bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental analysis of innovative dissipative bolted double split tee beam‐to‐column connections
Authors: Latour Massimo , Piluso Vincenzo , Rizzano Gianvittorio
Published: June 2011

The use of double split tee (DST) connections in seismic zones may represent an interesting solution from the technological point of view because of easy substitution of damaged components after destructive seismic events. But despite this significant advantage, partial‐strength DST connections have found limited application so far because their use requires that tee elements are characterized by high plastic deformation capacity to assure adequate energy dissipation. Therefore, in order to overcome the limitations to the energy dissipation capacity of traditional DST connections due to significant pinching of hysteresis loops and aiming at the development of a structural solution able to withstand severe seismic events without damage to members and connecting elements, this paper proposes two different innovative dissipative solutions for DST connections and investigates their performance by means of an experimental programme whose results are presented and discussed.
Review of steel buckling‐restrained braces
Authors: Della Corte Gaetano , D’Aniello Mario , Landolfo Raffaele , Mazzolani Federico M.
Published: June 2011

Buckling‐restrained braces (BRBs) are a relatively recent development in the field of seismic‐resistant steel structures. Their distinctive feature is the non‐buckling behaviour typically achieved by encasing a steel core in a concrete‐filled tube, but alternatives have been proposed. Restraining the brace from buckling enhances ductility significantly and allows a symmetric response under tension or compression forces. The design of BRB frames must consider a number of specific issues that are currently not covered by European standards and regulations. This paper presents a brief summary of the most recent research results and attempts to summarize the basic design issues as they emerge from both research and the codification rules of non‐European Countries. Conclusions are drawn regarding future research required to address the development of design rules in Europe, too.
Toughness requirements for plastic design with structural steel
Authors: Feldmann Markus , Eichler Björn , Schäfer Dirk , Sedlacek Gerhard , Vayas Ioannis , Karlos Vasilis , Spiliopoulos Andreas
Published: June 2011

This report deals with the results of an international research project ”Plastotough”, the aim of which is to discover the toughness requirements for structural steel to make it suitable for plastic design for ”static loads” and for loads that vary over time, as from seismic events. These toughness requirements should be specified as the Charpy energy value KVUS in the upper shelf domain of the toughness‐temperature diagram and as the extension of KVUS to the minimum temperature TUS for which it is still valid. This report, after recalling empirical rules for toughness requirements, first gives the methodological tools from fracture mechanics and damage mechanics to tackle the task. The use of these tools is connected with experimental tests on specimens that are detailed such that they are representative of local (from notch effects) and global (from plastic hinges with plastic rotations) ductility demands. The steels for the test specimens were taken from regular ”European production”; rolled sections in particular exhibit a quality level that far exceeds the minimum requirements of EN 10025. For the steels considered, it was proved that they follow the EricksonKirk correlation between the T27J values and TUS so that they can be classified in a group of steels together with pressure vessel steels and naval steels. All strain requirements from local strain raisers and from global plastic rotations could be met on the safe side using the fracture mechanics and damage mechanics resistances determined for these steels. For seismic design in particular it could be shown that the cracking associated with ultra‐low‐cycle fatigue is not relevant for buildings if the behaviour factor q is determined using reasonable limits for inter‐storey drift. Therefore, the key conclusion is that for the safe use of plastic design in ”static” and ”seismic” situations, the elevated level of toughness quality of steels usually available from European producers must be used. To this end it is recommended to specify these steels either in the context of brandnames or by additional options in EN 10025.
The Modern Teahouse — a contemporary nomadic building
Authors: Schmid Gerd
Published: June 2011

The Modern Teahouse is a small nomadic building formTL designed together with Kengo Kuma. It is used for Japanese tea ceremonies in the garden of the ”Museum für Angewandte Kunst” in Frankfurt am Main. The mattress‐like structure can be erected and taken down by just four people. The internal air pressure of this single‐chamber air house is 1500 Pa — only 1 % that of a high‐pressure beam but five times higher than a normal pneumatic structure. The Modern Teahouse ”wanders” between the entrance hall of the museum and a little hill in the museum garden. When it is not in use, it is packed away on a trolley.
Assessing bee species richness in two Mediterranean communities: importance of habitat type and sampling techniques
Authors: Nielsen Anders , Steffan‐Dewenter Ingolf , Westphal Catrin , Messinger Olivia , Potts Simon G. , Roberts Stuart P. M. , Settele Josef , Szentgyörgyi Hajnalka , Vaissière Bernard E. , Vaitis Michalis , Woyciechowski Michal , Bazos Ioannis , Biesmeijer Jacobus C. , Bommarco Riccardo , Kunin William E. , Tscheulin Thomas , Lamborn Ellen , Petanidou Theodora
Published: June 2011

