Unsupervised Bayesian linear unmixing of gene expression microarrays

Background: This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expression microarrays. The basis for uBLU is a Bayesian model for the data samples which are represented as an additive mixture of random positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a specific sample. The particularity of the proposed method is that uBLU constrains the factor loadings to be non-negative and the factor scores to be probability distributions over the factors. Furthermore, it also provides estimates of the number of factors. A Gibbs sampling strategy is adopted here to generate random samples according to the posterior distribution of the factors, factor scores, and number of factors. These samples are then used to estimate all the unknown parameters. Results: Firstly, the proposed uBLU method is applied to several simulated datasets with known ground truth and compared with previous factor decomposition methods, such as principal component analysis (PCA), non negative matrix factorization (NMF), Bayesian factor regression modeling (BFRM), and the gradient-based algorithm for general matrix factorization (GB-GMF). Secondly, we illustrate the application of uBLU on a real time-evolving gene expression dataset from a recent viral challenge study in which individuals have been inoculated with influenza A/H3N2/Wisconsin. We show that the uBLU method significantly outperforms the other methods on the simulated and real data sets considered here. Conclusions: The results obtained on synthetic and real data illustrate the accuracy of the proposed uBLU method when compared to other factor decomposition methods from the literature (PCA, NMF, BFRM, and GB-GMF). The uBLU method identifies an inflammatory component closely associated with clinical symptom scores collected during the study. Using a constrained model allows recovery of all the inflammatory genes in a single factor

Regular languages and partial commutations

[EN] The closure of a regular language under a [partial] commutation I has been extensively studied. We present new advances on two problems of this area: (1) When is the closure of a regular language under [partial] commutation still regular? (2) Are there any robust classes of languages closed under [partial] commutation? We show that the class Pol(G) of polynomials of group languages is closed under commutation, and under partial commutation when the complement of I in A2 is a transitive relation. We also give a su¿cient graph theoretic condition on I to ensure that the closure of a language of Pol(G) under I-commutation is regular. We exhibit a very robust class of languages W which is closed under commutation. This class contains Pol(G), is decidable and can be de¿ned as the largest positive variety of languages not containing (ab)¿. It is also closed under intersection, union, shu¿e, concatenation, quotients, length-decreasing morphisms and inverses of morphisms. If I is transitive, we show that the closure of a language of W under I-commutation is regular. The proofs are nontrivial and combine several advanced techniques, including combinatorial Ramsey type arguments, algebraic properties of the syntactic monoid, ¿niteness conditions on semigroups and properties of insertion systems. © 2013 Elsevier Inc. All rights reserved[ES] El cierre de un lenguaje regular bajo una conmutación [parcial] $I$ se ha estudiado extensivamente. Presentamos nuevos avances sobre los dos problemas de esta zona: (1) cuando es el cierre de un lenguaje regular bajo ¿conmutación [parcial] todavía regular? (2) Hay alguna clase robusta ¿de idiomas cerraron bajo conmutación [parcial]? Demostramos que la clase \PolG de polinomios de grupo idiomas está cerrada bajo conmutación y bajo conmutación parcial cuando el complemento de $$I en $A ^ 2$ es una relación transitiva. También damos un gráfico suficiente condición teórica en $$I para asegurarse de que el cierre de un lenguaje de \PolG$$ bajo $lo$-conmutación es regular. Exhibimos un muy robusto clase de idiomas \cW que es cerrado bajo conmutación. Esta clase contiene \PolG$$, es decidible y puede definirse como el más grande positiva variedad de idiomas que no contengan $(ab) ^ *$. También es cerrado bajo intersección, Unión, shuffle, concatenación, cocientes, longitud decreciente morfismos e inversas de morfismos. Si $$I es transitivo, demostramos que el cierre de un lenguaje de \cW bajo $Lo$-conmutación es regular. Las pruebas son no triviales y se combinan varias técnicas avanzadas, incluyendo el tipo de Ramsey combinatoria argumentos, propiedades algebraicas de la monoid sintáctica, finito condiciones sobre semigrupos y propiedades de los sistemas de inserción.The first author was supported by the project Automatas en dispositivos moviles: interfaces de usuario y realidad aumentada (PAID 2019-06-11) supported by Universidad Politecnica de Valencia. The third author was supported by the project ANR 2010 BLAN 0202 02 FREC.Cano Gómez, A.; Guaiana, G.; Pin, J. (2013). Regular languages and partial commutations. Information and Computation. 230:76-96. https://doi.org/10.1016/j.ic.2013.07.003S769623

