Modeling and visualizing uncertainty in gene expression clusters using Dirichlet process mixtures

Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data, little attention has been paid to uncertainty in the results obtained. Dirichlet process mixture (DPM) models provide a nonparametric Bayesian alternative to the bootstrap approach to modeling uncertainty in gene expression clustering. Most previously published applications of Bayesian model-based clustering methods have been to short time series data. In this paper, we present a case study of the application of nonparametric Bayesian clustering methods to the clustering of high-dimensional nontime series gene expression data using full Gaussian covariances. We use the probability that two genes belong to the same cluster in a DPM model as a measure of the similarity of these gene expression profiles. Conversely, this probability can be used to define a dissimilarity measure, which, for the purposes of visualization, can be input to one of the standard linkage algorithms used for hierarchical clustering. Biologically plausible results are obtained from the Rosetta compendium of expression profiles which extend previously published cluster analyses of this data

Tissue-Specific Transcriptomes Reveal Gene Expression Trajectories in Two Maturing Skin Epithelial Layers in Zebrafish Embryos.

Epithelial cells are the building blocks of many organs, including skin. The vertebrate skin initially consists of two epithelial layers, the outer periderm and inner basal cell layers, which have distinct properties, functions, and fates. The embryonic periderm ultimately disappears during development, whereas basal cells proliferate to form the mature, stratified epidermis. Although much is known about mechanisms of homeostasis in mature skin, relatively little is known about the two cell types in pre-stratification skin. To define the similarities and distinctions between periderm and basal skin epithelial cells, we purified them from zebrafish at early development stages and deeply profiled their gene expression. These analyses identified groups of genes whose tissue enrichment changed at each stage, defining gene flow dynamics of maturing vertebrate epithelia. At each of 52 and 72 hr post-fertilization (hpf), more than 60% of genes enriched in skin cells were similarly expressed in both layers, indicating that they were common epithelial genes, but many others were enriched in one layer or the other. Both expected and novel genes were enriched in periderm and basal cell layers. Genes encoding extracellular matrix, junctional, cytoskeletal, and signaling proteins were prominent among those distinguishing the two epithelial cell types. In situ hybridization and BAC transgenes confirmed our expression data and provided new tools to study zebrafish skin. Collectively, these data provide a resource for studying common and distinguishing features of maturing epithelia

A Reading Study Skills Course for a Community College

The ability to read is no longer limited to the literal meaning of the word, but is increasingly dependent upon the reader\u27s ability to recognize the style of writing, so that he knows whether to apply denotative or connotative meanings to what he is reading. Because reading needs have changed and will continue to change as rapidly as our culture changes, it is necessary to continuously develop and improve reading skills. The purpose of this study is to: (1) enumerate the reading study skills needed by college students, (2) describe the details of a reading study skills program, (3) and to list materials needed for that program

Discovering transcriptional modules by Bayesian data integration

Motivation: We present a method for directly inferring transcriptional modules (TMs) by integrating gene expression and transcription factor binding (ChIP-chip) data. Our model extends a hierarchical Dirichlet process mixture model to allow data fusion on a gene-by-gene basis. This encodes the intuition that co-expression and co-regulation are not necessarily equivalent and hence we do not expect all genes to group similarly in both datasets. In particular, it allows us to identify the subset of genes that share the same structure of transcriptional modules in both datasets. Results: We find that by working on a gene-by-gene basis, our model is able to extract clusters with greater functional coherence than existing methods. By combining gene expression and transcription factor binding (ChIP-chip) data in this way, we are better able to determine the groups of genes that are most likely to represent underlying TMs

Cooperative mixing induced surface roughening in bilayer metals: a possible novel surface damage mechanism

Molecular dynamics simulations have been used to study a collective atomic transport phenomenon by repeated Ar$^+$ irradiations in the Ti/Pt interfacial system. The ion-induced injection of surface atoms to the bulk, the ejection of bulk atoms to the top layers together with surface erosion is strongly enhanced by interfacial mixing. This process leads to a dense interfacial material, and broadening of the interface region. The process scales with the relative difference of the atomic masses. We find that surface roughening and interfacial mixing is strongly coupled via an enhanced counterflow material transport normal to the surface which might be a novel surface damage mechanism. This cooperative phenomenon is active when the bilayer system is subjected to a high dose ion irradiation (multiple ion irradiations) and leads to surface cavity growth.Comment: 6 pages, 6 figures. accepted in Nucl. Instrum. Meth.

