bluuebunny/crossref_metadata_2025 huggingface dataset:
Frequency-frequency correlation functions and apodization in two-dimensional infrared vibrational echo spectroscopy: A new approach
Authors: Kwak Kyungwon , Park Sungnam , Finkelstein Ilya J. , Fayer M. D.
Published: September 2007

Ultrafast two-dimensional infrared (2D-IR) vibrational echo spectroscopy can probe structural dynamics under thermal equilibrium conditions on time scales ranging from femtoseconds to ∼100ps and longer. One of the important uses of 2D-IR spectroscopy is to monitor the dynamical evolution of a molecular system by reporting the time dependent frequency fluctuations of an ensemble of vibrational probes. The vibrational frequency-frequency correlation function (FFCF) is the connection between the experimental observables and the microscopic molecular dynamics and is thus the central object of interest in studying dynamics with 2D-IR vibrational echo spectroscopy. A new observable is presented that greatly simplifies the extraction of the FFCF from experimental data. The observable is the inverse of the center line slope (CLS) of the 2D spectrum. The CLS is the inverse of the slope of the line that connects the maxima of the peaks of a series of cuts through the 2D spectrum that are parallel to the frequency axis associated with the first electric field-matter interaction. The CLS varies from a maximum of 1 to 0 as spectral diffusion proceeds. It is shown analytically to second order in time that the CLS is the Tw (time between pulses 2 and 3) dependent part of the FFCF. The procedure to extract the FFCF from the CLS is described, and it is shown that the Tw independent homogeneous contribution to the FFCF can also be recovered to yield the full FFCF. The method is demonstrated by extracting FFCFs from families of calculated 2D-IR spectra and the linear absorption spectra produced from known FFCFs. Sources and magnitudes of errors in the procedure are quantified, and it is shown that in most circumstances, they are negligible. It is also demonstrated that the CLS is essentially unaffected by Fourier filtering methods (apodization), which can significantly increase the efficiency of data acquisition and spectral resolution, when the apodization is applied along the axis used for obtaining the CLS and is symmetrical about τ=0. The CLS is also unchanged by finite pulse durations that broaden 2D spectra.
Understanding fragility in supercooled Lennard-Jones mixtures. II. Potential energy surface
Authors: Coslovich D. , Pastore G.
Published: September 2007

The connection between isobaric fragility and the properties of high-order stationary points of the potential energy surface in different supercooled Lennard-Jones mixtures was investigated. The increase of effective activation energies upon supercooling appears to be driven by the increase of average potential energy barriers measured by the energy dependence of the fraction of unstable modes. Such an increase is sharper, the more fragile the mixture. Correlations between fragility and other properties of high-order stationary points, including the vibrational density of states and the localization features of unstable modes, are also discussed.
Controlling the leader-laggard dynamics in delay-synchronized lasers
Authors: González Cristina M. , Torrent M. C. , García-Ojalvo Jordi
Published: September 2007

We study experimentally the collective dynamics of two delay-coupled semiconductor lasers. The lasers are coupled by mutual injection of their emitted light beams, at a distance for which coupling delay times are non-negligible. This system is known to exhibit lag synchronization, with one laser leading and the other one lagging the dynamics. Our setup is designed such that light travels along different paths in the two coupling directions, which allows independent control of the two coupling strengths. A comparison of unidirectional and bidirectional coupling reveals that the leader-laggard roles can be switched by acting upon the coupling architecture of the system. Additionally, numerical simulations show that a more extensive control of the network architecture can also lead to changes in the dynamics of the system. Finally, we discuss the relevance of these results for bidirectional chaotic communications.
Formation and growth of nanoindentation-induced high pressure phases in crystalline and amorphous silicon
Authors: Ruffell S. , Bradby J. E. , Williams J. S. , Munroe P.
Published: September 2007

Nanoindentation-induced formation of high pressure crystalline phases (Si-III and Si-XII) during unloading has been studied by Raman micro-spectroscopy, cross-sectional transmission electron microscopy (XTEM), and postindentation electrical measurements. For indentation in crystalline silicon (c-Si), rapid unloading (∼1000 mN∕s) results in the formation of amorphous silicon (a-Si) only; a result we have exploited to quench the formation of high pressure phases at various stages during unloading to study their formation and evolution. This reveals that seed volumes of Si-III and Si-XII form during the early stages of unloading with substantial volumes only forming after the pop-out event that occurs at about 50% of the maximum load. In contrast, high pressure phases form much more readily in an a-Si matrix, with substantial volumes forming without an observable pop-out event with rapid unloading. Postindentation electrical measurements have been used to further investigate the end phases and to identify differences between indentations which otherwise appear to be identical from the XTEM and Raman analyses.
Electromechanical analysis for a piezo-optical fiber subjected to harmonic loading
Authors: Huang Jin H. , Ding Desheng
Published: September 2007

