ALBERT

Description: The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we find that differences in population size have minimal impact on the distribution of population-scaled fitness effects, as well as on the rate of molecular evolution. This is because larger populations result in selection for more stable proteins that are less affected by mutations. This reduction in the magnitude of the fitness effects almost exactly cancels the greater selective pressure resulting from the larger population size. Conversely, changes in the population size in either direction cause transient increases in the substitution rate. As differences in population size often correspond to changes in population size, this makes comparisons of substitution rates in different lineages difficult to interpret.

Description: The aim of this study was to examine racial differences in long-term survival among hemodialysis patients after coronary artery bypass grafting (CABG). To our knowledge this has not been previously addressed in the literature. Black and white hemodialysis patients undergoing first-time, isolated CABG procedures between 1992 and 2011 were compared. Survival probabilities were computed using the Kaplan-Meier product-limit method and stratified by race. Hazard ratios (HR) and 95% confidence intervals (CI) were computed using a Cox regression model. A total of 207 (2%) patients were on hemodialysis at the time of CABG. White (n = 80) hemodialysis patients had significantly decreased 5-year survival compared with black (n = 127) patients (adjusted HR = 1.9, 95% CI = 1.2–2.8). Our finding provides useful outcome information for surgeons, primary care providers, and their patients.

Description: Background: Limited by data availability, most disease maps in the literature are for relatively large and subjectively-defined areal units, which are subject to problems associated with polygon maps. High resolution maps based on objective spatial units are needed to more precisely detect associations between disease and environmental factors. Method: We propose to use a Restricted and Controlled Monte Carlo (RCMC) process to disaggregate polygon-level location data to achieve mapping aggregate data at an approximated individual level. RCMC assigns a random point location to a polygon-level location, in which the randomization is restricted by the polygon and controlled by the background (e.g., population at risk). RCMC allows analytical processes designed for individual data to be applied, and generates high-resolution raster maps. Results: We applied RCMC to the town-level birth defect data for New Hampshire and generated raster maps at the resolution of 100 m. Besides the map of significance of birth defect risk represented by p-value, the output also includes a map of spatial uncertainty and a map of hot spots. Conclusions: RCMC is an effective method to disaggregate aggregate data. An RCMC-based disease mapping maximizes the use of available spatial information, and explicitly estimates the spatial uncertainty resulting from aggregation.

Description: The predominant microorganisms in samples taken from shower heads in residences in the Korean city “N” were Stenotrophomonas maltophilia, Sphingomonas paucimobilis, Acidovorax temperans, and Microbacterium lacticum. Legionella was not detected in this case. The volatile organic compounds (VOCs) vinylacetate, NN-DMA, cis-1,2-dichloroethylene, epichlorohydrin, and styrene were measured in five types of plastic pipes: PVC, PB, PP, PE, and cPVC. The rate of multiplication of the heterotrophic plate count (HPC) attached on the copper pipe in contact with hot tap water was higher than the rate for the copper pipe in contact with cold tap water. Biofilm accumulation on stainless steel pipes with added acetate (3 mg/L) was 2.56 times higher than the non-supplemented condition. Therefore, the growth of HPC in the pipe system was affected by the type and availability of nutrients and depended on variables such as heating during the hot water supply.

Description: Bile acid diarrhoea (BAD) is a common disease that requires expensive imaging to diagnose. We have tested the efficacy of a new method to identify BAD, based on the detection of differences in volatile organic compounds (VOC) in urine headspace of BAD vs. ulcerative colitis and healthy controls. A total of 110 patients were recruited; 23 with BAD, 42 with ulcerative colitis (UC) and 45 controls. Patients with BAD also received standard imaging (Se75HCAT) for confirmation. Urine samples were collected and the headspace analysed using an AlphaMOS Fox 4000 electronic nose in combination with an Owlstone Lonestar Field Asymmetric Ion Mobility Spectrometer (FAIMS). A subset was also tested by gas chromatography, mass spectrometry (GCMS). Linear Discriminant Analysis (LDA) was used to explore both the electronic nose and FAIMS data. LDA showed statistical differences between the groups, with reclassification success rates (using an n-1 approach) at typically 83%. GCMS experiments confirmed these results and showed that patients with BAD had two chemical compounds, 2-propanol and acetamide, that were either not present or were in much reduced quantities in the ulcerative colitis and control samples. We believe that this work may lead to a new tool to diagnose BAD, which is cheaper, quicker and easier that current methods.

Description: This paper is a theoretical analysis of mirror tilt in a Michelson interferometer and its effect on the radiant flux over the active area of a rectangular photodetector or image sensor pixel. It is relevant to sensor applications using homodyne interferometry where these opto-electronic devices are employed for partial fringe counting. Formulas are derived for radiant flux across the detector for variable location within the fringe pattern and with varying wave front angle. The results indicate that the flux is a damped sine function of the wave front angle, with a decay constant of the ratio of wavelength to detector width. The modulation amplitude of the dynamic fringe pattern reduces to zero at wave front angles that are an integer multiple of this ratio and the results show that the polarity of the radiant flux changes exclusively at these multiples. Varying tilt angle causes radiant flux oscillations under an envelope curve, the frequency of which is dependent on the location of the detector with the fringe pattern. It is also shown that a fringe count of zero can be obtained for specific photodetector locations and wave front angles where the combined effect of fringe contraction and fringe tilt can have equal and opposite effects. Fringe tilt as a result of a wave front angle of 0.05° can introduce a phase measurement difference of 16° between a photodetector/pixel located 20 mm and one located 100 mm from the optical origin.

Description: Various types of grafts have been traditionally used to restore damaged bones. In the late 1960s, a strong interest was raised in studying ceramics as potential bone grafts due to their biomechanical properties. A bit later, such synthetic biomaterials were called bioceramics. In principle, bioceramics can be prepared from diverse materials but this review is limited to calcium orthophosphate-based formulations only, which possess the specific advantages due to the chemical similarity to mammalian bones and teeth. During the past 40 years, there have been a number of important achievements in this field. Namely, after the initial development of bioceramics that was just tolerated in the physiological environment, an emphasis was shifted towards the formulations able to form direct chemical bonds with the adjacent bones. Afterwards, by the structural and compositional controls, it became possible to choose whether the calcium orthophosphate-based implants remain biologically stable once incorporated into the skeletal structure or whether they were resorbed over time. At the turn of the millennium, a new concept of regenerative bioceramics was developed and such formulations became an integrated part of the tissue engineering approach. Now calcium orthophosphate scaffolds are designed to induce bone formation and vascularization. These scaffolds are often porous and harbor different biomolecules and/or cells. Therefore, current biomedical applications of calcium orthophosphate bioceramics include bone augmentations, artificial bone grafts, maxillofacial reconstruction, spinal fusion, periodontal disease repairs and bone fillers after tumor surgery. Perspective future applications comprise drug delivery and tissue engineering purposes because calcium orthophosphates appear to be promising carriers of growth factors, bioactive peptides and various types of cells.

Description: O -GlcNAcylation is an inducible, highly dynamic and reversible post-translational modification, mediated by a unique enzyme named O -linked N -acetyl- d -glucosamine ( O -GlcNAc) transferase (OGT). In response to nutrients, O -GlcNAc levels are differentially regulated on many cellular proteins involved in gene expression, translation, immune reactions, protein degradation, protein–protein interaction, apoptosis and signal transduction. In contrast to eukaryotic cells, little is known about the role of O -GlcNAcylation in the viral life cycle. Here, we show that the overexpression of the OGT reduces the replication efficiency of Kaposi's sarcoma-associated herpesvirus (KSHV) in a dose-dependent manner. In order to investigate the global impact of O -GlcNAcylation in the KSHV life cycle, we systematically analyzed the 85 annotated KSHV-encoded open reading frames for O -GlcNAc modification. For this purpose, an immunoprecipitation (IP) strategy with three different approaches was carried out and the O -GlcNAc signal of the identified proteins was properly controlled for specificity. Out of the 85 KSHV-encoded proteins, 18 proteins were found to be direct targets for O -GlcNAcylation. Selected proteins were further confirmed by mass spectrometry for O -GlcNAc modification. Correlation of the functional annotation and the O -GlcNAc status of KSHV proteins showed that the predominant targets were proteins involved in viral DNA synthesis and replication. These results indicate that O -GlcNAcylation plays a major role in the regulation of KSHV propagation.

Description: Galectins are potent adhesion/growth-regulatory effectors with characteristic expression profiles. Understanding the molecular basis of gene regulation in each case requires detailed information on copy number of genes and sequence(s) of their promoter(s). Our report reveals plasticity in this respect between galectins and species. We here describe occurrence of a two-gene constellation for human galectin (Gal)-7 and define current extent of promoter-sequence divergence. Interestingly, cross-species genome analyses also detected single-copy display. Because the regulatory potential will then be different, extrapolations of expression profiles are precluded between respective species pairs. Gal-4 coding in chromosomal vicinity was found to be confined to one gene, whereas copy-number variation also applied to Gal-9. The example of rat Gal-9 teaches the lesson that the presence of multiple bands in Southern blotting despite a single-copy gene constellation is attributable to two pseudogenes. The documented copy-number variability should thus be taken into consideration when studying regulation of galectin genes, in a species and in comparison between species.

Description: In studying the molecular basis for the potent immune activity of previously described gamma and delta inulin particles and to assist in production of inulin adjuvants under Good Manufacturing Practice, we identified five new inulin isoforms, bringing the total to seven plus the amorphous form. These isoforms comprise the step-wise inulin developmental series amorphous -〉 alpha-1 (AI-1) -〉 alpha-2 (AI-2) -〉 gamma (GI) -〉 delta (DI) -〉 zeta (ZI) -〉 epsilon (EI) -〉 omega (OI) in which each higher isoform can be made either by precipitating dissolved inulin or by direct conversion from its precursor, both cases using regularly increasing temperatures. At higher temperatures, the shorter inulin polymer chains are released from the particle and so the key difference between isoforms is that each higher isoform comprises longer polymer chains than its precursor. An increasing trend of degree of polymerization is confirmed by end-group analysis using 1 H nuclear magnetic resonance spectroscopy. Inulin isoforms were characterized by the critical temperatures of abrupt phase-shifts (solubilizations or precipitations) in water suspensions. Such (aqueous) "melting" or "freezing" points are diagnostic and occur in strikingly periodic steps reflecting quantal increases in noncovalent bonding strength and increments in average polymer lengths. The (dry) melting points as measured by modulated differential scanning calorimetry similarly increase in regular steps. We conclude that the isoforms differ in repeated increments of a precisely repeating structural element. Each isoform has a different spectrum of biological activities and we show the higher inulin isoforms to be more potent alternative complement pathway activators.

Description: The methylotrophic yeast, Pichia pastoris , is an important organism used for the production of therapeutic proteins. Previously, we have reported the glycoengineering of this organism to produce human-like N -linked glycans but up to now no one has addressed engineering the O -linked glycosylation pathway. Typically, O -linked glycans produced by wild-type P. pastoris are linear chains of four to five α-linked mannose residues, which may be capped with β- or phospho-mannose. Previous genetic engineering of the N-linked glycosylation pathway of P. pastoris has eliminated both of these two latter modifications, resulting in O -linked glycans which are linear α-linked mannose structures. Here, we describe a method for the co-expression of an α-1,2-mannosidase, which reduces these glycans to primarily a single O -linked mannose residue. In doing so, we have reduced the potential of these glycans to interact with carbohydrate-binding proteins, such as dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin. Furthermore, the introduction of the enzyme protein- O -linked-mannose β-1,2- N -acetylglucosaminyltransferase 1, resulted in the capping of the single O -linked mannose residues with N -acetylglucosamine. Subsequently, this glycoform was extended into human-like sialylated glycans, similar in structure to α-dystroglycan-type glycoforms. As such, this represents the first example of sialylated O -linked glycans being produced in yeast and extends the utility of the P. pastoris production platform beyond N -linked glycosylated biotherapeutics to include molecules possessing O -linked glycans.

