Clustering via kernel decomposition

Spectral clustering methods were proposed recently which rely on the eigenvalue decomposition of an affinity matrix. In this letter, the affinity matrix is created from the elements of a nonparametric density estimator and then decomposed to obtain posterior probabilities of class membership. Hyperparameters are selected using standard cross-validation methods

Prioritising targets for biological control of weeds - a decision support tool for policy makers

This report outlines a framework of the overall process of prioritising targets for biological control and includes a decision support tool that enables policy makers to determine whether biological control is a suitable option for a proposed target species.Introduction Establishing effective biological control agents in Australia is costly in both resources and time, yet it is often a valuable component of weed control. It has been estimated that biological control of weeds in Australia has provided around $10 billion worth of agricultural protection over the past century. To date significant investment has been made in the selection process of biocontrol agents and the identification of priority weeds for biocontrol. However there is no nationally agreed system that facilitates prioritisation of weed targets for biological control. The Department of Agriculture commissioned ABARES to develop:• a framework that outlines the overall process of prioritising targets for biological control and• a decision support tool that enables policy makers to determine whether biological control is a suitable option for the proposed target species.A recent work related to the selection and prioritisation of weeds for biological control targets was published by Paynter et al 2009 (hereafter \u27Paynter\u27). Paynter was used as a basis for discussion about how to assist policy makers in assessing whether biocontrol is an appropriate option for weed control.The proposal for a decision support tool for policy makers was discussed at a workshop fully recognising that such a system would need to have a science basis that is both transparent and repeatable to be rigorous. The participants were experts in biocontrol or other weed science, state representatives and other relevant stakeholders. The proposal was outlined in a background/discussion paper and provided to participants prior to the workshop. The purpose of the paper was to provide participants with relevant background information and a proposed approach for a decision support tool for policy makers to be debated and progressed at the workshop.Aim of the workshop and background/discussion paper The workshop was held in Canberra on 4 April 2013. The objectives of the workshop were to:• discuss whether the approach based on Paynter is suitable as a decision support tool at the policy level to prioritise targets for biological control• reach a consensus amongst workshop participants on key principles that need to be considered in the prioritisation process of biological control targetsSuggestions made at the workshop are addressed in this report. Many of the concerns raised at the workshop corresponded with the common \u27core\u27 issues recorded in Paynter. These include concerns about lack of data, the tendency of the framework to overlook weeds outside the Weeds of National Significance, concerns that weightings are arbitrary, and a need for the framework to be able to anticipate emergent weeds and potential future problems. Here, those issues that are relevant to policy have been considered with the acknowledgement that remaining \u27core\u27 issues need to be addressed elsewhere

The MCGA (multiple cubic gradient approximation) method for the analysis of Raman spectra

An easily accessible interactive method for the analysis of Raman spectra consisting of many overlapping peaks is presented. A combination of a three- or four-dimensional grid and gradient searching is applied. The method can handle spectra with up to about 50 lines, based on a broad background. Analytical and user-defined or tabulated basic functions can be included. The merits of the method are discussed with both artificial and real spectra

Prevention of obesity : weighing ethical arguments

Taxes on unhealthy food, limits to commercial advertising, a ban on chocolate drink at schools, or compulsory physical exercise for obese employees: efforts to counter the rise in overweight and obesity sometimes rais

HMMER cut-off threshold tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold

Background: Protein superfamilies can be divided into subfamilies of proteins with different functional characteristics. Their sequences can be classified hierarchically, which is part of sequence function assignation. Typically, there are no clear subfamily hallmarks that would allow pattern-based function assignation by which this task is mostly achieved based on the similarity principle. This is hampered by the lack of a score cut-off that is both sensitive and specific. Results: HMMER Cut-off Threshold Tool (HMMERCTTER) adds a reliable cut-off threshold to the popular HMMER. Using a high quality superfamily phylogeny, it clusters a set of training sequences such that the cluster-specific HMMER profiles show cluster or subfamily member detection with 100% precision and recall (P&R), thereby generating a specific threshold as inclusion cut-off. Profiles and thresholds are then used as classifiers to screen a target dataset. Iterative inclusion of novel sequences to groups and the corresponding HMMER profiles results in high sensitivity while specificity is maintained by imposing 100% P&R self detection. In three presented case studies of protein superfamilies, classification of large datasets with 100% precision was achieved with over 95% recall. Limits and caveats are presented and explained. Conclusions: HMMERCTTER is a promising protein superfamily sequence classifier provided high quality training datasets are used. It provides a decision support system that aids in the difficult task of sequence function assignation in the twilight zone of sequence similarity. All relevant data and source codes are available from the Github repository at the following.Fil: Pagnuco, Inti Anabela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica; ArgentinaFil: Revuelta, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Bondino, Hernán Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Brun, Marcel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica; ArgentinaFil: Ten Have, Arjen. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; Argentin

