A higher order perfectly matched layer formulation for finite-difference time-domain seismic wave modeling

We have developed a higher order perfectly matched layer (PML) formulation to improve the absorption performance for finite-difference time-domain seismic modeling. First, we outlined a new unsplit “correction” approach, which allowed for traditional, first-order PMLs to be added directly to existing codes in a straightforward manner. Then, using this framework, we constructed a PML formulation that can be used to construct higher order PMLs of arbitrary order. The greater number of degrees of freedom associated with the higher order PML allow for enhanced flexibility of the PML stretching functions, thus potentially facilitating enhanced absorption performance. We found that the new approach can offer increased elastodynamic absorption, particularly for evanescent waves. We also discovered that the extra degrees of freedom associated with the higher order PML required careful optimization if enhanced absorption was to be achieved. Furthermore, these extra degrees of freedom increased the computational requirements in comparison with first-order schemes. We reached our formulations using one compact equation thus increasing the ease of implementation. Additionally, the formulations are based on a recursive integration approach that reduce PML memory requirements, and do not require special consideration for corner regions. We tested the new formulations to determine their ability to absorb body waves and surface waves. We also tested standard staggered grid stencils and rotated staggered grid stencils

Detection of Airborne Biological Particles in Indoor Air Using a Real-Time Advanced Morphological Parameter UV-LIF Spectrometer and Gradient Boosting Ensemble Decision Tree Classifiers

We present results from a study evaluating the utility of supervised machine learning to classify single particle ultraviolet laser-induced fluorescence (UV-LIF) signatures to investigate airborne primary biological aerosol particle (PBAP) concentrations in a busy, multifunctional building using a Multiparameter Bioaerosol Spectrometer. First we introduce and demonstrate a gradient boosting ensemble decision tree algorithm’s ability to accurately classify laboratory generated PBAP samples into broad taxonomic classes with a high level of accuracy. We then develop a framework to appraise the classification accuracy and performance using the Hellinger distance metric to compare product parameter probability density function similarity; this framework showed that key training classes were sufficiently different in terms of particle fluorescence and morphology to facilitate classification. We also demonstrate the utility of including advanced morphological parameters to minimise inter-class conflation and improve classification confidence, where relying on the fluorescent spectra alone would likely result in misattribution. Finally, we apply these methods to ambient data collected within a large multi-functional building where ambient bacterial- and fungal-like classes were identified to display trends corresponding to human activity; fungal-like classes displayed a consistent diurnal trend with a maximum at midday and hourly peaks correlating to movements within the building; bacteria-like aerosol displayed complex, episodic events during opening hours. All PBAP classes fell to low baseline concentrations when the building was unoccupied overnight and at weekendsPeer reviewe

Mechanisms involved in acquisition of blaNDM genes by IncA/C2 and IncFIIY plasmids

blaNDM genes confer carbapenem resistance and have been identified on transferable plasmids belonging to different incompatibility (Inc) groups. Here we present the complete sequences of four plasmids carrying a blaNDM gene, pKP1-NDM-1, pEC2-NDM-3, pECL3-NDM-1, and pEC4-NDM-6, from four clinical samples originating from four different patients. Different plasmids carry segments that align to different parts of the blaNDM region found on Acinetobacter plasmids. pKP1-NDM-1 and pEC2-NDM-3, from Klebsiella pneumoniae and Escherichia coli, respectively, were identified as type 1 IncA/C2 plasmids with almost identical backbones. Different regions carrying blaNDM are inserted in different locations in the antibiotic resistance island known as ARI-A, and ISCR1 may have been involved in the acquisition of blaNDM-3 by pEC2-NDM-3. pECL3-NDM-1 and pEC4-NDM-6, from Enterobacter cloacae and E. coli, respectively, have similar IncFIIY backbones, but different regions carrying blaNDM are found in different locations. Tn3-derived inverted-repeat transposable elements (TIME) appear to have been involved in the acquisition of blaNDM-6 by pEC4-NDM-6 and the rmtC 16S rRNA methylase gene by IncFIIY plasmids. Characterization of these plasmids further demonstrates that even very closely related plasmids may have acquired blaNDM genes by different mechanisms. These findings also illustrate the complex relationships between antimicrobial resistance genes, transposable elements, and plasmids and provide insights into the possible routes for transmission of blaNDM genes among species of the Enterobacteriaceae family

