Band bending and quasi-2DEG in the metallized β\beta-SiC(001) surface

We study the mechanism leading to the metallization of the $\beta$-SiC(001) Si-rich surface induced by hydrogen adsorption. We analyze the effects of band bending and demonstrate the existence of a quasi-2D electron gas, which originates from the donation of electrons from adsorbed hydrogen to bulk conduction states. We also provide a simple model that captures the main features of the results of first-principles calculations, and uncovers the basic physics of the process.Comment: accepted for publication in physica status solidi - Rapid Research Letter

Cohesive and magnetic properties of grain boundaries in bcc Fe with Cr additions

Structural, cohesive, and magnetic properties of two symmetric $\Sigma3(111)$ and $\Sigma5(210)$ tilt grain boundaries (GBs) in pure bcc Fe and in dilute FeCr alloys are studied from first principles. Different concentration and position of Cr solute atoms are considered. We found that Cr atoms placed in the GB interstice enhance the cohesion by 0.5-1.2 J/m$^2$. Substitutional Cr in the layers adjacent to the boundary shows anisotropic effect on the GB cohesion: it is neutral when placed in the (111) oriented Fe grains, and enhances cohesion (by 0.5 J/m$^2$) when substituted in the boundary layer of the (210) grains. The strengthening effect of the Cr solute is dominated by the chemical component of the adhesive binding energy. Our calculations show that unlike the free iron surfaces, Cr impurities segregate to the boundaries of the Fe grains. The magnetic moments on GB atoms are substantially changed and their variation correlates with the corresponding relaxation pattern of the GB planes. The moments on Cr additions are 2-4 times enhanced in comparison with that in a Cr crystal and are antiparallel to the moments on the Fe atoms

Inferring Unusual Crowd Events From Mobile Phone Call Detail Records

The pervasiveness and availability of mobile phone data offer the opportunity of discovering usable knowledge about crowd behaviors in urban environments. Cities can leverage such knowledge in order to provide better services (e.g., public transport planning, optimized resource allocation) and safer cities. Call Detail Record (CDR) data represents a practical data source to detect and monitor unusual events considering the high level of mobile phone penetration, compared with GPS equipped and open devices. In this paper, we provide a methodology that is able to detect unusual events from CDR data that typically has low accuracy in terms of space and time resolution. Moreover, we introduce a concept of unusual event that involves a large amount of people who expose an unusual mobility behavior. Our careful consideration of the issues that come from coarse-grained CDR data ultimately leads to a completely general framework that can detect unusual crowd events from CDR data effectively and efficiently. Through extensive experiments on real-world CDR data for a large city in Africa, we demonstrate that our method can detect unusual events with 16% higher recall and over 10 times higher precision, compared to state-of-the-art methods. We implement a visual analytics prototype system to help end users analyze detected unusual crowd events to best suit different application scenarios. To the best of our knowledge, this is the first work on the detection of unusual events from CDR data with considerations of its temporal and spatial sparseness and distinction between user unusual activities and daily routines.Comment: 18 pages, 6 figure

An Extended, Boolean Model of the Septation Initiation Network in S.Pombe Provides Insights into Its Regulation.

Cytokinesis in fission yeast is controlled by the Septation Initiation Network (SIN), a protein kinase signaling network using the spindle pole body as scaffold. In order to describe the qualitative behavior of the system and predict unknown mutant behaviors we decided to adopt a Boolean modeling approach. In this paper, we report the construction of an extended, Boolean model of the SIN, comprising most SIN components and regulators as individual, experimentally testable nodes. The model uses CDK activity levels as control nodes for the simulation of SIN related events in different stages of the cell cycle. The model was optimized using single knock-out experiments of known phenotypic effect as a training set, and was able to correctly predict a double knock-out test set. Moreover, the model has made in silico predictions that have been validated in vivo, providing new insights into the regulation and hierarchical organization of the SIN

A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis.

