bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ratchet effect of Davydov's solitons in nonlinear low‐dimensional nanosystems
Authors: Brizhik Larissa , Eremko Alexander , Piette Bernard , Zakrzewski Wojtek 
Published: May 2009

AbstractWe study the ratchet behavior of polarons in diatomic molecular chains under the influence of an external electromagnetic field which is periodic in time. We show that in asymmetric chains a harmonic unbiased field causes a drift of polarons. This phenomenon has a threshold with respect to the intensity and the frequency of the field. In spatially symmetric chains, a harmonic periodic electric field generates oscillations of polarons but does not result in their movement. Such a drift current can be induced in symmetric chains by a time periodic asymmetric external field. This complex dynamics of polarons is generated by the interplay between the Peierls–Nabarro barrier and dissipative effects in the system. The dependence of the amplitude of soliton oscillations and the velocity of the drift are calculated depending on the intensity of the field, its frequency, and the coefficient of the energy dissipation. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Structural analysis of ABAD point mutations causing 2‐methyl‐3‐hydroxylbutyryl‐coA deficiency
Authors: Marques Alexandra T. , Fernandes Pedro A. , Ramos Maria João 
Published: May 2009

AbstractHere, we report a structural analysis of three human amyloid‐beta binding alcohol dehydrogenase (ABAD) mutations, identified in patients with 2‐methyl‐3‐hydroxylbutyryl‐coA dehydrogenase (MHBD) deficiency. Mapping of the mutations (R130C, L122V, and N247S) on ABAD crystal structure revealed that they occur in the interfaces of the enzyme tetramer. The wild‐type and mutant enzymes were then subjected to molecular dynamics simulations with the intention of studying the local effects of the mutations on protein structure. A computational alanine scanning mutagenesis study has been carried out to study the possible impact of the mutations in the energetic contribution of the mutation sites to the binding free energy of ABAD subunit association. In this study, the MMPB‐SA (molecular mechanics/Poisson‐Boltzmann surface area) approach has been used to calculate the free energy differences on alanine mutation. The interactions and conservation of the mutation sites have been also evaluated. Our results provide an explanation for the strong effect of the R130C mutation on protein stability, evidenced from experimental results. Possibly, the primary effect of this mutation is to impair dimer assembly, as it changes the hot spot character of position 130 to null spot and causes the loss of important hydrogen bonds mediated by the R130 side chain, including a conserved interface hydrogen bond. The other two mutations do not significantly change the energetic contribution of residues 122 and 247 to subunit association, but they are predicted to cause structural changes that affect the enzymatic activity. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Calibration of new model core potentials for main group elements
Authors: Zeng Tao , Mori Hirotoshi , Miyoshi Eisaku , Klobukowski Mariusz 
Published: May 2009

AbstractThree newly developed families of model core potentials (MCPs) for the main group elements were calibrated in extensive calculations. In the calibration, 90 closed‐shell molecules of the main group elements from Li to Rn, with noble gases being excluded, were optimized using the MCPs at different levels of correlation. The optimized structural parameters were compared with the experimental values and the errors were evaluated. The distributions of the errors were studied, and diagnostic conclusions on the efficacies of the MCPs were obtained. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Electrostatic analysis of charge interactions in proteins
Authors: Tsironis G. P. , Ciudad A. , Sancho J. M. 
Published: May 2009

AbstractWe model proteins as continuous electrostatic media immersed in water to investigate charge mediated processes in their interior. We use a Green's function formalism and find analytical expressions for the electrostatic energy in the vicinity of the protein surfaces. We find that due to image charges generated by the protein dielectric medium embedded in water, the effective electrostatic interaction between the two charges in the interior of the protein has an energy larger than the thermal energy. We focus specifically on kinesin to asses the strength of the electrostatic interaction between ATP and ADP molecules. It is known experimentally that ADP expulsion is correlated to ATP kinesin binding while both processes are essential for the kinesin walk. We estimate that the Bjerrum length in the interior of the kinesin dimer protein is of the order of 4 nm and that the pure electrostatic ATP–ADP interaction is of the order of 3–5 kBT. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Isospectral potentials for the Schrödinger equation with a position‐dependent mass: Free‐particle potential model
Authors: Morales J. , Ovando G. , Peña J. J. , de Parga G. Ares 
Published: May 2009

