Anaphe - OO Libraries and Tools for Data Analysis

The Anaphe project is an ongoing effort to provide an Object Oriented software environment for data analysis in HENP experiments. A range of commercial and public domain libraries is used to cover basic functionalities; on top of these libraries a set of HENP-specific C++ class libraries for histogram management, fitting, plotting and ntuple-like data analysis has been developed. In order to comply with the user requirements for a command-line driven tool, we have chosen to use a scripting language (Python) as the front-end for a data analysis tool. The loose coupling provided by the consequent use of (AIDA compliant) Abstract Interfaces for each component in combination with the use of shared libraries for their implementation provides an easy integration of existing libraries into modern scripting languages thus allowing for rapid application development. This integration is simplified even further using a specialised toolkit (SWIG) to create "shadow classes" for the Python language, which map the definitions of the Abstract Interfaces almost at a one-to-one level. This paper will give an overview of the architecture and design choices and will present the current status and future developments of the project

The cephalopod arm crown:appendage formation and differentiation in the Hawaiian bobtail squid <i>Euprymna scolopes</i>

BACKGROUND: Cephalopods are a highly derived class of molluscs that adapted their body plan to a more active and predatory lifestyle. One intriguing adaptation is the modification of the ventral foot to form a bilaterally symmetric arm crown, which constitutes a true morphological novelty in evolution. In addition, this structure shows many diversifications within the class of cephalopods and therefore offers an interesting opportunity to study the molecular underpinnings of the emergence of phenotypic novelties and their diversification. Here we use the sepiolid Euprymna scolopes as a model to study the formation and differentiation of the decabrachian arm crown, which consists of four pairs of sessile arms and one pair of retractile tentacles. We provide a detailed description of arm crown formation in order to understand the basic morphology and the developmental dynamics of this structure. RESULTS: We show that the morphological formation of the cephalopod appendages occurs during distinct phases, including outgrowth, elongation, and tissue differentiation. Early outgrowth is characterized by uniform cell proliferation, while the elongation of the appendages initiates tissue differentiation. The latter progresses in a gradient from proximal to distal, whereas cell proliferation becomes restricted to the distal-most end of the arm. Differences in the formation of arms and tentacles exist, with the tentacles showing an expedite growth rate and higher complexity at younger stages. CONCLUSION: The early outgrowth and differentiation of the E. scolopes arm crown shows similarities to the related, yet derived cephalopod Octopus vulgaris. Parallels in the growth and differentiation of appendages seem to exist throughout the animal kingdom, raising the question of whether these similarities reflect a recruitment of similar molecular patterning pathways. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12983-016-0175-8) contains supplementary material, which is available to authorized users

High temperature, low neutron cross-section highentropy alloys in the Nb-Ti-V-Zr system

High-entropy alloys (HEAs) with high melting points and low thermal neutron cross-section are promising new cladding materials for generation III+ and IV power reactors. In this study a recently developed high throughput computational screening tool Alloy Search and Predict (ASAP) has been used to identify the most likely candidate single-phase HEAs with low thermal neutron cross-section, from over a million four-element equimolar combinations. The selected NbTiVZr HEA was further studied by density functional theory (DFT) for moduli and lattice parameter, and by CALPHAD to predict phase formation with temperature. HEAs of NbTiVZrx (x = 0.5, 1, 2) were produced experimentally, with Zr varied as the dominant cross-section modifier. Contrary to previous experimental work, these HEAs were demonstrated to constitute a single-phase HEA system; a result obtained using a faster cooling rate following annealing at 1200 °C. However, the beta (BCC) matrix decomposed following aging at 700 °C, into a combination of nano-scale beta, alpha (HCP) and C15 Laves phases

Back-hopping in Spin-Transfer-Torque switching of perpendicularly magnetized tunnel junctions

We analyse the phenomenon of back-hopping in spin-torque induced switching of the magnetization in perpendicularly magnetized tunnel junctions. The analysis is based on single-shot time-resolved conductance measurements of the pulse-induced back-hopping. Studying several material variants reveals that the back-hopping is a feature of the nominally fixed system of the tunnel junction. The back-hopping is found to proceed by two sequential switching events that lead to a final state P' of conductance close to --but distinct from-- that of the conventional parallel state. The P' state does not exist at remanence. It generally relaxes to the conventional antiparallel state if the current is removed. The P' state involves a switching of the sole spin-polarizing part of the fixed layers. The analysis of literature indicates that back-hopping occurs only when the spin-polarizing layer is too weakly coupled to the rest of the fixed system, which justifies a posteriori the mitigation strategies of back-hopping that were implemented empirically in spin-transfer-torque magnetic random access memories.Comment: submitted to Phys Rev.