This article investigates the electromechanical responses of a piezocoated optical fiber subjected to time-harmonic excitation of mechanical load as a sensor or to electric voltages as an actuator. Piezoelectric coatings, functioning as sensors or actuators, have potential in the development of acousto-optic devices. Despite the growing demand for optical fibers coated with piezoelectric materials, pertinent research work on their electromechanical responses in integrated systems still remains very scarce indeed. By application of Hamilton’s principle to piezoelectric fundamentals, the equations of motion under dynamic excitations are solved with proper boundary conditions to give the analytical forms of the integrated system’s electromechanical responses. For numerical illustration of the responses, an example is investigated to give the instantaneous response for the direct and converse effects.
Influence of defects and processing parameters on the properties of indium tin oxide films on polyethylene napthalate substrate
Authors: Han H. , Zoo Yeongseok , Bhagat S. K. , Lewis J. S. , Alford T. L.
Published: September 2007

Indium tin oxide (ITO) thin films were deposited on polyethylene napthalate (PEN) by rf sputtering using different rf powers (60 and 120W) and at different substrate temperatures (room temperature and 100°C). Selected PEN substrates were pretreated using an Ar plasma before ITO sputter deposition. Rutherford backscattering spectrometry was used to determine the oxygen content in the films. Hall effect measurements were used to evaluate the electrical properties. In this paper the influence of defect structure, sputtering conditions, and the effect of annealing on the electrical and optical properties of ITO on PEN have been investigated. Electrical properties such as carrier concentration, mobility, and resistivity of the ITO films varied with rf power and substrate temperature. The electrical and optical properties of the films changed after annealing in air. This study also describes how the as-deposited amorphous ITO changes from amorphous to crystalline as a result of heat treatment, and investigates the effects of Sn defect clustering on electrical and optical properties of the ITO films.
Analysis of transverse wave as a propagation mode for the pressure pulse in large arteries
Authors: Lin Wang Yuh-Ying , Chiu Wei-Bin , Jan Ming-Yie , Bau Jian-Guo , Li Sai-Ping , Wang Wei-Kung
Published: September 2007

A general axial momentum equation for fluid inside a transverse vibrating elastic tube is derived here. In a system with high pressure and low elastic modulus, transverse motion of the wall contributes important nonlinear forces, and the longitudinal fluid wave which assumes that flow is governed by the Navier-Stokes equation cannot describe the pulse wave completely. By comparing the transverse elastic wave with the longitudinal fluid wave, we conclude that transverse wave is a significant wave mode in large arteries. The longitudinal stress force, commonly ignored in the literature, can be considered as a significant factor that influences the propagation of the arterial pulse.
Electron density modulation in an asymmetric bipolar pulsed dc magnetron discharge
Authors: Karkari S. K. , Ellingboe A. R. , Gaman C. , Swindells I. , Bradley J. W.
Published: September 2007

This paper investigates the spatial and temporal variation in plasma electron density over a region between 5 and 10cm above the race-track region of a pulsed magnetron sputtering target. The pulse operation is performed using an asymmetric bipolar pulsed dc power supply, which provides a sequence of large negative “on-phase” voltage (−350V) and a small positive “reverse-phase” voltage (+10V) for 55% of the pulse duration (10μs). The electron density is measured using a floating microwave hairpin resonance probe. The results show electron expulsion from the target in the initial on phase, which propagates with a characteristic speed exceeding the ion thermal speed. In the steady state on phase, a consistent higher density is observed. A quantitative model has been developed to explain the resultant density drops in the initial on phase. While in the reverse phase, we observed an anomalous growth in density at a specific location from the target (d>7cm). The mechanism behind the increase in electron density has been attributed to the modulation in spatial plasma potential, which was measured earlier in the same apparatus using a floating emissive probe [J. W. Bradley et al., Plasma Sources Sci. Technol. 13, 189 (2004)].
Semiconducting properties of zinc-doped cubic boron nitride thin films
Authors: Nose K. , Yoshida T.
Published: September 2007

We have examined the electronic properties of zinc-doped cubic boron nitride (cBN) thin films prepared by sputter deposition. The electric conductivity of films deposited in pure Ar increased as the concentration of zinc dopant increased, and hole conduction was identified by the measurement of thermoelectric currents. It was also found that the conductivity increment in such films was accompanied by a linear increase in the B∕(B+N) ratio. At the same time, no modification of the composition and the conductivity by incorporated zinc was observed when film growth took place in presence of nitrogen gas. The effect of the excess boron on the conductivity emerged only when films show semi-insulating behavior. These results suggest that Zn substitution for nitrogen causes high electric conductivity of cBN. The electric contact between Ti electrode and semiconducting cBN was examined by the transfer length method, and Ohmic conduction was observed in the Ti∕cBN contact. The specific contact resistance was affected by the specific resistance of cBN films, and it was reduced from 105to100Ωcm2 by increasing the concentration of incorporated Zn.
High-efficiency transmission of nanoscale information by surface plasmon polaritons from near field to far field
Authors: Zhang Zhiyou , Du Jinglei , Guo Xiaowei , Luo Xiangang , lei Du Chun
Published: October 2007

