Development of probabilistic models for quantitative pathway analysis of plant pest introduction for the EU territory

This report demonstrates a probabilistic quantitative pathway analysis model that can be used in risk assessment for plant pest introduction into EU territory on a range of edible commodities (apples, oranges, stone fruits and wheat). Two types of model were developed: a general commodity model that simulates distribution of an imported infested/infected commodity to and within the EU from source countries by month; and a consignment model that simulates the movement and distribution of individual consignments from source countries to destinations in the EU. The general pathway model has two modules. Module 1 is a trade pathway model, with a Eurostat database of five years of monthly trade volumes for each specific commodity into the EU28 from all source countries and territories. Infestation levels based on interception records, commercial quality standards or other information determine volume of infested commodity entering and transhipped within the EU. Module 2 allocates commodity volumes to processing, retail use and waste streams and overlays the distribution onto EU NUTS2 regions based on population densities and processing unit locations. Transfer potential to domestic host crops is a function of distribution of imported infested product and area of domestic production in NUTS2 regions, pest dispersal potential, and phenology of susceptibility in domestic crops. The consignment model covers the several routes on supply chains for processing and retail use. The output of the general pathway model is a distribution of estimated volumes of infested produce by NUTS2 region across the EU28, by month or annually; this is then related to the accessible susceptible domestic crop. Risk is expressed as a potential volume of infested fruit in potential contact with an area of susceptible domestic host crop. The output of the consignment model is a volume of infested produce retained at each stage along the specific consignment trade chain

Egg shape changes at the theropod–bird transition, and a morphometric study of amniote eggs

The eggs of amniotes exhibit a remarkable variety of shapes, from spherical to elongate and from symmetrical to asymmetrical. We examine eggshell geometry in a diverse sample of fossil and living amniotes using geometric morphometrics and linear measurements. Our goal is to quantify patterns of morphospace occupation and shape variation in the eggs of recent through to Mesozoic birds (neornithe plus non-neornithe avialans), as well as in eggs attributed to non-avialan theropods. In most amniotes, eggs show significant deviation from sphericity, but departure from symmetry around the equatorial axis is mostly confined to theropods and birds. Mesozoic bird eggs differ significantly from extant bird eggs, but extinct Cenozoic bird eggs do not. This suggests that the range of egg shapes in extant birds had already been attained in the Cenozoic. We conclude with a discussion of possible biological factors imparting variation to egg shapes during their formation in the oviduct

A Regional Decision Support Scheme for Pest Risk Analysis in Southeast Asia

A key justification to support plant health regulations is the ability of quarantine services to conduct pest risk analyses (PRA). Despite the supranational nature of biological invasions and the close proximity and connectivity of Southeast Asian countries, PRAs are conducted at the national level. Furthermore, some countries have limited experience in the development of PRAs, which may result in inadequate phytosanitary responses that put their plant resources at risk to pests vectored via international trade. We review existing decision support schemes for PRAs and, following international standards for phytosanitary measures, propose new methods that adapt existing practices to suit the unique characteristics of Southeast Asia. Using a formal written expert elicitation survey, a panel of regional scientific experts was asked to identify and rate unique traits of Southeast Asia with respect to PRA. Subsequently, an expert elicitation workshop with plant protection officials was conducted to verify the potential applicability of the developed methods. Rich biodiversity, shortage of trained personnel, social vulnerability, tropical climate, agriculture-dependent economies, high rates of land-use change, and difficulties in implementing risk management options were identified as challenging Southeast Asian traits. The developed methods emphasize local Southeast Asian conditions and could help support authorities responsible for carrying out PRAs within the region. These methods could also facilitate the creation of other PRA schemes in low- and middle-income tropical countries

Recognizing detachment-mode seafloor spreading in the deep geological past.