The decline of bees has raised concerns regarding their conservation and the maintenance of ecosystem services they provide to bee‐pollinated wild flowers and crops. Although the Mediterranean region is a hotspot for bee species richness, their status remains poorly studied. There is an urgent need for cost‐effective, reliable, and unbiased sampling methods that give good bee species richness estimates. This study aims: (a) to assess bee species richness in two common Mediterranean habitat types: semi‐natural scrub (phrygana) and managed olive groves; (b) to compare species richness in those systems to that of other biogeographic regions, and (c) to assess whether six different sampling methods (pan traps, variable and standardized transect walks, observation plots and trap nests), previously tested in other European biogeographic regions, are suitable in Mediterranean communities. Eight study sites, four per habitat type, were selected on the island of Lesvos, Greece. The species richness observed was high compared to other habitat types worldwide for which comparable data exist. Pan traps collected the highest proportion of the total bee species richness across all methods at the scale of a study site. Variable and standardized transect walks detected the highest total richness over all eight study sites. Trap nests and observation plots detected only a limited fraction of the bee species richness. To assess the total bee species richness in bee diversity hotspots, such as the studied habitats, we suggest a combination of transect walks conducted by trained bee collectors and pan trap sampling.
Effect of Varietal Differences on Composition and Thermal Characteristics of Avocado Oil
Authors: Yanty N. A. M. , Marikkar J. M. N. , Long K.
Published: June 2011

A study was carried out to compare the characteristics of oils from three Malaysian avocado (Persea americana) cultivars with those of the oil from the Australian Hass avocado variety. Oil samples extracted from matured‐avocado fruits were assessed for basic physico‐chemical parameters, fatty acid and triacylglycerol (TAG) compositions, and melting and solidification characteristics. In comparison to Hass variety, the oil contents of the local avocado cultivars were significantly lower and found to be mostly in semisolid form. As a common feature, oils of both local cultivars and Hass variety are found to have oleic acid as the most dominant fatty acid. However, there are differences between them with regard to the proportional distributions of palmitic and linoleic acids. While the major TAG of local avocado cultivars were POO, followed by POL, OOO and PPO, the dominant TAG of Hass variety were OOO, followed by PPO, OOL and POL. Due to these differences in fatty acid and TAG distributional patterns, the oils of local avocado cultivars are found to possess iodine value, slip melting point, melting and solidification characteristics, which are completely different from those of the imported Hass avocado variety.
II Freestanding Sculpture
Authors: Sparkes Brian A.
Published: June 2011

In 2003, the 150th anniversary of the birth of Adolf Furtwängler was celebrated with an exhibition in his home town of Freiburg, accompanied by a memorial volume and an international symposium. His influence on Greek sculptural studies through emphasis on the search for individual craftsmen via Roman copies continues, particularly in Germany and the USA. The mystery of the ‘whodunit’ is still strong, and the cult of the creative artist is too deeply ingrained in our own thinking to be totally jettisoned for other, more impersonal considerations. There is such an innate desire to link a work of art to a name that, over the years, there has been a tendency to concentrate on the few names that have been vouchsafed to us from classical texts and the random discovery of inscriptions carrying the names of sculptors (the earliest dating from c.600 BC). Recent major exhibitions have centred round the sculptors Polykleitos, Praxiteles, and Lysippos, and there are studies that have highlighted the conjectural personalities of these and other named artists. Pollitt has declared his allegiance to this traditional approach:

Those who believe that ancient Greek art, like that of all other places and times, was the result of the insights, instincts, taste and choices of individual artists and not the product of impersonal, mechanical, evolutionary forces have good reason for wanting to carry on the tradition of Furtwängler.
A generalized power law approximation for fluvial incision of bedrock channels
Authors: Gasparini Nicole M. , Brandon Mark T.
Published: June 2011

Sediment flux is known to influence bedrock incision rates in mountain rivers. Although the widely used stream power incision model lacks any explicit representation of sediment flux, the model appears to work in a variety of real settings. We address this apparent contradiction using numerical experiments to explore the morphology of fluvial landscapes evolved with four different incision models, three of which include the influence of sediment flux on incision rate. The numerical landscapes have different spatial patterns of uplift and are at steady state. We analyze these landscape using the common “stream power” approach, which views incision rates to be primarily a function of the local channel gradient S and the upstream drainage area A. We find that incision rates I for these landscapes are well described by an empirical power law equation I = K′Am′Sn′. This equation is functionally equivalent to the widely used stream power model, with the important distinction that the parameters K′, m′, and n′ are entirely empirical. These parameters take on constant values within a single landscape, but can otherwise be quite different between landscapes mainly due to differences in the pattern of rock uplift within the drainage. In particular, the parameters m′ and n′ decrease as the rate of rock uplift becomes more focused in the upland part of a mountain belt. The parameter m′ is particularly important in that it describes the sensitivity of a tectonically active mountain belt to changes in precipitation or tectonic accretion. It also defines how incision rates will change as the discharge becomes flashier.
The role of trimerization in the osmoregulated betaine transporter BetP
Authors: Perez Camilo , Khafizov Kamil , Forrest Lucy R , Krämer Reinhard , Ziegler Christine
Published: June 2011

