Magnetotelluric data processing: a case study

Magnetotelluric (MT) data collected simultaneously at one or more sites may be processed by a number of different methods. Such methods attempt to remove or suppress the effect of noise on the data channels. The desired results are accurate, unbiased and repeatable estimates of the impedance tensor as a function of frequency and location. In this study we perform an investigation of the analysis of an MT data set sampled at 5 s. Both single-site (SS) and remote-reference (RR) techniques are employed to estimate the impedance tensor Z. Two biased SS estimates of Z are used to compare the performance of five coherence­ based acceptance criteria. It is demonstrated that the RR predicted coherence between local fields can be used for selecting data windows, and provides a necessary assessment of the reliability of a given RR estimate. It is demonstrated that the variance of an RR estimate depends strongly on the local signal-to-noise ratios (as monitored by the local predicted coherence) and depends weakly on the number of data windows, as long as coherences are above a moderate threshold. Although, for our data, an estimate of Z obtained using a remote electric field is grossly inaccurate, its associated predicted coherence is as efficient in selecting low-noise-level data windows as its counterpart obtained using a remote magnetic field. The relation between SS and RR predicted coherences, the latter estimated using both electric and magnetic fields, is investigated. A hybrid selection technique that uses a remote electric field is suggested

Transmission of primary resistance mutation K103N in a cluster of Belgian young patients from different risk groups

Background: We analysed the distribution of an HIV-1 subtype B strain resistant to efavirenz and nevirapine among incident infections in the Belgian population. Method: The Belgian AIDS reference laboratories searched their databases for HIV-1 subtype B sequences harbouring the K103N mutation in the reverse transcriptase (RT) or the C67S and V77I mutations in the protease (PR). We included the earliest RT sequence available of drug-naïve patients as well as sequences related to treatment failure. Fifty sequences were aligned omitting the codon 103 and submitted to phylogenetic analysis. Epidemiological data were collected through the Institute of Public Health national database. In addition, three sequences from the cluster were analysed by deep sequencing using the Roche GS Junior platform. Results: Phylogenetic analysis revealed the presence of a 24 virus sequences cluster. All except one of those sequences resulted from patients who were ARV-naïve at the time of sampling, and 21 had the K103N mutation. Two thirds of the clustered patients were infected through homosexual or bisexual contacts while the others were heterosexuals. No case was related to migrants contaminated abroad. Fifteen of the clustered patients were diagnosed between January 2011 and June 2012; 87% of them were aged between 20 and 29 at the time of diagnosis. Interestingly, 60% of them reside in the province of Namur. Deep sequencing analysis of 3 individuals sampled near seroconversion revealed no other resistance mutations at a frequency > 1% than those already picked up by Sanger sequencing (RT A98S, K103N; PR V77I), except the RT V90I. Conclusion: We identified a transmission cluster of drug resistant HIV-1 variants mainly including homo- and heterosexual young adults. Most individuals are of Belgian origin and are living around the city of Namur (Belgium). The K103N mutation had no apparent impact on transmission fitness as its spread raised during the last years. These observations may impact on local prevention and ARV prophylaxis strategies

Superconducting cavity transducer for resonant gravitational radiation antennas

Parametric transducers, such as superconducting rf cavities, can boost the bandwidth and sensitivity of the next generation resonant antennas, thanks to a readily available technology. We have developed a fully coupled dynamic model of the system "antenna--transducer" and worked out some estimates of signal--to--noise ratio and the stability conditions in various experimental configurations. We also show the design and the prototype of a rf cavity which, together with a suitable read--out electronic, will be used as a test bench for the parametric transducer.Comment: 7 pages, 3 eps figures. Presented at the 6th Amaldi Conference on Gravitational Waves (2005). Accepted for publication in Journal of Physics: Conference Serie

Experimental simulation of quantum graphs by microwave networks

We present the results of experimental and theoretical study of irregular, tetrahedral microwave networks consisting of coaxial cables (annular waveguides) connected by T-joints. The spectra of the networks were measured in the frequency range 0.0001-16 GHz in order to obtain their statistical properties such as the integrated nearest neighbor spacing distribution and the spectral rigidity. The comparison of our experimental and theoretical results shows that microwave networks can simulate quantum graphs with time reversal symmetry. In particular, we use the spectra of the microwave networks to study the periodic orbits of the simulated quantum graphs. We also present experimental study of directional microwave networks consisting of coaxial cables and Faraday isolators for which the time reversal symmetry is broken. In this case our experimental results indicate that spectral statistics of directional microwave networks deviate from predictions of Gaussian orthogonal ensembles (GOE) in random matrix theory approaching, especially for small eigenfrequency spacing s, results for Gaussian unitary ensembles (GUE). Experimental results are supported by the theoretical analysis of directional graphs.Comment: 16 pages, 7 figures, to be published in Phys. Rev.

