bluuebunny/crossref_metadata_2025 huggingface dataset:
Asymptotic regulation for distributed parameter systems via zero dynamics inverse design
Authors: Byrnes C.I. , Gilliam D.S. , Hu C. , Shubov V.I.
Published: November 2011

In this paper, we introduce a new approach, zero dynamics inverse (ZDI) design, for designing a feedback compensation scheme achieving asymptotic regulation for a linear or nonlinear distributed parameter system in the case when the value w(t) at time t of the signal w to be tracked or rejected is a measured variable. Following the nonequilibrium formulation of output regulation, we formulate the problem of asymptotic regulation by requiring zero steady‐state error together with ultimate boundedness of the state of the system and the controller(s), with a bound determined by bounds on the norms of the initial data and w. Because a controller solving this problem depends only on a bound on the norm of w not on the particular choice of w, this formulation is in sharp contrast to both exact tracking, asymptotic tracking or dynamic inversion of a completely known trajectory and to output regulation with a known exosystem. The ZDI design consists of the interconnection, via a memoryless filter, of a stabilizing feedback compensator and a cascade controller, designed in a simple, universal way from the zero dynamics of the closed‐loop feedback system. This design philosophy is illustrated with a problem of asymptotic regulation for a boundary controlled viscous Burgers' equation, for which we prove that the ZDI is input‐to‐state stable. In infinite dimensions, however, input‐to‐state stable compactness arguments are supplanted by smoothing arguments to accommodate crucial technical details, including the global existence, uniqueness, and regularity of solutions to the interconnected systems. Copyright © 2011 John Wiley & Sons, Ltd.
Weak quasi‐randomness for uniform hypergraphs
Authors: Conlon David , Hàn Hiêp , Person Yury , Schacht Mathias
Published: November 2011

We study quasi‐random properties of k‐uniform hypergraphs. Our central notion is uniform edge distribution with respect to large vertex sets. We will find several equivalent characterisations of this property and our work can be viewed as an extension of the well known Chung‐Graham‐Wilson theorem for quasi‐random graphs.

Moreover, let Kk be the complete graph on k vertices and M(k) the line graph of the graph of the k‐dimensional hypercube. We will show that the pair of graphs (Kk,M(k)) has the property that if the number of copies of both Kk and M(k) in another graph G are as expected in the random graph of density d, then G is quasi‐random (in the sense of the Chung‐Graham‐Wilson theorem) with density close to d. © 2011 Wiley Periodicals, Inc. Random Struct. Alg., 2011
Relative survival multistate Markov model
Authors: Huszti Ella , Abrahamowicz Michal , Alioum Ahmadou , Binquet Christine , Quantin Catherine
Published: November 2011

Prognostic studies often have to deal with two important challenges: (i) separating effects of predictions on different ‘competing’ events and (ii) uncertainty about cause of death. Multistate Markov models permit multivariable analyses of competing risks of, for example, mortality versus disease recurrence. On the other hand, relative survival methods help estimate disease‐specific mortality risks even in the absence of data on causes of death. In this paper, we propose a new Markov relative survival (MRS) model that attempts to combine these two methodologies. Our MRS model extends the existing multistate Markov piecewise constant intensities model to relative survival modeling. The intensity of transitions leading to death in the MRS model is modeled as the sum of an estimable excess hazard of mortality from the disease of interest and an ‘offset’ defined as the expected hazard of all‐cause ‘natural’ mortality obtained from relevant life‐tables. We evaluate the new MRS model through simulations, with a design based on registry‐based prognostic studies of colon cancer. Simulation results show almost unbiased estimates of prognostic factor effects for the MRS model. We also applied the new MRS model to reassess the role of prognostic factors for mortality in a study of colorectal cancer. The MRS model considerably reduces the bias observed with the conventional Markov model that does not permit accounting for unknown causes of death, especially if the ‘true’ effects of a prognostic factor on the two types of mortality differ substantially. Copyright © 2011 John Wiley & Sons, Ltd.
Probing Diffusion of Single Nanoparticles at Water–Oil Interfaces
Authors: Wang Dapeng , Yordanov Stoyan , Paroor Harsha Mohan , Mukhopadhyay Ashis , Li Christopher Y. , Butt Hans‐Jürgen , Koynov Kaloian
Published: November 2011

The diffusion of nanoparticles at a water–alkane interface is studied using fluorescence correlation spectroscopy. Hydrophilic and hydrophobic quantum dots of 5, 8, and 11 nm radius are used. A slow‐down of nanoparticle diffusion at the liquid–liquid interface is observed. The effect is most evident when the viscosities of both liquid phases are similar, here, at the water–decane interface. In this case, the interfacial diffusion coefficients of the hydrophilic particles are 1.5 times and those of the hydrophobic particles 2 times lower than the corresponding bulk values.
Left hepatectomy or left trisectionectomy with resection of the caudate lobe and extrahepatic bile duct for hilar cholangiocarcinoma (with video)
Authors: Uesaka Katsuhiko
Published: November 2011

Purpose

Although left‐sided hepatectomy, such as a left hepatectomy or left trisectionectomy with resection of the caudate lobe and extrahepatic bile duct, is used to treat hilar cholangiocarcinoma predominantly involving the left side of the hepatic hilum, it is associated with several difficult technical points. The important points during left‐sided hepatectomy are described here.

