Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies.

BACKGROUND: Nonparametric Bayesian techniques have been developed recently to extend the sophistication of factor models, allowing one to infer the number of appropriate factors from the observed data. We consider such techniques for sparse factor analysis, with application to gene-expression data from three virus challenge studies. Particular attention is placed on employing the Beta Process (BP), the Indian Buffet Process (IBP), and related sparseness-promoting techniques to infer a proper number of factors. The posterior density function on the model parameters is computed using Gibbs sampling and variational Bayesian (VB) analysis. RESULTS: Time-evolving gene-expression data are considered for respiratory syncytial virus (RSV), Rhino virus, and influenza, using blood samples from healthy human subjects. These data were acquired in three challenge studies, each executed after receiving institutional review board (IRB) approval from Duke University. Comparisons are made between several alternative means of per-forming nonparametric factor analysis on these data, with comparisons as well to sparse-PCA and Penalized Matrix Decomposition (PMD), closely related non-Bayesian approaches. CONCLUSIONS: Applying the Beta Process to the factor scores, or to the singular values of a pseudo-SVD construction, the proposed algorithms infer the number of factors in gene-expression data. For real data the "true" number of factors is unknown; in our simulations we consider a range of noise variances, and the proposed Bayesian models inferred the number of factors accurately relative to other methods in the literature, such as sparse-PCA and PMD. We have also identified a "pan-viral" factor of importance for each of the three viruses considered in this study. We have identified a set of genes associated with this pan-viral factor, of interest for early detection of such viruses based upon the host response, as quantified via gene-expression data.

Sticky central limit theorems on open books

Given a probability distribution on an open book (a metric space obtained by gluing a disjoint union of copies of a half-space along their boundary hyperplanes), we define a precise concept of when the Fréchet mean (barycenter) is sticky. This nonclassical phenomenon is quantified by a law of large numbers (LLN) stating that the empirical mean eventually almost surely lies on the (codimension 1 and hence measure 0) spine that is the glued hyperplane, and a central limit theorem (CLT) stating that the limiting distribution is Gaussian and supported on the spine.We also state versions of the LLN and CLT for the cases where the mean is nonsticky (i.e., not lying on the spine) and partly sticky (i.e., is, on the spine but not sticky). © Institute of Mathematical Statistics, 2013.

Local kinetic interpretation of entropy production through reversed diffusion.

The time reversal of stochastic diffusion processes is revisited with emphasis on the physical meaning of the time-reversed drift and the noise prescription in the case of multiplicative noise. The local kinematics and mechanics of free diffusion are linked to the hydrodynamic description. These properties also provide an interpretation of the Pope-Ching formula for the steady-state probability density function along with a geometric interpretation of the fluctuation-dissipation relation. Finally, the statistics of the local entropy production rate of diffusion are discussed in the light of local diffusion properties, and a stochastic differential equation for entropy production is obtained using the Girsanov theorem for reversed diffusion. The results are illustrated for the Ornstein-Uhlenbeck process.

Opportunistic Control Over Shared Wireless Channels

© 2015 IEEE.We consider a wireless control architecture with multiple control loops over a shared wireless medium. A scheduler observes the random channel conditions that each control system experiences over the shared medium and opportunistically selects systems to transmit at a set of non-overlapping frequencies. The transmit power of each system also adapts to channel conditions and determines the probability of successfully receiving and closing the loop. We formulate the optimal design of channel-aware scheduling and power allocation that minimize the total power consumption while meeting control performance requirements for all systems. In particular, it is required that for each control system a given Lyapunov function decreases at a specified rate in expectation over the random channel conditions. We develop an offline algorithm to find the optimal communication design, as well as an online protocol which selects scheduling and power variables based on a random observed channel sequence and converges almost surely to the optimal operating point. Simulations illustrate the power savings of our approach compared to other non-channel-aware schemes.

Influence of network topology and data collection on network inference.

