Single crystal raman spectroscopy of natural finnemanite and comparison with the synthesised analogue

The single crystal Raman spectra of natural mineral finnemanite Pb5(AsO3)3Cl from the Långban locality, Filipstad district, Värmland province, Sweden are presented for the first time. It is a hexagonal mineral belonging to the ortho arsenite group, where the [AsO3]3- ion is isolated. The spectra of finnemanite are characterized by a strong band at 734 cm-1 overlying a shoulder at 726 cm-1, and broad overlapping bands in the lower wavenumber with the strongest band positioned at 174 cm-1. Band assignments were made based on band symmetry, experimental band positions from literature and DFT calculated Raman spectrum, and spectral comparison with other ortho arsenite minerals reinerite, cafarsite, and nealite and synthetic lead arsenite compounds Pb2(AsO2)3Cl, Pb2As2O5, and PbAs2O4 . The band at 734 cm-1 was assigned to υ1(AsO3), bands at 726 and 640 cm-1 assigned to υ3, 372 and 357 cm-1 to υ2, and 244, 239 and 207 cm-1 to υ4. The single crystal spectra of finnemanite showed good mode separation, allowing bands to be assigned a symmetry species of Ag, E1g, or E2g.

Single crystal raman spectroscopy of natural paulmooreite Pb2As2O5 and in comparison with the synthesised analogue

The single crystal Raman spectra of natural mineral paulmooreite Pb2As2O5 from the Långban locality, Filipstad district, Värmland province, Sweden are presented for the first time. It is a monoclinic mineral containing an isolated [As2O5]4-. Depolarised and single crystal spectra of the natural and synthetic sample compare favorably and are characterized by strong bands around 186 and 140 cm-1 and three medium bands at 800 – 700 cm-1. Band assignments were made based on band symmetry and spectral comparison between experimental band positions and those resulting from Hartree-Fock calculation of an isolated [As2O5]4- ion. Spectral comparison was also made with lead arsenites such as synthetic PbAs2O4 and Pb2(AsO2)3Cl and natural finnemanite in order to determine the contribution of the terminal and bridging O in paulmooreite. Bands at 760 – 733 cm-1 were assigned to terminal As-O vibrations, whereas stretches of the bridging O occur at 562 and 503 cm-1. The single crystal spectra showed good mode separation, allowing bands to be assigned a symmetry species of Ag or Bg.

Can partial coherence interferometry be used to determine retinal shape?

Purpose: To determine likely errors in estimating retinal shape using partial coherence interferometric instruments when no allowance is made for optical distortion. Method: Errors were estimated using Gullstrand’s No. 1 schematic eye and variants which included a 10 D axial myopic eye, an emmetropic eye with a gradient-index lens, and a 10.9 D accommodating eye with a gradient-index lens. Performance was simulated for two commercial instruments, the IOLMaster (Carl Zeiss Meditec) and the Lenstar LS 900 (Haag-Streit AG). The incident beam was directed towards either the centre of curvature of the anterior cornea (corneal-direction method) or the centre of the entrance pupil (pupil-direction method). Simple trigonometry was used with the corneal intercept and the incident beam angle to estimate retinal contour. Conics were fitted to the estimated contours. Results: The pupil-direction method gave estimates of retinal contour that were much too flat. The cornea-direction method gave similar results for IOLMaster and Lenstar approaches. The steepness of the retinal contour was slightly overestimated, the exact effects varying with the refractive error, gradient index and accommodation. Conclusion: These theoretical results suggest that, for field angles ≤30º, partial coherence interferometric instruments are of use in estimating retinal shape by the corneal-direction method with the assumptions of a regular retinal shape and no optical distortion. It may be possible to improve on these estimates out to larger field angles by using optical modeling to correct for distortion.

SOA for business networks - service delivery framework

The next generation of SOA needs to scale for flexible service consumption, beyond organizational boundaries and current B2B applications, into communities, eco-systems, and business networks. In the wider and, ultimately, global settings, new capabilities are needed so that business partners can efficiently and reliably enable, adapt, and expose services where they can be discovered, ordered, consumed, metered, and paid for, through new applications and opportunities, driven by third parties in the global "village". This trend is already underway, in different ways, through various early adopter market segments. For the small medium enterprises segment, Google, Intuit-Microsoft, and others have launched appstores, through which an open-ended array of hosted applications are sourced from the development community and procured as maketplace commondities. In the corporate sector, the marketplace model and business network hubs are being put in place on top of connectivity and network orchestration investments for capitalizing services as tradable assets, seen in banking/finance (e.g. American Express Intelligent Marketplace), logistics (e.g., the E2open hub), and the public sector (e.g., UK DirectGov whole-of-government citizen services delivery).