Description: Neurons and other cells require intracellular transport of essential components for viability and function. Previous work has shown that while net amyloid precursor protein (APP) transport is generally anterograde, individual vesicles containing APP move bi-directionally. This discrepancy highlights our poor understanding of the in vivo regulation of APP-vesicle transport. Here, we show that reduction of presenilin (PS) or suppression of gamma-secretase activity substantially increases anterograde and retrograde velocities for APP vesicles. Strikingly, PS deficiency has no effect on an unrelated cargo vesicle class containing synaptotagmin, which is powered by a different kinesin motor. Increased velocities caused by PS or gamma-secretase reduction require functional kinesin-1 and dynein motors. Together, our findings suggest that a normal function of PS is to repress kinesin-1 and dynein motor activity during axonal transport of APP vesicles. Furthermore, our data suggest that axonal transport defects induced by loss of PS-mediated regulatory effects on APP-vesicle motility could be a major cause of neuronal and synaptic defects observed in Alzheimer's Disease (AD) pathogenesis. Thus, perturbations of APP/PS transport could contribute to early neuropathology observed in AD, and highlight a potential novel therapeutic pathway for early intervention, prior to neuronal loss and clinical manifestation of disease.

Description: With age, muscle mass and integrity are progressively lost leaving the elderly frail, weak and unable to independently care for themselves. Defined as sarcopenia, this age-related muscle atrophy appears to be multifactorial but its definite cause is still unknown. Mitochondrial dysfunction has been implicated in this process. Using a novel transgenic mouse model of mitochondrial DNA (mtDNA) double-strand breaks (DSBs) that presents a premature aging-like phenotype, we studied the role of mtDNA damage in muscle wasting. We caused DSBs in mtDNA of adult mice using a ubiquitously expressed mitochondrial-targeted endonuclease, mito- Pst I. We found that a short, transient systemic mtDNA damage led to muscle wasting and a decline in locomotor activity later in life. We found a significant decline in muscle satellite cells, which decreases the muscle's capacity to regenerate and repair during aging. This phenotype was associated with impairment in acetylcholinesterase (AChE) activity and assembly at the neuromuscular junction (NMJ), also associated with muscle aging. Our data suggests that systemic mitochondrial dysfunction plays important roles in age-related muscle wasting by preferentially affecting the myosatellite cell pool.

Description: Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation.

Description: We present a methodology for infrasonic remote sensing of winds in the stratosphere that does not require discrete ground-truth events. Our method uses measured time delays between arrays of sensors to provide group velocities (referred to here as celerities) and then minimizes the difference between observed and predicted celerities by perturbing an initial atmospheric specification. Because we focus on interarray propagation effects, it is not necessary to simulate the full propagation path from source to receiver. This feature allows us to use a relatively simple forward model that is applicable over short-regional distances. By focusing on stratospheric returns, we show that our non-linear inversion scheme converges much better if the starting model contains a strong stratospheric duct. Using the Horizontal Wind Model (HWM)/Mass Spectrometer Incoherent Scatter (MSISE) empirical climatology as a starting model, we demonstrate that the inversion scheme is robust to large uncertainties in backazimuth, but that uncertainties in the measured trace velocity and celerity require the use of prior constraints to ensure suitable convergence. The inversion of synthetic data, using realistic estimates of measurement error, shows that our scheme will nevertheless improve upon a starting model under most scenarios. The inversion scheme is applied to infrasound data recorded from a large event on 2010 December 25, which is presumed to be a bolide, using data from a nine-element infrasound network in Utah. We show that our recorded data require a stronger zonal wind speed in the stratosphere than is present in the HWM profile, and are more consistent with the Ground-to-Space (G2S) profile.

Description: Coda- Q is a stochastic parameter reflecting the heterogeneities of medium that seismic waves travel through. We confirmed that coda- Q would vary with the stress loaded to an elastic medium using numerical simulations of seismic wave propagation. When the stress is loaded, cracks in the crust could either close or newly open. The closure and opening of the cracks are not random but depending on the magnitude and the direction of the stress and the crack aspect ratio. The cracks in the medium after loading stress could be aligned in a specific orientation, and elastic wave velocity field would become anisotropic due to the alignment of specific crack orientations. Elastic wave velocity is in general faster along the direction corresponding with the crack orientation while slower along the perpendicular direction. In the numerical simulation, the effect of anisotropy in elastic wave velocity field due to the selective closure and opening of the cracks is calculated using a 2-D finite difference method assuming elastic wave velocity to be a function of the magnitude of loaded stress. The coda- Q calculated from seismic waves simulated for a model varies when the averaged normal stress changes. Our simulation indicated that the sensitivity of coda- Q –1 , that is the reciprocal of the coda- Q , would be 1.0 10 –2 (1.0 MPa –1 ) against the magnitude of the confining pressure and 1.0 10 –3 (1.0 deg –1 ) against the direction of principal stress. We would like to conclude that coda- Q , a stochastic parameter reflecting heterogeneities of subsurface medium, could become a quantitative state indicator of the stress field of the medium where seismic waves propagate through. Spatiotemporal variation of coda- Q reflects change in the stress field in the crust.

Description: How do body-wave traveltimes constrain the Earth's radial (1-D) seismic structure? Existing 1-D seismological models underpin 3-D seismic tomography and earthquake location algorithms. It is therefore crucial to assess the quality of such 1-D models, yet quantifying uncertainties in seismological models is challenging and thus often ignored. Ideally, quality assessment should be an integral part of the inverse method. Our aim in this study is twofold: (i) we show how to solve a general Bayesian non-linear inverse problem and quantify model uncertainties, and (ii) we investigate the constraint on spherically symmetric P -wave velocity ( V P ) structure provided by body-wave traveltimes from the EHB bulletin (phases Pn , P , PP and PKP ). Our approach is based on artificial neural networks, which are very common in pattern recognition problems and can be used to approximate an arbitrary function. We use a Mixture Density Network to obtain 1-D marginal posterior probability density functions (pdfs), which provide a quantitative description of our knowledge on the individual Earth parameters. No linearization or model damping is required, which allows us to infer a model which is constrained purely by the data. We present 1-D marginal posterior pdfs for the 22 V P parameters and seven discontinuity depths in our model. P -wave velocities in the inner core, outer core and lower mantle are resolved well, with standard deviations of ~0.2 to 1 per cent with respect to the mean of the posterior pdfs. The maximum likelihoods of V P are in general similar to the corresponding ak135 values, which lie within one or two standard deviations from the posterior means, thus providing an independent validation of ak135 in this part of the radial model. Conversely, the data contain little or no information on P -wave velocity in the D '' layer, the upper mantle and the homogeneous crustal layers. Further, the data do not constrain the depth of the discontinuities in our model. Using additional phases available in the ISC bulletin, such as PcP , PKKP and the converted phases SP and ScP , may enhance the resolvability of these parameters. Finally, we show how the method can be extended to obtain a posterior pdf for a multidimensional model space. This enables us to investigate correlations between model parameters.

Description: We have developed a network optimization method for regional-scale microseismic monitoring networks and applied it to optimize the densification of the existing seismic network in northeastern Switzerland. The new network will build the backbone of a 10-yr study on the neotectonic activity of this area that will help to better constrain the seismic hazard imposed on nuclear power plants and waste repository sites. This task defined the requirements regarding location precision (0.5 km in epicentre and 2 km in source depth) and detection capability [magnitude of completeness M c  = 1.0 ( M L )]. The goal of the optimization was to find the geometry and size of the network that met these requirements. Existing stations in Switzerland, Germany and Austria were considered in the optimization procedure. We based the optimization on the simulated annealing approach proposed by Hardt & Scherbaum, which aims to minimize the volume of the error ellipsoid of the linearized earthquake location problem ( D -criterion). We have extended their algorithm to: calculate traveltimes of seismic body waves using a finite difference ray tracer and the 3-D velocity model of Switzerland, calculate seismic body-wave amplitudes at arbitrary stations assuming the Brune source model and using scaling and attenuation relations recently derived for Switzerland, and estimate the noise level at arbitrary locations within Switzerland using a first-order ambient seismic noise model based on 14 land-use classes defined by the EU-project CORINE and open GIS data. We calculated optimized geometries for networks with 10–35 added stations and tested the stability of the optimization result by repeated runs with changing initial conditions. Further, we estimated the attainable magnitude of completeness ( M c ) for the different sized optimal networks using the Bayesian Magnitude of Completeness (BMC) method introduced by Mignan et al. The algorithm developed in this study is also applicable to smaller optimization problems, for example, small local monitoring networks. Possible applications are volcano monitoring, the surveillance of induced seismicity associated with geotechnical operations and many more. Our algorithm is especially useful to optimize networks in populated areas with heterogeneous noise conditions and if complex velocity structures or existing stations have to be considered.

Description: Fluid injection in and withdrawal from wells are basic procedures in mining activities and deep resources exploitation, such as oil and gas extraction, permeability enhancement for geothermal exploitation and waste fluid disposal. All of these activities have the potential to induce seismicity, as exemplified by the 2006 Basel earthquake ( M L 3.4). Despite several decades of experience, the mechanisms of induced seismicity are not known in detail, which prevents effective risk assessment and/or mitigation. In this study, we provide an interpretation of induced seismicity based on computation of Coulomb stress changes that result from fluid injection/withdrawal at depth, mainly focused on the interpretation of induced seismicity due to stimulation of a geothermal reservoir. Seismicity is, theoretically, more likely where Coulomb stress changes are larger. For modeling purposes, we simulate the thermodynamic evolution of a system after fluid injection/withdrawal. The associated changes in pressure and temperature are subsequently considered as sources of incremental stress changes, which are then converted to Coulomb stress changes on favourably oriented faults, taking into account the background regional stress. Numerical results are applied to the water injection that was performed to create the fractured reservoir at the enhanced-geothermal-system site, Soultz-sous-Forets (France). Our approach describes well the observed seismicity, and provides an explanation for the different behaviors of a system when fluids are injected or withdrawn.

Description: We report on a broad-band high-resolution attenuation model for the North China Craton and surrounding regions based on regional Lg -wave data. Vertical broad-band waveforms recorded at 39 stations from 176 crustal earthquakes are collected to extract the Lg -wave amplitude spectra between 0.05 and 10.0 Hz. We use the dual-station method to generate a preliminary Q Lg model and use it as the initial model. Then, we combine the dual- and single-station data together to jointly invert the Q Lg distribution and Lg source excitation functions. These inversions are conducted independently at individual frequencies without using any a priori assumption about the frequency dependences in Q Lg and source terms. The maximum spatial resolution is approximately 1° x 1° in well-covered areas for frequencies between 0.05 and 2.0 Hz. The Q Lg image is then used to determine the relationship between the attenuation and different geological structures. Results show an average Q 0 (1 Hz Q Lg ) of 374 for the entire North China Craton with an increasing trend from east to west. Average Q 0 values are 337, 361 and 421 for the east, central and west blocks, respectively. For the surrounding regions, the Eastern Tibetan plateau has a very low Q 0 of 188, while the Northeast China Plate and the Tianshan–Xingmeng fold belts are characterized by high Q 0 values of 506 and 424, respectively. We also investigate regional variations of the Lg attenuation in low-frequency band between 0.2 and 1.0 Hz.

