On Coupling FCA and MDL in Pattern Mining

International audiencePattern Mining is a well-studied field in Data Mining and Machine Learning. The modern methods are based on dynamically updating models, among which MDL-based ones ensure high-quality pattern sets. Formal concepts also characterize patterns in a condensed form. In this paper we study MDL-based algorithm called Krimp in FCA settings and propose a modified version that benefits from FCA and relies on probabilistic assumptions that underlie MDL. We provide an experimental proof that the proposed approach improves quality of pattern sets generated by Krimp

Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs

<div><p>In many parts of the world the damaging potato late blight pathogen, <i>Phytophthora infestans</i>, is spread as a succession of clonal lineages. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and drivers of pathogen evolution and dissemination at local and global scales. This knowledge, in turn, helps optimise management practices. Here we combine two key methods for dissecting mitochondrial and nuclear diversity and resolve intra and inter-lineage diversity of over 100 <i>P</i>. <i>infestans</i> isolates representative of key clonal lineages found globally. A novel set of PCR primers that amplify five target regions are provided for mitochondrial DNA sequence analysis. These five loci increased the number of mtDNA haplotypes resolved from four with the PCR RFLP method to 37 (17, 6, 8 and 4 for Ia, Ib, IIa, and IIb haplotypes, respectively, plus 2 Herb-1 haplotypes). As with the PCR RFLP method, two main lineages, I and II were defined. Group I contained 25 mtDNA haplotypes that grouped broadly according to the Ia and Ib types and resolved several sub-clades amongst the global sample. Group II comprised two distinct clusters with four haplotypes corresponding to the RFLP type IIb and eight haplotypes resolved within type IIa. The 12-plex SSR assay revealed 90 multilocus genotypes providing accurate discrimination of dominant clonal lineages and other genetically diverse isolates. Some association of genetic diversity and geographic region of contemporary isolates was observed; US and Mexican isolates formed a loose grouping, distinct from isolates from Europe, South America and other regions. Diversity within clonal lineages was observed that varied according to the age of the clone. In combination, these fine-scale nuclear and maternally inherited mitochondrial markers enabled a greater level of discrimination among isolates than previously available and provided complementary perspectives on evolutionary questions relating to the diversity, phylogeography and the origins and spread of clonal lineages of <i>P</i>. <i>infestans</i>.</p></div

The role of trust and hope in antipsychotic medication reviews between GPs and service users a realist review

Abstract Background Increasing number of service users diagnosed with schizophrenia and psychosis are being discharged from specialist secondary care services to primary care, many of whom are prescribed long-term antipsychotics. It is unclear if General Practitioners (GPs) have the confidence and experience to appropriately review and adjust doses of antipsychotic medication without secondary care support. Aim To explore barriers and facilitators of conducting antipsychotic medication reviews in primary care for individuals with no specialist mental health input. Design &amp; setting Realist review in general practice settings. Method A realist review has been conducted to synthesise evidence on antipsychotic medication reviews conducted in primary care with service users diagnosed with schizophrenia or psychosis. Following initial scoping searches and discussions with stakeholders, a systematic search and iterative secondary searches were conducted. Articles were systematically screened and analysed to develop a realist programme theory explaining the contexts (C) and mechanisms (M) which facilitate or prevent antipsychotic medication reviews (O) in primary care settings, and the potential outcomes of medication reviews. Results Meaningful Antipsychotic medication reviews may not occur for individuals with only primary care medical input. Several, often mutually reinforcing, mechanisms have been identified as potential barriers to conducting such reviews, including low expectations of recovery for people with severe mental illness, a perceived lack of capability to understand and participate in medication reviews, linked with a lack of information shared in appointments between GPs and Service Users, perceived risk and uncertainty regarding antipsychotic medication and illness trajectory. Conclusions The review identified reciprocal and reinforcing stereotypes affecting both GPs and service users. Possible mechanisms to counteract these barriers are discussed, including realistic expectations of medication, and the need for increased information sharing and trust between GPs and service users. </jats:sec

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.Keywords: Clone correction, Microbiology, Genotypic diversity, Genetics, Bootstrap, Computational Science, Bioinformatics, Population genetics, Hierarchy, Mycology, Clonality, Permutation, Minimum spanning networks, Index of association, Bruvo’s distanceThis is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by PeerJ. The published article can be found at: https://peerj.com/

Diversity of Foliar Phytophthora Species on Rhododendron in Oregon Nurseries

The genus Phytophthora contains some of the most notorious plant pathogens affecting nursery crops. Given the recent emergence of the sudden oak death pathogen Phytophthora ramorum, particularly in association with Rhododendron spp., characterization of Phytophthora communities associated with this host in nursery environments is prudent. Many taxa may present symptoms similar to P. ramorum but we do not necessarily know their identity, frequency, and importance. Here, we present a survey of Phytophthora taxa observed from seven nurseries in the U.S. state of Oregon. Incidence and diversity of Phytophthora communities differed significantly among nurseries and among seasons within nursery. The taxa P. syringae and P. plurivora were widespread and detected at most of the nurseries sampled. Nine other taxa were also detected but were found either in a single nursery or were shared among only a few nurseries. Characterization of the Phytophthora communities present in nurseries is an important step toward understanding the ecology of these organisms as well as an aid to nursery managers in determining what risks may be present when symptomatic plants are observed. This study builds on an increasing literature, which characterizes Phytophthora community structure in nurseries.This is the publisher’s final pdf. The published article is copyrighted by American Phytopathological Society and can be found at: http://apsjournals.apsnet.org/loi/pdi