A requirements framework for semantic business process modelling

The emergence of semantic technologies to deal with the underlying meaning of things, instead of a purely syntactical representation, has led to new developments in various fields, including business process modeling. Inspired by artificial intelligence research, technologies for semantic Web services have been proposed and extended to process modeling. However, the applicablility of semantic Web services for semantic business processes is limited because business processes encompass wider requirements of business than Web services. In particular, processes are concerned with the composition of tasks, that is, in which order activities are carried out, regardless of their implementation details; resources assigned to carry out tasks, such as machinery, people, and goods; data exchange; and security and compliance concerns.

Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

Despite recent methodological advances in inferring the time-scale of biological evolution from molecular data, the fundamental question of whether our substitution models are sufficiently well specified to accurately estimate branch-lengths has received little attention. I examine this implicit assumption of all molecular dating methods, on a vertebrate mitochondrial protein-coding dataset. Comparison with analyses in which the data are RY-coded (AG → R; CT → Y) suggests that even rates-across-sites maximum likelihood greatly under-compensates for multiple substitutions among the standard (ACGT) NT-coded data, which has been subject to greater phylogenetic signal erosion. Accordingly, the fossil record indicates that branch-lengths inferred from the NT-coded data translate into divergence time overestimates when calibrated from deeper in the tree. Intriguingly, RY-coding led to the opposite result. The underlying NT and RY substitution model misspecifications likely relate respectively to “hidden” rate heterogeneity and changes in substitution processes across the tree, for which I provide simulated examples. Given the magnitude of the inferred molecular dating errors, branch-length estimation biases may partly explain current conflicts with some palaeontological dating estimates.

A fundamental numerical and theoretical study for the vibrational properties of nanowires

Based on the molecular dynamics (MD) simulation and the classical Euler-Bernoulli beam theory, a fundamental study of the vibrational performance of the Ag nanowire (NW) is carried out. A comprehensive analysis of the quality (Q)-factor, natural frequency, beat vibration, as well as high vibration mode is presented. Two excitation approaches, i.e., velocity excitation and displacement excitation, have been successfully implemented to achieve the vibration of NWs. Upon these two kinds of excitations, consistent results are obtained, i.e., the increase of the initial excitation amplitude will lead to a decrease to the Q-factor, and moderate plastic deformation could increase the first natural frequency. Meanwhile, the beat vibration driven by a single relatively large excitation or two uniform excitations in both two lateral directions is observed. It is concluded that the nonlinear changing trend of external energy magnitude does not necessarily mean a nonconstant Q-factor. In particular, the first order natural frequency of the Ag NW is observed to decrease with the increase of temperature. Furthermore, comparing with the predictions by Euler- Bernoulli beam theory, the MD simulation provides a larger and smaller first vibration frequencies for the clamped-clamped and clamped-free thin Ag NWs, respectively. Additionally, for thin NWs, the first order natural frequency exhibits a parabolic relationship with the excitation magnitudes. The frequencies of the higher vibration modes tend to be low in comparison to Euler-Bernoulli beam theory predictions. A combined initial excitation is proposed which is capable to drive the NW under a multi-mode vibration and arrows the coexistence of all the following low vibration modes. This work sheds lights on the better understanding of the mechanical properties of NWs and benefits the increasing utilities of NWs in diverse nano-electronic devices.

A novel SNP in COMT is associated with alcohol dependence but not opiate or nicotine dependence: a case control study

Background It is well established that COMT is a strong candidate gene for substance use disorder and schizophrenia. Recently we identified two SNPs in COMT (rs4680 and rs165774) that are associated with schizophrenia in an Australian cohort. Individuals with schizophrenia were more than twice as likely to carry the GG genotype compared to the AA genotype for both the rs165774 and rs4680 SNPs. Association of both rs4680 and rs165774 with substance dependence, a common comorbidity of schizophrenia has not been investigated. Methods To determine whether COMT is important in substance dependence, rs165774 and rs4680 were genotyped and haplotyped in patients with nicotine, alcohol and opiate dependence. Results The rs165774 SNP was associated with alcohol dependence. However, it was not associated with nicotine or opiate dependence. Individuals with alcohol dependence were more than twice as likely to carry the GG or AG genotypes compared to the AA genotype, indicating a dominant mode of inheritance. The rs4680 SNP showed a weak association with alcohol dependence at the allele level that did not reach significance at the genotype level but it was not associated with nicotine or opiate dependence. Analysis of rs165774/rs4680 haplotypes also revealed association with alcohol dependence with the G/G haplotype being almost 1.5 times more common in alcohol-dependent cases. Conclusions Our study provides further support for the importance of the COMT in alcohol dependence in addition to schizophrenia. It is possible that the rs165774 SNP, in combination with rs4680, results in a common molecular variant of COMT that contributes to schizophrenia and alcohol dependence susceptibility. This is potentially important for future studies of comorbidity. As our participant numbers are limited our observations should be viewed with caution until they are independently replicated.

