Validation of water vapour profiles (version 13) retrieved by the IMK / IAA scientific retrieval processor based on full resolution spectra measured by MIPAS on board Envisat

Vertical profiles of stratospheric water vapour measured by the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) with the full resolution mode between September 2002 and March 2004 and retrieved with the IMK/IAA scientific retrieval processor were compared to a number of independent measurements in order to estimate the bias and to validate the existing precision estimates of the MIPAS data. The estimated precision for MIPAS is 5 to 10% in the stratosphere, depending on altitude, latitude, and season. The independent instruments were: the Halogen Occultation Experiment (HALOE), the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS), the Improved Limb Atmospheric Spectrometer-II (ILAS-II), the Polar Ozone and Aerosol Measurement (POAM III) instrument, the Middle Atmospheric Water Vapour Radiometer (MIAWARA), the Michelson Interferometer for Passive Atmospheric Sounding, balloon-borne version (MIPAS-B), the Airborne Microwave Stratospheric Observing System (AMSOS), the Fluorescent Stratospheric Hygrometer for Balloon (FLASH-B), the NOAA frostpoint hygrometer, and the Fast In Situ Hygrometer (FISH). For the in-situ measurements and the ground based, air- and balloon borne remote sensing instruments, the measurements are restricted to central and northern Europe. The comparisons to satellite-borne instruments are predominantly at mid- to high latitudes on both hemispheres. In the stratosphere there is no clear indication of a bias in MIPAS data, because the independent measurements in some cases are drier and in some cases are moister than the MIPAS measurements. Compared to the infrared measurements of MIPAS, measurements in the ultraviolet and visible have a tendency to be high, whereas microwave measurements have a tendency to be low. The results of χ2-based precision validation are somewhat controversial among the comparison estimates. However, for comparison instruments whose error budget also includes errors due to uncertainties in spectrally interfering species and where good coincidences were found, the χ2 values found are in the expected range or even below. This suggests that there is no evidence of systematically underestimated MIPAS random errors.

Tn6198, a novel transposon containing the trimethoprim resistance gene dfrG embedded into a Tn916 element in Listeria monocytogenes

OBJECTIVES: To characterize Tn6198, a novel conjugative transposon from the clinical Listeria monocytogenes strain TTH-2007, which contains the tetracycline and trimethoprim resistance genes tet(M) and dfrG, respectively, and to assess its transferability in vitro and in situ. METHODS: The complete sequence of Tn6198 was determined using a primer walking strategy. Horizontal gene transfer studies were performed by filter matings, as well as on the surface of smear-ripened cheese and smoked salmon. The presence of Tn916-like circular intermediates was determined by PCR. Antibiotic resistance was determined by the broth microdilution method and microarray hybridization. RESULTS: Sequencing of Tn6198 revealed that a 3.3 kb fragment containing dfrG was integrated between open reading frames 23 and 24 of Tn916. Furthermore, an additional copy of Tn916 was present in L. monocytogenes TTH-2007. Both elements were transferred simultaneously and separately in vitro to recipients L. monocytogenes 10403S and Enterococcus faecalis JH2-2 by conjugation, resulting in either tetracycline- and trimethoprim-resistant or solely tetracycline-resistant transconjugants. On the surface of cheese and salmon, only L. monocytogenes 10403S transconjugants were detected. CONCLUSIONS: This study reports the first Tn916-like element associated with a trimethoprim resistance gene, as well as the first fully characterized transposon conferring multidrug resistance in L. monocytogenes. This is of concern, as trimethoprim is administered to listeriosis patients with β-lactam allergy and as Tn6198 has a large potential for dissemination, indicated by both intra-species and inter-genus transfer.