Techniques

There are anatomical variations of the sectional artery and bile duct. It is essential to understand the individual intrahepatic and hilar anatomy preoperatively. Surgical procedures consist of lymph node clearance, dissection of the distal bile duct, skeletonization resection of the hepatoduodenal ligament, mobilization of the liver and liver resection, dissection of the intrahepatic bile ducts, and biliary reconstruction. During lymph node dissection and skeletonization resection of the hepatoduodenal ligament, the nerve plexus around the hepatic artery is dissected, and its adventitia is exposed with great care to avoid injuring the hepatic artery. Mobilization of the caudate lobe is performed only from the left side. There is no clear landmark between the caudate lobe and the right posterior section during liver resection. In the final step of liver resection, it progresses toward the right edge of the inferior vena cava. When dividing intrahepatic bile ducts, extreme care should be used to avoid injury to the corresponding hepatic arteries, especially the anomalous supraportal posterior sectional artery.

Conclusions

Left‐sided hepatectomy for hilar cholangiocarcinoma should be considered a more complicated and technically demanding procedure than right‐sided hepatectomy. Surgeons need to pay close attention to anatomical variations in order to perform a left‐sided hepatectomy safely and successfully.
Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes
Authors: Turner Peter C , Yomano Lorraine P , Jarboe Laura R , York Sean W , Baggett Christy L , Moritz Brélan E , Zentz Emily B , Shanmugam K T , Ingram Lonnie O
Published: November 2011

Escherichia coli KO11 (ATCC 55124) was engineered in 1990 to produce ethanol by chromosomal insertion of the Zymomonas mobilis pdc and adhB genes into E. coli W (ATCC 9637). KO11FL, our current laboratory version of KO11, and its parent E. coli W were sequenced, and contigs assembled into genomic sequences using optical NcoI restriction maps as templates. E. coli W contained plasmids pRK1 (102.5 kb) and pRK2 (5.4 kb), but KO11FL only contained pRK2. KO11FL optical maps made with AflII and with BamHI showed a tandem repeat region, consisting of at least 20 copies of a 10-kb unit. The repeat region was located at the insertion site for the pdc, adhB, and chloramphenicol-resistance genes. Sequence coverage of these genes was about 25-fold higher than average, consistent with amplification of the foreign genes that were inserted as circularized DNA. Selection for higher levels of chloramphenicol resistance originally produced strains with higher pdc and adhB expression, and hence improved fermentation performance, by increasing the gene copy number. Sequence data for an earlier version of KO11, ATCC 55124, indicated that multiple copies of pdc adhB were present. Comparison of the W and KO11FL genomes showed large inversions and deletions in KO11FL, mostly enabled by IS10, which is absent from W but present at 30 sites in KO11FL. The early KO11 strain ATCC 55124 had no rearrangements, contained only one IS10, and lacked most accumulated single nucleotide polymorphisms (SNPs) present in KO11FL. Despite rearrangements and SNPs in KO11FL, fermentation performance was equal to that of ATCC 55124.
Effect of modified glucose catabolism on xanthan production in Xanthomonas oryzae pv. oryzae
Authors: Jang Se-Gul , Lee Byoung-Moo , Cho Jae-Yong
Published: November 2011

In this study, the glucose 6-phosphate dehydrogenase gene (XOO2314) was inactivated in order to modulate the intracellular glucose 6-phosphate, and its effects on xanthan production in a wild-type strain of Xanthomonas oryzae were evaluated. The intracellular glucose 6-phosphate was increased from 17.6 to 99.4 μmol g−1 (dry cell weight) in the gene-disrupted mutant strain. The concomitant increase in the glucose 6-phosphate was accompanied by an increase in xanthan production of up to 2.23 g l−1 (culture medium). However, in defined medium supplemented with 0.4% glucose, the growth rate of the mutant strain was reduced to 52.9% of the wild-type level. Subsequently, when a family B ATP-dependent phosphofructokinase from Escherichia coli was overexpressed in the mutant strain, the growth rate was increased to 142.9%, whereas the yields of xanthan per mole of glucose remained approximately the same.
Calcium Chelating Sugar‐Based Surfactants for Hard‐Water Detergency
Authors: Ferlin Nadège , Grassi Diego , Ojeda Carlos , Castro Mariano J. L. , Fernández‐Cirelli Alicia , Kovensky José , Grand Eric
Published: November 2011

Hard water can decrease the detergency efficiency of surfactants due to a significant concentration of divalent cations as Ca2+ or Mg2+. The formulation of a cleaning detergent must be modified and it is usual to add more surfactants or a huge quantity of sequestrating agents. This supplementary addition can have deleterious effects on the environment and increases the price of the formulation. A surfactant, presenting both detergency capacities in the presence of Ca2+ and Ca2+ chelating properties, would be of great interest. In this paper, we report on Ca2+ extraction with sugar‐based chelating surfactants using an experimental device, namely a flotation column, as both chelating properties and foaming properties in the presence of Ca2+ are important in the flotation process as well as in detergency. Among all the sugar‐based surfactants tested, a few of them were able to extract calcium and thus demonstrated the expected characteristics.
Rente mit 67 - Notwendige Rahmenbedingungen
Authors: Haaf Hans-Günter , Sewöster Daniela
Published: November 2011