Mutans Streptococci and Lactobacilli Colonization in Predentate Children from the Neonatal Period to Seven Months of Age

Background/Aims: The aim of this study was to investigate the colonization of mutans streptococci (MS) and lactobacilli (LB) in predentate children from the neonatal period to 7 months. Methods: A total of 957 mother-and-child pairs were recruited from birth and followed up at 7 months. The 283 children who did not have erupted teeth at the second visit were included in the study. Oral mucosal swabs were taken, and the presence of MS and LB was determined using a commercial microbiological culture kit. Results: At mean ages of 34 days and 7 months, 9 and 11% of the infants, respectively, showed the presence of MS. In contrast, LB presence increased from 24 to 47% (p < 0.0001). MS presence in the neonatal period was associated with maternal MS counts of >105 CFU/ml (p = 0.05), while LB presence was associated with natural birth (p = 0.03) and maternal LB presence (p = 0.02). At 7 months, MS presence was associated with maternal MS counts (p = 0.02) and LB counts of >105 CFU/ml (p = 0.007). Additional predictors of MS presence at 7 months were a child’s MS counts of >105 CFU/ml at the neonatal visit (p = 0.019) and nighttime bottle feeding (p = 0.024). LB presence at 7 months was associated with maternal LB (p < 0.001) and MS presence (p = 0.02). Conclusions: MS and LB can be detected by culture in the oral cavity as early as 34 days after birth. Their infection rates increase to 11 and 47%, respectively, by the time the children reach the end of the predentate stage of oral development.

A review of the pharmacobiotic regulation of gastrointestinal inflammation by probiotics, commensal bacteria and prebiotics.

The idea that microbes induce disease has steered medical research toward the discovery of antibacterial products for the prevention and treatment of microbial infections. The twentieth century saw increasing dependency on antimicrobials as mainline therapy accentuating the notion that bacterial interactions with humans were to be avoided or desirably controlled. The last two decades, though, have seen a refocusing of thinking and research effort directed towards elucidating the critical inter-relationships between the gut microbiome and its host that control health/wellness or disease. This research has redefined the interactions between gut microbes and vertebrates, now recognizing that the microbial active cohort and its mammalian host have shared co-evolutionary metabolic interactions that span millennia. Microbial interactions in the gastrointestinal tract provide the necessary cues for the development of regulated pro- and anti-inflammatory signals that promotes immunological tolerance, metabolic regulation and other factors which may then control local and extra-intestinal inflammation. Pharmacobiotics, using nutritional and functional food additives to regulate the gut microbiome, will be an exciting growth area of therapeutics, developing alongside an increased scientific understanding of gut-microbiome symbiosis in health and disease.

Beat phenomena in metal nanowires, and their implications for resonance-based elastic property measurements

The elastic properties of 1D nanostructures such as nanowires are often measured experimentally through actuation of the nanowire at its resonance frequency, and then relating the resonance frequency to the elastic stiffness using elementary beam theory. In the present work, we utilize large scale molecular dynamics simulations to report a novel beat phenomenon in [110]oriented Ag nanowires. The beat phenomenon is found to arise from the asymmetry of the lattice spacing in the orthogonal elementary directions of the [110] nanowire, i.e. the [-110] and [001] directions, which results in two different principal moments of inertia. Because of this, actuations imposed along any other direction are found to decompose into two orthogonal vibrational components based on the actuation angle relative to these two elementary directions, with this phenomenon being generalizable to <110> FCC nanowires of different materials (Cu, Au, Ni, Pd and Pt). The beat phenomenon is explained using a discrete moment of inertia model based on the hard sphere assumption, the model is utilized to show that surface effects enhance the beat phenomenon, while the effect is reduced with increasing nanowires cross-sectional size or aspect ratio. Most importantly, due to the existence of the beat phenomena, we demonstrate that in resonance experiments only a single frequency component is expected to be observed, particularly when the damping ratio is relatively large or very small. Furthermore, for a large range of actuation angles, the lower frequency is more likely to be detected than the higher one, which implies that experimental predictions of Young’s modulus obtained from resonance may in fact be under predictions. The present study therefore has significant implications for experimental interpretations of Young’s modulus as obtained via resonance testing.