The osmoregulated betaine transporter BetP is a stable trimer. Structural studies have shown that individual protomers can adopt distinct transport conformations, implying a functional role for the trimeric state in transport, although the role of trimerization in regulation is not yet understood. We designed putative monomeric mutants by molecular‐dynamics simulations and in silico alanine‐scanning mutagenesis. Several mutants including BetP‐W101A/T351A were monomeric in detergent as well as in the membrane, as shown by blue native gel electrophoresis, crosslinking and electron microscopy. This monomeric form retains the ability to accumulate betaine, but is no longer regulated by hyperosmotic shock.
State‐ and Payer‐Specific Estimates of Annual Medical Expenditures Attributable to Obesity
Authors: Trogdon Justin G. , Finkelstein Eric A. , Feagan Charles W. , Cohen Joel W.
Published: June 2011

The goal of this study is to expand prior analyses by presenting current state‐level estimates of the costs of obesity in total and separately for Medicare and Medicaid. Quantifying current Medicare and Medicaid expenditures attributable to obesity is important because high public sector costs of obesity have been a primary motivation for publicly funded obesity prevention efforts at the state level. We also present estimates of the obesity‐attributable fraction (OAF) of total, Medicare, and Medicaid expenditures and the percentage of total obesity costs within each state that is funded by the public sector. We used the 2006 Medical Expenditure Panel Survey, nationally representative data that include information on obesity and medical expenditures, to generate an equation that predicts annual medical expenditures as a function of obesity status. We used the 2006 Behavioral Risk Factor Surveillance System, state representative data, and the equation generated from the national model to predict state (and payer within state) expenditures and the fraction of expenditures attributable to obesity for each state. Across states, annual medical expenditures would be between 6.7 and 10.7% lower in the absence of obesity. Between 22% (Virginia) and 55% (Rhode Island) of the state‐level costs of obesity are financed by the public sector via Medicare and Medicaid. The high costs of obesity at the state level emphasize the need to prevent and control obesity as a way to manage state medical costs.
High‐Volume Exercise Program in Obese Bariatric Surgery Patients: A Randomized, Controlled Trial
Authors: Shah Meena , Snell Peter G. , Rao Sneha , Adams‐Huet Beverley , Quittner Claudia , Livingston Edward H. , Garg Abhimanyu
Published: June 2011

Weight regain is a problem among many bariatric surgery patients. Whether a high‐volume exercise program (HVEP), a strategy to limit weight regain, is feasible in these patients is unknown. The feasibility of an HVEP in obese post‐bariatric‐surgery patients was determined by randomizing 33 Roux‐en‐Y gastric bypass (RYGB) and gastric banding (GB) surgery patients with a mean BMI of 41 ± 6 kg/m2 to an HVEP or control group for 12 weeks. The HVEP group was instructed to expend ≥2,000 kcal/week in moderate‐intensity exercise. All patients were counseled to limit energy intake. Treatment effect was assessed by repeated measures analysis. During the last 4 weeks of the study, 53% of the HVEP group expended ≥2,000 kcal/week and 82% expended ≥1,500 kcal/week. Step count, reported time spent and energy expended during moderate physical activity, maximal oxygen consumption relative to weight, and incremental area under the postprandial blood glucose curve were significantly improved over 12 weeks in the HVEP group compared to controls (group‐by‐week effect: P = 0.009–0.03). Both groups reported significant improvement in some quality‐of‐life scales. Changes in weight, energy and macronutrient intake, resting energy expenditure (REE), fasting lipids and glucose, and fasting and postprandial insulin concentrations were not different between the two groups. HVEP is feasible in about 50% of the patients and enhances physical fitness and reduces postprandial blood glucose in bariatric surgery patients.
Synchronization of continuous complex networks based on asynchronously discontinuous controllers
Authors: Xiong Wenjun , Yu Wenwu
Published: June 2011

In this paper, our purpose is to design asynchronously discontinuous controllers (ADCs) to achieve the synchronization of linear coupled continuous complex network models (LCCNMs). The LCCNMs with ADCs are proposed for two reasons: (1) The controllers may not transmit their information simultaneously; (2) The performing process of the controllers is difficult to be active continuously. The synchronization is then discussed for the designed network models. Moreover, time-delays are considered into the designed models and the synchronization is also presented.
Acoustic wave levitation: Handling of components
Authors: Vandaele Vincent , Delchambre Alain , Lambert Pierre
Published: June 2011

Apart from contact micromanipulation, there exists a large variety of levitation techniques among which standing wave levitation will be proposed as a way to handle (sub)millimetric components. This paper will compare analytical formulas to calculate the order of magnitude of the levitation force. It will then describe digital simulation and experimental levitation setup. Stable levitation of various components (cardboard, steel washer, ball, ceramic capacity, water droplet) was shown along 5 degrees of freedom: The only degree of freedom that could not be mastered was the rotation about the symmetry axis of the acoustic field. More importantly, the present work will show the modification of the orientation of the radial force component in the presence of an object disturbing the acoustic field. This property can be used as a new feeding strategy as it means that levitating components are spontaneously pushed toward grippers in an acoustic plane standing wave.
Domain engineered switchable strain states in ferroelectric (011) [Pb(Mg1/3Nb2/3)O3](1−x)-[PbTiO3]x (PMN-PT, x≈0.32) single crystals
Authors: Wu Tao , Zhao Ping , Bao Mingqiang , Bur Alexandre , Hockel Joshua L. , Wong Kin , Mohanchandra Kotekar P. , Lynch Christopher S. , Carman Gregory P.
Published: June 2011

