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

Magnetic behavior of the spin-chain compounds,Ca3CuIrO6 and Ca3CuRhO6

The spin-chain compounds, Ca3CuIrO6 and Ca3CuRhO6, crystallizing in a K4CdCl6-derived monoclinic structure, are investigated by ac and dc magnetization, isothermal remnant magnetization as well as heat capacity measurements. The results reveal the existence of a magnetic ordering in the vicinity of 15 K for both the compounds, but the transition appears to be of a complex nature. The existence of a spin-glass component is strongly indicated by the results. We propose that topological effects play a role on magnetism of these compounds. The magnetic properties for these two compounds are interestingly similar as though isoelectronic chemical substitution at the octahedral coordination site does not significantly interfere in the magnetic exchange process.Comment: Physical Review B, in pres

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

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

Inhomogeneous magnetism in single crystalline Sr3_3CuIrO6+δ_{6+\delta}: Implications to phase-separation concepts

The single crystalline form of an insulator, Sr$_3$CuIrO$_{6+\delta}$, is shown to exhibit unexpectedly more than one magnetic transition (at 5 and 19 K) with spin-glass-like magnetic susceptibility behaviour. On the basis of this finding, viz., inhomogeneous magnetism in a chemically homogeneous material, we propose that the idea of "phase- separation" described for manganites [1] is more widespread in different ways. The observed experimental features enable us to make a comparison with the predictions of a recent toy model [2] on {\it magnetic} phase separation in an insulating environment.Comment: 4 pages, 4 figure

Magnetic anomalies in the spin chain system, Sr3_3Cu1−x_{1-x}Znx_xIrO6_6

We report the results of ac and dc magnetization (M) and heat-capacity (C) measurements on the solid solution, Sr$_3$Cu$_{1-x}$Zn$_x$IrO$_6$. While the Zn end member is known to form in a rhombohedral pseudo one-dimensional K$_4$CdCl$_6$ structure with an antiferromagnetic ordering temperature of (T$_N$ =) 19 K, the Cu end member has been reported to form in a monoclinically distorted form with a Curie temperature of (T$_C$ =) 19 K. The magnetism of the Zn compound is found to be robust to synthetic conditions and is broadly consistent with the behavior known in the literature. However, we find a lower magnetic ordering temperature (T$_o$) for our Cu compound (~ 13 K), thereby suggesting that T$_o$ is sensitive to synthetic conditions. The Cu sample appears to be in a spin-glass-like state at low temperatures, judged by a frequency dependence of ac magnetic susceptibility and a broadening of the C anomaly at the onset of magnetic ordering, in sharp contrast to earlier proposals. Small applications of magnetic field, however, drive this system to ferromagnetism as inferred from the M data. Small substitutions for Cu/Zn (x = 0.75 or 0.25) significantly depress magnetic ordering; in other words, T$_o$ varies non-monotonically with x (T$_o$ ~ 6, 3 and 4 K for x = 0.25, 0.5, and 0.67 respectively). The plot of inverse susceptibility versus temperature is non-linear in the paramagnetic state as if correlations within (or among) the magnetic chains continuously vary with temperature. The results establishComment: 7 pages, 7 figures, Revte

Modified spin-wave study of random antiferromagnetic-ferromagnetic spin chains

We study the thermodynamics of one-dimensional quantum spin-1/2 Heisenberg ferromagnetic system with random antiferromagnetic impurity bonds. In the dilute impurity limit, we generalize the modified spin-wave theory for random spin chains, where local chemical potentials for spin-waves in ferromagnetic spin segments are introduced to ensure zero magnetization at finite temperature. This approach successfully describes the crossover from behavior of pure one-dimensional ferromagnet at high temperatures to a distinct Curie behavior due to randomness at low temperatures. We discuss the effects of impurity bond strength and concentration on the crossover and low temperature behavior.Comment: 14 pages, 7 eps figure

A systematic review on the effects of group singing on persistent pain in people with long‐term health conditions

Singing can have a range of health benefits; this paper reviews the evidence of the effects of group singing for chronic pain in people with long‐term health conditions. We searched for published peer‐reviewed singing studies reporting pain measures (intensity, interference and depression) using major electronic databases (last search date 31 July 2018). After screening 123 full texts, 13 studies met the inclusion criteria: five randomized controlled trials (RCTs), seven non‐RCTs and one qualitative study. Included studies were appraised using Downs and Black and the Critical Appraisals Skills Programme quality assessments. Included studies reported differences in the type of singing intervention, long‐term condition and pain measures. Due to the high heterogeneity, we conducted a narrative review. Singing interventions were found to reduce pain intensity in most studies, but there was more equivocal support for reducing pain interference and depression. Additionally, qualitative data synthesis identified three key linked and complementary themes: physical, psychological and social benefits. Group singing appears to have the potential to reduce pain intensity, pain interference and depression; however, we conclude that there is only partial support for singing on some pain outcomes based on the limited available evidence of varied quality. Given the positive findings of qualitative studies, this review recommends that practitioners are encouraged to continue this work. More studies of better quality are needed. Future studies should adopt more robust methodology and report their singing intervention in details. Group singing may be an effective and safe approach for reducing persistent pain and depression in people with long‐term health conditions.Health and Social Care Research Centr

The Status of Glaucous Gulls Larus hyperboreus in the Circumpolar Arctic

The entire world population of the Glaucous Gull Larus hyperboreus breeds in the circumpolar Arctic. Some local populations appear to be declining significanty. In this paper, we summarize the current state of knowledge on Glaucous Gull populations and trends. The total Arctic population is estimated at approximately 171 000 breeding pairs (> 342 000 breeding individuals) distributed among at least 2700 colonies (many not documented). Population declines may be attributable to egg harvest, contaminants, or food shortages, but other factors operating outside the breeding season should not be excluded. We recommend collaborative conservation efforts that will include better population estimates in most countries, as well as standardized monitoring programs.Toute la population mondiale de goélands bourgmestres Larus hyperboreus se reproduit dans l’Arctique circumpolaire. Certaines populations locales semblent diminuer considérablement. Dans cette communication, nous résumons l’état actuel des connaissances sur les populations et les tendances concernant le goéland bourgmestre. La population arctique totale est estimée à environ 171 000 couples reproducteurs (> 342 000 individus reproducteurs) répartis dans au moins 2 700 colonies (dont grand nombre n’ont pas été consignées). Les déclins de population peuvent être attribuables à la récolte des œufs, aux contaminants ou aux pénuries de nourriture, bien qu’il ne faille pas exclure d’autres facteurs ne se rapportant pas à la saison de reproduction. Nous recommandons des efforts de conservation communs qui comprendront de meilleures estimations de population dans la plupart des pays de même que des programmes de surveillance normalisés