Discovering a junction tree behind a Markov network by a greedy algorithm

In an earlier paper we introduced a special kind of k-width junction tree, called k-th order t-cherry junction tree in order to approximate a joint probability distribution. The approximation is the best if the Kullback-Leibler divergence between the true joint probability distribution and the approximating one is minimal. Finding the best approximating k-width junction tree is NP-complete if k>2. In our earlier paper we also proved that the best approximating k-width junction tree can be embedded into a k-th order t-cherry junction tree. We introduce a greedy algorithm resulting very good approximations in reasonable computing time. In this paper we prove that if the Markov network underlying fullfills some requirements then our greedy algorithm is able to find the true probability distribution or its best approximation in the family of the k-th order t-cherry tree probability distributions. Our algorithm uses just the k-th order marginal probability distributions as input. We compare the results of the greedy algorithm proposed in this paper with the greedy algorithm proposed by Malvestuto in 1991.Comment: The paper was presented at VOCAL 2010 in Veszprem, Hungar

Simpson's Paradox, Lord's Paradox, and Suppression Effects are the same phenomenon – the reversal paradox

This article discusses three statistical paradoxes that pervade epidemiological research: Simpson's paradox, Lord's paradox, and suppression. These paradoxes have important implications for the interpretation of evidence from observational studies. This article uses hypothetical scenarios to illustrate how the three paradoxes are different manifestations of one phenomenon – the reversal paradox – depending on whether the outcome and explanatory variables are categorical, continuous or a combination of both; this renders the issues and remedies for any one to be similar for all three. Although the three statistical paradoxes occur in different types of variables, they share the same characteristic: the association between two variables can be reversed, diminished, or enhanced when another variable is statistically controlled for. Understanding the concepts and theory behind these paradoxes provides insights into some controversial or contradictory research findings. These paradoxes show that prior knowledge and underlying causal theory play an important role in the statistical modelling of epidemiological data, where incorrect use of statistical models might produce consistent, replicable, yet erroneous results

Cytogerontology since 1881: A reappraisal of August Weismann and a review of modern progress

Cytogerontology, the science of cellular ageing, originated in 1881 with the prediction by August Weismann that the somatic cells of higher animals have limited division potential. Weismann's prediction was derived by considering the role of natural selection in regulating the duration of an organism's life. For various reasons, Weismann's ideas on ageing fell into neglect following his death in 1914, and cytogerontology has only reappeared as a major research area following the demonstration by Hayflick and Moorhead in the early 1960s that diploid human fibroblasts are restricted to a finite number of divisions in vitro. In this review we give a detailed account of Weismann's theory, and we reveal that his ideas were both more extensive in their scope and more pertinent to current research than is generally recognised. We also appraise the progress which has been made over the past hundred years in investigating the causes of ageing, with particular emphasis being given to (i) the evolution of ageing, and (ii) ageing at the cellular level. We critically assess the current state of knowledge in these areas and recommend a series of points as primary targets for future research

Vaccinia Virus G8R Protein: A Structural Ortholog of Proliferating Cell Nuclear Antigen (PCNA)

BACKGROUND: Eukaryotic DNA replication involves the synthesis of both a DNA leading and lagging strand, the latter requiring several additional proteins including flap endonuclease (FEN-1) and proliferating cell nuclear antigen (PCNA) in order to remove RNA primers used in the synthesis of Okazaki fragments. Poxviruses are complex viruses (dsDNA genomes) that infect eukaryotes, but surprisingly little is known about the process of DNA replication. Given our previous results that the vaccinia virus (VACV) G5R protein may be structurally similar to a FEN-1-like protein and a recent finding that poxviruses encode a primase function, we undertook a series of in silico analyses to identify whether VACV also encodes a PCNA-like protein. RESULTS: An InterProScan of all VACV proteins using the JIPS software package was used to identify any PCNA-like proteins. The VACV G8R protein was identified as the only vaccinia protein that contained a PCNA-like sliding clamp motif. The VACV G8R protein plays a role in poxvirus late transcription and is known to interact with several other poxvirus proteins including itself. The secondary and tertiary structure of the VACV G8R protein was predicted and compared to the secondary and tertiary structure of both human and yeast PCNA proteins, and a high degree of similarity between all three proteins was noted. CONCLUSIONS: The structure of the VACV G8R protein is predicted to closely resemble the eukaryotic PCNA protein; it possesses several other features including a conserved ubiquitylation and SUMOylation site that suggest that, like its counterpart in T4 bacteriophage (gp45), it may function as a sliding clamp ushering transcription factors to RNA polymerase during late transcription