The ferroelectric properties of (011) [Pb(Mg1/3Nb2/3)O3](1−x)-[PbTiO3]x (PMN-PT, x≈0.32) single crystals with focus on piezoelectric strain response were reported. Two giant reversible and stable remanent strain states and tunable remanent strain properties are achieved by properly reversing the electric field from the depolarized direction. The unique piezoelectric strain response, especially along the [100] direction, mainly stems from the non-180° ferroelectric polarization reorientation in the rhombohedral phase crystal structure. Such giant strain hysteresis with tunable remanent strain properties may be useful for magnetoelectric based memory devices as well as a potential candidate for other applications.
A continuous-wave optical parametric oscillator around 5-μm wavelength for high-resolution spectroscopy
Authors: Krieg J. , Klemann A. , Gottbehüt I. , Thorwirth S. , Giesen T. F. , Schlemmer S.
Published: June 2011

We present a continuous-wave optical parametric oscillator (OPO) capable of high resolution spectroscopy at wavelengths between 4.8 μm and 5.4 μm. It is based on periodically poled lithium niobate (PPLN) and is singly resonant for the signal radiation around 1.35 μm. Because of the strong absorption of PPLN at wavelengths longer than 4.5 μm, the OPO threshold rises to the scale of several watts, while it produces idler powers of more than 1 mW and offers continuous tuning over 15 GHz. A supersonic jet spectrometer is used in combination with the OPO to perform measurements of the transient linear molecule Si2C3 at 1968.2 cm−1. Fifty rovibrational transition frequencies of the ν3 antisymmetric stretching mode have been determined with an accuracy on the order of 10−4 cm−1, and molecular parameters for the ground and the v3 = 1 state have been determined most precisely.
Exploration of the relationship between topology and designability of conformations
Authors: Leelananda Sumudu P. , Towfic Fadi , Jernigan Robert L. , Kloczkowski Andrzej
Published: June 2011

Protein structures are evolutionarily more conserved than sequences, and sequences with very low sequence identity frequently share the same fold. This leads to the concept of protein designability. Some folds are more designable and lots of sequences can assume that fold. Elucidating the relationship between protein sequence and the three-dimensional (3D) structure that the sequence folds into is an important problem in computational structural biology. Lattice models have been utilized in numerous studies to model protein folds and predict the designability of certain folds. In this study, all possible compact conformations within a set of two-dimensional and 3D lattice spaces are explored. Complementary interaction graphs are then generated for each conformation and are described using a set of graph features. The full HP sequence space for each lattice model is generated and contact energies are calculated by threading each sequence onto all the possible conformations. Unique conformation giving minimum energy is identified for each sequence and the number of sequences folding to each conformation (designability) is obtained. Machine learning algorithms are used to predict the designability of each conformation. We find that the highly designable structures can be distinguished from other non-designable conformations based on certain graphical geometric features of the interactions. This finding confirms the fact that the topology of a conformation is an important determinant of the extent of its designability and suggests that the interactions themselves are important for determining the designability.
Capacities of Grassmann channels
Authors: Brádler Kamil , Jochym-O’Connor Tomas , Jáuregui Rocío
Published: June 2011

A new class of quantum channels called Grassmann channels is introduced and their classical and quantum capacity is calculated. The channel class appears in a study of the two-mode squeezing operator constructed from operators satisfying the fermionic algebra. We compare Grassmann channels with the channels induced by the bosonic two-mode squeezing operator. Among other results, we challenge the relevance of calculating entanglement measures to assess or compare the ability of bosonic and fermionic states to send quantum information to uniformly accelerated frames.
Nucleation and growth of tin whiskers
Authors: Cheng Jing , Vianco Paul T. , Zhang Bei , Li James C. M.
Published: June 2011

Pure tin film of one micron thick was evaporated onto a silicon substrate with chromium and nickel underlayers. The tinned silicon disk was bent by applying a dead load at the center and supported below around the edge to apply biaxial compressive stresses to the tin layer. After 180 C vacuum annealing for 1,2,4,6, and 8 weeks, tin whiskers/hillocks grew. A quantitative method revealed that the overall growth rate decreased with time with a tendency for saturation. A review of the literature showed in general, tin whisker growth has a nucleation period, a growth period and a period of saturation, very similar to recrystallization or phase transformation. In fact we found our data fit Avrami equation very well. This equation shows that the nucleation period was the first week.
A general approach to low noise readout of terahertz imaging arrays
Authors: Chisum Jonathan D. , Grossman Erich N. , Popović Zoya
Published: June 2011

