Computational challenges of systems biology

Progress in the study of biological systems such as the heart, brain, and liver will require computer scientists to work closely with life scientists and mathematicians. Computer science will play a key role in shaping the new discipline of systems biology and addressing the significant computational challenges it poses

Encoding of Marginal Utility across Time in the Human Brain

Marginal utility theory prescribes the relationship between the objective property of the magnitude of rewards and their subjective value. Despite its pervasive influence, however, there is remarkably little direct empirical evidence for such a theory of value, let alone of its neurobiological basis. We show that human preferences in an intertemporal choice task are best described by a model that integrates marginally diminishing utility with temporal discounting. Using functional magnetic resonance imaging, we show that activity in the dorsal striatum encodes both the marginal utility of rewards, over and above that which can be described by their magnitude alone, and the discounting associated with increasing time. In addition, our data show that dorsal striatum may be involved in integrating subjective valuation systems inherent to time and magnitude, thereby providing an overall metric of value used to guide choice behavior. Furthermore, during choice, we show that anterior cingulate activity correlates with the degree of difficulty associated with dissonance between value and time. Our data support an integrative architecture for decision making, revealing the neural representation of distinct subcomponents of value that may contribute to impulsivity and decisiveness

Herwig++ 2.0 Release Note

A new release of the Monte Carlo program Herwig++ (version 2.0) is now available. This is the first version of the program which can be used for hadron-hadron physics and includes the full simulation of both initial- and final-state QCD radiation.Comment: Source code and additional information available at http://hepforge.cedar.ac.uk/herwig

Bursting emission from PSR B0611+22

Over the past decade it has become apparent that a class of `bursting pulsars\u27 exist with the discovery of PSR J1752+2359 and PSR J1938+2213. In these pulsars, a sharp increase in the emission is observed that then tends to systematically drop-off from pulse-to-pulse. In this paper we describe the discovery of such a relationship in high-sensitivity observations of the young (characteristic age of 90,000 yrs) 0.33 s pulsar B0611+22 at both 327 MHz and 1400 MHz with the Arecibo radio telescope. While Nowakowski previously showed that B0611+22 has mode-switching properties, the data presented here show, for the first time, that this pulsar emits bursts with characteristic time-scales of several hundred seconds. At 327 MHz, the pulsar shows steady behaviour in one emission mode which is enhanced by bursting emission slightly offset in pulse phase from this steady emission. Contrastingly at 1400 MHz, the two modes appear to behave in a competing operation while still offset in phase. Using a fluctuation spectrum analysis, we also investigate each mode independently for sub-pulse drifting. Neither emission mode (i.e. during bursts or persistent emission) shows the presence of the drifting sub-pulse phenomenon. The bursting phenomena seen here appears to be a hybrid between bursting seen in other pulsars and the bistable profile illumination behaviour reported in two other pulsars by Rankin et al. Further examples of this cross-frequency behaviour are required, as this phenomenon may be quite common among the pulsar population

Herwig++1.0: an event generator for e(+)e(-) annihilation

Results from the new Monte Carlo event generator Herwig++ are presented. This first version simulates Hadron Emission Reactions With Interfering Gluons in electron-positron annihilation. The parton shower evolution is carried out using new evolution variables suited to describing radiation from heavy quarks as well as light partons. The partonic final state is fragmented into hadrons by means of an improved cluster hadronization model. The results are compared with a wide variety of data from LEP and SLC

A rare presentation of the Klinefelter's syndrome

A 16 years old boy with Chronic Renal Failure (CRF) was not suspected of having Klinefelter's syndrome until he complained of painful gynecomastia. He was under haemodialysis for 2 years. At first, he was in an approximately full pubertal development (P5, G5), but he had a small and a firm testis (length 2.2cm) and some degree of facial male pattern hair. He also had a decreased upper to lower body segment ratio and despite having chronic renal failure, he was taller than his parents and siblings. His laboratory tests showed high levels of FSH and normal levels of LH and testosterone. With regards to all these findings, we suspected that there might be an occult Klinefelter's syndrome. So, we made his karyotype that showed a 47XXY pattern. Because there are only a few number of cases that have occult Klinefelter's syndrome in the basis of chronic renal failure, we decided to report this case

Floral temperature and optimal foraging: is heat a feasible floral reward for pollinators?

