Quantitative modeling of \textit{in situ} x-ray reflectivity during organic molecule thin film growth

Synchrotron-based x-ray reflectivity is increasingly employed as an \textit{in situ} probe of surface morphology during thin film growth, but complete interpretation of the results requires modeling the growth process. Many models have been developed and employed for this purpose, yet no detailed, comparative studies of their scope and accuracy exists in the literature. Using experimental data obtained from hyperthermal deposition of pentane and diindenoperylene (DIP) on SiO$_2$, we compare and contrast three such models, both with each other and with detailed characterization of the surface morphology using ex-situ atomic force microscopy (AFM). These two systems each exhibit particular phenomena of broader interest: pentacene/SiO$_2$ exhibits a rapid transition from rough to smooth growth. DIP/SiO$_2$, under the conditions employed here, exhibits growth rate acceleration due to a different sticking probability between the substrate and film. In general, \textit{independent of which model is used}, we find good agreement between the surface morphology obtained from fits to the \insitu x-ray data with the actual morphology at early times. This agreement deteriorates at later time, once the root-mean squared (rms) film roughness exceeds about 1 ML. A second observation is that, because layer coverages are under-determined by the evolution of a single point on the reflectivity curve, we find that the best fits to reflectivity data --- corresponding to the lowest values of $\chi_\nu^2$ --- do not necessarily yield the best agreement between simulated and measured surface morphologies. Instead, it appears critical that the model reproduce all local extrema in the data. In addition to showing that layer morphologies can be extracted from a minimal set of data, the methodology established here provides a basis for improving models of multilayer growth by comparison to real systems.Comment: 34 pages (double-spaced, including figures and references), 10 figures, 3 appendice

Validity and reliability of computerized measurement of lumbar intervertebral disc height and volume from magnetic resonance images

BACKGROUND CONTEXT: Magnetic resonance (MR) examinations of morphologic characteristics of intervertebral discs (IVDs) have been used extensively for biomechanical studies and clinical investigations of the lumbar spine. Traditionally, the morphologic measurements have been performed using time- and expertise-intensive manual segmentation techniques not well suited for analyses of large-scale studies.

Reduced Deadtime and Higher Rate Photon-Counting Detection using a Multiplexed Detector Array

We present a scheme for a photon-counting detection system that can be operated at incident photon rates higher than otherwise possible by suppressing the effects of detector deadtime. The method uses an array of N detectors and a 1-by-N optical switch with a control circuit to direct input light to live detectors. Our calculations and models highlight the advantages of the technique. In particular, using this scheme, a group of N detectors provides an improvement in operation rate that can exceed the improvement that would be obtained by a single detector with deadtime reduced by 1/N, even if it were feasible to produce a single detector with such a large improvement in deadtime. We model the system for continuous and pulsed light sources, both of which are important for quantum metrology and quantum key distribution applications.Comment: 6 figure

Circulating alpha1-antitrypsin in the general population: Determinants and association with lung function

BACKGROUND: Severe alpha1-antitrypsin (AAT) deficiency associated with low AAT blood concentrations is an established genetic COPD risk factor. Less is known about the respiratory health impact of variation in AAT serum concentrations in the general population. We cross-sectionally investigated correlates of circulating AAT concentrations and its association with FEV1. METHODS: In 5187 adults (2669 females) with high-sensitive c-reactive protein (CRP) levels < or = 10 mg/l from the population-based Swiss SAPALDIA cohort, blood was collected at the time of follow-up examination for measuring serum AAT and CRP. RESULTS: Female gender, hormone intake, systolic blood pressure, age in men and in postmenopausal women, as well as active and passive smoking were positively, whereas alcohol intake and BMI inversely correlated with serum AAT levels, independent of CRP adjustment. We observed an inverse association of AAT with FEV1 in the total study population (p < 0.001), that disappeared after adjustment for CRP (p = 0.28). In addition, the AAT and FEV1 association was modified by gender, menopausal status in women, and smoking. CONCLUSION: The results of this population-based study reflect a complex interrelationship between tobacco exposure, gender related factors, circulating AAT, systemic inflammatory status and lung function

Seizures, CSF neurofilament light and tau in patients with subarachnoid haemorrhage

