A new purge and trap headspace technique to analyze low volatile compounds from fluid inclusions of rocks and minerals

A new method for the analysis of trace gases from fluid inclusions of minerals has been developed. The purge and trap GC-MS system is based on the system described by Nolting et al. (1988) and was optimized for the analyses of halogenated volatile organic compounds (VOCs) having boiling points as low as -128. °C (carbon tetrafluoride).The sample preconcentration cold trap consists of a U-shaped glass lined steel tube (GLT™), that is immersed into a small liquid nitrogen Dewar vessel for cooling. A rapid desorption step heats up the preconcentration tube in <30s from -196°C to 200°C. The process is carried out by using a pressurized air stream to dissipate the liquid nitrogen followed by resistive heating of the trap. The design of the cold trap and the direct transfer of desorbed analytes onto the GC column via a deactivated capillary column retention gap made sample refocusing within the GC oven unnecessary. Furthermore, a special air-tight grinding device was developed in which samples ranging from soft halite (hardness 2, Mohs scale) to hard quartz (hardness 7) are effectively ground to average diameters of 1000nm or below, thereby releasing gases from fluid inclusions of minerals. The gases are then purged from the grinding chamber with a He carrier gas flow. The detection and quantitative determination of gases, such as SF6 and CF4 released from fluorites and CH3Cl from halite samples is demonstrated.DFG/FOR/76

Susceptibility to collagen-induced arthritis is modulated by TGFβ responsiveness of T cells

The objective of our study was to determine the regulatory effects that endogenous transforming growth factor β (TGFβ) exerts on T cells in the pathogenesis of collagen-induced arthritis (CIA). CIA was induced in transgenic mice expressing a dominant negative TGFβ type II receptor in T cells under the control of the human CD2 promoter. Clinical and histological arthritis scores were determined and experiments on disease induction and the healing phase of disease were performed. The proliferation and cytokine production of draining lymph node cells in vitro were analyzed. Transgenic mice were more susceptible to induction of CIA. The overall incidence was higher in transgenic mice than in wild-type mice (57% vs 35%, P < 0.05). Affected transgenic animals displayed a significantly higher clinical (4.5 ± 0.6 vs 1.67 ± 0.19, P = 0.001) and histological arthritis score (8.01 ± 0.9 vs 4.06 ± 1.1, P < 0.05). Draining lymph node cells of transgenic mice secreted more tumor necrosis factor α and IFNγ and proliferated more vigorously in response to collagen type II and upon CD3/CD28 costimulation in vitro. Therefore, the regulation of T cells by endogenous TGFβ is important for the maintenance of joint integrity after arthritis induction. Defects in TGFβ-signalling as a susceptibility factor for rheumatoid arthritis may warrant further investigation

Correlation of EGFR expression, gene copy number and clinicopathological status in NSCLC

Background: Epidermal Growth Factor Receptor (EGFR) targeting therapies are currently of great relevance for the treatment of lung cancer. For this reason, in addition to mutational analysis immunohistochemistry (IHC) of EGFR in lung cancer has been discussed for the decision making of according therapeutic strategies. The aim of this study was to obtain standardization of EGFR-expression methods for the selection of patients who might benefit of EGFR targeting therapies. Methods: As a starting point of a broad investigation, aimed at elucidating the expression of EGFR on different biological levels, four EGFR specific antibodies were analyzed concerning potential differences in expression levels by Immunohistochemistry (IHC) and correlated with fluorescence in situ hybridization (FISH) analysis and clinicopathological data. 206 tumor tissues were analyzed in a tissue microarray format employing immunohistochemistry with four different antibodies including Dako PharmDx kit (clone 2-18C9), clone 31G7, clone 2.1E1 and clone SP84 using three different scoring methods. Protein expression was compared to FISH utilizing two different probes. Results: EGFR protein expression determined by IHC with Dako PharmDx kit, clone 31G7 and clone 2.1E1 (≤ 0.05) correlated significantly with both FISH probes independently of the three scoring methods; best correlation is shown for 31G7 using the scoring method that defined EGFR positivity when ≥ 10% of the tumor cells show membranous staining of moderate and severe intensity (p = 0.001). Conclusion: Overall, our data show differences in EGFR expression determined by IHC, due to the applied antibody. Highest concordance with FISH is shown for antibody clone 31G7, evaluated with score B (p = 0.001). On this account, this antibody clone might by utilized for standard evaluation of EGFR expression by IHC