Einleitung

Rehabilitationsleistungen tragen zum Erhalt der Erwerbsfähigkeit und damit zu einer längeren Lebensarbeitszeit von Beschäftigten bei. Der demografische Wandel und die Einführung der Rente mit 67 werden zu einem wachsenden Reha-Bedarf führen und auch die Anforderungen an die Rehabilitation verändern. Die Deutsche Rentenversicherung richtet ihre Reha-Leistungen zurzeit stärker auf berufliche Erfordernisse aus. Aufbauend auf den vorhandenen Reha-Strukturen strebt die Rentenversicherung zudem die Entwicklung betriebsnaher präventiver Angebote an.
The chronostratigraphic space of the lithosphere and the Vendian as a geohistorical subdivision of the Neoproterozoic
Authors: Sokolov B.S.
Published: November 2011

Chronostratigraphic space is defined as information about the geologic history and paleobiosphere that elucidates the Earth’s evolution as the interaction of different layers of the geosphere. Stratigraphic subdivisions act as information-carrying medium. Elementary units in the Phanerozoic chronostratigraphic space are biostratigraphic zones, whereas in the Proterozoic space, sequenthemes. The Vendian sequentheme has a unique paleontological characteristic, which continuously expands and is refined. Its lower boundary determines the top of cryogenic suberatheme and is marked by deposition of the last diamictite (Varangerian, Marinoan) and the largest postglacial transgression. In the chronostratigraphic space, the Vendian is surely Neoproterozoic, but constitutes a single acrochrone of the biosphere evolution with the Phanerozoic. The Vendian stage divides and connects two different-sized intervals in the evolution of Geomerida: a long interval of time (from the origin of life to the beginning of the Vendian) marked by a predominance of prokaryotic ecosystems and a relatively short interval with the incredible biodiversity of modern-type ecosystems dominated by eukaryotes.
The physicochemical conditions of hydrothermal ore-forming systems of “black smokers” associated with mantle ultrabasites in the Central Atlantic region
Authors: Bortnikov N.S. , Simonov V.A. , Amplieva E.E. , Stavrova O.O. , Fouquet Y.
Published: November 2011

Study of fluid inclusions in minerals from sulfide ores sampled in the Ashadze and Logatchev hydrothermal fields during the Serpentine cruise of the R/V Pourquoi Pas? in 2007 gave an insight into the physicochemical conditions of ore-forming systems of “black smokers” associated with mantle ultrabasites in the Central Atlantic region. It was established that the studied hydrothermal systems differ in mineral formation temperatures, fluid salinity, and hydrothermal processes running within basaltic complexes in both low-spreading (Mid-Atlantic Ridge) and high-spreading (East Pacific Rise) mid-ocean ridges. It was shown for the Ashadze and Logatchev hydrothermal fields that the temperatures and salinity of inclusion solutions in the minerals vary over a wider range of values than those of fluids flowing out from the ridge vents onto the ocean floor. Study of fluid inclusions showed that the Ashadze and Logatchev sulfide structures resulted from the action of both high-temperature (up to 355 °C) and low-temperature (no lower than 170 °C) solutions. The salinity of fluid in the inclusions (mainly 8 wt.%) is more than twice as high as the salinity of seawater. The data obtained substantiate the phase separation of fluid in the deepest-water submarine hydrothermal Ashadze system and give an idea of the chemical composition and temperature of fluids forming sulfide deposits in the Ashadze and Logatchev hydrothermal fields in the Central Atlantic region.
Migration of immiscible hydrocarbons recorded in calcite-hosted fluid inclusions, Ordos Basin: a case study from Northern China
Authors: Rongxi Li , Guzmics T. , Xiaojie Liu , Guangcheng Xie
Published: November 2011

In this study one- (hydrocarbon liquid), two- (hydrocarbon liquid and vapor) and three- (hydrocarbon liquid and vapor, and aqueous liquid) phase fluid inclusions have been investigated in calcites occurring in veinlets in fine grained sandstones of Chang 7 source rock and Chang 8 reservoir rock. These rocks are parts of the Upper Triassic Yangchang Formation in Ordos Basin, Northern China. The hydrocarbon inclusions studied show high variance in vapor-liquid volume ratio at ambient temperature, suggesting a heterogeneous entrapment of vapor and liquid phases those existed before or during formation of the calcite. This is supported by homogenizations happened into both liquid and vapor phase. Homogenization temperatures are ranging between 70 and 120 °C. We consider that this wide range are rather resulted in heterogeneous entrapment of immiscible liquid and vapor phases than high temperature (e.g., 120 °C) formation of the hydrocarbon inclusions. Therefore, the lower range of homogenization temperatures (around 80 °C) seem to be probable for formation of the hydrocarbon inclusions studied. Fluorescent microscopic results on the hydrocarbon inclusions show bright yellow color for the oil. Fluorescence spectra indexes indicate that oil in the inclusions is quite mature, similarly to the oil extract from Chang 7 source rock. The differences in fluorescent spectra among the hydrocarbon inclusions suggest their chemical modification during evolution, which might be determined by continuous separation of vapor phase (gas condensate) from the system. On the basis of organic geochemistry of the studied samples (e.g., akin distribution of normal-alkanes and similar isoprenoid ratios), it can be concluded that the oil in the inclusions and the crude oil from the reservoir rock Chang 8 are actually derived from the Chang 7 source rock. During tectonic evolution, the hydrocarbon might suffer phase separation (boiling) forming two phases (a liquid and a vapor phase) due to intensive uplifting of Ordos Basin after the Late Cretaceous. The boiling in the accumulated hydrocarbon could result in overpressure in the source rock. This phenomenon might favor formation of fractures and migration of hydrocarbons from their source toward into sandstone reservoirs. Our study demonstrates the significance of detailed analytical investigation of hydrocarbon inclusions in correlation with their potential source rock.
Toward an evolutionary basis for resilience to drug addiction
Authors: Ahmed Serge H.
Published: November 2011

