Separable time-causal and time-recursive spatio-temporal receptive fields

We present an improved model and theory for time-causal and time-recursive spatio-temporal receptive fields, obtained by a combination of Gaussian receptive fields over the spatial domain and first-order integrators or equivalently truncated exponential filters coupled in cascade over the temporal domain. Compared to previous spatio-temporal scale-space formulations in terms of non-enhancement of local extrema or scale invariance, these receptive fields are based on different scale-space axiomatics over time by ensuring non-creation of new local extrema or zero-crossings with increasing temporal scale. Specifically, extensions are presented about parameterizing the intermediate temporal scale levels, analysing the resulting temporal dynamics and transferring the theory to a discrete implementation in terms of recursive filters over time.Comment: 12 pages, 2 figures, 2 tables. arXiv admin note: substantial text overlap with arXiv:1404.203

Provably scale-covariant networks from oriented quasi quadrature measures in cascade

This article presents a continuous model for hierarchical networks based on a combination of mathematically derived models of receptive fields and biologically inspired computations. Based on a functional model of complex cells in terms of an oriented quasi quadrature combination of first- and second-order directional Gaussian derivatives, we couple such primitive computations in cascade over combinatorial expansions over image orientations. Scale-space properties of the computational primitives are analysed and it is shown that the resulting representation allows for provable scale and rotation covariance. A prototype application to texture analysis is developed and it is demonstrated that a simplified mean-reduced representation of the resulting QuasiQuadNet leads to promising experimental results on three texture datasets.Comment: 12 pages, 3 figures, 1 tabl

Affine Subspace Representation for Feature Description

This paper proposes a novel Affine Subspace Representation (ASR) descriptor to deal with affine distortions induced by viewpoint changes. Unlike the traditional local descriptors such as SIFT, ASR inherently encodes local information of multi-view patches, making it robust to affine distortions while maintaining a high discriminative ability. To this end, PCA is used to represent affine-warped patches as PCA-patch vectors for its compactness and efficiency. Then according to the subspace assumption, which implies that the PCA-patch vectors of various affine-warped patches of the same keypoint can be represented by a low-dimensional linear subspace, the ASR descriptor is obtained by using a simple subspace-to-point mapping. Such a linear subspace representation could accurately capture the underlying information of a keypoint (local structure) under multiple views without sacrificing its distinctiveness. To accelerate the computation of ASR descriptor, a fast approximate algorithm is proposed by moving the most computational part (ie, warp patch under various affine transformations) to an offline training stage. Experimental results show that ASR is not only better than the state-of-the-art descriptors under various image transformations, but also performs well without a dedicated affine invariant detector when dealing with viewpoint changes.Comment: To Appear in the 2014 European Conference on Computer Visio

Effect of slow-release FSH on embryo recovery in dairy cows

AETE, Bath, UK, 8-9 September, 2017201

PHI-base update: additions to the pathogen–host interaction database

The pathogen–host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/

Common and contrasting themes in host cell-targeted effectors from bacterial, fungal, oomycete and nematode plant symbionts described using the Gene Ontology

A wide diversity of plant-associated symbionts, including microbes, produce proteins that can enter host cells, or are injected into host cells in order to modify the physiology of the host to promote colonization. These molecules, termed effectors, commonly target the host defense signaling pathways in order to suppress the defense response. Others target the gene expression machinery or trigger specific modifications to host morphology or physiology that promote the nutrition and proliferation of the symbiont. When recognized by the host's surveillance machinery, which includes cognate resistance (R) gene products, defense responses are engaged to restrict pathogen proliferation. Effectors from diverse symbionts may be delivered into plant cells via varied mechanisms, including whole organism cellular entry (viruses, some bacteria and fungi), type III and IV secretion (in bacteria), physical injection (nematodes and insects) and protein translocation signal sequences (oomycetes and fungi). This mini-review will summarize both similarities and differences in effectors and effector delivery systems found in diverse plant-associated symbionts as well as how these are described with Plant-Associated Microbe Gene Ontology (PAMGO) terms

Whole blood transcriptome analysis reveals footprints of cattle adaptation to sub‐arctic conditions

201

Regulated expression of a transgene introduced on an oriP/EBNA-1 PAC shuttle vector into human cells

<p>Abstract</p> <p>Background</p> <p>Sequencing of the human genome has led to most genes being available in BAC or PAC vectors. However, limited functional information has been assigned to most of these genes. Techniques for the manipulation and transfer of complete functional units on large DNA fragments into human cells are crucial for the analysis of complete genes in their natural genomic context. One limitation of the functional studies using these vectors is the low transfection frequency.</p> <p>Results</p> <p>We have constructed a shuttle vector, pPAC7, which contains both the <it>EBNA-1 </it>gene and <it>ori</it>P from the Epstein-Barr virus allowing stable maintenance of PAC clones in the nucleus of human cells. The pPAC7 vector also contains the <it>EGFP </it>reporter gene, which allows direct monitoring of the presence of PAC constructs in transfected cells, and the <it>Bsr</it>-cassette that allows highly efficient and rapid selection in mammalian cells by use of blasticidin. Positive selection for recombinant PAC clones is obtained in pPAC7 because the cloning sites are located within the SacBII gene. We show regulated expression of the <it>CDH3 </it>gene carried as a 132 kb genomic insert cloned into pPAC7, demonstrating that the pPAC7 vector can be used for functional studies of genes in their natural genomic context. Furthermore, the results from the transfection of a range of pPAC7 based constructs into two human cell lines suggest that the transfection efficiencies are not only dependent on construct size.</p> <p>Conclusion</p> <p>The shuttle vector pPAC7 can be used to transfer large genomic constructs into human cells. The genes transferred could potentially contain all long-range regulatory elements, including their endogenous regulatory promoters. Introduction of complete genes in PACs into human cells would potentially allow complementation assays to identify or verify the function of genes affecting cellular phenotypes.</p