Generation of Realistic Synthetic Raw Radar Data for Automated Driving Applications using Generative Adversarial Networks

The main approaches for simulating FMCW radar are based on ray tracing, which is usually computationally intensive and do not account for background noise. This work proposes a faster method for FMCW radar simulation capable of generating synthetic raw radar data using generative adversarial networks (GAN). The code and pre-trained weights are open-source and available on GitHub. This method generates 16 simultaneous chirps, which allows the generated data to be used for the further development of algorithms for processing radar data (filtering and clustering). This can increase the potential for data augmentation, e.g., by generating data in non-existent or safety-critical scenarios that are not reproducible in real life. In this work, the GAN was trained with radar measurements of a motorcycle and used to generate synthetic raw radar data of a motorcycle traveling in a straight line. For generating this data, the distance of the motorcycle and Gaussian noise are used as input to the neural network. The synthetic generated radar chirps were evaluated using the Frechet Inception Distance (FID). Then, the Range-Azimuth (RA) map is calculated twice: first, based on synthetic data using this GAN and, second, based on real data. Based on these RA maps, an algorithm with adaptive threshold and edge detection is used for object detection. The results have shown that the data is realistic in terms of coherent radar reflections of the motorcycle and background noise based on the comparison of chirps, the RA maps and the object detection results. Thus, the proposed method in this work has shown to minimize the simulation-to-reality gap for the generation of radar data

Sleep homeostasis, seizures, and cognition in children with focal epilepsy

AIM: To investigate the link between sleep disruption and cognitive impairment in childhood epilepsy by studying the effect of epilepsy on sleep homeostasis, as reflected in slow-wave activity (SWA). METHOD: We examined SWA from overnight EEG-polysomnography in 19 children with focal epilepsy (mean [SD] age 11 years 6 months [3 years], range 6 years 6 months-15 years 6 months; 6 females, 13 males) and 18 age- and sex-matched typically developing controls, correlating this with contemporaneous memory consolidation task scores, full-scale IQ, seizures, and focal interictal discharges. RESULTS: Children with epilepsy did not differ significantly from controls in overnight SWA decline (p = 0.12) or gain in memory performance with sleep (p = 0.27). SWA was lower in patients compared to controls in the first hour of non-rapid eye movement sleep (p = 0.021), although not in those who remained seizure-free (p = 0.26). Full-scale IQ did not correlate with measures of SWA in patients or controls. There was no significant difference in SWA measures between focal and non-focal electrodes. INTERPRETATION: Overnight SWA decline is conserved in children with focal epilepsy and may underpin the preservation of sleep-related memory consolidation in this patient group. Reduced early-night SWA may reflect impaired or immature sleep homeostasis in those with a higher seizure burden

Sleep homeostasis, seizures, and cognition in children with focal epilepsy

AIM To investigate the link between sleep disruption and cognitive impairment in childhood epilepsy by studying the effect of epilepsy on sleep homeostasis, as reflected in slow-wave activity (SWA). METHOD We examined SWA from overnight EEG-polysomnography in 19 children with focal epilepsy (mean [SD] age 11 years 6 months [3 years], range 6 years 6 months-15 years 6 months; 6 females, 13 males) and 18 age- and sex-matched typically developing controls, correlating this with contemporaneous memory consolidation task scores, full-scale IQ, seizures, and focal interictal discharges. RESULTS Children with epilepsy did not differ significantly from controls in overnight SWA decline (p = 0.12) or gain in memory performance with sleep (p = 0.27). SWA was lower in patients compared to controls in the first hour of non-rapid eye movement sleep (p = 0.021), although not in those who remained seizure-free (p = 0.26). Full-scale IQ did not correlate with measures of SWA in patients or controls. There was no significant difference in SWA measures between focal and non-focal electrodes. INTERPRETATION Overnight SWA decline is conserved in children with focal epilepsy and may underpin the preservation of sleep-related memory consolidation in this patient group. Reduced early-night SWA may reflect impaired or immature sleep homeostasis in those with a higher seizure burden

