Groups of diffeomorphisms and geometric loops of manifolds over ultra-normed fields

The article is devoted to the investigation of groups of diffeomorphisms and loops of manifolds over ultra-metric fields of zero and positive characteristics. Different types of topologies are considered on groups of loops and diffeomorphisms relative to which they are generalized Lie groups or topological groups. Among such topologies pairwise incomparable are found as well. Topological perfectness of the diffeomorphism group relative to certain topologies is studied. There are proved theorems about projective limit decompositions of these groups and their compactifications for compact manifolds. Moreover, an existence of one-parameter local subgroups of diffeomorphism groups is investigated.Comment: Some corrections excluding misprints in the article were mad

Engineering chemistry: integrating batch and flow reactions on a single, automated reactor platform

Synthesis chemistry need not be limited to either only batch or only flow; rather, in the future we expect that it will consist of an amalgamation of the best and most appropriate methods. We have therefore devised a single reactor platform to conduct both batch and flow reactions, either singly or in concert, using open source technologies to automate, control and monitor individual processes. We illustrate this concept with the multistep synthesis of 5-methyl-4-propylthiophene-2-carboxylic acid to showcase the utility of this approach in a telescoped manner. Automated downstream processing techniques, consisting of continuous extraction and solvent switching steps, were also included, further freeing the chemist from routine laboratory tasks.Woolf Fisher Trust, Engineering and Physical Sciences Research Council (Grant IDs: EP/K009494/1, EP/M004120/1 and EP/K039520/1

Comparative functional genomics and the bovine macrophage response to strains of the Mycobacterium genus

Mycobacterial infections are major causes of morbidity and mortality in cattle and are also potential zoonotic agents with implications for human health. Despite the implementation of comprehensive animal surveillance programs, many mycobacterial diseases have remained recalcitrant to eradication in several industrialized countries. Two major mycobacterial pathogens of cattle are Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis (MAP), the causative agents of bovine tuberculosis (BTB) and Johne's disease (JD), respectively. BTB is a chronic, granulomatous disease of the respiratory tract that is spread via aerosol transmission, while JD is a chronic granulomatous disease of the intestines that is transmitted via the fecal-oral route. Although these diseases exhibit differential tissue tropism and distinct complex etiologies, both M. bovis and MAP infect, reside, and replicate in host macrophages - the key host innate immune cell that encounters mycobacterial pathogens after initial exposure and mediates the subsequent immune response. The persistence of M. bovis and MAP in macrophages relies on a diverse series of immunomodulatory mechanisms, including the inhibition of phagosome maturation and apoptosis, generation of cytokine-induced necrosis enabling dissemination of infection through the host, local pathology, and ultimately shedding of the pathogen. Here, we review the bovine macrophage response to infection with M. bovis and MAP. In particular, we describe how recent advances in functional genomics are shedding light on the host macrophage-pathogen interactions that underlie different mycobacterial diseases. To illustrate this, we present new analyses of previously published bovine macrophage transcriptomics data following in vitro infection with virulent M. bovis, the attenuated vaccine strain M. bovis BCG, and MAP, and discuss our findings with respect to the differing etiologies of BTB and JD

A Novel Internet-Based Reaction Monitoring, Control and Autonomous Self-Optimization Platform for Chemical Synthesis

We have developed a modular software system that enables researchers to monitor and control chemical reactions via the internet, using any device from any location in the world. It facilitates the automation of synthetic procedures and is able to autonomously self-optimize reaction parameters to find the best conditions meeting customizable, multi-component optimization functions. In this report, we demonstrate its utility as applied to reaction automation to maximize the output from a fixed volume of catalyst. We also showcase its ability to optimize a three dimension heterogeneous catalytic reaction and a five dimension Appel reaction against various target functions.We are grateful to the Woolf Fisher Trust (D.E.F), Pfizer Worldwide Research and Development (C.B.) and EPSRC (S.V.L., grant codes EP/K009494/1, EP/M004120/1 and EP/K039520/1) for financial assistance.This is the final version of the article. It was first available from American Chemical Society via http://dx.doi.org/10.1021/acs.oprd.5b0031

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data

Background: Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors. Results: We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples. Conclusions: GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines.Department of Agriculture, Food and the MarineEuropean Commission - Seventh Framework Programme (FP7)Science Foundation IrelandUniversity College Dubli

A tutored discourse on microcontrollers, single board computers and their applications to monitor and control chemical reactions

This Tutored Discourse constitutes a preliminary exposure on how synthesis chemists can engage positively with inexpensive, low-power microcontrollers to aid control, monitoring and optimisation of chemical reactions.H2020-FETOPEN-2016-2017 programme of the European Commission (grant agreement number: 737266-ONE FLOW

RNA-seq transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis

Bovine tuberculosis, caused by infection with Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including gene expression microarrays and RNA-sequencing (RNA-seq), has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix(®) GeneChip(®) Bovine Genome Array platform from the same PBL-extracted RNA. A total of 3,250 differentially expressed (DE) annotated genes were detected in the M. bovis-infected samples relative to the controls (adjusted P-value ≤0.05), with the number of genes displaying decreased relative expression (1,671) exceeding those with increased relative expression (1,579). Ingenuity(®) Systems Pathway Analysis (IPA) of all DE genes revealed enrichment for genes with immune function. Notably, transcriptional suppression was observed among several of the top-ranking canonical pathways including Leukocyte Extravasation Signaling. Comparative platform analysis demonstrated that RNA-seq detected a larger number of annotated DE genes (3,250) relative to the microarray (1,398), of which 917 genes were common to both technologies and displayed the same direction of expression. Finally, we show that RNA-seq had an increased dynamic range compared to the microarray for estimating differential gene expression