An idea is proposed to convert optical information of the near field into propagation waves by an isosceles triangle phase-grating coated metal film for super-resolution imaging. We analyzed the reverse process of exciting surface plasmon polaritons (SPPs) by attenuated total reflection coupling mode, and found it was possible and effective to transfer the nanoscale information from near field to far field by the special phase grating. In this article, the excitation mechanisms of the SPPs and the details of the high-efficiency coupling output of the near-field light waves were explored. A special coupling microstructure was designed so that the near-field information could be collected in the far field. We also built an optical transfer function of the superlens imaging system, and reconstructed the simulation image of nanoscale object. Analysis and calculation shows that the isosceles triangle phase-grating coated metal film plays an important role in far-field imaging beyond the diffraction limit, namely, converting evanescent waves to propagating waves and changing the direction of the optical wave by the phase modulation. The methods provide a way to quickly get the near-field information without complicated requirements.
Generalized infimum and sequential product of quantum effects
Authors: Li Yuan , Sun Xiu-Hong , Chen Zheng-Li
Published: October 2007

The quantum effects for a physical system can be described by the set E(H) of positive operators on a complex Hilbert space H that are bounded above by the identity operator I. For A, B∊E(H), the operation of sequential product A∘B=A1∕2BA1∕2 was proposed as a model for sequential quantum measurements. A nice investigation of properties of the sequential product has been carried over [Gudder, S. and Nagy, G., “Sequential quantum measurements,” J. Math. Phys. 42, 5212 (2001)]. In this note, we extend some results of this reference. In particular, a gap in the proof of Theorem 3.2 in this reference is overcome. In addition, some properties of generalized infimum A⨅B are studied.
Experimental technique for reducing contact and background noise in voltage spectral density measurements
Authors: Barone C. , Galdi A. , Pagano S. , Quaranta O. , Méchin L. , Routoure J.-M. , Perna P.
Published: September 2007

Electric noise measurements can give useful information on the conduction mechanisms and the dynamic behaviors of the charge carriers in new materials. However, it is well known that not all the electronic fluctuations are originated from the material itself, but some noise sources depend on the experimental procedures used for the measurements. In this article, an experimental technique to reduce “external” noise components, not associated with the bulk system, is presented. The proposed method is based on measurements of the voltage spectral density, using in sequence a four- and a two-probe technique. From the measurements it is possible to evaluate the contact and the background noise contributions and to recover the real spectral trace of the sample. The proposed procedure is demonstrated to be valid in spectral density measurements performed on La0.7Sr0.3MnO3 thin films.
The electronic structure change with Gd doping of HfO2 on silicon
Authors: Losovyj Ya. B. , Ketsman Ihor , Sokolov A. , Belashchenko K. D. , Dowben P. A. , Tang Jinke , Wang Zhenjun
Published: September 2007

Gd-doped HfO2 films deposited on silicon substrates undergo a crystallographic change from monoclinic to fluorite (cubic) phase with increasing Gd concentrations. The crystallographic phase change is accompanied by a small increase in the valence bandwidth and in the apparent band offset in the surface region. Electrical measurements show pronounced rectification properties for lightly doped Gd:HfO2 films on p-Si and for heavily-doped Gd:HfO2 films on n-Si, suggesting a crossover from n-type to p-type behavior with increasing doping level.
The nature of fluctuations in a double arc argon-nitrogen plasma jet
Authors: Tu Xin , Yan Jianhua , Yu Liang , Cen Kefa , Chéron Bruno
Published: September 2007

The dynamic behavior of the double arc argon-nitrogen plasma jet is investigated by combined means of the fast Fourier transform, correlation function, and Wigner distribution. The restrike mode is identified as the fluctuation behavior in an argon-nitrogen plasma jet. The Fourier spectra exhibit two characteristic frequencies of 150Hz and 4.1kHz, which indicates that the nature of fluctuations in the double arc argon-nitrogen plasma can be ascribed to the power supply undulation and both arc roots motion on the anode channels. It is further found that the double anode torch could inhibit and reduce the restrike phenomenon.
Single dot spectroscopy of site-controlled InAs quantum dots nucleated on GaAs nanopyramids
Authors: Tran T. , Muller A. , Shih C. K. , Wong P. S. , Balakrishnan G. , Nuntawong N. , Tatebayashi J. , Huffaker D. L.
Published: September 2007

Single InAs quantum dots, site-selectively grown by a patterning and regrowth technique, were probed using high-resolution low-temperature microphotoluminescence spectroscopy. Systematic measurements on many individual dots show a statistical distribution of homogeneous linewidths with a peak value of ∼120μeV, exceeding that of unpatterned dots but comparing well with previously reported patterning approaches. The linewidths do not appear to depend upon the specific facet on which the dots grow and often can reach the spectrometer resolution limit (<100μeV). These measurements show that the site-selective growth approach can controllably position the dots with good optical quality, suitable for constrained structures such as microcavities.
Magnetotunable left-handed material consisting of yttrium iron garnet slab and metallic wires
Authors: Zhao Hongjie , Zhou Ji , Zhao Qian , Li Bo , Kang Lei , Bai Yang
Published: September 2007