BACKGROUND: The yeast Schizosaccharomyces pombe is frequently used as a model for studying the cell cycle. The cells are rod-shaped and divide by medial fission. The process of cell division, or cytokinesis, is controlled by a network of signaling proteins called the Septation Initiation Network (SIN); SIN proteins associate with the SPBs during nuclear division (mitosis). Some SIN proteins associate with both SPBs early in mitosis, and then display strongly asymmetric signal intensity at the SPBs in late mitosis, just before cytokinesis. This asymmetry is thought to be important for correct regulation of SIN signaling, and coordination of cytokinesis and mitosis. In order to study the dynamics of organelles or large protein complexes such as the spindle pole body (SPB), which have been labeled with a fluorescent protein tag in living cells, a number of the image analysis problems must be solved; the cell outline must be detected automatically, and the position and signal intensity associated with the structures of interest within the cell must be determined. RESULTS: We present a new 2D and 3D image analysis system that permits versatile and robust analysis of motile, fluorescently labeled structures in rod-shaped cells. We have designed an image analysis system that we have implemented as a user-friendly software package allowing the fast and robust image-analysis of large numbers of rod-shaped cells. We have developed new robust algorithms, which we combined with existing methodologies to facilitate fast and accurate analysis. Our software permits the detection and segmentation of rod-shaped cells in either static or dynamic (i.e. time lapse) multi-channel images. It enables tracking of two structures (for example SPBs) in two different image channels. For 2D or 3D static images, the locations of the structures are identified, and then intensity values are extracted together with several quantitative parameters, such as length, width, cell orientation, background fluorescence and the distance between the structures of interest. Furthermore, two kinds of kymographs of the tracked structures can be established, one representing the migration with respect to their relative position, the other representing their individual trajectories inside the cell. This software package, called "RodCellJ", allowed us to analyze a large number of S. pombe cells to understand the rules that govern SIN protein asymmetry. CONCLUSIONS: "RodCell" is freely available to the community as a package of several ImageJ plugins to simultaneously analyze the behavior of a large number of rod-shaped cells in an extensive manner. The integration of different image-processing techniques in a single package, as well as the development of novel algorithms does not only allow to speed up the analysis with respect to the usage of existing tools, but also accounts for higher accuracy. Its utility was demonstrated on both 2D and 3D static and dynamic images to study the septation initiation network of the yeast Schizosaccharomyces pombe. More generally, it can be used in any kind of biological context where fluorescent-protein labeled structures need to be analyzed in rod-shaped cells. AVAILABILITY: RodCellJ is freely available under http://bigwww.epfl.ch/algorithms.html, (after acceptance of the publication)

Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN.

The Schizosaccharomyces pombe septation initiation network (SIN) regulates cytokinesis, and asymmetric association of SIN proteins with the mitotic spindle pole bodies (SPBs) is important for its regulation. Here, we have used semi-automated image analysis to study SIN proteins in large numbers of wild-type and mutant cells. Our principal conclusions are: first, that the association of Cdc7p with the SPBs in early mitosis is frequently asymmetric, with a bias in favour of the new SPB; second, that the early association of Cdc7p-GFP to the SPB depends on Plo1p but not Spg1p, and is unaffected by mutations that influence its asymmetry in anaphase; third, that Cdc7p asymmetry in anaphase B is delayed by Pom1p and by activation of the spindle assembly checkpoint, and is promoted by Rad24p; and fourth, that the length of the spindle, expressed as a fraction of the length of the cell, at which Cdc7p becomes asymmetric is similar in cells dividing at different sizes. These data reveal that multiple regulatory mechanisms control the SIN in mitosis and lead us to propose a two-state model to describe the SIN

Proteome changes in platelets activated by arachidonic acid, collagen, and thrombin

<p>Abstract</p> <p>Background</p> <p>Platelets are small anucleated blood particles that play a key role in the control of bleeding. Platelets need to be activated to perform their functions and participate in hemostasis. The process of activation is accompanied by vast protein reorganization and posttranslational modifications. The goal of this study was to identify changes in proteins in platelets activated by different agonists. Platelets were activated by three different agonists - arachidonic acid, collagen, and thrombin. 2D SDS-PAGE (pI 4-7) was used to separate platelet proteins. Proteomes of activated and resting platelets were compared with each other by Progenesis SameSpots statistical software; and proteins were identified by nanoLC-MS/MS.</p> <p>Results</p> <p>190 spots were found to be significantly different. Of these, 180 spots were successfully identified and correspond to 144 different proteins. Five proteins were found that had not previously been identified in platelets: protein CDV3 homolog, protein ETHE1, protein LZIC, FGFR1 oncogene partner 2, and guanine nucleotide-binding protein subunit beta-5. Using spot expression profile analysis, we found two proteins (WD repeat-containing protein 1 and mitochondrial glycerol-3-phosphate dehydrogenase) that may be part of thrombin specific activation or signal transduction pathway(s).</p> <p>Conclusions</p> <p>Our results, characterizing the differences within proteins in both activated (by various agonists) and resting platelets, can thus contribute to the basic knowledge of platelets and to the understanding of the function and development of new antiplatelet drugs.</p