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

Hedgehog Spin-texture and Berry's Phase tuning in a Magnetic Topological Insulator

Understanding and control of spin degrees of freedom on the surfaces of topological materials are key to future applications as well as for realizing novel physics such as the axion electrodynamics associated with time-reversal (TR) symmetry breaking on the surface. We experimentally demonstrate magnetically induced spin reorientation phenomena simultaneous with a Dirac-metal to gapped-insulator transition on the surfaces of manganese-doped Bi2Se3 thin films. The resulting electronic groundstate exhibits unique hedgehog-like spin textures at low energies, which directly demonstrate the mechanics of TR symmetry breaking on the surface. We further show that an insulating gap induced by quantum tunnelling between surfaces exhibits spin texture modulation at low energies but respects TR invariance. These spin phenomena and the control of their Fermi surface geometrical phase first demonstrated in our experiments pave the way for the future realization of many predicted exotic magnetic phenomena of topological origin.Comment: 38 pages, 18 Figures, Includes new text, additional datasets and interpretation beyond arXiv:1206.2090, for the final published version see Nature Physics (2012

Degeneracy: a link between evolvability, robustness and complexity in biological systems

A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as ecosystem services and resilience is well recognized, the broader relationship between robustness and evolution is only starting to be fully appreciated. A renewed interest in this relationship has been prompted by evidence that mutational robustness can play a positive role in the discovery of adaptive innovations (evolvability) and evidence of an intimate relationship between robustness and complexity in biology. This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms. In support of this hypothesis, we present evidence that degeneracy is a fundamental source of robustness, it is intimately tied to multi-scaled complexity, and it establishes conditions that are necessary for system evolvability

Functional hemizygosity in the human genome: direct estimate from twelve erythrocyte enzyme loci

Cord blood samples from 2020 unrelated newborns were screened for levels of enzyme activity for twelve enzymes. The level of enzymatic activity for 100 determinations were consistent with the existence of an enzyme-deficiency allele. The frequency of deficiency alleles in the Black population (0.0071) was four times higher (after removal of the G6PD * A - variant) than in the Caucasian sample (0.0016). These frequencies are approximately double the frequency of rare electrophoretic mobility variants at similar loci in the same population. Given the number of functionally important loci in the human genome, these enzyme deficiency variants could constitute a significant health burden.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47620/1/439_2004_Article_BF00284477.pd

Are one or two simple questions sufficient to detect depression in cancer and palliative care? A Bayesian meta-analysis

The purpose of this study is to examine the value of one or two simple verbal questions in the detection of depression in cancer settings. This study is a systematic literature search of abstract and full text databases to January 2008. Key authors were contacted for unpublished studies. Seventeen analyses were found. Of these, 13 were conducted in late stage palliative settings. (1) Single depression question: across nine studies, the prevalence of depression was 16%. A single ‘depression' question enabled the detection of depression in 160 out of 223 true cases, a sensitivity of 72%, and correctly reassured 964 out of 1166 non-depressed cancer sufferers, a specificity of 83%. The positive predictive value (PPV) was 44% and the negative predictive value (NPV) 94%. (2) Single interest question: there were only three studies examining the ‘loss-of-interest' question, with a combined prevalence of 14%. This question allowed the detection of 60 out of 72 cases (sensitivity 83%) and excluded 394 from 459 non-depressed cases (specificity of 86%). The PPV was 48% and the NPV 97%. (3) Two questions (low mood and low interest): five studies examined two questions with a combined prevalence of 17%. The two-question combination facilitated a diagnosis of depression in 138 of 151 true cases (sensitivity 91%) and gave correct reassurance to 645 of 749 non-cases (specificity 86%). The PPV was 57% and the NPV 98%. Simple verbal methods perform well at excluding depression in the non-depressed but perform poorly at confirming depression. The ‘two question' method is significantly more accurate than either single question but clinicians should not rely on these simple questions alone and should be prepared to assess the patient more thoroughly

School Effects on the Wellbeing of Children and Adolescents

Well-being is a multidimensional construct, with psychological, physical and social components. As theoretical basis to help understand this concept and how it relates to school, we propose the Self-Determination Theory, which contends that self-determined motivation and personality integration, growth and well-being are dependent on a healthy balance of three innate psychological needs of autonomy, relatedness and competence. Thus, current indicators involve school effects on children’s well-being, in many diverse modalities which have been explored. Some are described in this chapter, mainly: the importance of peer relationships; the benefits of friendship; the effects of schools in conjunction with some forms of family influence; the school climate in terms of safety and physical ecology; the relevance of the teacher input; the school goal structure and the implementation of cooperative learning. All these parameters have an influence in promoting optimal functioning among children and increasing their well-being by meeting the above mentioned needs. The empirical support for the importance of schools indicates significant small effects, which often translate into important real-life effects as it is admitted at present. The conclusion is that schools do make a difference in children’s peer relationships and well-being

Determinants of health facility utilization for childbirth in rural western Kenya: cross-sectional study

Background: Skilled attendance at delivery is recognized as one of the most important factors in preventing maternal death. However, more than 50% of births in Kenya still occur in non-institutional locations supported by family members and/or traditional birth attendants (TBAs). To improve this situation, a study of the determinants of facility delivery, including individual, family and community factors, was necessary to consider effective intervention in Kenya.Methods: This study was conducted to identify the factors which influence the place of delivery in rural western Kenya, and to recommend ways to improve women\u27s access to skilled attendants at delivery. A community-based cross-sectional survey was carried out from August to September 2011 in all 64 sub-locations which were covered by community health workers (CHWs). An interviewer-administered questionnaire on seventeen comprehensive variables was administered to 2,560 women who had children aged 12-24 months.Results: The response rate was 79% (n = 2,026). Of the respondents, 48% of births occurred in a health facility and 52% in a non-institutional location. The significant determinants of facility delivery examined using multivariate analysis were: maternal education level, maternal health knowledge, ANC visits, birth interval, economic status of household, number of household members, household sanitation practices and traveling time to nearest health facility.Conclusions: The results suggest that the involvement of TBAs to promote facility delivery is still one of the most important strategies. Strengthening CHWs\u27 performance by focusing on a limited number of topics and clear management guidance might also be an effective intervention. Stressing the importance of regular attendance at ANC (at least four times) would be effective in enhancing motivation for a facility delivery. Based on our findings, those actions to improve the facility delivery rate should focus more on pregnant women who have a low education level, poor health knowledge and short pregnancy spacing. In addition, women with low economic status, a large number of family members and a long distance to travel to a health facility should also be targeted by further interventions

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe