Genetics in psychiatry: common variant association studies.

Many psychiatric conditions and traits are associated with significant heritability. Genetic risk for psychiatric conditions encompass rare variants, identified due to major effect, as well as common variants, the latter analyzed by association analyses. We review guidelines for common variant association analyses, undertaking after assessing evidence of heritability. We highlight the importance of: suitably large sample sizes; an experimental design that controls for ancestry; careful data cleaning; correction for multiple testing; small P values for positive findings; assessment of effect size for positive findings; and, inclusion of an independent replication sample. We also note the importance of a critical discussion of any prior findings, biological follow-up where possible, and a means of accessing the raw data.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Octonions and the Triple Articulation

Num artigo anterior descrevemos a nossa abordagem para modelar as relações que um ecossistema de negócios pode sustentar para as demandas multi-facetadas dos seus clientes. Esta abordagem distinguia dois tipos de tempo, chronos e kairos, e era triplamente articulada, descrevendo uma empresa como uma realização de possíveis composições de 'capacidades tecnológicas', 'modelos sociais de orquestração e sincronização' e as antecipações de satisfações ‘da diferenciação das organizações dos clientes individuais'. Este artigo descreve os trabalhos subsequentes que necessitaram abandonar os Números Complexos como sua base matemática em favor dos Quaterniones e finalmente adoptar os Octoniones que fornecem um modelo da trialidade, necessário para abstrair as relações entre as articulações. Identificam-se uma série de questões de pesquisa derivadas da abordagem que fornece um meio para relacionar a agilidade necessária para apoiar uma relação dinâmica entre a situação de um cliente individual e a abordagem adoptada para instituir a empresa como um todo.A previous paper described our approach to modeling the relations that a business ecosystem can sustain to the multi-sided demands of its clients. This approach distinguished two kinds of time, chronos and kairos, and was triply articulated, describing an enterprise as a realization of possible compositions of ‘technological capabilities’, ‘social models of orchestration and synchronization’ and ‘the differing organizations of individual clients' anticipations of satisfaction’. This paper describes subsequent work that necessitated abandoning the Complex Numbers as its mathematical basis in favour of the Quaternions and finally adopting the Octonions which provide a model of triality necessary for abstracting the relations between the articulations. It identifies a number of research questions derived from the approach which provides a means of relating the agility needed to support a dynamic relation to an individual client’s situation with the approach taken to instituting the enterprise as a whole

Deconstruction of plant biomass by a Cellulomonas strain isolated from an ultra-basic (lignin-stripping) spring.

Plant material falling into the ultra-basic (pH 11.5-11.9) springs within The Cedars, an actively serpentinizing site in Sonoma County, California, is subject to conditions that mimic the industrial pretreatment of lignocellulosic biomass for biofuel production. We sought to obtain hemicellulolytic/cellulolytic bacteria from The Cedars springs that are capable of withstanding the extreme alkaline conditions wherein calcium hydroxide-rich water removes lignin, making cell wall polysaccharides more accessible to microorganisms and their enzymes. We enriched for such bacteria by adding plant debris from the springs into a synthetic alkaline medium with ground tissue of the biofuel crop switchgrass (Panicum virgatum L.) as the sole source of carbon. From the enrichment culture we isolated the facultative anaerobic bacterium Cellulomonas sp. strain FA1 (NBRC 114238), which tolerates high pH and catabolizes the major plant cell wall-associated polysaccharides cellulose, pectin, and hemicellulose. Strain FA1 in monoculture colonized the plant material and degraded switchgrass at a faster rate than the community from which it was derived. Cells of strain FA1 could be acclimated through subculturing to grow at a maximal concentration of 13.4% ethanol. A strain FA1-encoded β-1, 4-endoxylanase expressed in E. coli was active at a broad pH range, displaying near maximal activity at pH 6-9. Discovery of this bacterium illustrates the value of extreme alkaline springs in the search for microorganisms with potential for consolidated bioprocessing of plant biomass to biofuels and other valuable bio-inspired products

Higher Education Exchange:2005

This annual publication serves as a forum for new ideas and dialogue between scholars and the larger public. Essays explore ways that students, administrators, and faculty can initiate and sustain an ongoing conversation about the public life they share.The Higher Education Exchange is founded on a thought articulated by Thomas Jefferson in 1820: "I know no safe depository of the ultimate powers of the society but the people themselves; and if we think them not enlightened enough to exercise their control with a wholesome discretion, the remedy is not to take it from them, but to inform their discretion by education."In the tradition of Jefferson, the Higher Education Exchange agrees that a central goal of higher education is to help make democracy possible by preparing citizens for public life. The Higher Education Exchange is part of a movement to strengthen higher education's democratic mission and foster a more democratic culture throughout American society.Working in this tradition, the Higher Education Exchange publishes interviews, case studies, analyses, news, and ideas about efforts within higher education to develop more democratic societies