Large-offset oceanic detachment faults are a characteristic of slow- and ultraslow-spreading ridges, leading to the formation of oceanic core complexes (OCCs) that expose upper mantle and lower crustal rocks on the seafloor. The lithospheric extension accommodated by these structures is now recognized as a fundamentally distinct “detachment-mode” of seafloor spreading compared to classical magmatic accretion. Here we demonstrate a paleomagnetic methodology that allows unequivocal recognition of detachment-mode seafloor spreading in ancient ophiolites and apply this to a potential Jurassic detachment fault system in the Mirdita ophiolite (Albania). We show that footwall and hanging wall blocks either side of an inferred detachment have significantly different magnetizations that can only be explained by relative rotation during seafloor spreading. The style of rotation is shown to be identical to rolling hinge footwall rotation documented recently in OCCs in the Atlantic, confirming that detachment-mode spreading operated at least as far back as the Jurassic

Capturing egocentric biases in reference reuse during collaborative dialogue

Words that are produced aloud—and especially self-produced ones—are remembered better than words that are not, a phenomenon labeled the production effect in the field of memory research. Two experiments were conducted to determine whether this effect can be generalized to dialogue, and how it might affect dialogue management. Triads (Exp. 1) or dyads (Exp. 2) of participants interacted to perform a collaborative task. Analyzing reference reuse during the interaction revealed that the participants were more likely to reuse the references that they had presented themselves, on the one hand, and those that had been accepted through verbatim repetition, on the other. Analyzing reference recall suggested that the greater accessibility of self-presented references was only transient. Moreover, among partner-presented references, those discussed while the participant had actively taken part in the conversation were more likely to be recalled than those discussed while the participant had been inactive. These results contribute to a better understanding of how individual memory processes might contribute to collaborative dialogue

Investigation of attentional bias in obsessive compulsive disorder with and without depression in visual search

Copyright: © 2013 Morein-Zamir et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedWhether Obsessive Compulsive Disorder (OCD) is associated with an increased attentional bias to emotive stimuli remains controversial. Additionally, it is unclear whether comorbid depression modulates abnormal emotional processing in OCD. This study examined attentional bias to OC-relevant scenes using a visual search task. Controls, non-depressed and depressed OCD patients searched for their personally selected positive images amongst their negative distractors, and vice versa. Whilst the OCD groups were slower than healthy individuals in rating the images, there were no group differences in the magnitude of negative bias to concern-related scenes. A second experiment employing a common set of images replicated the results on an additional sample of OCD patients. Although there was a larger bias to negative OC-related images without pre-exposure overall, no group differences in attentional bias were observed. However, OCD patients subsequently rated the images more slowly and more negatively, again suggesting post-attentional processing abnormalities. The results argue against a robust attentional bias in OCD patients, regardless of their depression status and speak to generalized difficulties disengaging from negative valence stimuli. Rather, post-attentional processing abnormalities may account for differences in emotional processing in OCD.Peer reviewedFinal Published versio

The genome sequence of <i>Trypanosoma brucei gambiense</i>, causative agent of chronic Human African Trypanosomiasis

&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; &lt;i&gt;Trypanosoma brucei gambiense&lt;/i&gt; is the causative agent of chronic Human African Trypanosomiasis or sleeping sickness, a disease endemic across often poor and rural areas of Western and Central Africa. We have previously published the genome sequence of a &lt;i&gt;T. b. brucei&lt;/i&gt; isolate, and have now employed a comparative genomics approach to understand the scale of genomic variation between &lt;i&gt;T. b. gambiense&lt;/i&gt; and the reference genome. We sought to identify features that were uniquely associated with &lt;i&gt;T. b. gambiense&lt;/i&gt; and its ability to infect humans.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Methods and findings:&lt;/b&gt; An improved high-quality draft genome sequence for the group 1 &lt;i&gt;T. b. gambiense&lt;/i&gt; DAL 972 isolate was produced using a whole-genome shotgun strategy. Comparison with &lt;i&gt;T. b. brucei&lt;/i&gt; showed that sequence identity averages 99.2% in coding regions, and gene order is largely collinear. However, variation associated with segmental duplications and tandem gene arrays suggests some reduction of functional repertoire in &lt;i&gt;T. b. gambiense&lt;/i&gt; DAL 972. A comparison of the variant surface glycoproteins (VSG) in &lt;i&gt;T. b. brucei&lt;/i&gt; with all &lt;i&gt;T. b. gambiense&lt;/i&gt; sequence reads showed that the essential structural repertoire of VSG domains is conserved across &lt;i&gt;T. brucei&lt;/i&gt;.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This study provides the first estimate of intraspecific genomic variation within &lt;i&gt;T. brucei&lt;/i&gt;, and so has important consequences for future population genomics studies. We have shown that the &lt;i&gt;T. b. gambiense&lt;/i&gt; genome corresponds closely with the reference, which should therefore be an effective scaffold for any &lt;i&gt;T. brucei&lt;/i&gt; genome sequence data. As VSG repertoire is also well conserved, it may be feasible to describe the total diversity of variant antigens. While we describe several as yet uncharacterized gene families with predicted cell surface roles that were expanded in number in &lt;i&gt;T. b. brucei&lt;/i&gt;, no &lt;i&gt;T. b. gambiense&lt;/i&gt;-specific gene was identified outside of the subtelomeres that could explain the ability to infect humans.&lt;/p&gt