Objectives: Patients with severe subarachnoid haemorrhage (SAH) often suffer from complications with delayed cerebral ischaemia (DCI) due to vasospasm that is difficult to identify by clinical examination. The purpose of this study was to monitor seizures and to measure cerebrospinal fluid (CSF) concentrations of neurofilament light (NFL) and tau, and to see whether they could be used for predicting preclinical DCI. Methods: We prospectively studied 19 patients with aneurysmal SAH who underwent treatment with endovascular coiling. The patients were monitored with continuous EEG (cEEG) and received external ventricular drainage (EVD). CSF samples of neurofilament light (NLF) and total tau (T‐tau) protein were collected at day 4 and day 10. Cox regression analysis was applied to evaluate whether seizures and protein biomarkers were associated with DCI and poor outcome. Results: Seven patients developed DCI (37%), and 4 patients (21%) died within the first 2 months. Six patients (32%) had clinical seizures, and electrographic seizures were noted in one additional patient (4.5%). Increased tau ratio (proportion tau10/tau4) was significantly associated with DCI and hazard ratio [HR=1.33, 95% confidence interval (CI) 1.055‐1.680. P = .016]. Conclusion: Acute symptomatic seizures are common in SAH, but their presence is not predictive of DCI. High values of the tau ratio in the CSF may be associated with development of DCI

Challenges and strategies of children and adolescents with inflammatory bowel disease: a qualitative examination

© 2007 Nicholas et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Orbit structure and (reversing) symmetries of toral endomorphisms on rational lattices

We study various aspects of the dynamics induced by integer matrices on the invariant rational lattices of the torus in dimension 2 and greater. Firstly, we investigate the orbit structure when the toral endomorphism is not invertible on the lattice, characterising the pretails of eventually periodic orbits. Next we study the nature of the symmetries and reversing symmetries of toral automorphisms on a given lattice, which has particular relevance to (quantum) cat maps.Comment: 29 pages, 3 figure

GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database

GeneHub-GEPIS is a web application that performs digital expression analysis in human and mouse tissues based on an integrated gene database. Using aggregated expressed sequence tag (EST) library information and EST counts, the application calculates the normalized gene expression levels across a large panel of normal and tumor tissues, thus providing rapid expression profiling for a given gene. The backend GeneHub component of the application contains pre-defined gene structures derived from mRNA transcript sequences from major databases and includes extensive cross references for commonly used gene identifiers. ESTs are then linked to genes based on their precise genomic locations as determined by GMAP. This genome-based approach reduces incorrect matches between ESTs and genes, thus minimizing the noise seen with previous tools. In addition, the gene-centric design makes it possible to add several important features, including text searching capabilities, the ability to accept diverse input values, expression analysis for microRNAs, basic gene annotation, batch analysis and linking between mouse and human genes. GeneHub-GEPIS is available at http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/ or http://www.gepis.org/

Autoreactivity to malondialdehyde-modifications in rheumatoid arthritis is linked to disease activity and synovial pathogenesis

Oxidation-associated malondialdehyde (MDA) modification of proteins can generate immunogenic neo-epitopes that are recognized by autoantibodies. In health, IgM antibodies to MDA-adducts are part of the natural antibody pool, while elevated levels of IgG anti-MDA are associated with inflammatory conditions. Yet, in human autoimmune disease IgG anti-MDA responses have not been well characterized and their potential contribution to disease pathogenesis is not known. Here, we investigate MDA-modifications and anti-MDA-modified protein autoreactivity in rheumatoid arthritis (RA). While RA is primarily associated with autoreactivity to citrullinated antigens, we also observed increases in serum IgG anti-MDA in RA patients compared to controls. IgG anti-MDA levels significantly correlated with disease activity by DAS28-ESR and serum TNF-alpha, IL-6, and CRP. Mass spectrometry analysis of RA synovial tissue identified MDA-modified proteins and revealed shared peptides between MDA-modified and citrullinated actin and vimentin. Furthermore, anti-MDA autoreactivity among synovial B cells was discovered when investigating recombinant monoclonal antibodies (mAbs) cloned from single B cells. Several clones were highly specific for MDA-modification with no cross-reactivity to other antigen modifications. The mAbs recognized MDA-adducts in a variety of proteins. Interestingly, the most reactive clone, originated from an IgG1-bearing memory B cell, was encoded by germline variable genes, and showed similarity to previously reported natural IgM. Other anti-MDA clones display somatic hypermutations and lower reactivity. These anti-MDA antibodies had significant in vitro functional properties and induced enhanced osteoclastogenesis, while the natural antibody related high-reactivity clone did not. We postulate that these may represent distinctly different facets of anti-MDA autoreactive responses