A generalized collectively compact operator theory with an application to integral equations on unbounded domains

In this paper a generalization of collectively compact operator theory in Banach spaces is developed. A feature of the new theory is that the operators involved are no longer required to be compact in the norm topology. Instead it is required that the image of a bounded set under the operator family is sequentially compact in a weaker topology. As an application, the theory developed is used to establish solvability results for a class of systems of second kind integral equations on unbounded domains, this class including in particular systems of Wiener-Hopf integral equations with L1 convolutions kernels

Very high resolution bioclimatic zoning of Portuguese wine regions: present and future scenarios

Wine production is strongly affected by weather and climate and thus highly vulnerable to climate change. In Portugal, viticulture and wine production are an important economic activity. In the present study, current bioclimatic zoning in Portugal (1950–2000) and its projected changes under future climate conditions (2041–2070) are assessed through the analysis of an aggregated, categorized bioclimatic index (CatI) at a very high spatial resolution (near 1 km). CatI incorporates the most relevant bioclimatic characteristics of a given region, thus allowing the direct comparison between different regions. Future viticultural zoning is achieved using data from 13 climate model transient experiments following the A1B emission scenario. These data are downscaled using a two-step method of spatial pattern downscaling. This downscaling approach allows characterizing mesoclimatic influences on viticulture throughout Portugal. Results for the recent past depict the current spatial variability of Portuguese viticultural regions. Under future climate conditions, the current viticultural zoning is projected to undergo significant changes, which may represent important challenges for the Portuguese winemaking sector. The changes are quite robust across the different climate models. A lower bioclimatic diversity is also projected, resulting from a more homogeneous warm and dry climate in most of the wine regions. This will lead to changes in varietal suitability and wine characteristics of each region.

Knowledge-based clinical pathway for medical quality improvement

Clinical pathways have been adopted for various diseases in clinical departments for quality improvement as a result of standardization of medical activities in treatment process. Using knowledge-based decision support on the basis of clinical pathways is a promising strategy to improve medical quality effectively. However, the clinical pathway knowledge has not been fully integrated into treatment process and thus cannot provide comprehensive support to the actual work practice. Therefore this paper proposes a knowledgebased clinical pathway management method which contributes to make use of clinical knowledge to support and optimize medical practice. We have developed a knowledgebased clinical pathway management system to demonstrate how the clinical pathway knowledge comprehensively supports the treatment process. The experiences from the use of this system show that the treatment quality can be effectively improved by the extracted and classified clinical pathway knowledge, seamless integration of patient-specific clinical pathway recommendations with medical tasks and the evaluating pathway deviations for optimization.

Making the most of PAS data: Macro- and micro-level studies of Romano-British settlement

The Portable Antiquities Scheme (PAS) database includes records of over 225,000 artefacts of Roman date, with a wide geographical coverage and the potential to contribute to our understanding of Romano-British landscapes and settlement at several scales of analysis. This paper draws upon the author’s doctoral research to describe regional case studies from six counties (Wiltshire, Worcestershire, Warwickshire, Northamptonshire, North Lincolnshire and Cumbria) on the use of PAS data. The data have value nationally and regionally as general guides to ancient settlement patterns, but it is arguably at the micro-scale that they have the most potential. With reference to detailed landscape studies from parts of Warwickshire and Wiltshire, the paper argues that sites represented by PAS data are often rural settlements that show evidence for continued activity throughout the Roman period. The paper demonstrates that with an appropriate methodology PAS data can be an immensely valuable archaeological resource, particularly when interpreted at multiple scales, and can be considerably more than a guide to broad distributions of Roman finds.

Atmospheric blocking in a high resolution climate model: influences of mean state, orography and eddy forcing

An underestimate of atmospheric blocking occurrence is a well-known limitation of many climate models. This article presents an analysis of Northern Hemisphere winter blocking in an atmospheric model with increased horizontal resolution. European blocking frequency increases with model resolution, and this results from an improvement in the atmospheric patterns of variability as well as a simple improvement in the mean state. There is some evidence that the transient eddy momentum forcing of European blocks is increased at high resolution, which could account for this. However, it is also shown that the increase in resolution of the orography is needed to realise the improvement in blocking, consistent with the increase in height of the Rocky Mountains acting to increase the tilt of the Atlantic jet stream and giving higher mean geopotential heights over northern Europe. Blocking frequencies in the Pacific sector are also increased with atmospheric resolution, but in this case the improvement in orography actually leads to a decrease in blocking

Comparative genomics of Salmonella enterica serovars Derby and Mbandaka, two prevalent serovars associated with different livestock species in the UK

