Overcoming the risk of inaction from emissions uncertainty in smallholder agriculture

The potential for improving productivity and increasing the resilience of smallholder agriculture, while also contributing to climate change mitigation, has recently received considerable political attention (Beddington et al 2012). Financial support for improving smallholder agriculture could come from performance-based funding including sale of carbon credits or certified commodities, payments for ecosystem services, and nationally appropriate mitigation action (NAMA) budgets, as well as more traditional sources of development and environment finance. Monitoring the greenhouse gas fluxes associated with changes to agricultural practice is needed for performance-based mitigation funding, and efforts are underway to develop tools to quantify mitigation achieved and assess trade-offs and synergies between mitigation and other livelihood and environmental priorities (Olander 2012)

Nitrogen abundances in Planet-harbouring stars

We present a detailed spectroscopic analysis of nitrogen abundances in 91 solar-type stars, 66 with and 25 without known planetary mass companions. All comparison sample stars and 28 planet hosts were analysed by spectral synthesis of the near-UV NH band at 3360 \AA observed at high resolution with the VLT/UVES,while the near-IR NI 7468 \AA was measured in 31 objects. These two abundance indicators are in good agreement. We found that nitrogen abundance scales with that of iron in the metallicity range -0.6 <[Fe/H]< +0.4 with the slope 1.08 \pm 0.05. Our results show that the bulk of nitrogen production at high metallicities was coupled with iron. We found that the nitrogen abundance distribution in stars with exoplanets is the high [Fe/H] extension of the curve traced by the comparison sample of stars with no known planets. A comparison of our nitrogen abundances with those available in the literature shows a good agreement.Comment: 15 pages, 7 figures, Accepted for publication in A&

The role of configurality in the Thatcher illusion: an ERP study.

The Thatcher illusion (Thompson in Perception, 9, 483-484, 1980) is often explained as resulting from recognising a distortion of configural information when 'Thatcherised' faces are upright but not when inverted. However, recent behavioural studies suggest that there is an absence of perceptual configurality in upright Thatcherised faces (Donnelly et al. in Attention, Perception & Psychophysics, 74, 1475-1487, 2012) and both perceptual and decisional sources of configurality in behavioural tasks with Thatcherised stimuli (Mestry, Menneer et al. in Frontiers in Psychology, 3, 456, 2012). To examine sources linked to the behavioural experience of the illusion, we studied inversion and Thatcherisation of faces (comparing across conditions in which no features, the eyes, the mouth, or both features were Thatcherised) on a set of event-related potential (ERP) components. Effects of inversion were found at the N170, P2 and P3b. Effects of eye condition were restricted to the N170 generated in the right hemisphere. Critically, an interaction of orientation and eye Thatcherisation was found for the P3b amplitude. Results from an individual with acquired prosopagnosia who can discriminate Thatcherised from typical faces but cannot categorise them or perceive the illusion (Mestry, Donnelly et al. in Neuropsychologia, 50, 3410-3418, 2012) only differed from typical participants at the P3b component. Findings suggest the P3b links most directly to the experience of the illusion. Overall, the study showed evidence consistent with both perceptual and decisional sources and the need to consider both in relation to configurality

Chemical evolution of local galaxies in a hierarchical model

We investigate the chemical properties of local galaxies within a cosmological framework in the hierarchical picture of galaxy formation. To this aim, we use a hierarchical semi-analytic model which includes the contribution from (i) low and intermediate mass stars, (ii) type Ia Supernovae (SNe) and (iii) massive stars. - Abridged - We compare our predictions with available observations in the Milky Way (MW), in local dwarf galaxies and in local ellipticals. For Milky-Way-like galaxies, we can successfully reproduce the [O-Fe] vs [Fe/H] relation observed in disc stars and the stellar metallicity distribution (SMD). For dwarf galaxies, the stellar metallicity vs mass relation is reproduced by assuming that a substantial fraction of the heavy elements is lost through metal-enhanced outflows and a type Ia SN realization probability lower than the one of MW-like galaxies. - Abridged - In ellipticals, the observations indicate higher [alpha/Fe] values in larger galaxies. - Abridged - Our results computed with a standard Salpeter initial mass function (IMF) indicate a flat [alpha/Fe]-sigma relation. However, we suggest a possible solution to this problem and show how, by assuming a star formation-dependent IMF with a slope x=1.35 in systems with star formation rates < 100 M_sun/yr and slightly flatter (i.e. with x=1) in object with stronger star formation, the observed correlation between [alpha/Fe] and sigma can be accounted for on a large velocity dispersion range. Fundamental roles are played also by interaction-triggered starbursts and AGN.Comment: MNRAS, accepted, 27 pages, 22 figure