According to Müller & Schumann (M&S), people would have evolved adaptations for learning to use psychoactive plants and drugs as instruments that reveal particularly advantageous in modern urban environments. Here I “instrumentalize” this framework to propose an evolutionary basis for the existence of a biological resilience to drug addiction in people.
But is it evolution…?
Authors: Sullivan Roger J. , Hagen Edward H.
Published: November 2011

We applaud Müller & Schumann (M&S) for bringing needed attention to the problem of motivation for common non-addictive drug use, as opposed to the usual focus on exotic drugs and addiction. Unfortunately, their target article has many underdeveloped and sometimes contradictory ideas. Here, we will focus on three key issues.
Why do we take drugs? From the drug-reinforcement theory to a novel concept of drug instrumentalization
Authors: Spanagel Rainer
Published: November 2011

The drug-reinforcement theory explains why humans get engaged in drug taking behavior. This theory posits that drugs of abuse serve as biological rewards by activating the reinforcement system. Although from a psychological and neurobiological perspective this theory is extremely helpful, it does not tell us about the drug-taking motives and motivation of an individual. The definition of drug instrumentalization goals will improve our understanding of individual drug-taking profiles.
Theoretical predictions of mass, semimajor axis and eccentricity distributions of super-Earths
Authors: Ida Shigeru
Published: November 2011

We discuss the effects of close scattering and merging between planets on distributions of mass, semimajor axis and orbital eccentricity, using population synthesis model of planet formation, focusing on the distributions of close-in super-Earths, which are being observed recently. We found that a group of compact embryos emerge interior to the ice line, grow, migrate, and congregate into closely-packed convoys which stall in the proximity of their host stars. After the disk-gas depletion, they undergo orbit crossing, close scattering, and giant impacts to form multiple rocky Earths or super-Earths in non-resonant orbits around ~ 0.1AU with moderate eccentricities of ~ 0.01–0.1. The formation of these planets does not depend on model parameters such as type I migration speed. The fraction of solar-type stars with these super-Earths is anti-correlated with the fraction of stars with gas giants. The newly predicted family of close-in super-Earths makes less clear “planet desert” at intermediate mass range than our previous prediction.
Composition of massive giant planets
Authors: Helled Ravit , Bodenheimer Peter , Lissauer Jack J.
Published: November 2011

The two current models for giant planet formation are core accretion and disk instability. We discuss the core masses and overall planetary enrichment in heavy elements predicted by the two formation models, and show that both models could lead to a large range of final compositions. For example, both can form giant planets with nearly stellar compositions. However, low-mass giant planets, enriched in heavy elements compared to their host stars, are more easily explained by the core accretion model. The final structure of the planets, i.e., the distribution of heavy elements, is not firmly constrained in either formation model.
Direct imaging and spectroscopy of planets and brown dwarfs in wide orbits
Authors: Bonavita Mariangela , Jayawardhana Ray , Janson Markus , Lafrenière David
Published: November 2011

Recent direct imaging discoveries of exoplanets have raised new questions about the formation of very low-mass objects in very wide orbits. Several explanations have been proposed, but all of them run into some difficulties, trying to explain all the properties of these objects at once. Here we present the results of a deep adaptive optics imaging survey of 85 stars in the Upper Scorpius young association with Gemini, reaching contrasts of up to 10 magnitudes. In addition to identifying numerous stellar binaries and a few triples, we also found several interesting sub-stellar companions. We discuss the implications of these discoveries, including the possibility of a second pathway to giant planet formation.
Understanding exoplanet formation, structure and evolution in 2010
Authors: Chabrier Gilles , Leconte Jérémy , Baraffe Isabelle
Published: November 2011

In this short review, we summarize our present understanding (and non-understanding) of exoplanet formation, structure and evolution, in the light of the most recent discoveries. Recent observations of transiting massive brown dwarfs seem to remarkably confirm the predicted theoretical mass-radius relationship in this domain. This mass-radius relationship provides, in some cases, a powerful diagnostic to distinguish planets from brown dwarfs of same mass, as for instance for Hat-P-20b. If confirmed, this latter observation shows that planet formation takes place up to at least 8 Jupiter masses. Conversely, observations of brown dwarfs down to a few Jupiter masses in young, low-extinction clusters strongly suggests an overlapping mass domain between (massive) planets and (low-mass) brown dwarfs, i.e. no mass edge between these two distinct (in terms of formation mechanism) populations. At last, the large fraction of heavy material inferred for many of the transiting planets confirms the core-accretion scenario as been the dominant one for planet formation.
Exoplanet atmospheres: A theoretical outlook
Authors: Seager Sara
Published: November 2011