AbstractIn this work, a method to obtain exactly solvable potentials for the one‐dimensional Schrödinger equation with a position‐dependent mass (SEPDM) and a procedure to determine their isospectral potential partners are presented. In the first case, the problem of exactly solvable SEPDM is worked by means of the point canonical transformation method which permit to convert the SEPDM problem into a standard Schrödinger‐like equation with a position‐independent mass (SLEPIM). In the second case, the procedure to obtain the partner isospectral potentials that fulfill with the SEPDM involves the Darboux transform applied to the SLEPIM. As example of the usefulness of the proposals, it is considered the special case of the free particle potential model as former potential of the SEPDM which leads to different exactly solvable potentials, and to their isospectral partners, depending on the choice of the position‐dependent mass distribution. The proposals are general and can be used in the search of those potentials leading to exactly solvable SEPDM and their isospectral partners, which could be useful in the modeling of quantum chemical properties in condensed matter applications. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Self‐organization effects in reactions of macromolecules
Authors: Christophorov L. N. 
Published: May 2009

AbstractThe ability of biomacromolecules to coordinate fast reaction events in their active centers with slow rearrangements of their structure is focused upon. Under real conditions of many sequential reaction turnovers of the macromolecule, the structural shifts caused by single turnovers can be of cumulative character. This, in turn, leads to drastic threshold‐like changes of the reaction cycle. In this way, the creative role of dynamical substrate‐conformation interactions in the formation of functional regimes of the macromolecule is consistently uncovered. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Design and preliminary in vivo validation of a robotic laparoscope holder for minimally invasive surgery
Authors: Herman Benoît , Dehez Bruno , Duy Khanh Tran , Raucent Benoît , Dombre Etienne , Krut Sébastien 
Published: May 2009

AbstractBackgroundManual manipulation of the camera is a major source of difficulties encountered by surgeons while performing minimally invasive laparoscopic surgery.MethodsA survey of laparoscopic procedures and a review of existing active and passive holders were conducted. Based on these analyses, essential requirements were highlighted for such devices. Pursuant to this, a novel active laparoscope manipulator was designed, paying particular attention to ergonomics and ease of use. Several trials on the pelvitrainer and a first in vivo procedure were performed to validate the original design of our device.ResultsPhantom experiments demonstrated ease of use of the robot and advantages of the intuitive joystick with omnidirectional displacements and speed control. The compactness of the device and image stability were appreciated during the surgical trial.ConclusionsA novel robotic laparoscope holder has been developed and produced. An in vivo trial proved its value in clinical practice, enabling surgeons to work more comfortably. Copyright © 2009 John Wiley & Sons, Ltd.
Impact of IQ, computer‐gaming skills, general dexterity, and laparoscopic experience on performance with the da Vinci® surgical system
Authors: Hagen Monika E. , Wagner Oliver J. , Inan Ihsan , Morel Philippe 
Published: May 2009

