Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5

Chromosome 7q22 has been the focus of many cytogenetic and molecular studies aimed at delineating regions commonly deleted in myeloid leukemias and myelodysplastic syndromes. We have compared a gene-dense, GC-rich sub-region of 7q22 with the orthologous region on mouse chromosome 5. A physical map of 640 kb of genomic DNA from mouse chromosome 5 was derived from a series of overlapping bacterial artificial chromosomes. A 296 kb segment from the physical map, spanning Ache to Tfr2, was compared with 267 kb of human sequence. We identified a conserved linkage of 12 genes including an open reading frame flanked by Ache and Asr2, a novel cation-chloride cotransporter interacting protein Cip1, Ephb4, Zan and Perq1. While some of these genes have been previously described, in each case we present new data derived from our comparative sequence analysis. Adjacent unfinished sequence data from the mouse contains an orthologous block of 10 additional genes including three novel cDNA sequences that we subsequently mapped to human 7q22. Methods for displaying comparative genomic information, including unfinished sequence data, are becoming increasingly important. We supplement our printed comparative analysis with a new, Web-based program called Laj (local alignments with java). Laj provides interactive access to archived pairwise sequence alignments via the WWW. It displays synchronized views of a dot-plot, a percent identity plot, a nucleotide-level local alignment and a variety of relevant annotations. Our mouse–human comparison can be viewed at http://web.uvic.ca/~bioweb/laj.html. Laj is available at http://bio.cse.psu.edu/, along with online documentation and additional examples of annotated genomic regions.

Synthesis and characterization of Pd(II) and Pt(II) complexes with triazolopyrimidine derivatives: The crystal structure of [Pd2L2Cl4] where L=5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine

The Pd(II) and Pt(II) complexes with triazolopyrimidine C-nucleosides L-1 (5,7-dimethyl-3-(2',3',5'-tri-O-benzoyl-beta-D-ribofuranosyl-s-triazolo)[4,3-a]pyrimidine), L-2 (5,7-dimethyl-3-beta-D-ribofuranosyl-s-triazolo [4,3-a]pyrimidine) and L-3 (5,7-dimethyl[1,5-a]-s-triazolopyrimidine), [Pd(en)(L-1)](NO3)(2), (Pd(bpy)(L-1)](NO3)(2), cis-Pd(L-3)(2)Cl-2, [Pd-2(L-3)(2)Cl-4]center dot H2O, cis-Pd(L-2)(2)Cl-2 and [Pt-3(L-1)(2)Cl-6] were synthesized and characterized by elemental analysis and NMR spectroscopy. The structure of the [Pd-2(L-3)(2)Cl-4]center dot H2O complex was established by Xray crystallography. The two L-3 ligands are found in a head to tail orientation, with a (PdPd)-Pd-... distance of 3.1254(17) angstrom.L-1 coordinates to Pd(II) through N8 and N1 forming polymeric structures. L-2 coordinates to Pd(II) through N8 in acidic solutions (0.1 M HCl) forming complexes of cis-geometry. The Pd(II) coordination to L-2 does not affect the sugar conformation probably due to the high stability of the C-C glycoside bond. (c) 2006 Elsevier B.V. All rights reserved.

Feature analysis of spammers in social networks with active honeypots:a case study of Chinese microblogging networks

In this poster we presented our preliminary work on the study of spammer detection and analysis with 50 active honeypot profiles implemented on Weibo.com and QQ.com microblogging networks. We picked out spammers from legitimate users by manually checking every captured user's microblogs content. We built a spammer dataset for each social network community using these spammer accounts and a legitimate user dataset as well. We analyzed several features of the two user classes and made a comparison on these features, which were found to be useful to distinguish spammers from legitimate users. The followings are several initial observations from our analysis on the features of spammers captured on Weibo.com and QQ.com. ¦The following/follower ratio of spammers is usually higher than legitimate users. They tend to follow a large amount of users in order to gain popularity but always have relatively few followers. ¦There exists a big gap between the average numbers of microblogs posted per day from these two classes. On Weibo.com, spammers post quite a lot microblogs every day, which is much more than legitimate users do; while on QQ.com spammers post far less microblogs than legitimate users. This is mainly due to the different strategies taken by spammers on these two platforms. ¦More spammers choose a cautious spam posting pattern. They mix spam microblogs with ordinary ones so that they can avoid the anti-spam mechanisms taken by the service providers. ¦Aggressive spammers are more likely to be detected so they tend to have a shorter life while cautious spammers can live much longer and have a deeper influence on the network. The latter kind of spammers may become the trend of social network spammer. © 2012 IEEE.