As well as nutritional rewards, some plants also reward ectothermic pollinators with warmth. Bumble bees have some control over their temperature, but have been shown to forage at warmer flowers when given a choice, suggesting that there is some advantage to them of foraging at warm flowers (such as reducing the energy required to raise their body to flight temperature before leaving the flower). We describe a model that considers how a heat reward affects the foraging behaviour in a thermogenic central-place forager (such as a bumble bee). We show that although the pollinator should spend a longer time on individual flowers if they are warm, the increase in total visit time is likely to be small. The pollinator's net rate of energy gain will be increased by landing on warmer flowers. Therefore, if a plant provides a heat reward, it could reduce the amount of nectar it produces, whilst still providing its pollinator with the same net rate of gain. We suggest how heat rewards may link with plant life history strategies

Galaxy protocluster candidates around z ~ 2.4 radio galaxies

We study the environments of 6 radio galaxies at 2.2 < z < 2.6 using wide-field near-infrared images. We use colour cuts to identify galaxies in this redshift range, and find that three of the radio galaxies are surrounded by significant surface overdensities of such galaxies. The excess galaxies that comprise these overdensities are strongly clustered, suggesting they are physically associated. The colour distribution of the galaxies responsible for the overdensity are consistent with those of galaxies that lie within a narrow redshift range at z ~ 2.4. Thus the excess galaxies are consistent with being companions of the radio galaxies. The overdensities have estimated masses in excess of 10^14 solar masses, and are dense enough to collapse into virizalised structures by the present day: these structures may evolve into groups or clusters of galaxies. A flux-limited sample of protocluster galaxies with K < 20.6 mag is derived by statistically subtracting the fore- and background galaxies. The colour distribution of the protocluster galaxies is bimodal, consisting of a dominant blue sequence, comprising 77 +/- 10% of the galaxies, and a poorly populated red sequence. The blue protocluster galaxies have similar colours to local star-forming irregular galaxies (U -V ~ 0.6), suggesting most protocluster galaxies are still forming stars at the observed epoch. The blue colours and lack of a dominant protocluster red sequence implies that these cluster galaxies form the bulk of their stars at z < 3.Comment: Accepted for publication in MNRA

On the Monadic Second-Order Transduction Hierarchy

We compare classes of finite relational structures via monadic second-order transductions. More precisely, we study the preorder where we set C \subseteq K if, and only if, there exists a transduction {\tau} such that C\subseteq{\tau}(K). If we only consider classes of incidence structures we can completely describe the resulting hierarchy. It is linear of order type {\omega}+3. Each level can be characterised in terms of a suitable variant of tree-width. Canonical representatives of the various levels are: the class of all trees of height n, for each n \in N, of all paths, of all trees, and of all grids

Neural correlates of mentalizing-related computations during strategic interactions in humans

Competing successfully against an intelligent adversary requires the ability to mentalize an opponent's state of mind to anticipate his/her future behavior. Although much is known about what brain regions are activated during mentalizing, the question of how this function is implemented has received little attention to date. Here we formulated a computational model describing the capacity to mentalize in games. We scanned human subjects with functional MRI while they participated in a simple two-player strategy game and correlated our model against the functional MRI data. Different model components captured activity in distinct parts of the mentalizing network. While medial prefrontal cortex tracked an individual's expectations given the degree of model-predicted influence, posterior superior temporal sulcus was found to correspond to an influence update signal, capturing the difference between expected and actual influence exerted. These results suggest dissociable contributions of different parts of the mentalizing network to the computations underlying higher-order strategizing in humans