A Mixture model with random-effects components for clustering correlated gene-expression profiles

Motivation: The clustering of gene profiles across some experimental conditions of interest contributes significantly to the elucidation of unknown gene function, the validation of gene discoveries and the interpretation of biological processes. However, this clustering problem is not straightforward as the profiles of the genes are not all independently distributed and the expression levels may have been obtained from an experimental design involving replicated arrays. Ignoring the dependence between the gene profiles and the structure of the replicated data can result in important sources of variability in the experiments being overlooked in the analysis, with the consequent possibility of misleading inferences being made. We propose a random-effects model that provides a unified approach to the clustering of genes with correlated expression levels measured in a wide variety of experimental situations. Our model is an extension of the normal mixture model to account for the correlations between the gene profiles and to enable covariate information to be incorporated into the clustering process. Hence the model is applicable to longitudinal studies with or without replication, for example, time-course experiments by using time as a covariate, and to cross-sectional experiments by using categorical covariates to represent the different experimental classes. Results: We show that our random-effects model can be fitted by maximum likelihood via the EM algorithm for which the E(expectation) and M(maximization) steps can be implemented in closed form. Hence our model can be fitted deterministically without the need for time-consuming Monte Carlo approximations. The effectiveness of our model-based procedure for the clustering of correlated gene profiles is demonstrated on three real datasets, representing typical microarray experimental designs, covering time-course, repeated-measurement and cross-sectional data. In these examples, relevant clusters of the genes are obtained, which are supported by existing gene-function annotation. A synthetic dataset is considered too.

Timed Up and Go Tests in cardiac rehabilitation : reliability and comparison with the 6-minute walk test

PURPOSE: To test the reliability of Timed Up and Go Tests (TUGTs) in cardiac rehabilitation (CR) and compare TUGTs to the 6-Minute Walk Test (6MWT) for outcome measurement. METHODS: Sixty-one of 154 consecutive community-based CR patients were prospectively recruited. Subjects undertook repeated TUGTs and 6MWTs at the start of CR (start-CR), postdischarge from CR (post-CR), and 6 months postdischarge from CR (6 months post-CR). The main outcome measurements were TUGT time (TUGTT) and 6MWT distance (6MWD). RESULTS: Mean (SD) TUGTT1 and TUGTT2 at the 3 assessments were 6.29 (1.30) and 5.94 (1.20); 5.81 (1.22) and 5.53 (1.09); and 5.39 (1.60) and 5.01 (1.28) seconds, respectively. A reduction in TUGTT occurred between each outcome point (P ≤ .002). Repeated TUGTTs were strongly correlated at each assessment, intraclass correlation (95% CI) = 0.85 (0.76–0.91), 0.84 (0.73–0.91), and 0.90 (0.83–0.94), despite a reduction between TUGTT1 and TUGTT2 of 5%, 5%, and 7%, respectively (P ≤ .006). Relative decreases in TUGTT1 (TUGTT2) occurred from start-CR to post-CR and from start-CR to 6 months post-CR of −7.5% (−6.9%) and −14.2% (−15.5%), respectively, while relative increases in 6MWD1 (6MWD2) occurred, 5.1% (7.2%) and 8.4% (10.2%), respectively (P < .001 in all cases). Pearson correlation coefficients for 6MWD1 to TUGTT1 and TUGTT2 across all times were −0.60 and −0.68 (P < .001) and the intraclass correlations (95% CI) for the speeds derived from averaged 6MWDs and TUGTTs were 0.65 (0.54, 0.73) (P < .001). CONCLUSIONS: Similar relative changes occurred for the TUGT and the 6MWT in CR. A significant correlation between the TUGTT and 6MWD was demonstrated, and we suggest that the TUGT may provide a related or a supplementary measurement of functional capacity in CR.

Sex discrimination and non-random sampling in the Australian labour market

Historically a significant gap between male and female wages has existed in the Australian labour market. Indeed this wage differential was institutionalised in the 1912 arbitration decision which determined that the basic female wage would be set at between 54 and 66 per cent of the male wage. More recently however, the 1969 and 1972 Equal Pay Cases determined that male/female wage relativities should be based upon the premise of equal pay for work of equal value. It is important to note that the mere observation that average wages differ between males and females is not sine qua non evidence of sex discrimination. Economists restrict the definition of wage discrimination to cases where two distinct groups receive different average remuneration for reasons unrelated to differences in productivity characteristics. This paper extends previous studies of wage discrimination in Australia (Chapman and Mulvey, 1986; Haig, 1982) by correcting the estimated male/female wage differential for the existence of non-random sampling. Previous Australian estimates of male/female human capital basedwage specifications together with estimates of the corresponding wage differential all suffer from a failure to address this issue. If the sample of females observed to be working does not represent a random sample then the estimates of the male/female wage differential will be both biased and inconsistent.