Finite element analyses of human vertebral bodies embedded in polymethylmethalcrylate or loaded via the hyperelastic intervertebral disc models provide equivalent predictions of experimental strength

Quantitative computer tomography (QCT)-based finite element (FE) models of vertebral body provide better prediction of vertebral strength than dual energy X-ray absorptiometry. However, most models were validated against compression of vertebral bodies with endplates embedded in polymethylmethalcrylate (PMMA). Yet, loading being as important as bone density, the absence of intervertebral disc (IVD) affects the strength. Accordingly, the aim was to assess the strength predictions of the classic FE models (vertebral body embedded) against the in vitro and in silico strengths of vertebral bodies loaded via IVDs. High resolution peripheral QCT (HR-pQCT) were performed on 13 segments (T11/T12/L1). T11 and L1 were augmented with PMMA and the samples were tested under a 4° wedge compression until failure of T12. Specimen-specific model was generated for each T12 from the HR-pQCT data. Two FE sets were created: FE-PMMA refers to the classical vertebral body embedded model under axial compression; FE-IVD to their loading via hyperelastic IVD model under the wedge compression as conducted experimentally. Results showed that FE-PMMA models overestimated the experimental strength and their strength prediction was satisfactory considering the different experimental set-up. On the other hand, the FE-IVD models did not prove significantly better (Exp/FE-PMMA: R²=0.68; Exp/FE-IVD: R²=0.71, p=0.84). In conclusion, FE-PMMA correlates well with in vitro strength of human vertebral bodies loaded via real IVDs and FE-IVD with hyperelastic IVDs do not significantly improve this correlation. Therefore, it seems not worth adding the IVDs to vertebral body models until fully validated patient-specific IVD models become available.

(Non)-Dissipative Hydrodynamics on Embedded Surfaces

We construct the theory of dissipative hydrodynamics of uncharged fluids living on embedded space-time surfaces to first order in a derivative expansion in the case of codimension-1 surfaces (including fluid membranes) and the theory of non-dissipative hydrodynamics to second order in a derivative expansion in the case of codimension higher than one under the assumption of no angular momenta in transverse directions to the surface. This construction includes the elastic degrees of freedom, and hence the corresponding transport coefficients, that take into account transverse fluctuations of the geometry where the fluid lives. Requiring the second law of thermodynamics to be satisfied leads us to conclude that in the case of codimension-1 surfaces the stress-energy tensor is characterized by 2 hydrodynamic and 1 elastic independent transport coefficient to first order in the expansion while for codimension higher than one, and for non-dissipative flows, the stress-energy tensor is characterized by 7 hydrodynamic and 3 elastic independent transport coefficients to second order in the expansion. Furthermore, the constraints imposed between the stress-energy tensor, the bending moment and the entropy current of the fluid by these extra non-dissipative contributions are fully captured by equilibrium partition functions. This analysis constrains the Young modulus which can be measured from gravity by elastically perturbing black branes.

Graphics Processor Unit Based Parallelization of Optimized Baseline Wander Filtering Algorithms for Long-term Electrocardiography

Long-term electrocardiogram (ECG) often suffers from relevant noise. Baseline wander in particular is pronounced in ECG recordings using dry or esophageal electrodes, which are dedicated for prolonged registration. While analog high-pass filters introduce phase distortions, reliable offline filtering of the baseline wander implies a computational burden that has to be put in relation to the increase in signal-to-baseline ratio (SBR). Here we present a graphics processor unit (GPU) based parallelization method to speed up offline baseline wander filter algorithms, namely the wavelet, finite, and infinite impulse response, moving mean, and moving median filter. Individual filter parameters were optimized with respect to the SBR increase based on ECGs from the Physionet database superimposed to auto-regressive modeled, real baseline wander. A Monte-Carlo simulation showed that for low input SBR the moving median filter outperforms any other method but negatively affects ECG wave detection. In contrast, the infinite impulse response filter is preferred in case of high input SBR. However, the parallelized wavelet filter is processed 500 and 4 times faster than these two algorithms on the GPU, respectively, and offers superior baseline wander suppression in low SBR situations. Using a signal segment of 64 mega samples that is filtered as entire unit, wavelet filtering of a 7-day high-resolution ECG is computed within less than 3 seconds. Taking the high filtering speed into account, the GPU wavelet filter is the most efficient method to remove baseline wander present in long-term ECGs, with which computational burden can be strongly reduced.

Speech Intelligibility in Noise With a Single-Unit Cochlear Implant Audio Processor.

