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

Torsion and the Gravity Dual of Parity Symmetry Breaking in AdS4/CFT3 Holography

We study four dimensional gravity with a negative cosmological constant deformed by the Nieh-Yan torsional topological invariant with a spacetime-dependent coefficient. We find an exact solution of the Euclidean system, which we call the torsion vortex, having two asymptotic AdS4 regimes supported by a pseudoscalar with a kink profile. We propose that the torsion vortex is the holographic dual of a three dimensional system that exhibits distinct parity breaking vacua. The torsion vortex represents a (holographic) transition between these distinct vacua. We expect that from the boundary point of view, the torsion vortex represents a `domain wall' between the two distinct vacua. From a bulk point of view, we point out an intriguing identification of the parameters of the torsion vortex with those of an Abrikosov vortex in a Type I superconductor. Following the analogy, we find that external Kalb-Ramond flux then appears to support bubbles of flat spacetime within an asymptotically AdS geometry.Comment: 26 pages, 4 figures; v2: minor improvements, references adde

Lianas Have A Seasonal Growth Advantage Over Co‐Occurring Trees

The seasonal growth advantage hypothesis posits that plant species that grow well during seasonal drought will increase in abundance in forests with increasing seasonality of rainfall both in absolute numbers and also relative to co‐occurring plant species that grow poorly during seasonal drought. That is, seasonal drought will give some plant species a growth advantage that they lack in aseasonal forests, thus allowing them attain higher abundance. For tropical forest plants, the seasonal growth advantage hypothesis may explain the distribution of drought‐adapted species across large‐scale gradients of rainfall and seasonality. We tested the seasonal growth advantage hypothesis with lianas and trees in a seasonal tropical forest in central Panama. We measured the dry‐season and wet‐season diameter growth of 1,117 canopy trees and 648 canopy lianas from 2011 to 2016. We also evaluated how lianas and trees responded to the 2015–2016 El Niño, which was the third strongest el Niño drought on record in Panama. We found that liana growth rate was considerably higher during the dry‐season months than the wet‐season months in each of the five years. Lianas achieved one‐half of their annual growth during the 4‐month dry season. By contrast, trees grew far more during the wet season; they realized only one‐quarter of their annual growth during the dry season. During the strong 2015–2016 El Niño dry season, trees essentially stopped growing, whereas lianas grew unimpeded and as well as during any of the previous four dry seasons. Our findings support the hypothesis that seasonal growth gives lianas a decided growth advantage over trees in seasonal forests compared to aseasonal forests, and may explain why lianas peak in both absolute and relative abundance in highly seasonal tropical forests. Furthermore, the ability of lianas to grow during a strong el Niño drought suggests that lianas will benefit from the predicted increasing drought severity, whereas trees will suffer, and thus lianas are predicted to increase in relative abundance in seasonal tropical forests

Tau Boo b: Hunting for reflected starlight

Aims. We attempt to detect starlight reflected from the hot Jupiter orbiting the main-sequence star Tau Boo, in order to determine the albedo of the planetary atmosphere, the orbital inclination of the planetary system and the exact mass of the planetary companion. Methods. We analyze high-precision, high-resolution spectra, collected over two half nights using UVES at the VLT/UT2, by way of data synthesis. We interpret our data using two different atmospheric models for hot Jupiters. Results. Although a weak candidate signal appears near the most probable radial velocity amplitude, its statistical significance is insufficient for us to claim a detection. However, this feature agrees very well with a completely independently obtained result by another research group, which searched for reflected light from Tau Boo b. As a consequence of the non-detection of reflected light, we place upper limits to the planet-to-star flux ratio at the 99.9% significance level. For the most probable orbital inclination around i = 46 degrees, we can limit the relative reflected radiation to be less than 5.7 x 10^-5 for grey albedo. This implies a geometric albedo smaller than 0.40, assuming a planetary radius of 1.2 R_Jup .Comment: 7 page