A cross-discipline and collaborative approach to identifying the predictors of environmentally friendly and health protective behaviour

Background. As a society, our interaction with the environment is having a negative impact on human health. For example, an increase in car use for short trips, over walking or cycling, has contributed to an increase in obesity, diabetes and poor heart health and also contributes to pollution, which is associated with asthma and other respiratory diseases. In order to change the nature of that interaction, to be more positive and healthy, it is recommended that individuals adopt a range of environmentally friendly behaviours (such as walking for transport and reducing the use of plastics). Effective interventions aimed at increasing such behaviours will need to be evidence based and there is a need for the rapid communication of information from the point of research, into policy and practice. Further, a number of health disciplines, including psychology and public health, share a common mission to promote health and well-being. Therefore, the objective of this project is to take a cross-discipline and collaborative approach to reveal psychological mechanisms driving environmentally friendly behaviour. This objective is further divided into three broad aims, the first of which is to take a cross-discipline and collaborative approach to research. The second aim is to explore and identify the salient beliefs which most strongly predict environmentally friendly behaviour. The third aim is to build an augmented model to explain environmentally friendly behaviour. The thesis builds on the understanding that an interdisciplinary collaborative approach will facilitate the rapid transfer of knowledge to inform behaviour change interventions. Methods. The application of this approach involved two surveys which explored the psycho-social predictors of environmentally friendly behaviour. Following a qualitative pilot study, and in collaboration with an expert panel comprising academics, industry professionals and government representatives, a self-administered, Theory of Planned Behaviour (TPB) based, mail survey was distributed to a random sample of 3000 residents of Brisbane and Moreton Bay Region (Queensland, Australia). This survey explored specific beliefs including attitudes, norms, perceived control, intention and behaviour, as well as environmental altruism and green identity, in relation to walking for transport and switching off lights when not in use. Following analysis of the mail survey data and based on feedback from participants and key stakeholders, an internet survey was employed (N=451) to explore two additional behaviours, switching off appliances at the wall when not in use, and shopping with reusable bags. This work is presented as a series of interrelated publications which address each of the research aims. Presentation of Findings. Chapter five of this thesis consists of a published paper which addresses the first aim of the research and outlines the collaborative and multidisciplinary approach employed in the mail survey. The paper argued that forging alliances with those who are in a position to immediately utilise the findings of research has the potential to improve the quality and timely communication of research. Illustrating this timely communication, Chapter six comprises a report presented to Moreton Bay Regional Council (MBRC). This report addresses aim's one and two. The report contains a summary of participation in a range of environmentally friendly behaviours and identifies the beliefs which most strongly predicted walking for transport and switching off lights (from the mail survey). These salient beliefs were then recommended as targets for interventions and included: participants believing that they might save money; that their neighbours also switch off lights; that it would be inconvenient to walk for transport and that their closest friend also walks for transport. Chapter seven also addresses the second aim and presents a published conference paper in which the salient beliefs predicting the four specified behaviours (from both surveys) are identified and potential applications for intervention are discussed. Again, a range of TPB based beliefs, including descriptive normative beliefs, were predictive of environmentally friendly behaviour. This paper was also provided to MBRC, along with recommendations for applying the findings. For example, as descriptive normative beliefs were consistently correlated with environmentally friendly behaviour, local councils could engage in marketing and interventions (workshops, letter box drops, internet promotions) which encourage parents and friends to model, rather than simply encourage, environmentally friendly behaviour. The final two papers, presented in Chapters eight and nine, addresses the third aim of the project. These papers each present two behaviours together to inform a TPB based theoretical model with which to predict environmentally friendly behaviour. A generalised model is presented, which is found to predict the four specific behaviours under investigation. The role of demographics was explored across each of the behaviour specific models. It was found that some behaviour's differ by age, gender, income or education. In particular, adjusted models predicted more of the variance in walking for transport amongst younger participants and females. Adjusted models predicted more variance in switching off lights amongst those with a bachelor degree or higher and predicted more variance in switching off appliances amongst those on a higher income. Adjusted models predicted more variance in shopping with reusable bags for males, people 40 years or older, those on a higher income and those with a bachelor degree or higher. However, model structure and general predictability was relatively consistent overall. The models provide a general theoretical framework from which to better understand the motives and predictors of environmentally friendly behaviour. Conclusion. This research has provided an example of the benefits of a collaborative interdisciplinary approach. It has identified a number of salient beliefs which can be targeted for social marketing campaigns and educational initiatives; and these findings, along with recommendations, have been passed on to a local council to be used as part of their ongoing community engagement programs. Finally, the research has informed a practical model, as well as behaviour specific models, for predicting sustainable living behaviours. Such models can highlight important core constructs from which targeted interventions can be designed. Therefore, this research represents an important step in undertaking collaborative approaches to improving population health through human-environment interactions.

