Femtosecond resolution of ligand-heme interactions in the high-affinity quinol oxidase bd: A di-heme active site?

Interaction of the two high-spin hemes in the oxygen reduction site of the bd-type quinol oxidase from Escherichia coli has been studied by femtosecond multicolor transient absorption spectroscopy. The previously unidentified Soret band of ferrous heme b595 was determined to be centered around 440 nm by selective excitation of the fully reduced unliganded or CO-bound cytochrome bd in the α-band of heme b595. The redox state of the b-type hemes strongly affects both the line shape and the kinetics of the absorption changes induced by photodissociation of CO from heme d. In the reduced enzyme, CO photodissociation from heme d perturbs the spectrum of ferrous cytochrome b595 within a few ps, pointing to a direct interaction between hemes b595 and d. Whereas in the reduced enzyme no heme d-CO geminate recombination is observed, in the mixed-valence CO-liganded complex with heme b595 initially oxidized, a significant part of photodissociated CO does not leave the protein and recombines with heme d within a few hundred ps. This caging effect may indicate that ferrous heme b595 provides a transient binding site for carbon monoxide within one of the routes by which the dissociated ligand leaves the protein. Taken together, the data indicate physical proximity of the hemes d and b595 and corroborate the possibility of a functional cooperation between the two hemes in the dioxygen-reducing center of cytochrome bd.

Theory of single-spin inelastic tunneling spectroscopy

I show that recent experiments of inelastic scanning tunneling spectroscopy of single and a few magnetic atoms are modeled with a phenomenological spin-assisted tunneling Hamiltonian so that the inelastic dI/dV line shape is related to the spin spectral weight of the magnetic atom. This accounts for the spin selection rules and dI/dV spectra observed experimentally for single Fe and Mn atoms deposited on Cu2N. In the case of chains of Mn atoms it is found necessary to include both first and second-neighbor exchange interactions as well as single-ion anisotropy.

Optical Bloch equations and enhanced decay of Rabi oscillations in strong driving fields

Optical Bloch equations are widely used for describing dynamics in a system consisting molecules, electromagnetic waves, and a thermal bath. We analyze applicability of these equations to a single molecule imbedded in a solid matrix. Classical Bloch equations and the limits of their applicability are derived from more general master equations. Simple and intuitively appealing picture based on stochastic Bloch equations shows that at low temperatures, contrary to common believes, a strong driving field can not only suppress but can also increase decay rates of Rabi oscillations. A physical system where predicted effects can be observed experimentally is suggested. (c) 2005 Elsevier B.V. All rights reserved.

Transmission Spectra of Rb 87 atoms near an Optical Nanofiber.

We present measurements of the transmission spectra of 87Rb atoms at 780 nm in the vicinity of a nanofiber. A uniform distribution of fixed atoms around a nanofiber should produce a spectrum that is broadened towards the red due to shifts from the van der Waals potential. If the atoms are free, this also produces an attractive force that accelerates them until they collide with the fiber which depletes the steady-state density of near-surface atoms. It is for this reason that measurements of the van der Waals interaction are sparse. We confirm this by measuring the spectrum cold atoms from a magneto-optical trap around the fiber, revealing a symmetric line shape with nearly the natural linewidth of the transition. When we use an auxiliary 750 nm laser we are able to controllably desorb a steady flux of atoms from the fiber that reside near the surface (less than 50 nm) long enough to feel the van der Walls interaction and produce an asymmetric spectrum. We quantify the spectral asymmetry as a function of 750 nm laser power and find a maximum. Our model, which that takes into account the change in the density distribution, qualitatively explains the observations. In the future this can be used as a tool to more comprehensively study atom-surface interactions.

Development of a robotic system for switchgear cabling

Industrial robots are an inalienable part of modern automated production. Typical applications of robots include welding, painting, (dis)assembly, packaging, labeling, palletizing, pick and place and others. Many of that applications includes object manipulation. If the shape and position of the object are known in advance, it is possible to design the trajectory of the robot’s end-effector to take and place. Such a strategy is applicable for rigid objects and widely used in the manufacturing field. But flexible (deformable) objects can change their shape and position upon contact with the robot’s end-effector or environment. That is the reason why the general approach is unacceptable. It means that the robot can fail to grasp such an object and can’t place it in the desired position. This thesis has addressed the problem of cable manipulation by bilateral robotic setup for the industrial manufacturing of electrical switchgear. The considered solution is based on the idea of tensioned cable. If the cable was grasped by the ends and tensioned, it has a line shape. Since the position of the robot’s end-effectors known, the position of the cable is known as well. Such an approach is capable to place cable in cable ducts of switchgear. The considered solution has been tested experimentally on a real bilateral robotic setup.

