A rapid urban de-carbonization scenario analysis tool

A rapid urban de-carbonization scenario analysis tool has been developed. The tool is able to efficiently and effectively generate and populate spatially resolved large scale building scenes, to generate XML input files for the building energy simulation engine CitySim [1], to quickly modify building thermal attributes and develop and analyze de-carbonization scenarios as snapshot modifications to the building scene. The tool has been developed as a series of plugins to the Quantum Geographical Information System (QGIS) [2] application, whereby it can make use of much of the QGIS existing functionality and software libraries. A tip to tail test of the tool is performed on a basic scenario

Efficient 2.87 μm fiber laser passively switched using a semiconductor saturable absorber mirror

A passively switched Ho3+, Pr3+ codoped fluoride fiber laser using a semiconductor saturable absorber mirror (SESAM) is demonstrated. Q-switching and partial mode-locking were observed with the output power produced at a slope efficiency of 24% with respect to the absorbed pump power. The partially mode-locked 2.87 µm pulses operated at a repetition rate of 27.1 MHz with an average power of 132 mW, pulse energy of 4.9 nJ, and pulse width of 24 ps

New insights into the evolutionary history of plant sorbitol dehydrogenase

BACKGROUND: Sorbitol dehydrogenase (SDH, EC 1.1.1.14) is the key enzyme involved in sorbitol metabolism in higher plants. SDH genes in some Rosaceae species could be divided into two groups. L-idonate-5-dehydrogenase (LIDH, EC 1.1.1.264) is involved in tartaric acid (TA) synthesis in Vitis vinifera and is highly homologous to plant SDHs. Despite efforts to understand the biological functions of plant SDH, the evolutionary history of plant SDH genes and their phylogenetic relationship with the V. vinifera LIDH gene have not been characterized RESULTS: A total of 92 SDH genes were identified from 42 angiosperm species. SDH genes have been highly duplicated within the Rosaceae family while monocot, Brassicaceae and most Asterid species exhibit singleton SDH genes. Core Eudicot SDHs have diverged into two phylogenetic lineages, now classified as SDH Class I and SDH Class II. V. vinifera LIDH was identified as a Class II SDH. Tandem duplication played a dominant role in the expansion of plant SDH family and Class II SDH genes were positioned in tandem with Class I SDH genes in several plant genomes. Protein modelling analyses of V. vinifera SDHs revealed 19 putative active site residues, three of which exhibited amino acid substitutions between Class I and Class II SDHs and were influenced by positive natural selection in the SDH Class II lineage. Gene expression analyses also demonstrated a clear transcriptional divergence between Class I and Class II SDH genes in V. vinifera and Citrus sinensis (orange) CONCLUSIONS: Phylogenetic, natural selection and synteny analyses provided strong support for the emergence of SDH Class II by positive natural selection after tandem duplication in the common ancestor of core Eudicot plants. The substitutions of three putative active site residues might be responsible for the unique enzyme activity of V. vinifera LIDH, which belongs to SDH Class II and represents a novel function of SDH in V. vinifera that may be true also of other Class II SDHs. Gene expression analyses also supported the divergence of SDH Class II at the expression level. This study will facilitate future research into understanding the biological functions of plant SDH

Partial sex linkage and linkage disequilibrium on the guppy sex chromosome

The guppy Y chromosome has been considered a model system for the evolution of suppressed recombination between sex chromosomes, and it has been proposed that complete sex‐linkage has evolved across about 3 Mb surrounding this fish's sex‐determining locus, followed by recombination suppression across a further 7 Mb of the 23 Mb XY pair, forming younger “evolutionary strata”. Sequences of the guppy genome show that Y is very similar to the X chromosome. Knowing which parts of the Y are completely nonrecombining, and whether there is indeed a large completely nonrecombining region, are important for understanding its evolution. Here, we describe analyses of PoolSeq data in samples from within multiple natural populations from Trinidad, yielding new results that support previous evidence for occasional recombination between the guppy Y and X. We detected recent demographic changes, notably that downstream populations have higher synonymous site diversity than upstream ones and other expected signals of bottlenecks. We detected evidence of associations between sequence variants and the sex‐determining locus, rather than divergence under a complete lack of recombination. Although recombination is infrequent, it is frequent enough that associations with SNPs can suggest the region in which the sex‐determining locus must be located. Diversity is elevated across a physically large region of the sex chromosome, conforming to predictions for a genome region with infrequent recombination that carries one or more sexually antagonistic polymorphisms. However, no consistently male‐specific variants were found, supporting the suggestion that any completely sex‐linked region may be very small

Molecular Evolution of Human H1N1 and H3N2 Influenza A Virus in Thailand, 2006–2009

