Intelligent modelling of bioprocesses: A comparison of structured and unstructured approaches

This contribution moves in the direction of answering some general questions about the most effective and useful ways of modelling bioprocesses. We investigate the characteristics of models that are good at extrapolating. We trained 3 fully predictive models with different representational structures (diff eqns, inheritance of rates, network of reactions) on Saccharopolyspora erythraea shake flask fermentation data using genetic programming. The models were then tested on unseen data outside the range of the training data and the resulting performances compared. It was found that constrained models with mathematical forms analogous to internal mass balancing and stoichiometric were superior to flexible unconstrained models even though no A priori knowledge of this fermentation was used

A Novel Approach in Constraining Electron Spectra in Blazar Jets: The Case of Markarian 421

We report results from the observations of the well studied TeV blazar Mrk 421 with the Swift and the Suzaku satellites in December 2008. During the observation, Mrk 421 was found in a relatively low activity state, with the corresponding 2-10 keV flux of $3 \times 10^{-10}$ erg/s/cm^2. For the purpose of robust constraining the UV-to-X-ray emission continuum we selected only the data corresponding to truly simultaneous time intervals between Swift and Suzaku, allowing us to obtain a good-quality, broad-band spectrum despite a modest length (0.6 ksec) exposure. We analyzed the spectrum with the parametric forward-fitting SYNCHROTRON model implemented in XSPEC assuming two different representations of the underlying electron energy distribution, both well motivated by the current particle acceleration models: a power-law distribution above the minimum energy $\gamma_{\rm min}$ with an exponential cutoff at the maximum energy $\gamma_{\rm max}$, and a modified ultra-relativistic Maxwellian with an equilibrium energy $\gamma_{\rm eq}$. We found that the latter implies unlikely physical conditions within the blazar zone of Mrk 421. On the other hand, the exponentially moderated power-law electron distribution gives two possible sets of the model parameters: (i) flat spectrum $dN'_e/d\gamma \propto \gamma^{-1.91}$ with low minimum electron energy $\gamma_{\rm min}<10^3$, and (ii) steep spectrum $\propto \gamma^{-2.77}$ with high minimum electron energy $\gamma_{\rm min}\simeq 2\times10^4$. We discuss different interpretations of both possibilities in the context of a diffusive acceleration of electrons at relativistic, sub- or superluminal shocks. We also comment on how exactly the gamma-ray data can be used to discriminate between the proposed different scenarios.Comment: 18 pages, 2 figures; accepted for publication in the Astrophysical Journa

Characterizing upward lightning with and without a terrestrial gamma-ray flash

We compare two observations of gamma-rays before, during, and after lightning flashes initiated by upward leaders from a tower during low-altitude winter thunderstorms on the western coast of Honshu, Japan. While the two leaders appear similar, one produced a terrestrial gamma-ray flash (TGF) so bright that it paralyzed the gamma-ray detectors while it was occurring, and could be observed only via the weaker flux of neutrons created in its wake, while the other produced no detectable TGF gamma-rays at all. The ratio between the indirectly derived gamma-ray fluence for the TGF and the 95% confidence gamma-ray upper limit for the gamma-ray quiet flash is a factor of $1\times10^7$. With the only two observations of this type providing such dramatically different results -- a TGF probably as bright as those seen from space and a powerful upper limit -- we recognize that weak, sub-luminous TGFs in this situation are probably not common, and we quantify this conclusion. While the gamma-ray quiet flash appeared to have a faster leader and more powerful initial continuous current pulse than the flash that produced a TGF, the TGF-producing flash occurred during a weak gamma-ray "glow", while the gamma-ray quiet flash did not, implying a higher electric field aloft when the TGF was produced. We suggest that the field in the high-field region approached by a leader may be more important for whether a TGF is produced than the characteristics of the leader itself.Comment: 21 pages, 6 figures, accepted for publication by the Journal of Geophysical Research - Atmosphere

