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

Treatment of avoidant/restrictive food intake disorder: a systematic review

Objective: This study aimed to conduct a systematic review on the effects of available treatments for avoidant/restrictive food intake disorder (ARFID). Methods: Literature searches, study selection, method development, and quality appraisal were performed independently by one author, and data were synthesized using a narrative approach. Studies published in English and in peer-reviewed journals that evaluated the outcomes of ARFID treatments in at least three participants were taken into consideration, while non-original studies, editorials and letters to the editor were excluded. Results: The review had three main findings. First, in all of the studies by the end of the treatment there was a significant weight gain in the ARFID participants. Second, weight recovery was maintained at follow-up in a good percentage of participants with an associated improvement of eating behavior and a reduction in anxiety, depression, and fear for the adverse consequences of eating. Third, there was weak or missing evidence regarding the treatment of ARFID in adults and the difference in outcome in the three different ARFID profiles. Eighteen studies were selected and eleven were included. Conclusion: The treatments for ARFID, although promising, have focused only on young participants and addressed the normalization of eating with behavioral procedures, but not the underlying psychopathology. Moreover, the lack of randomized controlled trials with adequate statistical power does not allow to draw conclusions on the difference in the effectiveness of the interventions tested

Fixation locations when grasping partly occluded objects

When grasping an object, subjects tend to look at the contact positions of the digits (A. M. Brouwer, V. H. Franz, D. Kerzel, & K. R. Gegenfurtner, 2005; R. S. Johansson, G. Westling, A. Bäckström, & J. R. Flanagan, 2001). However, these contact positions are not always visible due to occlusion. Subjects might look at occluded parts to determine the location of the contact positions based on extrapolated information. On the other hand, subjects might avoid looking at occluded parts since no object information can be gathered there. To find out where subjects fixate when grasping occluded objects, we let them grasp flat shapes with the index finger and thumb at predefined contact positions. Either the contact position of the thumb or the finger or both was occluded. In a control condition, a part of the object that does not involve the contact positions was occluded. The results showed that subjects did look at occluded object parts, suggesting that they used extrapolated object information for grasping. Additionally, they preferred to look in the direction of the index finger. When the contact position of the index finger was occluded, this tendency was inhibited. Thus, an occluder does not prevent fixations on occluded object parts, but it does affect fixation locations especially in conditions where the preferred fixation location is occluded. © ARVO

Maize nitrogen use efficiency is affected by pig slurry composting and anaerobic digestion.

ABSTRACT: We assessed the nitrogen use efficiency of maize amended with mineral and organic N sources in a Nitisol from Southern Brazil under contrasting soil tillage systems: conventional tillage (CT) and no-tillage (NT). The tested N sources were: 140 kg N ha-1 (total N input) either as mineral fertilizer (urea; MIN), pig slurry (PS), anaerobically digested pig slurry (ADS) and composted pig slurry (CS), besides a control without fertilization (CTR). The N-based application of PS and ADS supplied less than 74% of the maize requirements for P2O5 (115 kg ha-1 ), while CS exceeded P2O5 demand by up to 109%. PS and ADS promoted maize N uptake, biomass production and grain yield similar or higher than maize receiving mineral fertilizer (urea). However, CS promoted significantly lower N agronomic efficiency (AEN) and recovery efficiency (REN) than other fertilizers. CS should be primarily used as a source of P and K or as an amendment to recover SOM stocks in degraded soils

Soil organic carbon pools as affected by tillage systems and organic nitrogen sources.

ABSTRACT: We assessed the impact of organic N sources on total organic carbon (TOC), particulate organic carbon (POC), and mineral-associated organic carbon (MAOC) pools in a Nitisol from Southern Brazil under contrasting soil tillage systems. The tillage systems were conventional tillage (CT) and no-tillage (NT). The tested N sources were: 140 kg N ha-1 (total N input) either as mineral fertilizer (urea; MIN), pig slurry (PS), anaerobically digested pig slurry (ADS) and composted pig slurry (CS), besides a control without fertilization (CTR). TOC stocks decreased by 1.0 and 5.1 Mg C ha-1 after two years of CT in both 0-5 and 0-30 cm soil layers, respectively. NT increased TOC stocks by 2.3 Mg C ha-1 at the soil surface and decrease by 1.7 Mg C ha-1 at the 0-30 cm soil layer. NT had higher POC and MAOC stocks than the CT soil. POC was a more sensitive pool than MAOC in response to soil tillage and fertilization practices. Long-term and continuous assessment of SOC pools is needed for evaluation of the impact of organic N sources for C sequestration in NT soil

Atyidae and Palaemonidae (Crustacea: Decapoda: Caridea) of Bocas del Toro, Panama.