Rare germline variants in DNA repair genes and the angiogenesis pathway predispose prostate cancer patients to develop metastatic disease

Background Prostate cancer (PrCa) demonstrates a heterogeneous clinical presentation ranging from largely indolent to lethal. We sought to identify a signature of rare inherited variants that distinguishes between these two extreme phenotypes. Methods We sequenced germline whole exomes from 139 aggressive (metastatic, age of diagnosis < 60) and 141 non-aggressive (low clinical grade, age of diagnosis ≥60) PrCa cases. We conducted rare variant association analyses at gene and gene set levels using SKAT and Bayesian risk index techniques. GO term enrichment analysis was performed for genes with the highest differential burden of rare disruptive variants. Results Protein truncating variants (PTVs) in specific DNA repair genes were significantly overrepresented among patients with the aggressive phenotype, with BRCA2, ATM and NBN the most frequently mutated genes. Differential burden of rare variants was identified between metastatic and non-aggressive cases for several genes implicated in angiogenesis, conferring both deleterious and protective effects. Conclusions Inherited PTVs in several DNA repair genes distinguish aggressive from non-aggressive PrCa cases. Furthermore, inherited variants in genes with roles in angiogenesis may be potential predictors for risk of metastases. If validated in a larger dataset, these findings have potential for future clinical application

Code Reuse in Open Source Software

Code reuse is a form of knowledge reuse in software development that is fundamental to innovation in many fields. However, to date there has been no systematic investigation of code reuse in open source software projects. This study uses quantitative and qualitative data gathered from a sample of six open source software projects to explore two sets of research questions derived from the literature on software reuse in firms and open source software development. We find that code reuse is extensive across the sample and that open source software developers, much like developers in firms, apply tools that lower their search costs for knowledge and code, assess the quality of software components, and have incentives to reuse code. Open source software developers reuse code because they want to integrate functionality quickly, because they want to write preferred code, because they operate under limited resources in terms of time and skills, and because they can mitigate development costs through code reuse

modMine: flexible access to modENCODE data.

In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium has generated an enormous library of genomic data along with detailed, structured information on all aspects of the experiments. The modMine database (http://intermine.modencode.org) described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data sets of interest among the thousands generated by modENCODE; (ii) access the data in an integrated form together with non-modENCODE data sets; and (iii) facilitate fine-grained analysis of the above data. The sophisticated search features are possible because of the collection of extensive experimental metadata by the consortium. Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response.

Integrated, up-to-date data about SARS-CoV-2 and COVID-19 is crucial for the ongoing response to the COVID-19 pandemic by the biomedical research community. While rich biological knowledge exists for SARS-CoV-2 and related viruses (SARS-CoV, MERS-CoV), integrating this knowledge is difficult and time-consuming, since much of it is in siloed databases or in textual format. Furthermore, the data required by the research community vary drastically for different tasks; the optimal data for a machine learning task, for example, is much different from the data used to populate a browsable user interface for clinicians. To address these challenges, we created KG-COVID-19, a flexible framework that ingests and integrates heterogeneous biomedical data to produce knowledge graphs (KGs), and applied it to create a KG for COVID-19 response. This KG framework also can be applied to other problems in which siloed biomedical data must be quickly integrated for different research applications, including future pandemics

The challenge of policy coordination for sustainable sociotechnical transitions: the case of the zero-carbon homes agenda in England

Emerging in recent research on sociotechnical transitions towards a low-carbon economy is the question of the extent to which such transitions require centralised, intentional coordination by government. Drawing from Hayek's conceptualisation of coordination, I evaluate the effectiveness of policy for low-carbon and zero-carbon homes in England. A detailed analysis is presented of how policy makers address complex choices and trade-offs as well as significant uncertainty. Particular attention is given to those policy decisions which are widely agreed by stakeholders to cause distortive effects. The focus here on the impacts of policy definition and delivery in terms of multiple evaluative criteria can complement and enrich the more process-orientated cross-sector and multilevel analyses that predominate in existing research on policy coordination. Furthermore, the coordination problems identified yield further insights into the actual and potential effectiveness of policy processes in shaping complex sociotechnical transitions