This article describes the theory and design of an ultra-low noise electronic readout circuit for use with room temperature video-rate terahertz imaging arrays. First, the noise characteristics of various imaging detectors, including low resistance bolometers and high resistance diodes are discussed. Theoretical approaches to white and 1/f noise mitigation are examined, and a corresponding low-noise readout circuit is designed, built, and tested. It is shown that the circuit is capable of achieving detector limited noise performance for use in room temperature terahertz imaging systems. A thorough noise analysis of the circuit provides the necessary information for applying the readout circuit to any type of imaging detector, and more generally, any measurement of small signals from various source impedances in the presence of white and 1/f noise. W-band measurements of an 8-element, high-resistance detector array, and a 32-element, low-resistance detector array demonstrate the usefulness of the readout circuit. Finally, recommended circuit configurations for various detectors in the literature are provided, with theoretical performance metrics summarized.
The photovoltaic performance of ZnO nanorods in bulk heterojunction solar cells
Authors: Das N. C. , Biswas S. , Sokol Paul E.
Published: June 2011

A novel approach has been followed for synthesizing vertically aligned ZnO nanorods (ZONRs) on indium tin oxide (ITO) coated glass substrates for photovoltaic applications. The fabricated ZONR arrays have been used to construct bulk heterojunction photovoltaic devices together with pristine poly-(3-hexylthiophene) (P3HT) or (6,6)-phenyl C61 butyric acid methyl ester (PCBM) and P3HT blends, respectively. Scanning electron microscopy, X-ray diffraction, photoluminescence, UV-vis absorption spectroscopy, and photovoltaic measurements were performed to study the morphology and device performance of the prepared structures. The typical microstructure of the vertically aligned ZONR arrays plays an important role in collecting the photo-generated electrons and acts as conducting paths to the ITO electrode. Fill factor of the devices increased from 35% to 47% when the PCBM was introduced, which directly contributed to the enhancement of the power conversion efficiencies up to 1.23%.
Conductive response of a photo-excited sample in a radio-frequent driven resonance cavity
Authors: Schins Juleon M. , Talgorn Elise
Published: June 2011

An expression is derived for the perturbative response of a lumped resonance circuit to a sudden change in the circuit parameters. This expression is shown to describe also the photo-induced conductivity of a semiconductor mounted in a single-mode microwave cavity. The power dissipated in the cavity is measured in the two dimensions corresponding to time (after photo-excitation of the sample) and frequency (of the microwave driving source). Analysis of the experimental data for different semiconductor materials demonstrates the general applicability of the presented analytical expression here, by retrieving the time dependence of the sample's photo-induced conductivity.
In situ conductance measurements of copper phthalocyanine thin film growth on sapphire [0001]
Authors: Murdey Richard , Sato Naoki
Published: June 2011

The current flowing through a thin film of copper phthalocyanine vacuum deposited on a single crystal sapphire [0001] surface was measured during film growth from 0 to 93 nm. The results, expressed as conductance vs. nominal film thickness, indicate three distinct film growth regions. Conductive material forms below about 5 nm and again above 35 nm, but in the intermediate thicknesses the film conductance was observed to decrease with increasing film thickness. With the aid of ac-AFM topology images taken ex situ, the conductance results are explained based on the Stranski–Krastanov (2D + 3D) film growth mechanism, in which the formation of a thin wetting layer is followed by the growth of discrete islands that eventually coalesce into an interpenetrating, conductive network.
Second-order dispersion interactions in π-conjugated polymers
Authors: Barford William , Paiboonvorachat Nattapong , Yaron David
Published: June 2011

We calculate the ground state and excited state second-order dispersion interactions between parallel π-conjugated polymers. The unperturbed eigenstates and energies are calculated from the Pariser-Parr-Pople model using CI-singles theory. Based on large-scale calculations using the molecular structure of trans-polyacetylene as a model system and by exploiting dimensional analysis, we find that: (1) For inter-chain separations, R, greater than a few lattice spacings, the ground-state dispersion interaction, \documentclass[12pt]{minimal}\begin{document}$\Delta E_{\text{GS}}$\end{document}ΔEGS, satisfies, \documentclass[12pt]{minimal}\begin{document}$\Delta E_{\text{GS}} \sim L^2/R^6$\end{document}ΔEGS∼L2/R6 for L ≪ R and \documentclass[12pt]{minimal}\begin{document}$\Delta E_{\text{GS}} \sim L/R^5$\end{document}ΔEGS∼L/R5 for R ≪ L, where L is the chain length. The former is the London fluctuating dipole-dipole interaction while the latter is a fluctuating line dipole-line dipole interaction. (2) The excited state screening interaction exhibits a crossover from fluctuating monopole-line dipole interactions to either fluctuating dipole-dipole or fluctuating line dipole-line dipole interactions when R exceeds a threshold Rc, where Rc is related to the root-mean-square separation of the electron-hole excitation. Specifically, the excited state screening interaction, ΔEn, satisfies, ΔEn ∼ L/R6 for Rc < L ≪ R and ΔEn ∼ L0/R5 for Rc < R ≪ L. For R < Rc < L, ΔEn ∼ R−ν, where ν ≃ 3. We also investigate the relative screening of the primary excited states in conjugated polymers, namely the n = 1, 2, and 3 excitons. We find that a larger value of n corresponds to a larger value of ΔEn. For example, for poly(para-phenylene), ΔEn = 1 ≃ 0.1 eV, ΔEn = 2 ≃ 0.6 eV, and ΔEn = 3 ≃ 1.2 eV (where n = 1 is the 11B1 state, n = 2 is the m1A state, and n = 3 is the n1B1 state). Finally, we find that the strong dependence of ΔEn on inter-chain separation implies a strong dependency of ΔEn on density fluctuations. In particular, a 10% density fluctuation implies a fluctuation of 13 meV, 66 meV, and 120 meV for the 11B1, m1A state, and n1B1 states of poly(para-phenylene), respectively. Our results for the ground-state dispersion are applicable to all types of conjugated polymers. However, our excited state results are only applicable to conjugated polymers, such as the phenyl-based class of light emitting polymers, in which the primary excitations are particle-hole (or ionic) states.
Perpendicular magnetization of Co2FeAl full-Heusler alloy films induced by MgO interface
Authors: Wen Zhenchao , Sukegawa Hiroaki , Mitani Seiji , Inomata Koichiro
Published: June 2011