AbstractBackgroundDue to improved ergonomics and dexterity, robotic surgery is promoted as being easily performed by surgeons with no special skills necessary. We tested this hypothesis by measuring IQ elements, computer gaming skills, general dexterity with chopsticks, and evaluating laparoscopic experience in correlation to performance ability with the da Vinci® robot.MethodsThirty‐four individuals were tested for robotic dexterity, IQ elements, computer‐gaming skills and general dexterity. Eighteen surgically inexperienced and 16 laparoscopically trained surgeons were included. Each individual performed three different tasks with the da Vinci surgical system and their times were recorded. An IQ test (elements: logical thinking, 3D imagination and technical understanding) was completed by each participant. Computer skills were tested with a simple computer game (hand–eye coordination) and general dexterity was evaluated by the ability to use chopsticks.ResultsWe found no correlation between logical thinking, 3D imagination and robotic skills. Both computer gaming and general dexterity showed a slight but non‐significant improvement in performance with the da Vinci robot (p > 0.05). A significant correlation between robotic skills, technical understanding and laparoscopic experience was observed (p < 0.05).ConclusionsThe data support the conclusion that there are no significant correlations between robotic performance and logical thinking, 3D understanding, computer gaming skills and general dexterity. A correlation between robotic skills and technical understanding may exist. Laparoscopic experience seems to be the strongest predictor of performance with the da Vinci surgical system. Generally, it appears difficult to determine non‐surgical predictors for robotic surgery. Copyright © 2009 John Wiley & Sons, Ltd.
The impact of robotics on practice management of endometrial cancer: transitioning from traditional surgery
Authors: Hoekstra Anna V. , Jairam‐Thodla Arati , Rademaker Alfred , Singh Diljeet K. , Buttin Barbara M. , Lurain John R. , Schink Julian C. , Lowe M. Patrick 
Published: May 2009

AbstractBackgroundEvaluation of the impact of a new robotic surgery programme on perioperative outcomes for endometrial cancerMethodsA prospective database of all patients undergoing staging for endometrial cancer during July 2007–July 2008 was collected and analysed. Demographic data and perioperative outcomes were compared between cases performed via laparotomy, laparoscopy and robotics.ResultsSixty‐five patients underwent staging during the time of data collection (LAP‐26, LSC‐7, ROB‐32). No difference in surgical volume in the year before vs. after robotics was identified. Median operative time for robotics and laparotomy was significantly less than for laparoscopy (p = 0.023). There was no significant difference in lymph node yields between the three groups (p = 0.92). Robotics was associated with significantly less blood loss (p < 0.0001). Complication rates were significantly lower in the robotic group compared to the laparotomy group (p = 0.05). Median hospital stay was 1 day for the minimally invasive groups. Total number of perioperative inpatient days decreased from 331 to 150 in one year. Practice management of endometrial cancer transitioned from a predominantly open approach (5.6% LSC) to robotics (11% LSC, 49% ROB) within 12 months.ConclusionsRobotic surgery dramatically altered our management of endometrial cancer and was associated with a significant improvement in several perioperative outcomes when compared to laparotomy and laparoscopy. Copyright © 2009 John Wiley & Sons, Ltd.
Teleoperated master–slave needle insertion
Authors: Abolhassani Niki , Patel Rajni V. 
Published: May 2009

AbstractBackgroundAccuracy of needle tip placement and needle tracking in soft tissue are of particular importance in many medical procedures. In recent years, developing autonomous and teleoperated systems for needle insertion has become an active area of research.MethodsIn this study, needle insertion was performed using a master–slave set‐up with multi‐degrees of freedom. The effect of force feedback on the accuracy of needle insertion was investigated. In addition, this study compared autonomous, teleoperated and semi‐autonomous needle insertion.ResultsThe results of this study show that incorporation of force feedback can improve teleoperated needle insertion. However, autonomous and semi‐autonomous needle insertions, which use feedback from a deflection model, provide significantly better performance.ConclusionsDevelopment of a haptic master–slave needle insertion system, which is capable of performing some autonomous tasks based on feedback from tissue deformation and needle deflection models, can improve the performance of autonomous robotics‐based insertions as well as non‐autonomous teleoperated manual insertions. Copyright © 2009 John Wiley & Sons, Ltd.
Hybrid model predictive control based on wireless sensor feedback: An experimental study
Authors: Bemporad Alberto , Di Cairano Stefano , Henriksson Erik , Johansson Karl Henrik 
Published: May 2009

