bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Approach for a Toxicity Prediction Model of Environmental Pollutants by Using a Quantitative Structure-Activity Relationship Method Based on Toxicogenomics
Authors: Hosoya Junichi , Tamura Kumiko , Muraki Naomi , Okumura Hiroki , Ito Tsuyoshi , Maeno Mitsugu
Published: August 2011

The development of automobile emission reduction technologies has decreased dramatically the particle concentration in emissions; however, there is a possibility that unexpected harmful chemicals are formed in emissions due to new technologies and fuels. Therefore, we attempted to develop new and efficient toxicity prediction models for the myriad environmental pollutants including those in automobile emissions. We chose 54 compounds related to engine exhaust and, by use of the DNA microarray, examined their effect on gene expression in human lung cells. We focused on IL-8 as a proinflammatory cytokine and developed a prediction model with quantitative structure-activity relationship (QSAR) for the IL-8 gene expression by using an in silico system. Our results demonstrate that this model showed high accuracy in predicting upregulation of the IL-8 gene. These results suggest that the prediction model with QSAR based on the gene expression from toxicogenomics may have great potential in predictive toxicology of environmental pollutants.
Familial Parkinson's Disease Mutant E46Kα-Synuclein Localizes to Membranous Structures, Forms Aggregates, and Induces Toxicity in Yeast Models
Authors: Fiske Michael , White Michael , Valtierra Stephanie , Herrera Sara , Solvang Keith , Konnikova Alina , DebBurman Shubhik
Published: August 2011

In Parkinson’s disease (PD), midbrain dopaminergic neuronal death is linked to the accumulation of aggregatedα-synuclein. The familial PD mutant form ofα-synuclein, E46K, has not been thoroughly evaluated yet in an organismal model system. Here, we report that E46K resembled wild-type (WT)α-synuclein inSaccharomyces cerevisiaein that it predominantly localized to the plasma membrane, and it did not induce significant toxicity or accumulation. In contrast, inSchizosaccharomyces pombe, E46K did not associate with the plasma membrane. Instead, in one strain, it extensively aggregated in the cytoplasm and was as toxic as WT. Remarkably, in another strain, E46K extensively associated with the endomembrane system and was more toxic than WT. Our studies recapitulate and extend aggregation and phospholipid membrane association properties of E46K previously observedin vitroand cell culture. Furthermore, it supports the notion that E46K generates toxicity partly due to increased association with endomembrane systems within cells.
Estimating Free Energies of Formation of Titanate () and Zirconate () Pyrochlore Phases of Trivalent Lanthanides and Actinides
Authors: Ragavan Anpalaki J. , Adams Dean V.
Published: August 2011

A linear free energy relationship was developed to predict the Gibbs free energies of formation (, in kJ/mol) of crystalline titanate (M2Ti2O7) and zirconate (M2Zr2O2) pyrochlore families of trivalent lanthanides and actinides (M3+) from the Shannon-Prewitt radius of M3+ in a given coordination state (, in nm) and the nonsolvation contribution to the Gibbs free energy of formation of the aqueous M3+ (). The linear free energy relationship for M2Ti2O7 is expressed as . The linear free energy relationship for M2Zr2O7 is expressed as . Estimated free energies were within 0.73 percent of those calculated from the first principles for M2Ti2O7 and within 0.50 percent for M2Zr2O7. Entropies of formation were estimated from constituent oxides (J/mol), based on an empirical parameter defined as the difference between the measured entropies of formation of the oxides and the measured entropies of formation of the aqueous cation.
Fabrication of Superhydrophobic Nanocomposite Coatings Using Polytetrafluoroethylene and Silica Nanoparticles
Authors: Basu Bharathibai J. , Dinesh Kumar V.
Published: August 2011