INTRODUCTION The Rondo is a single-unit cochlear implant (CI) audio processor comprising the identical components as its behind-the-ear predecessor, the Opus 2. An interchange of the Opus 2 with the Rondo leads to a shift of the microphone position toward the back of the head. This study aimed to investigate the influence of the Rondo wearing position on speech intelligibility in noise. METHODS Speech intelligibility in noise was measured in 4 spatial configurations with 12 experienced CI users using the German adaptive Oldenburg sentence test. A physical model and a numerical model were used to enable a comparison of the observations. RESULTS No statistically significant differences of the speech intelligibility were found in the situations in which the signal came from the front and the noise came from the frontal, ipsilateral, or contralateral side. The signal-to-noise ratio (SNR) was significantly better with the Opus 2 in the case with the noise presented from the back (4.4 dB, p < 0.001). The differences in the SNR were significantly worse with the Rondo processors placed further behind the ear than closer to the ear. CONCLUSION The study indicates that CI users with the receiver/stimulator implanted in positions further behind the ear are expected to have higher difficulties in noisy situations when wearing the single-unit audio processor.

Reliable LC3 and p62 autophagy marker detection in formalin fixed paraffin embedded human tissue by immunohistochemistry

Autophagy assures cellular homeostasis, and gains increasing importance in cancer, where it impacts on carcinogenesis, propagation of the malignant phenotype and development of resistance. To date, its tissue-based analysis by immunohistochemistry remains poorly standardized. Here we show the feasibility of specifically and reliably assessing the autophagy markers LC3B and p62 (SQSTM1) in formalin fixed and paraffin embedded human tissue by immunohistochemistry. Preceding functional experiments consisted of depleting LC3B and p62 in H1299 lung cancer cells with subsequent induction of autophagy. Western blot and immunofluorescence validated antibody specificity, knockdown efficiency and autophagy induction prior to fixation in formalin and embedding in paraffin. LC3B and p62 antibodies were validated on formalin fixed and paraffin embedded cell pellets of treated and control cells and finally applied on a tissue microarray with 80 human malignant and non-neoplastic lung and stomach formalin fixed and paraffin embedded tissue samples. Dot-like staining of various degrees was observed in cell pellets and 18/40 (LC3B) and 22/40 (p62) tumors, respectively. Seventeen tumors were double positive for LC3B and p62. P62 displayed additional significant cytoplasmic and nuclear staining of unknown significance. Interobserver-agreement for grading of staining intensities and patterns was substantial to excellent (kappa values 0.60 - 0.83). In summary, we present a specific and reliable IHC staining of LC3B and p62 on formalin fixed and paraffin embedded human tissue. Our presented protocol is designed to aid reliable investigation of dysregulated autophagy in solid tumors and may be used on large tissue collectives.

Speech Intelligibility in Noise With a Pinna Effect Imitating Cochlear Implant Processor.

OBJECTIVE To evaluate the speech intelligibility in noise with a new cochlear implant (CI) processor that uses a pinna effect imitating directional microphone system. STUDY DESIGN Prospective experimental study. SETTING Tertiary referral center. PATIENTS Ten experienced, unilateral CI recipients with bilateral severe-to-profound hearing loss. INTERVENTION All participants performed speech in noise tests with the Opus 2 processor (omnidirectional microphone mode only) and the newer Sonnet processor (omnidirectional and directional microphone mode). MAIN OUTCOME MEASURE The speech reception threshold (SRT) in noise was measured in four spatial settings. The test sentences were always presented from the front. The noise was arriving either from the front (S0N0), the ipsilateral side of the CI (S0NIL), the contralateral side of the CI (S0NCL), or the back (S0N180). RESULTS The directional mode improved the SRTs by 3.6 dB (p < 0.01), 2.2 dB (p < 0.01), and 1.3 dB (p < 0.05) in the S0N180, S0NIL, and S0NCL situations, when compared with the Sonnet in the omnidirectional mode. There was no statistically significant difference in the S0N0 situation. No differences between the Opus 2 and the Sonnet in the omnidirectional mode were observed. CONCLUSION Speech intelligibility with the Sonnet system was statistically different to speech recognition with the Opus 2 system suggesting that CI users might profit from the pinna effect imitating directionality mode in noisy environments.

High-resolution MALDI-FT-ICR MS imaging for the analysis of metabolites from formalin-fixed, paraffin-embedded clinical tissue samples.

