Experimental and computational approaches to quantitative proteomics: status quo and outlook.

Proteomics has come a long way from the initial qualitative analysis of proteins present in a given sample at a given time ("cataloguing") to large-scale characterization of proteomes, their interactions and dynamic behavior. Originally enabled by breakthroughs in protein separation and visualization (by two-dimensional gels) and protein identification (by mass spectrometry), the discipline now encompasses a large body of protein and peptide separation, labeling, detection and sequencing tools supported by computational data processing. The decisive mass spectrometric developments and most recent instrumentation news are briefly mentioned accompanied by a short review of gel and chromatographic techniques for protein/peptide separation, depletion and enrichment. Special emphasis is placed on quantification techniques: gel-based, and label-free techniques are briefly discussed whereas stable-isotope coding and internal peptide standards are extensively reviewed. Another special chapter is dedicated to software and computing tools for proteomic data processing and validation. A short assessment of the status quo and recommendations for future developments round up this journey through quantitative proteomics.

Error and attack tolerance of layered complex networks.

Many complex systems may be described by not one but a number of complex networks mapped on each other in a multi-layer structure. Because of the interactions and dependencies between these layers, the state of a single layer does not necessarily reflect well the state of the entire system. In this paper we study the robustness of five examples of two-layer complex systems: three real-life data sets in the fields of communication (the Internet), transportation (the European railway system), and biology (the human brain), and two models based on random graphs. In order to cover the whole range of features specific to these systems, we focus on two extreme policies of system's response to failures, no rerouting and full rerouting. Our main finding is that multi-layer systems are much more vulnerable to errors and intentional attacks than they appear from a single layer perspective.

Genetic team composition and level of selection in the evolution of cooperation

In cooperative multiagent systems, agents interac to solve tasks. Global dynamics of multiagent teams result from local agent interactions, and are complex and difficult to predict. Evolutionary computation has proven a promising approach to the design of such teams. The majority of current studies use teams composed of agents with identical control rules ("geneti- cally homogeneous teams") and select behavior at the team level ("team-level selection"). Here we extend current approaches to include four combinations of genetic team composition and level of selection. We compare the performance of genetically homo- geneous teams evolved with individual-level selection, genetically homogeneous teams evolved with team-level selection, genetically heterogeneous teams evolved with individual-level selection, and genetically heterogeneous teams evolved with team-level selection. We use a simulated foraging task to show that the optimal combination depends on the amount of cooperation required by the task. Accordingly, we distinguish between three types of cooperative tasks and suggest guidelines for the optimal choice of genetic team composition and level of selection

THE ROLE OF PUNISHMENT IN MANAGING DISCIPLINE: Best Practices and Lessons Learned

Now more than ever Capeverdean teachers are faced with student acts of violence which reverberate to the outer limits of our society at large. These situations have caused teachers to reflect upon their roles as educator and “promoter” of discipline. Some are even questioning their effectiveness in this process as they are challenged to discover if they are in the right place. How do teachers manage discipline? In the past, punishment was the rule of thumb and to some extent remains the measure of choice. But is this the most effective form of behavior management? What is the relationship between punishment and corrective behavior? This paper will discuss the affect that punishment has on the learning process as it attempts to suggest strategies in managing discipline with the objective of creating an effective learning environment.

Processes and consequences in business ethical dilemmas: The oil industry and climate changes

This paper proposes a framework to examine business ethical dilemmas andbusiness attitudes towards such dilemmas. Business ethical dilemmas canbe understood as reflecting a contradiction between a socially detrimentalprocess and a self-interested profitable consequence. This representationallows us to distinguish two forms of behavior differing by whetherpriority is put on consequences or on processes. We argue that theseforms imply very different business attitudes towards society:controversial or competitive for the former and aligned or cooperativefor the latter. These attitudes are then analyzed at the discursive level in order to address the question of good faith in businessargumentation, i.e. to which extent are these attitudes consistent withactual business behaviors. We argue that consequential attitudes mostlyinvolve communication and lobbying actions aiming at eluding the dilemma.Therefore, the question of good faith for consequential attitudes liesin the consistency between beliefs and discourse. On the other hand,procedural attitudes acknowledge the dilemma and claim a change of theprocess of behavior. They thus raise the question of the consistencybetween discourses and actual behavior. We apply this processes/consequencesframework to the case of the oil industry s climate change ethical dilemmawhich comes forth as a dilemma between emitting greenhouse gases and making more profits . And we examine the different attitudes of two oilcorporations-BP Amoco and ExxonMobil-towards the dilemma.