With over two dozen exoplanet atmospheres observed today, the field of exoplanet atmospheres is solidly established. The highlights of exoplanet atmosphere studies include: detection of molecular spectral features; constraints on atmospheric vertical temperature structure; detection of day-night temperature gradients; and a new numerical approach to atmosphere temperature and abundance retrieval. As hot Jupiter observations and interpretation are maturing, the next frontier is super Earth atmospheres. Theoretical models of super Earth atmospheres are moving forward with observational hopes pinned on the James Webb Space Telescope, scheduled for launch in 2014. Further in the future lies direct imaging attempts to answer the enigmatic and ancient question, “Are we alone?” via atmospheric biosignatures.
The diverse origin of exoplanets' eccentricities & inclinations
Authors: Ford Eric B.
Published: November 2011

Radial velocity surveys have discovered over 400 exoplanets. While measuring eccentricities of low-mass planets remains a challenge, giant exoplanets display a broad range of orbital eccentricities. Recently, spectroscopic measurements during transit have demonstrated that the short-period giant planets (“hot-Jupiters”) also display a broad range of orbital inclinations (relative to the rotation axis of the host star). Both properties pose a challenge for simple disk migration models and suggest that late-stage orbital evolution can play an important role in determining the final architecture of planetary systems. One possible formation mechanism for the inclined hot-Jupiters is some form of eccentricity excitation (e.g., planet scattering, secular perturbations due to a distant planet or wide binary) followed tidal circularization. The planet scattering hypothesis also makes predictions for the population of planets at large separations. Recent discoveries of planets on wide orbits via direct imaging and highly anticipated results from upcoming direct imaging campaigns are poised to provide a new type of constraint on planet formation. This proceedings describes recent progress in understanding the formation of giant exoplanets.
Towards habitable Earths with EUCLID and WFIRST
Authors: Beaulieu Jean-Philippe , Bennett David P. , Kerins Eamonn , Penny Matthew
Published: November 2011

The discovery of extrasolar planets is arguably the most exciting development in astrophysics during the past 15 years, rivalled only by the detection of dark energy. Two projects are now at the intersection of the two communities of exoplanet scientists and cosmologists: EUCLID, proposed as an ESA M-class mission; and WFIRST, the top-ranked large space mission for the next decade by the Astro 2010 Decadal Survey report. The missions are to have several important science programs: a dark energy survey using weak lensing, baryon acoustic oscillations, Type Ia supernova, a survey of exoplanetary architectures using microlensing, and different surveys. The WFIRST and EUCLID microlensing planet search programs will provide a statistical census of exoplanets with masses greater than the mass of Mars and orbital separations ranging from 0.5 AU outwards, including free-floating planets. This will include analogs of all Solar System planets except for Mercury, as well as most types of planets predicted by planet formation theories. In combination with Kepler's census of planets in shorter period orbits, EUCLID and WFIRST's planet search programs will provide a complete statistical census of the planets that populate our Galaxy. As of today, EUCLID is proposed to ESA as a M class mission (the result of the selection will be known in october 2011). We are presenting here preliminary results about the expected planet yields. WFIRST has just appointed a Science Definition Team.
Super-Earths and life - a fascinating puzzle: Example GJ 581d
Authors: Kaltenegger Lisa , Segura Antígona , Mohanty Subhanjoy
Published: November 2011

Spurred by the recent large number of radial velocity detections and the discovery of several transiting system and among those two planets, that are consistent with rocky composition, the study of planets orbiting nearby stars has now entered an era of characterizing massive terrestrial planets (aka super-Earths). One prominent question is, if such planets could be habitats. Here we focuss on one particular planet Gl581d. For Earth-like assumptions, we investigate the minimal atmospheric conditions for Gl581d to be potentially habitable at its current position, and if habitability could be remotely detected in its spectra. The model we present here only represents one possible nature an Earth-like composition - of a planet like Gl581d in a wide parameter space. Future observations of atmospheric features of such super-Earths can be used to examine if our concept of habitability and its dependence on the carbonate-silicate cycle is correct, and also assess whether Gl581d is indeed the first detected habitable super-Earth. We will need spectroscopic measurements to probe the atmosphere of such planets to break the degeneracy of mass and radius measurements and characterize a planetary environment.
Metallicity of M dwarfs: The link to exoplanets
Authors: Neves V. , Bonfils X. , Santos N. C.
Published: November 2011

The determination of the stellar parameters of M dwarfs is of prime importance in the fields of galactic, stellar and planetary astronomy. M stars are the least studied galactic component regarding their fundamental parameters. Yet, they are the most numerous stars in the galaxy and contribute to most of its total (baryonic) mass. In particular, we are interested in their metallicity in order to study the star-planet connection and to refine the planetary parameters. As a preliminary result we present a test of the metallicity calibrations of Bonfils et al. (2005), Johnson & Apps (2009), and Schlaufman & Laughlin (2010) using a new sample of 17 binaries with precise V band photometry.
Observable signatures of dust evolution mechanisms which shape the planet forming regions
Authors: Panić Olja , Birnstiel Tilman , Visser Ruud , van Kampen Elco
Published: November 2011