We recently developed an approach for testing the accuracy of network inference algorithms by applying them to biologically realistic simulations with known network topology. Here, we seek to determine the degree to which the network topology and data sampling regime influence the ability of our Bayesian network inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks. NETWORKINFERENCE performed well at recovering feedback loops and multiple targets of a regulator with small amounts of data, but required more data to recover multiple regulators of a gene. When collecting the same number of data samples at different intervals from the system, the best recovery was produced by sampling intervals long enough such that sampling covered propagation of regulation through the network but not so long such that intervals missed internal dynamics. These results further elucidate the possibilities and limitations of network inference based on biological data.

A Video Game-Integrated Electromyography Biofeedback Device for Use in Physical Therapy

We present a novel system to be used in the rehabilitation of patients with forearm injuries. The system uses surface electromyography (sEMG) recordings from a wireless sleeve to control video games designed to provide engaging biofeedback to the user. An integrated hardware/software system uses a neural net to classify the signals from a user’s muscles as they perform one of a number of common forearm physical therapy exercises. These classifications are used as input for a suite of video games that have been custom-designed to hold the patient’s attention and decrease the risk of noncompliance with the physical therapy regimen necessary to regain full function in the injured limb. The data is transmitted wirelessly from the on-sleeve board to a laptop computer using a custom-designed signal-processing algorithm that filters and compresses the data prior to transmission. We believe that this system has the potential to significantly improve the patient experience and efficacy of physical therapy using biofeedback that leverages the compelling nature of video games.

Relations, residuals, regular interiors, and relative regular equivalence

Given a relation α (a binary sociogram) and an a priori equivalence relation π, both on the same set of individuals, it is interesting to look for the largest equivalence πo that is contained in and is regular with respect to α. The equivalence relation πo is called the regular interior of π with respect to α. The computation of πo involves the left and right residuals, a concept that generalized group inverses to the algebra of relations. A polynomial-time procedure is presented (Theorem 11) and illustrated with examples. In particular, the regular interior gives meet in the lattice of regular equivalences: the regular meet of regular equivalences is the regular interior of their intersection. Finally, the concept of relative regular equivalence is defined and compared with regular equivalence.

Applications of Feller-Reuter-Riley transition functions

A Feller–Reuter–Riley function is a Markov transition function whose corresponding semigroup maps the set of the real-valued continuous functions vanishing at infinity into itself. The aim of this paper is to investigate applications of such functions in the dual problem, Markov branching processes, and the Williams-matrix. The remarkable property of a Feller–Reuter–Riley function is that it is a Feller minimal transition function with a stable q-matrix. By using this property we are able to prove that, in the theory of branching processes, the branching property is equivalent to the requirement that the corresponding transition function satisfies the Kolmogorov forward equations associated with a stable q-matrix. It follows that the probabilistic definition and the analytic definition for Markov branching processes are actually equivalent. Also, by using this property, together with the Resolvent Decomposition Theorem, a simple analytical proof of the Williams' existence theorem with respect to the Williams-matrix is obtained. The close link between the dual problem and the Feller–Reuter–Riley transition functions is revealed. It enables us to prove that a dual transition function must satisfy the Kolmogorov forward equations. A necessary and sufficient condition for a dual transition function satisfying the Kolmogorov backward equations is also provided.

What students can tell about lecturers when they are teaching: manifestations of confident and under-confident lecturers

