A probabilistic energy model for non-domestic building sectors applied to analysis of school buildings in greater London

The diversity of non-domestic buildings at urban scale poses a number of difficulties to develop models for large scale analysis of the stock. This research proposes a probabilistic, engineering-based, bottom-up model to address these issues. In a recent study we classified London's non-domestic buildings based on the service they provide, such as offices, retail premise, and schools, and proposed the creation of one probabilistic representational model per building type. This paper investigates techniques for the development of such models. The representational model is a statistical surrogate of a dynamic energy simulation (ES) model. We first identify the main parameters affecting energy consumption in a particular building sector/type by using sampling-based global sensitivity analysis methods, and then generate statistical surrogate models of the dynamic ES model within the dominant model parameters. Given a sample of actual energy consumption for that sector, we use the surrogate model to infer the distribution of model parameters by inverse analysis. The inferred distributions of input parameters are able to quantify the relative benefits of alternative energy saving measures on an entire building sector with requisite quantification of uncertainties. Secondary school buildings are used for illustrating the application of this probabilistic method. © 2012 Elsevier B.V. All rights reserved.

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A > T, C > G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA. (c) 2008 Published by Elsevier Inc.

Characterization and phylogenetic analysis of the chitinase gene from the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus

A putative chitinase gene was identified within the fragment EcoRI-K of the Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HearNPV, also called HaSNPIV) genome. The open reading frame (ORF) contains 1713 nucleotides (nt) and encodes a protein of 570 amino acids (aa) with a predicted molecular weight of 63.6 kDa. Transcription started at about 18 h post infection (p.i.) and the protein was first detected at 20 h p.i. The times of transcription and expression are characteristic of a late baculovirus gene. 5' and 3' RACE indicated that transcription was initiated from the adenine residue located at -246 nt upstream from the ATG start site and the poly (A) tail was added at 267 nt downstream from the stop codon. This is the first report on the molecular characterization of a chitinase from a single nucleocapsid NPV. The phylogeny of baculoviral chitinase genes were extensively examined in comparison with chitinases derived from bacteria, fungi, nematode, actinomycetes, viruses, insects and mammals. Neighbor-joining and most parsimony analyses showed that the baculoviral chitinases were clustered exclusively within gamma-proteobacteria. Our results strongly suggest that baculoviruses acquired their chitinase genes from bacteria. (C) 2004 Elsevier B.V. All rights reserved.

PIXE analysis of Fe content in Fe-implanted GaN film

The diluted magnetic semiconductors (DMSs) were achieved by the ion implantation. Fe+ ions (250 keV) were implanted into n-type GaN at room temperature with doses ranging from 8 X 10(15) cm(-2) to 8 X 10(16) cm(-2) and subsequently rapidly annealed at 800 degrees C for 5 m in N-2 ambient. PIXE was employed to determine the Fe-implanted content. The magnetic property was measured by the Quantum Design MPMS SQUID magnetometer. No secondary phases or clusters are detected within the sensitivity of XRD. Apparent ferromagnetic hysteresis loops measured at 10 K were presented. The relationships between the Fe-implanted content and the ferromagnetic property are discussed. (c) 2006 Elsevier B.V. All rights reserved.

Leakage current analysis in AlGaInP/GaInP multi-quantum well lasers by the electrical derivative method - art. no. 60202F

In AlGaInP/GaInP multi-quantum well (MQW) lasers, the electron leakage current is a much more serious problem than that in laser diodes with longer wavelength. To further improve the output performance, the leakage current should be analyzed. In this letter, the temperature dependence of electrical derivative characteristics in AlGaInP/GaInP multi-quantum well lasers was measured, and the potential barrier for electron leakage was obtained. With the help of secondary ion mass spectroscopy (SIMS) measurement, theoretical analysis of the potential barrier was presented and compared with the measurement result. The influence of p-cladding doping level and doping profile on the potential barrier was discussed, and this can be helpful in metalorganic chemical vapor deposition (MOCVD) growth.