Overdensity of dust with respect to the gas in the planet forming regions is a crucial prerequisite to form larger bodies and eventually planets. We use a state-of-the-art code to simulate dust evolution processes in gas-rich circumstellar discs, including the viscous gas evolution. We find significant deviations of the radial distribution of dust from that of the gas as early as 1-2Myr. These deviations are closely related to the efficiency of grain growth. Apparent discrepancies between dust and gas distributions are suggested by the current millimetre interferometer observations, and ALMA will allow us tointerpret any such discrepancies in the context of dust evolution.
Observational signs of planet infall and Roche lobe overflow outward migration
Authors: Taylor Stuart F. , Jiang Ing-Guey
Published: November 2011

Outward migration of planets due to Roche lobe overflow may play an important role in producing the presently observed distribution of planet parameters. We suggest that many of the currently known short period planets may have already migrated into the Roche distance from the star, and then deposited at their current semi-major axes by being migrated outwards due to angular momentum transfer from an episode of Roche lobe overflow (RLO). This RLO outward migration (RLOOM) could be sustained in the region where planetary radius increases with decreasing mass. We are modeling how RLOOM may leave what kind of planet parameter statistics. This modeling seeks to predict what observable signs of RLOOM there may be. Overflow of planetary mass may leave behind characteristic hot dust and gas as well as produce luminous signatures.
Detectability of Earth mass planets with RV techniques around Sun-like stars. The example of the Sun
Authors: Lagrange Anne-Marie , Meunier Nadege , Desort Morgan
Published: November 2011

We present the results of detailed simulations of the RV and astrometric signals expected from the Sun, when taking into account its activity (spots, plages, convection). To do so, we considered all structures (2,000,000) identified on the Sun surface over a full cycle. We show that the Sun activity would prevent the detection of the Earth in the Habitable Zone with RV technics with today or future forthcoming instruments, mainly because of inhomogeneous convection. We also show that the activity-induced signal would be comparatively easier for the astrometric detection of the Earth of similar planets.
Imaging faint companions very close to stars
Authors: Serabyn Eugene , Mawet Dimitri , Burruss Rick
Published: November 2011

A vortex coronagraph on our extreme adaptive optics “well-corrected subaperture” on the Hale telescope has recently allowed the imaging of the triple-planet HR8799 system with a 1.5 m subaperture. Moreover, a faint, low-mass companion to a second star was imaged only one diffraction beam width away from the primary. These results illustrate the potential of the vortex coronagraph, which can enable exoplanet imaging and characterization with smaller telescopes than previously thought.
) Cues-of-Being-Watched Paradigm Revisited
Authors: Carbon Claus-Christian , Hesslinger Vera M.
Published: November 2011

Bateson, Nettle, and Roberts (2006 ) provided an intriguing experimental paradigm for investigating the effects of social cues on cooperative behavior in a real-world setting. By placing an image of a pair of eyes on a cupboard door above an “honesty box” for hot beverages, they induced substantially higher amounts of contributions. As this finding has a significant impact on the social sciences and assumptions concerning the meaning of social cues for human behavior, we systematically reanalyzed their procedure and statistical analyses and tried to replicate the results while taking personality factors into account. The overall results of our analysis and replication efforts do not unequivocally support conclusions about the effects of eyes as social cues for cooperative behavior. Problems start with the definition of cooperative behavior, underspecified methods, confounding variables, invalid statistical analyses, and a lack of insight into the factors – including personality factors – that modulate the expected effect. A follow-up experiment with 138 participants showed no effect of eyes on socially relevant concepts and attitudes. Furthermore, none of the personality factors that, according to Bateson et al.’s explanation of reputational concerns, might be a source of effects interacted with any of the measures we used to operationalize these socially relevant concepts and attitudes.
Sequential Patterning of Facial Actions in the Production and Perception of Emotional Expressions
Authors: With Stéphane , Kaiser Susanne
Published: November 2011

Despite the fact that the facial expressions of emotions are naturally dynamic social signals, their communicative value has typically been studied using static photographs. In this paper, we focus on the perception of emotions from naturally occurring, dynamic facial displays produced in social interactions. In describing their impressions of 200 video records of spontaneous emotional expressions produced during a face-to-face emotional sharing task, observers were found to agree on five emotional factors: enjoyment, hostility, embarrassment, surprise, and sadness. FACS coding and sequential analysis using a pattern detection algorithm showed that recordings rated high on one emotional factor were characterized by unique sequences of facial actions coordinated with eye and/or gaze actions. Our results suggest that the dynamic unfolding of facial displays and their combination with additional nonverbal signals may play an important and still under-investigated role in emotion perception in face-to-face interactions.
Spectroscopic studies of the $\tilde{A}$Ã–$\tilde{X}$X̃ electronic spectrum of the β-hydroxyethylperoxy radical: Structure and dynamics
Authors: Chen Ming-Wei , Just Gabriel M. P. , Codd Terrance , Miller Terry A.
Published: November 2011

