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

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

Barriers and enablers to implementation of the therapeutic engagement questionnaire in acute mental health inpatient wards in England: A qualitative study.

A strong association exists between the quality of nurse-service user therapeutic relationship and care outcomes on acute mental health inpatient wards. Despite evidence that service users desire improved therapeutic engagement, and registered mental health nurses recognize the benefits of therapeutic relationships, such interactions remain sub-optimal. There is a dearth of evidence on factors influencing implementation of interventions to support and encourage therapeutic engagement. This study aimed to understand the barriers and enablers to implementation of the Therapeutic Engagement Questionnaire (TEQ), across fifteen acute inpatient wards in seven English mental health organizations. Qualitative methods were used in which data were collected from ethnographic field notes and documentary review, coded, and analysed using thematic analysis. Theoretical framing supported data analysis and interpretation. Reporting adheres to the Standards for Reporting Qualitative Research. The TEQ as an evidence-based intervention co-produced with service users and nurses was valued and welcomed by many nurse directors, senior clinicians, and ward managers. However, a range of practical and perceptual factors impeded implementation. Furthermore, many existing contextual challenges for intervention implementation in acute inpatient wards were magnified by the COVID-19 pandemic. Suitable facilitation to address these barriers can help support implementation of the TEQ, with some transferability to implementation of other interventions in these settings. Our study suggests several facilitation methods, brought together in a conceptual model, including encouragement of reflective, facilitative discussion meetings among stakeholders and researchers, effort put into winning nurse 'buy-in' and identifying and supporting ward-level agents of change

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

The acheulean handaxe : More like a bird's song than a beatles' tune?

© 2016 Wiley Periodicals, Inc. KV is supported by the Netherlands Organization for Scientific Research. MC is supported by the Canada Research Chairs Program, the Social Sciences and Humanities Research of Canada, the Canada Foundation for Innovation, the British Columbia Knowledge Development Fund, and Simon Fraser UniversityPeer reviewedPublisher PD

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

Making connections: technological interventions to support students in using, and tutors in creating, assessment feedback

This paper explores the potential of technology to enhance the assessment and feedback process for both staff and students. The ‘Making Connections’ project aimed to better understand the connections that students make between the feedback that they receive and future assignments, and explored whether technology can help them in this activity. The project interviewed 10 tutors and 20 students, using a semi-structured approach. Data were analysed using a thematic approach, and the findings have identified a number of areas in which improvements could be made to the assessment and feedback process through the use of technology. The findings of the study cover each stage of the assessment process from the perspective of both staff and students. The findings are discussed in the context of current literature, and special attention is given to projects from the UK higher education sector intended to address the same issues. Keywords: feed-forward; assessment; practices; technology; technology-enhanced learnin

The implications of service quality gaps for strategy implementation

This article addresses the problem of service quality strategy implementation and proposes three interrelated models: a static model of the organisation; a comprehensive dynamic model of the implementation process, both synthesised from the literature; and a mixed model, which integrates static and dynamic models. The mixed model is combined with the service quality gaps (SQGs) model, drawn at a previous congress paper, to propose a map of the pattern of SQGs occurring at each implementation stage; the organisational variables that can be manipulated to eliminate SQGs; and several implications to practising managers