Modeling of very high frequency large-electrode capacitively coupled plasmas with a fully electromagnetic particle-in-cell code

Phenomena taking place in capacitively coupled plasmas with large electrodes and driven at very high frequencies are studied numerically utilizing a novel energy- and charge-conserving implicit fully electromagnetic particle-in-cell / Monte Carlo code ECCOPIC2M. The code shows a good agreement with different cases having various collisionality and absorbed power. Although some aspects of the underlying physics were demonstrated in the previous literature with other models, the particle-in-cell method is advantageous for the predictive modeling due to a complex interplay between the surface mode excitations and the nonlocal physics of the corresponding type of plasma discharges operated at low pressures, which is hard to reproduce in other models realistically

Simultaneous non-negative matrix factorization for multiple large scale gene expression datasets in toxicology

Non-negative matrix factorization is a useful tool for reducing the dimension of large datasets. This work considers simultaneous non-negative matrix factorization of multiple sources of data. In particular, we perform the first study that involves more than two datasets. We discuss the algorithmic issues required to convert the approach into a practical computational tool and apply the technique to new gene expression data quantifying the molecular changes in four tissue types due to different dosages of an experimental panPPAR agonist in mouse. This study is of interest in toxicology because, whilst PPARs form potential therapeutic targets for diabetes, it is known that they can induce serious side-effects. Our results show that the practical simultaneous non-negative matrix factorization developed here can add value to the data analysis. In particular, we find that factorizing the data as a single object allows us to distinguish between the four tissue types, but does not correctly reproduce the known dosage level groups. Applying our new approach, which treats the four tissue types as providing distinct, but related, datasets, we find that the dosage level groups are respected. The new algorithm then provides separate gene list orderings that can be studied for each tissue type, and compared with the ordering arising from the single factorization. We find that many of our conclusions can be corroborated with known biological behaviour, and others offer new insights into the toxicological effects. Overall, the algorithm shows promise for early detection of toxicity in the drug discovery process

Genome-Wide Gene Expression Analysis Implicates the Immune Response and Lymphangiogenesis in the Pathogenesis of Fetal Chylothorax

Fetal chylothorax (FC) is a rare condition characterized by lymphocyte-rich pleural effusion. Although its pathogenesis remains elusive, it may involve inflammation, since there are increased concentrations of proinflammatory mediators in pleural fluids. Only a few hereditary lymphedema-associated gene loci, e.g. VEGFR3, ITGA9 and PTPN11, were detected in human fetuses with this condition; these cases had a poorer prognosis, due to defective lymphangiogenesis. In the present study, genome-wide gene expression analysis was conducted, comparing pleural and ascitic fluids in three hydropic fetuses, one with and two without the ITGA9 mutation. One fetus (the index case), from a dizygotic pregnancy (the cotwin was unaffected), received antenatal OK-432 pleurodesis and survived beyond the neonatal stage, despite having the ITGA9 mutation. Genes and pathways involved in the immune response were universally up-regulated in fetal pleural fluids compared to those in ascitic fluids. Furthermore, genes involved in the lymphangiogenesis pathway were down-regulated in fetal pleural fluids (compared to ascitic fluid), but following OK-432 pleurodesis, they were up-regulated. Expression of ITGA9 was concordant with overall trends of lymphangiogenesis. In conclusion, we inferred that both the immune response and lymphangiogenesis were implicated in the pathogenesis of fetal chylothorax. Furthermore, genome-wide gene expression microarray analysis may facilitate personalized medicine by selecting the most appropriate treatment, according to the specific circumstances of the patient, for this rare, but heterogeneous disease

Actively Q-switched dual-wavelength pumped Er3+ :ZBLAN fiber laser at 3.47 micrometers

We demonstrate the first actively -switched fiber laser operating in the 3.5 μm regime. The dual-wavelength pumped system makes use of an Er3+ doped ZBLAN fiber and a germanium acousto-optic modulator. Robust -switching saw a pulse energy of 7.8 μJ achieved at a repetition rate of 15 kHz, corresponding to a peak power of 14.5 W.Nathaniel Bawden, Hiraku Matsukuma, Ori Henderson-Sapir, Elizaveta Klantsataya, Shigeki Tokita, and David J. Ottawa

Spatiotemporal structure of low frequency waves in a magnetized plasma device

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