A Countermeasure for Space Motion Sickness

Overall, the results obtained in both the U.S. and the Russian space programs indicate that most space crews will experience some symptoms of motion sickness (MS) causing significant impact on the operational objectives that must be accomplished to assure mission success. At this time the primary countermeasure for MS requires the administration of Promethazine. Promethazine is not a benign drug, and is most frequently administered just prior to the sleep cycle to prevent its side effects from further compromising mission objectives. Clearly other countermeasures for SMS must be developed. Currently the primary focus is on two different technologies: (1) developing new and different pharmacological compounds with less significant side effects, (2) preflight training. The primary problem with all of these methods for controlling MS is time. New drugs that may be beneficial are years from testing and development, and preflight training requires a significant investment of crew time during an already intensive pre-launch schedule. Granted, motion sickness symptoms can be minimized with either of the two methods detailed above, however, it may be possible to develop a countermeasure that does not require either extensive adaptation time or exposure to motion sickness. Approximately 25 years ago Professor Geoffrey Melvill Jones presented his work on adaptation of the vestibuloocular reflex (VOR) using optically reversed vision (left-right prisms) during head rotations in the horizontal plane. It was of no surprise that most subjects experienced motion sickness while wearing the optically reversing prisms. However, a serendipitous finding emerged during this research showing that the same subjects did not experience motion sickness symptoms when wearing the reversing prisms under stroboscopic illumination. The mechanism, by which this side-effect was believed to have occurred, is not clearly understood. However, the fact that no motion sickness was ever noted, suggests the possibility of producing functionally useful adaptation during space flight without the penalty of disabling motion sickness by controlling the rate of the adaptive process by means of an appropriate stroboscopically presented environment. After several recent meetings with Professor Melvill Jones, we were encouraged to repeat the motion sickness portions of his and Mandl's 1981 stroboscopic experiment. In conducting this experiment we used a randomized cross-over design where subjects were randomly assigned to either a stroboscopic flash or no strobe for their first exposure in the experimental design. Twenty subjects (19 subjects completed the study) read a short passage from Treasure Island mounted on the wall approximately 1 m from their eyes while wearing left-right reversing prisms. The strobe on time of 3 microseconds and flash frequency of 4 Hz was set to equal that used in the original study. Motion sickness was scored using a modified Miller and Graybiel scale that we constructed to include symptoms that may be elicited under conditions where reversing prisms are worn. On this scale a score of 5 represented Malaise IIa (mild motion sickness) and a score of 8 or above is approaching frank sickness. Symptoms were tracked and recorded every 5 min during the task. Testing was limited to 30 min unless the subject had reached the MIIa score, at which time the test was terminated. Performance under stroboscopic illumination was significantly better than when the subjects read under normal room illumination while wearing the left-right reversing prisms. Based on these results we developed a goggle system using LCD material that can be strobed. To evaluate the effectiveness of stroboscopic goggles we tested an additional 9 subjects in addition to retesting 10 used in the stroboscopic pilot study described above. These 19 subjects wore a pair of strobing LCD goggles that could be cycled at 4 Hz. These subjects wore the goggles while also wearing left-right reversg prisms. Results while wearing the goggles showed that none of the 19 subjects scored at the MIIa level on the motion sickness rating scale. When the goggles did not flash (no strobe), 11 of the 19 developed symptoms above the MIIa criteria. As a countermeasure the goggles seem to be effective, even with an on time of 10 msec (time the goggles are clear). We have also collected anecdotal data, from our personnel in the Neuroscience Laboratory at the Johnson Space Center, suggesting that the goggles may effective in preventing carsickness

Authorship in Ecology: Attribution, Accountability, and Responsibility

Quality and quantity of publications are among the most important measures determining the success of ecologists. The past 50 years have seen a steady rise in the number of researchers and collaborative manuscripts, and a corresponding increase in multi-authored articles. Despite these increases, there remains a shortage of useful and definitive guidelines to aid ecologists in addressing authorship issues, leading to a lack of consistency in what the term “author” really means. Deciding where to draw the line between those who have earned authorship and those who are more appropriately credited in the acknowledgments may be one of the more challenging aspects of authorship. Here, we borrow ideas from other scientific disciplines and propose a simple solution to help ecologists who are making such decisions. We recommend improving communication between co-authors throughout the research process, and propose that authors publish their contributions to a manuscript in a separate byline