Promoter effects in the polymerisation of a mixed hydrocarbon feed with silica-supported BF3

The activity of a silica-supported BF3–methanol solid acid catalyst in the cationic polymerisation of an industrial aromatic C9 feedstock has been investigated. Reuse has been achieved under continuous conditions. Titration of the catalyst acid sites with triethylphosphine oxide (TEPO) in conjunction with 31P MAS NMR shows the catalyst to have two types of acid sites. Further analysis with 2,6 di-tert-butyl-4-methylpyridine (DBMP) has revealed the majority of these acid sites to be Brønsted in nature. The role of α-methylstyrene in promoting resin polymerisation via chain transfer is proposed.

Quantitative analysis of solid-state processes studied with isothermal microcalorimetry

Quantitative analysis of solid-state processes from isothermal microcalorimetric data is straightforward if data for the total process have been recorded and problematic (in the more likely case) when they have not. Data are usually plotted as a function of fraction reacted (α); for calorimetric data, this requires knowledge of the total heat change (Q) upon completion of the process. Determination of Q is difficult in cases where the process is fast (initial data missing) or slow (final data missing). Here we introduce several mathematical methods that allow the direct calculation of Q by selection of data points when only partial data are present, based on analysis with the Pérez-Maqueda model. All methods in addition allow direct determination of the reaction mechanism descriptors m and n and from this the rate constant, k. The validity of the methods is tested with the use of simulated calorimetric data, and we introduce a graphical method for generating solid-state power-time data. The methods are then applied to the crystallization of indomethacin from a glass. All methods correctly recovered the total reaction enthalpy (16.6 J) and suggested that the crystallization followed an Avrami model. The rate constants for crystallization were determined to be 3.98 × 10-6, 4.13 × 10-6, and 3.98 × 10 -6 s-1 with methods 1, 2, and 3, respectively. © 2010 American Chemical Society.

Comparative genome analysis of human bifidobacteria with commercial potential

This thesis describes two newly sequenced B. longum subsp. longum genomes and subsequent comparative analysis with publicly available B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis genomes (Chapter 2). The acquired data revealed a closed pan-genome for this bifidobacterial species and furthermore facilitated the definition of the B. longum core genome. The comparative analysis also highlights differences in the potential metabolic abilities of all three sub-species. Interestingly, phylogenetic analysis of the B. longum core genome indicated the existence of a novel B. longum subspecies. Characterisation of restriction-modification systems from two B. longum subsp. longum strains is described in Chapter 3. These defence mechanisms limit the uptake of genetic material, which was successfully demonstrated for some of the identified systems. When these systems were by-passed by methylation of DNA prior to the transformation procedure, the resulting transformation efficiency of both B. longum subsp. longum strains was increased to a level that allowed for the generation of mutants via homologous recombination. Arabinoxylan metabolism by B. longum subsp. longum NCIMB 8809 was investigated in Chapter 4 of this thesis. Transcriptome analysis allowed the identification of a number of genes involved in the degradation, uptake and utilisation of arabinoxylan. Biochemical analysis revealed that three of the identified genes encode arabinofuranosidase activity. Phenotypic assessment of a number of insertion mutants in genes identified by the transcriptome analysis revealed the essential role of two of these enzymes in arabinoxylan metabolism, and a third enzyme in the metabolism of debranched arabinan. Furthermore, this investigation revealed that B. longum subsp. longum NCIMB 8809 does not completely degrade arabinoxylan, but utilises the arabinose substitutions only, while leaving the xylan backbone untouched.Finally, Chapter 5 outlines that B. longum subsp. longum NCIMB 8809 is capable of removing ferulic and p-coumaric acid substitutions that originate from arabinoxylan. Analysis of the genome sequence led to the identification of a candidate gene for this activity, which was subsequently cloned and expressed in E. coli. Biochemical analysis revealed that the enzyme, designated here as FaeA, is indeed capable of releasing both ferulic and p-coumaric acid from arabinoxylan. Furthermore, it is shown that a derivative of B. longum subsp. longum NCIMB 8809 carrying an insertion mutation in faeA had lost the ability to release ferulic and p-coumaric acid from arabinoxylan, and that growth of this mutant strain is negatively affected when cultivated on growth-limiting levels of arabinoxylan.