The jet-cooled $\tilde{A}$Ã–$\tilde{X}$X̃ near IR origin band spectra of the G1G2G3 conformer of four β-hydroxyethylperoxy isotopologues, β-HEP (HOCH2CH2OO), β-DHEP (DOCH2CH2OO), β-HEP-d4 (HOCD2CD2OO), and β-DHEP-d4 (DOCD2CD2OO), have been recorded by a cavity ringdown spectrometer with a laser source linewidth of ∼70 MHz. The spectra of all four isotopologues have been analyzed and successfully simulated with an evolutionary algorithm, confirming the cyclic structure of the molecule responsible for the observed origin band. The analysis also provides experimental $\tilde{A}$Ã and $\tilde{X}$X̃ state rotational constants and the orientation of the transition dipole moment in the inertial axis system; these quantities are compared to results from electronic structure calculations. The observed, broad linewidth (Δν > 2 GHz) is attributed to a shortened lifetime of the $\tilde{A}$Ã state associated with dynamics along the reaction path for hydrogen transfer from the OH to OO group.
Design of experiments to observe radiation stabilized Rayleigh-Taylor instability growth at an embedded decelerating interface
Authors: Huntington C. M. , Kuranz C. C. , Drake R. P. , Miles A. R. , Prisbrey S. T. , Park H.-S. , Robey H. F. , Remington B. A.
Published: November 2011

Using a hohlraum produced thermal x-ray drive at the National Ignition Facility (NIF) to create pressure by material ablation, a shock exceeding 200 Mbar can be driven through a planar, solid-density target and into a lower-density foam material. The shock driven through the foam is strongly radiative, and this radiation significantly alters the dynamics of the system, including those of the Rayleigh-Taylor (RT) fluid instability at the interface between the two materials. We discuss here the design of experiments that can produce such radiative conditions. One will be able to compare the observed growth rates with an extensive body of hydrodynamic experiments performed previously. In this paper, we describe a set of 1D simulations performed to understand the mechanisms of stabilization in a strongly radiative Rayleigh-Taylor unstable system. Simulation results are used to calculate modified analytic RT growth rates which have been proposed in the literature. Calculations predict reduced RT spike growth as a result of increases in density gradient scale length and mass ablation from the unstable interface. This work has direct applicability to the observable features in upcoming NIF experiments.
Equation of state of partially ionized argon plasma
Authors: Chen Q. F. , Zheng J. , Gu Y. J. , Chen Y. L. , Cai L. C.
Published: November 2011

The ionization degree, Hugoniots, and equation of state of partially ionized argon plasma were calculated by using self-consistent fluid variational theory for temperature of 6–50 kK and density of 0.05–4.0 g/cm3. The corrections of lowering of ionization energy of fluid argon caused by the interactions among all particles of Ar, Ar+, Ar2+, and e have been taken into consideration in terms of the correlation contributions to the chemical potential which is determined self-consistently by the free energy function. The initial density effects of gas argon under shock compression have been discussed. Comparison is performed with available shock-wave experiments and other theoretical calculations.
Maximal slicings in spherical symmetry: Local existence and construction
Authors: Cordero-Carrión Isabel , Ibáñez José María , Morales-Lladosa Juan Antonio
Published: November 2011

We show that any spherically symmetric spacetime locally admits a maximal space-like slicing and we give a procedure allowing its construction. The designed construction procedure is based on purely geometrical arguments and, in practice, leads to solve a decoupled system of first-order quasi-linear partial differential equations. We have explicitly built up maximal foliations in Minkowski and Friedmann spacetimes. Our approach admits further generalizations and efficient computational implementation. As by-product, we suggest some applications of our work in the task of calibrating numerical relativity complex codes, usually written in Cartesian coordinates.
Improved reliability of magnetic field programmable gate arrays through the use of memristive tunnel junctions
Authors: Münchenberger Jana , Krzysteczko Patryk , Reiss Günter , Thomas Andy
Published: November 2011

Since the recent successful implementation of the long-hypothesized memristor, its use in neuronal computing and in the reproduction of biological neural networks has gained increasing attention. In addition to the development of these new applications, the growing number of devices with memristive properties is promising to improve already established technologies. Herein, we use the recently reported memristance in magnesium-oxide-based magnetic tunnel junctions to improve the error tolerance in magnetic random access memory and magnetic field programmable logic arrays.
Nicotinamide mononucleotide adenylyl transferase 1 protects against acute neurodegeneration in developing CNS by inhibiting excitotoxic-necrotic cell death
Authors: Verghese Philip B. , Sasaki Yo , Yang Donghan , Stewart Floy , Sabar Fatima , Finn Mary Beth , Wroge Christine M. , Mennerick Steven , Neil Jeffrey J. , Milbrandt Jeffrey , Holtzman David M.
Published: November 2011