The perpendicular magnetization of Co2FeAl (CFA) full-Heusler alloy films was achieved in the structures of CFA/MgO and MgO/CFA with the perpendicular magnetic anisotropy energy density (KU) of 2–3×106 erg/cm3, which can be used as the perpendicular ferromagnetic electrodes of MgO-based magnetic tunnel junctions (MTJs) with high thermal stability at sub-50-nm dimension. The CFA thickness dependence of KU was investigated at different annealing temperatures, indicating that the perpendicular anisotropy of CFA is contributed by the interfacial anisotropy between CFA and MgO. This letter will open up a way for obtaining perpendicular magnetization of Co-based full-Heusler alloys, which is promising for further reduction in the critical current of current induced magnetization switching in MgO-based MTJ nanopillars with perpendicular full-Heusler alloy electrodes.
Uniform saturation of a strongly coupled spin system by two-frequency irradiation
Authors: Lee Jae-Seung , Khitrin Anatoly K. , Regatte Ravinder R. , Jerschow Alexej
Published: June 2011

The theoretical basis of two-frequency saturation is given here in the framework of Provotorov theory. The parameters influencing the saturation efficiency are discussed and studied experimentally using a liquid-crystalline test system. It is shown that double-frequency irradiation can be extremely efficient when the irradiation frequencies are placed at opposite sides of the characteristic frequency of the spin system, and that the frequency separation in the double-frequency irradiation can be varied over a large range. Provotorov theory is also shown to provide good insights into the experimental findings, which would otherwise be difficult to obtain from simulations.
Driving intervalley scattering and impact ionization in InAs with intense terahertz pulses
Authors: Ho I-Chen , Zhang X.-C.
Published: June 2011

We report intense terahertz (THz) pulses inducing intervalley scattering and impact ionization mechanisms in doped InAs crystals by THz pump-THz probe measurements. Two competing mechanisms are observed by varying the impurity doping type of the semiconductors and the strength of the THz field. For p-doped InAs, a cascaded carrier generation dominates while for n-doped InAs, both mechanisms have to be considered. Electron fractional occupancy between the Γ and L valleys is estimated at different field strengths.
LOCALIZING SAGITTARIUS A* AND M87 ON MICROARCSECOND SCALES WITH MILLIMETER VERY LONG BASELINE INTERFEROMETRY
Authors: Broderick Avery E. , Loeb Abraham , Reid Mark J.
Published: June 2011

With the advent of the Event Horizon Telescope (EHT), a millimeter/submillimeter very long baseline interferometer (VLBI), it has become possible to image a handful of black holes with sub-horizon resolutions. However, these images do not translate into microarcsecond absolute positions due to the lack of absolute phase information when an external phase reference is not used. Due to the short atmospheric coherence time at these wavelengths, nodding between the source and phase reference is impractical. However, here we suggest an alternative scheme which makes use of the fact that many of the VLBI stations within the EHT are arrays in their own right. With this we show that it should be possible to absolutely position the supermassive black holes at the centers of the Milky Way (Sgr A*) and M87 relative to nearby objects with precisions of roughly 1 μas. This is sufficient to detect the perturbations to Sgr A*'s position resulting from interactions with the stars and stellar-mass black holes in the Galactic cusp on year timescales, and severely constrain the astrophysically relevant parameter space for an orbiting intermediate-mass black hole, implicated in some mechanisms for producing the young massive stars in the Galactic center. For M87, it allows the registering of millimeter images, in which the black hole may be identified by its silhouette against nearby emission, and existing larger-scale radio images, eliminating present ambiguities in the nature of the radio core and inclination, opening angle, and source of the radio jet.
Dystroglycan is involved in skin morphogenesis downstream of the Notch signaling pathway
Authors: Sirour Cathy , Hidalgo Magdalena , Bello Valérie , Buisson Nicolas , Darribère Thierry , Moreau Nicole
Published: June 2011

