Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network

BACKGROUND It is widely accepted that genetic regulatory systems are 'modular', in that the whole system is made up of smaller 'subsystems' corresponding to specific biological functions. Most attempts to identify modules in genetic regulatory systems have relied on the topology of the underlying network. However, it is the temporal activity (dynamics) of genes and proteins that corresponds to biological functions, and hence it is dynamics that we focus on here for identifying subsystems. RESULTS Using Boolean network models as an exemplar, we present a new technique to identify subsystems, based on their dynamical properties. The main part of the method depends only on the stable dynamics (attractors) of the system, thus requiring no prior knowledge of the underlying network. However, knowledge of the logical relationships between the network components can be used to describe how each subsystem is regulated. To demonstrate its applicability to genetic regulatory systems, we apply the method to a model of the Drosophila segment polarity network, providing a detailed breakdown of the system. CONCLUSION We have designed a technique for decomposing any set of discrete-state, discrete-time attractors into subsystems. Having a suitable mathematical model also allows us to describe how each subsystem is regulated and how robust each subsystem is against perturbations. However, since the subsystems are found directly from the attractors, a mathematical model or underlying network topology is not necessarily required to identify them, potentially allowing the method to be applied directly to experimental expression data

Advanced Solid-State Array Spectrometer (ASAS) data sets from the 1990 field season: A unique look at two forested ecosystems

The Advanced Solid-state Array Spectrometer (ASAS) is a pointable imaging spectrometer which uses a solid-state array to acquire imagery of terrestrial targets in 29 spectral bands from .4 to .8 microns. Performance and calibration of the instrument are described. The ASAS data sets obtained in 1990 provide a unique look at forest canopies from two different forest regions of the North America continent under varying temporal, spectral, and bidirectional conditions. These data sets will be used to study such parameters as the albedo of forest canopies, the dynamics of scene radiation due to factors such as canopy architecture, moisture stress, leaf chemistry, topography, and understory composition

Singing for people with Parkinson's disease

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: To compare the efficacy and effectiveness of singing interventions with non‐singing intervention or usual care on QoL, wellbeing, and speech and communication among people with PD. We will assess the QoL and the physical, psychological, and social health and wellbeing of people with PD who receive a singing intervention, compared to non‐singing intervention or usual care

Creative Assessment in Programming: Diversity and Divergence

Negative stereotypes persist in computing, and align poorly with research into the motivations of female students. In particular, female students are more inclined to want to work creatively and have a positive impact through their work. However programming assignments are often tightly constrained and rather pointless in themselves so are doubly unattractive. Alongside this, concerns are often raised about plagiarism in programming assignments, particularly when the assessment process is automated. We attempt to address both of these issues by designing more creative programming assignments, allowing students to engage in work aligned with whatever their interests are. By providing a more divergent assessment, automated plagiarism detectors are much more effective because the likelihood of false positives is much lower than in more constrained, convergent assessments. We also show how to combine this with partial automation of assessment. To examine this approach we compare the results of two subsequent years of delivery of the same second-year undergraduate programming module, and find that, using more creative assessments, female students average scores were substantially increased so that they outperform male students. While the results are not quite statistically significant (according to 2-way ANOVA), they demonstrate potential that could be verified with a larger sample

The coupling constant averaged exchange–correlation energy density

The exchange–correlation energy, central to density-functional theory, may be represented in terms of the coupling constant averaged (CCA) exchange–correlation energy density. We present an approach to calculate the CCA energy density using accurate ab initio methods and its application to simple atomic systems. This function provides a link between intrinsically non-local, many-body electronic structure methods and simple local and semi-local density-functional approximations (DFAs). The CCA energy density is resolved into separate exchange and correlation terms and the features of each compared with those of quantities commonly used to construct DFAs. In particular, the more complex structure of the correlation energy density is found to exhibit features that align well with those present in the Laplacian of the density, suggesting its role as a key variable to be used in the construction of improved semi-local correlation functionals. The accurate results presented in this work are also compared with those provided by the Laplacian-dependent Becke–Roussel model for the exchange energy

ac susceptibility of Sr\u3csub\u3e3\u3c/sub\u3eCuPt\u3csub\u3ex\u3c/sub\u3eIr\u3csub\u3e1-x\u3c/sub\u3eO\u3csub\u3e6\u3c/sub\u3e: A magnetic system with competing interactions and dimensionality