AbstractDesign and experimental validation of model predictive control (MPC) of a hybrid dynamical laboratory process with wireless sensors is presented. The laboratory process consists of four infrared lamps, controlled in pairs by two on/off switches, and of a transport belt, where moving parts equipped with wireless sensors are heated by the lamps. The process, which is motivated by heating processes in the plastic and printing industry, presents interesting hybrid dynamics. By approximating the stationary heat spatial distribution as a piecewise affine function of the position along the belt, the resulting plant model is a hybrid dynamical system. The control architecture is based on the reference governor approach: the process is actuated by a local controller, while a hybrid MPC algorithm running on a remote base station sends optimal belt velocity setpoints and lamp on/off commands over a wireless link, exploiting the sensor information received through the wireless network. A discrete‐time hybrid model of the process is used for the hybrid MPC algorithm and for the state estimator. The physical modelling of the process and the hybrid MPC algorithm are presented in detail, together with the hardware and software architectures. The experimental results show that the presented theoretical framework is well suited for control of the new laboratory process, and that the process can be used as a prototype system for evaluating hybrid and networked control strategies. Copyright © 2009 John Wiley & Sons, Ltd.
Indirect estimation of a discrete‐state discrete‐time model using secondary data analysis of regression data
Authors: Isaman Deanna J. M. , Barhak Jacob , Ye Wen 
Published: May 2009

AbstractMulti‐state models of chronic disease are becoming increasingly important in medical research to describe the progression of complicated diseases. However, studies seldom observe health outcomes over long time periods. Therefore, current clinical research focuses on the secondary data analysis of the published literature to estimate a single transition probability within the entire model. Unfortunately, there are many difficulties when using secondary data, especially since the states and transitions of published studies may not be consistent with the proposed multi‐state model. Early approaches to reconciling published studies with the theoretical framework of a multi‐state model have been limited to data available as cumulative counts of progression. This paper presents an approach that allows the use of published regression data in a multi‐state model when the published study may have ignored intermediary states in the multi‐state model. Colloquially, we call this approach the Lemonade Method since when study data give you lemons, make lemonade. The approach uses maximum likelihood estimation. An example is provided for the progression of heart disease in people with diabetes. Copyright © 2009 John Wiley & Sons, Ltd.
Do doctors need statistics? Doctors' use of and attitudes to probability and statistics
Authors: Swift Louise , Miles Susan , Price Gill M. , Shepstone Lee , Leinster Sam J. 
Published: May 2009

AbstractThere is little published evidence on what doctors do in their work that requires probability and statistics, yet the General Medical Council (GMC) requires new doctors to have these skills. This study investigated doctors' use of and attitudes to probability and statistics with a view to informing undergraduate teaching.An email questionnaire was sent to 473 clinicians with an affiliation to the University of East Anglia's Medical School.Of 130 respondents approximately 90 per cent of doctors who performed each of the following activities found probability and statistics useful for that activity: accessing clinical guidelines and evidence summaries, explaining levels of risk to patients, assessing medical marketing and advertising material, interpreting the results of a screening test, reading research publications for general professional interest, and using research publications to explore non‐standard treatment and management options.Seventy‐nine per cent (103/130, 95 per cent CI 71 per cent, 86 per cent) of participants considered probability and statistics important in their work. Sixty‐three per cent (78/124, 95 per cent CI 54 per cent, 71 per cent) said that there were activities that they could do better or start doing if they had an improved understanding of these areas and 74 of these participants elaborated on this. Themes highlighted by participants included: being better able to critically evaluate other people's research; becoming more research‐active, having a better understanding of risk; and being better able to explain things to, or teach, other people.Our results can be used to inform how probability and statistics should be taught to medical undergraduates and should encourage today's medical students of the subjects' relevance to their future careers. Copyright © 2009 John Wiley & Sons, Ltd.
Imputing missing covariate values for the Cox model
Authors: White Ian R. , Royston Patrick 
Published: May 2009

