Links between metamorphism and deformation in feldspar at mid-crustal conditions

Feldspar is the most common mineral in the Earth’s mid-to-lower crust, and therefore exerts fundamental controls on crustal strength. However, due to the relatively complex chemistry of the feldspar series, particularly its temperature dependence on composition, interactions between metamorphism and deformation, and thus overall deformation behaviour, remain poorly understood. Metagabbroic rocks from a crustal-scale shear zone were studied using electron backscatter diffraction and transmission electron microscopy, to investigate the deformation behaviour of plagioclase at greenschist facies. Numerical modelling was subsequently employed to characterise the microstructural evolution of features observed in the natural samples, specifically the effect that large grains have on the evolution of a fine-grained matrix. The results of this study showed that mm–cm-scale albite grains were formed through fluid-assisted, interface-coupled replacement reactions, which produced a high dislocation density in those grains through a chemical, rather than mechanical, mechanism. Small albite grains of the same composition were formed either through classical precipitation mechanisms, or by growth from strain-free nuclei that consumed the large grains, in response to the stored strain energy in the large grains. The reduction in grain size led to fluid-assisted diffusion creep (pressure solution) becoming the dominant deformation mechanism that accommodated high strains in the samples. Despite this type of deformation being expected to destroy crystallographic preferred orientation, or texture, preferred orientation domains are preserved to high strains in the albite-rich matrix of the rocks. Metagabbroic samples were studied at five different strain levels to characterise how albite grain size, aspect ratio, and texture strength, and second phase abundance, evolved and interacted during deformation. Although the secondary phases produced during metamorphic reactions have generally been reported to inhibit grain growth, which promotes GSS creep, the results of this study show their presence may also limit texture modification by inhibiting the rotations normally associated with diffusion creep and grain boundary sliding, to preserve CPO domains to high strain. The modelling results showed that large grains can have a significant effect on the microstructural evolution of a fine-grained matrix undergoing diffusion creep. In particular, rotations of matrix grains were strongly influenced by the rotation direction and velocity of large grains. The study also showed that the rotation direction of large grains does not have to be simply either synthetic or antithetic; rotation directions changed due to interactions with the matrix. The model output also showed that large grains create stress heterogeneities that focus the effects of diffusion creep. The stress heterogeneities resulted in the alignment of grain boundaries, and led to a profound drop in strength of the deforming material. These results indicate the microstructural evolution of rocks undergoing (fluid-assisted) diffusion creep is more complex than previously realised, and the mechanisms and processes at work during deformation by diffusion creep require further study

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie

Measurements of the vertical fluxes of atomic Fe and Na at the mesopause: implications for the velocity of cosmic dust entering the atmosphere

The downward fluxes of Fe and Na, measured near the mesopause with the University of Colorado lidars near Boulder, and a chemical ablation model developed at the University of Leeds, are used to constrain the velocity/mass distribution of the meteoroids entering the atmosphere and to derive an improved estimate for the global influx of cosmic dust. We find that the particles responsible for injecting a large fraction of the ablated material into the Earth's upper atmosphere enter at relatively slow speeds and originate primarily from the Jupiter Family of Comets. The global mean Na influx is 17,200 ± 2800 atoms/cm2/s, which equals 298 ± 47 kg/d for the global input of Na vapor and 150 ± 38 t/d for the global influx of cosmic dust. The global mean Fe influx is 102,000 ± 18,000 atoms/cm2/s, which equals 4.29 ± 0.75 t/d for the global input of Fe vapor

A scattering rate approach to the understanding of absorption line broadening in near-infrared AlGaN/GaN quantum wells

There has been much interest in the advancement of III-Nitride growth technology to fabricate AlGaN/GaN heterostructures for intersubband transitions (ISBTs). The large conduction band offset in these structures (up to 2 eV) allows transition energies in the near- to the far-infrared region, which have applications from telecommunications, such as in all-optical switches, to infra-red detectors for sensing and imaging. To date, ISBT electroluminescence has been elusive and absorption measurements remain an important method to verify band structure calculations. The growth quality can be inferred from the absorption spectrum, which will have line broadening with contributions that are both inhomogeneous (large-scale interface roughness, and non-parabolicity) and homogeneous (electron scattering related lifetime broadening). In the present work we calculated the contributions of various homogeneous broadening mechanisms (electron interaction with longitudinal-optical (LO) phonons, acoustic phonons, impurities and alloy disorder) to the full linewidth, and also the contribution of band non-parabolicity, which contributes to the inhomogeneous broadening. Calculations are then compared to the measured absorption spectra of several samples

Time esophageal pH < 4 overestimates the prevalence of pathologic esophageal reflux in subjects with gastroesophageal reflux disease treated with proton pump inhibitors

<p>Abstract</p> <p>Background</p> <p>A Stanford University study reported that in asymptomatic GERD patients who were being treated with a proton pump inhibitor (PPI), 50% had pathologic esophageal acid exposure.</p> <p>Aim</p> <p>We considered the possibility that the high prevalence of pathologic esophageal reflux might simply have resulted from calculating acidity as time pH < 4.</p> <p>Methods</p> <p>We calculated integrated acidity and time pH < 4 from the 49 recordings of 24-hour gastric and esophageal pH from the Stanford study as well as from another study of 57 GERD subjects, 26 of whom were treated for 8 days with 20 mg omeprazole or 20 mg rabeprazole in a 2-way crossover fashion.</p> <p>Results</p> <p>The prevalence of pathologic 24-hour esophageal reflux in both studies was significantly higher when measured as time pH < 4 than when measured as integrated acidity. This difference was entirely attributable to a difference between the two measures during the nocturnal period. Nocturnal gastric acid breakthrough was not a useful predictor of pathologic nocturnal esophageal reflux.</p> <p>Conclusion</p> <p>In GERD subjects treated with a PPI, measuring time esophageal pH < 4 will significantly overestimate the prevalence of pathologic esophageal acid exposure over 24 hours and during the nocturnal period.</p