Description: We present a systematic study on the influence of pressure (0.1–600 MPa), temperature (750–1200 °C), carbon dioxide fugacity (log f CO 2  = –4.41 to 3.60) and time (2–12 hr) on the chemical and physical properties of carbonate rock. Our experiments aim to reproduce the conditions at the periphery of magma chamber where carbonate host rock is influenced by, but not readily assimilated by, magma. This permits the investigation of the natural conditions at which circulating fluids/gases promote infiltration reactions typical of metasomatic skarns that can involve large volumes of subvolcanic carbonate basements. Results show that, providing that carbon dioxide is retained in the pore space, decarbonation does not proceed at any magmatic pressure and temperature. However, when the carbon dioxide is free to escape, decarbonation can occur rapidly and is not hindered by a low initial porosity or permeability. Together with carbon dioxide and lime, portlandite, a mineral commonly found in voluminous metasomatic skarns, readily forms during carbonate decomposition. Post-experimental analyses highlight that thermal microcracking, a result of the highly anisotropic thermal expansion of calcite, exerts a greater influence on rock physical properties (porosity, ultrasonic wave velocities and elastic moduli) than decarbonation. Our data suggest that this will be especially true at the margins of dykes or magma bodies, where temperatures can reach up to 1200 °C. However, rock compressive strength is significantly reduced by both thermal cracking and decarbonation, explained by the relative weakness of lime + portlandite compared to calcite, and an increase in grain size with increasing temperature. Metasomatic skarns, whose petrogenetic reactions may involve a few tens of cubic kilometres, could therefore represent an important source of volcanic instability.

Description: The scattering of plane SH waves incident on a circular sectorial canyon is considered. An accurate region-matching technique is applied to derive a rigorous series solution. Appropriate wavefunctions are employed to describe antiplane motions. Judicious basis functions, involving Gegenbauer polynomials, are well utilized to correctly capture the singular behaviour in stress fields near the canyon bottom. The enforcement of matching conditions on the auxiliary boundary leads to the determination of unknown coefficients. Plotted results demonstrate the influence of pertinent parameters on surface and subsurface motions. Both steady-state and transient results are included. The solution technique proposed achieves a considerable reduction in the computational effort, facilitating benchmark computations. The derived series solution enriches the limited list of series solutions presently known for canyon problems related to SH -wave scattering.

Description: We present 3-D models of the P- and S -wave velocity distributions in the crust and uppermost mantle beneath Sicily, Calabria (Southern Italy), and surrounding submerged areas, obtained by tomographic inversion of traveltimes of regional body waves phases. Our method combines double-difference tomographic inversion with a post-processing procedure [Weighted Average Model method (WAM)]. This procedure was applied to a set of models consistent with the experimental data. We tested the ability of the WAM procedure to mitigate the uncertainty associated with the arbitrary nature of the many input parameters required for each inversion. The local reliability and resolution of the obtained models have been assessed through: synthetic tests, experimental tests carried out with independent data sets and unconventional tests based on the analysis of the internal consistency of the P - and S -velocity models. The tomographic images provide a detailed sketch of P- and S- wave velocity anomalies. These clearly show the shape of the Sicilian-Maghrebian belt beneath Sicily and Calabrian Arc at different depths. Low V P and Vs bodies are imaged beneath Stromboli and Marsili volcanoes in the southern Tyrrhenian, whereas high and low seismic velocities alternate beneath the Etna giving inferences on the possible depth of the mantle melting feeding the volcano. In the upper crust, the main sedimentary basins and tectonic features are also well imaged. Finally, tomographic cross sections show the trend of the Moho in the study area, where its depth ranges between 35 and 40 km beneath the Sicilian belt and between 15 and 22 km in the southern Tyrrhenian basin and Ionian Sea.

Description: We used two tracks of ALOS PALSAR images to investigate the focal mechanism and slip distribution of the 2011 March 24, M W 6.8 Burma strike-slip earthquake. Three different SAR techniques, namely conventional interferometry, SAR pixel offsets (SPO) and multiple-aperture InSAR (MAI), were employed to obtain the coseismic surface deformation fields along the ~30 km length of the fault rupture. Along-track measurements from SPO and MAI techniques show a high correlation, and were subsequently used to precisely determine the location and extent of the surface fault trace. The best-fitting fault model geometry derived from an iterative inversion technique suggests that the rupture occurred on a near-vertical sinistral strike-slip fault west of the Nam Ma fault with a strike of 70°. A maximum slip of 4.2 m occurs at a depth of 2.5 km, with significant slip constrained only to the upper 10 km of the crust.

Description: Knowledge of the mantle reflectivity structure is highly dependent on our ability to efficiently extract, and properly interpret, small seismic arrivals. Among the various data types and techniques, long-period SS/PP precursors and high-frequency receiver functions are routinely utilized to increase the confidence of the recovered mantle stratifications at distinct spatial scales. However, low resolution and a complex Fresnel zone are glaring weaknesses of SS precursors, while over-reliance on receiver distribution is a formidable challenge for the analysis of converted waves from oceanic regions. A promising high frequency alternative to receiver functions is P ' P ' precursors, which are capable of resolving mantle structures at vertical and lateral resolution of ~5 and ~200 km, respectively, owing to their spectral content, shallow angle of incidence and near-symmetric Fresnel zones. This study presents a novel processing method for both SS (or PP) and P ' P ' precursors based on deconvolution, stacking, Radon transform and depth migration. A suite of synthetic tests is performed to quantify the fidelity and stability of this method under different data conditions. Our multiresolution survey of the mantle at targeted areas near Nazca-South America subduction zone reveal both olivine and garnet related transitions at depths below 400 km. We attribute a depressed 660 to thermal variations, whereas compositional variations atop the upper-mantle transition zone are needed to explain the diminished or highly complex reflected/scattered signals from the 410 km discontinuity. We also observe prominent P ' P ' reflections within the transition zone, and the anomalous amplitudes near the plate boundary zone indicate a sharp (~10 km thick) transition that likely resonates with the frequency content of P ' P ' precursors. The migration of SS precursors in this study shows no evidence of split 660 reflections, but potential majorite–ilmenite (590–640 km) and ilmenite–perovskite transitions (740–750 km) are identified based on similarly processed high-frequency P ' P ' precursors. Additional findings of severely scattered energy in the lithosphere and distinct lower mantle reflections at ~800 km could be potentially important but require further verifications. Overall, our improved imaging methods and the strong sensitivity of P ' P ' precursors to the existence, depth, sharpness and strength of reflective structures offer significant future promise for the understanding of mantle mineralogy and dynamics.

Description: Time-dependent probabilistic seismic hazard assessment requires a stochastic description of earthquake occurrences. While short-term seismicity models are well-constrained by observations, the recurrences of characteristic on-fault earthquakes are only derived from theoretical considerations, uncertain palaeo-events or proxy data. Despite the involved uncertainties and complexity, simple statistical models for a quasi-period recurrence of on-fault events are implemented in seismic hazard assessments. To test the applicability of statistical models, such as the Brownian relaxation oscillator or the stress release model, we perform a systematic comparison with deterministic simulations based on rate- and state-dependent friction, high-resolution representations of fault systems and quasi-dynamic rupture propagation. For the specific fault network of the Lower Rhine Embayment, Germany, we run both stochastic and deterministic model simulations based on the same fault geometries and stress interactions. Our results indicate that the stochastic simulators are able to reproduce the first-order characteristics of the major earthquakes on isolated faults as well as for coupled faults with moderate stress interactions. However, we find that all tested statistical models fail to reproduce the characteristics of strongly coupled faults, because multisegment rupturing resulting from a spatiotemporally correlated stress field is underestimated in the stochastic simulators. Our results suggest that stochastic models have to be extended by multirupture probability distributions to provide more reliable results.

Description: Stress waves, known as acoustic emissions (AEs), are released by localized inelastic deformation events during the progressive failure of brittle rocks. Although several numerical models have been developed to simulate the deformation and damage processes of rocks, such as non-linear stress–strain behaviour and localization of failure, only a limited number have been capable of providing quantitative information regarding the associated seismicity. Moreover, the majority of these studies have adopted a pseudo-static approach based on elastic strain energy dissipation that completely disregards elastodynamic effects. This paper describes a new AE modelling technique based on the combined finite-discrete element method (FEM/DEM), a numerical tool that simulates material failure by explicitly considering fracture nucleation and propagation in the modelling domain. Given the explicit time integration scheme of the solver, stress wave propagation and the effect of radiated seismic energy can be directly captured. Quasi-dynamic seismic information is extracted from a FEM/DEM model with a newly developed algorithm based on the monitoring of internal variables (e.g. relative displacements and kinetic energy) in proximity to propagating cracks. The AE of a wing crack propagation model based on this algorithm are cross-analysed by traveltime inversion and energy estimation from seismic recordings. Results indicate a good correlation of AE initiation times and locations, and scaling of energies, independently calculated with the two methods. Finally, the modelling technique is validated by simulating a laboratory compression test on a granite sample. The micromechanical parameters of the heterogeneous model are first calibrated to reproduce the macroscopic stress–strain response measured during standard laboratory tests. Subsequently, AE frequency–magnitude statistics, spatial clustering of source locations and the evolution of AE rate are investigated. The distribution of event magnitude tends to decay as power law while the spatial distribution of sources exhibits a fractal character, in agreement with experimental observations. Moreover, the model can capture the decrease of seismic b value associated with the macrorupture of the rock sample and the transition of AE spatial distribution from diffuse, in the pre-peak stage, to strongly localized at the peak and post-peak stages, as reported in a number of published laboratory studies. In future studies, the validated FEM/DEM-AE modelling technique will be used to obtain further insights into the micromechanics of rock failure with potential applications ranging from laboratory-scale microcracking to engineering-scale processes (e.g. excavations within mines, tunnels and caverns, petroleum and geothermal reservoirs) to tectonic earthquakes triggering.

