Absolute Free Energies for Biomolecules in Implicit or Explicit Solvent

in Physics Procedia (2014), 57

Quel avenir pour la recherche en histoire religieuse au Luxembourg?

in Hemecht : Zeitschrift für Luxemburger Geschichte = Revue d'Histoire Luxembourgeoise (2014), 66(3/4), 547-550

Influence and interaction indexes for pseudo-Boolean functions: a unified least squares approach

in Discrete Applied Mathematics (2014), 179

The Banzhaf power and interaction indexes for a pseudo-Boolean function (or a cooperative game) appear naturally as leading coefficients in the standard least squares approximation of the function by a ... [more ▼]

The Banzhaf power and interaction indexes for a pseudo-Boolean function (or a cooperative game) appear naturally as leading coefficients in the standard least squares approximation of the function by a pseudo-Boolean function of a specified degree. We first observe that this property still holds if we consider approximations by pseudo-Boolean functions depending only on specified variables. We then show that the Banzhaf influence index can also be obtained from the latter approximation problem. Considering certain weighted versions of this approximation problem, we introduce a class of weighted Banzhaf influence indexes, analyze their most important properties, and point out similarities between the weighted Banzhaf influence index and the corresponding weighted Banzhaf interaction index. We also discuss the issue of reconstructing a pseudo-Boolean function from prescribed influences and point out very different behaviors in the weighted and non-weighted cases. [less ▲]

An essential role of syntaxin 3 protein for granule exocytosis and secretion of IL-1α, IL-1β, IL-12b, and CCL4 from differentiated HL-60 cells

in Journal of Leukocyte Biology (2014), 97

Besides their roles in the killing of pathogens, neutrophils have the capacity to package a variety of cytokines into cytoplasmic granules for subsequent release upon inflammatory conditions. Because the ... [more ▼]

Besides their roles in the killing of pathogens, neutrophils have the capacity to package a variety of cytokines into cytoplasmic granules for subsequent release upon inflammatory conditions. Because the rapid secretion of cytokines orchestrates the action of other immune cells at the infection site and thus, can contribute to the development and chronicity of inflammatory diseases, we aimed to determine the intracellular SNARE machinery responsible for the regulation of cytokine secretion and degranulation. From a constructed gene-expression network, we first selected relevant cytokines for functional validation by the CBA approach. We established a cytokine-secretion profile for human neutrophils and dHL-60 cells, underlining their similar ability to secrete a broad variety of cytokines within proinflammatory conditions mimicked by LPS stimulation. Secondly, after screening of SNARE genes by microarray experiments, we selected STX3 for further functional studies. With the use of a siRNA strategy, we show that STX3 is clearly required for the maximal release of IL-1α, IL-1β, IL-12b, and CCL4 without alteration of other cytokine secretion in dHL-60 cells. In addition, we demonstrate that STX3 is involved in MMP-9 exocytosis from gelatinase granules, where STX3 is partly localized. Our results suggest that the secretion of IL-1α, IL-1β, IL-12b, and CCL4 occurs during gelatinase degranulation, a process controlled by STX3. In summary, these findings provide first evidence that STX3 has an essential role in trafficking pathways of cytokines in neutrophil granulocytes. [less ▲]

Empirical assessment of machine learning-based malware detectors for Android: Measuring the Gap between In-the-Lab and In-the-Wild Validation Scenarios

in Empirical Software Engineering (2014)

To address the issue of malware detection through large sets of applications, researchers have recently started to investigate the capabilities of machine-learning techniques for proposing effective ... [more ▼]

To address the issue of malware detection through large sets of applications, researchers have recently started to investigate the capabilities of machine-learning techniques for proposing effective approaches. So far, several promising results were recorded in the literature, many approaches being assessed with what we call in the lab validation scenarios. This paper revisits the purpose of malware detection to discuss whether such in the lab validation scenarios provide reliable indications on the performance of malware detectors in real-world settings, aka in the wild. To this end, we have devised several Machine Learning classifiers that rely on a set of features built from applications’ CFGs. We use a sizeable dataset of over 50 000 Android applications collected from sources where state-of-the art approaches have selected their data. We show that, in the lab, our approach outperforms existing machine learning-based approaches. However, this high performance does not translate in high performance in the wild. The performance gap we observed—F-measures dropping from over 0.9 in the lab to below 0.1 in the wild —raises one important question: How do state-of-the-art approaches perform in the wild ? [less ▲]

Computer Simulations of Crystallization Mechanism in Polymeric Materials

Doctoral thesis (2014)

In this work, we have studied crystallization in short polymer chains using molec- ular dynamics simulations. We use a realistic united atom model which is able to reproduce the physical quantities ... [more ▼]