MHV-Vertices for Gravity Amplitudes

We obtain a CSW-style formalism for calculating graviton scattering amplitudes and prove its validity through the use of a special type of BCFW-like parameter shift. The procedure is illustrated with explicit examples.Comment: 21 pages, minor typos corrected, proof added in section

Recursive Calculation of One-Loop QCD Integral Coefficients

We present a new procedure using on-shell recursion to determine coefficients of integral functions appearing in one-loop scattering amplitudes of gauge theories, including QCD. With this procedure, coefficients of integrals, including bubbles and triangles, can be determined without resorting to integration. We give criteria for avoiding spurious singularities and boundary terms that would invalidate the recursion. As an example where the criteria are satisfied, we obtain all cut-constructible contributions to the one-loop n-gluon scattering amplitude, A_n^{oneloop}(...--+++...), with split-helicity from an N=1 chiral multiplet and from a complex scalar. Using the supersymmetric decomposition, these are ingredients in the construction of QCD amplitudes with the same helicities. This method requires prior knowledge of amplitudes with sufficiently large numbers of legs as input. In many cases, these are already known in compact forms from the unitarity method.Comment: 36 pages; v2 clarification added and typos fixed, v3 typos fixe

Explaining co-movements between equity and CDS bid-ask spreads

In this paper I show that the co-movements between bid-ask spreads of equities and credit default swaps vary over time and increase over crisis periods. The co-movements are strongly related to systematic risk factors and to the theoretical debt-to-equity hedge ratio. I document that hedging and asymmetric information, besides higher funding costs and market volatility risk, are driving factors of the commonality and are significantly priced in CDS bid-ask spreads

Nasty Viruses, Costly Plasmids, Population Dynamics, and the Conditions for Establishing and Maintaining CRISPR-Mediated Adaptive Immunity in Bacteria

Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR) abound in the genomes of almost all archaebacteria and nearly half the eubacteria sequenced. Through a genetic interference mechanism, bacteria with CRISPR regions carrying copies of the DNA of previously encountered phage and plasmids abort the replication of phage and plasmids with these sequences. Thus it would seem that protection against infecting phage and plasmids is the selection pressure responsible for establishing and maintaining CRISPR in bacterial populations. But is it? To address this question and provide a framework and hypotheses for the experimental study of the ecology and evolution of CRISPR, I use mathematical models of the population dynamics of CRISPR-encoding bacteria with lytic phage and conjugative plasmids. The results of the numerical (computer simulation) analysis of the properties of these models with parameters in the ranges estimated for Escherichia coli and its phage and conjugative plasmids indicate: (1) In the presence of lytic phage there are broad conditions where bacteria with CRISPR-mediated immunity will have an advantage in competition with non-CRISPR bacteria with otherwise higher Malthusian fitness. (2) These conditions for the existence of CRISPR are narrower when there is envelope resistance to the phage. (3) While there are situations where CRISPR-mediated immunity can provide bacteria an advantage in competition with higher Malthusian fitness bacteria bearing deleterious conjugative plasmids, the conditions for this to obtain are relatively narrow and the intensity of selection favoring CRISPR weak. The parameters of these models can be independently estimated, the assumption behind their construction validated, and the hypotheses generated from the analysis of their properties tested in experimental populations of bacteria with lytic phage and conjugative plasmids. I suggest protocols for estimating these parameters and outline the design of experiments to evaluate the validity of these models and test these hypotheses