A cascaded approach to normalising gene mentions in biomedical literature

Linking gene and protein names mentioned in the literature to unique identifiers in referent genomic databases is an essential step in accessing and integrating knowledge in the biomedical domain. However, it remains a challenging task due to lexical and terminological variation, and ambiguity of gene name mentions in documents. We present a generic and effective rule-based approach to link gene mentions in the literature to referent genomic databases, where pre-processing of both gene synonyms in the databases and gene mentions in text are first applied. The mapping method employs a cascaded approach, which combines exact, exact-like and token-based approximate matching by using flexible representations of a gene synonym dictionary and gene mentions generated during the pre-processing phase. We also consider multi-gene name mentions and permutation of components in gene names. A systematic evaluation of the suggested methods has identified steps that are beneficial for improving either precision or recall in gene name identification. The results of the experiments on the BioCreAtIvE2 data sets (identification of human gene names) demonstrated that our methods achieved highly encouraging results with F-measure of up to 81.20%

Democracia monitorizada en España. Nuevas formas de participación política en el marco de la era digital

Se ofrece una reflexión sobre el complejo contexto político español desde la propuesta de la democracia monitorizada. Los resultados muestran la consolidación de heterogéneos procesos de escrutinio público a través del uso del potencial ofrecido por las TIC.This article aims to reflect on the complex political context of Spain using the monitory democracy framework. The results indicate the consolidation of heterogeneous processes of public scrutiny through the exploitation of the potential offered by the ICT

Resilience–Recovery Factors in Post-traumatic Stress Disorder Among Female and Male Vietnam Veterans: Hardiness, Postwar Social Support, and Additional Stressful Life Events

Structural equation modeling procedures were used to examine relationships among several war zone stressor dimensions, resilience-recovery factors, and post-traumatic stress disorder symptoms in a national sample of 1,632 Vietnam veterans (26% women and 74% men). A 9-factor measurement model was specified on a mixed-gender subsample of the data and then replicated on separate subsamples of female and male veterans. For both genders, the structural models supported strong mediation effects for the intrapersonal resource characteristic of hardiness, postwar structural and functional social support, and additional negative life events in the postwar period. Support for moderator effects or buffering in terms of interactions between war zone stressor level and resiliencerecovery factors was minimal

Stochastic parameterization: uncertainties from convection

In 2005, the ECMWF held a workshop on stochastic parameterisation, at which the convection was seen as being a key issue. That much is clear from the working group reports and particularly the statement from working group 1 that “it is clear that a stochastic convection scheme is desirable”. The present note aims to consider our current status in comparison with some of the issues raised and hopes expressed in that working group report

A formal approach to determining parallel resource bindings

The paper investigates the nature of the design process for parallel operating systems. It proposes a temporal logic-based formal methodology addressing the high-level design of such systems. In operating systems design, much use is made of the informal notion of resource bindings. A way of improving the high-level design of parallel systems is proposed by providing a formal language for enumerating the design space and thus enabling all high-level design alternatives to be represented. A design process to be used with this language is given, the aim being to establish the most appropriate binding. The process is temporal logic-based and permits high level design of parallel systems to be analysed, tested and, in certain cases, formally verified before implementation is embarked upo

A method of verification in design: an operating system case study

This paper reports a study of verification in the high-level design phase of operating system development in which both a rigorous and formal verification are used, where the rigorous argument is used to determine a manageable formal proof to be carried out. A 2-sorted first order temporal language is used to express several possible high-level designs and the required properties of an operating system store manager. The case of large system limits is reduced to a case of small system limits by use of a rigorous argument. Corresponding proportional temporal logic (PTL) formulae are then verified using a PTL theorem prover

The use of formal methods in parallel operating systems

The authors report on the use of formal methods for the development of parallel operating systems for two experimental declarative systems over a five-year period. A common specification approach has evolved as part of the development of these two very different systems: one being for a parallel graph reduction machine and written in a functional language enhanced with state-based objects, the other was written in C++. A brief overview of each system is given before concentrating on the use of formal methods. A description is given of how both a technique for formally specifying sequential systems (VDM) and a technique for specifying concurrent systems (temporal logic) have been used together. In both cases, the issue of verification is addresse

Representation of coherency classes for parallel systems

Some parallel applications do not require a precise imitation of the behaviour of the physically shared memory programming model. Consequently, certain parallel machine architectures have elected to emphasise different required coherency properties because of possible efficiency gains. This has led to various definitions of models of store coherency. These definitions have not been amenable to detailed analysis and, consequently, inconsistencies have resulted. In this paper a unified framework is proposed in which different models of store coherency are developed systematically by progressively relaxing the constraints that they have to satisfy. A demonstration is given of how formal reasoning can be cam’ed out to compare different models. Some real-life systems are considered and a definition of a version of weak coherency is found to be incomplete

Asking sensitive questions using the Unmatched Count Technique: Applications and guidelines for conservation

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordData accessibility: All data used in the analyses are freely available in the University of Oxford research archive at this link: https://ora.ox.ac.uk/objects/uuid:556a8a97-2d3d-4bf2-8fc1-359ce9786986. Data were gathered from 101 English language publications that empirically tested the UCT method. For each paper, information on 17 variables was collected, including the context (e.g. discipline, behaviour studied, rationale for using UCT, location), details of survey administration (e.g. whether a pilot study was conducted, whether design assumptions were checked), type of analysis, and comparisons to other methods (e.g. direct questions). Full data collection protocol and citations for all 101 reviewed publications are included in Appendix III and IV.1.Researchers and practitioners are increasingly using methods from the social sciences to address complex conservation challenges. This brings benefits but also the responsibility to understand the suitability and limitations of these methods in different contexts. After years of use in other disciplines, the Unmatched Count Technique (UCT) has recently been adopted by conservation scientists to investigate illegal and socially undesirable human behaviours. Here we provide guidance for practitioners and researchers on how to apply UCT effectively, and outline situations where it will be most and least appropriate. 2.We reviewed 101 publications in refereed journals that used UCT to draw conclusions on its use to date and provide recommendations on when and how to use the method effectively in conservation. In particular, we explored: type of studies undertaken (e.g. disciplines; behaviour being studied; rationale for using UCT); survey administration (e.g. sample size, pilot studies, administration mode); UCT outcomes (e.g. type of analyses, estimates, comparison with other methods); and type of recommendations. 3.We show that UCT has been used across multiple disciplines and contexts, with 10 studies that focus on conservation and natural resource use. The UCT has been used to investigate topics falling into five categories: socially undesirable behaviours, socially undesirable views, illegal or non‐compliant behaviours, socially desirable behaviours; and personal topics (e.g. being HIV positive). It has been used in 51 countries and is suitable to several situations, but limitations do exist, and the method does not always improve reporting of sensitive topics. 4.We provide best‐practice guidance to researchers and practitioners considering using UCT. We highlight that alternate methods should be considered if sample sizes are likely to be small, the behaviour in question is likely to be extremely rare, or if the behaviour is not particularly sensitive. UCT can be a useful tool for estimating the extent of non‐compliance within a conservation context, but as with all scientific investigation, careful study design, robust sampling and consistent implementation are required in order for it to be effective.Oxford Martin Programme on the Illegal Wildlife TradeNational Environment Research Council (NERC)Darwin Initiativ