A new determination of the orbit and masses of the Be binary system delta Scorpii

The binary star delta Sco (HD143275) underwent remarkable brightening in the visible in 2000, and continues to be irregularly variable. The system was observed with the Sydney University Stellar Interferometer (SUSI) in 1999, 2000, 2001, 2006 and 2007. The 1999 observations were consistent with predictions based on the previously published orbital elements. The subsequent observations can only be explained by assuming that an optically bright emission region with an angular size of > 2 +/- 1 mas formed around the primary in 2000. By 2006/2007 the size of this region grew to an estimated > 4 mas. We have determined a consistent set of orbital elements by simultaneously fitting all the published interferometric and spectroscopic data as well as the SUSI data reported here. The resulting elements and the brightness ratio for the system measured prior to the outburst in 2000 have been used to estimate the masses of the components. We find Ma = 15 +/- 7 Msun and Mb = 8.0 +/- 3.6 Msun. The dynamical parallax is estimated to be 7.03 +/- 0.15 mas, which is in good agreement with the revised HIPPARCOS parallax.Comment: 8 pages, 4 figs. Accepted for publication in MNRA

The q-exponential family in statistical physics

The notion of generalised exponential family is considered in the restricted context of nonextensive statistical physics. Examples are given of models belonging to this family. In particular, the q-Gaussians are discussed and it is shown that the configurational probability distributions of the microcanonical ensemble belong to the q-exponential family.Comment: 18 pages, 4 figures, proceedings of SigmaPhi 200

Spatial and Temporal Analysis of Populations of the Sudden Oak Death Pathogen in Oregon Forests

Sudden oak death caused by the oomycete Phytophthora ramorum was first discovered in California toward the end of the 20th century and subsequently emerged on tanoak forests in Oregon before its first detection in 2001 by aerial surveys. The Oregon Department of Forestry has since monitored the epidemic and sampled symptomatic tanoak trees from 2001 to the present. Populations sampled over this period were genotyped using microsatellites and studied to infer the population genetic history. To date, only the NA1 clonal lineage is established in this region, although three lineages exist on the North American west coast. The original introduction into the Joe Hall area eventually spread to several regions: mostly north but also east and southwest. A new introduction into Hunter Creek appears to correspond to a second introduction not clustering with the early introduction. Our data are best explained by both introductions originating from nursery populations in California or Oregon and resulting from two distinct introduction events. Continued vigilance and eradication of nursery populations of P. ramorum are important to avoid further emergence and potential introduction of other clonal lineages

Data Set Models and Exponential Families in Statistical Physics and Beyond

The exponential family of models is defined in a general setting, not relying on probability theory. Some results of information geometry are shown to remain valid. Exponential families both of classical and of quantum mechanical statistical physics fit into the new formalism. Other less obvious applications are predicted. For instance, quantum states can be modeled as points in a classical phase space and the resulting model belongs to the exponential family

Identification and distribution of mating-type idiomorphs in populations of Podosphaera macularis and development of chasmothecia of the fungus

Podosphaera macularis, the causal agent of hop powdery mildew, is known to produce chasmothecia (formerly cleistothecia) in eastern North America and Europe. Ascocarps have not yet been reported from the Pacific Northwestern region of North America. Reasons for the apparent absence of chasmothecia in the Pacific Northwest were unknown. This study established that P. macularis is heterothallic and ascocarp ontogeny, maturation, dehiscence and ascospore infection proceed similarly to other powdery mildew fungi. Genome sequencing of a MAT1-1 isolate revealed the structure of the MAT1 locus and presence of MAT1-1-3, demonstrating further similarities to other powdery mildew fungi. PCR assays with primers designed from conserved domains of the MAT1 idiomorphs were developed to characterize the frequency of idiomorphs in populations of P. macularis. Amongst 317 samples of P. macularis collected during 2012 and 2013 from the Pacific Northwest only the MAT1-1 idiomorph was found. In contrast, among 56 samples from the eastern United States and Europe, MAT1-1 and MAT1-2 idiomorphs were detected at equivalent frequencies. At temperatures representative of late season conditions in the Pacific Northwest, chasmothecia formed readily when a Pacific Northwest MAT1-1 isolate was paired with a MAT1-2 isolate collected from outside the region. Although these findings do not encompass all climatic, geographic or temporal barriers that could inhibit the formation of chasmothecia, the current absence of the ascigerious stage of P. macularis in the Pacific Northwest could be explained by the absence of the MAT1-2 mating type idiomorph.Keywords: Humulus lupulus, powdery mildew, Podosphaera macularis, chasmothecia, cleistothecia, ho