How to survive pig farming: Mechanism of SCCmec element deletion and metabolic stress adaptation in livestock-associated MRSA

Previous research on methicillin susceptible Staphylococcus aureus (MSSA) belonging to livestock-associated (LA-) sequence type (ST) 398, isolated from pigs and their local surroundings, indicated that differences between these MSSA and their methicillin resistant predecessors (MRSA) are often limited to the absence of the staphylococcal cassette chromosome mec (SCCmec) and few single nucleotide polymorphisms. So far, our understanding on how LA-MRSA endure the environmental conditions associated with pig-farming as well as the putative impact of this particular environment on the mobilisation of SCCmec elements is limited. Thus, we performed in-depth genomic and transcriptomic analyses using the LA-MRSA ST398 strain IMT38951 and its methicillin susceptible descendant. We identified a mosaic-structured SCCmec region including a putative replicative SCCmecVc which is absent from the MSSA chromosome through homologous recombination. Based on our data, such events occur between short repetitive sequences identified within and adjacent to two distinct alleles of the large cassette recombinase genes C (ccrC). We further evaluated the global transcriptomic response of MRSA ST398 to particular pig-farm associated conditions, i.e., contact with host proteins (porcine serum) and a high ammonia concentration. Differential expression of global regulators involved in stress response control were identified, i.e., ammonia-induced alternative sigma factor B-depending activation of genes for the alkaline shock protein 23, the heat shock response and the accessory gene regulator (agr)-controlled transcription of virulence factors. Exposure to serum transiently induced the transcription of distinct virulence factor encoding genes. Transcription of genes reported for mediating the loss of methicillin resistance, especially ccrC, was not significantly different compared to the unchallenged controls. We concluded that, from an evolutionary perspective, bacteria may save energy by incidentally dismissing a fully replicative SCCmec element in contrast to the induction of ccr genes on a population scale. Since the genomic SCCmec integration site is a hot-spot of recombination, occasional losses of elements of 16 kb size may restore capacities for the uptake of foreign genetic material. Subsequent spread of resistance, on the other hand, might depend on the autonomous replication machinery of the deleted SCCmec elements that probably enhance chances for reintegration of SCCmec into susceptible genomes by mere multiplication

Excellent Silicon Surface Passivation Achieved by Industrial Inductively Coupled Plasma Deposited Hydrogenated Intrinsic Amorphous Silicon Suboxide

We present an alternative method of depositing a high-quality passivation film for heterojunction silicon wafer solar cells, in this paper. The deposition of hydrogenated intrinsic amorphous silicon suboxide is accomplished by decomposing hydrogen, silane, and carbon dioxide in an industrial remote inductively coupled plasma platform. Through the investigation on CO2 partial pressure and process temperature, excellent surface passivation quality and optical properties are achieved. It is found that the hydrogen content in the film is much higher than what is commonly reported in intrinsic amorphous silicon due to oxygen incorporation. The observed slow depletion of hydrogen with increasing temperature greatly enhances its process window as well. The effective lifetime of symmetrically passivated samples under the optimal condition exceeds 4.7 ms on planar n-type Czochralski silicon wafers with a resistivity of 1 Ωcm, which is equivalent to an effective surface recombination velocity of less than 1.7 cms−1 and an implied open-circuit voltage (Voc) of 741 mV. A comparison with several high quality passivation schemes for solar cells reveals that the developed inductively coupled plasma deposited films show excellent passivation quality. The excellent optical property and resistance to degradation make it an excellent substitute for industrial heterojunction silicon solar cell production

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples