Stability analysis of mixtures of mutagenetic trees

<p>Abstract</p> <p>Background</p> <p>Mixture models of mutagenetic trees are evolutionary models that capture several pathways of ordered accumulation of genetic events observed in different subsets of patients. They were used to model HIV progression by accumulation of resistance mutations in the viral genome under drug pressure and cancer progression by accumulation of chromosomal aberrations in tumor cells. From the mixture models a genetic progression score (GPS) can be derived that estimates the genetic status of single patients according to the corresponding progression along the tree models. GPS values were shown to have predictive power for estimating drug resistance in HIV or the survival time in cancer. Still, the reliability of the exact values of such complex markers derived from graphical models can be questioned.</p> <p>Results</p> <p>In a simulation study, we analyzed various aspects of the stability of estimated mutagenetic trees mixture models. It turned out that the induced probabilistic distributions and the tree topologies are recovered with high precision by an EM-like learning algorithm. However, only for models with just one major model component, also GPS values of single patients can be reliably estimated.</p> <p>Conclusion</p> <p>It is encouraging that the estimation process of mutagenetic trees mixture models can be performed with high confidence regarding induced probability distributions and the general shape of the tree topologies. For a model with only one major disease progression process, even genetic progression scores for single patients can be reliably estimated. However, for models with more than one relevant component, alternative measures should be introduced for estimating the stage of disease progression.</p

Natural images from the birthplace of the human eye

Here we introduce a database of calibrated natural images publicly available through an easy-to-use web interface. Using a Nikon D70 digital SLR camera, we acquired about 5000 six-megapixel images of Okavango Delta of Botswana, a tropical savanna habitat similar to where the human eye is thought to have evolved. Some sequences of images were captured unsystematically while following a baboon troop, while others were designed to vary a single parameter such as aperture, object distance, time of day or position on the horizon. Images are available in the raw RGB format and in grayscale. Images are also available in units relevant to the physiology of human cone photoreceptors, where pixel values represent the expected number of photoisomerizations per second for cones sensitive to long (L), medium (M) and short (S) wavelengths. This database is distributed under a Creative Commons Attribution-Noncommercial Unported license to facilitate research in computer vision, psychophysics of perception, and visual neuroscience.Comment: Submitted to PLoS ON

Interplay of quantum and classical fluctuations near quantum critical points

For a system near a quantum critical point (QCP), above its lower critical dimension $d_L$, there is in general a critical line of second order phase transitions that separates the broken symmetry phase at finite temperatures from the disordered phase. The phase transitions along this line are governed by thermal critical exponents that are different from those associated with the quantum critical point. We point out that, if the effective dimension of the QCP, $d_{eff}=d+z$ ($d$ is the Euclidean dimension of the system and $z$ the dynamic quantum critical exponent) is above its upper critical dimension $d_C$, there is an intermingle of classical (thermal) and quantum critical fluctuations near the QCP. This is due to the breakdown of the generalized scaling relation $\psi=\nu z$ between the shift exponent $\psi$ of the critical line and the crossover exponent $\nu z$, for $d+z>d_C$ by a \textit{dangerous irrelevant interaction}. This phenomenon has clear experimental consequences, like the suppression of the amplitude of classical critical fluctuations near the line of finite temperature phase transitions as the critical temperature is reduced approaching the QCP.Comment: 10 pages, 6 figures, to be published in Brazilian Journal of Physic

Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.)

The date palm (Phoenix dactylifera L.), famed for its sugar-rich fruits (dates) and cultivated by humans since 4,000 B.C., is an economically important crop in the Middle East, Northern Africa, and increasingly other places where climates are suitable. Despite a long history of human cultivation, the understanding of P. dactylifera genetics and molecular biology are rather limited, hindered by lack of basic data in high quality from genomics and transcriptomics. Here we report a large-scale effort in generating gene models (assembled expressed sequence tags or ESTs and mapped to a genome assembly) for P. dactylifera, using the long-read pyrosequencing platform (Roche/454 GS FLX Titanium) in high coverage. We built fourteen cDNA libraries from different P. dactylifera tissues (cultivar Khalas) and acquired 15,778,993 raw sequencing reads—about one million sequencing reads per library—and the pooled sequences were assembled into 67,651 non-redundant contigs and 301,978 singletons. We annotated 52,725 contigs based on the plant databases and 45 contigs based on functional domains referencing to the Pfam database. From the annotated contigs, we assigned GO (Gene Ontology) terms to 36,086 contigs and KEGG pathways to 7,032 contigs. Our comparative analysis showed that 70.6 % (47,930), 69.4 % (47,089), 68.4 % (46,441), and 69.3 % (47,048) of the P. dactylifera gene models are shared with rice, sorghum, Arabidopsis, and grapevine, respectively. We also assigned our gene models into house-keeping and tissue-specific genes based on their tissue specificity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11103-012-9924-z) contains supplementary material, which is available to authorized users

Religious Experience and the Modernist Novel

Output Type: Book Revie