bNAber: database of broadly neutralizing HIV antibodies.

The discovery of broadly neutralizing antibodies (bNAbs) has provided an enormous impetus to the HIV vaccine research and to entire immunology. The bNAber database at http://bNAber.org provides open, user-friendly access to detailed data on the rapidly growing list of HIV bNAbs, including neutralization profiles, sequences and three-dimensional structures (when available). It also provides an extensive list of visualization and analysis tools, such as heatmaps to analyse neutralization data as well as structure and sequence viewers to correlate bNAbs properties with structural and sequence features of individual antibodies. The goal of the bNAber database is to enable researchers in this field to easily compare and analyse available information on bNAbs thereby supporting efforts to design an effective vaccine for HIV/AIDS. The bNAber database not only provides easy access to data that currently is scattered in the Supplementary Materials sections of individual papers, but also contributes to the development of general standards of data that have to be presented with the discovery of new bNAbs and a universal mechanism of how such data can be shared

In-medium Hadrons - Properties, Interaction and Formation

In this talk various aspects of in-medium behavior of hadrons are discussed with an emphasis on observable effects. Examples for theoretical predictions of in-medium spectral functions are given and the importance of resonance-hole excitations is stressed. It is also stressed that final state interactions can have a major effect on observables and thus have to be considered as part of the theory. This is demonstrated with examples from neutrino-nucleus interactions. Finally, the possibility to access hadron formation times in high-energy photonuclear (or neutrino-induced) reactions is illustrated.Comment: Invited talk given by U. Mosel at Vth Conference on Hadronic Physics, ICTP, Trieste, May 200

Assessment of human immediate response capability related to tsunami threats in Indonesia at a sub-national scale

Human immediate response is contextualized into different time compartments reflecting the tsunami early warning chain. Based on the different time compartments the available response time and evacuation time is quantified. The latter incorporates accessibility of safe areas determined by a hazard assessment, as well as environmental and demographic impacts on evacuation speed properties assessed using a Cost Distance Weighting GIS approach. Approximately 4.35 million Indonesians live in tsunami endangered areas on the southern coasts of Sumatra, Java and Bali and have between 20 and 150 min to reach a tsunami-safe area. Most endangered areas feature longer estimated-evacuation times and hence the population possesses a weak immediate response capability leaving them more vulnerable to being directly impacted by a tsunami. At a sub-national scale these hotspots were identified and include: the Mentawai islands off the Sumatra coast, various sub-districts on Sumatra and west and east Java. Based on the presented approach a temporal dynamic estimation of casualties and displacements as a function of available response time is obtained for the entire coastal area. As an example, a worst case tsunami scenario for Kuta (Bali) results in casualties of 25 000 with an optimal response time (direct evacuation when receiving a tsunami warning) and 120 000 for minimal response time (no evacuation). The estimated casualties correspond well to observed/reported values and overall model uncertainty is low with a standard error of 5%. The results obtained allow for prioritization of intervention measures such as early warning chain, evacuation and contingency planning, awareness and preparedness strategies down to a sub-district level and can be used in tsunami early warning decision support

Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae

A similarity statistic for codon usage was developed and used to compare novel gene sequences found in clinical isolates of Haemophilus influenzae with a reference set of 80 prokaryotic, eukaryotic and viral genomes. These analyses were performed to obtain an indication as to whether individual genes were Haemophilus-like in nature, or if they probably had more recently entered the H.influenzae gene pool via horizontal gene transfer from other species. The average and SD values were calculated for the similarity statistics from a study of the set of all genes in the H.influenzae Rd reference genome that encoded proteins of 100 amino acids or longer. Approximately 80% of Rd genes gave a statistic indicating that they were most like other Rd genes. Genes displaying codon usage statistics >1 SD above this range were either considered part of the highly expressed group of H.influenzae genes, or were considered of foreign origin. An alternative determinant for identifying genes of foreign origin was when the similarity statistics produced a value that was much closer to a non-H.influenzae reference organism than to any of the Haemophilus species contained in the reference set. Approximately 65% of the novel sequences identified in the H.influenzae clinical isolates displayed codon usages most similar to Haemophilus sp. The remaining novel sequences produced similarity statistics closer to one of the other reference genomes thereby suggesting that these sequences may have entered the H.influenzae gene pool more recently via horizontal transfer

Monitoring of lung edema by microwave reflectometry during lung ischemia-reperfusion injury in vivo

It is still unclear whether lung edema can be monitored by microwave reflectometry and whether the measured changes in lung dry matter content (DMC) are accompanied by changes in PaO(2) and in pro-to anti-inflammatory cytokine expression (IFN-gamma and IL-10). Right rat lung hili were cross-clamped at 37 degrees C for 0, 60, 90 or 120 min ischemia followed by 120 min reperfusion. After 90 min (DMC: 15.9 +/- 1.4%; PaO(2): 76.7 +/- 18 mm Hg) and 120 min ischemia (DMC: 12.8 +/- 0.6%; PaO(2): 43 +/- 7 mm Hg), a significant decrease in DMC and PaO(2) throughout reperfusion compared to 0 min ischemia (DMC: 19.5 +/- 1.11%; PaO(2): 247 +/- 33 mm Hg; p < 0.05) was observed. DMC and PaO(2) decreased after 60 min ischemia but recovered during reperfusion (DMC: 18.5 +/- 2.4%; PaO(2) : 173 +/- 30 mm Hg). DMC values reflected changes on the physiological and molecular level. In conclusion, lung edema monitoring by microwave reflectometry might become a tool for the thoracic surgeon. Copyright (c) 2006 S. Karger AG, Basel