Surface effects on the dual-mode vibration of <110> silver nanowires with different cross-sections

Dual-mode vibration of nanowires has been reported experimentally through actuation of the nanowire at its resonance frequency, which is expected to open up a variety of new modalities for the NEMS that could operate in the nonlinear regime. In the present work, we utilize large scale molecular dynamics simulations to investigate the dual-mode vibration of <110> Ag nanowires with triangular, rhombic and truncated rhombic cross-sections. By incorporating the generalized Young-Laplace equation into Euler-Bernoulli beam theory, the influence of surface effects on the dual-mode vibration is studied. Due to the different lattice spacing in principal axes of inertia of the {110} atomic layers, the NW is also modeled as a discrete system to reveal the influence from such specific atomic arrangement. It is found that the <110> Ag NW will under a dual-mode vibration if the actuation direction is deviated from the two principal axes of inertia. The predictions of the two first mode natural frequencies by the classical beam model appear underestimated comparing with the MD results, which are found to be enhanced by the discrete model. Particularly, the predictions by the beam theory with the contribution of surface effects are uniformly larger than the classical beam model, which exhibit better agreement with MD results for larger cross-sectional size. However, for ultrathin NWs, current consideration of surface effects is still experiencing certain inaccuracy. In all, for all different cross-sections, the inclusion of surface effects is found to reduce the difference between the two first mode natural frequencies. This trend is observed consistent with MD results. This study provides a first comprehensive investigation on the dual-mode vibration of <110> oriented Ag NWs, which is supposed to benefit the applications of NWs that acting as a resonating beam.

Analysis of genome survey sequences and SSR marker development for Siamese Mud Carp, Henicorhynchus siamensis, using 454 Pyrosequencing

Siamese mud carp (Henichorynchus siamensis) is a freshwater teleost of high economic importance in the Mekong River Basin. However, genetic data relevant for delineating wild stocks for management purposes currently are limited for this species. Here, we used 454 pyrosequencing to generate a partial genome survey sequence (GSS) dataset to develop simple sequence repeat (SSR) markers from H. siamensis genomic DNA. Data generated included a total of 65,954 sequence reads with average length of 264 nucleotides, of which 2.79% contain SSR motifs. Based on GSS-BLASTx results, 10.5% of contigs and 8.1% singletons possessed significant similarity (E value < 10–5) with the majority matching well to reported fish sequences. KEGG analysis identified several metabolic pathways that provide insights into specific potential roles and functions of sequences involved in molecular processes in H. siamensis. Top protein domains detected included reverse transcriptase and the top putative functional transcript identified was an ORF2-encoded protein. One thousand eight hundred and thirty seven sequences containing SSR motifs were identified, of which 422 qualified for primer design and eight polymorphic loci have been tested with average observed and expected heterozygosity estimated at 0.75 and 0.83, respectively. Regardless of their relative levels of polymorphism and heterozygosity, microsatellite loci developed here are suitable for further population genetic studies in H. siamensis and may also be applicable to other related taxa.

The active site residue V266 of Chlamydial HtrA is critical for substrate binding during both in vitro and in vivo conditions

HtrA is a complex, multimeric chaperone and serine protease important for the virulence and survival of many bacteria. Chlamydia trachomatis is an obligate, intracellular bacterial pathogen that is responsible for severe disease pathology. C. trachomatis HtrA (CtHtrA) has been shown to be highly expressed in laboratory models of disease. In this study, molecular modelling of CtHtrA protein active site structure identified putative S1-S3 subsite residues I242, I265, and V266. These residues were altered by site-directed mutagenesis, and these changes were shown to considerably reduce protease activity on known substrates and resulted in a narrower and distinct range of substrates compared to wild type. Bacterial two-hybrid analysis revealed that CtHtrA is able to interact in vivo with a broad range of protein sequences with high affinity. Notably, however, the interaction was significantly altered in 35 out of 69 clones when residue V266 was mutated, indicating that this residue has an important function during substrate binding.