AbstractMultiple imputation is commonly used to impute missing data, and is typically more efficient than complete cases analysis in regression analysis when covariates have missing values. Imputation may be performed using a regression model for the incomplete covariates on other covariates and, importantly, on the outcome. With a survival outcome, it is a common practice to use the event indicator D and the log of the observed event or censoring time T in the imputation model, but the rationale is not clear.We assume that the survival outcome follows a proportional hazards model given covariates X and Z. We show that a suitable model for imputing binary or Normal X is a logistic or linear regression on the event indicator D, the cumulative baseline hazard H0(T), and the other covariates Z. This result is exact in the case of a single binary covariate; in other cases, it is approximately valid for small covariate effects and/or small cumulative incidence. If we do not know H0(T), we approximate it by the Nelson–Aalen estimator of H(T) or estimate it by Cox regression.We compare the methods using simulation studies. We find that using logT biases covariate‐outcome associations towards the null, while the new methods have lower bias. Overall, we recommend including the event indicator and the Nelson–Aalen estimator of H(T) in the imputation model. Copyright © 2009 John Wiley & Sons, Ltd.
Determination of mineral element concentrations in wheat, sunflower, chickpea and lentil cultivars in response to P fertilization by polarized energy dispersive X‐ray fluorescence
Authors: Gunes Aydin , Inal Ali , Kadioglu Yusuf K. 
Published: May 2009

AbstractConcentrations of elements (P, K, S, Ca, Mg, Si, Cl, Fe, Zn, Cu, Mn, Mo, Na, Al, Ti, Ni, Ba, As, Br, Rb and Sr) of wheat, sunflower, chickpea and lentil cultivars grown in low and high phosphorus soil were investigated by polarized energy dispersive X‐ray fluorescence (PEDXRF). The phosphorus treatment x cultivars interaction was significant for the growth and element concentrations, and cultivars within plant species differed considerably with respect to element concentrations as the result of P fertilization. Shoot growth of the cultivars of each plant species was increased in response to phosphorus fertilization. Application of P increased the P concentrations of wheat, sunflower, chickpea and lentil cultivars. Under high P conditions, mean K concentrations of wheat and sunflower cultivars were decreased while the mean K concentrations of chickpea and lentil were increased. With the exception of sunflower cultivars, applied P significantly increased S concentration of the cultivars of wheat, chickpea and lentil. Calcium concentrations of wheat and sunflower cultivars were reduced by P fertilization and that of chickpea and lentil were increased. Applied P decreased mean Mg concentrations in sunflower, increased in chickpea and lentil cultivars and showed no effects on the wheat cultivars. Applied P significantly decreased mean Si concentrations of wheat and sunflower while mean Si concentrations of the chickpea and lentil cultivars were increased. Chloride concentrations of the wheat and sunflower cultivars were decreased and those of the chickpea and lentil cultivars were increased by applied P. In general, Fe concentrations of the wheat and chickpea cultivars were significantly increased by applied P. Zinc and Cu concentrations of all the cultivars of the four plant species were reduced by P, particularly Zn concentrations. However, applied P increased mean Mn concentrations of wheat and chickpea and decreased those of chickpea cultivars. Mean Mo concentrations of wheat and chickpea increased but decreased in sunflower and lentil cultivars. In general, applied P increased mean Na concentration of wheat and decreased that of chickpea and lentil. Aluminum concentrations of wheat and chickpea cultivars were decreased by applied P. Applied P decreased Ti concentrations of wheat and sunflower cultivars and increased Ti concentrations of chickpea and lentil. Nickel concentrations of wheat and chickpea were increased and those of sunflower and lentil were decreased by applied P. Applied P reduced the Ba and increased As and Rb concentrations of all the cultivars within the plant species. Bromine concentrations of wheat and lentil were decreased and those of sunflower and chickpea were increased by applied P. Finally, Sr concentrations in wheat and sunflower cultivars were reduced, and increased in chickpea cultivars with applied P. Copyright © 2009 John Wiley & Sons, Ltd.