Accommodation of tin in tetragonal ZrO2

Atomic scale computer simulations using density functional theory were used to investigate the behaviour of tin in the tetragonal phase oxide layer on Zr-based alloys. The Sn×ZrSnZr× defect was shown to be dominant across most oxygen partial pressures, with Sn′′ZrSnZr″ charge compensated by V∙∙OVO•• occurring at partial pressures below 10−31 atm. Insertion of additional positive charge into the system was shown to significantly increase the critical partial pressure at which Sn′′ZrSnZr″ is stable. Recently developed low-Sn nuclear fuel cladding alloys have demonstrated an improved corrosion resistance and a delayed transition compared to Sn-containing alloys, such as Zircaloy-4. The interaction between the positive charge and the tin defect is discussed in the context of alloying additions, such as niobium and their influence on corrosion of cladding alloys

Steady-state modulation of voltage-gated K+ channels in rat arterial smooth muscle by cyclic AMP-dependent protein kinase and protein phosphatase 2B

Voltage-gated potassium channels (Kv) are important regulators of membrane potential in vascular smooth muscle cells, which is integral to controlling intracellular Ca2+ concentration and regulating vascular tone. Previous work indicates that Kv channels can be modulated by receptor-driven alterations of cyclic AMP-dependent protein kinase (PKA) activity. Here, we demonstrate that Kv channel activity is maintained by tonic activity of PKA. Whole-cell recording was used to assess the effect of manipulating PKA signalling on Kv and ATP-dependent K+ channels of rat mesenteric artery smooth muscle cells. Application of PKA inhibitors, KT5720 or H89, caused a significant inhibition of Kv currents. Tonic PKA-mediated activation of Kv appears maximal as application of isoprenaline (a β-adrenoceptor agonist) or dibutyryl-cAMP failed to enhance Kv currents. We also show that this modulation of Kv by PKA can be reversed by protein phosphatase 2B/calcineurin (PP2B). PKA-dependent inhibition of Kv by KT5720 can be abrogated by pre-treatment with the PP2B inhibitor cyclosporin A, or inclusion of a PP2B auto-inhibitory peptide in the pipette solution. Finally, we demonstrate that tonic PKA-mediated modulation of Kv requires intact caveolae. Pre-treatment of the cells with methyl-β-cyclodextrin to deplete cellular cholesterol, or adding caveolin-scaffolding domain peptide to the pipette solution to disrupt caveolae-dependent signalling each attenuated PKA-mediated modulation of the Kv current. These findings highlight a novel, caveolae-dependent, tonic modulatory role of PKA on Kv channels providing new insight into mechanisms and the potential for pharmacological manipulation of vascular tone

Combined expression of caveolin-1 and an activated AKT/mTOR pathway predicts reduced disease-free survival in clinically confined renal cell carcinoma

We previously reported that tumour-associated caveolin-1 is a potential biomarker in renal cell carcinoma (RCC), whose overexpression predicts metastasis following surgical resection for clinically confined disease. Much attention has recently focused on the AKT/mTOR pathway in a number of malignancies, including RCC. Since caveolin-1 and the AKT/mTOR signalling cascade are independently shown to be important regulators of tumour angiogenesis, we hypothesised that caveolin-1 interacts with the AKT/mTOR pathway to drive disease progression and metastasis in RCC. The aims of this study were to determine (i) the expression status of the activated AKT/mTOR pathway components (phosphorylated forms) in RCC and (ii) their prognostic value when combined with caveolin-1. Immunohistochemistry for caveolin-1, pAKT, pmTOR, pS6 and p4E-BP1 was performed on tissue microarrays from 174 clinically confined RCCs. Significantly decreased mean disease-free survival was observed when caveolin-1 was coexpressed with either pAKT (2.95 vs 6.14 years), pmTOR (3.17 vs 6.28 years), pS6 (1.45 vs 6.62 years) or p4E-BP1 (2.07 vs 6.09 years) than when neither or any one single biomarker was expressed alone. On multivariate analysis, the covariate of ‘caveolin-1/AKT' (neither alone were influential covariates) was a significant influential indicator of poor disease-free survival with a hazard ratio of 2.13 (95% CI: 1.15–3.92), higher than that for vascular invasion. Tumours that coexpressed caveolin-1 and activated mTOR components were more likely to be larger, higher grade and to show vascular invasion. Our results provide the first clinical evidence that caveolin-1 cooperates with an activated AKT/mTOR pathway in cancer and may play an important role in disease progression. We conclude that evaluation of the ‘caveolin-1/AKT/mTOR axis' in primary kidney tumours will identify subsets of RCC patients who require greater postoperative surveillance and more intensive treatment