Automated categorisation of e-journals by synonym analysis of n-grams

Automatic keyword or keyphrase extraction is concerned with assigning keyphrases to documents based on words from within the document. Previous studies have shown that in a significant number of cases author-supplied keywords are not appropriate for the document to which they are attached. This can either be because they represent what the author believes a paper is about not what it actually is, or because they include keyphrases which are more classificatory than explanatory e.g., “University of Poppleton” instead of “Knowledge Discovery in Databases”. Thus, there is a need for a system that can generate an appropriate and diverse range of keyphrases that reflect the document. This paper proposes two possible solutions that examine the synonyms of words and phrases in the document to find the underlying themes, and presents these as appropriate keyphrases. Using three different freely available thesauri, the work undertaken examines two different methods of producing keywords and compares the outcomes across multiple strands in the timeline. The primary method explores taking n-grams of the source document phrases, and examining the synonyms of these, while the secondary considers grouping outputs by their synonyms. The experiments undertaken show the primary method produces good results and that the secondary method produces both good results and potential for future work. In addition, the different qualities of the thesauri are examined and it is concluded that the more entries in a thesaurus, the better it is likely to perform. The age of the thesaurus or the size of each entry does not correlate to performance.

Constrained principal component analysis reveals functionally connected load-dependent networks involved in multiple stages of working memory

Constrained principal component analysis (CPCA) with a finite impulse response (FIR) basis set was used to reveal functionally connected networks and their temporal progression over a multistage verbal working memory trial in which memory load was varied. Four components were extracted, and all showed statistically significant sensitivity to the memory load manipulation. Additionally, two of the four components sustained this peak activity, both for approximately 3 s (Components 1 and 4). The functional networks that showed sustained activity were characterized by increased activations in the dorsal anterior cingulate cortex, right dorsolateral prefrontal cortex, and left supramarginal gyrus, and decreased activations in the primary auditory cortex and "default network" regions. The functional networks that did not show sustained activity were instead dominated by increased activation in occipital cortex, dorsal anterior cingulate cortex, sensori-motor cortical regions, and superior parietal cortex. The response shapes suggest that although all four components appear to be invoked at encoding, the two sustained-peak components are likely to be additionally involved in the delay period. Our investigation provides a unique view of the contributions made by a network of brain regions over the course of a multiple-stage working memory trial.

Multiple-project discount rates for cost-benefit analysis in construction projects: A formal risk model for microgeneration renewable energy technologies

The traditional economic approach for appraising the costs and benefits of construction project Net Present Values involves the calculation of net returns for each investment option under different discount rates. An alternative approach consists of multiple-project discount rates based on risk modelling. The example of a portfolio of microgeneration renewable energy technology (MRET) is presented to demonstrate that risks and future available budget for re-investment can be taken into account when setting discount rates for construction project specifications in presence of uncertainty. A formal demonstration is carried out through a reversed intertemporal approach of applied general equilibrium. It is demonstrated that risk and the estimated available budget for future re-investment can be included in the simultaneous assessment of the costs and benefits of multiple projects.

Analysis of Direct Outdoor Air Cooling Efficency for Combined Variable Air Volume Air-conditioning System in Stores in Cold Climates of China

Direct outdoor air cooling contributes a lot not only to the improvement of the indoor air quality but also to the energy saving. Its full use will reduce the water chiller’s running time especially in some stores where cooling load keeps much higher and longer than that in other buildings. A novel air-conditioning system named Combined Variable Air Volume system (CVAV), combining a normal AHU with a separate outdoor air supply system, was proposed firstly by the authors. The most attractive feature of the system is its full utilization of cooling capacity and freshness of outdoor air in the transition period of the year round. On the basis of the obtain of the dynamic cooling loads of the typical shopping malls in different four cities located in cold climates in China with the aid of DOE-2, the possibility of increasing the amount of outdoor air volume of CVAV system in the transition period instead of operating the water chillers was confirmed. Moreover, a new concept, Direct Outdoor Air Cooling Efficiency (DOACE), was defined as the ratio of cooling capacity of outdoor air to the water chiller, indicating the degree of outdoor air’s utilization. And the DOACE of the CVAV was calculated and compared with that of conventional all-air constant volume air-conditioning systems, the results showed that CVAV bear much more energy saving potential with the 10%~19% higher DOACE and it is a kind of energy efficient systems and can improve the indoor air quality as well.

