Geodesic acoustic modes in a fluid model of tokamak plasma : the effects of finite beta and collisionality

Starting from the Braginskii equations, relevant for the tokamak edge region, a complete set of nonlinear equations for the geodesic acoustic modes (GAM) has been derived which includes collisionality, plasma beta and external sources of particle, momentum and heat. Local linear analysis shows that the GAM frequency increases with collisionality at low radial wave number $k_{r}$ and decreases at high $k_{r}$. GAM frequency also decreases with plasma beta. Radial profiles of GAM frequency for two Tore Supra shots, which were part of a collisionality scan, are compared with these calculations. Discrepency between experiment and theory is observed, which seems to be explained by a finite $k_{r}$ for the GAM when flux surface averaged density $\langle n \rangle$ and temperature $\langle T \rangle$ are assumed to vanish. It is shown that this agreement is incidental and self-consistent inclusion of $\langle n \rangle$ and $\langle T \rangle$ responses enhances the disagreement more with $k_r$ at high $k_{r}$ . So the discrepancy between the linear GAM calculation, (which persist also for more "complete" linear models such as gyrokinetics) can probably not be resolved by simply adding a finite $k_{r}$

Multi-branch Convolutional Neural Network for Multiple Sclerosis Lesion Segmentation

In this paper, we present an automated approach for segmenting multiple sclerosis (MS) lesions from multi-modal brain magnetic resonance images. Our method is based on a deep end-to-end 2D convolutional neural network (CNN) for slice-based segmentation of 3D volumetric data. The proposed CNN includes a multi-branch downsampling path, which enables the network to encode information from multiple modalities separately. Multi-scale feature fusion blocks are proposed to combine feature maps from different modalities at different stages of the network. Then, multi-scale feature upsampling blocks are introduced to upsize combined feature maps to leverage information from lesion shape and location. We trained and tested the proposed model using orthogonal plane orientations of each 3D modality to exploit the contextual information in all directions. The proposed pipeline is evaluated on two different datasets: a private dataset including 37 MS patients and a publicly available dataset known as the ISBI 2015 longitudinal MS lesion segmentation challenge dataset, consisting of 14 MS patients. Considering the ISBI challenge, at the time of submission, our method was amongst the top performing solutions. On the private dataset, using the same array of performance metrics as in the ISBI challenge, the proposed approach shows high improvements in MS lesion segmentation compared with other publicly available tools.Comment: This paper has been accepted for publication in NeuroImag

Sleeve resections with unprotected bronchial anastomoses are safe even after neoadjuvant therapy†

OBJECTIVES Sleeve resection is the operation of choice in patients with centrally located tumours, in order to avoid a pneumonectomy. Most surgeons protect the bronchial anastomoses with tissue to prevent insufficiencies. The purpose of this study is to report on outcome of unwrapped bronchial anastomoses, especially after neoadjuvant chemo- or chemoradiotherapy. METHODS Between 2000 and 2010, 103 patients [59 years (range 16-80), 40 females] underwent bronchial sleeve resections without coverage of the anastomosis with a tissue flap. We retrospectively reviewed the data for morbidity, mortality and survival, especially with regard to the type of resection, neoadjuvant therapy and stage. RESULTS Sleeve lobectomy was performed in 88, sleeve bilobectomy in 8, sleeve pneumonectomy in 4 and sleeve resection of the main bronchus in 3 patients. Twenty-seven patients had a combined vascular sleeve resection. Neoadjuvant chemotherapy was performed in 20 and radiochemotherapy in 5 patients. Non-small cell lung cancer (NSCLC) was present in 76 patients (squamous cell carcinoma in 44, adenocarcinoma in 24, large cell carcinoma in 6and mixed cell in 2) and neuroendocrine tumour in 20 and other histological types in 7 patients. The pathologic tumour stage in NSCLC was stage I in 26, stage II in 26, stage IIIA in 16, stage IIIB in 7 and stage IV in 1 patient. There were no anastomotic complications, especially no fistulas. One patient developed narrowing of the intermediate bronchus without need for intervention. Twenty-four patients had early postoperative complications, including 11 surgery-related complications (air leakage, nerve injury, haemothorax or mediastinal emphysema). The 30-day mortality was 3% (one patient died due to heart failure and two with multiorgan failure). The 5-year survival rate was 63% in NSCLC patients and 86% in neuroendocrine tumour patients. CONCLUSIONS Sleeve resection without wrapping the bronchial anastomoses with a tissue flap is safe even in patients who underwent neoadjuvant chemo- or chemoradiotherapy. Therefore, wrapping of the bronchial anastomoses is not routinely mandator

Feeding ecology of five commercial shark species of the Celtic Sea through stable isotope and trace metal analysis