Superhydrophobic nanocomposite coatings were fabricated by incorporating hydrophobically modified silica (HMS) nanoparticles in polytetrafluoroethylene (PTFE) emulsion. Hydrophobicity of the coating was dependent on the concentration of HMS. Coatings containing optimum amounts of PTFE and HMS exhibited superhydrophobic property with high water contact angle (WCA) of 165∘ and low sliding angle <2∘. Scanning electron microscopic (SEM) studies have shown a binary surface topography composed of microbumps and nanoscale granules. The synergistic effect of the micro-nano-binary structure and low surface energy of PTFE was responsible for the superhydrophobicity of the coating. The method is simple and cost-effective and can be used for preparing self-cleaning superhydrophobic coatings on large areas of different kinds of substrates like glass, metal, and composites.
Boundary Layer under Oscillatory Wave
Authors: Adityawan Mohammad Bagus , Tanaka Hitoshi
Published: August 2011

Turbulence due to wave motion and propagation is a very important aspect in sediment transport modeling. The boundary layer characteristic during the process will highly influence the sediment transport mechanism at the bottom. 1D model approach has been widely used to assess the turbulent boundary layer. However, the need for a more detailed model leads to the development of a more sophisticated models. This study presents a 2D turbulent model using k-ω equation to approach the turbulent boundary layer characteristic in oscillatory wave. The equations are solved using finite-difference center scheme. The model is applied to the case of oscillatory sinusoidal and skew wave. The velocity profile and bed stress were compared to those obtained from wind channel experimental data and 1D k-ω model from previous study.
Evaluation of the Biocompatibility of a Bilayer Chitosan Skin Regenerating Template, Human Skin Allograft, and Integra Implants in Rats
Authors: Mohd Yussof Shah Jumaat , Halim Ahmad Sukari , Mat Saad Arman Zaharil , Jaafar Hasnan
Published: August 2011

Introduction. Chitosan is a nontoxic, biocompatible, and biodegradable polymer obtained from chitin by N-deacetylation using strong alkali. Chitosan in a form of a bilayer skin regenerating template can act as a scaffold for regeneration. Integra is a two-layer skin regeneration system, constructed of a matrix of crosslinked fibers that acts as a scaffold for regenerating dermal skin cells. Human skin allografts (HSAs) are the “gold standard” for temporary coverage of clean burn wounds. Objectives. The objective of this study was to conduct in-vivo, preclinical biocompatibility evaluations of Integra, HSA, and Chitosan skin regenerating template (SRT). Methods. Paravertebral subcutaneous pockets were created for the implantation of test materials. Implants were retrieved after 4, 7, 14, 21, and 28 days. Slides of sections through the implants were examined to determine biocompatibility. Results. Chitosan SRT and Integra showed similar inflammatory patterns. HSA showed a higher inflammatory reaction initially which then reduced to levels similar to Integra and Chitosan SRT. Chitosan SRT and Integra also shared similar angiogenesis levels. Towards the end, all implants were degraded with decreased tissue response. Conclusion. Integra, Chitosan SRT, and HSA have been shown to be biocompatible. Integra and Chitosan SRT seem to illicit similar tissue responses.
Translation, Cross-Cultural Adaptation, and Validation of the Parkinson's Disease Quality of Life Questionnaire (PDQL), the “PDQL-BR”, into Brazilian Portuguese
Authors: Campos Marcos , Rezende Carlos Henrique A. de , Farnese Virgilio da C. , da Silva Carlos Henrique M. , Morales Nívea Macedo de O. , Pinto Rogério de Melo C.
Published: August 2011

Translate, culturally adapt, and validate the “Parkinson's Disease Quality of Life” (PDQL) BR, into Brazilian Portuguese. Fifty-two patients answered the PDQL-BR. Twenty-one patients answered the PDQL-BR again 14 days later. The UPDRS and HY scale was applied. Validation was evaluated using psychometric properties, checking the quality of the data, reliability, and validity. Quality of the data was evaluated based on occurrence of ceiling and floor effects. Reliability was evaluated based on: internal consistency of an item, homogeneity, and reproducibility. Validation was checked through the evaluation of convergent and discriminatory validation. There was no ceiling and floor effect. When evaluating reliability, items 20, 30, and 37 showed correlation of 0.34, 0.26, and 0.37, respectively, to your scale; the other items was higher than 0.4. The alpha Cronbach coefficient was higher than 0.7 for most domains. There was good reproducibility. There were no meaningful changes in the PDQL-BR translation and cross-cultural adaptation.
Antiphospholipid Antibody Syndrome
Authors: Sangle Nikhil A , Smock Kristi J
Published: August 2011