Random existence of charge ordered stripes and its influence on the magnetotransport properties of La0.6Sr0.4MnO3 perovskite substituted with diamagnetic ions at Mn sublattice

Phase-singular solid solutions of La0.6Sr0.4Mn1-yMeyO3 (0 <= y <= 0.3) [Me=Li1+, Mg2+, Al3+, Ti4+, Nb5+, Mo6+ or W6+] [LSMey] perovskite of rhombohedral symmetry (space group: R (3) over barc) have been prepared wherein the valence of the diamagnetic substituent at Mn site ranged from 1 to 6. With increasing y-content in LSMey, the metal-insulator (TM-I) transition in resistivity-temperature rho(T) curves shifted to low temperatures. The magnetization studies M(H) as well as the M(T) indicated two groups for LSMey. (1) Group A with Me=Mg, Al, Ti, or Nb which are paramagnetic insulators (PIs) at room temperature with low values of M (< 0.5 mu(B)/Mn); the magnetic transition [ferromagnetic insulator (FMI)-PI] temperature (T-C) shifts to low temperatures and nearly coincides with that of TM-I and the maximum magnetoresistance (MR) of similar to 50% prevails near T-C (approximate to TM-I). (2) Group-B samples with Me=Li, Mo, or W which are FMIs with M-s=3.3-3.58 mu(B)/Mn and marginal reduction in T-C similar to 350 K as compared to the undoped LSMO (T-C similar to 378 K). The latter samples show large temperature differences Delta T=T-c-TM-I, reaching up to similar to 288 K. The maximum MR (similar to 60%) prevails at low temperatures corresponding to the M-I transition TM-I rather than around T-C. High resolution lattice images as well as microscopy analysis revealed the prevalence of inhomogeneous phase mixtures of randomly distributed charge ordered-insulating (COI) bistripes (similar to 3-5 nm width) within FMI charge-disordered regions, yet maintaining crystallographically single phase with no secondary precipitate formation. The averaged ionic radius < r(B)>, valency, or charge/radius ratio < CRR > cannot be correlated with that of large Delta T; hence cannot be used to parametrize the discrepancy between T-C and TM-I. The M-I transition is controlled by the charge conduction within the electronically heterogeneous mixtures (COI bistripes+FMI charge disordered); large MR at TM-I suggests that the spin-ordered FM-insulating regions assist the charge transport, whereas the T-C is associated with the bulk spin ordered regions corresponding to the FMI phase of higher volume fraction of which anchors the T-C to higher temperatures. The present analysis showed that the double-exchange model alone cannot account for the wide bifurcation of the magnetic and electric transitions, contributions from the charge as well as lattice degrees of freedom to be separated from spin/orbital ordering. The heterogeneous phase mixtures (COI+FMI) cannot be treated as of granular composite behavior. (c) 2008 American Institute of Physics.

Distributed Transmission of Functions of Correlated Sources over a Fading Multiple Access Channel

In this paper we address the problem of distributed transmission of functions of correlated sources over a fast fading multiple access channel (MAC). This is a basic building block in a hierarchical sensor network used in estimating a random field where the cluster head is interested only in estimating a function of the observations. The observations are transmitted to the cluster head through a fast fading MAC. We provide sufficient conditions for lossy transmission when the encoders and decoders are provided with partial information about the channel state. Furthermore signal side information maybe available at the encoders and the decoder. Various previous studies are shown as special cases. Efficient joint-source channel coding schemes are discussed for transmission of discrete and continuous alphabet sources to recover function values.