A magnetotunable left-handed material (LHM) consisting of yttrium iron garnet (YIG) slab and metallic wires has been demonstrated by experiments and simulations. The left-handed passband through the LHM can be dynamically and continuously tuned in a wide frequency region by an applied magnetic field. The tunability of the passband is attributed to that of the negative permeability induced by ferromagnetic resonance in the YIG slab. The authors proposed a convenient means to design tunable LHM based on the ferromagnetic materials as an alternative to tunable split ring resonators.
Green light-emitting diodes with self-assembled In-rich InGaN quantum dots
Authors: Park Il-Kyu , Kwon Min-Ki , Kim Jeom-Oh , Seo Seong-Bum , Kim Ja-Yeon , Lim Jae-Hong , Park Seong-Ju , Kim Yoon-Seok
Published: September 2007

A green light-emitting diode (LED) was fabricated using self-assembled In-rich InGaN quantum dots (QDs). The photoluminescence studies showed that the QDs provide thermally stable deeply localized recombination sites for carriers with negligibly small piezoelectric field. The electroluminescence spectra of the LED showed a peak in the green spectral range and the dominant peak was blueshifted with increasing injection current due to the distribution of depth of the potential wells of QDs. The output power of the LED increased with increasing injection current, indicating that the potential wells are thermally stable and deeply localized in the QDs.
Melting curve analysis in a snapshot
Authors: Baaske Philipp , Duhr Stefan , Braun Dieter
Published: September 2007

The thermal denaturation of molecules is an essential method in biochemistry and diagnostics, including the measurement of single nucleotide polymorphisms and the binding analysis of proteins. We present a method for the all-optical high speed measurement of melting curves. A thin sheet of water is locally heated with an infrared laser to obtain a spatial temperature distribution between 20 and 100°C. Using a fluorescence microscope a melting curve is recorded within 50ms. This is about 10 000-times faster than state-of-the-art fluorometry and yields the same results for the validation example of a DNA hairpin.
Application of hydrogenated amorphous silicon oxide layers to c-Si heterojunction solar cells
Authors: Fujiwara Hiroyuki , Kaneko Tetsuya , Kondo Michio
Published: September 2007

Wide-gap hydrogenated amorphous silicon oxide (a-SiO:H), fabricated by plasma process using SiH4 and CO2 gas mixture, has been applied to crystalline silicon (c-Si) heterojunction solar cells. It has been demonstrated that incorporation of an a-SiO:H p layer, instead of a hydrogenated amorphous silicon (a-Si:H) p layer, improves the conversion efficiency slightly. Moreover, when an a-SiO:H i layer is formed on the c-Si substrate, Si epitaxial growth that occurs at an a-Si:H∕c-Si heterointerface at high deposition temperatures can be prevented entirely. Accordingly, high-efficiency solar cells are fabricated more easily by applying a-SiO:H p-i layers to n-type c-Si heterojunction solar cells.
An active energy harvesting scheme with an electroactive polymer
Authors: Ren Kailiang , Liu Yiming , Hofmann H. , Zhang Q. M. , Blottman John
Published: September 2007

We investigate the energy harvesting with an electrostrictive polymer, possessing high electromechanical response and elastic energy density, which make it possible to generate high electric energy density and attractive for the active energy harvesting scheme. It is shown that combining the active energy harvesting scheme and high electromechanical response of the polymer yields a harvested electric energy density of ∼40mJ∕cm3 with a 10% efficiency.
Air flow through carbon nanotube arrays
Authors: Hu Ming , Shenogin Sergei , Keblinski Pawel , Raravikar Nachiket
Published: September 2007

Using molecular dynamics simulations, we studied the air flow through carbon nanotube arrays. We found that for 1.4nm diameter tubes separated by 25nm, the air flow can be well described by the free molecular flow theory. We estimate that for such array, the pressure gradient is about 0.1atm∕μm at 1atm air pressure and 5m∕s flow velocity, indicating that the flowing air can only pass through an array of no more than about 400 carbon nanotubes in series. Our findings provide design rules for arrays of nanotubes for thermal energy exchange with air.
Design and fabrication of segmented, slotted waveguides for electro-optic modulation
Authors: Wang Guangxi , Baehr-Jones Tom , Hochberg Michael , Scherer Axel
Published: October 2007

Recently, slotted waveguides have been used in conjunction with second order nonlinear optical polymers to provide a platform for electro-optic modulation at telecommunication frequencies. A challenge with these devices is the need to provide high-frequency electrical driving signals to the slots. The silicon resistivity must be high to reduce optical loss, and as a result electrical performance can be severely limited. We have designed and fabricated a class of waveguide that achieves quasicontinuous electrical contact with subwavelength segmentations and has low optical losses of 4dB∕cm, allowing both millimeter-wave and optical fields to be concentrated in the same area.
Large-area, ordered hexagonal arrays of nanoscale holes or dots from block copolymer templates
Authors: Vedrine Josee , Hong Young-Rae , Marencic Andrew P. , Register Richard A. , Adamson Douglas H. , Chaikin Paul M.
Published: October 2007

Hexagonal arrays of nanoscale holes or metal dots (25nm in diameter and 39nm in period), with orientational order extending over the entire square-centimeter array area, were fabricated on unpatterned silicon wafer substrates using a shear-aligned sphere-forming diblock copolymer template. Since two or more layers of spherical nanodomains are required to achieve alignment in the block copolymer film, but pattern transfer requires a single layer, a multistep etching process was developed, whereby the top layer of a shear-aligned bilayer was evenly removed, leaving the ordered bottom layer as the fabrication template for hole and dot arrays free from grain boundaries.
Complete in-plane polarization anisotropy of the A exciton in unstrained A-plane GaN films
Authors: Misra Pranob , Brandt O. , Grahn H. T. , Teisseyre H. , Siekacz M. , Skierbiszewski C. , Łucznik B.
Published: October 2007