Annual seasonal influenza outbreaks are associated with high morbidity and mortality.To index and document evolutionary changes among influenza A H1N1 and H3N2 viruses isolated from Thailand during 2006-2009, using complete genome sequences.Nasopharyngeal aspirates were collected from patients diagnosed with respiratory illness in Thailand during 2006-2009. All samples were screened for Influenza A virus. A total of 13 H1N1 and 21 H3N2 were confirmed and whole genome sequenced for the evolutionary analysis using standard phylogenetic approaches.Phylogenetic analysis of HA revealed a clear diversification of seasonal from vaccine strain lineages. H3N2 seasonal clusters were closely related to the WHO recommended vaccine strains in each season. Most H1N1 isolates could be differentiated into 3 lineages. The A/Brisbane/59/2007 lineage, a vaccine strain for H1N1 since 2008, is closely related with the H1N1 subtypes circulating in 2009. HA sequences were conserved at the receptor-binding site. Amino acid variations in the antigenic site resulted in a possible N-linked glycosylation motif. Recent H3N2 isolates had higher genetic variations compared to H1N1 isolates. Most substitutions in the NP protein were clustered in the T-cell recognition domains.In this study we performed evolutionary genetic analysis of influenza A viruses in Thailand between 2006-2009. Although the current vaccine strain is efficient for controlling the circulating outbreak subtypes, surveillance is necessary to provide unambiguous information on emergent viruses. In summary, the findings of this study contribute the understanding of evolution in influenza A viruses in humans and is useful for routine surveillance and vaccine strain selection

Thermodynamic entropy as an indicator for urban sustainability?

As foci of economic activity, resource consumption, and the production of material waste and pollution, cities represent both a major hurdle and yet also a source of great potential for achieving the goal of sustainability. Motivated by the desire to better understand and measure sustainability in quantitative terms we explore the applicability of thermodynamic entropy to urban systems as a tool for evaluating sustainability. Having comprehensively reviewed the application of thermodynamic entropy to urban systems we argue that the role it can hope to play in characterising sustainability is limited. We show that thermodynamic entropy may be considered as a measure of energy efficiency, but must be complimented by other indices to form part of a broader measure of urban sustainability

ElevatedpCO2drives lower growth and yet increased calcification in the early life history of the cuttlefish Sepia officinalis (Mollusca: Cephalopoda)

Ocean acidification is an escalating environmental issue and associated changes in the ocean carbonate system have implications for many calcifying organisms. The present study followed the growth of Sepia officinalis from early-stage embryos, through hatching, to 7-week-old juveniles. Responses of cuttlefish to elevated pCO(2) (hypercapnia) were investigated to test the impacts of near-future and extreme ocean acidification conditions on growth, developmental time, oxygen consumption, and yolk utilization as proxies for individual fitness. We further examined gross morphological characteristics of the internal calcareous cuttlebone to determine whether embryonically secreted shell lamellae are impacted by environmental hypercapnia. Embryonic growth was reduced and hatching delayed under elevated pCO(2), both at environmentally relevant levels (0.14 kPa pCO(2) similar to predicted ocean conditions in 2100) and extreme conditions (0.40 kPa pCO(2)). Comparing various metrics from control and intermediate treatments generally showed no significant difference in experimental measurements. Yet, results from the high pCO(2) treatment showed significant changes compared with controls and revealed a consistent general trend across the three treatment levels. The proportion of animal mass contributed by the cuttlebone increased in both elevated pCO(2) treatments. Gross cuttlebone morphology was affected under such conditions and cuttlebones of hypercapnic individuals were proportionally shorter. Embryonic shell morphology was maintained consistently in all treatments, despite compounding hypercapnia in the perivitelline fluid; however, post-hatching, hypercapnic animals developed denser cuttlebone laminae in shorter cuttlebones. Juvenile cuttlefish in acidified environments thus experience lower growth and yet increased calcification of their internal shell. The results of this study support recent findings that early cuttlefish life stages are more vulnerable towards hypercapnia than juveniles and adults, which may have negative repercussions on the biological fitness of cuttlefish hatchlings in future oceans

Integrating Slacks-based Measure of Efficiency and Super-efficiency in Data Envelopment Analysis

In this paper, we develop an integrated model for slacks- based measure (SBM) simultaneously of both the efficiency and the super-efficiency for decision-making units (DMUs) in data envelopment analysis (DEA). Unlike the traditional solution approaches in which we need to identify the efficient DMUs by the SBM model of Tone [20] before applying the super SBM model of Tone [21] for the DMUs to achieve their super-effciency scores, our integration can obtain the efficiency scores of the infficient DMUs and the super-efficiency scores of the efficient DMUs by solving simultaneously these two models by an onestage approach. Therefore, it may save computational time for large-scale practical applications. Due to the non-linearity in the objective function of this integrated model, we develop a linearisation technique to deal with the non-linear model. The numerical experiments, carried out on several examples in the literature and a case study, have demonstrated the accuracy and the computational time effectiveness of our proposed model as compared with the traditional solution approache