Quantified MS analysis applied to combinatorial heterogeneous catalyst libraries

A high-throughput screening system for secondary catalyst libraries has been developed by incorporation of an 80-pass reactor and a quantified multistream mass spectrometer screening (MSMSS) technique. With a low-melting alloy as the heating medium, a uniform reaction temperature could be obtained in the multistream reactor (maximum temperature differences are less than 1 K at 673 K). Quantification of the results was realized by combination of a gas chromatogram with the MSMSS, which could provide the product selectivities of each catalyst in a heterogeneous catalyst library. Because the catalyst loading of each reaction tube is comparable to that of the conventional microreaction system and because the parallel reactions could be operated under identical conditions (homogeneous temperature, same pressure and WHSV), the reaction results of a promising catalyst selected from the library could be reasonably applied to the further scale-up of the system. The aldol condensation of acetone, with obvious differences in the product distribution over different kind of catalysts, was selected as a model reaction to validate the screening system.

Effect of secondary ligands' size on energy transfer and electroluminescent efficiencies for a series of europium(III) complexes, a density functional theory study

In this paper, a quantum chemistry method was used to investigate the effect of different sizes of substituted phenanthrolines on absorption, energy transfer, and the electroluminescent performance of a series of Eu(TTA)(3)L (L = [1,10] phenanthroline (Phen), Pyrazino[2,3-f][1,10]phenanthroline (PyPhen), 2-methylprrazino[2,3-f][1,10] phenanthroline(MPP), dipyrido[3,2-a:2',3'-c]phenazine(DPPz), 11-methyldipyrido[3,2-a:2',3'c]phenazine(MDPz), 11.12-dimethyldipyrido[3,2-a:2',3'-c]phenazine(DDPz), and benzo[i]dipyrido[3,2-a:2',3'-c]phenazine (BDPz)) complexes. Absorption spectra calculations show that different sizes of secondary ligands have different effects on transition characters, intensities, and absorption peak positions.

A three-dimensional metal-organic framework based on a triazine derivative: syntheses, structure analysis, and sorption studies

A novel metal-organic framework [Cu-3(m-TATB)(2)Py(CH3OH)(2)] (1) constructed of a triazine-based trigonal-planar ligand, 3,3',3 ''-s-triazine-2,4,6- triyltribenzoate (m-H(3)TATB), has been synthesized and structurally characterized. Compound 1 features three-dimensional (3D) channels and cavities together, and exhibits high carbon dioxide sorption at normal pressure.

Assignment of absolute configuration of cyclic secondary amines by NMR techniques using Mosher's method: a general procedure exemplified with (-)-isoanabasine

A general procedure to determine the absolute configuration of cyclic secondary amines with Mosher's NMR method is demonstrated, with assignment of absolute configuration of isoanabasine as an example. Each Mosher amide can adopt two stable conformations (named rotamers) caused by hindered rotation around amide C-N bond. Via a three-step structural analysis of four rotamers, the absolute configuration of (-)-isoanabasine is deduced to be (R) on the basis of Newman projections, which makes it easy to understand and clarify the application of Mosher's method to cyclic secondary amines. Furthermore, it was observed that there was an unexpected ratio of rotamers of Mosher amide derived from (R)-isoanabasine and (R)-Mosher acid. This phenomenon implied that it is necessary to distinguish the predominant rotamer from the minor one prior to determining the absolute configuration while using this technique.

QUANTITATIVE STRUCTURE-ACTIVITY-RELATIONSHIPS FOR TOXICITY OF PHENOLS USING REGRESSION-ANALYSIS AND COMPUTATIONAL NEURAL NETWORKS

Quantitative structure-toxicity models were developed that directly link the molecular structures of a et of 50 alkYlated and/or halogenated phenols with their polar narcosis toxicity, expressed as the negative logarithm of the IGC50 (50% growth inhibitor

Analysis of Sequence Periodicity in E. coli Proteins: Empirical Investigation of the ?Duplication and Divergence? Theory of Protein Evolution

Gatherer, D., and McEwan, N.R. (2003). Analysis of sequence periodicity in E. coli proteins: empirical investigation of the 'duplication and divergence' theory of protein evolution. Journal of Molecular Evolution 57, 149-158. RAE2008

