Maximum likelihood estimation of Gaussian mixture models using stochastic search

Cataloged from PDF version of article.Gaussian mixture models (GMM), commonly used in pattern recognition and machine learning, provide a flexible probabilistic model for the data. The conventional expectation-maximization (EM) algorithm for the maximum likelihood estimation of the parameters of GMMs is very sensitive to initialization and easily gets trapped in local maxima. Stochastic search algorithms have been popular alternatives for global optimization but their uses for GMM estimation have been limited to constrained models using identity or diagonal covariance matrices. Our major contributions in this paper are twofold. First, we present a novel parametrization for arbitrary covariance matrices that allow independent updating of individual parameters while retaining validity of the resultant matrices. Second, we propose an effective parameter matching technique to mitigate the issues related with the existence of multiple candidate solutions that are equivalent under permutations of the GMM components. Experiments on synthetic and real data sets show that the proposed framework has a robust performance and achieves significantly higher likelihood values than the EM algorithm. (C) 2012 Elsevier Ltd. All rights reserved

Heating of magnetic fluid systems driven by circularly polarized magnetic field

Cataloged from PDF version of article.A theory is presented to calculate the heat dissipation of a magnetic suspension, a ferrofluid, driven by7 circularly polarized magnetic field. Theory is tested by in vitro experiments and it is shown that, regardless of the character of the relaxation process, linearly and circularly polarized magnetic field excitations, having the same root-mean-square magnitude, are equivalent in terms of heating efficiency. (C) 2010 Elsevier B.V. All rights reserved

Tsetse fly (Glossina pallidipes) midgut responses to Trypanosoma brucei challenge

Abstract Background Tsetse flies (Glossina spp.) are the prominent vector of African trypanosome parasites (Trypanosoma spp.) in sub-Saharan Africa, and Glossina pallidipes is the most widely distributed species in Kenya. This species displays strong resistance to infection by parasites, which are typically eliminated in the midgut shortly after acquisition from the mammalian host. Although extensive molecular information on immunity for the related species Glossina morsitans morsitans exists, similar information is scarce for G. pallidipes. Methods To determine temporal transcriptional responses of G. pallidipes to Trypanosoma brucei brucei challenge, we conducted Illumina based RNA-seq on midgut organ and carcass from teneral females G. pallidipes at 24 and 48 h post-challenge (hpc) with T. b. brucei relative to their respective controls that received normal blood meals (without the parasite). We used a suite of bioinformatics tools to determine differentially expressed and enriched transcripts between and among tissues, and to identify expanded transcripts in G. pallidipes relative to their orthologs G. m. morsitans. Results Midgut transcripts induced at 24 hpc encoded proteins were associated with lipid remodelling, proteolysis, collagen metabolism, apoptosis, and cell growth. Midgut transcripts induced at 48 hpc encoded proteins linked to embryonic growth and development, serine endopeptidases and proteosomal degradation of the target protein, mRNA translation and neuronal development. Temporal expression of immune responsive transcripts at 48 relative to 24 hpc was pronounced, indicative of a gradual induction of host immune responses the following challenge. We also searched for G. m. morsitans orthologous groups that may have experienced expansions in the G. pallidipes genome. We identified ten expanded groups in G. pallidipes with putative immunity-related functions, which may play a role in the higher refractoriness exhibited by this species. Conclusions There appears to be a lack of strong immune responses elicited by gut epithelia of teneral adults. This in combination with a compromised peritrophic matrix at this stage during the initial phase of T. b. brucei challenge may facilitate the increased parasite infection establishment noted in teneral flies relative to older adults. Although teneral flies are more susceptible than older adults, the majority of tenerals are still able to eliminate parasite infections. Hence, robust responses elicited at a later time point, such as 72 hpc, may clear parasite infections from the majority of flies. The expanded G. m. morsitans orthologous groups in G. pallidipes may also be functionally associated with the enhanced refractoriness to trypanosome infections reported in G. pallidipes relative to G. m. morsitans