Mactinin, a fragment of cytoskeletal α-actinin, is a novel inducer of heat shock protein (Hsp)-90 mediated monocyte activation

<p>Abstract</p> <p>Background</p> <p>Monocytes, their progeny such as dendritic cells and osteoclasts and products including tumor necrosis factor (TNF)-α, interleukin (IL)-1α and IL-1β play important roles in cancer, inflammation, immune response and atherosclerosis. We previously showed that mactinin, a degradative fragment of the cytoskeletal protein α-actinin, is present at sites of monocytic activation in vivo, has chemotactic activity for monocytes and promotes monocyte/macrophage maturation. We therefore sought to determine the mechanism by which mactinin stimulates monocytes.</p> <p>Results</p> <p>Radiolabeled mactinin bound to a heterocomplex on monocytes comprised of at least 3 proteins of molecular weight 88 kD, 79 kD and 68 kD. Affinity purification, mass spectroscopy and Western immunoblotting identified heat shock protein (Hsp)-90 as the 88 kD component of this complex. Hsp90 was responsible for mediating the functional effects of mactinin on monocytes, since Hsp90 inhibitors (geldanamycin and its analogues 17-allylamino-17-demethoxygeldanamycin [17-AAG] and 17-(dimethylaminoethylamino)-17-demethoxygeldanamycin [17-DMAG]) almost completely abrogated the stimulatory activity of mactinin on monocytes (production of the pro-inflammatory cytokines IL-1α, IL-1β and TNF-α, as well as monocyte chemotaxis).</p> <p>Conclusion</p> <p>Mactinin is a novel inducer of Hsp90 activity on monocytes and may serve to perpetuate and augment monocytic activation, thereby functioning as a "matrikine." Blockage of this function of mactinin may be useful in diseases where monocyte/macrophage activation and/or Hsp90 activity are detrimental.</p

Queueing Theory an Index Factor for Production Inventory Control in Automotive Industry—A Review

In this paper, various approaches to inventory control within the automotive industry were reviewed using queueing theory. Different models used in past literature were stated and the model considered to be most effective in this review is dock management modeling. This model was used to analyze inventory control and how effectively automotive industries can minimize inventory by getting the component needed in the assembly line just in time, this helps to reduce additional costs for warehouse maintenance and capital tied down in form of excess inventory. Analytical and simulation models are the mathematical models that are considered in this review as they are used in several papers by different authors

Older adult loneliness: myths and realities

The focus in this paper is on the social domain of quality of life, and more particularly loneliness. The empirical literature on older adult loneliness is reviewed, thereby challenging three often-held assumptions that figure prominently in public debates on loneliness. The first assumption that loneliness is a problem specifically for older people finds only partial support. Loneliness is common only among the very old. The second assumption is that people in individualistic societies are most lonely. Contrary to this belief, findings show that older adults in northern European countries tend to be less lonely than those in the more familialistic southern European countries. The scarce data on Central and Eastern Europe suggest a high prevalence of older adult loneliness in those countries. The third assumption that loneliness has increased over the past decades finds no support. Loneliness levels have decreased, albeit slightly. The review notes the persistence of ageist attitudes, and underscores the importance of considering people’s frame of reference and normative orientation in analyses of loneliness