Antiphospholipid antibodies are directed against phospholipid-protein complexes and include lupus anticoagulant, anticardiolipin antibodies, and anti–beta-2 glycoprotein I antibodies. Antiphospholipid antibody syndrome is a common cause of acquired thrombophilia and is characterized by venous or arterial thromboembolism or pregnancy morbidity and the presence of antiphospholipid antibodies. Antibodies should be demonstrable on at least 2 occasions separated by 12 weeks. Heterogeneity of the autoantibodies and absence of gold standard assays makes interpretation of laboratory results a challenge for both laboratorians and clinicians. This review discusses the key laboratory and clinical aspects of antiphospholipid antibody syndrome. Particular focus is given to lupus anticoagulant detection, in view of recently updated laboratory guidelines.
Solution Densities and Estimated Total Protein Contents Associated With Inappropriate Flotation of Separator Gel in Different Blood Collection Tubes
Authors: Faught Ronald C , Marshall James , Bornhorst Joshua
Published: August 2011

Context.—Clinical samples that have densities greater than that of separator gel in specimen tubes may exhibit gel flotation to the top of the specimen upon centrifugation. Inappropriate separator gel flotation can occur in specimens with high protein content. In automated analytical systems, gel flotation can lead to mechanical disruption and potential inaccurate result reporting upon aspiration into instrument sampling probes.

Objective.—To determine the relative specimen densities and estimated total protein contents at which specimen gel flotation would occur upon centrifugation in commonly used commercial specimen tubes, a comparative study of separator gel density was initiated using prepared dextran solutions.

Design.—Specific gravity of several dextran solutions was determined by direct hydrometry. The dextran solutions were introduced to serum and plasma lithium heparin BD Vacutainer specimen tubes manufactured by Becton, Dickinson and Company and into Vacuette specimen tubes manufactured by Greiner Bio-One containing separator gel. Following centrifugation the specimen tubes were examined for gel flotation.

Results.—Flotation was observed at a lower dextran solution density for Greiner than for BD tubes in both serum and plasma separator gel specimen tubes. Additionally, some differences between specimen tube lots were observed for both BD and Greiner tubes. The total protein content in clinical samples that would result in gel flotation can be estimated for different specimen container types.

Conclusions.—Differences were observed for the gel separator specific gravity in different blood collection containers. Laboratories wishing to avoid problems with inappropriate gel flotation in high protein samples should consider these observations.
Three‐dimensional focusing of particles using negative dielectrophoretic force in a microfluidic chip with insulating microstructures and dual planar microelectrodes
Authors: Jen Chun‐Ping , Weng Cheng‐Hsin , Huang Ching‐Te
Published: August 2011

The focusing of biological and synthetic particles in microfluidic devices is a prerequisite for the construction of microstructured materials, as well as for medical applications. In the present study, a microdevice that can effectively focus particles in three dimensions using a combination of insulator‐based and metal‐electrode dielectrophoresis (DEP) has been designed and fabricated. The DEP force is employed to confine the particles using a negative DEP response. Four insulating microstructures, which form an X‐pattern in the microchannel, were employed to distort the electric field between the insulators in a conducting solution, thereby generating regions with a high electric‐field gradient. Two strips of microelectrodes on the top and bottom surfaces were placed in the middle of the microchannel and connected to an electric pole. Two sets of dual‐planar electrodes connected to the opposite pole were placed at the sides of the microchannel at the top and bottom surfaces. The results of a transient simulation of tracks of polystyrene particles, which was performed using the commercial software package CFD‐ACE+ (ESI Group, France), demonstrate that the three‐dimensional focusing of particles was achieved when the applied voltage was larger than 35 V at a frequency of 1 MHz. Furthermore, the focusing performance increased with the increased strength of the applied electric field and decreased inlet flow rate. Experiments on particle focusing, employing polystyrene particles 10 μm in diameter, were conducted to demonstrate the feasibility of the proposed design; the results agree with the trend predicted by numerical simulations.
Reconfigurable bowtie electromagnetic bandgap‐based microwave filters
Authors: Assimonis Stylianos D. , Lalas Antonios X. , Kantartzis Nikolaos V. , Yioultsis Traianos V.
Published: August 2011