Dystroglycan (Dg) is a transmembrane protein involved both in the assembly and maintenance of basement membrane structures essential for tissue morphogenesis, and the transmission of signals across the plasma membrane. We used a morpholino knockdown approach to investigate the function of Dg during Xenopus laevis skin morphogenesis. The loss of Dg disrupts epidermal differentiation by affecting the intercalation of multiciliated cells, deposition of laminin, and organization of fibronectin in the extracellular matrix (ECM). Depletion of Dg also affects cell–cell adhesion, as shown by the reduction of E-cadherin expression at the intercellular contacts, without affecting the distribution of β1integrins. This was associated with a decrease of cell proliferation, a disruption of multiciliated-cell intercalation, and the down-regulation of the transcription factor P63, a marker of differentiated epidermis. In addition, we demonstrated that inhibition or activation of the Notch pathway prevents and promotes transcription of X-dg. Our study showed for the first time in vivo that Dg, in addition to organizing laminin in the ECM, also acts as a key signaling component in the Notch pathway.
RINQ: Reference-based Indexing for Network Queries
Authors: Gülsoy Günhan , Kahveci Tamer
Published: June 2011

We consider the problem of similarity queries in biological network databases. Given a database of networks, similarity query returns all the database networks whose similarity (i.e. alignment score) to a given query network is at least a specified similarity cutoff value. Alignment of two networks is a very costly operation, which makes exhaustive comparison of all the database networks with a query impractical. To tackle this problem, we develop a novel indexing method, named RINQ (Reference-based Indexing for Biological Network Queries). Our method uses a set of reference networks to eliminate a large portion of the database quickly for each query. A reference network is a small biological network. We precompute and store the alignments of all the references with all the database networks. When our database is queried, we align the query network with all the reference networks. Using these alignments, we calculate a lower bound and an approximate upper bound to the alignment score of each database network with the query network. With the help of upper and lower bounds, we eliminate the majority of the database networks without aligning them to the query network. We also quickly identify a small portion of these as guaranteed to be similar to the query. We perform pairwise alignment only for the remaining networks. We also propose a supervised method to pick references that have a large chance of filtering the unpromising database networks. Extensive experimental evaluation suggests that (i) our method reduced the running time of a single query on a database of around 300 networks from over 2 days to only 8 h; (ii) our method outperformed the state of the art method Closure Tree and SAGA by a factor of three or more; and (iii) our method successfully identified statistically and biologically significant relationships across networks and organisms.

Contact:  ggulsoy@cise.ufl.edu; tamer@cise.ufl.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The role of proteosome-mediated proteolysis in modulating potentially harmful transcription factor activity in Saccharomyces cerevisiae
Authors: Bonzanni Nicola , Zhang Nianshu , Oliver Stephen G. , Fisher Jasmin
Published: June 2011

Motivation: The appropriate modulation of the stress response to variable environmental conditions is necessary to maintain sustained viability in Saccharomyces cerevisiae. Particularly, controlling the abundance of proteins that may have detrimental effects on cell growth is crucial for rapid recovery from stress-induced quiescence.

Results: Prompted by qualitative modeling of the nutrient starvation response in yeast, we investigated in vivo the effect of proteolysis after nutrient starvation showing that, for the Gis1 transcription factor at least, proteasome-mediated control is crucial for a rapid return to growth. Additional bioinformatics analyses show that potentially toxic transcriptional regulators have a significantly lower protein half-life, a higher fraction of unstructured regions and more potential PEST motifs than the non-detrimental ones. Furthermore, inhibiting proteasome activity tends to increase the expression of genes induced during the Environmental Stress Response more than those in the rest of the genome. Our combined results suggest that proteasome-mediated proteolysis of potentially toxic transcription factors tightly modulates the stress response in yeast.

Contact:  jasmin.fisher@microsoft.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity
Authors: Furlotte Nicholas A. , Kang Hyun Min , Ye Chun , Eskin Eleazar
Published: June 2011

Motivation: The analysis of gene coexpression is at the core of many types of genetic analysis. The coexpression between two genes can be calculated by using a traditional Pearson's correlation coefficient. However, unobserved confounding effects may cause inflation of the Pearson's correlation so that uncorrelated genes appear correlated. Many general methods have been suggested, which aim to remove the effects of confounding from gene expression data. However, the residual confounding which is not accounted for by these generic correction procedures has the potential to induce correlation between genes. Therefore, a method that specifically aims to calculate gene coexpression between gene expression arrays, while accounting for confounding effects, is desirable.

Results: In this article, we present a statistical model for calculating gene coexpression called mixed model coexpression (MMC), which models coexpression within a mixed model framework. Confounding effects are expected to be encoded in the matrix representing the correlation between arrays, the inter-sample correlation matrix. By conditioning on the information in the inter-sample correlation matrix, MMC is able to produce gene coexpressions that are not influenced by global confounding effects and thus significantly reduce the number of spurious coexpressions observed. We applied MMC to both human and yeast datasets and show it is better able to effectively prioritize strong coexpressions when compared to a traditional Pearson's correlation and a Pearson's correlation applied to data corrected with surrogate variable analysis (SVA).