Fuzzy Rings in D6-Branes and Magnetic Field Background

We use the Myers T-dual nonabelin Born-Infeld action to find some new nontrivial solutions for the branes in the background of D6-branes and Melvin magnetic tube field. In the D6-Branes background we can find both of the fuzzy sphere and fuzzy ring solutions, which are formed by the gravitational dielectric effect. We see that the fuzzy ring solution has less energy then that of the fuzzy sphere. Therefore the fuzzy sphere will decay to the fuzzy ring configuration. In the Melvin magnetic tube field background there does not exist fuzzy sphere while the fuzzy ring configuration may be formed by the magnetic dielectric effect. The new solution shows that $D_0$ propagating in the D6-branes and magnetic tube field background may expand into a rotating fuzzy ring. We also use the Dirac-Born-Infeld action to construct the ring configuration from the D-branes.Comment: Latex, 15 pages, detailed comments in section 2, typos correcte

Asymptotic generators of fermionic charges and boundary conditions preserving supersymmetry

We use a covariant phase space formalism to give a general prescription for defining Hamiltonian generators of bosonic and fermionic symmetries in diffeomorphism invariant theories, such as supergravities. A simple and general criterion is derived for a choice of boundary condition to lead to conserved generators of the symmetries on the phase space. In particular, this provides a criterion for the preservation of supersymmetries. For bosonic symmetries corresponding to diffeomorphisms, our prescription coincides with the method of Wald et al. We then illustrate these methods in the case of certain supergravity theories in $d=4$. In minimal AdS supergravity, the boundary conditions such that the supercharges exist as Hamiltonian generators of supersymmetry transformations are unique within the usual framework in which the boundary metric is fixed. In extended ${\mathcal N}=4$ AdS supergravity, or more generally in the presence of chiral matter superfields, we find that there exist many boundary conditions preserving ${\mathcal N}=1$ supersymmetry for which corresponding generators exist. These choices are shown to correspond to a choice of certain arbitrary boundary ``superpotentials,'' for suitably defined ``boundary superfields.'' We also derive corresponding formulae for the conserved bosonic charges, such as energy, in those theories, and we argue that energy is always positive, for any supersymmetry-preserving boundary conditions. We finally comment on the relevance and interpretation of our results within the AdS-CFT correspondence.Comment: 45 pages, Latex, no figures, v2: extended discussion of positive energy theorem and explicit form of fermionic generators, references adde

The Multiple Origin of Blue Straggler Stars: Theory vs. Observations

In this chapter we review the various suggested channels for the formation and evolution of blue straggler stars (BSSs) in different environments and their observational predictions. These include mass transfer during binary stellar evolution - case A/B/C and D (wind Roche-lobe overflow) mass transfer, stellar collisions during single and binary encounters in dense stellar cluster, and coupled dynamical and stellar evolution of triple systems. We also explore the importance of the BSS and binary dynamics in stellar clusters. We review the various observed properties of BSSs in different environments (halo and bulge BSSs, BSSs in globular clusters and BSSs in old open clusters), and compare the current observations with the theoretical predictions for BSS formation. We try to constrain the likely progenitors and processes that play a role in the formation of BSSs and their evolution. We find that multiple channels of BSS formation are likely to take part in producing the observed BSSs, and we point out the strengths and weaknesses of each the formation channel in respect to the observational constraints. Finally we point out directions to further explore the origin of BSS, and highlight eclipsing binary BSSs as important observational tool.Comment: Chapter 11, in Ecology of Blue Straggler Stars, H.M.J. Boffin, G. Carraro & G. Beccari (Eds), Astrophysics and Space Science Library, Springe