Description: We used strong-motion records from the 2012 May 20 and 29 Emilia-Romagna earthquakes ( M w 6.1 and 5.9, respectively) and four aftershocks with magnitudes ranging between 4.9 and 5.5 to analyse the S -wave spectral amplitude decay with distance and estimate acceleration source functions and site effects. The data set consists of six earthquakes, 44 stations and 248 records with hypocentral distances in the range 10 〈 r  〈 100 km. We rotated the accelerograms to calculate transverse and radial components of the acceleration spectrum. We found non-parametric attenuation functions that describe the spectral amplitude decay of SH and SV waves with distance at 60 different frequencies between 0.1 and 40 Hz. These attenuation functions provide an estimate of the quality factor Q at each frequency analysed. Assuming that geometrical spreading is 1/ r for r  ≤ r x and 1/( r x r ) 0.5 for r  〉 r x with r x  = 60 km and normalizing at 15 km (the recording distance where the attenuation functions start to decay), we find that the average Q for SH waves can be approximated by Q SH  = 82 ± 1 f  1.2±0.02 and by Q SV  = 79 ± 1 f  1.24±0.03 for SV waves in the frequency range 0.10 ≤ f  ≤ 10.7 Hz. At higher frequencies, 11.8 ≤ f  ≤ 40 Hz, the frequency dependence of Q weakens and is approximated by Q SH  = 301 ± 1 f   0.36±0.04 and Q SV  = 384 ± 1 f  0.28±0.04 . These results indicate that the S -wave attenuation is radially isotropic at local distances in the epicentral area. Nevertheless, we used these attenuation parameters separately to correct the radial (with Q SV ) and transverse (with Q SH ) components of the acceleration spectra and to separate source and site effects using a non-parametric spectral inversion scheme. We found that the source function of the main event and the bigger aftershocks show enhanced low frequency radiation between 0.4 and 3.0 Hz. We converted the source functions into far-field source acceleration spectra and interpreted the resulting source spectra in terms of Brune's model. The stress drops obtained range between approximately 0.9 and 2.9 MPa. Although all the recording stations used are located in the Po Plain, the site functions obtained from the spectral inversion show important amplification variability between the sites. We compared these site functions with the average horizontal to vertical spectral ratios calculated for each station, and we found consistent results for most stations.

Description: In this study, a miniaturized high fundamental frequency quartz crystal microbalance (QCM) is fabricated for sensor applications using a wet etching technique. The vibration area is reduced in the fabrication of the high frequency QCM with an inverted mesa structure. To reduce the complexity of the side wall profile that results from anisotropic quartz etching, a rectangular vibration area is used instead of the conventional circular structure. QCMs with high Q values exceeding 25,000 at 47 MHz, 27,000 at 60 MHz, 24,000 at 73 MHz and 25,000 at 84 MHz are fabricated on 4 × 4 mm2 chips with small vibration areas of 1.2 × 1.4 mm2. A PMMA-based flow cell is designed and manufactured to characterize the behavior of the fabricated QCM chip in a liquid. Q values as high as 1,006 at 47 MHz, 904 at 62 MHz, 867 at 71 MHz and 747 at 84 MHz are obtained when one side of the chip is exposed to pure water. These results show that fabricated QCM chips can be used for bio- and chemical sensor applications in liquids.

Description: Finger vein recognition is a promising biometric recognition technology, which verifies identities via the vein patterns in the fingers. Binary pattern based methods were thoroughly studied in order to cope with the difficulties of extracting the blood vessel network. However, current binary pattern based finger vein matching methods treat every bit of feature codes derived from different image of various individuals as equally important and assign the same weight value to them. In this paper, we propose a finger vein recognition method based on personalized weight maps (PWMs). The different bits have different weight values according to their stabilities in a certain number of training samples from an individual. Firstly we present the concept of PWM, and then propose the finger vein recognition framework, which mainly consists of preprocessing, feature extraction, and matching. Finally, we design extensive experiments to evaluate the effectiveness of our proposal. Experimental results show that PWM achieves not only better performance, but also high robustness and reliability. In addition, PWM can be used as a general framework for binary pattern based recognition.

Description: The aim of this work is to study the sensing behavior of Sr-doped hematite for soil water content measurement. The material was prepared by solid state reaction from commercial hematite and strontium carbonate heat treated at 900 °C. X-Ray diffraction, scanning electron microscopy and mercury intrusion porosimetry were used for microstructural characterization of the synthesized powder. Sensors were then prepared by uniaxially pressing and by screen-printing, on an alumina substrate, the prepared powder and subsequent firing in the 800–1,000 °C range. These sensors were first tested in a laboratory apparatus under humid air and then in an homogenized soil and finally in field. The results evidenced that the screen printed film was able to give a response for a soil matric potential from about 570 kPa, that is to say well below the wilting point in the used soil.

Description: Salinity and trace mineral accumulation threaten the sustainability of crop production in many semi-arid parts of the world, including California’s western San Joaquin Valley (WSJV). We used data from a multi-year field-scale trial in Kings County and related container trials to simulate a forage-grazing system under saline conditions. The model uses rainfall and irrigation water amounts, irrigation water quality, soil, plant, and atmospheric variables to predict Bermuda grass (Cynodon dactylon (L.) Pers.) growth, quality, and use by cattle. Simulations based on field measurements and a related container study indicate that although soil chemical composition is affected by irrigation water quality, irrigation timing and frequency can be used to mitigate salt and trace mineral accumulation. Bermuda grass yields of up to 12 Mg dry matter (DM)·ha−1 were observed at the field site and predicted by the model. Forage yield and quality supports un-supplemented cattle stocking rates of 1.0 to 1.2 animal units (AU)·ha−1. However, a balance must be achieved between stocking rate, desired average daily gain, accumulation of salts in the soil profile, and potential pollution of ground water from drainage and leaching. Using available weather data, crop-specific parameter values and field scale measurements of soil salinity and nitrogen levels, the model can be used by farmers growing forages on saline soils elsewhere, to sustain forage and livestock production under similarly marginal conditions.

Description: The tension between the meaning of causality in science and law or public policy is well-known; however, defendants in product liability cases or industries that might be affected by a government regulation may try to convince the factfinder to require evidence of a causal relationship that meets the standards of science. From the perspective of public health, however, people may be exposed unnecessarily to a health risk during the time period between the establishment of reasonably strong evidence of a causal relationship and the overwhelming evidence required for scientific causality. The Bayesian paradigm enables one to update information from epidemiologic studies as they accumulate, providing estimates of the probability that the relative risk of a particular harm from exposure exceeds a threshold value, e.g. 2.0 or 4.0 that is sufficient to meet the preponderance of the evidence standard or to support a health initiative. In order to diminish the role of the initial prior distribution, which may be quite subjective, the first case-control study or an analysis of adverse event and case reports is used to determine two prior distributions. One is the most favourable to the defendant, or industry that might be regulated, which is consistent with the previous data. The other is centred on or near the estimated relative risk from the first study. The method is applied to the studies that linked aspirin use to Reye syndrome and demonstrates that the evidence of a causal association was sufficiently strong in 1982, when the Food and Drug Administration first proposed that the public be warned of the risk, to support the regulation. Thus, lives would have been saved had the warning been given at the end of 1982 rather than in early 1985.

Description: In law, inferences of causation are sometimes made through a structured process in which multiple participants play various roles, and make decisions concerning various logical components of the overall inference (such as legal rules, policy objectives, presumptions, evidence, burdens of proof and findings of fact). This article illustrates such a process using empirical research into compensation decisions in the USA for injuries allegedly caused by vaccinations. Empirical research into actual legal processes is essential, in order to discover how various players approach their sub-tasks of decision-making. It also provides insights for areas outside of law, such as non-monotonic logic, cognitive science, sociology and artificial intelligence.

Description: Situations of causal factual uncertainty are relatively common in law. The problems and difficulties regarding ‘factual causation’ in law point to the need of ‘evidence’ and ‘proof’ models that are adequate and capable to accommodate the tests and methodologies used to explain and demonstrate it in a legal context. Given the configuration of the situations of causal factual uncertainty and the available ‘evidence’ and ‘proof’ models, I argue that it is justified to use an ‘argumentative-narrative’ model for ‘proving causation’ in law. However, considering that each model of ‘evidence’ and ‘proof’ reveals a different kind of ‘rationality’ that can still be viewed in different ways, I also argue that we must try to match the perspective we have on the ‘rationality’ behind the chosen model of ‘evidence’ and ‘proof’ with the ‘rationality’ underlying ‘causation’ in law.

Description: At least in some cases, the values confronted in legal decision-making appear to be incommensurable. Some legal theorists resist incommensurability because they fear that this presents an overwhelming obstacle to rational decision-making. By offering a close analysis of proportionality and, more particularly, measures of proportional value satisfaction, I show that this fear is unfounded. Comparative measures of proportional value satisfaction do not require the values to be commensurable. However, assuming incommensurability presents us with the problem of public significance in the proportional satisfaction of values. When two values are commensurable, this public significance is provided by the mediating effects of the overarching third value that provides the common measure of the values. However, when this common measure is removed, then the public significance of value satisfaction must be otherwise achieved. This is why I propose an equal proportional value satisfaction as the most appropriate proportionality maximand. Under equal proportional value satisfaction, the proportional satisfaction of any one value has significance for each and every other value. This kind of public significance is interpersonal rather than impersonal (or second-personal rather than third-personal). The article then shows that the legal process that is most appropriate to equal proportionality is a process that implements defeasible legal rules.

Description: In order to allocate the risk between parties in legal adjudication, we use evidentiary techniques with the main device among them being the standard of proof (SoP). The traditional view holds the grade of probability to be the parameter that shifts when moving to different standards. However, as soon as we dig slightly deeper, an incoherent picture is being revealed. In this article, I challenge the accepted view and try to show that it faces insurmountable problems concerning the rationality, the grammatical consistency and the impact of the SoP for the acceptability of verdicts. At the end of the article, I shortly discuss the theory of epistemological contextualism and propose a framework that allows rational distinctions to be drawn between different standards of proof. In the second part of this project (forthcoming), I will defend a contextualist view according to which shifting parameter is not the grade of (aleatory) probability, but instead the Set of Epistemic Defeaters in play.

Description: This paper presents experimental characterization of plasmoids (fireballs) obtained by directing localized microwave power (〈1 kW at 2.45 GHz) onto a silicon-based substrate in a microwave cavity. The plasmoid emerges up from the hotspot created in the solid substrate into the air within the microwave cavity. The experimental diagnostics employed for the fireball characterization in this study include measurements of microwave scattering, optical spectroscopy, small-angle X-ray scattering (SAXS), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). Various characteristics of these plasmoids as dusty plasma are drawn by a theoretical analysis of the experimental observations. Aggregations of dust particles within the plasmoid are detected at nanometer and micrometer scales by both in-situ SAXS and ex-situ SEM measurements. The resemblance of these plasmoids to the natural ball-lightning (BL) phenomenon is discussed with regard to silicon nano-particle clustering and formation of slowly-oxidized silicon micro-spheres within the BL. Potential applications and practical derivatives of this study (e.g., direct conversion of solids to powders, material identification by breakdown spectroscopy (MIBS), thermite ignition, and combustion) are discussed.

Description: In this study, we simulate the electrophoretic motion of a bio-polymer through a synthetic nanopore in the presence of an external bias voltage by considering the hydrodynamic interactions between the polymer and the fluid explicitly. The motion of the polymer is simulated by 3D Langevin dynamics technique by modeling the polymer as a worm-like-chain, while the hydrodynamic interactions are incorporated by the lattice Boltzmann equation. We report the simulation results for three different lengths of the nanopore. The translocation time increases with the pore length even though the electrophoretic force on the polymer is the same irrespective of the pore length. This is attributed to the fact that the translocation velocity of each bead inside the nanopore decreases with the pore length due to the increased fluid resistance force caused by the increase in the straightened portion of the polymer. We confirmed this using a theoretical formula.