Functional metagenomic analysis of the human gut microbiome to identify novel salt tolerance genes

The ability to adapt to and respond to increases in external osmolarity is an important characteristic that enables bacteria to survive and proliferate in different environmental niches. When challenged with increased osmolarity, due to sodium chloride (NaCl) for example, bacteria elicit a phased response; firstly via uptake of potassium (K+), which is known as the primary response. This primary response is followed by the secondary response which is characterised by the synthesis or uptake of compatible solutes (osmoprotectants). The overall osmotic stress response is much broader however, involving many diverse cellular systems and processes. These ancillary mechanisms are arguably more interesting and give a more complete view of the osmotic stress response. The aim of this thesis was to identify novel genetic loci from the human gut microbiota that confer increased tolerance to osmotic stress using a functional metagenomic approach. Functional metagenomics is a powerful tool that enables the identification of novel genes from as yet uncultured bacteria from diverse environments through cloning, heterologous expression and phenotypic identification of a desired trait. Functional metagenomics does not rely on any previous sequence information to known genes and can therefore enable the discovery of completely novel genes and assign functions to new or known genes. Using a functional metagenomic approach, we have assigned a novel function to previously annotated genes; murB, mazG and galE, as well as a putative brp/blh family beta-carotene 15,15’-monooxygenase. Finally, we report the identification of a completely novel salt tolerance determinant with no current known homologues in the databases. Overall the genes identified originate from diverse taxonomic and phylogenetic groups commonly found in the human gastrointestinal (GI) tract, such as Collinsella and Eggerthella, Akkermansia and Bacteroides from the phyla Actinobacteria, Verrucomicrobia and Bacteroidetes, respectively. In addition, a number of the genes appear to have been acquired via lateral gene transfer and/or encoded on a prophage. To our knowledge, this thesis represents the first investigation to identify novel genes from the human gut microbiota involved in the bacterial osmotic stress response.

Identification and analysis of mechanisms involved in a broad-spectrum disease resistant mutant of the winter wheat cv. Guardian

M66 an X-ray induced mutant of winter wheat (Triticum aestivum) cv. Guardian exhibits broad-spectrum resistance to powdery mildew (Blumeria graminis f. sp. tritici), yellow rust (Puccinia striiformis f. sp. tritici), and leaf rust (Puccinia recondita f. sp. tritici), along with partial resistance to stagnonospora nodorum blotch (caused by the necrotroph Stagonosporum nodorum) and septoria tritici blotch (caused by the hemibiotroph Mycosphaerella graminicola) compared to the parent plant ‘Guardian’. Analysis revealed that M66 exhibited no symptoms of infection following artificial inoculation with Bgt in the glasshouse after adult growth stage (GS 45). Resistance in M66 was associated with widespread leaf flecking which developed during tillering. Flecking also occurred in M66 leaves without Bgt challenge; as a result grain yields were reduced by approximately 17% compared to ‘Guardian’ in the absence of disease. At the seedling stage, M66 exhibited partial resistance. M66, along with Tht mutants (Tht 12, Tht13), also exhibit increased tolerance to environmental stresses (abiotic), such as drought and heat stress at seedling and adult growth stages, However, adult M66 exhibited increased susceptibility to the aphid Schizaphis graminum compared to ‘Guardian’. Resistance to Bgt in M66 was characterized with increased and earlier H2O2 accumulation at the site of infection which resulted in increased papilla formation in epidermal cells, compared to ‘Guardian’. Papilla formation was associated with reduced pathogen ingress and haustorium formation, indicating that the primary cause of resistance in M66 was prevention of pathogen penetration. Heat treatment at 46º C prior to challenge with Bgt also induced partial disease resistance to Blumeria graminis f. sp. tritici in ‘Guardian’ and M66 seedlings. This was characterized by a delay in primary infection, due to increased production of ROS species, such as hydrogen peroxide, ROS-scavenging enzymes and Hsp70, resulting in cross-linking of cell wall components prior to inoculation. This actively prevented the fungus from penetrating the epidermal cell wall. Proteomics analysis using 2-D gel electrophoresis identified primary and secondary disease resistance effects in M66 including detection of ROS scavenging enzymes (4, 24 hai), such as ascorbate peroxidase and a superoxidase dismutase isoform (CuZnSOD) in M66 which were absent from ‘Guardian’. Chitinase (PR protein) was also upregulated (24 hai) in M66 compared to ‘Guardian’.Monosomic and ditelosomic analysis of M66 revealed that the mutation in M66 is located on the long arm of chromosome 2B (2BL). Chromosome 2BL is known to have key genes involved in resistance to pathogens such as those causing stripe rust and powdery mildew. The TaMloB1 gene, an orthologue of the barley Mlo gene, is also located on chromosome 2BL. Sanger sequencing of part of the coding sequence revealed no deletions in the TaMloB1 gene between ‘Guardian’ and M66.