Using reflectance spectroscopy, the in-plane polarization behavior of unstrained C- and A-plane GaN films is experimentally investigated. While no in-plane polarization anisotropy is observed for all three band-gap related excitons (A, B, and C) in unstrained C-plane GaN films, the A exciton is completely linearly polarized perpendicular to the c axis in unstrained A-plane GaN films. However, the B and C excitons are only partially polarized. This observation is in excellent agreement with results based on band-structure calculations using the Bir-Pikus Hamiltonian for the wurtzite crystal structure.
Statistical physics is for the birds
Authors: Feder Toni
Published: October 2007

Three-dimensional mapping of starling flocks could shed light not only on the birds' collective behavior but also on a broad range of other aggregate systems.
Fermilab forms backup plan to avoid science gap
Authors: Feder Toni
Published: October 2007

High-intensity beams of rare particles could give Fermilab a vibrant scientific program if delays in the International Linear Collider spell a dry period for the lab.
Frontiers of surface science
Authors: Somorjai Gabor A. , Park Jeong Y.
Published: October 2007

The field of surface physics is evolving to include molecular-scale studies of nanoparticle surfaces, as well as single-crystal surfaces in contact with liquids or high-pressure gases.
Wavelets, a modern tool for signal processing
Authors: Selesnick Ivan W.
Published: October 2007

The simplest wavelet transform is based on sums and differences of nearby points in a function. A variety of sophisticated variations allow signals and images to be effectively compressed, cleaned, and analyzed.
Institutional Barriers to Incorporating Climate Responsive Design in Commercial Redevelopment
Authors: Ryser Laura , Halseth Greg
Published: October 2007

For decades the literature on the winter cities and on urban design has explored the implications of poorly designed urban spaces on pedestrian mobility during various seasons. In Canada, however, practice in using climate responsive design principles tends to be the exception. Using a case study methodology, this paper explores the application of climate responsive design principles in the commercial redevelopment process in Prince George, British Columbia. Findings indicate that, despite expressed interest in winter city development, professionals and decision makers involved in the development permit process do not possess sufficient knowledge about climate responsive design to apply these principles to everyday practice. More importantly, knowledge about climate responsive design did not appear to be a major consideration in creating or evaluating commercial redevelopment projects. A range of educational, attitudinal, regulatory, structural, and political barriers impede the development of an institutional framework to support the implementation of climate responsive design.
Load fluctuations drive actin network growth
Authors: Shaevitz Joshua W. , Fletcher Daniel A.
Published: September 2007

The growth of actin filament networks is a fundamental biological process that drives a variety of cellular and intracellular motions. During motility, eukaryotic cells and intracellular pathogens are propelled by actin networks organized by nucleation-promoting factors that trigger the formation of nascent filaments off the side of existing filaments in the network. A Brownian ratchet (BR) mechanism has been proposed to couple actin polymerization to cellular movements, whereby thermal motions are rectified by the addition of actin monomers at the end of growing filaments. Here, by following actin-propelled microspheres using three-dimensional laser tracking, we find that beads adhered to the growing network move via an object-fluctuating BR. Velocity varies with the amplitude of thermal fluctuation and inversely with viscosity as predicted for a BR. In addition, motion is saltatory with a broad distribution of step sizes that is correlated in time. These data point to a model in which thermal fluctuations of the microsphere or entire actin network, and not individual filaments, govern motility. This conclusion is supported by Monte Carlo simulations of an adhesion-based BR and suggests an important role for membrane tension in the control of actin-based cellular protrusions.
In vivo
mouse inferior olive neurons exhibit heterogeneous subthreshold oscillations and spiking patterns
Authors: Khosrovani S. , Van Der Giessen R. S. , De Zeeuw C. I. , De Jeu M. T. G.
Published: September 2007

In vitro
whole-cell recordings of the inferior olive have demonstrated that its neurons are electrotonically coupled and have a tendency to oscillate. However, it remains to be shown to what extent subthreshold oscillations do indeed occur in the inferior olive
in vivo
and whether its spatiotemporal firing pattern may be dynamically generated by including or excluding different types of oscillatory neurons. Here, we did whole-cell recordings of olivary neurons
in vivo
to investigate the relation between their subthreshold activities and their spiking behavior in an intact brain. The vast majority of neurons (85%) showed subthreshold oscillatory activities. The frequencies of these subthreshold oscillations were used to distinguish four main olivary subtypes by statistical means. Type I showed both sinusoidal subthreshold oscillations (SSTOs) and low-threshold Ca
2+
oscillations (LTOs) (16%); type II showed only sinusoidal subthreshold oscillations (13%); type III showed only low-threshold Ca
2+
oscillations (56%); and type IV did not reveal any subthreshold oscillations (15%). These subthreshold oscillation frequencies were strongly correlated with the frequencies of preferred spiking. The frequency characteristics of the subthreshold oscillations and spiking behavior of virtually all olivary neurons were stable throughout the recordings. However, the occurrence of spontaneous or evoked action potentials modified the subthreshold oscillation by resetting the phase of its peak toward 90°. Together, these findings indicate that the inferior olive in intact mammals offers a rich repertoire of different neurons with relatively stable frequency settings, which can be used to generate and reset temporal firing patterns in a dynamically coupled ensemble.
Inner ear hair cells produced
in vitro
by a mesenchymal-to-epithelial transition
Authors: Hu Zhengqing , Corwin Jeffrey T.
Published: September 2007