A controllable bowtie‐like electromagnetic bandgap (EBG)‐based microwave filter is proposed in this article. The device exploits EBG properties to form the desired stopband, whereas tunability is used by means of switching elements. Numerical analysis is performed by a finite element scheme revealing the DC‐extending bandstop behavior of the structure. In addition, a prototype of the proposed filter is constructed and measured. Experimental data demonstrate the robustness of the conducted simulations, while an adequate tuning range is observed. The simple, yet efficient and easily fabricated, design promises operational reconfigurability combined with amplitude tunability. © 2011 Wiley Periodicals, Inc. Microwave Opt Technol Lett 53:2472–2474, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/mop.26316
Improved axial feeding of Fabry–Perot resonator for high‐resolution spectroscopy applications
Authors: Černý Petr , Piksa Petr , Zvánovec Stanislav , Kořínek Tomáš , Kabourek Václav
Published: August 2011

This article presents the methods of broadband axial feeding of a Fabry–Perot resonator. The resonator was originally designed with the radial excitation for the absorption measurement in the frequency band ranging from 18 to 80 GHz. If the frequency stays below ∼26.4 GHz, the excitation of resonator is less satisfactory, since at the frequency in question, the value of Fresnel number of resonator drops to one. For the broadband measurement of gaseous samples' emission spectra, the excitations for frequencies lower than 26.4 GHz were analyzed using the capacitive coupling and two newly proposed couplings. © 2011 Wiley Periodicals, Inc. Microwave Opt Technol Lett 53:2456–2462, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/mop.26344
An algorithm to identify avoidance behavior in moving object trajectories
Authors: Alvares Luis Otavio , Loy Alisson Moscato , Renso Chiara , Bogorny Vania
Published: August 2011

Research on trajectory behavior has increased significantly in the last few years. The focus has been on the search for patterns considering the movement of the moving object in space and time, essentially looking for similar geometric properties and dense regions. This paper proposes an algorithm to detect a new kind of behavior pattern that identifies when a moving object is avoiding specific spatial regions, such as security cameras. This behavior pattern is called avoidance. The algorithm was evaluated with real trajectory data and achieved very good results.
Unique relations of age and delinquency with cognitive control☆
Authors: Iselin Anne‐Marie R. , DeCoster Jamie
Published: August 2011

Context processing has significant empirical support as an explanation of age‐ and psychopathology‐related deficiencies in cognitive control. We examined whether context processing generalizes to younger individuals who are in trouble with the law. We tested whether age and delinquency might have unique relations to context processing skills in four samples of male participants: adolescent offenders (n = 43), control adolescents (n = 33), young adult offenders (n = 40), and control young adults (n = 31). We used a modified Stroop task to measure context processing (i.e., attention, memory, and response inhibition). Task performance was superior for older participants in conditions most demanding of context processing skills. Adolescent offenders and control adolescents showed difficulties engaging selective attention to filter out irrelevant information, even after controlling for the effects of age. Control adolescents made the most errors in the condition most demanding of context processing, whereas the other three samples showed slower processing but fewer errors in context processing.
Recent advances in cytochrome bc1: Inter monomer electronic communication?
Authors: Khalfaoui-Hassani Bahia , Lanciano Pascal , Lee Dong-Woo , Darrouzet Elisabeth , Daldal Fevzi
Published: August 2011

The ubihydroquinone: cytochrome c oxidoreductase, or cytochrome bc
1, is a central component of photosynthetic and respiratory energy transduction pathways in many organisms. It contributes to the generation of membrane potential and proton gradient used for cellular energy production (ATP). The three‐dimensional structures of cytochrome bc
1 indicate that its two monomers are intertwined to form a symmetrical homodimer. This unusual architecture raises the issue of whether the monomers operate independently, or function cooperatively during the catalytic cycle of the enzyme. In this review, recent progresses achieved in our understanding of the mechanism of function of dimeric cytochrome bc
1 are presented. New genetic approaches producing heterodimeric enzymes, and emerging insights related to the inter monomer electron transfer between the heme b cofactors of cytochrome bc
1 are described.
Ovarian cancer during pregnancy
Authors: Gezginç Kazım , Karataylı Rengin , Yazıcı Fatma , Acar Ali , Çelik Çetin , Çapar Metin
Published: August 2011

Objective

To evaluate the clinical features, pregnancy outcome, and treatment of patients with ovarian cancer diagnosed during pregnancy.