Change points detection in crime-related time series: an on-line fuzzy approach based on a shape space representation

The extension of traditional data mining methods to time series has been effectively applied to a wide range of domains such as finance, econometrics, biology, security, and medicine. Many existing mining methods deal with the task of change points detection, but very few provide a flexible approach. Querying specific change points with linguistic variables is particularly useful in crime analysis, where intuitive, understandable, and appropriate detection of changes can significantly improve the allocation of resources for timely and concise operations. In this paper, we propose an on-line method for detecting and querying change points in crime-related time series with the use of a meaningful representation and a fuzzy inference system. Change points detection is based on a shape space representation, and linguistic terms describing geometric properties of the change points are used to express queries, offering the advantage of intuitiveness and flexibility. An empirical evaluation is first conducted on a crime data set to confirm the validity of the proposed method and then on a financial data set to test its general applicability. A comparison to a similar change-point detection algorithm and a sensitivity analysis are also conducted. Results show that the method is able to accurately detect change points at very low computational costs. More broadly, the detection of specific change points within time series of virtually any domain is made more intuitive and more understandable, even for experts not related to data mining.

Elongated shape isomers in the (36)Ar nucleus

A recent analysis of the (12)C + (24)Mg scattering [W. Sciani et al., Phys. Rev. C 80, 034319 (2009)] suggests the existence of a hyperdeformed band in the (36)Ar nucleus, completely in line with the predictions of alpha [W. D. M. Rae and A. C. Merchant, Phys. Lett. B279, 207 (1992)] and binary cluster calculations [J. Cseh et al., Phys. Rev. C 70, 034311 (2004)]. Here we review the structural understanding of the superdeformed and the hyperdeformed states of (36)Ar and present new results on the shape isomers as well. Special attention is paid to the clusterization of these states, which indicates the appropriate reaction channels for their formation.

Development of preferences for the human body shape in infancy

Two studies investigated the development of infants' visual preferences for the human body shape. In Study 1, infants of 12,15 and 18 months were tested in a standard preferential looking experiment, in which they were shown paired line drawings of typical and scrambled bodies. Results indicated that the 18-month-olds had a reliable preference for the scrambled body shapes over typical body shapes, while the younger infants did not show differential responding. In Study 2, 12- and 18-month-olds were tested with the same procedure, except that the typical and scrambled body stimuli were photographic images. The results of Study 2 again indicated that only the 18-month-olds had a reliable preference for the scrambled body shapes. This finding contrasts sharply with infants' precocious preferences for human faces, suggesting that infants' learning about human faces and human bodies follow different developmental trajectories. (C) 2002 Elsevier Science B.V. All rights reserved.

Capturing the essence of shape of polygonal meshes

Polygonal meshes, essential shape representation, feature detection, external skeleton, mesh decimation, progrssive meshes, silhouettes, hidden line removal, non-photorealistic rendering, OpenNPAR

Cost-effectiveness analysis of the first-line therapies for nicotine dependence.