Experimental and numerical investigation of the reflection coefficient and the distributions of Wigner's reaction matrix for irregular graphs with absorption

We present the results of experimental and numerical study of the distribution of the reflection coefficient P(R) and the distributions of the imaginary P(v) and the real P(u) parts of the Wigner's reaction K matrix for irregular fully connected hexagon networks (graphs) in the presence of strong absorption. In the experiment we used microwave networks, which were built of coaxial cables and attenuators connected by joints. In the numerical calculations experimental networks were described by quantum fully connected hexagon graphs. The presence of absorption introduced by attenuators was modelled by optical potentials. The distribution of the reflection coefficient P(R) and the distributions of the reaction K matrix were obtained from the measurements and numerical calculations of the scattering matrix S of the networks and graphs, respectively. We show that the experimental and numerical results are in good agreement with the exact analytic ones obtained within the framework of random matrix theory (RMT).Comment: 15 pages, 8 figure

Transmitted drug resistance, selection of resistance mutations and moderate antiretroviral efficacy in HIV-2: Analysis of the HIV-2 Belgium and Luxembourg database

BACKGROUND: Guidelines established for the treatment of HIV-1 infection and genotype interpretation do not apply for HIV-2. Data about antiretroviral (ARV) drug efficacy and resistance mutations is scarce. METHODS: Clinical data about HIV-2 infected patients in Belgium and Luxembourg were collected and the effect of ARV therapy on plasma viral load and CD4 counts were analysed. Viral RNA encoding for protease (PR) and reverse transcriptase (RT) from ARV-naive and treated patients were sequenced. RESULTS: Sixty-five HIV-2 infected patients were included in this cohort. Twenty patients were treated with 25 different ARV combinations in a total of 34 regimens and six months after the start of ARV therapy, only one third achieved viral load suppression. All of these successful regimens bar one contained protease inhibitors (PIs). Mean CD4 gains in the group of viral load suppressors and the group of patients treated with PI-containing regimens were respectively significantly higher than in the group of non-suppressors and the group of PI-sparing regimens. The most frequent mutations selected under therapy (compared to HIV-2 ROD) were V71I, L90M and I89V within PR. Within RT, they were M184V, Q151M, V111I and K65R. All of these mutations, except K65R and M184V, were also found in variable proportions in ARV-naive patients. CONCLUSION: Despite a high rate of ARV treatment failure, better virological and immunological results were achieved with PI-containing regimens. The analysis of polymorphic positions and HIV-2 specific mutations selected during therapy showed for the first time that transmission of drug resistant viruses has occurred in Belgium and Luxembourg. The high heterogeneity in ARV combinations reflects a lack of guidelines for the treatment of HIV-2 infection

Clinical profile of patients with ATP1A3 mutations in alternating hemiplegia of childhood-a study of 155 patients.

BACKGROUND: Mutations in the gene ATP1A3 have recently been identified to be prevalent in patients with alternating hemiplegia of childhood (AHC2). Based on a large series of patients with AHC, we set out to identify the spectrum of different mutations within the ATP1A3 gene and further establish any correlation with phenotype. METHODS: Clinical data from an international cohort of 155 AHC patients (84 females, 71 males; between 3 months and 52 years) were gathered using a specifically formulated questionnaire and analysed relative to the mutational ATP1A3 gene data for each patient. RESULTS: In total, 34 different ATP1A3 mutations were detected in 85 % (132/155) patients, seven of which were novel. In general, mutations were found to cluster into five different regions. The most frequent mutations included: p.Asp801Asn (43 %; 57/132), p.Glu815Lys (16 %; 22/132), and p.Gly947Arg (11 %; 15/132). Of these, p.Glu815Lys was associated with a severe phenotype, with more severe intellectual and motor disability. p.Asp801Asn appeared to confer a milder phenotypic expression, and p.Gly947Arg appeared to correlate with the most favourable prognosis, compared to the other two frequent mutations. Overall, the comparison of the clinical profiles suggested a gradient of severity between the three major mutations with differences in intellectual (p = 0.029) and motor (p = 0.039) disabilities being statistically significant. For patients with epilepsy, age at onset of seizures was earlier for patients with either p.Glu815Lys or p.Gly947Arg mutation, compared to those with p.Asp801Asn mutation (p < 0.001). With regards to the five mutation clusters, some clusters appeared to correlate with certain clinical phenotypes. No statistically significant clinical correlations were found between patients with and without ATP1A3 mutations. CONCLUSIONS: Our results, demonstrate a highly variable clinical phenotype in patients with AHC2 that correlates with certain mutations and possibly clusters within the ATP1A3 gene. Our description of the clinical profile of patients with the most frequent mutations and the clinical picture of those with less common mutations confirms the results from previous studies, and further expands the spectrum of genotype-phenotype correlations. Our results may be useful to confirm diagnosis and may influence decisions to ensure appropriate early medical intervention in patients with AHC. They provide a stronger basis for the constitution of more homogeneous groups to be included in clinical trials