Numerical analysis of wooden slabs with perforations under fire conditions

Wood is considered an ideal solution for floors and roofs building construction, due the mechanical and thermal properties, associated with acoustic conditions. These constructions have good sound absorption, heat insulation and relevant architectonic characteristics. They are used in many civil applications: concert and conference halls, auditoriums, ceilings, walls… However, the high vulnerability of wooden elements submitted to fire conditions requires the evaluation of its structural behaviour with accuracy. The main objective of this work is to present a numerical model to assess the fire resistance of wooden cellular slabs with different perforations. Also the thermal behaviour of the wooden slabs will be compared considering different material insulation, with different sizes, inside the cavities. A transient thermal analysis with nonlinear material behaviour will be solved using ANSYS© program. This study allows to verify the fire resistance, the temperature evolution and the char-layer, throughout a wooden cellular slab with perforations and considering the insulation effect inside the cavities.

The Melbourne Decision-Making Questionnaire : an instrument for measuring patterns for coping with decisional conflict

A study was conducted to examine the factorial validity of the Flinders Decision Making Questionnaire (Mann, 1982), a 31-item self-report inventory designed to measure tendencies to use three major coping patterns identified in the conflict theory of decision making (Janis and Mann, 1977): vigilance, hypervigilance, and defensive avoidance (procrastination, buck-passing, and rationalization). A sample of 2051 university students, comprising samples from Australia (n=262), New Zealand (n=260), the USA (n=475), Japan (n=359), Hong Kong (n=281) and Taiwan (n=414) was administered the DMQ. Factorial validity of the instrument was tested by confirmatory factor analysis with LISREL. Five different substantive models, representing different structural relationships between the decision-coping patterns had unsatisfactory fit to the data and could not be validated. A shortened instrument, containing 22 items, yielded a revised model comprising four identifiable factors-vigilance, hypervigilance, buck-passing, and procrastination. The revised model had adequate fit with data for each country sample and for the total sample, and was confirmed. It is recommended that the 22-item instrument, named the Melbourne DMQ, replace the Flinders DMQ for measurement of decision-coping patterns.

Downtime reduction analysis of the Australia Post flat mail optical character reader

Machine downtime, whether planned or unplanned, is intuitively costly to manufacturing organisations, but is often very difficult to quantify. The available literature showed that costing processes are rarely undertaken within manufacturing organisations. Where cost analyses have been undertaken, they generally have only valued a small proportion of the affected costs, leading to an overly conservative estimate. This thesis aimed to develop a cost of downtime model, with particular emphasis on the application of the model to Australia Post’s Flat Mail Optical Character Reader (FMOCR). The costing analysis determined a cost of downtime of $5,700,000 per annum, or an average cost of $138 per operational hour. The second section of this work focused on the use of the cost of downtime to objectively determine areas of opportunity for cost reduction on the FMOCR. This was the first time within Post that maintenance costs were considered along side of downtime for determining machine performance. Because of this, the results of the analysis revealed areas which have historically not been targeted for cost reduction. Further exploratory work was undertaken on the Flats Lift Module (FLM) and Auto Induction Station (AIS) Deceleration Belts through the comparison of the results against two additional FMOCR analysis programs. This research has demonstrated the development of a methodical and quantifiable cost of downtime for the FMOCR. This has been the first time that Post has endeavoured to examine the cost of downtime. It is also one of the very few methodologies for valuing downtime costs that has been proposed in literature. The work undertaken has also demonstrated how the cost of downtime can be incorporated into machine performance analysis with specific application to identifying high costs modules. The outcome of this report has both been the methodology for costing downtime, as well as a list of areas for cost reduction. In doing so, this thesis has outlined the two key deliverables presented at the outset of the research.