Description: Shadows in high resolution imagery create significant problems for urban land cover classification and environmental application. We first investigated whether shadows were intrinsically different and hypothetically possible to separate from each other with ground spectral measurements. Both pixel-based and object-oriented methods were used to evaluate the effects of shadow detection on QuickBird image classification and spectroradiometric restoration. In each method, shadows were detected and separated either with or without histogram thresholding, and subsequently corrected with a k-nearest neighbor algorithm and a linear correlation correction. The results showed that shadows had distinct spectroradiometric characteristics, thus, could be detected with an optimal brightness threshold and further differentiated with a scene-based near infrared ratio. The pixel-based methods generally recognized more shadow areas and with statistically higher accuracy than the object-oriented methods. The effects of the prior shadow thresholding were not statistically significant. The accuracy of the final land cover classification, after accounting for the shadow detection and separation, was significantly higher for the pixel-based methods than for the object-oriented methods, although both achieved similar accuracy for the non-shadow classes. Both radiometric restoration algorithms significantly reduced shadow areas in the original satellite images.

Description: Since the mechanical properties of single cells together with the intercellular adhesive properties determine the macro-mechanical properties of plants, a method for evaluation of the cell elastic properties is needed to help explanation of the behavior of fruits and vegetables in handling and food processing. For this purpose, indentation of tomato mesocarp cells with an atomic force microscope was used. The Young’s modulus of a cell using the Hertz and Sneddon models, and stiffness were calculated from force-indentation curves. Use of two probes of distinct radius of curvature (20 nm and 10,000 nm) showed that the measured elastic properties were significantly affected by tip geometry. The Young’s modulus was about 100 kPa ± 35 kPa and 20 kPa ± 14 kPa for the sharper tip and a bead tip, respectively. Moreover, large variability regarding elastic properties (>100%) among cells sampled from the same region in the fruit was observed. We showed that AFM provides the possibility of combining nano-mechanical properties with topography imaging, which could be very useful for the study of structure-related properties of fruits and vegetables at the cellular and sub-cellular scale.

Description: Despite longstanding contributions to oceanography, similar use of fluorescence light detection and ranging (LiDAR) in lake settings is not routine. The potential for ship-mounted, multispectral Ultraviolet Fluorescence LiDAR (UFL) to provide rapid, high-resolution data in variably turbid and productive lake conditions are investigated here through a series of laboratory tank and field measurements carried out on Lake Balaton, Hungary. UFL data, calibrated empirically to a set of coinciding conventionally-analyzed samples, provide simultaneous estimates of three important parameters-chlorophyll a(chla), total suspended matter (TSM) and colored dissolved organic matter (CDOM). Successful UFL retrievals from both laboratory and field measurements were achieved for chla (0.01–378 mg∙m−3; R = 0.83–0.92), TSM (0.1–130 g∙m−3; R = 0.90–0.96) and CDOM (0.003–0.125 aCDOM(440); R = 0.80–0.97). Fluorescence emission at 685 nm is shown through tank measurements to display robust but distinct relationships with chla concentration for the two cultured algae species investigated (cyanobacteria, Cylindrospermopsis raciborskii, and chlorophyta, Scenedesmus armatus). The ratio between fluorescence emissions measured at 650 nm, related to the phycocyanin fluorescence maximum, to that at 685 nm is demonstrated to effectively distinguish these two species. Validation through both laboratory measurements and field measurements confirmed that site specific calibration is necessary. This study presents the first known assessment and application of ship-mounted fluorescence LiDAR in freshwater lake conditions and demonstrates the use of UFL in measuring important water quality parameters despite the more complicated hydro-optic conditions of inland waters.

Description: Active magnetic bearings (AMBs) have become a key technology in various industrial applications. Self-sensing AMBs provide an integrated sensorless solution for position estimation, consolidating the sensing and actuating functions into a single electromagnetic transducer. The approach aims to reduce possible hardware failure points, production costs, and system complexity. Despite these advantages, self-sensing methods must address various technical challenges to maximize the performance thereof. This paper presents the direct current measurement (DCM) approach for self-sensing AMBs, denoting the direct measurement of the current ripple component. In AMB systems, switching power amplifiers (PAs) modulate the rotor position information onto the current waveform. Demodulation self-sensing techniques then use bandpass and lowpass filters to estimate the rotor position from the voltage and current signals. However, the additional phase-shift introduced by these filters results in lower stability margins. The DCM approach utilizes a novel PA switching method that directly measures the current ripple to obtain duty-cycle invariant position estimates. Demodulation filters are largely excluded to minimize additional phase-shift in the position estimates. Basic functionality and performance of the proposed self-sensing approach are demonstrated via a transient simulation model as well as a high current (10 A) experimental system. A digital implementation of amplitude modulation self-sensing serves as a comparative estimator.

Description: The stability of radiance measurements taken by the Sky Quality Meter (SQM)was tested under rapidly changing temperature conditions during exposure to a stable lightfield in the laboratory. The reported radiance was found to be negatively correlated withtemperature, but remained within 7% of the initial reported radiance over a temperaturerange of -15 °C to 35 °C, and during temperature changes of -33 °C/h and +70 °C/h.This is smaller than the manufacturer’s quoted unit-to-unit systematic uncertainty of 10%,indicating that the temperature compensation of the SQM is adequate under expected outdooroperating conditions.

Description: There is much interest in using high-throughput DNA sequencing methodology to monitor microorganisms, complex plant and animal communities. However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects. Many of these issues have been highlighted by recent microbial studies. Understanding how high-throughput sequencing is best implemented is important for the interpretation of recent results and the success of future applications. Addressing complex biological questions with metagenomics requires the interaction of researchers who bring different skill sets to problem solving. Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving. Educators are in a position to help students, teachers, the public and policy makers interpret the new knowledge that metagenomics brings. To do this, they need to understand, not only the excitement of the science but also the pitfalls and shortcomings of methodology and research designs. We review these issues and some of the research directions that are helping to move the field forward.

Description: We believe that undergraduate biology students must acquire a foundational background in computing including how to formulate a computational problem; develop an algorithmic solution; implement their solution in software and then test, document and use their code to explore biological phenomena. Moreover, by learning these skills in the first year, students acquire a powerful tool set that they can use and build on throughout their studies. To address this need, we have developed a first-year undergraduate course that teaches students the foundations of computational thinking and programming in the context of problems in biology. This article describes the structure and content of the course and summarizes assessment data on both affective and learning outcomes.

Description: Bioinformatics is an integral part of modern life sciences. It has revolutionized and redefined how research is carried out and has had an enormous impact on biotechnology, medicine, agriculture and related areas. Yet, it is only rarely integrated into high school teaching and learning programs, playing almost no role in preparing the next generation of information-oriented citizens. Here, we describe the design principles of bioinformatics learning environments, including our own, that are aimed at introducing bioinformatics into senior high school curricula through engaging learners in scientifically authentic inquiry activities. We discuss the bioinformatics-related benefits and challenges that high school teachers and students face in the course of the implementation process, in light of previous studies and our own experience. Based on these lessons, we present a new approach for characterizing the questions embedded in bioinformatics teaching and learning units, based on three criteria: the type of domain-specific knowledge required to answer each question (declarative knowledge, procedural knowledge, strategic knowledge, situational knowledge), the scientific approach from which each question stems (biological, bioinformatics, a combination of the two) and the associated cognitive process dimension (remember, understand, apply, analyze, evaluate, create). We demonstrate the feasibility of this approach using a learning environment, which we developed for the high school level, and suggest some of its implications. This review sheds light on unique and critical characteristics related to broader integration of bioinformatics in secondary education, which are also relevant to the undergraduate level, and especially on curriculum design, development of suitable learning environments and teaching and learning processes.

Description: The aim of this paper is to study the relations between the Hausdorff dimensions of k -quasilines and the theory of extremal quasiconformal mappings. We show that there is an open and dense subset (Strebel points) of the universal Teichmüller space T (H) such that, for every [ f ] in the set, the Hausdorff dimension of the k -quasiline determined by [ f ] is strictly less than 1 + k 2 . We also show that there are some points [ f ] != [id] outside the open and dense set in the universal Teichmüller space such that the Hausdorff dimension of the quasiline determined by [ f ] is 1. Moreover, some results on the Hausdorff dimensions of the quasilines varying in the asymptotic Teichmüller space are also obtained.

Description: Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.

Description: A new uniqueness result for a general n th order differential equation is obtained. We show that some previous results follow immediately from our theorem.

Description: Consider a discrete uniformly elliptic divergence form equation on the d ≥3 dimensional lattice Z d with random coefficients. In Conlon and Spencer [ Trans. Amer. Math. Soc. , http://www.math.lsa.umich.edu/~conlon/paper/hom10.pdf ], rate of convergence results in homogenization and estimates on the difference between the averaged Green's function and the homogenized Green's function for random environments which satisfy a Poincaré inequality were obtained. Here, these results are extended to certain environments in which correlations can have arbitrarily small power law decay. These environments are simply related via a convolution to environments which do satisfy a Poincaré inequality.

Description: In this paper, we prove that, for any a , M N with ( a , M ) = 1, there are infinitely many Carmichael numbers m such that m a mod M .

Description: We give a topological analogue for openness of a criterion for flatness that originates with Auslander. Over a normal base of dimension n , failure of openness is detected by a vertical component in the n th fibred power of the morphism.

Description: Investigated are regular maps from real algebraic varieties into real Fermat varieties. It is proved that under some natural assumptions, all such maps are null homotopic.

Description: Let ( M , g ) be a complete non-compact Riemannian manifold. We consider operators of the form g + V , where g is the non-negative Laplacian associated with the metric g , and V a locally integrable function. Let be a Riemannian covering, with Laplacian g and potential . If the operator + V is non-negative on ( M , g ), then the operator is non-negative on . In this note, we show that the converse statement is true provided that is a co-amenable subgroup of 1 ( M ).

Description: Peak interpolation is concerned with a foundational kind of mathematical task: building functions in a fixed algebra A , which have prescribed values or behaviour on a fixed closed subset (or on several disjoint subsets). In this paper, we do the same but now A is an algebra of operators on a Hilbert space. We briefly survey this noncommutative peak interpolation , which we have studied with coauthors in a long series of papers, and whose basic theory now appears to be approaching its culmination. This programme developed from, and is based partly on, theorems of Hay and Read whose proofs were spectacular, but therefore inaccessible to an uncommitted reader. We give short proofs of these results, using recent progress in noncommutative peak interpolation, and conversely give examples of the use of these theorems in peak interpolation. For example, we prove a useful new noncommutative peak interpolation theorem.

Description: We show how a parameterized family of maps of the spine of a manifold can be used to construct a family of homeomorphisms of the ambient manifold which have the inverse limits of the spine maps as global attractors. We describe applications to unimodal families of interval maps, to rotation sets, and to the standard family of circle maps.

Description: High-entropy (H-E) alloys, bulk metallic glasses (BMGs) and high-entropy BMGs (HE-BMGs) were statistically analyzed with the help of a database of ternary amorphous alloys. Thermodynamic quantities corresponding to heat of mixing and atomic size differences were calculated as a function of composition of the multicomponent alloys. Actual calculations were performed for configurational entropy (Sconfig.) in defining the H-E alloys and mismatch entropy (Ss) normalized with Boltzmann constant (kB), together with mixing enthalpy (DHmix) based on Miedema’s empirical model and Delta parameter (d) as a corresponding parameter to Ss/kB. The comparison between DHmix–d and DHmix–  diagrams for the ternary amorphous alloys revealed Ss/kB ~ (d /22)2. The zones S, S′ and B’s where H-E alloys with disordered solid solutions, ordered alloys and BMGs are plotted in the DHmix–d diagram are correlated with the areas in the DHmix – Ss /kB diagram. The results provide mutual understandings among H-E alloys, BMGs and HE-BMGs.