The aspartic proteinase family of three Phytophthora species

Background - Phytophthora species are oomycete plant pathogens with such major social and economic impact that genome sequences have been determined for Phytophthora infestans, P. sojae and P. ramorum. Pepsin-like aspartic proteinases (APs) are produced in a wide variety of species (from bacteria to humans) and contain conserved motifs and landmark residues. APs fulfil critical roles in infectious organisms and their host cells. Annotation of Phytophthora APs would provide invaluable information for studies into their roles in the physiology of Phytophthora species and interactions with their hosts. Results - Genomes of Phytophthora infestans, P. sojae and P. ramorum contain 11-12 genes encoding APs. Nine of the original gene models in the P. infestans database and several in P. sojae and P. ramorum (three and four, respectively) were erroneous. Gene models were corrected on the basis of EST data, consistent positioning of introns between orthologues and conservation of hallmark motifs. Phylogenetic analysis resolved the Phytophthora APs into 5 clades. Of the 12 sub-families, several contained an unconventional architecture, as they either lacked a signal peptide or a propart region. Remarkably, almost all APs are predicted to be membrane-bound. Conclusions - One of the twelve Phytophthora APs is an unprecedented fusion protein with a putative G-protein coupled receptor as the C-terminal partner. The others appear to be related to well-documented enzymes from other species, including a vacuolar enzyme that is encoded in every fungal genome sequenced to date. Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aß peptide central to Alzheimer's Disease. The oomycetes also encode enzymes similar to plasmepsin V, a membrane-bound AP that cleaves effector proteins of the malaria parasite Plasmodium falciparum during their translocation into the host red blood cell. Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation. Indeed, elucidation of the physiological roles of the APs identified here offers areas for future study. The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design

Design and performance of a compact and stationary microSPECT system

Purpose: Over the last ten years, there has been an extensive growth in the development of microSPECT imagers. Most of the systems are based on the combination of conventional, relatively large gamma cameras with poor intrinsic spatial resolution and multipinhole collimators working in large magnification mode. Spatial resolutions range from 0.58 to 0.76 mm while peak sensitivities vary from 0.06% to 0.4%. While pushing the limits of performance is of major importance, the authors believe that there is a need for smaller and less complex systems that bring along a reduced cost. While low footprint and low-cost systems can make microSPECT available to more researchers, the ease of operation and calibration and low maintenance cost are additional factors that can facilitate the use of microSPECT in molecular imaging. In this paper, the authors simulate the performance of a microSPECT imager that combines high space-bandwidth detectors and pinholes with truncated projection, resulting in a small and stationary system. Methods: A system optimization algorithm is used to determine the optimal SPECT systems, given our high resolutions detectors and a fixed field-of-view. These optimal system geometries are then used to simulate a Defrise disk phantom and a hot rod phantom. Finally, a MOBY mouse phantom, with realistic concentrations of Tc99m-tetrofosmin is simulated. Results: Results show that the authors can successfully reconstruct a Defrise disk phantom of 24 mm in diameter without any rotating system components or translation of the object. Reconstructed spatial resolution is approximately 800 mu m while the peak sensitivity is 0.23%. Finally, the simulation of the MOBY mouse phantom shows that the authors can accurately reconstruct mouse images. Conclusions: These results show that pinholes with truncated projections can be used in small magnification or minification mode to obtain a compact and stationary microSPECT system. The authors showed that they can reach state-of-the-art system performance and can successfully reconstruct images with realistic noise levels in a preclinical context. Such a system can be useful for dynamic SPECT imaging. 2013 American Association of Physicists in Medicine