Methods

The present study was a retrospective review of 11 cases of ovarian cancer detected during pregnancy. The women were treated and followed up at Selçuk University, Meram Faculty of Medicine, Konya, Turkey, during 2006–2010.

Results

Approximately half the patients were asymptomatic (5 [45.5%]) and diagnosed during cesarean delivery (6 [54.5%]). The histopathologic tumor categories comprised malignant epithelial ovarian tumor (4 [36.4%]), borderline tumor (4 [36.4%]), malignant germ cell tumor (2 [18.2%]), and sex cord stromal tumor (1 [9.1%]). Nine (81.8%) tumors were classified as stage I. Conservative surgery was performed in 10 (90.9%) patients. A patient with stage IIIC serous papillary adenocarcinoma underwent hysterectomy with bilateral salpingo‐oophorectomy. A patient with dysgerminoma in stage IV died on follow‐up. Three infants were born premature; they were followed up in the neonatal intensive care unit with satisfactory outcomes.

Conclusion

Early diagnosis and appropriate treatment are crucial for patients with ovarian cancer diagnosed during pregnancy. Tumor staging is possible during pregnancy, but the appropriateness of surgery needs to be considered carefully. Ideally, the treatment strategy should be discussed and structured on an individual basis.
Stillbirth rate at an emerging tertiary health institution in Enugu, southeast Nigeria
Authors: Ezugwu Euzebus C. , Onah Hyacinth E. , Ezegwui Hygenius U. , Nnaji Chidi
Published: August 2011

Objectives

To determine the stillbirth rate and factors predisposing to a stillbirth delivery at a teaching hospital in Nigeria, with the aim of identifying solutions.

Method

A descriptive study of all stillbirths delivered at Enugu State University of Science and Technology Teaching Hospital, Parklane, Nigeria between January 1 and December 31, 2009. The sociodemographic characteristics of the mothers were documented and the possible causes of death were analyzed.

Results

There were 153 stillbirths and 2064 total deliveries, giving a stillbirth rate of 74 per 1000 deliveries. Of the stillbirths, 52.3% were fresh and 47.7% were macerated. Women who had not received prenatal care had a significantly higher stillbirth rate (P < 0.05). The most likely cause of a macerated stillbirth was a hypertensive disorder of pregnancy, whereas the likely causes of fresh stillbirths were labor‐related. The “3 levels of delay” and injudicious use of oxytocin in labor contributed to the intrapartum stillbirths (P < 0.05).

Conclusion

The stillbirth rate recorded in the study institution is unacceptably high. Appropriate prenatal care, timely intervention, and prompt and appropriate intrapartum care are key to achieving a reduction in the stillbirth rate.
A 5‐day educational program for teaching cervical cancer screening using visual inspection with acetic acid in low‐resource settings
Authors: Levine Lisa D. , Chudnoff Scott G. , Taylor Kathleen , Baganizi Michael , Banks Erika
Published: August 2011

Objective

To assess the effectiveness of an educational program in visual inspection with acetic acid (VIA) for cervical cancer screening among healthcare providers in 2 low‐resource countries.

Methods

A cohort of multidisciplinary healthcare workers in Uganda and El Salvador were recruited to the study. A pretest was administered before the intervention of a 5‐day educational program on VIA. A posttest was performed immediately after the educational program and again at a 6‐month follow‐up visit to assess retention of knowledge.

Results

In total, 42 (93%) of the healthcare workers who participated in the educational program completed the initial posttest evaluation, and 18 (40%) healthcare workers completed the 6‐month follow‐up evaluation. Mean test scores increased after participation in the training session (62% versus 81%; P < 0.001). The self‐reported comfort level for identifying cellular abnormalities also increased (2.1 versus 3.3; P < 0.001). At 6‐month follow‐up, the mean test score remained higher than pretest scores (79% versus 57%; P < 0.001). There was no significant difference in the initial and 6‐month posttest scores (80% versus 79%; P = 0.20).

