The Dynamics of Hybrid Metabolic-Genetic Oscillators

The synthetic construction of intracellular circuits is frequently hindered by a poor knowledge of appropriate kinetics and precise rate parameters. Here, we use generalized modeling (GM) to study the dynamical behavior of topological models of a family of hybrid metabolic-genetic circuits known as "metabolators." Under mild assumptions on the kinetics, we use GM to analytically prove that all explicit kinetic models which are topologically analogous to one such circuit, the "core metabolator," cannot undergo Hopf bifurcations. Then, we examine more detailed models of the metabolator. Inspired by the experimental observation of a Hopf bifurcation in a synthetically constructed circuit related to the core metabolator, we apply GM to identify the critical components of the synthetically constructed metabolator which must be reintroduced in order to recover the Hopf bifurcation. Next, we study the dynamics of a re-wired version of the core metabolator, dubbed the "reverse" metabolator, and show that it exhibits a substantially richer set of dynamical behaviors, including both local and global oscillations. Prompted by the observation of relaxation oscillations in the reverse metabolator, we study the role that a separation of genetic and metabolic time scales may play in its dynamics, and find that widely separated time scales promote stability in the circuit. Our results illustrate a generic pipeline for vetting the potential success of a potential circuit design, simply by studying the dynamics of the corresponding generalized model

Riemann Invariant Manifolds for the Multidimensional Euler Equations Part I: Theoretical Development Part II: A Multidimensional Godunov Scheme and Applications

A new approach for studying wave propagation phenomena in an inviscid gas is presented. This approach can be viewed as the extension of the method of characteristics to the general case of unsteady multidimensional flow. The general case of the unsteady compressible Euler equations in several space dimensions is examined. A family of spacetime manifolds is found on which an equivalent one-dimensional problem holds. Their geometry depends on the spatial gradients of the flow, and they provide, locally, a convenient system of coordinate surfaces for spacetime. In the case of zero entropy gradients, functions analogous to the Riemann invariants of 1-D gas dynamics can be introduced. These generalized Riemann Invariants are constant on these manifolds and, thus, the manifolds are dubbed Riemann Invariant Manifolds (RIM). In this special case of zero entropy gradients, the equations of motion are integrable on these manifolds, and the problem of computing the solution becomes that of determining the manifold geometry in spacetime. This situation is completely to the traditional method of characteristics in one-dimensional flow. Explicit espressions for the local differential geometry of these manifolds can be found directly from the equations of motion. The local direction and speed of propagation of the waves that these manifolds represent, can be found as a function of the local spatial gradients of the flow. Their geometry is examined, and in particular, their relation to the characteristic surfaces. It turns out that they can be space-like or time-like, depending on the flow gradients. Wave propagation can be viewed as a superposition of these Riemann Invariant waves, whenever appropriate conditions of smoothness are met. This provides a means for decomposing the equations into a set of convective scalar fields in a way which is different and potentially more useful than the characteristic decomposition. The two decompositions become identical in the special case of one-dimellsional flow. This different approach can be used for computational purposes by discretizing the equivalent set of scalar equations. Such a computational application of this theory leads to the possibility of determining the solution at points in spacetime using information that propagates faster than the local characteristic speed, i.e., using information outside the domain of dependence. This possibility and its relation to the uniqueness theorems is discussed

The Radio Variability of the Gravitational Lens PMN J1838-3427

We present the results of a radio variability study of the gravitational lens PMN J1838-3427. Our motivation was to determine the Hubble constant by measuring the time delay between variations of the two quasar images. We monitored the system for 4 months (approximately 5 times longer than the expected delay) using the Australia Telescope Compact Array at 9 GHz. Although both images were variable on a time scale of a few days, no correlated intrinsic variability could be identified, and therefore no time delay could be measured. Notably, the fractional variation of the fainter image (8%) was greater than that of the brighter image (4%), whereas lensed images of a point source would have the same fractional variation. This effect can be explained, at least in part, as the refractive scintillation of both images due to the turbulent interstellar medium of the Galaxy.Comment: To appear in AJ (8 pages, including 4 figures

ALMA observations of PKS 1549-79: A case of feeding and feedback in a young radio quasar