In order to trace their feeding habits, stable carbon and nitrogen isotope ratios (delta(15)N and delta(13)C), as well as trace metal concentrations (Zn, Cd, Fe, Cu, Se and Hg) were analysed in the tissues of five commercial shark species from the Celtic Sea: the tope shark Galeorhinus galeus, the black-mouthed catshark Galeus melastomus, the starry smooth hound Mustelus asterias, the spiny dogfish Squalus acanthias and the lesser-spotted dogfish Scyliorhinus canicula. Our results were compared to previously described stomach contents and isotopic composition of potential preys. Isotopic ratio delta(15)N suggested that tope sharks fed at a higher trophic level (16.7 parts per thousand in the muscle) than the other species, reflecting its piscivorous diet. The lower values of spiny dogfish (11.6 parts per thousand in the muscle) might be explained, amongst other things, by either its migratory behaviour or its preference for preys from lower trophic levels. Cd and Hg were correlated with isotopic ratios delta(13)C and delta(15)N, and were shown to be diet-related whereas Zn, Fe and Cu seemed much more linked to species-specific metabolism. Although this multidisciplinary approach is revealed as a useful tool for the study of shark ecology, the lack of known trophic fractionation suggests that isotopic data be compared to traditional diet analyses. (c) 2005 Elsevier Ltd. All rights reserved.Peer reviewe

OMEGA-3 fatty acids contribute to plaque stability differentially affecting the release of matrix metalloproteinases and tissue inhibitors of metalloproteinases by human monocytes/macrophages in culture

Objectives. High intakes of omega-3 fatty acids has been associated with protection from plaque rupture. The secretion of metalloproteinases (MMPs) by macrophages is believed to play a key role in matrix degradation underlying plaque instability. Conversely, tissue inhibitors of metalloproteinases (TIMPs) would contribute to plaque stability. We therefore studied the effects of omega-3 fatty acids on the release and activity of MMPs and TIMPs in cultured human monocytoid cells. Methods. Human U937 monocytoid cells were differentiated into macrophages by exposure for 24 h to 30 ng/mL phorbol myristate acetate (PMA) and 10 ng/mL tumor necrosis factor(TNF)-α. Both monocytes and macrophages were treated for 48 h with the DHA (22:6 n-3) or EPA (22:6 n-3) (25-100 μmol/L) before stimulation for 24 h with 10 ng/ml TNFα. Cell supernatates were used to test the release of gelatinase A (MMP-2), gelatinase-B (MMP-9), collagenase-1 (MMP-1), TIMP-1 and TIMP-2, by ELISAs, and total gelatinase and anti-gelatinase activities by zymography and retro-zymography techniques, respectively. Results. The long term exposure to 50 μmol/L EPA and DHA, but not to arachidonic acid (20:4 n-6), significantly reduced MMP-9 protein release without affecting the release of MMP-1, MMP-2 and TIMP-1. Conversely, TIMP-2 protein release was significantly increased by EPA and DHA (Table). Zymography for MMP-9 and retro-zymography for TIMP-1 and -2 reproduced the same results. Conclusions. The long term exposure to omega-3 fatty acids significantly reduces MMP-9 release without affecting the release of MMP-1 and -2. This effect, associated with the increase of TIMP-2 protein production and activity, may contribute to explaining the plaque-stabilizing effect by omega-3 fatty acid observed in humans

Mixotrophic growth under micro-oxic conditions in the purple sulfur bacterium "Thiodictyon syntrophicum"

The microbial ecosystem of the meromictic Lake Cadagno (Ticino, Swiss Alps) has been studied intensively in order to understand structure and functioning of the anoxygenic phototrophic sulfur bacteria community living in the chemocline. It has been found that the purple sulfur bacterium “Thiodictyon syntrophicum” strain Cad16T, belonging to the Chromatiaceae, fixes around 26% of all bulk inorganic carbon in the chemocline, both during day and night. With this study, we elucidated for the first time the mode of carbon fixation of str. Cad16T under micro-oxic conditions with a combination of long-term monitoring of key physicochemical parameters with CTD, 14C-incorporation experiments and quantitative proteomics using in-situ dialysis bag incubations of str. Cad16T cultures. Regular vertical CTD profiling during the study period in summer 2017 revealed that the chemocline sank from 12 to 14 m which was accompanied by a bloom of cyanobacteria and the subsequent oxygenation of the deeper water column. Sampling was performed both day and night. CO2 assimilation rates were higher during the light period compared to those in the dark, both in the chemocline population and in the incubated cultures. The relative change in the proteome between day and night (663 quantified proteins) comprised only 1% of all proteins encoded in str. Cad16T. Oxidative respiration pathways were upregulated at light, whereas stress-related mechanisms prevailed during the night. These results indicate that low light availability and the co-occurring oxygenation of the chemocline induced mixotrophic growth in str. Cad16T. Our study thereby helps to further understand the consequences micro-oxic conditions for phototrophic sulfur oxidizing bacteria. The complete proteome data have been deposited to the ProteomeXchange database with identifier PXD010641

Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno

"Thiodictyon syntrophicum" sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences. Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans strain DSM 232T the most closely related species. Genes involved in sulfur oxidation, central carbon metabolism and transmembrane transport were found. Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed insight into the Cad16T genome and analyze it in the context of the microbial ecosystem of Lake Cadagno

Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno

"Thiodictyon syntrophicum" sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences. Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans strain DSM 232T the most closely related species. Genes involved in sulfur oxidation, central carbon metabolism and transmembrane transport were found. Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed insight into the Cad16T genome and analyze it in the context of the microbial ecosystem of Lake Cadagno

Peroxisome proliferator-activated receptory inhibits angiogenesis by suppressing creb-mediated cyclooxygenase-2 expression in human endothelium

Objetives. Neoangiogenesis contributes to diabetic vasculopathy and intraplaque hemorrhage in atherosclerosis. The activation of Peroxisome Proliferator-Activated Receptor(PPAR)γ is known to inhibit angiogenesis. We therefore examined the effects of PPARγ agonists on the pro-angiogenic enzyme cyclooxygenase(COX)-2 in human umbilical vein endothelial cells challenged with vascular endothelial growth factor (VEGF) and phorbol 12-myristate 13-acetate (PMA). Methods and Results.A 24 h exposure of HUVEC to the PPARγ agonists rosiglitazone (RSG) and GW1929 significantly attenuated VEGF- and PMA-stimulated COX-2 activity (by 30%, immunoassay for 6-keto-PGF1α), as well as protein (by 50%, Western analysis) and mRNA expression (by 50%, RT-PCR). This effect was abolished by the PPARγ antagonists bisphenol A diglycidyl ether and GW9662. COX-2 promoter activity experiments revealed that the induction of COX-2 promoter was significantly inhibited by RSG through an interference with the cAMP response element (CRE) site. COX-2 downregulation after siRNA knockdown of the transcription factor CRE binding protein (CREB) confirmed the role of CREB in mediating COX-2 transcription. Correspondingly, PPARγ agonists also attenuated CREB phosphorylation/activation. Since Protein Kinase(PK)C is involved in VEGF-induced COX-2 expression and CREB activation, we also investigated which isoforms of PKC were affected by RSG. While the inhibition of both conventional PKCα and β suppressed VEGF- and PMA-stimulated CREB activation and COX-2 expression, RGS only reduced VEGF- and PMA-stimulated PKCα membrane translocation. Conclusions. The anti-angiogenic effect of PPARγ agonists is due, at least in part, to their interference with the PKCα-mediated activation of CREB and the related expression of COX-2. PKCα may therefore be a novel therapeutic target for antidiabetic drugs in atherosclerosis

Hydroxytyrosol suppresses phorbol ester-induced matrix metalloproteinase-9 expression by inhibiting both PKCalpha/beta1 and NF-kB activation in human monocytoid cells

Objectives: Mediterranean diets, of which olive oil is an important component, are associated with low prevalence of cardiovascular diseases, but active dietary components and their mechanisms of action are incompletely understood. The local production of active matrix metalloproteinase (MMP)-9 by macrophages likely contributes to plaque matrix degradation and plaque instability, leading to acute coronary events. We sought to examine the effect of the olive oil phenolic antioxidant hydroxytyrosol (HT) on MMP-9 expression and activity in monocytoid cells and to explore mechanisms of action involved. Methods: U937 human monocytoid cells were pre-treated with HT (0-100 &#956;mol/L) for 30 min before stimulation with 50 nmol/L phorbol myristate acetate (PMA) in a serum-free medium for 24 h or alternatively with inhibitors of PKC iso-enzymes or of the NF-&#954;B pathway. Cell supernatants were then tested for gelatinase activity by zymography. MMP-9 protein and mRNA expression was assayed by ELISA and RT-PCR. We assessed the activation of transcription factor Nuclear Factor (NF)-&#954;B by EMSA and Western analysis of nuclear extracts, and the activation of PKC iso-enzymes by membrane translocation analysis. Results: HT (1-100 &#956;mol/L) reduced PMA-induced MMP-9 activity at zymography analysis in a concentration-dependent manner, with inhibitory concentration producing 50% of the effect (IC50) at 10 &#956;mol/L (p<0.01). In addition, 10 &#956;mol/L HT reduced MMP-9 protein release and mRNA levels by about (by 60?5% and 40?7%, respectively, p<0.01), without significantly affecting TIMP-1 and -2 release. HT (10 &#956;mol/L) also significantly inhibited NF-&#954;B activation (by 57?8%) and PMA-induced membrane translocation of PKC&#945; and &#946;1 (by 50?8% and 35?5%, respectively, for all, p<0.05), suggesting a plausible mechanism for the downregulation of MMP-9 expression by HT. Conclusions: HT, the major olive and olive oil phenolic antioxidant, inhibits MMP-9 expression and release, interfering with PKC&#945;/&#946;1 and NF-&#954;B activation in human monocytoid cells. This may contribute to plaque stabilization, explaining at least in part the cardiovascular protection by specific components of Mediterranean diets