Conclusion

The educational program in VIA provided healthcare workers with the tools potentially to decrease the morbidity and mortality of cervical cancer in the 2 low‐resource countries.
“The (Real) World is not Enough:” Motivational Drivers and User Behavior in Virtual Worlds
Authors: Eisenbeiss Maik , Blechschmidt Boris , Backhaus Klaus , Freund Philipp Alexander
Published: August 2011

Virtual worlds (VWs) have become increasingly prominent during the past decade, populated by individual users and more recently, even “real world” firms. To effectively use a VW for business purposes, a relevant question for those firms pertains to why people use VWs and which motivational drivers might influence their participation behavior. This study offers an early analysis of the topic by extending a social influence model to explain participation behavior in a new, marketing-relevant context and identify specific motivational drivers of VW participation. Socializing, creativity, and escape emerge as individual drivers. Accounting for user heterogeneity also reveals four latent segments, each characterized by a distinct motivational driver, and one segment that reflects mixed motives. The segments differ substantially in their descriptive characteristics (e.g., usage intensity, overall spending behavior). These results have significant implications for research, VW operators, and companies doing business in VWs.
Quantifying hyporheic exchange at high spatial resolution using natural temperature variations along a first‐order stream
Authors: Westhoff M. C. , Gooseff M. N. , Bogaard T. A. , Savenije H. H. G.
Published: August 2011

Hyporheic exchange is an important process that underpins stream ecosystem function, and there have been numerous ways to characterize and quantify exchange flow rates and hyporheic zone size. The most common approach, using conservative stream tracer experiments and 1‐D solute transport modeling, results in oversimplified representations of the system. Here we present a new approach to quantify hyporheic exchange and the size of the hyporheic zone (HZ) using high‐resolution temperature measurements and a coupled 1‐D transient storage and energy balance model to simulate in‐stream water temperatures. Distributed temperature sensing was used to observe in‐stream water temperatures with a spatial and temporal resolution of 2 and 3 min, respectively. The hyporheic exchange coefficient (which describes the rate of exchange) and the volume of the HZ were determined to range between 0 and 2.7 × 10−3 s−1 and 0 and 0.032 m3 m−1, respectively, at a spatial resolution of 1–10 m, by simulating a time series of in‐stream water temperatures along a 565 m long stretch of a small first‐order stream in central Luxembourg. As opposed to conventional stream tracer tests, two advantages of this approach are that exchange parameters can be determined for any stream segment over which data have been collected and that the depth of the HZ can be estimated as well. Although the presented method was tested on a small stream, it has potential for any stream where rapid (in regard to time) temperature change of a few degrees can be obtained.
A Pool of Queries: Interactive Multidimensional Query Visualization for Information Seeking in Digital Libraries
Authors: Seifert Inessa
Published: August 2011

In this article, I present a novel relational visualization that supports people at exploration of scientific literature in digital libraries. This visualization provides an integrated view of multiple dimensions concealed in the scientific literature. It displays, for example, authors and scientific organizations together with freely defined search queries and highlights the intersections between them. The proposed visual representation introduces interactive drag-and-drop operations for manipulation of queries in order to retrieve further results. These operations enable information seekers to employ efficient online search strategies that involve Boolean AND, OR and NOT operators. In doing so, an information seeker can refine (or relax) various search queries in an interactive way during a focusing or a defocusing phase. The intersections of queries are made explicitly visible to enable the information seeker to build an individual picture of the research area under investigation and to avoid frustrating ‘zero hit’ situations.
Mechanism of thermal conductivity reduction in few-layer graphene
Authors: Singh Dhruv , Murthy Jayathi Y. , Fisher Timothy S.
Published: August 2011

Using the linearized Boltzmann transport equation and perturbation theory, we analyze the reduction in the intrinsic thermal conductivity of few-layer graphene sheets accounting for all possible three-phonon scattering events. Even with weak coupling between layers, a significant reduction in the thermal conductivity of the out-of-plane acoustic modes is apparent. The main effect of this weak coupling is to open many new three-phonon scattering channels that are otherwise absent in graphene. However, reflection symmetry is only weakly broken with the addition of multiple layers, and out-of-plane acoustic phonons still dominate thermal conductivity. We also find that reduction in thermal conductivity is mainly caused by lower contributions of the higher-order overtones of the fundamental out-of-plane acoustic mode. The results compare remarkably well over the entire temperature range with measurements of graphene and graphite.
Magnetism and bonding in graphene nanodots with H modified interior, edge, and apex
Authors: Philpott Michael R. , Prabhat  , Kawazoe Yoshiyuki
Published: August 2011

