Representation of probabilistic scientific knowledge

This article is available through the Brunel Open Access Publishing Fund. Copyright © 2013 Soldatova et al; licensee BioMed Central Ltd.The theory of probability is widely used in biomedical research for data analysis and modelling. In previous work the probabilities of the research hypotheses have been recorded as experimental metadata. The ontology HELO is designed to support probabilistic reasoning, and provides semantic descriptors for reporting on research that involves operations with probabilities. HELO explicitly links research statements such as hypotheses, models, laws, conclusions, etc. to the associated probabilities of these statements being true. HELO enables the explicit semantic representation and accurate recording of probabilities in hypotheses, as well as the inference methods used to generate and update those hypotheses. We demonstrate the utility of HELO on three worked examples: changes in the probability of the hypothesis that sirtuins regulate human life span; changes in the probability of hypotheses about gene functions in the S. cerevisiae aromatic amino acid pathway; and the use of active learning in drug design (quantitative structure activity relation learning), where a strategy for the selection of compounds with the highest probability of improving on the best known compound was used. HELO is open source and available at https://github.com/larisa-soldatova/HELO.This work was partially supported by grant BB/F008228/1 from the UK Biotechnology & Biological Sciences Research Council, from the European Commission under the FP7 Collaborative Programme, UNICELLSYS, KU Leuven GOA/08/008 and ERC Starting Grant 240186

Flexural deformation and basin-mountain coupling in the northern Kyrgyz Tien Shan: transition from the Issyk-Kul basin to the Kumtor plateau

During the late stage of the India-Asia collision, deformation propagated northwards into the Asian foreland. North of the stable Tarim plate, the Tien Shan range – an old Palaeozoic fold belt – was strongly reactivated. It now accommodates more than one third of the total shortening rate between Stable Eurasia and the Indian continent.In the northern part of the Kyrgyz Tien-Shan Range, the 600 m deep Lake Issyk-Kul occupies a lense-shaped tectonic depression elongated in an E-W direction and bordered on its northern and southern sides by high mountain ranges (> 4000 m high). To the north, the Kungey Alatau range has the structure of an active positive flower structure with the Chon-Kemin – Chilik fault in its middle (location of several Ms > 8.0 historic earthquakes). To the south, the Terskey range forms the frontal scarp of the high and relatively flat Kumtor Plateau whose surface is undulating between 3800 and 5200 m high.Multidisciplinary investigation was performed during several summer campaigns, involving structural geology, paleostress reconstructions, tectono-stratigraphy and paleoseismology in the mountain ranges and lake shore, as well as high-resolution seismic profiling and heat flow measurements in Lake Issyk-Kul. Investigations included also the seismotectonics analysis of a large number of earthquake focal mechanisms determined from the local seismic network.All the results are best integrated in a model of lithospheric deformation by flexural folding and basin-mountain coupling. The Issyk-Kul basin probably formed as a flexural downwarp of the lithosphere rather than as a symmetric ramp basin, as once proposed. South of the Issyk-Kul depression, the Kumtor plateau still show large remains of the pre-Cainozoic flat erosion surface that is widespread in the Central Asia, now strongly uplifted and slightly undulating. Deformation at mountain-basin interface occurs mainly by tilting around a horizontal axis of the pre-Cainozoic basement (up to 60°from the horizontal), and top-to-the south reverse faulting at the southern margin of the basin (basin towards the range), in an opposite sense to what could be expected in the case of a ramp basin. The focal mechanism of a recent earthquake along the southern mountain-basin interface confirms this interpretation (25 December 2006 Ms 5.8)

Guidance on the Selection of Appropriate Indicators for Quantification of Antimicrobial Usage in Humans and Animals