Resistance fluctuations, phase randomness and noise in one-dimensional conductors with a long-range correlated potential

When the size (L) of a one-dimensional metallic conductor is less than the correlation length λ-1 of the Gaussian random potential, one expects transport properties to show ballistic behaviour. Using an invariant imbedding method, we study the exact distribution of the resistance, of the phase θ of the reflection amplitude of an incident electron of wave number k0, and of dθ/dk0, for λL ll 1. The resistance is non-self-averaging and the n-th resistance moment varies periodically as (1 - cos 2k0L)n. The charge fluctuation noise, determined by the distribution of dθ/dk0, is constant at low frequencies.

Male-biased adult sex ratios and their significance for cooperative breeding in dhole, Cuon alpinus, packs

Two free-ranging packs of dholes (Asiatic wild dog, Cuon alpinus) were monitored for a period of 6 yr (Sep. 1990-Sep. 1996) in the Mudumalai sanctuary, southern India. Demographic data on age structure, litter-size, sex ratio and age and sex specific dispersal were collected. Behavioural data on social interactions and reproductive behaviour among pack members were obtained to determine the frequencies of dominant and subordinate behaviours shown by malt: and female pack members and a measure of each male's reproductive access to females. Behaviours displayed by pack members at dens were recorded to determine whether any age- or sex-specific role specialization existed during pup care. Tenures for dominant males and females within the pack were calculated to ascertain the rate of breeding vacancies occurring within packs. Approximate levels of genetic relatedness within packs were determined by studying pedigrees. In most years one study pack had a male-biased adult sex ratio. This was caused by almost twofold higher dispersal of adult females over adult males. A considerable variance existed in the percentage of sub-adults dispersing from the two packs. Differences existed in the frequencies of dominant and subordinate behaviours shown by males. For males, dominance ranks and ranks based on submissive behaviours were not correlated with frequencies of reproductive behaviours. Subordinate males also displayed reproductive behaviours. In packs, dominant males had lower tenures than dominant females indicating that among males breeding vacancies arose more quickly. The litter size was found to be negatively correlated with the age of the breeding female. There were no significant differences across individuals of varying age or sex classes in the display of pup care behaviours. Significant differences did exist among individual adults. Genetic relatedness among packs tended to vary temporally as a consequence of possible mating by subordinate animals and immigration of new males into the pack. In conclusion, it appears that males delay dispersal and cooperate within their natal packs because of the variety of reproductive strategies they could pursue within. A combination of ecological constraints and the difficulties of achieving breeding status within non-natal packs may make early dispersal and independent breeding less beneficial.

Transmission of correlated sources over fading multiple access channel

In this paper we address the problem of transmission of correlated sources over a fading multiple access channel (MAC). We provide sufficient conditions for transmission with given distortions. Next these conditions are specialized to a Gaussian MAC (GMAC). Transmission schemes for discrete and Gaussian sources over a fading GMAC are considered. Various power allocation strategies are also compared. Keywords: Fading MAC, Power allocation, Random TDMA, Amplify and Forward, Correlated sources.

Completely random nanoporous Cu4O3-CuO-C composite thin films for potential application as multiple channel photonic band gap based filter in the telecommunication wavelengths

In 2003, Babin et al. theoretically predicted (J. Appl. Phys. 94:4244, 2003) that fabrication of organic-inorganic hybrid materials would probably be required to implement structures with multiple photonic band gaps. In tune with their prediction, we report synthesis of such an inorganic-organic nanocomposite, comprising Cu4O3-CuO-C thin films that experimentally exhibit the highest (of any known material) number (as many as eleven) of photonic band gaps in the near infrared. On contrary to the report by Wang et al. (Appl. Phys. Lett. 84:1629, 2004) that photonic crystals with multiple stop gaps require highly correlated structural arrangement such as multilayers of variable thicknesses, we demonstrate experimental realization of multiple stop gaps in completely randomized structures comprising inorganic oxide nanocrystals (Cu4O3 and CuO) randomly embedded in a randomly porous carbonaceous matrix. We report one step synthesis of such nanostructured films through the metalorganic chemical vapor deposition technique using a single source metalorganic precursor, Cu-4(deaH)(dea)(oAc)(5) a <...aEuro parts per thousand(CH3)(2)CO. The films displaying multiple (4/9/11) photonic band gaps with equal transmission losses in the infrared are promising materials to find applications as multiple channel photonic band gap based filter for WDM technology.