BACKGROUND: Nicotine dependence is the major obstacle for smokers who want to quit. Guidelines have identified five effective first-line therapies, four nicotine replacement therapies (NRTs)--gum, patch, nasal spray and inhaler--and bupropion. Studying the extent to which these various treatments are cost-effective requires additional research. OBJECTIVES: To determine cost-effectiveness (CE) ratios of pharmacotherapies for nicotine dependence provided by general practitioners (GPs) during routine visits as an adjunct to cessation counselling. METHODS: We used a Markov model to generate two cohorts of one-pack-a-day smokers: (1) the reference cohort received only cessation counselling from a GP during routine office visits; (2) the second cohort received the same counselling plus an offer to use a pharmacological treatment to help them quit smoking. The effectiveness of adjunctive therapy was expressed in terms of the resultant differential in mortality rate between the two cohorts. Data on the effectiveness of therapies came from meta-analyses, and we used odds ratio for quitting as the measure of effectiveness. The costs of pharmacotherapies were based on the cost of the additional time spent by GPs offering, prescribing and following-up treatment, and on the retail prices of the therapies. We used the third-party-payer perspective. Results are expressed as the incremental cost per life-year saved. RESULTS: The cost per life-year saved for only counselling ranged from Euro 385 to Euro 622 for men and from Euro 468 to Euro 796 for women. The CE ratios for the five pharmacological treatments varied from Euro 1768 to Euro 6879 for men, and from Euro 2146 to Euro 8799 for women. Significant variations in CE ratios among the five treatments were primarily due to differences in retail prices. The most cost-effective treatments were bupropion and the patch, and, then, in descending order, the spray, the inhaler and, lastly, gum. Differences in CE between men and women across treatments were due to the shape of their respective mortality curve. The lowest CE ratio in men was for the 45- to 49-year-old group and for women in the 50- to 54-year-old group. Sensitivity analysis showed that changes in treatment efficacy produced effects only for less-well proven treatments (spray, inhaler, and bupropion) and revealed a strong influence of the discount rate and natural quit rate on the CE of pharmacological treatments. CONCLUSION: The CE of first-line treatments for nicotine dependence varied widely with age and sex and was sensitive to the assumption for the natural quit rate. Bupropion and the nicotine patch were the two most cost-effective treatments.

Changes in volume, surface estimate, three-dimensional shape and total number of neurons of the human primary visual cortex from midgestation until old age.

Macroscopic features such as volume, surface estimate, thickness and caudorostral length of the human primary visual cortex (Brodman's area 17) of 46 human brains between midgestation and 93 years were studied by means of camera lucida drawings from serial frontal sections. Individual values were best fitted by a logistic function from midgestation to adulthood and by a regression line between adulthood and old age. Allometric functions were calculated to study developmental relationships between all the features. The three-dimensional shape of area 17 was also reconstructed from the serial sections in 15 cases and correlated with the sequence of morphological events. The sulcal pattern of area 17 begins to develop around 21 weeks of gestation but remains rather simple until birth, while it becomes more convoluted, particularly in the caudal part, during the postnatal period. Until birth, a large increase in cortical thickness (about 83% of its mean adult value) and caudorostral length (69%) produces a moderate increase in cortical volume (31%) and surface estimate (40%) of area 17. After birth, the cortical volume and surface undergo their maximum growth rate, in spite of a rather small increase in cortical thickness and caudorostral length. This is due to the development of the pattern of gyrification within and around the calcarine fissure. All macroscopic features have reached the mean adult value by the end of the first postnatal year. With aging, the only features to undergo significant regression are the cortical surface estimate and the caudorostral length. The total number of neurons in area 17 shows great interindividual variability at all ages. No decrease in the postnatal period or in aging could be demonstrated.

Design of adjustable packaging line

Diplomityön tavoite oli tutkia, mitä toimintoja ja tekniikoita uusi, joustava kartonkipakkauslinja sisältää ja mitkä suuntaukset pakkausteollisuudessa tulevat olemaan tärkeitä tulevaisuudessa. Pakkauslinjan päätoimintoja tarkasteltiin nykyisten jatulevaisuuden tekniikoiden pohjalta. Erityisesti tarkasteltiin laser-sovellusten käytön mahdollisuutta pakkauslinjan eri osatoiminnoissa. Katsaus pakkausteollisuuden tulevaisuuden näkymiin luotiin kirjallisuuden ja aikaisempien tutkimusten pohjalta, minkä perusteella työssä oletetaan, että yksilölliset ja monitoimipakkaukset tulevat lisääntymään tulevaisuudessa. Eri tuotantoerien välillä olevat asetusajat tulee saada minimoitua, mutta millä keinoin joustavuus on saavutettavissa? Yksi ratkaisu pakkausten valmistamisessa on käyttää robottisolua, mikä on mahdollista luultavasti ainakin kuppimuotoisten pakkausten kohdalla. Muutenkin robotiikka on lisääntymässä pakkausteollisuudessa. Digitaalisten painotekniikoiden kehitys on mahdollistanut yksilölliset painatukset. Tulevaisuudessa painatus on mahdollista tehdä pakkauslinjan loppupäässä, jopa vasta täytön ja suljennan jälkeen. Laserleikkaus on jo nyt käytössä, mutta tulevaisuudessa myös saumaus ja perinteinen nuuttaus on mahdollista tehdä lasersovelluksia käyttäen. Kehittynyt, väyläpohjainen ohjausjärjestelmä on tulevaisuudessa välttämätön joustavassa pakkauslinjassa. Internetin välityksellä toimiva etäohjattu virheenkorjausdiagnostiikka tulee myös olemaan itsestäänselvyys tulevaisuudessa. Kustannussäästöjä voidaan saavuttaa käyttämälläpakkauslinjassa modulaarista rakennetta. Standardiosien ja standardiosajärjestelmien käyttäminen pienentää myös käyttö- ja huoltokustannuksia. Tärkeää on kuitenkin muistaa, ettei joustavuutta voida saavuttaa pelkästään yhtä ominaisuutta tai tekniikkaa hyödyntäen vaan monia menetelmiä yhdistäen. Suunniteltavan pakkauslinjan toiminta on myös hyvä varmistaa käyttäen apuna mallinnusta ja simulointia.