Sensory hair cell loss is a major contributor to disabling hearing and balance deficits that affect >250 million people worldwide. Sound exposures, infections, drug toxicity, genetic disorders, and aging all can cause hair cell loss and lead to permanent sensory deficits. Progress toward treatments for these deficits has been limited, in part because hair cells have only been obtainable via microdissection of the anatomically complex internal ear. Attempts to produce hair cells
in vitro
have resulted in reports of some success but have required transplantation into embryonic ears or coculturing with other tissues. Here, we show that avian inner ear cells can be cultured and passaged for months, frozen, and expanded to large numbers without other tissues. At any point from passage 6 up to at least passage 23, these cultures can be fully dissociated and then aggregated in suspension to induce a mesenchymal-to-epithelial transition that reliably yields new polarized sensory epithelia. Those epithelia develop numerous hair cells that are crowned by hair bundles, composed of a single kinocilium and an asymmetric array of stereocilia. These hair cells exhibit rapid permeance to FM1-43, a dye that passes through open mechanotransducing channels. Because a vial of frozen cells can now provide the capacity to produce bona fide hair cells completely
in vitro
, these discoveries should open new avenues of research that may ultimately contribute to better treatments for hearing loss and other inner ear disorders.
A functional single-molecule binding assay via force spectroscopy
Authors: Cao Yi , Balamurali M. M. , Sharma Deepak , Li Hongbin
Published: September 2007

Protein–ligand interactions, including protein–protein interactions, are ubiquitously essential in biological processes and also have important applications in biotechnology. A wide range of methodologies have been developed for quantitative analysis of protein–ligand interactions. However, most of them do not report direct functional/structural consequence of ligand binding. Instead they only detect the change of physical properties, such as fluorescence and refractive index, because of the colocalization of protein and ligand, and are susceptible to false positives. Thus, important information about the functional state of protein–ligand complexes cannot be obtained directly. Here we report a functional single-molecule binding assay that uses force spectroscopy to directly probe the functional consequence of ligand binding and report the functional state of protein–ligand complexes. As a proof of principle, we used protein G and the Fc fragment of IgG as a model system in this study. Binding of Fc to protein G does not induce major structural changes in protein G but results in significant enhancement of its mechanical stability. Using mechanical stability of protein G as an intrinsic functional reporter, we directly distinguished and quantified Fc-bound and Fc-free forms of protein G on a single-molecule basis and accurately determined their dissociation constant. This single-molecule functional binding assay is label-free, nearly background-free, and can detect functional heterogeneity, if any, among protein–ligand interactions. This methodology opens up avenues for studying protein–ligand interactions in a functional context, and we anticipate that it will find broad application in diverse protein–ligand systems.
Estradiol-17β regulates mouse uterine epithelial cell proliferation through insulin-like growth factor 1 signaling
Authors: Zhu Liyin , Pollard Jeffrey W.
Published: September 2007

Estradiol-17β (E
2
) causes cell proliferation in the uterine epithelium of mice and humans by signaling through its transcription factor receptor α (ERα). In this work we show that this signaling is mediated by the insulin-like growth factor 1 receptor (IGF1R) expressed in the epithelium, whose activation leads to the stimulation of the phosphoinositide 3-kinase/protein kinase B pathway leading to cyclin D1 nuclear accumulation and engagement with the canonical cell cycle machinery. This cyclin D1 nuclear accumulation results from the inhibition of glycogen synthase kinase 3β (GSK3β) activity caused by an inhibitory phosphorylation by protein kinase B. Once the IGF1 pathway is activated, inhibition of ER signaling demonstrates that it is independent of ER. Inhibition of GSK3β in the absence of E
2
is sufficient to induce uterine epithelial cell proliferation, and GSK3β is epistatic to IGF1 signaling, indicating a linear pathway from E
2
to cyclin D1. Exposure to E
2
is the major risk factor for endometrial cancer, suggesting that downstream activation of this IGF1-mediated pathway by mutation could be causal in the progression to ER-independent tumors.
Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle
Authors: Şener Melih K. , Olsen John D. , Hunter C. Neil , Schulten Klaus
Published: September 2007