Description: For every prime p , we give infinitely many examples of torsors under abelian varieties over Q that are locally trivial but not divisible by p in the Weil–Châtelet group. We also give an example of a locally trivial torsor under an elliptic curve over Q that is not divisible by 4 in the Weil–Châtelet group. This gives a negative answer to a question of Cassels.

Description: We show that at least of the zeros of the Riemann zeta-function are simple, assuming the Riemann hypothesis. This was previously established by Conrey, Ghosh and Gonek [ Proc. London Math. Soc. 76 (1998) 497–522] under the additional assumption of the generalized Lindelöf hypothesis. We are able to remove this hypothesis by careful use of the generalized Vaughan identity.

Description: We construct an infinite family of hyperbolic, homologically thin knots that are not quasi-alternating. To establish the latter, we argue that the branched double-cover of each knot in the family does not bound a negative-definite 4-manifold with trivial first homology and bounded second Betti number. This fact depends in turn on information from the correction terms in Heegaard Floer homology, which we establish by way of a relationship to, and calculation of, the Turaev torsion.

Description: We observe that E -resultant of a very ample rank 2 vector bundle E on a real projective curve (with no real points) is nonnegative when restricted to the space of real sections. Moreover, we show that if E has a section vanishing at exactly two points and the degree d of E satisfies d ( d – 6) ≥ 4( g – 1), then this polynomial cannot be written as a sum of squares.

Description: Let G be one of the Ricci-flat holonomy groups SU( n ), Sp( n ), Spin(7) or G 2 , and M a compact manifold of dimension 2 n , 4 n , 8 or 7, respectively. We prove that the natural map from the moduli space of torsion-free G -structures on M to the moduli space of Ricci-flat metrics is open, and that the image is a smooth manifold. For the exceptional cases G = Spin(7) and G 2 , we extend the result to asymptotically cylindrical manifolds.

Description: We improve the results of Booker and Krishnamurthy ( Compos. Math. 147 (2011) 669–715) by allowing restricted sets of poles among the unramified twists. This allows for a clean statement of the GL(2) converse theorem which includes all cases of Eisenstein series.

Description: Let G be a solvable subgroup of the automorphism group Aut( X ) of a compact Kähler manifold X of complex dimension n , and let N ( G ) be the normal subgroup of G consisting of elements with null entropy. Let us denote by G * the image of G under the natural map from Aut( X ) to GL( V , R ), where V is the Dolbeault cohomology group H 1, 1 ( X , R ). Assume that the Zariski closure of G * in GL( V C ) is connected. The main aim of this paper is to show that, when the rank r ( G ) of the quotient group G / N ( G ) is equal to n – 1 and the identity component of Aut( X ) is trivial, then the normal subgroup N ( G ) of G is finite. This affirmatively answers a question in Invent. Math. posed by D.-Q. Zhang.

Description: Aquaculture coasts have become widely distributed in coastal zones as human activities are intensified. Due to the complexity in this type of coast, it is difficult to extract the coastline with traditional automated mapping approaches. In this paper, we present an automated method—object-based region growing integrating edge detection (OBRGIE) for the extraction of this type of coastline. In this method, a new object feature named OMI (object merging index) is proposed to separate land and sea. The OBRGIE method was applied to Landsat Thematic Mapper (TM) (pixel size 30m) and Satellite Pour l’Observation de la Terre (SPOT-5) (pixel size 10 m) images of two coastal segments with lengths of 272.7 km and 35.5 km respectively, and the accuracy of the extracted coastlines was assessed in comparison with the manually delineated coastlines. The mean and RMSE (root mean square error) are 16.0 m and 16.4 m respectively for the TM images, and 8.0 m and 8.6 m, respectively, for the SPOT-5 images, indicating that the proposed method derives coastlines with pixel accuracy. The OBRGIE method is also found to be robust to the segmentation scale parameter, and the OMI feature is much more effective than the spectral attribute in separating land and sea in aquaculture coasts. This method may provide an inexpensive means of fast coastline mapping from remotely sensed imagery with relatively fine-to-moderate spatial resolution in coastal sectors with intense human interference.

Description: A study was undertaken to assess Envisat Advanced Synthetic Aperture Radar (ASAR) ScanSAR data for quantifying forest growing stock volume (GSV) across three boreal regions with varying forest types, composition, and structure (Sweden, Central Siberia, and Québec). Estimates of GSV were obtained using hyper-temporal observations of the radar backscatter acquired by Envisat ASAR with the BIOMASAR algorithm. In total, 5.3×106 km2 were mapped with a 0.01° pixel size to obtain estimates representative for the year of 2005. Comparing the SAR-based estimates to spatially explicit datasets of GSV, generated from forest field inventory and/or Earth Observation data, revealed similar spatial distributions of GSV. Nonetheless, the weak sensitivity of C-band backscatter to forest structural parameters introduced significant uncertainty to the estimated GSV at full resolution. Further discrepancies were observed in the case of different scales of the ASAR and the reference GSV and in areas of fragmented landscapes. Aggregation to 0.1° and 0.5° was then undertaken to generate coarse scale estimates of GSV. The agreement between ASAR and the reference GSV datasets improved; the relative difference at 0.5° was consistently within a magnitude of 20–30%. The results indicate an improvement of the characterization of forest GSV in the boreal zone with respect to currently available information.

Description: This paper investigates the linear separation requirements for Angle-of-Arrival (AoA) and range sensors, in order to achieve the optimal performance in estimating the position of a target from multiple and typically noisy sensor measurements. We analyse the sensor-target geometry in terms of the Cramer–Rao inequality and the corresponding Fisher information matrix, in order to characterize localization performance with respect to the linear spatial distribution of sensors. Here in this paper, we consider both fixed and adjustable linear sensor arrays.

Description: The problem of drifting charge-induced currents is considered in order to predict the pulsed operational characteristics in photo-and particle-detectors with a junction controlled active area. The direct analysis of the field changes induced by drifting charge in the abrupt junction devices with a plane-parallel geometry of finite area electrodes is presented. The problem is solved using the one-dimensional approach. The models of the formation of the induced pulsed currents have been analyzed for the regimes of partial and full depletion. The obtained solutions for the current density contain expressions of a velocity field dependence on the applied voltage, location of the injected surface charge domain and carrier capture parameters. The drift component of this current coincides with Ramo’s expression. It has been illustrated, that the synchronous action of carrier drift, trapping, generation and diffusion can lead to a vast variety of possible current pulse waveforms. Experimental illustrations of the current pulse variations determined by either the rather small or large carrier density within the photo-injected charge domain are presented, based on a study of Si detectors.

Description: A visible light communication (VLC) system using an organic bulk heterojunction photodetector (OPD) is presented. The system has been successfully proven indoors with an audio signal. The emitter consists of three commercial high-power white LEDs connected in parallel. The receiver is based on an organic photodetector having as active layer a blend of poly(3-hexylthiophene) (P3HT) and phenyl C61-butyric acid methyl ester (PCBM). The OPD is opto-electrically characterized, showing a responsivity of 0.18 A/W and a modulation response of 790 kHz at −6 V.

Description: In form and in content, cities are the epitome of diversity. This state is the result of the accumulation of layers of history, of construction, of demolition and reconstruction cycles. These tensions are the catalyst for the emergence of new urban forms and participate in the construction of heritage. As such they should be encouraged. As important as the existing fabric of the city is, its evolution to accommodate the ever-changing needs and fashions of its inhabitants is paramount. For regeneration to be successful it must inscribe itself in this process and it must be driven by an understanding of the environment where it occurs. This paper explores, through the lens of an architectural practice, some design processes and architectural proposals that have been generated by working on the Valletta harbours. It also discusses the necessary dynamics required to accommodate stakeholder engagement and planning policy while ensuring design quality and the perpetuation of the creative process inherent to the city. Finally, the paper introduces, as a possible future, the experiments and studies of the practice on the wider Valletta, putting into perspective the benefits of theoretical research combined with formal and aesthetic explorations of the harbour region.

Description: An experimental campaign is undertaken in order to investigate the hydraulic features of a vertical drop shaft, also considering the influence of a venting system consisting of a coaxial vertical pipe, projecting within the drop shaft with different plunging rates. Three different flow regimes are observed: a “weir flow” for very low head values, where the flow profile is subject to the atmospheric pressure; a “full flow” for high head values, where water flows in a pressurized regime along the whole shaft; and a “transitional flow” for intermediate water head values. Weir flow and full flow can be experimentally investigated under steady-state conditions, whereas transitional flow is a pulsating condition, alternately switching from full flow to weir flow. Considering some significant geometric parameters, a head-discharge relation is sought both for the non-vented and for the vented configurations, by means of an energy balance equation, with specific assumptions about intake losses.

Description: Applying the particle filter (PF) technique, this paper proposes a PF-based algorithm to blindly demodulate the chaotic direct sequence spread spectrum (CDS-SS) signals under the colored or non-Gaussian noises condition. To implement this algorithm, the PFs are modified by (i) the colored or non-Gaussian noises are formulated by autoregressive moving average (ARMA) models, and then the parameters that model the noises are included in the state vector; (ii) the range-differentiating factor is imported into the intruder’s chaotic system equation. Since the range-differentiating factor is able to make the inevitable chaos fitting error advantageous based on the chaos fitting method, thus the CDS-SS signals can be demodulated according to the range of the estimated message. Simulations show that the proposed PF-based algorithm can obtain a good bit-error rate performance when extracting the original binary message from the CDS-SS signals without any knowledge of the transmitter’s chaotic map, or initial value, even when colored or non-Gaussian noises exist.

Description: As an important part of the smart grid, a wide-area measurement system (WAMS) provides the key technical support for power system monitoring, protection and control. But 20 uncertainties in system parameters and signal transmission time delay could worsen the damping effect and deteriorate the system stability. In the presented study, the subspace system identification technique (SIT) is used to firstly derive a low-order linear model of a power system from the measurements. Then, a novel adaptive wide-area damping control scheme for online tuning of the wide-area damping controller (WADC) parameters using the residue method is proposed. In order to eliminate the effects of the time delay to the signal transmission, a simple and practical time delay compensation algorithm is proposed to compensate the time delay in each wide-area control signal. Detailed examples, inspired by the IEEE test system under various disturbance scenarios, have been used to verify the effectiveness of the proposed adaptive wide-area damping control scheme.

Description: Model membrane approaches have attracted much attention in biomedical sciences to investigate and simulate biological processes. The application of model membrane systems for biosensor measurements is partly restricted by the fact that the integrity of membranes critically depends on the maintenance of an aqueous surrounding, while various biosensors require a preconditioning of dry sensors. This is for example true for the well-established surface acoustic wave (SAW) biosensor SAM®5 blue. Here, a simple drying procedure of sensor-supported model membranes is introduced using the protective disaccharide trehalose. Highly reproducible model membranes were prepared by the Langmuir-Blodgett technique, transferred to SAW sensors and supplemented with a trehalose solution. Membrane rehydration after dry incorporation into the SAW device becomes immediately evident by phase changes. Reconstituted model membranes maintain their full functionality, as indicated by biotin/avidin binding experiments. Atomic force microscopy confirmed the morphological invariability of dried and rehydrated membranes. Approximating to more physiological recognition phenomena, the site-directed immobilization of the integrin VLA-4 into the reconstituted model membrane and subsequent VCAM-1 ligand binding with nanomolar affinity were illustrated. This simple drying procedure is a novel way to combine the model membrane generation by Langmuir-Blodgett technique with SAW biosensor measurements, which extends the applicability of SAM®5 blue in biomedical sciences.