Design considerations for GaN/AlN based unipolar (opto-)electronic devices, and interface quality aspects

We describe the theoretical and experimental studies of GaN/AlGaN based resonant tunnelling diodes, and in particular analyse the effects and typical values of interface roughness, and then discuss the implications of these, realistic material quality parameters on performance of unipolar optoelectronic devices

Cooperative secretions facilitate host range expansion in bacteria

The majority of emergent human pathogens are zoonotic in origin, that is, they can transmit to humans from other animals. Understanding the factors underlying the evolution of pathogen host range is therefore of critical importance in protecting human health. There are two main evolutionary routes to generalism: organisms can tolerate multiple environments or they can modify their environments to forms to which they are adapted. Here we use a combination of theory and a phylogenetic comparative analysis of 191 pathogenic bacterial species to show that bacteria use cooperative secretions that modify their environment to extend their host range and infect multiple host species. Our results suggest that cooperative secretions are key determinants of host range in bacteria, and that monitoring for the acquisition of secreted proteins by horizontal gene transfer can help predict emerging zoonoses

Respiratory Insufficiency Correlated Strongly with Mortality of Rodents Infected with West Nile Virus

West Nile virus (WNV) disease can be fatal for high-risk patients. Since WNV or its antigens have been identified in multiple anatomical locations of the central nervous system of persons or rodent models, one cannot know where to investigate the actual mechanism of mortality without careful studies in animal models. In this study, depressed respiratory functions measured by plethysmography correlated strongly with mortality. This respiratory distress, as well as reduced oxygen saturation, occurred beginning as early as 4 days before mortality. Affected medullary respiratory control cells may have contributed to the animals' respiratory insufficiency, because WNV antigen staining was present in neurons located in the ventrolateral medulla. Starvation or dehydration would be irrelevant in people, but could cause death in rodents due to lethargy or loss of appetite. Animal experiments were performed to exclude this possibility. Plasma ketones were increased in moribund infected hamsters, but late-stage starvation markers were not apparent. Moreover, daily subcutaneous administration of 5% dextrose in physiological saline solution did not improve survival or other disease signs. Therefore, infected hamsters did not die from starvation or dehydration. No cerebral edema was apparent in WNV- or sham-infected hamsters as determined by comparing wet-to-total weight ratios of brains, or by evaluating blood-brain-barrier permeability using Evans blue dye penetration into brains. Limited vasculitis was present in the right atrium of the heart of infected hamsters, but abnormal electrocardiograms for several days leading up to mortality did not occur. Since respiratory insufficiency was strongly correlated with mortality more than any other pathological parameter, it is the likely cause of death in rodents. These animal data and a poor prognosis for persons with respiratory insufficiency support the hypothesis that neurological lesions affecting respiratory function may be the primary cause of human WNV-induced death

Mathematical modelling of a liver hollow fibre bioreactor

A mathematical model has been developed to assist with the development of a hollow fibre bioreactor (HFB) for hepatotoxicity testing of xenobiotics; specifically, to inform the HFB operating set-up, interpret data from HFB outputs and aid in optimizing HFB design to mimic certain hepatic physiological conditions. Additionally, the mathematical model has been used to identify the key HFB and compound parameters that will affect xenobiotic clearance. The analysis of this model has produced novel results that allow the operating set-up to be calculated, and predictions of compound clearance to be generated. The mathematical model predicts the inlet oxygen concentration and volumetric flow rate that gives a physiological oxygen gradient in the HFB to mimic a liver sinusoid. It has also been used to predict the concentration gradients and clearance of a test drug and paradigm hepatotoxin, paracetamol (APAP). The effect of altering the HFB dimensions and fibre properties on APAP clearance under the condition of a physiological oxygen gradient is analysed. These theoretical predictions can be used to design the most appropriate experimental set up and data analysis to quantitatively compare the functionality of cell types that are cultured within the HFB to those in other systems

Pathophysiology of acute experimental pancreatitis: Lessons from genetically engineered animal models and new molecular approaches

The incidence of acute pancreatitis is growing and worldwide population-based studies report a doubling or tripling since the 1970s. 25% of acute pancreatitis are severe and associated with histological changes of necrotizing pancreatitis. There is still no specific medical treatment for acute pancreatitis. The average mortality resides around 10%. In order to develop new specific medical treatment strategies for acute pancreatitis, a better understanding of the pathophysiology during the onset of acute pancreatitis is necessary. Since it is difficult to study the early acinar events in human pancreatitis, several animal models of acute pancreatitis have been developed. By this, it is hoped that clues into human pathophysiology become possible. In the last decade, while employing molecular biology techniques, a major progress has been made. The genome of the mouse was recently sequenced. Various strategies are possible to prove a causal effect of a single gene or protein, using either gain-of-function (i.e., overexpression of the protein of interest) or loss-of-function studies (i.e., genetic deletion of the gene of interest). The availability of transgenic mouse models and gene deletion studies has clearly increased our knowledge about the pathophysiology of acute pancreatitis and enables us to study and confirm in vitro findings in animal models. In addition, transgenic models with specific genetic deletion or overexpression of genes help in understanding the role of one specific protein in a cascade of inflammatory processes such as pancreatitis where different proteins interact and co-react. This review summarizes the recent progress in this field. Copyright (c) 2005 S. Karger AG, Basel