Future of the Sea: Health and Wellbeing of Coastal Communities

This is the final version of the report. Available from the Government Office for Science via the link in this recordThis review has been commissioned as part of the UK government’s Foresight Future of the Sea project. The views expressed do not represent policy of any government or organisationApproximately 17 per cent of the UK population live in coastal communities; some are prosperous and commercially successful, others experiencing socio- economic decline. Regardless, evidence suggests growing risks for the health and wellbeing of coastal communities. Communities along the coast are on the front line in facing climate change and marine pollution impacts, furthermore their economies are deeply embedded with coastal and other marine activities, making these communities particularly affected. Sea-level rise and extreme weather events, driven by climate change and ecosystem damage, expose coastal communities to flooding events now and in the future, damaging local economies, and threatening health and wellbeing. Continuing pollution of the sea has been underestimated as a threat to the health of coastal dwellers.Governtment Office for Scienc

LHC Signatures of a Minimal Supersymmetric Hidden Valley

We investigate the LHC signals of a minimal supersymmetric hidden valley. Our theory consists of the supersymmetric Standard Model along with a light hidden U(1)_x gauge multiplet and a pair of hidden chiral superfields that spontaneously break the new Abelian gauge symmetry near a GeV. The visible and hidden sectors interact exclusively through supersymmetric gauge kinetic mixing. We perform a thorough examination of the hidden decay cascades initiated by the lightest Standard Model superpartner and we study the range of LHC signals they can produce. In particular, we find parameter regions that give rise to missing energy, single and multiple lepton jets, and displaced vertices. Given the simplicity of the underlying theory and the broad range of collider signals it can produce, we propose that this model is a useful benchmark for LHC studies of (supersymmetric) hidden valleys.Comment: 45 pages, 15 figures; typos corrected but conclusions unchange

Computer vision and machine learning for robust phenotyping in genome-wide studies

Traditional evaluation of crop biotic and abiotic stresses are time-consuming and labor-intensive limiting the ability to dissect the genetic basis of quantitative traits. A machine learning (ML)-enabled image-phenotyping pipeline for the genetic studies of abiotic stress iron deficiency chlorosis (IDC) of soybean is reported. IDC classification and severity for an association panel of 461 diverse plant-introduction accessions was evaluated using an end-to-end phenotyping workflow. The workflow consisted of a multi-stage procedure including: (1) optimized protocols for consistent image capture across plant canopies, (2) canopy identification and registration from cluttered backgrounds, (3) extraction of domain expert informed features from the processed images to accurately represent IDC expression, and (4) supervised ML-based classifiers that linked the automatically extracted features with expert-rating equivalent IDC scores. ML-generated phenotypic data were subsequently utilized for the genome-wide association study and genomic prediction. The results illustrate the reliability and advantage of ML-enabled image-phenotyping pipeline by identifying previously reported locus and a novel locus harboring a gene homolog involved in iron acquisition. This study demonstrates a promising path for integrating the phenotyping pipeline into genomic prediction, and provides a systematic framework enabling robust and quicker phenotyping through ground-based systems

Genome-Wide Identification and Mapping of NBS-Encoding Resistance Genes in Solanum tuberosum Group Phureja

The majority of disease resistance (R) genes identified to date in plants encode a nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain containing protein. Additional domains such as coiled-coil (CC) and TOLL/interleukin-1 receptor (TIR) domains can also be present. In the recently sequenced Solanum tuberosum group phureja genome we used HMM models and manual curation to annotate 435 NBS-encoding R gene homologs and 142 NBS-derived genes that lack the NBS domain. Highly similar homologs for most previously documented Solanaceae R genes were identified. A surprising ∼41% (179) of the 435 NBS-encoding genes are pseudogenes primarily caused by premature stop codons or frameshift mutations. Alignment of 81.80% of the 577 homologs to S. tuberosum group phureja pseudomolecules revealed non-random distribution of the R-genes; 362 of 470 genes were found in high density clusters on 11 chromosomes

What Constitutes a Natural Fire Regime? Insight from the Ecology and Distribution of Coniferous Forest Birds in North America