An increasing variety of indicators of antimicrobial usage has become available in human and veterinary medicine, with no consensus on the most appropriate indicators to be used. The objective of this review is therefore to provide guidance on the selection of indicators, intended for those aiming to quantify antimicrobial usage based on sales, deliveries or reimbursement data. Depending on the study objective, different requirements apply to antimicrobial usage quantification in terms of resolution, comprehensiveness, stability over time, ability to assess exposure and comparability. If the aim is to monitor antimicrobial usage trends, it is crucial to use a robust quantification system that allows stability over time in terms of required data and provided output; to compare usage between different species or countries, comparability must be ensured between the different populations. If data are used for benchmarking, the system comprehensiveness is particularly crucial, while data collected to study the association between usage and resistance should express the exposure level and duration as a measurement of the exerted selection pressure. Antimicrobial usage is generally described as the number of technical units consumed normalized by the population at risk of being treated in a defined period. The technical units vary from number of packages to number of individuals treated daily by adding different levels of complexity such as daily dose or weight at treatment. These technical units are then related to a description of the population at risk, based either on biomass or number of individuals. Conventions and assumptions are needed for all of these calculation steps. However, there is a clear lack of standardization, resulting in poor transparency and comparability. By combining study requirements with available approaches to quantify antimicrobial usage, we provide suggestions on the most appropriate indicators and data sources to be used for a given study objective

Carbon Nanotubes by a CVD Method. Part I: Synthesis and Characterization of the (Mg, Fe)O Catalysts

The controlled synthesis of carbon nanotubes by chemical vapor deposition requires tailored and wellcharacterized catalyst materials. We attempted to synthesize Mg1-xFexO oxide solid solutions by the combustion route, with the aim of performing a detailed investigation of the influence of the synthesis conditions (nitrate/urea ratio and the iron content) on the valency and distribution of the iron ions and phases. Notably, characterization of the catalyst materials is performed using 57Fe Mo¨ssbauer spectroscopy, X-ray diffraction, and electron microscopy. Several iron species are detected including Fe2+ ions substituting for Mg2+ in the MgO lattice, Fe3+ ions dispersed in the octahedral sites of MgO, different clusters of Fe3+ ions, and MgFe2O4-like nanoparticles. The dispersion of these species and the microstructure of the oxides are discussed. Powders markedly different from one another that may serve as model systems for further study are identified. The formation of carbon nanotubes upon reduction in a H2/CH4 gas atmosphere of the selected powders is reported in a companion paper

Exploring the evidence base for national and regional policy interventions to combat resistance

The effectiveness of existing policies to control antimicrobial resistance is not yet fully understood. A strengthened evidence base is needed to inform effective policy interventions across countries with different income levels and the human health and animal sectors. We examine three policy domains—responsible use, surveillance, and infection prevention and control—and consider which will be the most effective at national and regional levels. Many complexities exist in the implementation of such policies across sectors and in varying political and regulatory environments. Therefore, we make recommendations for policy action, calling for comprehensive policy assessments, using standardised frameworks, of cost-effectiveness and generalisability. Such assessments are especially important in low-income and middle-income countries, and in the animal and environmental sectors. We also advocate a One Health approach that will enable the development of sensitive policies, accommodating the needs of each sector involved, and addressing concerns of specific countries and regions

Using a Stick Does Not Necessarily Alter Judged Distances or Reachability

Background It has been reported that participants judge an object to be closer after a stick has been used to touch it than after touching it with the hand. In this study we try to find out why this is so. Methodology We showed six participants a cylindrical object on a table. On separate trials (randomly intermixed) participants either estimated verbally how far the object is from their body or they touched a remembered location. Touching was done either with the hand or with a stick (in separate blocks). In three different sessions, participants touched either the object location or the location halfway to the object location. Verbal judgments were given either in centimeters or in terms of whether the object would be reachable with the hand. No differences in verbal distance judgments or touching responses were found between the blocks in which the stick or the hand was used. Conclusion Instead of finding out why the judged distance changes when using a tool, we found that using a stick does not necessarily alter judged distances or judgments about the reachability of objects