A distributed TDMA slot scheduling algorithm for spatially correlated contention in WSNs

In wireless sensor networks (WSNs) the communication traffic is often time and space correlated, where multiple nodes in a proximity start transmitting at the same time. Such a situation is known as spatially correlated contention. The random access methods to resolve such contention suffers from high collision rate, whereas the traditional distributed TDMA scheduling techniques primarily try to improve the network capacity by reducing the schedule length. Usually, the situation of spatially correlated contention persists only for a short duration and therefore generating an optimal or sub-optimal schedule is not very useful. On the other hand, if the algorithm takes very large time to schedule, it will not only introduce additional delay in the data transfer but also consume more energy. To efficiently handle the spatially correlated contention in WSNs, we present a distributed TDMA slot scheduling algorithm, called DTSS algorithm. The DTSS algorithm is designed with the primary objective of reducing the time required to perform scheduling, while restricting the schedule length to maximum degree of interference graph. The algorithm uses randomized TDMA channel access as the mechanism to transmit protocol messages, which bounds the message delay and therefore reduces the time required to get a feasible schedule. The DTSS algorithm supports unicast, multicast and broadcast scheduling, simultaneously without any modification in the protocol. The protocol has been simulated using Castalia simulator to evaluate the run time performance. Simulation results show that our protocol is able to considerably reduce the time required to schedule.

A Distributed TDMA Slot Scheduling Algorithm for Spatially Correlated Contention in WSNs

In WSNs the communication traffic is often time and space correlated, where multiple nodes in a proximity start transmitting simultaneously. Such a situation is known as spatially correlated contention. The random access method to resolve such contention suffers from high collision rate, whereas the traditional distributed TDMA scheduling techniques primarily try to improve the network capacity by reducing the schedule length. Usually, the situation of spatially correlated contention persists only for a short duration, and therefore generating an optimal or suboptimal schedule is not very useful. Additionally, if an algorithm takes very long time to schedule, it will not only introduce additional delay in the data transfer but also consume more energy. In this paper, we present a distributed TDMA slot scheduling (DTSS) algorithm, which considerably reduces the time required to perform scheduling, while restricting the schedule length to the maximum degree of interference graph. The DTSS algorithm supports unicast, multicast, and broadcast scheduling, simultaneously without any modification in the protocol. We have analyzed the protocol for average case performance and also simulated it using Castalia simulator to evaluate its runtime performance. Both analytical and simulation results show that our protocol is able to considerably reduce the time required for scheduling.

RD-TDMA: A Randomized and Distributed TDMA Scheduling for Correlated Contention in WSNs

In wireless sensor networks (WSNs), contention occurs when two or more nodes in a proximity simultaneously try to access the channel. The contention causes collisions, which are very likely to occur when traffic is correlated. The excessive collision not only affects the reliability and the QoS of the application, but also the lifetime of the network. It is well-known that random access mechanisms do not efficiently handle correlated-contention, and therefore, suffer from high collision rate. Most of the existing TDMA scheduling techniques try to find an optimal or a sub-optimal schedule. Usually, the situation of correlated-contention persists only for a short duration, and therefore, it is not worthwhile to take a long time to generate an optimal or a sub-optimal schedule. We propose a randomized distributed TDMA scheduling (RD-TDMA) algorithm to quickly generate a feasible schedule (not necessarily optimal) to handle correlated-contention in WSNs. In RD-TDMA, a node in the network negotiates a slot with its neighbors using the message exchange mechanism. The proposed protocol has been simulated using the Castalia simulator to evaluate its runtime performance. Simulation results show that the RD-TDMA algorithm considerably reduces the time required to schedule.

Autoregressive cascades on random networks

A network cascade model that captures many real-life correlated node failures in large networks via load redistribution is studied. The considered model is well suited for networks where physical quantities are transmitted, e.g., studying large scale outages in electrical power grids, gridlocks in road networks, and connectivity breakdown in communication networks, etc. For this model, a phase transition is established, i.e., existence of critical thresholds above or below which a small number of node failures lead to a global cascade of network failures or not. Theoretical bounds are obtained for the phase transition on the critical capacity parameter that determines the threshold above and below which cascade appears or disappears, respectively, that are shown to closely follow numerical simulation results. (C) 2015 Elsevier B.V. All rights reserved.