Photon generation by laser-Compton scattering at the KEK-ATF

We performed a photon generation experiment by laser-Compton scattering at the KEK-ATF, aiming to develop a Compton based polarized positron source for linear colliders. In the experiment, laser pulses with a 357 MHz repetition rate were accumulated and their power was enhanced by up to 250 times in the Fabry-Perot optical resonant cavity. We succeeded in synchronizing the laser pulses and colliding them with the 1.3 GeV electron beam in the ATF ring while maintaining the laser pulse accumulation in the cavity. As a result, we observed 26.0 +/- 0.1 photons per electron-laser pulse crossing, which corresponds to a yield of 10^8 photons in a second.Comment: 3 pages, 5 figures, Preprint submitted to TIPP09 Proceedings in NIM

Charge analysis on lightning discharges to the ground in Chinese inland plateau (close to Tibet)

International audienceSince the summer of 1996, scientists from China and Japan have conducted a joint observation of natural cloud-to-ground lightning discharges in the Zhongchuan area that is located close to Qinghai-Xizang (Tibet) Plateau, China. It has been found that the long-duration of intracloud discharge processes, just before the first return stroke, lasted more than 120 ms for 85% of cloud-to-ground flashes in this area, with a mean duration of 189.7 ms and a maximum of 300 ms. We present the results of charge sources neutralized by four ground flashes and two intracloud discharge processes, just before the first return stroke, by using the data from a 5-site slow antenna network synchronized by GPS with 1 µs time resolution. The result shows that the altitudes of the neutralized negative charge for three negative ground flashes were between 2.7 to 5.4 km above the ground, while that of neutralized positive charges for one positive ground flash and one continuing current process were at about 2.0 km above the ground. The comparison with radar echo showed that the negative discharges initiated in the region greater than 20 dBZ or near the edge of the region with intense echoes greater than 40 dBZ, while positive discharge initiated in the weak echo region.Key words: Meterology and atmospheric dynamics (atmospheric electricity; convective processes; lightning) <p style="line-height: 20px;"

The proton spin sum rule chiral bag prediction, an update

We reevaluate a quark model prediction using the new QCD evolution function calculated to the 3 loop order and conclude that this model compares favorably with the new experimental results.Comment: 10 pages, 2 figures available by request, give fax numbe

Direct Sensing of Endothelial Oxidants by Vascular Endothelial Growth Factor Receptor-2 and c-Src

BACKGROUND: ADPH oxidase-derived reactive oxygen species (ROS) play important roles in redox homeostasis and signal transduction in endothelial cells (ECs). We previously demonstrated that c-Src plays a key role in VEGF-induced, ROS-dependent selective activation of PI3K-Akt but not PLCγ-1-ERK1/2 signaling pathways. The aim of the present study was to understand how VEGFR-2-c-Src signaling axis 'senses' NADPH oxidase-derived ROS levels and couples VEGF activation of c-Src to the redox state of ECs. METHODOLOGY/PRINCIPAL FINDINGS: Using biotinylated probe that detects oxidation of cysteine thiol (cys-OH) in intracellular proteins, we demonstrate that VEGF induced oxidative modification in c-Src and VEGFR-2, and that reduction in ROS levels using siRNA against p47(phox) subunit of Rac1-dependent NADPH oxidase inhibited this phenomenon. Co-immunoprecipitation studies using human coronary artery ECs (HCAEC) showed that VEGF-induced ROS-dependent interaction between VEGFR-2 and c-Src correlated with their thiol oxidation status. Immunofluorescence studies using antibodies against internalized VEGFR-2 and c-Src demonstrated that VEGF-induced subcellular co-localization of these tyrosine kinases were also dependent on NADPH oxidsase-derived ROS. CONCLUSION/SIGNIFICANCE: These results demonstrate that VEGF induces cysteine oxidation in VEGFR-2 and c-Src in an NADPH oxidase-derived ROS-dependent manner, suggesting that VEGFR-2 and c-Src can 'sense' redox levels in ECs. The data also suggest that thiol oxidation status of VEGFR-2 and c-Src correlates with their ability to physically interact with each other and c-Src activation. Taken together, these findings suggest that prior to activating downstream c-Src-PI3K-Akt signaling pathway, VEGFR-2-c-Src axis requires an NADPH oxidase-derived ROS threshold in ECs