Clinical outcome of breast cancer patients with liver metastases alone in the anthracycline-taxane era: a retrospective analysis of two prospective, randomised metastatic breast cancer trials.

Liver metastases have long been known to indicate an unfavourable disease course in breast cancer (BC). However, a small subset of patients with liver metastases alone who were treated with pre-taxane chemotherapy regimens was reported to have longer survival compared with patients with liver and metastases at other sites. In the present study, we examined the clinical outcome of breast cancer patients with liver metastases alone in the context of two phase III European Organisation for Research and Treatment of Cancer (EORTC) trials which compared the efficacy of doxorubicin (A) versus paclitaxel (T) (trial 10923) and of AC (cyclophosphamide) versus AT (trial 10961), given as first-line chemotherapy in metastatic BC patients. The median follow-up for the patients with liver metastases was 90.5 months in trial 10923 and 56.6 months in trial 10961. Patients with liver metastases alone comprised 18% of all patients with liver metastases, in both the 10923 and 10961 trials. The median survival of patients with liver metastases alone and liver plus other sites of metastases were 22.7 and 14.2 months (log rank test, P=0.002) in trial 10923 and 27.1 and 16.8 months (log rank test, P=0.19) in trial 10961. The median TTP (time to progression) for patients with liver metastases alone was also longer compared with the liver plus other sites of metastases group in both trials: 10.2 versus 8.8 months (log rank test, P=0.02) in trial 10923 and 8.3 versus 6.7 months (log rank test, P=0.37) in trial 10961. Most patients with liver metastases alone have progression of their disease in their liver again (96 and 60% of patients in trials 10923 and 10961, respectively). Given the high prevalence of breast cancer, improved detection of liver metastases, encouraging survival achieved with currently available cytotoxic agents and the fact that a significant portion of patients with liver metastases alone have progression of their tumour in the liver again, a more aggressive multimodality treatment approach through prospective clinical trials seems worth exploring in this specific subset of women.

Hippocampus shape analysis and late-life depression.

Major depression in the elderly is associated with brain structural changes and vascular lesions. Changes in the subcortical regions of the limbic system have also been noted. Studies examining hippocampus volumetric differences in depression have shown variable results, possibly due to any volume differences being secondary to local shape changes rather than differences in the overall volume. Shape analysis offers the potential to detect such changes. The present study applied spherical harmonic (SPHARM) shape analysis to the left and right hippocampi of 61 elderly subjects with major depression and 43 non-depressed elderly subjects. Statistical models controlling for age, sex, and total cerebral volume showed a significant reduction in depressed compared with control subjects in the left hippocampus (F(1,103) = 5.26; p = 0.0240) but not right hippocampus volume (F(1,103) = 0.41; p = 0.5213). Shape analysis showed significant differences in the mid-body of the left (but not the right) hippocampus between depressed and controls. When the depressed group was dichotomized into those whose depression was remitted at time of imaging and those who were unremitted, the shape comparison showed remitted subjects to be indistinguishable from controls (both sides) while the unremitted subjects differed in the midbody and the lateral side near the head. Hippocampal volume showed no difference between controls and remitted subjects but nonremitted subjects had significantly smaller left hippocampal volumes with no significant group differences in the right hippocampus. These findings may provide support to other reports of neurogenic effects of antidepressants and their relation to successful treatment for depressive symptoms.