The Evolution of Bat Vestibular Systems in the Face of Potential Antagonistic Selection Pressures for Flight and Echolocation

PMCID: PMC3634842This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Community based needs assessment in an urban area; A participatory action research project

<p>Abstract</p> <p>Background</p> <p>Community assessment is a core function of public health. In such assessments, a commitment to community participation and empowerment is at the heart of the WHO European Healthy Cities Network, reflecting its origins in health for all and the Ottawa Charter for Health Promotion. This study employs a participation and empowerment plan in order to conduct community assessment.</p> <p>Methods</p> <p>The method of participatory action research (PAR) was used. The study was carried out in an area of high socio-economic deprivation in Ardabil, a city in the northwest of Iran, which is currently served by a branch of the Social Development Center (SDC). The steering committee of the project was formed by some university faculty members, health officials and delegates form Farhikhteh non-governmental organization and representatives from twelve blocks or districts of the community. Then, the representatives were trained and then conducted focus groups in their block. The focus group findings informed the development of the questionnaire. About six hundred households were surveyed and study questionnaires were completed either during face-to-face interviews by the research team (in case of illiteracy) or via self-completion. The primary question for the residents was: 'what is the most important health problem in your community? Each health problem identified by the community was weighted based on the frequency it was selected on the survey, and steering committee perception of the problem's seriousness, urgency, solvability, and financial load.</p> <p>Results</p> <p>The main problems of the area appeared to be <it>the asphalt problem</it>, <it>lack of easy access to medical centers</it>, <it>addiction among relatives </it>and <it>unemployment of youth</it>. High participation rates of community members in the steering committee and survey suggest that the PAR approach was greatly appreciated by the community and that problems identified through this research truly reflect community opinion.</p> <p>Conclusions</p> <p>Participatory action research is an effective method for community assessments. However, researchers must rigorously embrace principles of mutual cooperation, respect for public ideas, and a robust belief in community empowerment in order to pave the way for responsible and active citizen participation in the various stages of research.</p

Aldo-keto reductases are biomarkers of NRF2 activity and are co-ordinately overexpressed in non-small cell lung cancer

BACKGROUND: Although the nuclear factor-erythroid 2-related factor 2 (NRF2) pathway is one of the most frequently dysregulated in cancer, it is not clear whether mutational status is a good predictor of NRF2 activity. Here we utilise four members of the aldo-keto reductase (AKR) superfamily as biomarkers to address this question. METHODS: Twenty-three cell lines of diverse origin and NRF2-pathway mutational status were used to determine the relationship between AKR expression and NRF2 activity. AKR expression was evaluated in lung cancer biopsies and Cancer Genome Atlas (TCGA) and Oncomine data sets. RESULTS: AKRs were expressed at a high basal level in cell lines carrying mutations in the NRF2 pathway. In non-mutant cell lines, co-ordinate induction of AKRs was consistently observed following activation of NRF2. Immunohistochemical analysis of lung tumour biopsies and interrogation of TCGA data revealed that AKRs are enriched in both squamous cell carcinomas (SCCs) and adenocarcinomas that contain somatic alterations in the NRF2 pathway but, in the case of SCC, AKRs were also enriched in most other tumours. CONCLUSIONS: An AKR biomarker panel can be used to determine NRF2 status in tumours. Hyperactivation of the NRF2 pathway is far more prevalent in lung SCC than previously predicted by genomic analyses