Observation of secondary instability of 2/1 magnetic island in compass high density limit plasmas

Density limit disruptions (DLDs) have been observed in tokamak plasmas when high density regimes are explored. The DLDs are harmless in small size tokamaks like COMPASS,larger tokamaks like JET try to avoid them and they are extremely undesirable in ITER sizetokamaks due to the severe structural damages they can cause. It is very important to understand the dynamics of the DLDs so that better strategies to ameliorate or avoid them can bedeveloped. In this work, following detection in JET [1] of a secondary instability (SI) to thewell-known m/n = 2/1 MHD mode (where m and n are the poloidal and toroidal mode numbers, respectively) in the precursor of DLD, we analyse the evolution of the 2/1 magnetic islandin COMPASS DLD to look for the presence of this SI just close to the onset of energy quenchphase of the disruption. The presence of this SI to the magnetic island was associated with theoccurrence of minor disruptions preceding the major disruption and with the major disruptionitself in [1]. The coherence observed between the perturbations caused by the SI in the magneticpoloidal flux and in the electron temperature was very high (above 0.9), allowing to determinethat the SI perturbations came from the same position as the magnetic island. In the work presented here, only the perturbations in the magnetic poloidal flux are analysed since at the time ofthe experiments in COMPASS, no diagnostics was operational for measuring the time evolutionof the electron temperature with high time rate.Nonlinear MHD numerical simulations have also shown that island deformation during itsrapid growth can lead to the secondary magnetic island formation [2]. A recent review [3] ofthe theory of current sheet formation that leads to magnetic reconnection discusses the role ofplasmoids during magnetic island evolution. Since the validity ranges of the mentioned theoretical works are not directly comparable to the experimental conditions, one cannot claimwith certainty that the SI observed in JET [1] and in COMPASS disruptions (reported here)are the same as observed in those numerical works [2, 3]. However, there are some qualitative43rd EPS Conference on Plasma Physics P5.003similarities between them.The main COMPASS [4] diagnostics used for the analysis in the present work, are the threetoroidally separated arrays (A at 32.5◦, B at 212.5◦and C at 257.5◦from the vessel axis) ofMirnov coils (MCs), each with 24 MCs located poloidally. The MC arrays A and C, toroidallyseparated by 135◦, measure the change in poloidal magnetic flux, dBp/dt. The MC array B,toroidally separated by 180◦to the array A, measures the poloidal magnetic field, Bp. Thesemagnetic sensors have good responsivity to high frequency (up to 1 MHz)

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles

<p>Abstract</p> <p>Background</p> <p>Unicellular cyanobacteria of the genus <it>Cyanothece </it>are recognized for their ability to execute nitrogen (N₂)-fixation in the dark and photosynthesis in the light. An understanding of these mechanistic processes in an integrated systems context should provide insights into how <it>Cyanothece </it>might be optimized for specialized environments and/or industrial purposes. Systems-wide dynamic proteomic profiling with mass spectrometry (MS) analysis should reveal fundamental insights into the control and regulation of these functions.</p> <p>Results</p> <p>To expand upon the current knowledge of protein expression patterns in <it>Cyanothece </it>ATCC51142, we performed quantitative proteomic analysis using partial ("unsaturated") metabolic labeling and high mass accuracy LC-MS analysis. This dynamic proteomic profiling identified 721 actively synthesized proteins with significant temporal changes in expression throughout the light-dark cycles, of which 425 proteins matched with previously characterized cycling transcripts. The remaining 296 proteins contained a cluster of proteins uniquely involved in DNA replication and repair, protein degradation, tRNA synthesis and modification, transport and binding, and regulatory functions. Functional classification of labeled proteins suggested that proteins involved in respiration and glycogen metabolism showed increased expression in the dark cycle together with nitrogenase, suggesting that N₂-fixation is mediated by higher respiration and glycogen metabolism. Results indicated that <it>Cyanothece </it>ATCC51142 might utilize alternative pathways for carbon (C) and nitrogen (N) acquisition, particularly, aspartic acid and glutamate as substrates of C and N, respectively. Utilization of phosphoketolase (PHK) pathway for the conversion of xylulose-5P to pyruvate and acetyl-P likely constitutes an alternative strategy to compensate higher ATP and NADPH demand.</p> <p>Conclusion</p> <p>This study provides a deeper systems level insight into how <it>Cyanothece </it>ATCC51142 modulates cellular functions to accommodate photosynthesis and N₂-fixation within the single cell.</p

How metaphysical commitments shape the study of psychological mechanisms

The study of psychological mechanisms is an interdisciplinary endeavour, requiring insights from many different domains (from electrophysiology, to psychology, to theoretical neuroscience, to computer science). In this article, I argue that philosophy plays an essential role in this interdisciplinary project, and that effective scientific study of psychological mechanisms requires that working scientists be responsible metaphysicians. This means adopting deliberate metaphysical positions when studying mechanisms that go beyond what is empirically justified regarding the nature of the phenomenon being studied, the conditions of its occurrence, and its boundaries. Such metaphysical commitments are necessary in order to set up experimental protocols, determine which variables to manipulate under experimental conditions, and which conclusions to draw from different scientific models and theories. It is important for scientists to be aware of the metaphysical commitments they adopt, since they can easily be led astray if invoked carelessly

In vivo biomolecular imaging of zebrafish embryos using confocal Raman spectroscopy