Morphology, distribution and abundance of antennal sensilla of the oyster mushroom fly, Coboldia fuscipes (Meigen) (Diptera: Scatopsidae)

ABSTRACT We investigated the distribution, morphology and abundance of antennae sensilla of Coboldia fuscipes (Meigen) using scanning electron microscopy. Antennae of C. fuscipes consisted of scape, pedicel, and flagellum with eight flagellomeres. Antennal scape and pedicel had only one type of sensillum, i.e., sensilla chaetica. Significant differences were found between the number and distribution of these sensilla. Four types of morphologically distinct sensilla on the flagellum were identified, including sensilla chaetica, sensilla trichoidea, sensilla coeloconica, and sensilla basiconica (three subtypes). Significant differences were found in the abundance and distribution of sensilla among the antennal flagella and diverse flagellomeres in both sexes. Sensilla trichoidea is the most abundant of sensilla discovered on the antennal flagellum. Sensilla chaetica is the largest and longest sensilla among all the types of sensilla found on the antennal surface of C. fuscipes. Sensilla coeloconica is widely distributed all over the flagellum surface except for the first of female. Some significant differences in the abundance and distribution were also observed among sensilla basiconica of flagellum. The probable biological function of each sensillum type was deduced based on the basis of their structure. These results serve as important basis for further studies on the host location mechanism and mating behavior of C. fuscipes.

The Smiling Project: development of a new program for gait and balance training

Introduction: The SMILING project, a multicentric project fundedby the European Union, aims to develop a new gait and balance trainingprogram to prevent falls in older persons. The program includes the"SMILING shoe", an innovative device that generates mechanical perturbationwhile walking by changing the soles' inclination. Induced perturbationschallenge subjects' balance and force them to react to avoidfalls. By training specifically the complex motor reactions used to maintainbalance when walking on irregular ground, the program will improvesubjects' ability to react in situation of unsteadiness and reduce theirrisk of falling. Methods: The program will be evaluated in a multicentric,cross-over randomized controlled trial. Overall, 112 subjects (aged≥65 years, ≥1 falls, POMA score 22-26/28) will be enrolled. Subjectswill be randomised in 2 groups: group A begin the training with active"SMILING shoes", group B with inactive dummy shoes. After 4 weeksof training, group A and B will exchange the shoes. Supervised trainingsessions (30 minutes twice a week for 8 weeks) include walkingtasks of progressive difficulties.To avoid a learning effect, "SMILINGshoes" perturbations will be generated in a non-linear and chaotic way.Gait performance, fear of falling, and acceptability of the program willbe assessed. Conclusion: The SMILING program is an innovative interventionfor falls prevention in older persons based on gait and balancetraining using chaotic perturbations. Because of the easy use of the"SMILING shoes", this program could be used in various settings, suchas geriatric clinics or at home.

Construction and electrophoretic migration of single-stranded DNA knots and catenanes.

In recent years there has been growing interest in the question of how the particular topology of polymeric chains affects their overall dimensions and physical behavior. The majority of relevant studies are based on numerical simulation methods or analytical treatment; however, both these approaches depend on various assumptions and simplifications. Experimental verification is clearly needed but was hampered by practical difficulties in obtaining preparative amounts of knotted or catenated polymers with predefined topology and precisely set chain length. We introduce here an efficient method of production of various single-stranded DNA knots and catenanes that have the same global chain length. We also characterize electrophoretic migration of the produced single-stranded DNA knots and catenanes with increasing complexity.

White luminescence from Si+ and C+ ion-implanted SiO2 films

The microstructural and optical analysis of SiO2 layers emitting white luminescence is reported. These structures have been synthesized by sequential Si+ and C+ ion implantation and high-temperature annealing. Their white emission results from the presence of up to three bands in the photoluminescence (PL) spectra, covering the whole visible spectral range. The microstructural characterization reveals the presence of a complex multilayer structure: Si nanocrystals are only observed outside the main C-implanted peak region, with a lower density closer to the surface, being also smaller in size. This lack of uniformity in their density has been related to the inhibiting role of C in their growth dynamics. These nanocrystals are responsible for the band appearing in the red region of the PL spectrum. The analysis of the thermal evolution of the red PL band and its behavior after hydrogenation shows that carbon implantation also prevents the formation of well passivated Si/SiO2 interfaces. On the other hand, the PL bands appearing at higher energies show the existence of two different characteristics as a function of the implanted dose. For excess atomic concentrations below or equal to 10%, the spectra show a PL band in the blue region. At higher doses, two bands dominate the green¿blue spectral region. The evolution of these bands with the implanted dose and annealing time suggests that they are related to the formation of carbon-rich precipitates in the implanted region. Moreover, PL versus depth measurements provide a direct correlation of the green band with the carbon-implanted profile. These PL bands have been assigned to two distinct amorphous phases, with a composition close to elemental graphitic carbon or stoichiometric SiC.

The impact of cyclin D1 mRNA isoforms, morphology and p53 in mantle cell lymphoma: p53 alterations and blastoid morphology are strong predictors of a high proliferation index.