Alveolar macrophage-derived type I interferons orchestrate innate immunity to RSV through recruitment of antiviral monocytes

Type I interferons (IFNs) are important for host defense from viral infections, acting to restrict viral production in infected cells and to promote antiviral immune responses. However, the type I IFN system has also been associated with severe lung inflammatory disease in response to respiratory syncytial virus (RSV). Which cells produce type I IFNs upon RSV infection and how this directs immune responses to the virus, and potentially results in pathological inflammation, is unclear. Here, we show that alveolar macrophages (AMs) are the major source of type I IFNs upon RSV infection in mice. AMs detect RSV via mitochondrial antiviral signaling protein (MAVS)–coupled retinoic acid–inducible gene 1 (RIG-I)–like receptors (RLRs), and loss of MAVS greatly compromises innate immune restriction of RSV. This is largely attributable to loss of type I IFN–dependent induction of monocyte chemoattractants and subsequent reduced recruitment of inflammatory monocytes (infMo) to the lungs. Notably, the latter have potent antiviral activity and are essential to control infection and lessen disease severity. Thus, infMo recruitment constitutes an important and hitherto underappreciated, cell-extrinsic mechanism of type I IFN–mediated antiviral activity. Dysregulation of this system of host antiviral defense may underlie the development of RSV-induced severe lung inflammation

Clinical profile of patients with ATP1A3 mutations in Alternating Hemiplegia of Childhood\u2014a study of 155 patients

Background: Mutations in the gene ATP1A3 have recently been identified to be prevalent in patients with alternating hemiplegia of childhood (AHC2). Based on a large series of patients with AHC, we set out to identify the spectrum of different mutations within the ATP1A3 gene and further establish any correlation with phenotype. Methods: Clinical data from an international cohort of 155 AHC patients (84 females, 71 males; between 3 months and 52 years) were gathered using a specifically formulated questionnaire and analysed relative to the mutational ATP1A3 gene data for each patient. Results: In total, 34 different ATP1A3 mutations were detected in 85 % (132/155) patients, seven of which were novel. In general, mutations were found to cluster into five different regions. The most frequent mutations included: p.Asp801Asn (43 %; 57/132), p.Glu815Lys (16 %; 22/132), and p.Gly947Arg (11 %; 15/132). Of these, p.Glu815Lys was associated with a severe phenotype, with more severe intellectual and motor disability. p.Asp801Asn appeared to confer a milder phenotypic expression, and p.Gly947Arg appeared to correlate with the most favourable prognosis, compared to the other two frequent mutations. Overall, the comparison of the clinical profiles suggested a gradient of severity between the three major mutations with differences in intellectual (p = 0.029) and motor (p = 0.039) disabilities being statistically significant. For patients with epilepsy, age at onset of seizures was earlier for patients with either p.Glu815Lys or p.Gly947Arg mutation, compared to those with p.Asp801Asn mutation (p &lt; 0.001). With regards to the five mutation clusters, some clusters appeared to correlate with certain clinical phenotypes. No statistically significant clinical correlations were found between patients with and without ATP1A3 mutations. Conclusions: Our results, demonstrate a highly variable clinical phenotype in patients with AHC2 that correlates with certain mutations and possibly clusters within the ATP1A3 gene. Our description of the clinical profile of patients with the most frequent mutations and the clinical picture of those with less common mutations confirms the results from previous studies, and further expands the spectrum of genotype-phenotype correlations. Our results may be useful to confirm diagnosis and may influence decisions to ensure appropriate early medical intervention in patients with AHC. They provide a stronger basis for the constitution of more homogeneous groups to be included in clinical trial