The present contribution is a preliminary report on the freshwater caridean fauna of Bocas del Toro province, northeastern Panama, based on field collections carried out during a Shrimp Taxonomy Workshop at the STRI station in Bocas del Toro in August 2008. A total of eight species from two families, Atyidae and Palaemonidae, were collected at 17 different collection sites in the rivers, streams and ponds on several islands of the Bocas del Toro archipelago and the adjacent mainland. The species reported herein are Atya scabra (Leach, 1815), Jonga serrei (Bouvier, 1909), Micratya poeyi (Guérin-Méneville, 1855), Potimirim glabra (Kingsley, 1878), P. potimirim (Müller, 1881) (Atyidae), Palaemon pandaliformis (Stimpson, 1871), Macrobrachium acanthurus (Wiegmann, 1836) and M. crenulatum Holthuis, 1950 (Palaemonidae). The record of J. serrei is the first for Panama, and M. poeyi a P. glabra the first for Bocas del Toro province

Play, learn, explore: grasping complexity through gaming and photography

Increased demand for agricultural products, the aspirations of rural communities and a growing recognition of planetary boundaries outline the complex trade-offs resource users are facing on a daily basis. Management problems typically involve multiple stakeholders with diverse and often conflicting worldviews, needs and agendas, in an environment with growing uncertainty. How to improve the flow of information between decision makers? What future landscapes will best resolve the apparently conflicting demands? To address these questions, our methodology has been based on participatory modeling and ‘ethnophotography in environmental science’, a term we have coined to describe our use of photography to explore the perceptions of landscape by resource users. We apply these coupled methods in the social-ecological landscape of the Alaotra, Madagascar. Within the realms of the AlaReLa (Alaotra Resilience Landscape) project, we have developed conceptual models that link actors, resources, norms and institutions, ecological processes and social dynamics through participatory modeling workshops. These involved farmers, academics, conservationists and decision makers. Recognizing and understanding the multiple linkages and feedback loops between all of these components and processes is a crucial first step in the design of socially acceptable strategies. In this paper we highlight the interaction of participatory research and photography, to show how they exchange and nurture each other, and how this approach allows the evolution of a common understanding of a social-ecological system. RésuméL'augmentation de la demande de produits agricoles, les aspirations des communautés rurales et la reconnaissance croissante d’une planète aux frontières limités mettent en exergue les compromis complexes auxquels les utilisateurs des ressources sont confrontés de manière quotidienne. Ces problèmes de gestion impliquent généralement de multiples parties prenantes ayant des visions du monde et des besoins variés et souvent conflictuels, dans un environnement où l'incertitude augmente. Comment peut-on améliorer le flux d'information entre les preneurs de décision ? Quels futures utilisations du territoire résoudront au mieux des demandes apparemment contradictoires ? Pour répondre à ces questions, notre méthodologie a été basée sur la modélisation participative et l'« ethnophotographie en sciences de l'environnement », terme que nous avons créé pour décrire notre utilisation de la photographie afin d’explorer les perceptions de leur environnement par les utilisateurs de ressources. Nous appliquons ces méthodes couplées dans le paysage socio-écologique de l'Alaotra, à Madagascar. Dans le cadre du projet AlaReLa (Alaotra Resilience Landscape), nous avons développé des modèles conceptuels qui relient les acteurs, les ressources, les normes et institutions, les processus écologiques et la dynamique sociale à travers des ateliers de modélisation participative. Les participants en étaient des agriculteurs, des universitaires, des conservationistes et des décideurs. Mettre en évidence et comprendre les liens multiples et les boucles de renforcement entre tous les composants et processus est une première étape cruciale dans la conception de stratégies socialement acceptables. Dans cet article, nous soulignons l'interaction entre la recherche participative et la photographie, afin de montrer comment elles échangent et se nourrissent l’une de l’autre, et comment cette approche permet une évolution vers une compréhension commune d'un système socio-écologique