Phytophthora ramorum

Phytophthora ramorum is a recently emerged plant pathogen and causal agent of one of the most destructive and devastating diseases currently affecting US horticulture and forests (Rizzo et al. 2002, 2005). This oomycete pathogen was discovered in Marin County, California, in the mid-1990s, causing sudden oak death on coast live oak (Quercus agrifolia) and tanoak (Notholithocarpus densiflorus) and simultaneously discovered in Europe causing foliar blight on Rhododendron and Viburnum (Rizzo et al. 2002; Werres et al. 2001). It is now known to affect more than 100 plant species, including economically important nursery and forest host species (Frankel 2008; Rizzo et al. 2005; Tooley et al. 2004; Tooley and Kyde 2007)

Transplantation of progenitor cells and regeneration enhancement in acute myocardial infarction - (TOPCARE-AMI)

Background - Experimental studies suggest that transplantation of blood-derived or bone marrow–derived progenitor cells beneficially affects postinfarction remodeling. The safety and feasibility of autologous progenitor cell transplantation in patients with ischemic heart disease is unknown

The No-Free-Lunch Theorems of Supervised Learning

The no-free-lunch theorems promote a skeptical conclusion that all possible machine learning algorithms equally lack justification. But how could this leave room for a learning theory, that shows that some algorithms are better than others? Drawing parallels to the philosophy of induction, we point out that the no-free-lunch results presuppose a conception of learning algorithms as purely data-driven. On this conception, every algorithm must have an inherent inductive bias, that wants justification. We argue that many standard learning algorithms should rather be understood as model-dependent: in each application they also require for input a model, representing a bias. Generic algorithms themselves, they can be given a model-relative justification

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

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/

ТЕХНОГЕННІ РОДОВИЩА ТА ЇХ КЛАСИФІКАЦІЯ

На багатьох гірничодобувних підприємствах тих, що забезпечують мінера-льною сировиною чорну і кольорову металургію України та країн СНД, виник-ла проблема з розвіданими запасами. Резерв запасів багатьох видів корисних копалини на експлуатованих родовищах недостатній для забезпечення повної проектної потужності. Стан сировинних баз багатьох найважливіших гірничо-добувних регіонів і підприємств, що діють, різко погіршав у зв'язку з висна-женням запасів, зниженням їх якісних і економічних характеристик ускладнен-ням умов відробітку в результаті тривалої і інтенсивної експлуатації раніше освоєних родовищ. Основною причиною ситуації, що створилася, можна назва-ти зниження фінансування геологорозвідувальних робіт для освоєння нових ро-довищ необхідної мінеральної сировини

Transitions between Inherent Structures in Water

The energy landscape approach has been useful to help understand the dynamic properties of supercooled liquids and the connection between these properties and thermodynamics. The analysis in numerical models of the inherent structure (IS) trajectories -- the set of local minima visited by the liquid -- offers the possibility of filtering out the vibrational component of the motion of the system on the potential energy surface and thereby resolving the slow structural component more efficiently. Here we report an analysis of an IS trajectory for a widely-studied water model, focusing on the changes in hydrogen bond connectivity that give rise to many IS separated by relatively small energy barriers. We find that while the system \emph{travels} through these IS, the structure of the bond network continuously modifies, exchanging linear bonds for bifurcated bonds and usually reversing the exchange to return to nearly the same initial configuration. For the 216 molecule system we investigate, the time scale of these transitions is as small as the simulation time scale ($\approx 1$ fs). Hence for water, the transitions between each of these IS is relatively small and eventual relaxation of the system occurs only by many of these transitions. We find that during IS changes, the molecules with the greatest displacements move in small ``clusters'' of 1-10 molecules with displacements of $\approx 0.02-0.2$ nm, not unlike simpler liquids. However, for water these clusters appear to be somewhat more branched than the linear ``string-like'' clusters formed in a supercooled Lennar d-Jones system found by Glotzer and her collaborators.Comment: accepted in PR

Genomic investigation of the strawberry pathogen Phytophthora fragariae indicates pathogenicity is associated with transcriptional variation in three key races

The oomycete Phytophthora fragariae is a highly destructive pathogen of cultivated strawberry (Fragaria × ananassa), causing the root rotting disease, “red core”. The host-pathogen interaction has a well described gene-for-gene resistance relationship, but to date neither candidate avirulence nor resistance genes have been identified. We sequenced a set of American, Canadian, and United Kingdom isolates of known race type, along with three representatives of the closely related pathogen of the raspberry (Rubus idaeus), P. rubi, and found a clear population structure, with a high degree of nucleotide divergence seen between some race types and abundant private variation associated with race types 4 and 5. In contrast, between isolates defined as United Kingdom races 1, 2, and 3 (UK1-2-3) there was no evidence of gene loss or gain; or the presence of insertions/deletions (INDELs) or Single Nucleotide Polymorphisms (SNPs) within or in proximity to putative pathogenicity genes could be found associated with race variation. Transcriptomic analysis of representative UK1-2-3 isolates revealed abundant expression variation in key effector family genes associated with pathogen race; however, further long read sequencing did not reveal any long range polymorphisms to be associated with avirulence to race UK2 or UK3 resistance, suggesting either control in trans or other stable forms of epigenetic modification modulating gene expression. This work reveals the combined power of population resequencing to uncover race structure in pathosystems and in planta transcriptomic analysis to identify candidate avirulence genes. This work has implications for the identification of putative avirulence genes in the absence of associated expression data and points toward the need for detailed molecular characterisation of mechanisms of effector regulation and silencing in oomycete plant pathogens