Testing for an Unusual Distribution of Rare Variants

Technological advances make it possible to use high-throughput sequencing as a primary discovery tool of medical genetics, specifically for assaying rare variation. Still this approach faces the analytic challenge that the influence of very rare variants can only be evaluated effectively as a group. A further complication is that any given rare variant could have no effect, could increase risk, or could be protective. We propose here the C-alpha test statistic as a novel approach for testing for the presence of this mixture of effects across a set of rare variants. Unlike existing burden tests, C-alpha, by testing the variance rather than the mean, maintains consistent power when the target set contains both risk and protective variants. Through simulations and analysis of case/control data, we demonstrate good power relative to existing methods that assess the burden of rare variants in individuals

Filtering informal learning in everyday life: invoking ordinariness and moving to civic engagement

This article explores the role of informal learning from television as it is anchored within the ordinariness of daily life. It examines the consequences for pedagogy and civic engagement, questioning how informal learning from television can enhance civic engagement. For many, this learning was localized through personalized and interpersonal relations of everyday life. Learning was not viewed as a distant institutional force, but as an embedded part of an ordinary life. The invoking of ordinariness rendered the relationship between learning and civic engagement unproblematic. Learning was localized in subjective terms for self-identity and interpersonal relations rather than critically reflecting on the power structures of everyday life

Analysis of Rare, Exonic Variation amongst Subjects with Autism Spectrum Disorders and Population Controls

We report on results from whole-exome sequencing (WES) of 1,039 subjects diagnosed with autism spectrum disorders (ASD) and 870 controls selected from the NIMH repository to be of similar ancestry to cases. The WES data came from two centers using different methods to produce sequence and to call variants from it. Therefore, an initial goal was to ensure the distribution of rare variation was similar for data from different centers. This proved straightforward by filtering called variants by fraction of missing data, read depth, and balance of alternative to reference reads. Results were evaluated using seven samples sequenced at both centers and by results from the association study. Next we addressed how the data and/or results from the centers should be combined. Gene-based analyses of association was an obvious choice, but should statistics for association be combined across centers (meta-analysis) or should data be combined and then analyzed (mega-analysis)? Because of the nature of many gene-based tests, we showed by theory and simulations that mega-analysis has better power than meta-analysis. Finally, before analyzing the data for association, we explored the impact of population structure on rare variant analysis in these data. Like other recent studies, we found evidence that population structure can confound case-control studies by the clustering of rare variants in ancestry space; yet, unlike some recent studies, for these data we found that principal component-based analyses were sufficient to control for ancestry and produce test statistics with appropriate distributions. After using a variety of gene-based tests and both meta- and mega-analysis, we found no new risk genes for ASD in this sample. Our results suggest that standard gene-based tests will require much larger samples of cases and controls before being effective for gene discovery, even for a disorder like ASD. © 2013 Liu et al

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

A cure time model for joint prediction of outcome and time-to-outcome

The Cox model has been widely used in time-to-outcome predictions, particularly in studies of medical patients, where prediction of the time of death is desired. In addition, the cure model has been proposed to model times of death for discharged patients. However, neither the Cox model nor the cure model allow explicit cure information and prediction of patient cure times (discharge times). In this paper we propose a new model, the cure time model , which models the static data for dying patients, surviving patients, and their death/cure times jointly. It models (1) mortality via logistic regression and (2) death and discharge times via Cox models. We extend the cure time model to situations with censored data, where neither time of death nor discharge time are known, as well as to multiple (\u3e2) outcomes. In addition, we propose a joint log-odds ratio which can predict the mortality of patients using the information from both the logistic regression and Cox models. We compare our model with the Cox and cure models on a trauma patient dataset from UCSF/San Francisco General Hospital. Our results show that the cure time model more accurately predicts both mortality and time-to-mortality for patients from these datasets

Identification of disease states associated with coagulopathy in trauma.

BackgroundTrauma is the leading cause of death between the ages of 1 to 44 in the United States. Blood loss is the primary cause of these deaths. The discrimination of states through which patients transition would be helpful in understanding the disease process, and in identification of critical states and appropriate interventions. Even though these states are strongly associated with patients' blood composition data, there has not been a way to directly identify them. Statistical tools such as hidden Markov models can be used to infer the discrete latent states from the blood composition data.MethodsWe applied a hidden Markov model to time-series multivariate patient measurements from the UCSF/ San Francisco General Hospital and Trauma Center. Ten blood factor related measurements were used to identify the model: factors II, V, VII, VIII, IX, X, antithrombin III, protein C, prothrombin time and partial thromboplastin time. Missing data in the time-series dataset was considered in the hidden Markov model. The number of states was determined by minimizing the Bayesian information criterion across different numbers of states.ResultsAfter preprocessing, 1090 patients with a total number of 2176 time point measurements were included in the analysis. The hidden Markov model identified 6 disease states and 3 stages. We analyzed their relationships to the blood composition data and the coagulation cascade. The states are very indicative of the disease progression status of patients.ConclusionsSix disease states and 3 stages associated with Coagulopathy in trauma were identified in our study. The hidden Markov model can be useful in identifying latent states by using patients' time-series multivariate data. The information obtained from the states and stages can be useful in the clinical setting