Zebrafish embryos provide a unique opportunity to visualize complex biological processes, yet conventional imaging modalities are unable to access intricate biomolecular information without compromising the integrity of the embryos. Here, we report the use of confocal Raman spectroscopic imaging for the visualization and multivariate analysis of biomolecular information extracted from unlabeled zebrafish embryos. We outline broad applications of this method in: (i) visualizing the biomolecular distribution of whole embryos in three dimensions, (ii) resolving anatomical features at subcellular spatial resolution, (iii) biomolecular profiling and discrimination of wild type and ΔRD1 mutant Mycobacterium marinum strains in a zebrafish embryo model of tuberculosis and (iv) in vivo temporal monitoring of the wound response in living zebrafish embryos. Overall, this study demonstrates the application of confocal Raman spectroscopic imaging for the comparative bimolecular analysis of fully intact and living zebrafish embryos

Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142

Cyanothece sp. ATCC 51142 is a diazotrophic cyanobacterium notable for its ability to perform oxygenic photosynthesis and dinitrogen fixation in the same single cell. Previous transcriptional analysis revealed that the existence of these incompatible cellular processes largely depends on tightly synchronized expression programs involving ∼30% of genes in the genome. To expand upon current knowledge, we have utilized sensitive proteomic approaches to examine the impact of diurnal rhythms on the protein complement in Cyanothece 51142. We found that 250 proteins accounting for ∼5% of the predicted ORFs from the Cyanothece 51142 genome and 20% of proteins detected under alternating light/dark conditions exhibited periodic oscillations in their abundances. Our results suggest that altered enzyme activities at different phases during the diurnal cycle can be attributed to changes in the abundance of related proteins and key compounds. The integration of global proteomics and transcriptomic data further revealed that post-transcriptional events are important for temporal regulation of processes such as photosynthesis in Cyanothece 51142. This analysis is the first comprehensive report on global quantitative proteomics in a unicellular diazotrophic cyanobacterium and uncovers novel findings about diurnal rhythms

BALL - biochemical algorithms library 1.3

<p>Abstract</p> <p>Background</p> <p>The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms for molecular modeling and structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers. In the ten years since its original publication, BALL has seen a substantial increase in functionality and numerous other improvements.</p> <p>Results</p> <p>Here, we discuss BALL's current functionality and highlight the key additions and improvements: support for additional file formats, molecular edit-functionality, new molecular mechanics force fields, novel energy minimization techniques, docking algorithms, and support for cheminformatics.</p> <p>Conclusions</p> <p>BALL is available for all major operating systems, including Linux, Windows, and MacOS X. It is available free of charge under the Lesser GNU Public License (LPGL). Parts of the code are distributed under the GNU Public License (GPL). BALL is available as source code and binary packages from the project web site at <url>http://www.ball-project.org</url>. Recently, it has been accepted into the debian project; integration into further distributions is currently pursued.</p

An integer linear programming approach for finding deregulated subgraphs in regulatory networks

Deregulation of cell signaling pathways plays a crucial role in the development of tumors. The identification of such pathways requires effective analysis tools that facilitate the interpretation of expression differences. Here, we present a novel and highly efficient method for identifying deregulated subnetworks in a regulatory network. Given a score for each node that measures the degree of deregulation of the corresponding gene or protein, the algorithm computes the heaviest connected subnetwork of a specified size reachable from a designated root node. This root node can be interpreted as a molecular key player responsible for the observed deregulation. To demonstrate the potential of our approach, we analyzed three gene expression data sets. In one scenario, we compared expression profiles of non-malignant primary mammary epithelial cells derived from BRCA1 mutation carriers and of epithelial cells without BRCA1 mutation. Our results suggest that oxidative stress plays an important role in epithelial cells of BRCA1 mutation carriers and that the activation of stress proteins may result in avoidance of apoptosis leading to an increased overall survival of cells with genetic alterations. In summary, our approach opens new avenues for the elucidation of pathogenic mechanisms and for the detection of molecular key players

The study of atmospheric ice-nucleating particles via microfluidically generated droplets

Ice-nucleating particles (INPs) play a significant role in the climate and hydrological cycle by triggering ice formation in supercooled clouds, thereby causing precipitation and affecting cloud lifetimes and their radiative properties. However, despite their importance, INP often comprise only 1 in 10³–10⁶ ambient particles, making it difficult to ascertain and predict their type, source, and concentration. The typical techniques for quantifying INP concentrations tend to be highly labour-intensive, suffer from poor time resolution, or are limited in sensitivity to low concentrations. Here, we present the application of microfluidic devices to the study of atmospheric INPs via the simple and rapid production of monodisperse droplets and their subsequent freezing on a cold stage. This device offers the potential for the testing of INP concentrations in aqueous samples with high sensitivity and high counting statistics. Various INPs were tested for validation of the platform, including mineral dust and biological species, with results compared to literature values. We also describe a methodology for sampling atmospheric aerosol in a manner that minimises sampling biases and which is compatible with the microfluidic device. We present results for INP concentrations in air sampled during two field campaigns: (1) from a rural location in the UK and (2) during the UK’s annual Bonfire Night festival. These initial results will provide a route for deployment of the microfluidic platform for the study and quantification of INPs in upcoming field campaigns around the globe, while providing a benchmark for future lab-on-a-chip-based INP studies