Delivering a lecture requires confidence, a sound knowledge and well developed teaching skills (Cooper and Simonds, 2007, Quinn and Hughes, 2007). However, practitioners who are new to lecturing large groups in higher education may initially lack the confidence to do so which can manifest itself in their verbal and non-verbal cues and the fluency of their teaching skills. This results in the perception that students can identify the confident and non-confident teacher during a lecture (Street, 2007) and so potentially contributing to a lecturer’s level of anxiety prior to, and during, a lecture. Therefore, in the current educational climate of consumerisation, with the increased evaluation of teaching by students, having the ability to deliver high-quality, informed, and interesting lectures assumes greater significance for both lecturers and universities (Carr, 2007; Higher Education Founding Council 2008, Glass et al., 2006). This paper will present both the quantitative and qualitative data from a two-phase mixed method study with 75 nurse lecturers and 62 nursing students in one university in the United Kingdom. The study investigated the notion that lecturing has similarities to acting (Street, 2007). The findings presented here are concerned with how students perceived lecturers’ level of confidence and how lecturers believed they demonstrated confidence. In phase one a specifically designed questionnaire was distributed to both lecturers and students and a response rate of 91% (n=125) was achieved, while in phase two 12 in-depth semi-structured interviews were conducted with lecturers. Results suggested that students in a lecture could identify if the lecturer was confident or not by the way they performed a lecture. Students identified 57 manifestations of non-confidence and lecturers identified 85, while 57 manifestations of confidence were identified by students and 88 by lecturers. Overall, these fell into 12 main converse categories, ranging from body language to the use of space within the room. Both students and lecturers ranked body language, vocal qualities, delivery skills, involving the students and the ability to share knowledge as the most evident manifestations of confidence. Elements like good eye contact, smiling, speaking clearly and being fluent in the use of media recourses where all seen as manifestations confidence, conversely if these were poorly executed then a presentation of under confidence was evident. Furthermore, if the lecturer appeared enthusiastic it was clearly underpinned by the manifestation of a highly confidence lecturer who was secure in their knowledge base and teaching abilities: Some lecturers do appear enthusiastic but others don’t. I think the ones that do know what they are talking about, you can see it in their voice and in their lively body language. I think they are also good at involving the students even. I think the good ones are able to turn boring subjects into lively and interesting ones. (Student 50) Significantly more lecturers than students felt the lecturer should appear confident when lecturing. The lecturers stated it was particularly important to do so when they did not feel confident, because they were concerned with appearing capable. It seems that these students and lecturers perceived that expressive and apparently confident lecturers can make a positive impact on student groups in terms of involvement in lectures; the data also suggested the reverse, for the under confident lecturer. Findings from phase two indicated that these lecturers assumed a persona when lecturing, particularly, but not exclusively, when they were nervous. These lecturers went through a process of assuming and maintaining this persona before and during a lecture as a way of promoting their internal perceptions of confidence but also their outward manifestation of confidence. Although assuming a convincing persona may have a degree of deception about it, providing the knowledge communicated is accurate, the deception may aid rather than hinder learning, because enhances the delivery of a lecture. Therefore, the deception of acting a little more confidently than one feels might be justified when the lecturer knows the knowledge they are communicating is correct, unlike the Dr Fox Effect where the person delivering a lecture is an actor and does not know the subject in any detail or depth and where the deception to be justified (Naftulin, et al., 1973). In conclusion, these students and lecturers perceive that confident and enthusiastic lecturers communicate their passion for the subject in an interesting and meaningful manner through the use of their voice, body, space and interactions in such a way that shows confidence in their knowledge as well as their teaching abilities. If lecturers, therefore, can take a step back to consider how they deliver lectures in apparently confident ways this may increase their ability to engage their students and not only help them being perceived as good lecturers, but also contribute to the genuine act of education.

Effects Of Preservation On Wet Weight Dry-Weight Nitrogen And Carbon Contents Of Calanus-Helgolandicus (Crustacea Copepoda)

The lengths, wet and dry weights, nitrogen and carbon contents of fresh, frozen and formaldehyde-fixed specimens of Calanus helgolandicus (Claus) were determined. Samples were collected during May 1980 in the Celtic Sea. Individual Copepodite Stages 3, 4, 5, and Adult Male and Female Stage 6 were measured and analysed, and 36 linear regression equations derived for these variables together with mean values, standard deviations and 95% confidence limits. The range of nitrogen values in the fresh material, expressed as a percentage of dry weight, ranged from 8.08%±0.80 (Copepodite Stage 3) to 10.89%±0.27 (adult female); carbon values changed from 41.6%±3.05 (mean ±95% confidence limits) for Copepodite Stage 3 to 50.97%±2.63 in Copepodite Stage 5. The adult females had a high nitrogen and relatively low carbon content, while the converse was true for Stage 5 copepodites. There was a loss of dry weight from the frozen samples (57%) and the fixed samples (38%) compared with the mean of the fresh dry weight of all stages. The material lost from the copepods was rich in nitrogen, thus, artificially high percentage carbon values were determined from the frozen and fixed samples (52.0 to 60.3% and 44.7 to 58.5%, respectively).