The photosynthetic unit (PSU) of purple photosynthetic bacteria consists of a network of bacteriochlorophyll–protein complexes that absorb solar energy for eventual conversion to ATP. Because of its remarkable simplicity, the PSU can serve as a prototype for studies of cellular organelles. In the purple bacterium
Rhodobacter sphaeroides
the PSU forms spherical invaginations of the inner membrane, ≈70 nm in diameter, composed mostly of light-harvesting complexes, LH1 and LH2, and reaction centers (RCs). Atomic force microscopy studies of the intracytoplasmic membrane have revealed the overall spatial organization of the PSU. In the present study these atomic force microscopy data were used to construct three-dimensional models of an entire membrane vesicle at the atomic level by using the known structure of the LH2 complex and a structural model of the dimeric RC–LH1 complex. Two models depict vesicles consisting of 9 or 18 dimeric RC–LH1 complexes and 144 or 101 LH2 complexes, representing a total of 3,879 or 4,464 bacteriochlorophylls, respectively. The
in silico
reconstructions permit a detailed description of light absorption and electronic excitation migration, including computation of a 50-ps excitation lifetime and a 95% quantum efficiency for one of the model membranes, and demonstration of excitation sharing within the closely packed RC–LH1 dimer arrays.
Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling
Authors: Sweredoski Michael J. , Donovan Kevin J. , Nguyen Bao D. , Shaka A.J. , Baldi Pierre
Published: September 2007

Motivation: Recent advances in cell-free protein expression systems allow specific labeling of proteins with amino acids containing stable isotopes (15N, 13 C and 2H), an important feature for protein structure determination by nuclear magnetic resonance (NMR) spectroscopy. Given this labeling ability, we present a mathematical optimization framework for designing a set of protein isotopomers, or labeling schedules, to reduce the congestion in the NMR spectra. The labeling schedules, which are derived by the optimization of a cost function, are tailored to a specific protein and NMR experiment.

Results: For 2D 15N-1H HSQC experiments, we can produce an exact solution using a dynamic programming algorithm in under 2 h on a standard desktop machine. Applying the method to a standard benchmark protein, calmodulin, we are able to reduce the number of overlaps in the 500 MHz HSQC spectrum from 10 to 1 using four samples with a true cost function, and 10 to 4 if the cost function is derived from statistical estimates. On a set of 448 curated proteins from the BMRB database, we are able to reduce the relative percent congestion by 84.9% in their HSQC spectra using only four samples. Our method can be applied in a high-throughput manner on a proteomic scale using the server we developed. On a 100-node cluster, optimal schedules can be computed for every protein coded for in the human genome in less than a month.

Availability: A server for creating labeling schedules for 15N-1H HSQC experiments as well as results for each of the individual 448 proteins used in the test set is available at http://nmr.proteomics.ics.uci.edu.

Contact:  pfbaldi@ics.uci.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Clustering by soft-constraint affinity propagation: applications to gene-expression data
Authors: Leone Michele , Sumedha  , Weigt Martin
Published: September 2007

Motivation: Similarity-measure-based clustering is a crucial problem appearing throughout scientific data analysis. Recently, a powerful new algorithm called Affinity Propagation (AP) based on message-passing techniques was proposed by Frey and Dueck (2007a). In AP, each cluster is identified by a common exemplar all other data points of the same cluster refer to, and exemplars have to refer to themselves. Albeit its proved power, AP in its present form suffers from a number of drawbacks. The hard constraint of having exactly one exemplar per cluster restricts AP to classes of regularly shaped clusters, and leads to suboptimal performance, e.g. in analyzing gene expression data.

Results: This limitation can be overcome by relaxing the AP hard constraints. A new parameter controls the importance of the constraints compared to the aim of maximizing the overall similarity, and allows to interpolate between the simple case where each data point selects its closest neighbor as an exemplar and the original AP. The resulting soft-constraint affinity propagation (SCAP) becomes more informative, accurate and leads to more stable clustering. Even though a new a priori free parameter is introduced, the overall dependence of the algorithm on external tuning is reduced, as robustness is increased and an optimal strategy for parameter selection emerges more naturally. SCAP is tested on biological benchmark data, including in particular microarray data related to various cancer types. We show that the algorithm efficiently unveils the hierarchical cluster structure present in the data sets. Further on, it allows to extract sparse gene expression signatures for each cluster.

Contact:  leone@isi.it, sumedha@isi.it and weigt@isi.it
SnoReport: computational identification of snoRNAs with unknown targets
Authors: Hertel Jana , Hofacker Ivo L. , Stadler Peter F.
Published: September 2007

Summary: Unlike tRNAs and microRNAs, both classes of snoRNAs, which direct two distinct types of chemical modifications of uracil residues, have proved to be surprisingly difficult to find in genomic sequences. Most computational approaches so far have explicitly used the fact that snoRNAs predominantly target ribosomal RNAs and spliceosomal RNAs. The target is specified by a short stretch of sequence complementarity between the snoRNA and its target. This sequence complementarity to known targets crucially contributes to sensitivity and specificity of snoRNA gene finding algorithms.

The discovery of ‘orphan’ snoRNAs, which either have no known target, or which target ordinary protein-coding mRNAs, however, begs the question whether this class of ‘housekeeping’ non-coding RNAs is much more widespread and might have a diverse set of regulatory functions. In order to approach this question, we present here a combination of RNA secondary structure prediction and machine learning that is designed to recognize the two major classes of snoRNAs, box C/D and box H/ACA snoRNAs, among ncRNA candidate sequences. The snoReport approach deliberately avoids any usage of target information. We find that the combination of the conserved sequence boxes and secondary structure constraints as a pre-filter with SVM classifiers based on a small set of structural descriptors are sufficient for a reliable identification of snoRNAs.