Changes in cell shape, cytoskeletal proteins and adhesion sites of cultured cells after extracellular Ca2+ chelation

Although much is known about the molecules involved in extracellular Ca2+ regulation, the relationship of the ion with overall cell morphology is not understood. The objective of the present study was to determine the effect of the Ca2+ chelator EGTA on the major cytoskeleton components, at integrin-containing adhesion sites, and their consequences on cell shape. Control mouse cell line C2C12 has a well-spread morphology with long stress fibers running in many different directions, as detected by fluorescence microscopy using rhodamine-phalloidin. In contrast, cells treated with EGTA (1.75 mM in culture medium) for 24 h became bipolar and showed less stress fibers running in one major direction. The adhesion plaque protein alpha5-integrin was detected by immunofluorescence microscopy at fibrillar adhesion sites in both control and treated cells, whereas a dense labeling was seen only inside treated cells. Microtubules shifted from a radial arrangement in control cells to a longitudinal distribution in EGTA-treated cells, as analyzed by immunofluorescence microscopy. Desmin intermediate filaments were detected by immunofluorescence microscopy in a fragmented network dispersed within the entire cytoplasm in EGTA-treated cells, whereas a dense network was seen in the whole cytoplasm of control cells. The present results suggest that the role of extracellular Ca2+ in the regulation of C2C12 cell shape can be mediated by actin-containing stress fibers and microtubules and by intermediate filament reorganization, which may involve integrin adhesion sites.

Facilitatory effects of an auditory warning stimulus in a visual location identification task and a visual shape identification task

The occurrence of a weak auditory warning stimulus increases the speed of the response to a subsequent visual target stimulus that must be identified. This facilitatory effect has been attributed to the temporal expectancy automatically induced by the warning stimulus. It has not been determined whether this results from a modulation of the stimulus identification process, the response selection process or both. The present study examined these possibilities. A group of 12 young adults performed a reaction time location identification task and another group of 12 young adults performed a reaction time shape identification task. A visual target stimulus was presented 1850 to 2350 ms plus a fixed interval (50, 100, 200, 400, 800, or 1600 ms, depending on the block) after the appearance of a fixation point, on its left or right side, above or below a virtual horizontal line passing through it. In half of the trials, a weak auditory warning stimulus (S1) appeared 50, 100, 200, 400, 800, or 1600 ms (according to the block) before the target stimulus (S2). Twelve trials were run for each condition. The S1 produced a facilitatory effect for the 200, 400, 800, and 1600 ms stimulus onset asynchronies (SOA) in the case of the side stimulus-response (S-R) corresponding condition, and for the 100 and 400 ms SOA in the case of the side S-R non-corresponding condition. Since these two conditions differ mainly by their response selection requirements, it is reasonable to conclude that automatic temporal expectancy influences the response selection process.

Asymptotic model for shape resonance control of diatomics by intense non-resonant light

We derive a universal model for atom pairs interacting with non-resonant light via the polarizability anisotropy, based on the long range properties of the scattering. The corresponding dynamics can be obtained using a nodal line technique to solve the asymptotic Schrödinger equation. It consists of imposing physical boundary conditions at long range and vanishing the wavefunction at a position separating the inner zone and the asymptotic region. We show that nodal lines which depend on the intensity of the non-resonant light can satisfactorily account for the effect of the polarizability at short range. The approach allows to determine the resonance structure, energy, width, channel mixing and hybridization even for narrow resonances.