Ukrudt i fugleperspektiv

The article describes the possibilities for weed monitoring by small Unmanned Aircraft Systems (UAS). It also describes the ASETA project, which is a multidisciplinary project combining cooperating airborne and ground-based vehicles with advanced sensors to identify the positions of weeds in agricultural fields

My migraine voice survey. aA global study of disease burden among individuals with migraine for whom preventive treatments have failed

Background: Migraine is associated with many debilitating symptoms that affect daily functioning. My Migraine Voice is a large global cross-sectional study aimed at understanding the full burden and impact of migraine directly from patients suffering from ≥4 monthly migraine days (MMDs) with a history of prophylactic treatment failure. Methods: This study was conducted worldwide (31 countries across North and South Americas, Europe, the Middle East and Northern Africa, and the Asia-Pacific region) using an online survey administered to adults with migraine who reported ≥4 MMDs in the 3 months preceding survey administration, with pre-specified criteria of 90% having used preventive migraine treatment (80% with history of ≥1 treatment failure). Prophylactic treatment failure was defined as a reported change in preventive medication by individuals with migraine for any reason, at least once. Results: In total, 11,266 individuals participated in the survey. Seventy-four percent of the participants reported spending time in darkness/isolation due to migraine (average: 19 h/month). While 85% of all respondents reported negative aspects of living with migraine (feeling helpless, depressed, not understood), sleeping difficulties (83%), and fear of the next attack (55%), 57% shared ≥1 positive aspect (learning to cope, becoming a stronger person). Forty-nine percent reported feeling limited in daily activities throughout all migraine phases. Migraine impact on professional, private, or social domains was reported by 87% of respondents (51% in all domains). In the previous 12 months, 38% of respondents had visited the emergency department (average: 3.3 visits), whereas 23% stayed in hospital overnight (average: 3.2 nights) due to migraine. Conclusions: The burden of migraine is substantial among this cohort of individuals with at least 4 migraine days per month and for whom at least 1 preventive migraine treatment had failed. Interestingly, respondents reported some positive aspects in their migraine journey; the greater resilience and strength brought on by coping with migraine suggests that if future treatments could address existing unmet needs, these individuals with migraine will be able to maximize their contribution to society

Accuracy of a method based on atomic absorption spectrometry to determine inorganic arsenic in food : Outcome of the collaborative trial IMEP-41

Peer reviewedPublisher PD

Pottery firing temperatures: A new method for determining the firing temperature of ceramics and burnt clay

A new method for determining the maximum firing temperature of ceramics and burnt clay is presented. The technique relies on measuring the magnetic susceptibility on a step-wise re-fired sample. The validity of the method has been tested by determining firing temperatures of two sets of clay samples fired at temperatures ranging from 400 to 1000 C. Aliquots of the same samples have been studied petrographically by optical microscopy on thin sections and analyzed by powder X-ray diffraction in order to monitor structural and mineralogical changes as a function of temperature. The method is demonstrated on samples from four geographically widely different sites and it is applied to a larger set of ceramics of Late (ca. AD 900eAD 1450) and Inca (ca. AD 1480eAD 1532) periods from the Northwestern Argentine region, dating to a limited period of time prior to the fall of the Inca Empire. The method is shown to be a powerful tool in revealing archaeological information about the change in firing technologies in the pre-Hispanic societies in the Andean area through time.Fil: Rasmussen, Kaare Lund. Technical University of Denmark; DinamarcaFil: de la Fuente, Guillermo Adrian. Universidad Nacional de Catamarca. Escuela de Arqueología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bond, Andrew D.. Technical University of Denmark; DinamarcaFil: Mathiesen, Karsten Korsholm. Technical University of Denmark; DinamarcaFil: Vera, Sergio David. Universidad Nacional de Catamarca. Escuela de Arqueología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Application of Bayesian Networks to the Upper Guadiana Basin

The need for more stakeholder participation is becoming increasingly important in natural resource management and for water resources in particular. There are a number of methods to facilitate the participatory process but in many cases the quality of these methods is difficult to evaluate because of the lack of appropriate benchmarks. Therefore there is a need of researches evaluating participatory process with clear evaluation criteria. This paper describes the development of a participatory decision support system based on Bayesian networks (Bns) and evaluates the implementation of the methodology using selected criteria. The work has been conducted in the Upper Guadiana Basin (UGB) in central Spain, a site of serious water management conflict, where groundwater-based irrigation is the main water consumer, accounting for 95% of the total uses. The uncontrolled exploitation of groundwater resources along several decades has led to an important environmental degradation and significant conflicts among stakeholder groups. The need to find solutions is becoming more urgent since the implementation of the Water Framework requires a good state of water ecosystems in the short term. The participatory building of Bayesian networks was lead to three-fold objectives: (1) To develop a DSS in the UGB, which allows the impacts of different water management options on the groundwater levels and agricultural economy to be evaluated. (2) To improve the knowledge of key water users and provide a platform for dialogue among stakeholders. (3) To evaluate the ability of Bns to provide support in complex conflict situations and as a means to more effectively engage stakeholders in the decision making process. The results obtained show that, in this context, the elaboration of a Bayesian network requires simplification of the problem, which helps stakeholders to understand the elements involved in the problem and the relationships among them. In addition to this, Bayesian networks have proved to be a good tool to deal with stakeholder participation, due to their defined structured elaboration process