Background Despite the frequent isolation of Salmonella enterica sub. enterica serovars Derby and Mbandaka from livestock in the UK and USA little is known about the biological processes maintaining their prevalence. Statistics for Salmonella isolations from livestock production in the UK show that S. Derby is most commonly associated with pigs and turkeys and S. Mbandaka with cattle and chickens. Here we compare the first sequenced genomes of S. Derby and S. Mbandaka as a basis for further analysis of the potential host adaptations that contribute to their distinct host species distributions. Results Comparative functional genomics using the RAST annotation system showed that predominantly mechanisms that relate to metabolite utilisation, in vivo and ex vivo persistence and pathogenesis distinguish S. Derby from S. Mbandaka. Alignment of the genome nucleotide sequences of S. Derby D1 and D2 and S. Mbandaka M1 and M2 with Salmonella pathogenicity islands (SPI) identified unique complements of genes associated with host adaptation. We also describe a new genomic island with a putative role in pathogenesis, SPI-23. SPI-23 is present in several S. enterica serovars, including S. Agona, S. Dublin and S. Gallinarum, it is absent in its entirety from S. Mbandaka. Conclusions We discovered a new 37 Kb genomic island, SPI-23, in the chromosome sequence of S. Derby, encoding 42 ORFS, ten of which are putative TTSS effector proteins. We infer from full-genome synonymous SNP analysis that these two serovars diverged, between 182kya and 625kya coinciding with the divergence of domestic pigs. The differences between the genomes of these serovars suggest they have been exposed to different stresses including, phage, transposons and prolonged externalisation. The two serovars possess distinct complements of metabolic genes; many of which cluster into pathways for catabolism of carbon sources.

Impact of vegetation and preferential source areas on global dust aerosol: results from a model study

[1] We present a model of the dust cycle that successfully predicts dust emissions as determined by land surface properties, monthly vegetation and snow cover, and 6-hourly surface wind speeds for the years 1982–1993. The model takes account of the role of dry lake beds as preferential source areas for dust emission. The occurrence of these preferential sources is determined by a water routing and storage model. The dust source scheme also explicitly takes into account the role of vegetation type as well as monthly vegetation cover. Dust transport is computed using assimilated winds for the years 1987–1990. Deposition of dust occurs through dry and wet deposition, where subcloud scavenging is calculated using assimilated precipitation fields. Comparison of simulated patterns of atmospheric dust loading with the Total Ozone Mapping Spectrometer satellite absorbing aerosol index shows that the model produces realistic results from daily to interannual timescales. The magnitude of dust deposition agrees well with sediment flux data from marine sites. Emission of submicron dust from preferential source areas are required for the computation of a realistic dust optical thickness. Sensitivity studies show that Asian dust source strengths are particularly sensitive to the seasonality of vegetation cover.

Association learning for emotional harbinger cues: When do previous emotional associations impair and when do they facilitate subsequent learning of new associations?

Neutral cues that predict emotional events (emotional harbingers) acquire emotional properties and attract attention. Given the importance of emotional harbingers for future survival, it is desirable to flexibly learn new facts about emotional harbingers when needed. However, recent research revealed that it is harder to learn new associations for emotional harbingers than cues that predict non-emotional events (neutral harbingers). In the current study, we addressed whether this impaired association learning for emotional harbingers is altered by one’s awareness of the contingencies between cues and emotional outcomes. Across 3 studies, we found that one’s awareness of the contingencies determines subsequent association learning of emotional harbingers. Emotional harbingers produced worse association learning than neutral harbingers when people were not aware of the contingencies between cues and emotional outcomes, but produced better association learning when people were aware of the contingencies. These results suggest that emotional harbingers do not always suffer from impaired association learning and can show facilitated learning depending on one’s contingency awareness.

The pgip family in soybean and three other legume species: evidence for a birth-and-death model of evolution

Background Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) plant cell wall glycoproteins involved in plant immunity. They are typically encoded by gene families with a small number of gene copies whose evolutionary origin has been poorly investigated. Here we report the complete characterization of the full complement of the pgip family in soybean (Glycine max [L.] Merr.) and the characterization of the genomic region surrounding the pgip family in four legume species. Results BAC clone and genome sequence analyses showed that the soybean genome contains two pgip loci. Each locus is composed of three clustered genes that are induced following infection with the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary, and remnant sequences of pgip genes. The analyzed homeologous soybean genomic regions (about 126 Kb) that include the pgip loci are strongly conserved and this conservation extends also to the genomes of the legume species Phaseolus vulgaris L., Medicago truncatula Gaertn. and Cicer arietinum L., each containing a single pgip locus. Maximum likelihood-based gene trees suggest that the genes within the pgip clusters have independently undergone tandem duplication in each species. Conclusions The paleopolyploid soybean genome contains two pgip loci comprised in large and highly conserved duplicated regions, which are also conserved in bean, M. truncatula and C. arietinum. The genomic features of these legume pgip families suggest that the forces driving the evolution of pgip genes follow the birth-and-death model, similar to that proposed for the evolution of resistance (R) genes of NBS-LRR-type.