Sr3CuPtxIr1-xO6 has been cited as an example of a one-dimensional quantum spin chain with competing ferromagnetic and antiferromagnetic interactions. We have measured the ac susceptibility of Sr3CuPtxIr1-xO6 with x=0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, and 0.7, in magnetic fields of 0–60 kOe, and at temperatures down to 0.275 K. Our data show that the x=endpoint Sr3CuIrO6, exhibits long-range ferromagnetic order at T=20.1 K, contrary to results from dc susceptibility studies which indicated that it remained a one-dimensional ferromagnet to below 4 K. When platinum is substituted for iridium, antiferromagnetic couplings are introduced, and the susceptibility shows a diminishing signature of the three-dimensional ferromagnetic transition. Furthermore, the low-temperature susceptibility exhibits peaks which appear and evolve as x is increased. These results lead to a rich phase diagram in temperature and Pt concentration space. We find that the behavior of Sr3CuPtxIr1-xO6 cannot be simply described by the random quantum spin chain theories that were developed, in part, to address this system

Spin Waves in Random Spin Chains

We study quantum spin-1/2 Heisenberg ferromagnetic chains with dilute, random antiferromagnetic impurity bonds with modified spin-wave theory. By describing thermal excitations in the language of spin waves, we successfully observe a low-temperature Curie susceptibility due to formation of large spin clusters first predicted by the real-space renormalization-group approach, as well as a crossover to a pure ferromagnetic spin chain behavior at intermediate and high temperatures. We compare our results of the modified spin-wave theory to quantum Monte Carlo simulations.Comment: 3 pages, 3 eps figures, submitted to the 47th Conference on Magnetism and Magnetic Material

Long range magnetic ordering in a spin-chain compound, Ca3_3CuMnO6_6, with multiple bond distances

The results of ac and dc magnetization and heat capacity measurements as a function of temperature (T = 1.8 to 300 K) are reported for a quasi-one-dimensional compound, Ca$_3$CuMnO$_6$, crystallizing in a triclinically distorted K$_4$CdCl$_6$-type structure. The results reveal that this compound undergoes antiferromagnetic ordering close to 5.5 K. In addition, there is another magnetic transition below 3.6 K. Existence of two long-range magnetic transitions is uncommon among quasi-one-dimensional systems. It is interesting to note that both the magnetic transitions are of long-range type, instead of spin-glass type, in spite of the fact that the Cu-O and Mn-O bond distances are multiplied due to this crystallographic distortion. In view of this, this compound could serve as a nice example for studying "order-in-disorder" phenomena.Comment: Physical Review (in press

Biotransformation of an uncured composite material

The feasibility of biologically degrading prepreg wastes was studied. The work was conducted with the intention of obtaining baseline data that would facilitate the achievement of two long-range goals. These goals are: (1) the biological remediation of the hazardous components in the prepreg wastes, and (2) providing the potential for recycling the prepreg waste fibers. The experiments examined a prepreg that employs an bismaleimide resin system. Initial results demonstrated an obvious deterioration of the prepreg material when incubated with several bacterial strains. The most active cultures were identified as a mixture of 'Bacillus cereus' and 'Pseudomonas sp'. Gas chromatography analyses revealed seven primary compounds in the resin mixture. Biotransformation studies, using the complete prepreg material, demonstrated on obvious loss of all seven organic compounds. Gas chromatography-mass spectrometry analyses resulted in structure assignments for the two primary components of the resin. Both were analogs of Bisphenol A; one being bismaleimide, and the other being Bisphenol A containing a diglycidyl moiety. The 'diglycidyl analog' was purified using thin-layer chromatography and the biotransformation of this compound (at 27 ug/ml bacterial culture) was monitored. After a seven-day incubation, approximately 40% of the organic compound was biotransformed. These results demonstrate the biotransformation of the prepreg resin and indicate that biological remediation of the prepreg wastes is feasible