We present the first analytical approach to demonstrate the in situ imaging of metabolites from formalin-fixed, paraffin-embedded (FFPE) human tissue samples. Using high-resolution matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FT-ICR MSI), we conducted a proof-of-principle experiment comparing metabolite measurements from FFPE and fresh frozen tissue sections, and found an overlap of 72% amongst 1700 m/z species. In particular, we observed conservation of biomedically relevant information at the metabolite level in FFPE tissues. In biomedical applications, we analysed tissues from 350 different cancer patients and were able to discriminate between normal and tumour tissues, and different tumours from the same organ, and found an independent prognostic factor for patient survival. This study demonstrates the ability to measure metabolites in FFPE tissues using MALDI-FT-ICR MSI, which can then be assigned to histology and clinical parameters. Our approach is a major technical, histochemical, and clinicopathological advance that highlights the potential for investigating diseases in archived FFPE tissues.

Quantitative PCR for the diagnosis of cutaneous leishmaniasis from formalin-fixed and paraffin-embedded skin sections.

The present report describes a real-time PCR-based procedure to reliably determine the quantity of Leishmania amastigotes in relation to the amount of host tissue in histological skin sections from canine and equine cases of cutaneous leishmaniasis. The novel diagnostic Leishmania-PCR has a detection limit of <0.02 amastigotes per μg tissue, which corresponds well to the detection limit of immunohistochemistry and is far beyond that of conventional histology. Our results emphasise the importance of PCR to complement routine histology of cutaneous leishmaniasis cases, particularly in laboratories in which no immunohistochemical assay is available.

Issues related to HIV stigma: An embedded case study of PLHAS and community in Nepal

Little is known about HIV stigma in Nepal. Findings from other parts of the world suggest that HIV related stigma acts as a limiting factor for People Living with HIV & AIDS (PLHAs) from accessing needed health care and the subsequent psychological outcomes make PLHAs and their immediate family members more vulnerable. The purpose of this study is to understand and describe Nepalese PLHA's and community peoples' experiences regarding sources, types, causes and mechanism of HIV-associated stigma. This study aimed to best utilize the existing data. Study participants were recruited through local Community Based Organizations working in the field of HIV. The data, collected in the form of focus group discussions in workshop settings, were coded and analyzed. Study has revealed key issues related to HIV stigma in Nepal: hierarchy of stigma, denial and rejection, death as a form of punishment and Mumbaiya disease. A conceptual model was developed to explain the HIV stigma in Nepal. Our hope is that this finding, stigma being a contextual variable, will be helpful in triggering a novel public health discourse in the field of HIV stigma in Nepal, which will eventually be helpful for developing policies and interventions to eliminate HIV-associated stigma.^

A numerical discrete element study on the influence of an embedded viscoelastic-plastic layer at different viscosity values

The major aim of this study was to examine the influence of an embedded viscoelastic-plastic layer at different viscosity values on accretionary wedges at subduction zones. To quantify the effects of the layer viscosity, we analysed the wedge geometry, accretion mode, thrust systems and mass transport pattern. Therefore, we developed a numerical 2D 'sandbox' model utilising the Discrete Element Method. Starting with a simple pure Mohr Coulomb sequence, we added an embedded viscoelastic-plastic layer within the brittle, undeformed 'sediment' package. This layer followed Burger's rheology, which simulates the creep behaviour of natural rocks, such as evaporites. This layer got thrusted and folded during the subduction process. The testing of different bulk viscosity values, from 1 × 10**13 to 1 × 10**14 (Pa s), revealed a certain range where an active detachment evolved within the viscoelastic-plastic layer that decoupled the over- and the underlying brittle strata. This mid-level detachment caused the evolution of a frontally accreted wedge above it and a long underthrusted and subsequently basally accreted sequence beneath it. Both sequences were characterised by specific mass transport patterns depending on the used viscosity value. With decreasing bulk viscosities, thrust systems above this weak mid-level detachment became increasingly symmetrical and the particle uplift was reduced, as would be expected for a salt controlled forearc in nature. Simultaneously, antiformal stacking was favoured over hinterland dipping in the lower brittle layer and overturning of the uplifted material increased. Hence, we validated that the viscosity of an embedded detachment strongly influences the whole wedge mechanics, both the respective lower slope and the upper slope duplex, shown by e.g. the mass transport pattern.