Bdellovibrio bacteriovorus HD100 guards against Pseudomonas tolaasii brown-blotch lesions on the surface of post-harvest Agaricus bisporus supermarket mushrooms

BACKGROUND: Pseudomonas tolaasii is a problematic pathogen of cultured mushrooms, forming dark brown 'blotches' on mushroom surfaces and causing spoilage during crop growth and post-harvest . Treating P. tolaasii infection is difficult, as other, commensal bacterial species such as Pseudomonas putida are necessary for mushroom growth, so treatments must be relatively specific. RESULTS: We have found that P. tolaasii is susceptible to predation in vitro by the δ-proteobacterium Bdellovibrio bacteriovorus. This effect also occurred in funga, where B. bacteriovorus was administered to post-harvest mushroom caps before and after administration of the P. tolaasii pathogen. A significant, visible improvement in blotch appearance, after incubation, was observed on administration of Bdellovibrio. A significant reduction in viable P. tolaasii cell numbers, recovered from the mushroom tissue, was detected. This was accompanied by a more marked reduction in blotch severity on Bdellovibrio administration. We found that there was in some cases an accompanying overgrowth of presumed-commensal, non-Pseudomonas bacteria on post-harvest mushroom caps after Bdellovibrio-treatment. These bacteria were identified (by 16SrRNA gene sequencing) as Enterobacter species, which were seemingly resistant to predation. We visualised predatory interactions occuring between B. bacteriovorus and P. tolaasii on the post-harvest mushroom cap surface by Scanning Electron Microscopy, seeing predatory invasion of P. tolaasii by B. bacteriovorus in funga. This anti-P. tolaasii effect worked well in post-harvest supermarket mushrooms, thus Bdellovibrio was not affected by any pre-treatment of mushrooms for commercial/consumer purposes. CONCLUSIONS: The soil-dwelling B. bacteriovorus HD100 preys upon and kills P. tolaasii, on mushroom surfaces, and could therefore be applied to prevent spoilage in post-harvest situations where mushrooms are stored and packaged for sale.

Deglaciation of the Caucasus Mountains, Russia/Georgia, in the 21st century observed with ASTER satellite imagery and aerial photograpy

Changes in the map area of 498 glaciers located on the Main Caucasus ridge (MCR) and on Mt. Elbrus in the Greater Caucasus Mountains (Russia and Georgia) were assessed using multispectral ASTER and panchromatic Landsat imagery with 15 m spatial resolution in 1999/2001 and 2010/2012. Changes in recession rates of glacier snouts between 1987–2001 and 2001–2010 were investigated using aerial photography and ASTER imagery for a sub-sample of 44 glaciers. In total, glacier area decreased by 4.7 ± 2.1% or 19.2 ± 8.7 km2 from 407.3 ± 5.4 km2 to 388.1 ± 5.2 km2. Glaciers located in the central and western MCR lost 13.4 ± 7.3 km2 (4.7 ± 2.5%) in total or 8.5 km2 (5.0 ± 2.4%) and 4.9 km2 (4.1 ± 2.7%) respectively. Glaciers on Mt. Elbrus, although located at higher elevations, lost 5.8 ± 1.4 km2 (4.9 ± 1.2%) of their total area. The recession rates of valley glacier termini increased between 1987–2000/01 and 2000/01–2010 (2000 for the western MCR and 2001 for the central MCR and Mt.~Elbrus) from 3.8 ± 0.8, 3.2 ± 0.9 and 8.3 ± 0.8 m yr−1 to 11.9 ± 1.1, 8.7 ± 1.1 and 14.1 ± 1.1 m yr−1 in the central and western MCR and on Mt. Elbrus respectively. The highest rate of increase in glacier termini retreat was registered on the southern slope of the central MCR where it has tripled. A positive trend in summer temperatures forced glacier recession, and strong positive temperature anomalies in 1998, 2006, and 2010 contributed to the enhanced loss of ice. An increase in accumulation season precipitation observed in the northern MCR since the mid-1980s has not compensated for the effects of summer warming while the negative precipitation anomalies, observed on the southern slope of the central MCR in the 1990s, resulted in stronger glacier wastage.

A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely-related crop species, lentil, and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2 cM interval of Vf chromosome 2 which was highly collinear with Mt3. The obvious candidate gene from 77 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene (Mt3g092830, Mt3g092840) controlling anthocyanin production in Medicago and re-sequencing of the Vf orthologue showed a putative causative deletion of the entire 5’ end of the gene.

Sea level extremes at the coasts of China

Hourly sea level records from 1954 to 2012 at 20 tide gauges at and adjacent to the Chinese coasts are used to analyze extremes in sea level and in tidal residual. Tides and tropical cyclones determine the spatial distribution of sea level maxima. Tidal residual maxima are predominantly determined by tropical cyclones. The 50 year return level is found to be sensitive to the number of extreme events used in the estimation. This is caused by the small number of tropical cyclone events happening each year which lead to other local storm events included thus significantly affecting the estimates. Significant increase in sea level extremes is found with trends in the range between 2.0 and 14.1 mm yr−1. The trends are primarily driven by changes in median sea level but also linked with increases in tidal amplitudes at three stations. Tropical cyclones cause significant interannual variations in the extremes. The interannual variability in the sea level extremes is also influenced by the changes in median sea level at the north and by the 18.6 year nodal cycle at the South China Sea. Neither of PDO and ENSO is found to be an indicator of changes in the size of extremes, but ENSO appears to regulate the number of tropical cyclones that reach the Chinese coasts. Global mean atmospheric temperature appears to be a good descriptor of the interannual variability of tidal residual extremes induced by tropical cyclones but the trend in global temperature is inconsistent with the lack of trend in the residuals.