Accuracy assessment of supervised classification of submersed macrophytes: the case of the Gavaraget region of Lake Sevan,Armenia

The necessity of assessing the accuracy of spatial data derived from remote sensing methods and used in geographic information system (GIS) analyses has been regarded as a critical component of many projects. In this article, supervised classified QuickBird satellite imageries of submersed macrophytes of the Gavaraget region of Lake Sevan (Armenia) during 2006–2008 are validated in a GIS environment. The results of this assessment are represented by error matrices presenting the overall accuracy, the user and producer accuracies in each category, as well as the kappa coefficients. The assessments were done at three levels: the vegetation types, the growth (vertical) type, and the species levels. At the vegetation level, an overall accuracy of more than 86% was achieved in 2006 and 2007, while that in 2008 was about 72%. Substantial agreements were achieved between the classified remote sensing data and the reference (groundtruth) data for both 2006 and 2007. Only a fair agreement was attained in 2008. The kappa coefficients ranged from 0.39 to 0.89. At the growth type level, only the 2006 classification attained a substantial agreement, with an overall accuracy of 80%. The 2007 and 2008 classifications had above average and average overall accuracies of 72 and 64%, respectively. The kappa coefficient had a lowest value of 0.35 and a highest value of 0.70 at the growth type level. At the species level, Chara spp. or Zannichellia palustris and Potamogeton pectinatus had high user accuracies of more than 90% and a high overall accuracy of 82% in 2006. High user accuracies (>80%) occurred for P. pectinatus (for 2007 and 2008) and No Vegetation (for 2007). The remaining species, however, had low user and producer accuracies of less than 64%. The kappa coefficients ranged between 0.36 and 0.73 at the species level.     

The Long Term Impact of Cataract Surgery on Quality of Life,Activities and Poverty: Results from a Six Year Longitudinal Study in Bangladesh and the Philippines

Background

Cataract surgery has been shown to improve quality of life and household economy in the short term. However, it is unclear whether these benefits are sustained over time. This study aims to assess the six year impact of cataract surgery on health related quality of life (HRQoL), daily activities and economic poverty in Bangladesh and The Philippines.

Methods and Findings

This was a longitudinal study. At baseline people aged ≥50 years with visual impairment due to cataract (‘cases’) and age-, sex-matched controls without visual impairment were interviewed about vision specific and generic HRQoL, daily activities and economic indicators (household per capita expenditure, assets and self-rated wealth). Cases were offered free or subsidised cataract surgery. Cases and controls were re-interviewed approximately one and six years later. At baseline across the two countries there were 455 cases and 443 controls. Fifty percent of cases attended for surgery. Response rates at six years were 47% for operated cases and 53% for controls. At baseline cases had poorer health and vision related QoL, were less likely to undertake productive activities, more likely to receive assistance with activities and were poorer compared to controls (p<0.05). One year after surgery there were significant increases in HRQoL, participation and time spent in productive activities and per capita expenditure and reduction in assistance with activities so that the operated cases were similar to controls. These increases were still evident after six years with the exception that time spent on productive activities decreased among both cases and controls.

Conclusion

Cataract causing visual loss is associated with reduced HRQoL and economic poverty among older adults in low-income countries. Cataract surgery improves the HRQoL of the individual and economy of the household. The findings of this study suggest these benefits are sustained in the long term.     

Process challenges relating to hematopoietic stem cell cultivation in bioreactors

Hematopoietic stem cells (HSCs) are extremely useful in treating a wide range of diseases and have a variety of useful research applications. However, the routinely generated low in vitro concentrations of HSCs from current bioreactor manufacturing systems has been a hindrance to the full-scale application of these essential cellular materials. This has made the search for novel bioreactor systems for high-concentration HSC production a major research endeavour. This review addresses process challenges in relation to bioreactor development and optimisation for high-density HSC production under effective monitoring of essential culture parameters, such as pH, dissolved oxygen and nutrient uptake. It discusses different process strategies and bioreactor configurations for HSCs production from a commercial viability perspective, and also discusses recent advances in the field.     

