). Each of these parameters can have an effect on the final deposit properties, such as the physical dimensions, the composition, the morphology, or the conductivity. For each parameter-property combination, the available data are discussed and (as far as possible) interpreted. By combining models for electron scattering in a solid, two different growth regimes, and electron beam induced heating, the majority of the experimental results were explained qualitatively. This indicates that the physical processes are well understood, although quantitatively speaking the models can still be improved. The review makes clear that several major issues remain. One issue encountered when interpreting results from literature is the lack of data. Often, important parameters (such as the local precursor pressure) are not reported, which can complicate interpretation of the results. Another issue is the fact that the cross section for electron induced dissociation is unknown. In a number of cases, a correlation between the vertical growth rate and the secondary electron yield was found, which suggests that the secondary electrons dominate the dissociation rather than the primary electrons. Conclusive evidence for this hypothesis has not been found. Finally, there is a limited understanding of the mechanism of electron induced precursor dissociation. In many cases, the deposit composition is not directly dependent on the stoichiometric composition of the precursor and the electron induced decomposition paths can be very different from those expected from calculations or thermal decomposition. The dissociation mechanism is one of the key factors determining the purity of the deposits and a better understanding of this process will help develop electron beam induced deposition into a viable nanofabrication technique.Imaging Science and TechnologyApplied Science

Spatial resolution limits in electron-beam-induced deposition

Electron-beam-induced deposition (EBID) is a versatile micro- and nanofabrication technique based on electron-induced dissociation of metal-carrying gas molecules adsorbed on a target. EBID has the advantage of direct deposition of three-dimensional structures on almost any target geometry. This technique has occasionally been used in focused electron-beam instruments, such as scanning electron microscopes, scanning transmission electron microscopes (STEM), or lithography machines. Experiments showed that the EBID spatial resolution, defined as the lateral size of a singular deposited dot or line, always exceeds the diameter of the electron beam. Until recently, no one has been able to fabricate EBID features smaller than 15–20?nm diameter, even if a 2-nm-diam electron-beam writer was used. Because of this, the prediction of EBID resolution is an intriguing problem. In this article, a procedure to theoretically estimate the EBID resolution for a given energetic electron beam, target, and gaseous precursor is described. This procedure offers the most complete approach to the EBID spatial resolution problem. An EBID model was developed based on electron interactions with the solid target and with the gaseous precursor. The spatial resolution of EBID can be influenced by many factors, of which two are quantified: the secondary electrons, suspected by almost all authors working in this field, and the delocalization of inelastic electron scattering, a poorly known effect. The results confirm the major influence played by the secondary electrons on the EBID resolution and show that the role of the delocalization of inelastic electron scattering is negligible. The model predicts that a 0.2-nm electron beam can deposit structures with minimum sizes between 0.2 and 2?nm, instead of the formerly assumed limit of 15–20?nm. The modeling results are compared with recent experimental results in which 1-nm?W dots from a W(CO)6 precursor were written in a 200-kV STEM on a 30-nm SiN membrane.Imaging Science and TechnologyApplied Science