The multiple antibiotic resistance (mar) locus and its significance

Chromosomally encoded systems involved in low level resistance of bacteria to different classes of antibiotics (mainly beta-lactams, chloramphenicol, quinolones and tetracycline), disinfectants and in resistance to organic solvents have been the focus of considerable interest in recent years. The multiple antibiotic resistance (mar) locus of Escherichia coli and Salmonella is perhaps the best described system involved in this type of resistance which is induced by MarA, the activator protein encoded by the marRAB locus. The mar-locus is reported to mediate resistance primarily by up-regulating efflux of some antibiotics, disinfectants and organic solvents via the AcrAB-TolC efflux pump and down regulating influx through Outer Membrane Protein F (OmpF). Whilst the level of antibiotic resistance conferred by marRAB is only low level, there are increasing data to suggest that marRAB and related systems are important in clinical antibiotic resistance, possibly as a 'stepping stone' to higher levels of resistance. Other related systems include up-regulation of RobA, SoxS and AcrAB which give rise to a similar resistance phenotype to that conferred by up-regulation of MarA. The aim of this paper is to review the function and significance of the mar-locus and related systems with a particular focus on its implications in veterinary medicine. (C) 2002 Published by Elsevier Science Ltd.

Linking number analysis of a self-assembled lemniscular Möbius-metallamacrocycle

A 26 membered, 24π-electron metallamacrocycle containing two Ag(I) centers is shown to be a double-twist Möbius cycle by a linking number analysis.

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.

Haplotype analysis of vernalization loci in European barley germplasm reveals novel VRN-H1 alleles and a predominant winter VRN-H1/VRN-H2 multi-locus haplotype

In barley, variation in the requirement for vernalization (an extended period of low temperature before flowering can occur) is determined by the VRN-H1, -H2 and -H3 loci. In European cultivated germplasm, most variation in vernalization requirement is accounted for by alleles at VRN-H1 and VRN-H2 only, but the range of allelic variation is largely unexplored. Here we characterise VRN-H1 and VRN-H2 haplotypes in 429 varieties representing a large portion of the acreage sown to barley in Western Europe over the last 60 years. Analysis of genotype, intron I sequencing data and growth habit tests identified three novel VRN-H1 alleles and determined the most frequent VRN-H1 intron I rearrangements. Combined analysis of VRN-H1 and VRN-H2 alleles resulted in the classification of seventeen VRN-H1/VRN-H2 multi-locus haplotypes, three of which account for 79% of varieties. The molecular markers employed here represent powerful diagnostic tools for prediction of growth habit and assessment of varietal purity. These markers will also allow development of germplasm to test the behaviour of individual alleles with the aim of understanding the relationship between allelic variation and adaptation to specific agri-environments.

Characterization of the complex locus of bean encoding polygalacturonase-inhibiting proteins reveals subfunctionalization for defense against fungi and insects.

Polygalacturonase-inhibiting proteins (PGIPs) are extracellular plant inhibitors of fungal endopolygalacturonases (PGs) that belong to the superfamily of Leu-rich repeat proteins. We have characterized the full complement of pgip genes in the bean (Phaseolus vulgaris) genotype BAT93. This comprises four clustered members that span a 50-kb region and, based on their similarity, form two pairs (Pvpgip1/Pvpgip2 and Pvpgip3/Pvpgip4). Characterization of the encoded products revealed both partial redundancy and subfunctionalization against fungal-derived PGs. Notably, the pair PvPGIP3/PvPGIP4 also inhibited PGs of two mirid bugs (Lygus rugulipennis and Adelphocoris lineolatus). Characterization of Pvpgip genes of Pinto bean showed variations limited to single synonymous substitutions or small deletions. A three-amino acid deletion encompassing a residue previously identified as crucial for recognition of PG of Fusarium moniliforme was responsible for the inability of BAT93 PvPGIP2 to inhibit this enzyme. Consistent with the large variations observed in the promoter sequences, reverse transcription-PCR expression analysis revealed that the different family members differentially respond to elicitors, wounding, and salicylic acid. We conclude that both biochemical and regulatory redundancy and subfunctionalization of pgip genes are important for the adaptation of plants to pathogenic fungi and phytophagous insects.

