A text-mining system for extracting metabolic reactions from full-text articles

Background: Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway—metabolic pathways—has been largely neglected. Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein–protein interactions. Results: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task. Conclusions: We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein–protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed

Single Maximal versus Combination Punch Kinematics

The aim of this study was to determine the influence of punch type (Jab, Cross, Lead Hook and Reverse Hook) and punch modality (Single maximal, ‘In-synch’ and ‘Out of synch’ combination) on punch speed and delivery time. Ten competition-standard volunteers performed punches with markers placed on their anatomical landmarks for 3D motion capture with an eight-camera optoelectronic system. Speed and duration between key moments were computed. There were significant differences in contact speed between punch types (F 2,18,84.87 = 105.76, p = 0.001) with Lead and Reverse Hooks developing greater speed than Jab and Cross. There were significant differences in contact speed between punch modalities (F 2,64,102.87 = 23.52, p = 0.001) with the Single maximal (M ± SD: 9.26 ± 2.09 m/s) higher than ‘Out of synch’ (7.49 ± 2.32 m/s), ‘In-synch’ left (8.01 ± 2.35 m/s) or right lead (7.97 ± 2.53 m/s). Delivery times were significantly lower for Jab and Cross than Hook. Times were significantly lower ‘In-synch’ than a Single maximal or ‘Out of synch’ combination mode. It is concluded that a defender may have more evasion-time than previously reported. This research could be of use to performers and coaches when considering training preparations

Renormalized Vacuum Polarization and Stress Tensor on the Horizon of a Schwarzschild Black Hole Threaded by a Cosmic String

We calculate the renormalized vacuum polarization and stress tensor for a massless, arbitrarily coupled scalar field in the Hartle-Hawking vacuum state on the horizon of a Schwarzschild black hole threaded by an infinte straight cosmic string. This calculation relies on a generalized Heine identity for non-integer Legendre functions which we derive without using specific properties of the Legendre functions themselves.Comment: This is an expanded version of a previous submission, we have added the calculation of the stress tensor. 28 pages, 7 figure

Forest landscape restoration in the drylands of Latin America

Forest Landscape Restoration (FLR) involves the ecological restoration of degraded forest landscapes, with the aim of benefiting both biodiversity and human well-being. We first identify four fundamental principles of FLR, based on previous definitions. We then critically evaluate the application of these principles in practice, based on the experience gained during an international, collaborative research project conducted in six dry forest landscapes of Latin America. Research highlighted the potential for FLR; tree species of high socioeconomic value were identified in all study areas, and strong dependence of local communities on forest resources was widely encountered, particularly for fuelwood. We demonstrated that FLR can be achieved through both passive and active restoration approaches, and can be cost-effective if the increased provision of ecosystem services is taken into account. These results therefore highlight the potential for FLR, and the positive contribution that it could make to sustainable development. However, we also encountered a number of challenges to FLR implementation, including the difficulty of achieving strong engagement in FLR activities among local stakeholders, lack of capacity for community-led initiatives, and the lack of an appropriate institutional and regulatory environment to support restoration activities. Successful implementation of FLR will require new collaborative alliances among stakeholders, empowerment and capacity building of local communities to enable them to fully engage with restoration activities, and an enabling public policy context to enable local people to be active participants in the decision making process. © 2012 by the author(s). Published here under license by the Resilience Alliance

Rapid identification of Brucella isolates to the species level by real time PCR based single nucleotide polymorphism (SNP) analysis

<p>Abstract</p> <p>Background</p> <p>Brucellosis, caused by members of the genus <it>Brucella</it>, remains one of the world's major zoonotic diseases. Six species have classically been recognised within the family <it>Brucella </it>largely based on a combination of classical microbiology and host specificity, although more recently additional isolations of novel <it>Brucella </it>have been reported from various marine mammals and voles. Classical identification to species level is based on a biotyping approach that is lengthy, requires extensive and hazardous culturing and can be difficult to interpret. Here we describe a simple and rapid approach to identification of <it>Brucella </it>isolates to the species level based on real-time PCR analysis of species-specific single nucleotide polymorphisms (SNPs) that were identified following a robust and extensive phylogenetic analysis of the genus.</p> <p>Results</p> <p>Seven pairs of short sequence Minor Groove Binding (MGB) probes were designed corresponding to SNPs shown to possess an allele specific for each of the six classical <it>Brucella </it>spp and the marine mammal <it>Brucella</it>. Assays were optimised to identical reaction parameters in order to give a multiple outcome assay that can differentiate all the classical species and <it>Brucella </it>isolated from marine mammals. The scope of the assay was confirmed by testing of over 300 isolates of <it>Brucella</it>, all of which typed as predicted when compared to other phenotypic and genotypic approaches. The assay is sensitive being capable of detecting and differentiating down to 15 genome equivalents. We further describe the design and testing of assays based on three additional SNPs located within the 16S rRNA gene that ensure positive discrimination of <it>Brucella </it>from close phylogenetic relatives on the same platform.</p> <p>Conclusion</p> <p>The multiple-outcome assay described represents a new tool for the rapid, simple and unambiguous characterisation of <it>Brucella </it>to the species level. Furthermore, being based on a robust phylogenetic framework, the assay provides a platform that can readily be extended in the future to incorporate newly identified <it>Brucella </it>groups, to further type at the subspecies level, or to include markers for additional useful characteristics.</p

