Environment, Ram Pressure, and Shell Formation in HoII

Neutral hydrogen VLA D-array observations of the dwarf irregular galaxy HoII, a prototype galaxy for studies of shell formation, are presented. HI is detected to radii over 16' or 4 R_25, and M_HI=6.44x10^8 M_sun. The total HI map has a comet-like appearance suggesting that HoII is affected by ram pressure from an intragroup medium (IGM). A rotation curve corrected for asymmetric drift was derived and an analysis of the mass distribution yields a total mass 6.3x10^9 M_sun, of which about 80% is dark. HoII lies northeast of the M81 group's core, along with Kar52 (M81dwA) and UGC4483. No signs of interaction are observed and it is argued that HoII is part of the NGC2403 subgroup, infalling towards M81. A case is made for ram pressure stripping and an IGM in the M81 group. Stripping of the disk outer parts would require an IGM density n_IGM>=4.0x10^-6 atoms/cm^3 at the location of HoII. This corresponds to 1% of the virial mass of the group uniformly distributed over a volume just enclosing HoII and is consistent with the X-ray properties of small groups. It is argued that existing observations of HoII do not support self-propagating star formation scenarios, whereby the HI holes and shells are created by supernova explosions and stellar winds. Many HI holes are located in low surface density regions of the disk, where no star formation is expected or observed. Ram pressure has the capacity to enlarge preexisting holes and lower their creation energies, helping to bridge the gap between the observed star formation rate and that required to create the holes. (abridged)Comment: 43 pages, including 7 figures. 4 figures available as JPEG only. Complete manuscript including full resolution figures available at http://www.strw.leidenuniv.nl/~bureau/pub_list.html . Accepted for publication in The Astronomical Journa

Mapping genetic variations to three- dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods

Proceedings of the 2007 symposium on Component and framework technology in high-performance and scientific computing

Applying component-based development requires design support in the form of methods, frameworks, and tools. To this end, this paper first proposes a componentisation approach and then applies this approach to re-engineer a numerical application into a component-based application. The paper provides qualitative and quantitative evidence that componentisation has improved the modifiability and reusability of the application without significantly affecting performance

Message-passing performance of parallel computers

In this paper we investigate some of the important factors which affect the message-passing performance on parallel computers. Variations of low-level communication benchmarks that approximate realistic cases are tested and compared with the available Parkbench codes and benchmarking techniques. The results demonstrate a substantial divergence between message-passing performance measured by low-level benchmarks and message-passing performance achieved by real programs. In particular, the influence of different data types, the memory access patterns, and the communication structures of the NAS Parallel Benchmarks are analysed in detail, using performance measurements on the Cray-T3D in Edinburgh and the IBM-SP2 in Southampton

WMIN-MOBILE: a mobile learning platform for information and service provision

Educational organisations hold lots of valuable information and material in different forms that needs to be communicated to people with different profiles anytime, anywhere. Mobile phones offer great opportunities of accessing such information and services by using hardware owned by Educational Organizations’ members. This paper studies the requirements for such mobile learning (m-learning) tools for information and services provision to support learning and teaching and enhance student experience and satisfaction. To demonstrate this it uses the WMIN-MOBILE project as a case study. The WMIN-MOBILE is a prototype that provides general information about the School of Electronics and Computer Science (ECS) at the University of Westminster (UoW) and services like announcements, timetable and lab facilities and availability. The paper justifies the educational value of such m-learning tools and reports requirements for developing such tools. It further describes the WMIN-MOBILE system design and architecture and concludes with lessons learned and further work

Comparison of HPF-like Systems

This report describes our experience with some of the existing prototype HPF systems which were available to the members of the PPPE project. The comparison and evaluation of these early HPF compilers was equally difficult and important in order to gain some feedback to the compiler designers but also to accumulate some initial skills in writing efficient HPF programs

JavaGrande - high performance computing with Java

The JavaGrande Forum is a group of users, researchers, and interested parties from industry. The Forum members are either trying to use Java for resource-intensive applications or are trying to improve the Java platform, making it possible to create large-sized applications that run quickly and effciently in Java. In order to improve its floating point arithmetic, the Forum has suggested to add the keywords strictfp and fastfp to the Java programming lan- guage It has has worked on complex numbers, multidimensional arrays, fast object serializations, and a high-speed remote method invocation (RMI). Results about the new field of research that has been started by the JavaGrande Forum have been recognized both internationally and within Sun Microsystems. 1 Grande, as found in the phrase “Rio Grande” is the prevalent designation for the term large or big in many languages. In American English, the term Grande has established itself as describing size within the coffee house scene