Phase diagram of Fe-doped Ni-Mn-Ga ferromagnetic shape-memory alloys

We have studied the effect of Fe addition on the structural and magnetic transitions in the magnetic shape memory alloy Ni-Mn-Ga by substituting systematically each atomic species by Fe. Calorimetric and AC susceptibility measurements have been carried out in order to study the magnetic and structural transformation properties. We find that the addition of Fe modifies the structural and magnetic transformation temperatures. Magnetic transition temperatures are displaced to higher values when Fe is substituted into Ni-Mn-Ga, while martensitic and premartensitic transformation temperatures shift to lower values. Moreover, it has been found that the electron per atom concentration essentially governs the phase stability in the quaternary system. However, the observed scaling of transition temperatures with $e/a$ differs from that reported in the related ternary system Ni-Mn-Ga.Comment: 8 pages, 8 figures. Accepted for publication in the Physical Review

The atypical E2F family member E2F7 couples the p53 and RB pathways during cellular senescence

Oncogene-induced senescence is an anti-proliferative stress response program that acts as a fail-safe mechanism to limit oncogenic transformation and is regulated by the retinoblastoma protein (RB) and p53 tumor suppressor pathways. We identify the atypical E2F family member E2F7 as the only E2F transcription factor potently up-regulated during oncogene-induced senescence, a setting where it acts in response to p53 as a direct transcriptional target. Once induced, E2F7 binds and represses a series of E2F target genes and cooperates with RB to efficiently promote cell cycle arrest and limit oncogenic transformation. Disruption of RB triggers a further increase in E2F7, which induces a second cell cycle checkpoint that prevents unconstrained cell division despite aberrant DNA replication. Mechanistically, E2F7 compensates for the loss of RB in repressing mitotic E2F target genes. Together, our results identify a causal role for E2F7 in cellular senescence and uncover a novel link between the RB and p53 pathways

Integrating biological pathways and genomic profiles with ChiBE 2

Cataloged from PDF version of article.Background: Dynamic visual exploration of detailed pathway information can help researchers digest and interpret complex mechanisms and genomic datasets. Results: ChiBE is a free, open-source software tool for visualizing, querying, and analyzing human biological pathways in BioPAX format. The recently released version 2 can search for neighborhoods, paths between molecules, and common regulators/targets of molecules, on large integrated cellular networks in the Pathway Commons database as well as in local BioPAX models. Resulting networks can be automatically laid out for visualization using a graphically rich, process-centric notation. Profiling data from the cBioPortal for Cancer Genomics and expression data from the Gene Expression Omnibus can be overlaid on these networks. Conclusions: ChiBE's new capabilities are organized around a genomics-oriented workflow and offer a unique comprehensive pathway analysis solution for genomics researchers

Social Identity and Social Value Orientations

This study provides an extension of the social value orientation model and a tool, other-other Decomposed Games, to quantify the influence of social iden- tity on social value orientations. Social identity is induced experimentally using the minimal group paradigm. Subsequently, the weights subjects add to the outcomes of outgroup others relative to ingroup others and to the absolute difference between the outcomes of ingroup and outgroup others are estimated. Results are compared to a control condition in which social identity is not induced. Results show that when the outgroup is better off than the ingroup, the average subject is spiteful: they derive negative utility from the outcomes of the outgroup other. When the ougroup is worse off than the ingroup, the average subject attaches similar weights to the outcomes of outgroup and ingroup others. There is also significant variation across subjects with respect to the level of ingroup bias

H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence

Cellular senescence is a tumor-suppressive program that involves chromatin reorganization and specific changes in gene expression that trigger an irreversible cell-cycle arrest. Here we combine quantitative mass spectrometry, ChIP deep-sequencing, and functional studies to determine the role of histone modifications on chromatin structure and gene-expression alterations associated with senescence in primary human cells. We uncover distinct senescence-associated changes in histone-modification patterns consistent with a repressive chromatin environment and link the establishment of one of these patterns-loss of H3K4 methylation-to the retinoblastoma tumor suppressor and the H3K4 demethylases Jarid1a and Jarid1b. Our results show that Jarid1a/b-mediated H3K4 demethylation contributes to silencing of retinoblastoma target genes in senescent cells, suggesting a mechanism by which retinoblastoma triggers gene silencing. Therefore, we link the Jarid1a and Jarid1b demethylases to a tumor-suppressor network controlling cellular senescence