Algorithmic Complexity for Short Binary Strings Applied to Psychology: A Primer

Since human randomness production has been studied and widely used to assess executive functions (especially inhibition), many measures have been suggested to assess the degree to which a sequence is random-like. However, each of them focuses on one feature of randomness, leading authors to have to use multiple measures. Here we describe and advocate for the use of the accepted universal measure for randomness based on algorithmic complexity, by means of a novel previously presented technique using the the definition of algorithmic probability. A re-analysis of the classical Radio Zenith data in the light of the proposed measure and methodology is provided as a study case of an application.Comment: To appear in Behavior Research Method

The socio-economic impact of pre-trial detention in Kenya, Mozambique and Zambia

The presumed link between the rule of law and development suggests that an operational justice system is key to development. The research sought to understand and quantify how the decision to detain an accused person affects his or her socio-economic situation. Data was collected in Kenya, Mozambique and Zambia. The findings suggest that the use of the coercive power of the state exercised through the deprivation of an individual’s liberty has serious socio-economic consequences. While detention pending trial is justifiable sometimes, we argue that it is over-used, frequently resulting in excessively long detention. The deprivation of liberty interferes with the ability of individuals to be agents of their own development, infringing on socio-economic rights of individuals and their dependents. States can justify such infringements only if their coercive power is used within the ambit of democratic and rights-respecting laws complying with human rights standards

Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005

BACKGROUND The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.This work was partially supported by salaries from the NOAA Coral Reef Conservation Program to the NOAA Coral Reef Conservation Program authors. NOAA provided funding to Caribbean ReefCheck investigators to undertake surveys of bleaching and mortality. Otherwise, no funding from outside authors' institutions was necessary for the undertaking of this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

The stimulus for the water-balance response to dehydration in toads

1. 1. Changes in rates of water exchange similar to those caused by dehydration (enhanced cutaneous uptake and reduced urinary loss) are elicited by injection of hyperosmotic solutions of NaCl or sucrose.2. 2. Rates of water exchange bear the same relation to plasma sodium concentration in both dehydrated and NaCl loaded toads.3. 3. Injection of a hyperosmotic urea solution does not affect rates of water exchange.4. 4. Loss of blood causes toads to take up amounts of water greater than those excreted.5. 5. Small volumes of plasma from dehydrated toads cause cutaneous water uptake to exceed urine production when injected into hydrated individuals.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/32011/1/0000053.pd

"What Do They Want Me To Say?" The hidden curriculum at work in the medical school selection process: a qualitative study

<p>Abstract</p> <p>Background</p> <p>There has been little study of the role of the essay question in selection for medical school. The purpose of this study was to obtain a better understanding of how applicants approached the essay questions used in selection at our medical school in 2007.</p> <p>Methods</p> <p>The authors conducted a qualitative analysis of 210 essays written as part of the medical school admissions process, and developed a conceptual framework to describe the relationships, ideas and concepts observed in the data.</p> <p>Results</p> <p>Findings of this analysis were confirmed in interviews with applicants and assessors. Analysis revealed a tension between "genuine" and "expected" responses that we believe applicants experience when choosing how to answer questions in the admissions process. A theory named "What do they want me to say?" was developed to describe the ways in which applicants modulate their responses to conform to their expectations of the selection process; the elements of this theory were confirmed in interviews with applicants and assessors.</p> <p>Conclusions</p> <p>This work suggests the existence of a "hidden curriculum of admissions" and demonstrates that the process of selection has a strong influence on applicant response. This paper suggests ways that selection might be modified to address this effect. Studies such as this can help us to appreciate the unintended consequences of admissions processes and can identify ways to make the selection process more consistent, transparent and fair.</p