Experimenting with an intrusion detection system for encrypted networks

Network-based Intrusion Detection Systems (NIDSs) analyse network traffic to detect instances of malicious activity. Typically, this is only possible when the network traffic is accessible for analysis. With the growing use of Virtual Private Networks (VPNs) that encrypt network traffic, the NIDS can no longer access this crucial audit data. In this paper, we present an implementation and evaluation of our approach proposed in Goh et al. (2009). It is based on Shamir's secret-sharing scheme and allows a NIDS to function normally in a VPN without any modifications and without compromising the confidentiality afforded by the VPN.

Psychometric analysis of the Brisbane Practice Environment Measure (B-PEM)

Purpose: To undertake rigorous psychometric testing of the newly developed contemporary work environment measure (the Brisbane Practice Environment Measure [B-PEM]) using exploratory factor analysis and confirmatory factor analysis. Methods: Content validity of the 33-item measure was established by a panel of experts. Initial testing involved 195 nursing staff using principal component factor analysis with varimax rotation (orthogonal) and Cronbach's alpha coefficients. Confirmatory factor analysis was conducted using data from a further 983 nursing staff. Results: Principal component factor analysis yielded a four-factor solution with eigenvalues greater than 1 that explained 52.53% of the variance. These factors were then verified using confirmatory factor analysis. Goodness-of-fit indices showed an acceptable fit overall with the full model, explaining 21% to 73% of the variance. Deletion of items took place throughout the evolution of the instrument, resulting in a 26-item, four-factor measure called the Brisbane Practice Environment Measure-Tested. Conclusions: The B-PEM has undergone rigorous psychometric testing, providing evidence of internal consistency and goodness-of-fit indices within acceptable ranges. The measure can be utilised as a subscale or total score reflective of a contemporary nursing work environment. Clinical Relevance: An up-to-date instrument to measure practice environment may be useful for nursing leaders to monitor the workplace and to assist in identifying areas for improvement, facilitating greater job satisfaction and retention.

Associations among smoking status, lifestyle and lipoprotein subclasses

BACKGROUND: The relationship between cigarette smoking and cardiovascular disease is well established, yet the underlying mechanisms remain unclear. Although smokers have a more atherogenic lipid profile, this may be mediated by other lifestyle-related factors. Analysis of lipoprotein subclasses by the use of nuclear magnetic resonance spectroscopy (NMR) may improve characterisation of lipoprotein abnormalities. OBJECTIVE: We used NMR spectroscopy to investigate the relationships between smoking status, lifestyle-related risk factors, and lipoproteins in a contemporary cohort. METHODS: A total of 612 participants (360 women) aged 40–69 years at baseline (199021994) enrolled in the Melbourne Collaborative Cohort Study had plasma lipoproteins measured with NMR. Data were analysed separately by sex. RESULTS: After adjusting for lifestyle-related risk factors, including alcohol and dietary intake, physical activity, and weight, mean total low-density lipoprotein (LDL) particle concentration was greater for female smokers than nonsmokers. Both medium- and small-LDL particle concentrations contributed to this difference. Total high-density lipoprotein (HDL) and large-HDL particle concentrations were lower for female smokers than nonsmokers. The proportion with low HDL particle number was greater for female smokers than nonsmokers. For men, there were few smoking-related differences in lipoprotein measures. CONCLUSION: Female smokers have a more atherogenic lipoprotein profile than nonsmokers. This difference is independent of other lifestyle-related risk factors. Lipoprotein profiles did not differ greatly between male smokers and nonsmokers.