Description: Hull cleaning before repainting is a key operation in the maintenance of ships. For years, a method to improve such operation has been sought by means of the robotization of techniques such as grit blasting and ultra high pressure water jetting. Despite this, it continues to be standard practice in shipyards that this process is carried out manually because the developed robotized systems are too expensive to be widely accepted by shipyards. We have chosen to apply a more conservative and realistic approach to this problem, which has resulted in the development of several solutions that have been designed with different automation and operation range degrees. These solutions are fitted with most of the elements already available in many shipyards, so the installation of additional machinery in the workplace would not be necessary. This paper describes the evolutionary development of sensor systems for the automation of the preparation process of ship hull surfaces before the painting process is performed. Such evolution has given rise to the development of new technologies for coating removal.

Description: Stress corrosion cracks (SCC) in low-pressure steam turbine discs are serious hidden dangers to production safety in the power plants, and knowing the orientation and depth of the initial cracks is essential for the evaluation of the crack growth rate, propagation direction and working life of the turbine disc. In this paper, a method based on phased array ultrasonic transducer and artificial neural network (ANN), is proposed to estimate both the depth and orientation of initial cracks in the turbine discs. Echo signals from cracks with different depths and orientations were collected by a phased array ultrasonic transducer, and the feature vectors were extracted by wavelet packet, fractal technology and peak amplitude methods. The radial basis function (RBF) neural network was investigated and used in this application. The final results demonstrated that the method presented was efficient in crack estimation tasks.

Description: The dihedral angle formed at junctions between two plagioclase grains and a grain of augite is only very rarely in textural equilibrium in gabbros from kilometre-scale crustal layered intrusions. The median of a population of these disequilibrium angles, cpp , varies systematically within a single layered intrusion, remaining constant over large stretches of stratigraphy with significant increases and decreases associated with the addition or reduction respectively of the number of phases on the liquidus of the bulk magma. The stepwise changes in cpp are present in the Upper Zone of the Bushveld Complex, the Megacyclic Unit I of the Sept Iles Intrusion, and the Layered Series of the Skaergaard intrusion. The plagioclase-bearing cumulates of Rum have a bimodal distribution of cpp , dependent on whether the cumulus assemblage includes clinopyroxene. The presence of the stepwise changes is independent of the order of arrival of cumulus phases and of the composition of either the cumulus phases or the inferred composition of the interstitial liquid. The only parameter that behaves in an exactly analogous manner to cpp is the rate of change in enthalpy with temperature ( H / T ) during crystallization. Both H / T and cpp increase with the addition of a liquidus phase, and decrease with the removal of a liquidus phase. The replacement of one phase by another has little effect on H / T and no discernible effect on cpp . An increase of H / T results in an increase in the fraction of the total enthalpy budget that is the latent heat of crystallization (the fractional latent heat). It also increases the mass crystallized in each incremental temperature drop (the crystal productivity). These increases of both fractional latent heat and crystal productivity are likely to cause an increase in the time taken to form three-grain junctions in the mush via thermal buffering of a thickened mushy layer. We suggest these are the underlying causes of stepwise increases in cpp . Stepwise changes in the geometry of three-grain junctions in fully solidified gabbros thus provide a clear microstructural marker for the progress of fractionation down the liquid line of descent in layered intrusions.

Description: High-resolution sampling in monogenetic fields has the potential to reveal fine-scale heterogeneity of the mantle, a feature that may be overwhelmed by larger fluxes of magma, or missed by under-sampling. The Quaternary Auckland Volcanic Field (AVF) in northern New Zealand is a basaltic field of 51 small-volume volcanic centres, and is one of the best-sampled examples of a monogenetic volcanic field. We present data for 12 centres in the volcanic field. These show the large compositional variations between volcanoes as well as through single eruptive sequences. Whole-rock compositions range from subalkaline basalt in the larger centres, through alkali basalt to nephelinite in the smallest centres. Fractional crystallization has had a limited effect in many of the centres, but high-pressure clinopyroxene crystallization may have occurred in others. Three end-members are observed in Pb isotope space, indicating that distinct mantle source components are involved in the petrogenesis of the magmas. Whole-rock multi-element patterns show that the larger centres have prominent positive Sr anomalies and lack K anomalies, whereas the smaller centres have prominent negative K anomalies and lack Sr anomalies. The melting parameters and compositions of the sources involved are modelled using trace element ratios and multi-element patterns, and three components are characterized: (1) fertile peridotite with a Pb-isotope composition similar to Pacific mid-ocean ridge basalt; (2) eclogite domains with a HIMU-like isotope composition dispersed within the fertile peridotite; (3) slightly depleted subduction-metasomatized peridotitic lithospheric mantle (containing c . 3% subduction fluids). Modelling shows that melting in the AVF begins in garnet-bearing fertile asthenosphere (with preferential melting of eclogite domains) and that melts are variably diluted by melts of the lithospheric source. The U–Th isotope compositions of the end-members in the AVF show 230 Th excess [( 230 Th/ 232 Th) ratios of 1·11–1·38], with the samples of lower ( 230 Th/ 232 Th) exhibiting higher ( 238 U/ 232 Th), which we attribute to the dilution effect of the melts from the lithospheric mantle source. Modelling reveals a correlation between melting in the asthenosphere, the degree of melting and incorporation of the metasomatized lithospheric mantle source, and the resultant size of the volcanic centre. This suggests that the scale of the eruption may essentially be controlled by asthenospheric mantle dynamics.

Description: The origin of mafic and ultramafic sills exhibiting different whole-rock compositional profiles (e.g. I-, C-, D-, M- and S-shaped profiles) remains controversial. We have addressed this issue by revisiting three ~100 m thick Siberian dolerite sills (Vavukansky, Kuz’movsky and Vilyuysky) that display remarkable internal differentiation. The Vavukansky sill has an M-shaped profile with prominent basal and top reversals showing inward increases in whole-rock MgO, Mg-number [100Mg/(Mg + Fe)] and normative An content [100An/(An + Ab)], followed by the Layered and Upper Border Series with inward decreases in these indices. The Kuz’movsky and Vilyuysky sills both show S-shaped profiles similar to the Vavukansky sill, but lack a top reversal. These whole-rock M- and S-shaped profiles are accompanied by similar profiles in mineral compositions. Plagioclase and, to a lesser extent, olivine show systematic inward increases in An content and Mg-number, respectively, across basal and top reversals. These compositional trends are followed by inward decreases in these ratios in the interiors of the Vavukansky and Kuz’movsky sills. Currently accepted models attribute whole-rock M- and S-shaped compositional profiles to crystal settling, compositional convection or compaction operating in closed systems. Our observations challenge these traditional interpretations because variations in mineral compositions observed in marginal reversals cannot result from closed-system fractionation. We suggest instead that initially the sills evolved as open systems that were slowly inflated by magmas that became gradually more primitive with time. The inflation was accompanied by in situ crystallization that preserved the preceding fractionation history of the injected magmas by forming basal and top reversals with minerals becoming more primitive inwards. This process culminated with rapid inflation of the sills to their current size owing to a major influx of primitive magma. Subsequently, magma flow through the sills ceased and they evolved as closed systems by fractional crystallization. This resulted in the Layered and Upper Border Series with minerals becoming more evolved inwards. This model can be extended to explain other compositional profiles and petrological features in mafic and ultramafic sills.

Description: The genomes of related species contain valuable information on the history of the considered taxa. Great apes in particular exhibit variation of evolutionary patterns along their genomes. However, the great ape data also bring new challenges, such as the presence of incomplete lineage sorting and ancestral shared polymorphisms. Previous methods for genome-scale analysis are restricted to very few individuals or cannot disentangle the contribution of mutation rates and fixation biases. This represents a limitation both for the understanding of these forces as well as for the detection of regions affected by selection. Here, we present a new model designed to estimate mutation rates and fixation biases from genetic variation within and between species. We relax the assumption of instantaneous substitutions, modeling substitutions as mutational events followed by a gradual fixation. Hence, we straightforwardly account for shared ancestral polymorphisms and incomplete lineage sorting. We analyze genome-wide synonymous site alignments of human, chimpanzee, and two orangutan species. From each taxon, we include data from several individuals. We estimate mutation rates and GC-biased gene conversion intensity. We find that both mutation rates and biased gene conversion vary with GC content. We also find lineage-specific differences, with weaker fixation biases in orangutan species, suggesting a reduced historical effective population size. Finally, our results are consistent with directional selection acting on coding sequences in relation to exonic splicing enhancers.

Description: Genetic control of male or female gonad development displays between different groups of organisms a remarkable diversity of "master sex-determining genes" at the top of the genetic hierarchies, whereas downstream components surprisingly appear to be evolutionarily more conserved. Without much further studies, conservation of sequence has been equalized to conservation of function. We have used the medaka fish to investigate the generality of this paradigm. In medaka, the master male sex-determining gene is dmrt1bY , a highly conserved downstream regulator of sex determination in vertebrates. To understand its function in orchestrating the complex gene regulatory network, we have identified targets genes and regulated pathways of Dmrt1bY. Monitoring gene expression and interactions by transgenic fluorescent reporter fish lines, in vivo tissue-chromatin immunoprecipitation and in vitro gene regulation assays revealed concordance but also major discrepancies between mammals and medaka, notably amongst spatial, temporal expression patterns and regulations of the canonical Hedgehog and R-spondin/Wnt/Follistatin signaling pathways. Examination of Foxl2 protein distribution in the medaka ovary defined a new subpopulation of theca cells, where ovarian-type aromatase transcriptional regulation appears to be independent of Foxl2. In summary, these data show that the regulation of the downstream regulatory network of sex determination is less conserved than previously thought.

Description: Recently, the duality between values (words) and orderings (permutations) has been proposed by the authors as a basis to discuss the relationship between information theoretic measures for finite-alphabet stationary stochastic processes and their permutatio nanalogues. It has been used to give a simple proof of the equality between the entropy rate and the permutation entropy rate for any finite-alphabet stationary stochastic process and to show some results on the excess entropy and the transfer entropy for finite-alphabet stationary ergodic Markov processes. In this paper, we extend our previous results to hidden Markov models and show the equalities between various information theoretic complexity and coupling measures and their permutation analogues. In particular, we show the following two results within the realm of hidden Markov models with ergodic internal processes: the two permutation analogues of the transfer entropy, the symbolic transfer entropy and the transfer entropy on rank vectors, are both equivalent to the transfer entropy if they are considered as the rates, and the directed information theory can be captured by the permutation entropy approach.

Description: This work is devoted to the systematic study of the optical and magneto-optical properties of sputter deposited CuFe2O4 thin films in the photon energy region between 2 and 5 eV using spectroscopic ellipsometry and magneto-optical Kerr spectroscopy. The spectral dependence of both the diagonal and off-diagonal elements of the permittivity tensor is determined. A complete picture about the electron transitions in CuFe2O4 is suggested in the frame of intervalence charge transfer and intersublattice charge transfer transitions. The effect of deposition conditions and post-deposition treatment in CuFe2O4 films upon the optical and magneto-optical properties is discussed.