Vertical Distributions Of Calanus-Finmarchicus And Calanus-Helgolandicus (Crustacea Copepoda)

The vertical distributions of the spring populations of Calanus finmarchicus (Gunnerus) and C. helgolandicus Claus are described and compared. The differences we observed between the two species have probably confused the understanding of the vertical distribution and development of the populations of Calanus spp. in the shelf seas around the United Kingdom where the species occur together. The results imply that these two congeneric species have different behaviour patterns which minimise interspecific competition where the species have sympatric distributions. C. finmarchicus has its younger development stages overlying the older stages in the water column. In C. helgolandicus the converse is true; i. e., the majority of the populations of Stage I and II copepodites of the first spring generations are found below the thermocline. It is also suggested that the different behaviour patterns lead to different feeding regimes and strategies.

Oceans and Human Health (OHH): a European Perspective from the Marine Board of the European Science Foundation (Marine Board-ESF)

The oceans and coastal seas provide mankind with many benefits including food for around a third of the global population, the air that we breathe and our climate system which enables habitation of much of the planet. However, the converse is that generation of natural events (such as hurricanes, severe storms and tsunamis) can have devastating impacts on coastal populations, while pollution of the seas by pathogens and toxic waste can cause illness and death in humans and animals. Harmful effects from biogenic toxins produced by algal blooms (HABs) and from the pathogens associated with microbial pollution are also a health hazard in seafood and from direct contact with water. The overall global burden of human disease caused by sewage pollution of coastal waters has been estimated at 4 million lost person-years annually. Finally, the impacts of all of these issues will be exacerbated by climate change. A holistic systems approach is needed. It must consider whole ecosystems, and their sustainability, such as integrated coastal zone management, is necessary to address the highly interconnected scientific challenges of increased human population pressure, pollution and over-exploitation of food (and other) resources as drivers of adverse ecological, social and economic impacts. There is also an urgent and critical requirement for effective and integrated public health solutions to be developed through the formulation of politically and environmentally meaningful policies. The research community required to address "Oceans & Human Health" in Europe is currently very fragmented, and recognition by policy makers of some of the problems, outlined in the list of challenges above, is limited. Nevertheless, relevant key policy issues for governments worldwide include the reduction of the burden of disease (including the early detection of emerging pathogens and other threats) and improving the quality of the global environment. Failure to effectively address these issues will impact adversely on efforts to alleviate poverty, sustain the availability of environmental goods and services and improve health and social and economic stability; and thus, will impinge on many policy decisions, both nationally and internationally. Knowledge exchange (KE) will be a key element of any ensuing research. KE will facilitate the integration of biological, medical, epidemiological, social and economic disciplines, as well as the emergence of synergies between seemingly unconnected areas of science and socio-economic issues, and will help to leverage knowledge transfer across the European Union (EU) and beyond. An integrated interdisciplinary systems approach is an effective way to bring together the appropriate groups of scientists, social scientists, economists, industry and other stakeholders with the policy formulators in order to address the complexities of interfacial problems in the area of environment and human health. The Marine Board of the European Science Foundation Working Group on "Oceans and Human Health" has been charged with developing a position paper on this topic with a view to identifying the scientific, social and economic challenges and making recommendations to the EU on policy-relevant research and development activities in this arena. This paper includes the background to health-related issues linked to the coastal environment and highlights the main arguments for an ecosystem-based whole systems approach.