Tests of snoReport on data from several recent experimental surveys show that the approach is feasible; the application to a dataset from a large-scale comparative genomics survey for ncRNAs suggests that there are likely hundreds of previously undescribed ‘orphan’ snoRNAs still hidden in the human genome.

Availability: The snoReport software is implemented in ANSI C. The source code is available under the GNU Public License at http://www.bioinf.uni-leipzig.de/Software/snoReport.

Supplementary Material is available at http://www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/07-015

Contact:  jana@bioinf.uni-leipzig.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Reducing Beta‐Glucan Solubility in Oat Bran Muffins by Freeze‐Thaw Treatment Attenuates Its Hypoglycemic Effect
Authors: Lan‐Pidhainy Xiaomiao , Brummer Yolanda , Tosh Susan M. , Wolever Thomas M. , Wood Peter J.
Published: October 2007

The viscosity of soluble fibers such as β‐glucan depends on their concentration in solution and molecular weight (MW) distribution. We investigated whether freezing treatment of oat bran muffins affected the physicochemical properties of β‐glucan, and its physiological effectiveness in lowering postprandial blood glucose response. A controlled range of β‐glucan solubility was achieved by subjecting oat bran muffins containing two levels of β‐glucan to repeated freeze‐thaw temperature cycling. β‐Glucan solubilized by in vitro digestion extraction was measured by flow‐injection analysis. MW distributions of β‐glucan were analyzed using size‐exclusion chromatography. β‐Glucan solubility decreased as the number of freeze‐thaw cycles increased, while MW distribution of β‐glucan decreased slightly. Peak blood glucose rise (PBGR) after fresh muffins (8 and 12 g of β‐glucan/serving) was significantly lower than that after muffins (8 and 12 g of β‐glucan/serving) treated with four freeze‐thaw (FT) cycles (1.84 ± 0.2 vs. 2.31 ± 0.1 mmol/L, P = 0.007). Compared with the control whole wheat muffins, the reduction in incremental area under the glucose response curve (AUC) after fresh muffins (8 and 12 g of β‐glucan/serving) was nearly twice that after 4 FT cycles (43.3 ± 4.4% vs. 27.0 ± 5.4%, P = 0.016). A significant inverse linear relationship was found between the log [concentration] of extractable β‐glucan and PBGR (r2 = 0.85, P = 0.01), and AUC (r2 = 0.71, P = 0.03). The results show that reduction of β‐glucan solubility in foods attenuates its physiological effectiveness in lowering postprandial glycemia.
Strain-dependent twist–stretch elasticity in chiral filaments
Authors: Upmanyu M , Wang H.L , Liang H.Y , Mahajan R
Published: September 2007

Coupling between axial and torsional degrees of freedom often modifies the conformation and expression of natural and synthetic filamentous aggregates. Recent studies on chiral single-walled carbon nanotubes and B-DNA reveal a reversal in the sign of the twist–stretch coupling at large strains. The similarity in the response in these two distinct supramolecular assemblies and at high strains suggests a fundamental, chirality-dependent nonlinear elastic behaviour. Here we seek the link between the microscopic origin of the nonlinearities and the effective twist–stretch coupling using energy-based theoretical frameworks and model simulations. Our analysis reveals a sensitive interplay between the deformation energetics and the sign of the coupling, highlighting robust design principles that determine both the sign and extent of these couplings. These design principles have already been exploited by nature to dynamically engineer such couplings, and have broad implications in mechanically coupled actuation, propulsion and transport in biology and technology.
Bimodal degradation of MLL by SCFSkp2 and APCCdc20 assures cell cycle execution: a critical regulatory circuit lost in leukemogenic MLL fusions
Authors: Liu Han , Cheng Emily H.-Y. , Hsieh James J.-D.
Published: October 2007

Human chromosome 11q23 translocations disrupting MLL result in poor prognostic leukemias. It fuses the common MLL N-terminal ∼1400 amino acids in-frame with >60 different partners without shared characteristics. In addition to the well-characterized activity of MLL in maintaining Hox gene expression, our recent studies established an MLL–E2F axis in orchestrating core cell cycle gene expression including Cyclins. Here, we demonstrate a biphasic expression of MLL conferred by defined windows of degradation mediated by specialized cell cycle E3 ligases. Specifically, SCFSkp2 and APCCdc20 mark MLL for degradation at S phase and late M phase, respectively. Abolished peak expression of MLL incurs corresponding defects in G1/S transition and M-phase progression. Conversely, overexpression of MLL blocks S-phase progression. Remarkably, MLL degradation initiates at its N-terminal ∼1400 amino acids, and tested prevalent MLL fusions are resistant to degradation. Thus, impaired degradation of MLL fusions likely constitutes the universal mechanism underlying all MLL leukemias. Our data conclude an essential post-translational regulation of MLL by the cell cycle ubiquitin/proteasome system (UPS) assures the temporal necessity of MLL in coordinating cell cycle progression.