Description: In this paper, the formation of ZrO2 and yttria-stabilised-zirconia (YSZ) aqueous colloidal systems via microwave assisted hydrothermal synthesis is studied. Microwave synthesis allows a fast screening of the influence of different parameters such as time and temperature. The temperature varied from 140 °C up to 180 °C and the used reaction time varied from 5 min up to 1 h. The synthesised zirconia nanoparticles have a particle size of 50 nm confirmed by TEM. A 1H NMR (nuclear magnetic resonance) study helped to understand the stabilization mechanism of the synthesised particles. By the addition of ytrrium ions into the zirconia colloidal solution, YSZ could be formed via an additional thermal treatment. Hereby, the samples are heated up to 400 °C for 1 h. YSZ colloidal solutions are synthesised by making use of complexing agents such as nitrilotriacetic acid, ethylenediaminetetraacetic acid and citric acid to control the hydrolysis and condensation of both ions to avoid non-stoichiometric phases. The ratio of Zr/Y in the particles is quantified by XRF. The amorphous structure of those particles necessitates an additional thermal treatment up to 600 °C during 1 h in order to obtain crystalline YSZ.

Description: The recovery behavior for strength and impermeability of cementitious composites embedded with organic microcapsules was investigated in this study. Mortar specimens were formed by mixing the organic microcapsules and a catalyst with cement and sand. The mechanical behaviors of flexural and compression strength were tested. The results showed that strength could increase by up to nine percent with the addition of a small amount of microcapsules and then decrease with an increasing amount of microcapsules. An orthogonal test for investigating the strength recovery rate was designed and implemented for bending and compression using the factors of water/cement ratio, amount of microcapsules, and preloading rate. It is shown that the amount of microcapsules plays a key role in the strength recovery rate. Chloride ion permeability tests were also carried out to investigate the recovery rate and healing effect. The initial damage was obtained by subjecting the specimens to compression. Both the recovery rate and the healing effect were nearly proportional to the amount of microcapsules. The obtained cementitious composites can be seen as self-healing owing to their recovery behavior for both strength and permeability.

Description: We present measurements of higher order clustering of galaxies in the latest release of the Canada–France–Hawaii Telescope Legacy Survey (CFHTLS)-Wide. We construct a series of volume-limited sample of galaxies containing more than one million galaxies over the redshift range 0.2 〈  z  〈 1 in the four independent fields of the CFHTLS-Wide. Using a counts-in-cells technique we measure the variance ${\bar{\xi }}_2$ and the hierarchical moments $S_{n}= {{\bar{\xi }}_n / {\bar{\xi }}_2^{n-1}}$ (3 ≤  n  ≤ 5) as a function of redshift and angular scale. We find that the measured field-to-field scatter in our estimators is in excellent agreement with analytical predictions. At small scales, corresponding to the highly non-linear regime, we find tentative evidence at the 1 level that the hierarchical moments increase with redshift. At large scales, corresponding to the weakly non-linear regime, our measurements are marginally consistent with perturbation theory predictions for standard cold dark matter cosmology using a simple linear bias. The predictions of perturbation theory tend to slightly overestimate our measurements, which may be a signature of non-linear bias.

Description: We estimate cosmic microwave background (CMB) polarization power spectra and temperature–polarization cross-spectra, from the 9-year data of the Wilkinson Microwave Anisotropy Probe ( WMAP ). Foreground cleaning is implemented using minimum variance linear combinations of the coefficients of needlet decompositions of sky maps for all WMAP channels, to produce maps for CMB temperature anisotropies ( T -mode) and polarization ( E and B -modes), for nine different years of observation. The final power spectra are computed from averages of all possible cross-year power spectra obtained using foreground-cleaned maps for the different years. Our analysis technique yields a measurement of the EE spectrum that is in excellent agreement with theoretical expectations from the current cosmological model. By comparison, the publicly available WMAP EE power spectrum is higher on average (and significantly higher than the predicted EE spectrum from the current best fit) at scales larger than about a degree, an excess that is not confirmed by our analysis. Our TE and TB measurements are in good agreement overall with the WMAP ones and are compatible with the theoretical expectations, although a few data points are off by a few standard deviations, and yield a reduced 2 somewhat above expectation. As predicted for a standard cosmological model with low tensor-to-scalar ratio, the EB and BB power spectra obtained in our analysis are compatible with zero.

Description: We present optical integral field unit observations of two gas pillars surrounding the Galactic young massive star cluster NGC 3603. The high S/N and spectral resolution of these data have allowed us to accurately quantify the Hα, [N ii ] and [S ii ] emission line shapes, and we find a mixture of broad (FWHM ~ 70–100 km s –1 ) and narrow (〈50 km s –1 ) components. The broad components are found close to the edges of both pillars, suggesting that they originate in turbulent mixing layers (TMLs) driven by the effect of the star cluster wind. Both pillars exhibit surprisingly high ionized gas densities of 〉10 000 cm –3 . In one pillar we found that these high densities are only found in the narrow component, implying that they must originate from deeper within the pillar than the broad component. From this, together with our kinematical data, we conclude that the narrow component traces a photoevaporation flow, and that the TML forms at the interface with the hot wind. On the pillar surfaces, we find a consistent offset in radial velocity between the narrow (brighter) components of Hα and [N ii ] of ~5–8 km s –1 , for which we were unable to find a satisfactory explanation. We urge the theoretical community to simulate mechanical and radiative cloud interactions in more detail to address the many unanswered questions raised by this study.

Description: By exploiting the data base of early-type galaxy (ETG) members of the WINGS survey of nearby clusters, we address here the long debated question of the origin and shape of the Fundamental Plane (FP). Our data suggest that different physical mechanisms concur in shaping and ‘tilting’ the FP with respect to the virial plane (VP) expectation. In particular, a ‘hybrid solution’ in which the structure of galaxies and their stellar population are the main contributors to the FP tilt seems to be favoured. We find that the bulk of the tilt should be attributed to structural non-homology, while stellar population effects play an important but less crucial role. In addition, our data indicate that the differential FP tilt between the V and K band is due to a sort of entanglement between structural and stellar population effects, for which the inward steepening of colour profiles ( V  –  K ) tends to increase at increasing the stellar mass of ETGs. The same kind of analysis applied to the ATLAS 3 D and Sloan Digital Sky Survey (SDSS) data in common with WINGS ( WSDSS throughout the paper) confirms our results, the only remarkable difference being the less important role that our data attribute to the stellar mass-to-light-ratio (stellar populations) in determining the FP tilt . The ATLAS 3 D data also suggest that the FP tilt depends as well on the dark matter (DM) fraction and on the rotational contribution to the kinetic energy ( V rot /), thus again pointing towards the above-mentioned ‘hybrid solution’. We show that the global properties of the FP, i.e. its tilt and tightness, can be understood in terms of the underlying correlation among mass, structure and stellar population of ETGs, for which, at increasing the stellar mass, ETGs become (on average) ‘older’ and more centrally concentrated. Finally, we show that a Malmquist-like selection effect may mimic a differential evolution of the mass-to-light ratio for galaxies of different masses. This should be taken into account in the studies investigating the amount of the so-called ‘downsizing’ phenomenon.

Description: This paper provides an overview on our recent investigations on the consolidation of hierarchy-structured nanopowder agglomerates and related applications to net-shaping nanopowder materials. Understanding the nanopowder agglomerate sintering (NAS) process is essential to processing of net-shaped nanopowder materials and components with small and complex shape. The key concept of the NAS process is to enhance material transport through controlling the powder interface volume of nanopowder agglomerates. Based upon this concept, we have suggested a new idea of full density processing for fabricating micro-powder injection molded part using metal nanopowder agglomerates produced by hydrogen reduction of metal oxide powders. Studies on the full density sintering of die compacted- and powder injection molded iron base nano-agglomerate powders are introduced and discussed in terms of densification process and microstructure.

Description: I present a new algorithm, Curved-sky grAvitational Lensing for Cosmological Light conE simulatioNS ( calclens ), for efficiently computing weak gravitational lensing shear signals from large N -body light cone simulations over a curved sky. This new algorithm properly accounts for the sky curvature and boundary conditions, is able to produce redshift-dependent shear signals including corrections to the Born approximation by using multiple-plane ray tracing and properly computes the lensed images of source galaxies in the light cone. The key feature of this algorithm is a new, computationally efficient Poisson solver for the sphere that combines spherical harmonic transform and multigrid methods. As a result, large areas of sky (~10 000 square degrees) can be ray traced efficiently at high resolution using only a few hundred cores. Using this new algorithm and curved-sky calculations that only use a slower but more accurate spherical harmonic transform Poisson solver, I study the convergence, shear E-mode, shear B-mode and rotation mode power spectra. Employing full-sky E/B-mode decompositions, I confirm that the numerically computed shear B-mode and rotation mode power spectra are equal at high accuracy (1 per cent) as expected from perturbation theory up to second order. Coupled with realistic galaxy populations placed in large N -body light cone simulations, this new algorithm is ideally suited for the construction of synthetic weak lensing shear catalogues to be used to test for systematic effects in data analysis procedures for upcoming large-area sky surveys. The implementation presented in this work, written in c and employing widely available software libraries to maintain portability, is publicly available at http://code.google.com/p/calclens .

Description: Quasar accretion disc winds observed via broad absorption lines (BALs) in the UV produce strong continuous absorption in X-rays. The X-ray absorber is believed to serve critically as a radiative shield to keep the outflow ionizations low enough for radiative driving. However, previous studies have shown that ‘mini-BAL’ and narrow absorption line (NAL) outflows have dramatically less X-ray absorption than BALs. Here, we examine X-ray and rest-frame UV spectra of eight mini-BAL quasars with outflow speeds in the range 0.1–0.2c to test the hypothesis that these extreme speeds require a strong shield. We find that the X-ray absorption is weak or moderate, with neutral-equivalent column densities N H  〈 few 10 22 cm –2 , consistent with mini-BALs at lower speeds. We use photoionization models to show that the amount of shielding consistent with our data is too weak to control the outflow ionizations and, therefore, it is not important for the acceleration. Shielding in complex geometries also seems unlikely because the alleged shield would need to extinguish the ionizing far-UV flux while avoiding detection in X-rays and the near-UV. We argue that the outflow ionizations are kept moderate, instead, by high gas densities in small clouds. If the mini-BALs form at radial distances of the order of R ~ 2 pc from the central quasar (broadly consistent with theoretical models and with the mini-BAL variabilities observed here and in previous work), and the total column densities in the mini-BAL gas are N H 10 21 cm –2 , then the total radial extent of outflow clouds is only R clouds 3 x 10 13 cm in cases of no/weak shielding or R clouds 3 x 10 14 cm behind the maximum shield allowed by our data. This implies radial filling factors R clouds / R 5 x 10 – 6 or 5 x 10 – 5 for the unshielded or maximally shielded cases, respectively. Compared to the transverse sizes 8 x 10 15 cm (based on measured line depths), the outflows have shapes like thin ‘pancakes’ viewed face-on, or they occupy larger volumes like a spray of many dense clouds with a small volume filling factor. These results favour models with magnetic confinement in magnetic disc winds. To the extent that BALs, mini-BALs and NALs probe the same general outflow phenomenon, our result for dense substructures should apply to all three outflow types.