BACKGROUND: Mantle cell lymphoma is a clinically heterogeneous disease characterized by overexpression of cyclin D1 protein. Blastoid morphology, high proliferation, and secondary genetic aberrations are markers of aggressive behavior. Expression profiling of mantle cell lymphoma revealed that predominance of the 3'UTR-deficient, short cyclin D1 mRNA isoform was associated with high cyclin D1 levels, a high "proliferation signature" and poor prognosis. DESIGN AND METHODS: Sixty-two cases of mantle cell lymphoma were analyzed for cyclin D1 mRNA isoforms and total cyclin D1 levels by real-time reverse transcriptase polymerase chain reaction, and TP53 alterations were assessed by immunohistochemistry and molecular analysis. Results were correlated with proliferation index and clinical outcome. RESULTS: Predominance of the short cyclin D1 mRNA was found in 14 (23%) samples, including four with complete loss of the standard transcript. TP53 alterations were found in 15 (24%) cases. Predominance of 3'UTR-deficient mRNA was significantly associated with high cyclin D1 mRNA levels (P=0.009) and more commonly found in blastoid mantle cell lymphoma (5/11, P=0.060) and cases with a proliferation index of >20% (P=0.026). Both blastoid morphology (11/11, P<0.001) and TP53 alterations (15/15, P<0.001) were significantly correlated with a high proliferation index. A proliferation index of 10% was determined to be a significant threshold for survival in multivariate analysis (P=0.01). CONCLUSIONS: TP53 alterations are strongly associated with a high proliferation index and aggressive behavior in mantle cell lymphoma. Predominance of the 3'UTR-deficient transcript correlates with higher cyclin D1 levels and may be a secondary contributing factor to high proliferation, but failed to reach prognostic significance in this study.

Premartensitic and martensitic phase transitions in ferromagnetic Ni2MnGa

We present an experimental study of the premartensitic and martensitic phase transitions in a Ni2MnGa single crystal by using ultrasonic techniques. The effect of applied magnetic field and uniaxial compressive stress has been investigated. It has been found that they substantially modify the elastic and magnetic behavior of the alloy. These experimental findings are a consequence of magnetoelastic effects. The measured magnetic and vibrational behavior agrees with the predictions of a recently proposed Landau-type model [A. Planes et al., Phys. Rev. Lett. 79, 3926 (1997)] that incorporates a magnetoelastic coupling as a key ingredient.

Dissipation in quasistatically driven disordered systems

This work presents an analysis of hysteresis and dissipation in quasistatically driven disordered systems. The study is based on the random field Ising model with fluctuationless dynamics. It enables us to sort out the fraction of the energy input by the driving field stored in the system and the fraction dissipated in every step of the transformation. The dissipation is directly related to the occurrence of avalanches, and does not scale with the size of Barkhausen magnetization jumps. In addition, the change in magnetic field between avalanches provides a measure of the energy barriers between consecutive metastable states

Landscape structure affects dispersal in the greater white-toothed shrew: inference between genetic and simulated ecological distances

Animal dispersal in a fragmented landscape depends on the complex interaction between landscape structure and animal behavior. To better understand how individuals disperse, it is important to explicitly represent the properties of organisms and the landscape in which they move. A common approach to modelling dispersal includes representing the landscape as a grid of equal sized cells and then simulating individual movement as a correlated random walk. This approach uses a priori scale of resolution, which limits the representation of all landscape features and how different dispersal abilities are modelled. We develop a vector-based landscape model coupled with an object-oriented model for animal dispersal. In this spatially explicit dispersal model, landscape features are defined based on their geographic and thematic properties and dispersal is modelled through consideration of an organism's behavior, movement rules and searching strategies (such as visual cues). We present the model's underlying concepts, its ability to adequately represent landscape features and provide simulation of dispersal according to different dispersal abilities. We demonstrate the potential of the model by simulating two virtual species in a real Swiss landscape. This illustrates the model's ability to simulate complex dispersal processes and provides information about dispersal such as colonization probability and spatial distribution of the organism's path

Design and Evaluation of a Single-Span Bridge Using Ultra- High Performance Concrete, September 2009

Research presented herein describes an application of a newly developed material called Ultra-High Performance Concrete (UHPC) to a single-span bridge. The two primary objectives of this research were to develop a shear design procedure for possible code adoption and to provide a performance evaluation to ensure the viability of the first UHPC bridge in the United States. Two other secondary objectives included defining of material properties and understanding of flexural behavior of a UHPC bridge girder. In order to obtain information in these areas, several tests were carried out including material testing, large-scale laboratory flexure testing, large-scale laboratory shear testing, large-scale laboratory flexure-shear testing, small-scale laboratory shear testing, and field testing of a UHPC bridge. Experimental and analytical results of the described tests are presented. Analytical models to understand the flexure and shear behavior of UHPC members were developed using iterative computer based procedures. Previous research is referenced explaining a simplified flexural design procedure and a simplified pure shear design procedure. This work describes a shear design procedure based on the Modified Compression Field Theory (MCFT) which can be used in the design of UHPC members. Conclusions are provided regarding the viability of the UHPC bridge and recommendations are made for future research.

Selection, shape and relaxation of fronts: A numerical study of the effects of inertia.

We study the problem of front propagation in the presence of inertia. We extend the analytical approach for the overdamped problem to this case, and present numerical results to support our theoretical predictions. Specifically, we conclude that the velocity and shape selection problem can still be described in terms of the metastable, nonlinear, and linear overdamped regimes. We study the characteristic relaxation dynamics of these three regimes, and the existence of degenerate (¿quenched¿) solutions.