Hypoxic-ischemic (H-I) injury to the developing brain is a significant cause of morbidity and mortality in humans. Other than hypothermia, there is no effective treatment to prevent or lessen the consequences of neonatal H-I. Increased expression of the NAD synthesizing enzyme nicotinamide mononucleotide adenylyl transferase 1 (Nmnat1) has been shown to be neuroprotective against axonal injury in the peripheral nervous system. To investigate the neuroprotective role of Nmnat1 against acute neurodegeneration in the developing CNS, we exposed wild-type mice and mice overexpressing Nmnat1 in the cytoplasm (cytNmnat1-Tg mice) to a well-characterized model of neonatal H-I brain injury. As early as 6 h after H-I, cytNmnat1-Tg mice had strikingly less injury detected by MRI. CytNmnat1-Tg mice had markedly less injury in hippocampus, cortex, and striatum than wild-type mice as assessed by loss of tissue volume 7 d days after H-I. The dramatic protection mediated by cytNmnat1 is not mediated through modulating caspase3-dependent cell death in cytNmnat1-Tg brains. CytNmnat1 protected neuronal cell bodies and processes against NMDA-induced excitotoxicity, whereas caspase inhibition or B-cell lymphoma-extra large (Bcl-XL) protein overexpression had no protective effects in cultured cortical neurons. These results suggest that cytNmnat1 protects against neonatal HI-induced CNS injury by inhibiting excitotoxicity-induced, caspase-independent injury to neuronal processes and cell bodies. As such, the Nmnat1 protective pathway could be a useful therapeutic target for acute and chronic neurodegenerative insults mediated by excitotoxicity.
Large-scale motif discovery using DNA Gray code and equiprobable oligomers
Authors: Ichinose Natsuhiro , Yada Tetsushi , Gotoh Osamu
Published: November 2011

Motivation: How to find motifs from genome-scale functional sequences, such as all the promoters in a genome, is a challenging problem. Word-based methods count the occurrences of oligomers to detect excessively represented ones. This approach is known to be fast and accurate compared with other methods. However, two problems have hampered the application of such methods to large-scale data. One is the computational cost necessary for clustering similar oligomers, and the other is the bias in the frequency of fixed-length oligomers, which complicates the detection of significant words.

Results: We introduce a method that uses a DNA Gray code and equiprobable oligomers, which solve the clustering problem and the oligomer bias, respectively. Our method can analyze 18 000 sequences of ~1 kbp long in 30 s. We also show that the accuracy of our method is superior to that of a leading method, especially for large-scale data and small fractions of motif-containing sequences.

Availability: The online and stand-alone versions of the application, named Hegma, are available at our website: http://www.genome.ist.i.kyoto-u.ac.jp/~ichinose/hegma/

Contact:  ichinose@i.kyoto-u.ac.jp; o.gotoh@i.kyoto-u.ac.jp
AURA: Atlas of UTR Regulatory Activity
Authors: Dassi E. , Malossini A. , Re A. , Mazza T. , Tebaldi T. , Caputi L. , Quattrone A.
Published: November 2011

Summary: The Atlas of UTR Regulatory Activity (AURA) is a manually curated and comprehensive catalog of human mRNA untranslated regions (UTRs) and UTR regulatory annotations. Through its intuitive web interface, it provides full access to a wealth of information on UTRs that integrates phylogenetic conservation, RNA sequence and structure data, single nucleotide variation, gene expression and gene functional descriptions from literature and specialized databases.

Availability:  http://aura.science.unitn.it

Contact:  aura@science.unitn.it; dassi@science.unitn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Fast computation of minimum hybridization networks
Authors: Albrecht Benjamin , Scornavacca Celine , Cenci Alberto , Huson Daniel H.
Published: November 2011

Motivation: Hybridization events in evolution may lead to incongruent gene trees. One approach to determining possible interspecific hybridization events is to compute a hybridization network that attempts to reconcile incongruent gene trees using a minimum number of hybridization events.

Results: We describe how to compute a representative set of minimum hybridization networks for two given bifurcating input trees, using a parallel algorithm and provide a user-friendly implementation. A simulation study suggests that our program performs significantly better than existing software on biologically relevant data. Finally, we demonstrate the application of such methods in the context of the evolution of the Aegilops/Triticum genera.

Availability and implementation: The algorithm is implemented in the program Dendroscope 3, which is freely available from www.dendroscope.org and runs on all three major operating systems.

Contact:  scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mesorhizobium silamurunense sp. nov., isolated from root nodules of Astragalus species
Authors: Zhao Chun Tian , Wang En Tao , Zhang Yan Ming , Chen Wen Feng , Sui Xin Hua , Chen Wen Xin , Liu Hong Can , Zhang Xiao Xia
Published: November 2011

Four rhizobial strains representing a previously defined novel group in the genus

Mesorhizobium

and isolated from Astragalus species in China were further characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that these Gram-negative bacteria belonged to the genus

Mesorhizobium

, with

Mesorhizobium plurifarium

LMG 11892T as the closest neighbour sharing a sequence similarity of 99.8 %. Comparative sequence analysis of the atpD, recA, glnII, rpoB, nodC and nifH genes, SDS-PAGE of whole-cell soluble proteins, DNA–DNA hybridization, fatty acid profiles and a series of phenotypic and physiological tests differentitated the novel group from all recognized species of the genus

Mesorhizobium

. Based on the data obtained in the present and previous studies, this group represents a novel species within the genus

Mesorhizobium

, for which the name Mesorhizobium silamurunense sp. nov. is proposed. The type strain is CCBAU 01550T ( = HAMBI 3029T = LMG 24822T), and could form effective nodules on Astragalus membranaceus, Astragalus adsurgens and Caragana intermedia, and ineffective nodules on Phaseolus vulgaris in cross-nodulation tests.