Bird species that specialize in the use of burned forest conditions can provide insight into the prehistoric fire regimes associated with the forest types that they have occupied over evolutionary time. The nature of their adaptations reflects the specific post-fire conditions that occurred prior to the unnatural influence of humans after European settlement. Specifically, the post-fire conditions, nest site locations, and social systems of two species (Bachman\u27s sparrow [Aimophila aestivalis] and red-cockaded woodpecker [Picoides borealis]) suggest that, prehistorically, a frequent, low-severity fire regime characterized the southeastern pine system in which they evolved. In contrast, the patterns of distribution and abundance for several other bird species (black-backed woodpecker [Picoides arcticus], buff-breasted flycatcher [Empidonax fulvifrons], Lewis\u27 woodpecker [Melanerpes lewis], northern hawk owl [Surnia ulula], and Kirtland\u27s warbler [Dendroica kirtlandii]) suggest that severe fire has been an important component of the fire regimes with which they evolved. Patterns of habitat use by the latter species indicate that severe fires are important components not only of higher-elevation and high-latitude conifer forest types, which are known to be dominated by such fires, but also of mid-elevation and even low-elevation conifer forest types that are not normally assumed to have had high-severity fire as an integral part of their natural fire regimes. Because plant and animal adaptations can serve as reliable sources of information about what constitutes a natural fire regime, it might be wise to supplement traditional historical methods with careful consideration of information related to plant and animal adaptations when attempting to restore what are thought to be natural fire regimes

Ecological impacts of non-native Pacific oysters (Crassostrea gigas) and management measures for protected areas in Europe

Pacific oysters are now one of the most ‘globalised’ marine invertebrates. They dominate bivalve aquaculture production in many regions and wild populations are increasingly becoming established, with potential to displace native species and modify habitats and ecosystems. While some fishing communities may benefit from wild populations, there is now a tension between the continued production of Pacific oysters and risk to biodiversity, which is of particular concern within protected sites. The issue of the Pacific oyster therefore locates at the intersection between two policy areas: one concerning the conservation of protected habitats, the other relating to livelihoods and the socio-economics of coastal aquaculture and fishing communities. To help provide an informed basis for management decisions, we first summarise evidence for ecological impacts of wild Pacific oysters in representative coastal habitats. At local scales, it is clear that establishment of Pacific oysters can significantly alter diversity, community structure and ecosystem processes, with effects varying among habitats and locations and with the density of oysters. Less evidence is available to evaluate regional-scale impacts. A range of management measures have been applied to mitigate negative impacts of wild Pacific oysters and we develop recommendations which are consistent with the scientific evidence and believe compatible with multiple interests. We conclude that all stakeholders must engage in regional decision making to help minimise negative environmental impacts, and promote sustainable industry development

Practical guidelines for rigor and reproducibility in preclinical and clinical studies on cardioprotection

The potential for ischemic preconditioning to reduce infarct size was first recognized more than 30 years ago. Despite extension of the concept to ischemic postconditioning and remote ischemic conditioning and literally thousands of experimental studies in various species and models which identified a multitude of signaling steps, so far there is only a single and very recent study, which has unequivocally translated cardioprotection to improved clinical outcome as the primary endpoint in patients. Many potential reasons for this disappointing lack of clinical translation of cardioprotection have been proposed, including lack of rigor and reproducibility in preclinical studies, and poor design and conduct of clinical trials. There is, however, universal agreement that robust preclinical data are a mandatory prerequisite to initiate a meaningful clinical trial. In this context, it is disconcerting that the CAESAR consortium (Consortium for preclinicAl assESsment of cARdioprotective therapies) in a highly standardized multi-center approach of preclinical studies identified only ischemic preconditioning, but not nitrite or sildenafil, when given as adjunct to reperfusion, to reduce infarct size. However, ischemic preconditioning—due to its very nature—can only be used in elective interventions, and not in acute myocardial infarction. Therefore, better strategies to identify robust and reproducible strategies of cardioprotection, which can subsequently be tested in clinical trials must be developed. We refer to the recent guidelines for experimental models of myocardial ischemia and infarction, and aim to provide now practical guidelines to ensure rigor and reproducibility in preclinical and clinical studies on cardioprotection. In line with the above guideline, we define rigor as standardized state-of-the-art design, conduct and reporting of a study, which is then a prerequisite for reproducibility, i.e. replication of results by another laboratory when performing exactly the same experiment