Evidence of natural selection for disease resistance in Composite Cross Five (CCV) of barley

Cambridge Composite Cross Five (CCV) of barley was studied utilising hordeins, restriction fragment length polymorphisms (RFLPs) and reaction to powdery mildew with a view to understanding the genetic changes occurring in the population. Changes in the frequency of individual hordein patterns as well as pattern combinations showed directional trends in successive generations in three parallel populations maintained as discrete populations since 1977 in Cambridge. Certain hordein pattern combinations were more common in the resistance classes and there was a strong association between hordein patterns and mildew reaction. RFLP analysis revealed that 80% of a random sample taken from generation F₂₄ of Population I had the same restriction pattern as that of the cultivar Algerian, which was one of the original 30 parental lines of CCV. This cultivar is the source of the Mla1 allele in barley improvement programmes in Europe. We argue, based on supporting evidence from hordein analysis and tests of reaction to selected mildew isolates of known virulence isolates together with UK virulence surveys, that selection for Mla1 in Cambridge has been the predominant evolutionary force in CCV in Cambridge.     

Hordein Variation and Reaction to Powdery Mildew in Composite Cross XLII of Barley

A bulk hybrid population, CCXLII was investigated for hordein variation and reaction to powdery mildew. The results indicated that the population in F₄ was genetically variable and contained an appreciable proportion of heterozygotes. Evidence was found for differential viability within families. This was possibly the result of a high segregation load. The pattern of genetic variation suggests that although the population could be a useful source of breeding material for the selection of new lines, it may be risky as a method of conservation of germplasm.     

Plant MAPK cascades: Just rapid signaling modules?

Abscisic acid (ABA) is a major phytohormone mediating important stress-related processes. We recently unveiled an ABA-activated MAPK signaling module constituted of MAP3K17/18-MKK3-MPK1/2/7/14. Unlike classical rapid MAPK activation, we showed that the activation of the new MAPK module is delayed and relies on the MAP3K protein synthesis. In this addendum, we discuss the role of this original and unexpected activation mechanism of MAPK cascades which suggests that MAPKs can regulate both early and long-term plant stress responses.     

Phylogeography of the heavily poached African common pangolin (Pholidota,Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification

Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y‐borne gene fragments (totalizing 2602 bp). We used a time‐calibrated, Bayesian inference phylogenetic framework and conducted character‐based, genetic and phylogenetic delineation of species hypotheses within African common pangolins. We identified six geographic lineages partitioned into western Africa, Ghana, the Dahomey Gap, western central Africa, Gabon and central Africa, all diverging during the Middle to Late Pleistocene. MtDNA (cytochrome b + control region) was the sole locus to provide diagnostic characters for each of the six lineages. Tree‐based Bayesian delimitation methods using single‐ and multilocus approaches gave high support for ‘species’ level recognition of the six African common pangolin lineages. Although the diversification of African common pangolins occurred during Pleistocene cyclical glaciations, causative correlation with traditional rainforest refugia and riverine barriers in Africa was not straightforward. We conclude on the existence of six cryptic lineages within African common pangolins, which might be of major relevance for future conservation strategies. The high discriminative power of the mtDNA markers used in this study should allow an efficient molecular tracing of the regional origin of African common pangolin seizures.     

CorA, the magnesium/nickel/cobalt transporter, affects virulence and extracellular enzyme production in the soft rot pathogen Pectobacterium carotovorum

Pectobacterium carotovorum (formerly Erwinia carotovora ssp. carotovora) is a phytopathogenic bacterium that causes soft rot disease, characterized by water-soaked soft decay, resulting from the action of cell wall-degrading exoenzymes secreted by the pathogen. Virulence in soft rot bacteria is regulated by environmental factors, host and bacterial chemical signals, and a network of global and gene-specific bacterial regulators. We isolated a mini-Tn5 mutant of P. carotovorum that is reduced in the production of extracellular pectate lyase, protease, polygalacturonase and cellulase. The mutant is also decreased in virulence as it macerates less host tissues than its parent and is severely impaired in multiplication in planta. The inactivated gene responsible for the reduced virulent phenotype was identified as corA. CorA, a magnesium/nickel/cobalt membrane transporter, is the primary magnesium transporter for many bacteria. Compared with the parent, the CorA(-) mutant is cobalt resistant. The mutant phenotype was confirmed in parental strain P. carotovorum by marker exchange inactivation of corA. A functional corA(+) DNA from P. carotovorum restored exoenzyme production and pathogenicity to the mutants. The P. carotovorum corA(+) clone also restored motility and cobalt sensitivity to a CorA(-) mutant of Salmonella enterica. These data indicate that CorA is required for exoenzyme production and virulence in P. carotovorum.