Analysis of full-waveform LiDAR data for classification of an orange orchard scene

Full-waveform laser scanning data acquired with a Riegl LMS-Q560 instrument were used to classify an orange orchard into orange trees, grass and ground using waveform parameters alone. Gaussian decomposition was performed on this data capture from the National Airborne Field Experiment in November 2006 using a custom peak-detection procedure and a trust-region-reflective algorithm for fitting Gauss functions. Calibration was carried out using waveforms returned from a road surface, and the backscattering coefficient c was derived for every waveform peak. The processed data were then analysed according to the number of returns detected within each waveform and classified into three classes based on pulse width and c. For single-peak waveforms the scatterplot of c versus pulse width was used to distinguish between ground, grass and orange trees. In the case of multiple returns, the relationship between first (or first plus middle) and last return c values was used to separate ground from other targets. Refinement of this classification, and further sub-classification into grass and orange trees was performed using the c versus pulse width scatterplots of last returns. In all cases the separation was carried out using a decision tree with empirical relationships between the waveform parameters. Ground points were successfully separated from orange tree points. The most difficult class to separate and verify was grass, but those points in general corresponded well with the grass areas identified in the aerial photography. The overall accuracy reached 91%, using photography and relative elevation as ground truth. The overall accuracy for two classes, orange tree and combined class of grass and ground, yielded 95%. Finally, the backscattering coefficient c of single-peak waveforms was also used to derive reflectance values of the three classes. The reflectance of the orange tree class (0.31) and ground class (0.60) are consistent with published values at the wavelength of the Riegl scanner (1550 nm). The grass class reflectance (0.46) falls in between the other two classes as might be expected, as this class has a mixture of the contributions of both vegetation and ground reflectance properties.

Evidence for changes in stratospheric transport and mixing over the past three decades based on multiple data sets and tropical leaky pipe analysis

Variability in the strength of the stratospheric Lagrangian mean meridional or Brewer-Dobson circulation and horizontal mixing into the tropics over the past three decades are examined using observations of stratospheric mean age of air and ozone. We use a simple representation of the stratosphere, the tropical leaky pipe (TLP) model, guided by mean meridional circulation and horizontal mixing changes in several reanalyses data sets and chemistry climate model (CCM) simulations, to help elucidate reasons for the observed changes in stratospheric mean age and ozone. We find that the TLP model is able to accurately simulate multiyear variability in ozone following recent major volcanic eruptions and the early 2000s sea surface temperature changes, as well as the lasting impact on mean age of relatively short-term circulation perturbations. We also find that the best quantitative agreement with the observed mean age and ozone trends over the past three decades is found assuming a small strengthening of the mean circulation in the lower stratosphere, a moderate weakening of the mean circulation in the middle and upper stratosphere, and a moderate increase in the horizontal mixing into the tropics. The mean age trends are strongly sensitive to trends in the horizontal mixing into the tropics, and the uncertainty in the mixing trends causes uncertainty in the mean circulation trends. Comparisons of the mean circulation and mixing changes suggested by the measurements with those from a recent suite of CCM runs reveal significant differences that may have important implications on the accurate simulation of future stratospheric climate.

Analysis and compensation of power amplifier nonlinearity in MIMO transmit diversity systems

The nonlinearity of high-power amplifiers (HPAs) has a crucial effect on the performance of multiple-input-multiple-output (MIMO) systems. In this paper, we investigate the performance of MIMO orthogonal space-time block coding (OSTBC) systems in the presence of nonlinear HPAs. Specifically, we propose a constellation-based compensation method for HPA nonlinearity in the case with knowledge of the HPA parameters at the transmitter and receiver, where the constellation and decision regions of the distorted transmitted signal are derived in advance. Furthermore, in the scenario without knowledge of the HPA parameters, a sequential Monte Carlo (SMC)-based compensation method for the HPA nonlinearity is proposed, which first estimates the channel-gain matrix by means of the SMC method and then uses the SMC-based algorithm to detect the desired signal. The performance of the MIMO-OSTBC system under study is evaluated in terms of average symbol error probability (SEP), total degradation (TD) and system capacity, in uncorrelated Nakagami-m fading channels. Numerical and simulation results are provided and show the effects on performance of several system parameters, such as the parameters of the HPA model, output back-off (OBO) of nonlinear HPA, numbers of transmit and receive antennas, modulation order of quadrature amplitude modulation (QAM), and number of SMC samples. In particular, it is shown that the constellation-based compensation method can efficiently mitigate the effect of HPA nonlinearity with low complexity and that the SMC-based detection scheme is efficient to compensate for HPA nonlinearity in the case without knowledge of the HPA parameters.