The effects of blood pressure lowering on development of cognitive impairment and dementia in patients without apparent prior cerebrovascular disease

BACKGROUND: Hypertension and cognitive impairment are prevalent in older people. It is known that hypertension is a direct risk factor for vascular dementia and recent studies have suggested hypertension also impacts upon prevalence of Alzheimer's disease. The question is therefore whether treatment of hypertension lowers the rate of cognitive decline. OBJECTIVES: To assess the effects of blood pressure lowering treatments for the prevention of dementia and cognitive decline in patients with hypertension but no history of cerebrovascular disease. SEARCH STRATEGY: The trials were identified through a search of CDCIG's Specialised Register, CENTRAL, MEDLINE, EMBASE, PsycINFO and CINAHL on 27 April 2005. SELECTION CRITERIA: Randomized, double-blind, placebo controlled trials in which pharmacological or non-pharmacological interventions to lower blood pressure were given for at least six months. DATA COLLECTION AND ANALYSIS: Two independent reviewers assessed trial quality and extracted data. The following outcomes were assessed: incidence of dementia, cognitive change from baseline, blood pressure level, incidence and severity of side effects and quality of life. MAIN RESULTS: Three trials including 12,091 hypertensive subjects were identified. Average age was 72.8 years. Participants were recruited from industrialised countries. Mean blood pressure at entry across the studies was 170/84 mmHg. All trials instituted a stepped care approach to hypertension treatment, starting with a calcium-channel blocker, a diuretic or an angiotensin receptor blocker. The combined result of the three trials reporting incidence of dementia indicated no significant difference between treatment and placebo (Odds Ratio (OR) = 0.89, 95% CI 0.69, 1.16). Blood pressure reduction resulted in a 11% relative risk reduction of dementia in patients with no prior cerebrovascular disease but this effect was not statistically significant (p = 0.38) and there was considerable heterogeneity between the trials. The combined results from the two trials reporting change in Mini Mental State Examination (MMSE) did not indicate a benefit from treatment (Weighted Mean Difference (WMD) = 0.10, 95% CI -0.03, 0.23). Both systolic and diastolic blood pressure levels were reduced significantly in the two trials assessing this outcome (WMD = -7.53, 95% CI -8.28, -6.77 for systolic blood pressure, WMD = -3.87, 95% CI -4.25, -3.50 for diastolic blood pressure).Two trials reported adverse effects requiring discontinuation of treatment and the combined results indicated a significant benefit from placebo (OR = 1.18, 95% CI 1.06, 1.30). When analysed separately, however, more patients on placebo in SCOPE were likely to discontinue treatment due to side effects; the converse was true in SHEP 1991. Quality of life data could not be analysed in the three studies. There was difficulty with the control group in this review as many of the control subjects received antihypertensive treatment because their blood pressures exceeded pre-set values. In most cases the study became a comparison between the study drug against a usual antihypertensive regimen. AUTHORS' CONCLUSIONS: There was no convincing evidence from the trials identified that blood pressure lowering prevents the development of dementia or cognitive impairment in hypertensive patients with no apparent prior cerebrovascular disease. There were significant problems identified with analysing the data, however, due to the number of patients lost to follow-up and the number of placebo patients given active treatment. This introduced bias. More robust results may be obtained by analysing one year data to reduce differential drop-out or by conducting a meta-analysis using individual patient data.

Hall conditions for edge-weighted bipartite graphs

A weighted variant of Hall's condition for the existence of matchings is shown to be equivalent to the existence of a matching in a lexicographic product. This is used to introduce characterizations of those bipartite graphs whose edges may be replicated so as to yield semiregular multigraphs or, equivalently, semiregular edge-weightings. Such bipartite graphs will be called semiregularizable. Some infinite families of semiregularizable trees are described and all semiregularizable trees on at most 11 vertices are listed. Matrix analogues of some of the results are mentioned and are shown to imply some of the known characterizations of regularizable graphs.

On subspace lattices II. Continuity of Lat

We study the continuity of the map Lat sending an ultraweakly closed operator algebra to its invariant subspace lattice. We provide an example showing that Lat is in general discontinuous and give sufficient conditions for the restricted continuity of this map. As consequences we obtain that Lat is continuous on the classes of von Neumann and Arveson algebras and give a general approximative criterion for reflexivity, which extends Arvesonâ??s theorem on the reflexivity of commutative subspace lattices.