Bird evolution: testing the Metaves clade with six new mitochondrial genomes

Background Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade. Results Our mitochondrial trees did not return the Metaves clade that had been proposed based on one nuclear intron sequence. We suggest that the high number of indels within the seventh intron of the β-fibrinogen gene at this phylogenetic level, which left a dataset with not a single site across the alignment shared by all taxa, resulted in artifacts during analysis. With respect to the overall avian tree, we find the flamingo and grebe are sister taxa and basal to the shorebirds (Charadriiformes). Using a novel site-stripping technique for noise-reduction we found this relationship to be stable. The hummingbird/swift clade is outside the large and very diverse group of raptors, shore and sea birds. Unexpectedly the kagu is not closely related to the rail in our analysis, but because neither the kagu nor the rail have close affinity to any taxa within this dataset of 41 birds, their placement is not yet resolved. Conclusion Our phylogenetic hypothesis based on 41 avian mitochondrial genomes (13,229 bp) rejects monophyly of seven Metaves species and we therefore conclude that the members of Metaves do not share a common evolutionary history within the Neoaves.

Efficient solution of multiple cracks in great number using eigen COD boundary integral equations with iteration procedure

A newly developed computational approach is proposed in the paper for the analysis of multiple crack problems based on the eigen crack opening displacement (COD) boundary integral equations. The eigen COD particularly refers to a crack in an infinite domain under fictitious traction acting on the crack surface. With the concept of eigen COD, the multiple cracks in great number can be solved by using the conventional displacement discontinuity boundary integral equations in an iterative fashion with a small size of system matrix to determine all the unknown CODs step by step. To deal with the interactions among cracks for multiple crack problems, all cracks in the problem are divided into two groups, namely the adjacent group and the far-field group, according to the distance to the current crack in consideration. The adjacent group contains cracks with relatively small distances but strong effects to the current crack, while the others, the cracks of far-field group are composed of those with relatively large distances. Correspondingly, the eigen COD of the current crack is computed in two parts. The first part is computed by using the fictitious tractions of adjacent cracks via the local Eshelby matrix derived from the traction boundary integral equations in discretized form, while the second part is computed by using those of far-field cracks so that the high computational efficiency can be achieved in the proposed approach. The numerical results of the proposed approach are compared not only with those using the dual boundary integral equations (D-BIE) and the BIE with numerical Green's functions (NGF) but also with those of the analytical solutions in literature. The effectiveness and the efficiency of the proposed approach is verified. Numerical examples are provided for the stress intensity factors of cracks, up to several thousands in number, in both the finite and infinite plates.

Bubble extinction in Hele-Shaw flow with surface tension and kinetic undercooling regularisation

We perform an analytic and numerical study of an inviscid contracting bubble in a two-dimensional Hele-Shaw cell, where the effects of both surface tension and kinetic undercooling on the moving bubble boundary are not neglected. In contrast to expanding bubbles, in which both boundary effects regularise the ill-posedness arising from the viscous (Saffman-Taylor) instability, we show that in contracting bubbles the two boundary effects are in competition, with surface tension stabilising the boundary, and kinetic undercooling destabilising it. This competition leads to interesting bifurcation behaviour in the asymptotic shape of the bubble in the limit it approaches extinction. In this limit, the boundary may tend to become either circular, or approach a line or "slit" of zero thickness, depending on the initial condition and the value of a nondimensional surface tension parameter. We show that over a critical range of surface tension values, both these asymptotic shapes are stable. In this regime there exists a third, unstable branch of limiting self-similar bubble shapes, with an asymptotic aspect ratio (dependent on the surface tension) between zero and one. We support our asymptotic analysis with a numerical scheme that utilises the applicability of complex variable theory to Hele-Shaw flow.