High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes

Background: Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. Results: We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. Conclusions: Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service.

Causal relationship between obesity and vitamin D status: bi-directional mendelian randomization analysis of multiple cohorts

BACKGROUND: Obesity is associated with vitamin D deficiency, and both are areas of active public health concern. We explored the causality and direction of the relationship between body mass index (BMI) and 25-hydroxyvitamin D [25(OH)D] using genetic markers as instrumental variables (IVs) in bi-directional Mendelian randomization (MR) analysis. METHODS AND FINDINGS: We used information from 21 adult cohorts (up to 42,024 participants) with 12 BMI-related SNPs (combined in an allelic score) to produce an instrument for BMI and four SNPs associated with 25(OH)D (combined in two allelic scores, separately for genes encoding its synthesis or metabolism) as an instrument for vitamin D. Regression estimates for the IVs (allele scores) were generated within-study and pooled by meta-analysis to generate summary effects. Associations between vitamin D scores and BMI were confirmed in the Genetic Investigation of Anthropometric Traits (GIANT) consortium (n = 123,864). Each 1 kg/m(2) higher BMI was associated with 1.15% lower 25(OH)D (p = 6.52×10⁻²⁷). The BMI allele score was associated both with BMI (p = 6.30×10⁻⁶²) and 25(OH)D (-0.06% [95% CI -0.10 to -0.02], p = 0.004) in the cohorts that underwent meta-analysis. The two vitamin D allele scores were strongly associated with 25(OH)D (p≤8.07×10⁻⁵⁷ for both scores) but not with BMI (synthesis score, p = 0.88; metabolism score, p = 0.08) in the meta-analysis. A 10% higher genetically instrumented BMI was associated with 4.2% lower 25(OH)D concentrations (IV ratio: -4.2 [95% CI -7.1 to -1.3], p = 0.005). No association was seen for genetically instrumented 25(OH)D with BMI, a finding that was confirmed using data from the GIANT consortium (p≥0.57 for both vitamin D scores). CONCLUSIONS: On the basis of a bi-directional genetic approach that limits confounding, our study suggests that a higher BMI leads to lower 25(OH)D, while any effects of lower 25(OH)D increasing BMI are likely to be small. Population level interventions to reduce BMI are expected to decrease the prevalence of vitamin D deficiency.

Genetic analysis reveals a novel locus in Vicia faba decoupling pigmentation in the flower from that in the extra-floral nectaries

The genetics of the stipule spot pigmentation (SSP) in faba bean (Vicia faba L.) was studied using four inbred lines, of which Disco/2 was zero-tannin (zt2) with colourless stipule spots, ILB938/2 was normal-tannin (ZT2) with colourless stipule spots, and both Aurora/2 and Mélodie/2 were ZT2 with coloured stipule spots. Crosses Mélodie/2 × ILB 938/2, Mélodie/2 × Disco/2, ILB 938/2 × Aurora/2 and ILB 938/2 × Disco/2 (A, B, C and D, respectively) were prepared, along with reciprocals and backcrosses, and advanced through single-seed descent. All F1 hybrid plants had pigmented stipule spots, and in the F2 generation, the segregation ratio fit 3 coloured:1 colourless in crosses A, B and C and 9:7 in cross D. In the F3 generation, the ratio fit 5:3 in crosses A and C and 25:39 in cross D, and in the F4 generation, 9:7 in cross A. SSP was linked to the zero-tannin characteristics (white flower) only in cross B. The results show that coloured stipule spot is dominant to colourless and that colouration is determined by two unlinked complementary recessive genes. We propose the symbols ssp2 for the gene associated with zt2 in Disco/2 and ssp1 for the gene not associated with tannin content in ILB938/2. The novel ssp1 locus was mapped at F5 in cross ‘A’ using Medicago truncatula-derived single-nucleotide polymorphism and was on chromosome 1 of faba bean, in a well-conserved region of M. truncatula chromosome 5 containing some candidate Myb and basic helix–loop–helix transcription factor genes.