We present CO(1-0) and CO(3-2) ALMA observations of the molecular gas in PKS 1549-79, as well as mm and VLBI 2.3-GHz continuum observations of its radio jet. PKS 1549-79 is one of the closest young, radio-loud quasars caught in an on-going merger in which the AGN is in the first phases of its evolution. We detect three structures tracing the accretion and the outflow of molecular gas: kpc-scale tails of gas accreting onto PKS 1549-79, a circumnuclear disc (CND) in the inner few hundred parsec, and a very broad (>2300 \kms) component detected in CO(1-0) at the position of the AGN. Thus, in PKS 1549-79 we see the co-existence of accretion and the ejection of gas. The line ratio CO(1-0)/CO(3-2) suggests that the gas in the CND has both high densities and high kinetic temperatures. We estimate a mass outflow rate of at least 650 msun/yr. This massive outflow is confined to r < 120 pc, which suggests that the AGN drives the outflow. Considering the amount of molecular gas available in CND and the observed outflow rate, we estimate a time scale of ~10^5 yr over which the AGN would be able to destroy the CND, although gas from the merger may come in from larger radii, rebuilding this disc at the same time. The AGN appears to self-regulate gas accretion onto the super-massive black hole. From a comparison with HST data, we find that the ionised gas outflow is more extended. Nevertheless, the warm outflow is about two orders of magnitude less massive than the molecular outflow. PKS 1549-79 does not seem to follow the scaling relation between bolometric luminosity and the relative importance of warm ionised and molecular outflows claimed to exist for other AGN. We argue that, although PKS 1549-79 hosts a powerful quasar nucleus and an ultra-fast outflow, the radio jet plays a significant role in producing the outflow.Comment: Accepted for A&A Main Journa

Web conversations about complementary and alternative medicines and cancer: Content and sentiment analysis

Background: The use of complementary and alternative medicine (CAM) among cancer patients is widespread and mostly self-administrated. Today, one of the most relevant topics is the nondisclosure of CAM use to doctors. This general lack of communication exposes patients to dangerous behaviors and to less reliable information channels, such as the Web. The Italian context scarcely differs from this trend. Today, we are able to mine and analyze systematically the unstructured information available in the Web, to get an insight of people's opinions, beliefs, and rumors concerning health topics. Objective: Our aim was to analyze Italian Web conversations about CAM, identifying the most relevant Web sources, therapies, and diseases and measure the related sentiment. Methods: Data have been collected using the Web Intelligence tool ifMONITOR. The workflow consisted of 6 phases: (1) eligibility criteria definition for the ifMONITOR search profile; (2) creation of a CAM terminology database; (3) generic Web search and automatic filtering, the results have been manually revised to refine the search profile, and stored in the ifMONITOR database; (4) automatic classification using the CAM database terms; (5) selection of the final sample and manual sentiment analysis using a 1-5 score range; (6) manual indexing of the Web sources and CAM therapies type retrieved. Descriptive univariate statistics were computed for each item: absolute frequency, percentage, central tendency (mean sentiment score [MSS]), and variability (standard variation Ò). Results: Overall, 212 Web sources, 423 Web documents, and 868 opinions have been retrieved. The overall sentiment measured tends to a good score (3.6 of 5). Quite a high polarization in the opinions of the conversation partaking emerged from standard variation analysis (δ≥1). In total, 126 of 212 (59.4%) Web sources retrieved were nonhealth-related. Facebook (89; 21%) and Yahoo Answers (41; 9.7%) were the most relevant. In total, 94 CAM therapies have been retrieved. Most belong to the "biologically based therapies or nutrition" category: 339 of 868 opinions (39.1%), showing an MSS of 3.9 (δ=0.83). Within nutrition, "diets" collected 154 opinions (18.4%) with an MSS of 3.8 (δ=0.87); "food as CAM" overall collected 112 opinions (12.8%) with a MSS of 4 (δ=0.68). Excluding diets and food, the most discussed CAM therapy is the controversial Italian "Di Bella multitherapy" with 102 opinions (11.8%) with an MSS of 3.4 (δ=1.21). Breast cancer was the most mentioned disease: 81 opinions of 868. Conclusions: Conversations about CAM and cancer are ubiquitous. There is a great concern about the biologically based therapies, perceived as harmless and useful, under-rating all risks related to dangerous interactions or malnutrition. Our results can be useful to doctors to be aware of the implications of these beliefs for the clinical practice. Web conversation exploitation could be a strategy to gain insights of people's perspective for other controversial topics

First geodetic observations using new VLBI stations ASKAP-29 and WARK12M

We report the results of a successful 7 hour 1.4 GHz VLBI experiment using two new stations, ASKAP-29 located in Western Australia and WARK12M located on the North Island of New Zealand. This was the first geodetic VLBI observing session with the participation of these new stations. We have determined the positions of ASKAP-29 and WARK12M. Random errors on position estimates are 150-200 mm for the vertical component and 40-50 mm for the horizontal component. Systematic errors caused by the unmodeled ionosphere path delay may reach 1.3 m for the vertical component.Comment: 11 pages, 6 flgures, 4 table

São Pedro, uma Igreja do Brasil no Egito

O Brasil e o Egito, dois países tão distantes, mas que, em virtude do interêsse de D. Pedro II, pela terra dos Faraós, tornaram-se espiritualmente próximos no que diz às tradições é ao seu passado. Estão em hemisférios opostos, mas em latitudes idênticas, a partir do equador, com clima parecido e com muitos problemas, como o das sêcas, para resolver. A' grande admiração do Imperador Pedro II pelo velho Egito, é conhecida; realizou duas memoráveis viagens àquêle país, em 1871 e 1876, tendo planejado uma terceira para 1888, que não chegou a efetuar.