In this work, we have studied crystallization in short polymer chains using molec- ular dynamics simulations. We use a realistic united atom model which is able to reproduce the physical quantities related to phase transitions. We present a study of crystal nucleation from undercooled melts of n-alkanes and identify the molec- ular mechanism of homogeneous crystal nucleation under quiescent conditions and under shear flow. We choose n-eicosane (C20) the length of which is below the en- tanglement length and n-pentacontahectane (C150) the length of which is above the entanglement length so that we can compare results for unentangled and entangled polymer chains. We also provide the crystal growth mechanism of n-eicosane under quiescent conditions. For C150, we present crystal lamellae structure and compare our results with published simulation results. We use a mean first passage time analysis and a committor analysis to determine the critical nucleus size and then to compute the nucleation rate. We observe that the critical nucleus is of cylindrical shape. We report on the effects of shear rate and temperature on the nucleation rates and estimate the critical shear rates, beyond which the nucleation rate in- creases with the shear rate. We show that the critical shear rate corresponds to a Weissenberg number of order unity which is in agreement with previous experimen- tal observation and theoretical work. We also show that the power law behaviour between nucleation rate and shear rate is in agreement with experiments and theory. We compute the viscosity of the system during the formation of crystalline nuclei and we show that the viscosity of the system is not affected by the crystalline nuclei. Finally, we present results of crystallization in the polyethylene (C500) melt under quiescent conditions. [less ▲]

Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson’s disease

in BMC Genomics (2014), 15(1154),

Background: The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often ... [more ▼]

Background: The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellular model for Parkinson’s disease, the relevance of this cellular model in the context of Parkinson’s disease (PD) and other neurodegenerative diseases has not yet been systematically evaluated. Results: We have used a systems genomics approach to characterize the SH-SY5Y cell line using whole-genome sequencing to determine the genetic content of the cell line and used transcriptomics and proteomics data to determine molecular correlations. Further, we integrated genomic variants using a network analysis approach to evaluate the suitability of the SH-SY5Y cell line for perturbation experiments in the context of neurodegenerative diseases, including PD. Conclusions: The systems genomics approach showed consistency across different biological levels (DNA, RNA and protein concentrations). Most of the genes belonging to the major Parkinson’s disease pathways and modules were intact in the SH-SY5Y genome. Specifically, each analysed gene related to PD has at least one intact copy in SH-SY5Y. The disease-specific network analysis approach ranked the genetic integrity of SH-SY5Y as higher for PD than for Alzheimer’s disease but lower than for Huntington’s disease and Amyotrophic Lateral Sclerosis for loss of function perturbation experiments. [less ▲]

A propos de Life time contracts

in Revue Trimestrielle de Droit Civil (2014), 4

Laser Annealing of CuInSe2 Electrodeposited Precursors as the Absorber Layer in Thin Film Solar Cells

Doctoral thesis (2014)

This thesis demonstrates a method by which a non-vacuum deposited CuInSe2 precursor is transformed into a semiconductor absorber layer, suitable for completion into a photovoltaic device, using 1 s laser ... [more ▼]

This thesis demonstrates a method by which a non-vacuum deposited CuInSe2 precursor is transformed into a semiconductor absorber layer, suitable for completion into a photovoltaic device, using 1 s laser annealing. A final device produced using this absorber fabrication method gave a 1.6 % best conversion efficiency. This represents the first reported working device originating from electrodeposition - laser annealing. In this thesis, the steps taken to achieve this result are analysed in detail. This work is split into four parts. Firstly, the precursor structure and the optical properties of its component materials were investigated to ensure optimal interaction between the laser beam and sample. Using the selected codeposited CuInSe2 precursor it was shown that it is possible to stimulate grain growth and atomic diffusion by using a 1064 nm Nd:YAG laser with only a 1 s annealing time. Secondly, it is shown that even on these rapid annealing time-scales the thermodynamic equilibrium reactions between the ternary CuInSe2 and its constituent materials must be considered. This is proven by the formation of the first device from a laser annealed absorber only when a sufficiently elevated partial pressure of Se is supplied during the annealing process. Absorbers formed under lower Se activities led to devices which were shunted or showed negligible efficiency. A correlation was identified between the Se partial pressure and the absorber properties including its Se content, grain size and PL yield. Thirdly, a finite element model capable of predicting the film temperature during laser annealing is demonstrated. By considering the Gaussian nature of the irradiating beam it is seen that the peak temperature of the CuInSe2 film, which formed the 1.6 % device, fluctuated spatially by > 300 oC during processing. Variations in temperature led to different rates of atomic diffusion and grain growth and resulted in lateral inhomogeneities in the absorber. The low device efficiency is believed to be partially caused by these variations. Finally, the chemical composition of the film and its effect on absorber properties is established. Increasing the Cu/In ratio of CuInSe2 precursors and incorporating Na into CuInSe2 absorbers is shown to increase their crystal coherence length. However, the positive effects related to these elements must be balanced against their impact on the optoelectronic properties of the absorber when present in high concentrations. Therefore it is hoped that this initial ‘first device’ efficiency validates this fabrication route and motivates future research on this interesting topic. [less ▲]

Book review

in H-Soz-Kult: Kommunikation und Fachinformation für die Geschichtswissenschaften (2014)