From HIV infection to AIDS: A dynamically induced percolation transition?

The origin of the unusual incubation period distribution in the development of AIDS is largely unresolved. A key factor in understanding the observed distribution of latency periods, as well as the occurrence of infected individuals not developing AIDS at all, is the dynamics of the long lasting struggle between HIV and the immune system. Using a computer simulation, we study the diversification of viral genomes under mutation and the selective pressure of the immune system.In common infections vast spreading of viral genomes usually does not takes place. In the case of an HIV infection this may occur, as the virus successively weakens the immune system by depletion of CD4+ cells.In a sequence space framework, this leads to a dynamically induced percolation transition, corresponding to the onset of AIDS. As a result, we obtain the prolongated shape of the incubation period distribution, as well as a finite fraction of non-progressors that do not develop AIDS, comparing well with results from recent clinical research.Comment: 7 pages RevTeX, 4 figure

Nuclear weak interaction rates in primordial nucleosynthesis

We calculate the weak interaction rates of selected light nuclei during the epoch of Big Bang Nucleosynthesis (BBN), and we assess the impact of these rates on nuclear abundance flow histories and on final light element abundance yields. We consider electron and electron antineutrino captures on 3He and 7Be, and the reverse processes of positron capture and electron neutrino capture on 3H and 7Li. We also compute the rates of positron and electron neutrino capture on 6He. We calculate beta and positron decay transitions where appropriate. As expected, the final standard BBN abundance yields are little affected by addition of these weak processes, though there can be slight alterations of nuclear flow histories. However, non-standard BBN scenarios, e.g., those involving out of equilibrium particle decay with energetic final state neutrinos, may be affected by these processes.Comment: 10 pages, 6 figure

European precipitation connections with large-scale mean sea-level pressure (MSLP) fields

To advance understanding of hydroclimatological processes, this paper links spatiotemporal variability in gridded European precipitation and large-scale mean sea-level pressure (MSLP) time series (1957–2002) using monthly concurrent correlation. Strong negative (positive) correlation near Iceland and (the Azores) is apparent for precipitation in northwest Europe, confirming a positive North Atlantic Oscillation (NAO) association. An opposing pattern is found for southwest Europe, and the Mediterranean in winter. In the lee of mountains, MSLP correlation is lower reflecting reduced influence of westerlies on precipitation generation. Importantly, European precipitation is shown to be controlled by physically interpretable climate patterns that change in extent and position from month to month. In spring, MSLP–precipitation correlation patterns move and shrink, reaching a minimum in summer, before expanding in the autumn, and forming an NAO-like dipole in winter. These space–time shifts in correlation regions explain why fixed-point NAO indices have limited ability to resolve precipitation for some European locations and seasons

Weak Interaction Rate Coulomb Corrections in Big Bang Nucleosynthesis

We have applied a fully relativistic Coulomb wave correction to the weak reactions in the full Kawano/Wagoner Big Bang Nucleosynthesis (BBN) code. We have also added the zero temperature radiative correction. We find that using this higher accuracy Coulomb correction results in good agreement with previous work, giving only a modest 0.04 percent increase in helium mass fraction over correction prescriptions applied previously in BBN calculations. We have calculated the effect of these corrections on other light element abundance yields in BBN and we have studied these yields as functions of electron neutrino lepton number. This has allowed insights into the role of the Coulomb correction in the setting of the neutron-to-proton ratio during the BBN epoch. We find that the lepton capture processes' contributions to this ratio are only second order in the Coulomb correction.Comment: 8 pages, 3 figure

Big Bang Nucleosynthesis with Independent Neutrino Distribution Functions

We have performed new Big Bang Nucleosynthesis calculations which employ arbitrarily-specified, time-dependent neutrino and antineutrino distribution functions for each of up to four neutrino flavors. We self-consistently couple these distributions to the thermodynamics, the expansion rate and scale factor-time/temperature relationship, as well as to all relevant weak, electromagnetic, and strong nuclear reaction processes in the early universe. With this approach, we can treat any scenario in which neutrino or antineutrino spectral distortion might arise. These scenarios might include, for example, decaying particles, active-sterile neutrino oscillations, and active-active neutrino oscillations in the presence of significant lepton numbers. Our calculations allow lepton numbers and sterile neutrinos to be constrained with observationally-determined primordial helium and deuterium abundances. We have modified a standard BBN code to perform these calculations and have made it available to the community.Comment: 9 pages, 5 figure

Polyfluorinated systems resulting from free radical addition reactions

The first part of this work was to synthesise partially fluorinated reactive compounds and then to study their reactivity towards nucleophiles and electrophiles. These reactive compounds were obtained in a two step process from both cyclopentane and adamantane and in a three step process for cyclopentanol. The first step was the free radical addition of the cycloalkanes, cycloalcohol to hexafluoropropene via thermal and/or radiochemical alkylations. For the cyclic alkane derivatives, the second step was a stereospecific dehydrofluorination of the fluorocarbon chain, whereas for the cyclic alcohol, a dehydration and then dehydrofluorination were performed to give the conjugated diene. Finally, the fluoroalkene reactivity was studied via nucleophilic and electrophilic addition reactions. The second part of my work was to study the free radical addition of tertiary amines to hexafluoropropene, an example is illustrated below

Optimal decision making for sperm chemotaxis in the presence of noise

For navigation, microscopic agents such as biological cells rely on noisy sensory input. In cells performing chemotaxis, such noise arises from the stochastic binding of signaling molecules at low concentrations. Using chemotaxis of sperm cells as application example, we address the classic problem of chemotaxis towards a single target. We reveal a fundamental relationship between the speed of chemotactic steering and the strength of directional fluctuations that result from the amplification of noise in the chemical input signal. This relation implies a trade-off between slow, but reliable, and fast, but less reliable, steering. By formulating the problem of optimal navigation in the presence of noise as a Markov decision process, we show that dynamic switching between reliable and fast steering substantially increases the probability to find a target, such as the egg. Intriguingly, this decision making would provide no benefit in the absence of noise. Instead, decision making is most beneficial, if chemical signals are above detection threshold, yet signal-to-noise ratios of gradient measurements are low. This situation generically arises at intermediate distances from a target, where signaling molecules emitted by the target are diluted, thus defining a `noise zone' that cells have to cross. Our work addresses the intermediate case between well-studied perfect chemotaxis at high signal-to-noise ratios close to a target, and random search strategies in the absence of navigation cues, e.g. far away from a target. Our specific results provide a rational for the surprising observation of decision making in recent experiments on sea urchin sperm chemotaxis. The general theory demonstrates how decision making enables chemotactic agents to cope with high levels of noise in gradient measurements by dynamically adjusting the persistence length of a biased persistent random walk.Comment: 9 pages, 5 figure

Measuring the influence of concept detection on video retrieval

There is an increasing emphasis on including semantic concept detection as part of video retrieval. This represents a modality for retrieval quite different from metadata-based and keyframe similarity-based approaches. One of the premises on which the success of this is based, is that good quality detection is available in order to guarantee retrieval quality. But how good does the feature detection actually need to be? Is it possible to achieve good retrieval quality, even with poor quality concept detection and if so then what is the 'tipping point' below which detection accuracy proves not to be beneficial? In this paper we explore this question using a collection of rushes video where we artificially vary the quality of detection of semantic features and we study the impact on the resulting retrieval. Our results show that the impact of improving or degrading performance of concept detectors is not directly reflected as retrieval performance and this raises interesting questions about how accurate concept detection really needs to be