The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura

Abstract We sequenced the mitochondrial genomes of the spider crabs Maja crispata and Maja squinado (Majidae, Brachyura). Both genomes contain the whole set of 37 genes characteristic of Bilaterian genomes, encoded on both \u3b1- and \u3b2-strands. Both species exhibit the same gene order, which is unique among known animal genomes. In particular, all the genes located on the \u3b2-strand form a single block. This gene order was analysed together with the other nine gene orders known for the Brachyura. Our study confirms that the most widespread gene order (BraGO) represents the plesiomorphic condition for Brachyura and was established at the onset of this clade. All other gene orders are the result of transformational pathways originating from BraGO. The different gene orders exhibit variable levels of genes rearrangements, which involve only tRNAs or all types of genes. Local homoplastic arrangements were identified, while complete gene orders remain unique and represent signatures that can have a diagnostic value. Brachyura appear to be a hot-spot of gene order diversity within the phylum Arthropoda. Our analysis, allowed to track, for the first time, the fully evolutionary pathways producing the Brachyuran gene orders. This goal was achieved by coupling sophisticated bioinformatic tools with phylogenetic analysis

Boekbespreking

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Boring bivalve traces in modern reef and deeper-water macroid and rhodolith beds

Macroids and rhodoliths, made by encrusting acervulinid foraminifera and coralline algae, are widely recognized as bioengineers providing relatively stable microhabitats and increasing biodiversity for other species. Macroid and rhodolith beds occur in different depositional settings at various localities and bathymetries worldwide. Six case studies of macroid/rhodolith beds from 0 to 117m water depth in the Pacific Ocean (northern Central Ryukyu Islands, French Polynesia), eastern Australia (Fraser Island, One Tree Reef, Lizard Island), and the Mediterranean Sea (southeastern Spain) show that nodules in the beds are perforated by small-sized boring bivalve traces (Gastrochanolites). On average, boring bivalve shells (gastrochaenids and mytilids) are more slender and smaller than those living inside shallow-water rocky substrates. In the Pacific, Gastrochaena cuneiformis, Gastrochaena sp., Leiosolenus malaccanus, L. mucronatus, L. spp., and Lithophaga/Leiosolenus sp., for the first time identified below 20m water depth, occur as juvenile forms along with rare small-sized adults. In deep-water macroids and rhodoliths the boring bivalves are larger than the shallower counterparts in which growth of juveniles is probably restrained by higher overturn rates of host nodules. In general, most boring bivalves are juveniles that grew faster than the acervulinid foraminiferal and coralline red algal hosts and rarely reached the adult stage. As a consequence of phenotypic plasticity, small-sized adults with slow growth rates coexist with juveniles. Below wave base macroids and rhodoliths had the highest amounts of bioerosion, mainly produced by sponges and polychaete worms. These modern observations provide bases for paleobiological inferences in fossil occurrences.Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT) Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (KAKENHI) 25247083Erasmus+FAR2012-2017FIR2016FIR2018PRIN "Biotic resilience to global change: biomineralization of planktonic and benthic calcifiers in the past, present and future" 2017RX9XXXYBioMed Central-Prepay Membership at the University of FerraraJunta de Andalucía RNM 190Committee on ResearchMuseum of PaleontologyDepartment of Integrative Biology, UC BerkeleyUC Pacific Rim Projec

Atomic and electronic structure of twin growth defects in magnetite

We report the existence of a stable twin defect in Fe3O4 thin films. By using aberration corrected scanning transmission electron microscopy and spectroscopy the atomic structure of the twin boundary has been determined. The boundary is confined to the (111) growth plane and it is non-stoichiometric due to a missing Fe octahedral plane. By first principles calculations we show that the local atomic structural configuration of the twin boundary does not change the nature of the superexchange interactions between the two Fe sublattices across the twin grain boundary. Besides decreasing the half-metallic band gap at the boundary the altered atomic stacking at the boundary does not change the overall ferromagnetic (FM) coupling between the grains