Availability: The method is implemented in the R programming language and may be found at http://genetics.cs.ucla.edu/mmc.

Contact:  nfurlott@cs.ucla.edu; eeskin@cs.ucla.edu
Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning
Authors: Airoldi Edoardo M. , Heller Katherine A. , Silva Ricardo
Published: June 2011

Motivation: Proteins and protein complexes coordinate their activity to execute cellular functions. In a number of experimental settings, including synthetic genetic arrays, genetic perturbations and RNAi screens, scientists identify a small set of protein interactions of interest. A working hypothesis is often that these interactions are the observable phenotypes of some functional process, which is not directly observable. Confirmatory analysis requires finding other pairs of proteins whose interaction may be additional phenotypical evidence about the same functional process. Extant methods for finding additional protein interactions rely heavily on the information in the newly identified set of interactions. For instance, these methods leverage the attributes of the individual proteins directly, in a supervised setting, in order to find relevant protein pairs. A small set of protein interactions provides a small sample to train parameters of prediction methods, thus leading to low confidence.

Results: We develop RBSets, a computational approach to ranking protein interactions rooted in analogical reasoning; that is, the ability to learn and generalize relations between objects. Our approach is tailored to situations where the training set of protein interactions is small, and leverages the attributes of the individual proteins indirectly, in a Bayesian ranking setting that is perhaps closest to propensity scoring in mathematical psychology. We find that RBSets leads to good performance in identifying additional interactions starting from a small evidence set of interacting proteins, for which an underlying biological logic in terms of functional processes and signaling pathways can be established with some confidence. Our approach is scalable and can be applied to large databases with minimal computational overhead. Our results suggest that analogical reasoning within a Bayesian ranking problem is a promising new approach for real-time biological discovery.

Availability: Java code is available at: www.gatsby.ucl.ac.uk/~rbas.

Contact:  airoldi@fas.harvard.edu; kheller@mit.edu; ricardo@stats.ucl.ac.uk
Automatic 3D neuron tracing using all-path pruning
Authors: Peng Hanchuan , Long Fuhui , Myers Gene
Published: June 2011

Motivation: Digital reconstruction, or tracing, of 3D neuron structures is critical toward reverse engineering the wiring and functions of a brain. However, despite a number of existing studies, this task is still challenging, especially when a 3D microscopic image has low signal-to-noise ratio (SNR) and fragmented neuron segments. Published work can handle these hard situations only by introducing global prior information, such as where a neurite segment starts and terminates. However, manual incorporation of such global information can be very time consuming. Thus, a completely automatic approach for these hard situations is highly desirable.

Results: We have developed an automatic graph algorithm, called the all-path pruning (APP), to trace the 3D structure of a neuron. To avoid potential mis-tracing of some parts of a neuron, an APP first produces an initial over-reconstruction, by tracing the optimal geodesic shortest path from the seed location to every possible destination voxel/pixel location in the image. Since the initial reconstruction contains all the possible paths and thus could contain redundant structural components (SC), we simplify the entire reconstruction without compromising its connectedness by pruning the redundant structural elements, using a new maximal-covering minimal-redundant (MCMR) subgraph algorithm. We show that MCMR has a linear computational complexity and will converge. We examined the performance of our method using challenging 3D neuronal image datasets of model organisms (e.g. fruit fly).

Availability: The software is available upon request. We plan to eventually release the software as a plugin of the V3D-Neuron package at http://penglab.janelia.org/proj/v3d.

Contact:  pengh@janelia.hhmi.org
A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments
Authors: Mayhew Michael B. , Robinson Joshua W. , Jung Boyoun , Haase Steven B. , Hartemink Alexander J.
Published: June 2011

Motivation: To advance understanding of eukaryotic cell division, it is important to observe the process precisely. To this end, researchers monitor changes in dividing cells as they traverse the cell cycle, with the presence or absence of morphological or genetic markers indicating a cell's position in a particular interval of the cell cycle. A wide variety of marker data is available, including information-rich cellular imaging data. However, few formal statistical methods have been developed to use these valuable data sources in estimating how a population of cells progresses through the cell cycle. Furthermore, existing methods are designed to handle only a single binary marker of cell cycle progression at a time. Consequently, they cannot facilitate comparison of experiments involving different sets of markers.

Results: Here, we develop a new sampling model to accommodate an arbitrary number of different binary markers that characterize the progression of a population of dividing cells along a branching process. We engineer a strain of Saccharomyces cerevisiae with fluorescently labeled markers of cell cycle progression, and apply our new model to two image datasets we collected from the strain, as well as an independent dataset of different markers. We use our model to estimate the duration of post-cytokinetic attachment between a S.cerevisiae mother and daughter cell. The Java implementation is fast and extensible, and includes a graphical user interface. Our model provides a powerful and flexible cell cycle analysis tool, suitable to any type or combination of binary markers.

Availability: The software is available from: http://www.cs.duke.edu/~amink/software/cloccs/.

Contact:  michael.mayhew@duke.edu; amink@cs.duke.edu