The relationship between cognitive ability and BOLD activation across sleep–wake states

The sleep spindle, a waxing and waning oscillation in the sigma frequency range, has been shown to correlate with fluid intelligence; i.e. the ability to use logic, learn novel rules/patterns, and solve problems. Using simultaneous EEG and fMRI, we previously identified the neural correlates of this relationship, including activation of the thalamus, bilateral putamen, medial frontal gyrus, middle cingulate cortex, and precuneus. However, research to date has focussed primarily on non-rapid eye movement (NREM) sleep, and spindles per se, thus overlooking the possibility that brain activity that occurs in other sleep–wake states might also be related to cognitive abilities. In our current study, we sought to investigate whether brain activity across sleep/wake states is also related to human intelligence in N = 29 participants. During NREM sleep, positive correlations were observed between fluid intelligence and blood oxygen level dependent (BOLD) activations in the bilateral putamen and the paracentral lobule/precuneus, as well as between short-term memory (STM) abilities and activity in the medial frontal cortex and inferior frontal gyrus. During wake, activity in bilateral postcentral gyri and occipital lobe was positively correlated with short-term memory abilities. In participants who experienced REM sleep in the scanner, fluid intelligence was positively associated with midbrain activation, and verbal intelligence was associated with right postcentral gyrus activation. These findings provide evidence that the relationship between sleep and intellectual abilities exists beyond sleep spindles

A Systems Engineering Approach to Quantitative Comparison of Molecular Instruments for Use on the International Space Station

AbstractThe presence of microorganisms on the International Space Station (ISS) poses a threat to the health and safety of the ISS crew. Currently the ISS utilizes culture-based methods to detect and identify microorganisms. These methods are out dated and time-consuming. Molecular methods can deliver accurate results and require less processing time. This article details an approach to determine which molecular methods instrument most closely meets the Microbial Monitoring System (MMS) requirements for use on the ISS. We utilize the decision-theoretic Analytical Hierarchy Process and Quality Function Deployment while aligning the systems requirements vs. instrument capabilities in a Pugh Matrix to perform a quantitative assessment of six candidate systems, with the analysis yielding a single recommended instrument for use on the ISS. We demonstrate our techniques to be very effective for selection of the best instrument—the recommended system is currently under consideration for use on the ISS

From mantle to critical zone : a review of large and giant sized deposits of the rare earth elements

MS, AF and FW acknowledge the support of the NERC SoS:RARE consortium grant (NE/M011267/1). D. Kavecsanszki acknowledges the support of a postgraduate fellowship from the College of Engineering, Mathematics and Physical Sciences at the University of Exeter.The rare earth elements are unusual when defining giant-sized ore deposits, as resources are often quoted as total rare earth oxide, but the importance of a deposit may be related to the grade for individual, or a limited group of, the elements. Taking the total REE resource, only one currently known deposit (Bayan Obo) would class as giant (>1.7×107 tonnes contained metal), but a range of others classify as large (>1.7×106 tonnes). With the exception of unclassified resource estimates from the Olympic Dam IOCG deposit, all of these deposits are related to alkaline igneous activity – either carbonatites or agpaitic nepheline syenites. The total resource in these deposits must relate to the scale of the primary igneous source, but the grade is a complex function of igneous source, magmatic crystallisation, hydrothermal modification and supergene enrichment during weathering. Isotopic data suggest that the sources conducive to the formation of large REE deposits are developed in subcontinental lithospheric mantle, enriched in trace elements either by plume activity, or by previous subduction. The reactivation of such enriched mantle domains in relatively restricted geographical areas may have played a role in the formation of some of the largest deposits (e.g. Bayan Obo). Hydrothermal activity involving fluids from magmatic to meteoric sources may result in the redistribution of the REE and increases in grade, depending on primary mineralogy and the availability of ligands. Weathering and supergene enrichment of carbonatite has played a role in the formation of the highest grade deposits at Mount Weld (Australia) and Tomtor (Russia). For the individual REE with the current highest economic value (Nd and the HREE), the boundaries for the large and giant size classes are 2 orders of magnitude lower, and deposits enriched in these metals (agpaitic systems, ion absorption deposits) may have significant economic impact in the near future.Publisher PDFPeer reviewe