Ab initio density functional theory calculations of hexagonal shaped zigzag edged graphene nanodot molecules, modified by the addition of atomic H to interior and perimeter sites, predict significant changes to the hexagonally sectored spin distribution and chemical bonding of the originals. The redistribution of Kohn-Sham levels at the top of the valence manifold from parent to derivative hint at large changes in the electronic structure. A centrally added H atom creates an occupied level in the middle of the 0.3 eV band gap of the parent molecule and is surrounded by an island of spins. The latter is isolated enough from the perimeter to provide a calibration of the edge spins of the modified parent. Mid-edge addition of a H atom “quenches” the spin on the edge by drawing a pz-electron into the C-H bond without reducing the spin on the other edges. Addition of H to an apex carbon atom results in a localized spin freed from the double bond that coexists with the parent spin on the same edge. Saturating the apex double bond by adding two H atoms, returns π-levels shifted in energy and index and parent-like spin patterns on all edges, intact except for small changes on the edges joined at the apex. Taken in unison these results demonstrate how atomic hydrogen and other groups could be used to engineer the magnetism of graphene nanodots.
Modeling of nanocluster formation by ion beam implantation
Authors: Li Kun-Dar
Published: August 2011

A theoretical model was developed to investigate the mechanism of the formation of nanoclusters via ion beam implantation. The evolution of nanoclusters, including the nucleation and growth process known as Ostwald ripening, was rebuilt using numerical simulations. The effects of implantation parameters such as the ion energy, ion fluence, and temperature on the morphology of implanted microstructures were also studied through integration with the Monte Carlo Transport of Ions in Matter code calculation for the distribution profiles of implanted ions. With an appropriate ion fluence, a labyrinth-like nanostructure with broad size distributions of nanoclusters formed along the ion implantation range. In a latter stage, a buried layer of implanted impurity developed. With decreasing ion energy, the model predicted the formation of precipitates on the surface. These simulation results were fully consistent with many experimental observations. With increased temperature, the characteristic length and size of nanostructures would increase due to the high mobility. This theoretical model provides an efficient numerical approach for fully understanding the mechanism of the formation of nanoclusters, allowing for the design of ion beam experiments to form specific nanostructures through ion-implantation technology.
Mean velocity and length-scales in the overlap region of wall-bounded turbulent flows
Authors: Mizuno Yoshinori , Jiménez Javier
Published: August 2011

The length scales of the spectra and correlation functions of the velocity fluctuations in the overlap region of turbulent wall-bounded flows are analyzed. It is found that a mixing length based on the mean local shear works better as a normalization than the distance to the wall. To define an overlap range sufficiently long and independent of the Reynolds number to allow the two scalings to be tested, the classical asymptotic expansion of the mean shear is extended to include a near-wall virtual origin and a wake component. The result represents well the velocity profile in y+ > 70 and y/δ < 0.3 – 0.5 for Reτ≿2000, and the spectral scales for Reτ≿500. It is suggested that the scaling with a local mixing length could be interpreted as an indication that the size of the eddies is more related to the local shear time scale than to the interaction with the wall. It is also noted that the linearity of the mixing length is a more robust indicator of a logarithmic regime than those that rely on a zero virtual origin.
Polarized Raman scattering in monolayer, bilayer, and suspended bilayer graphene
Authors: Sahoo Satyaprakash , Palai R. , Katiyar R. S.
Published: August 2011

Polarized resonant Raman scattering studies have been performed on monolayer, bilayer, and suspended bilayer graphene. The intensity of the G band is found to be unchanged with polarization in monolayer and bilayer graphene, whereas it shows polarization dependence in suspended bilayer graphene. The 2D mode shows strong polarization depended behavior for all the samples, irrespective of layer thickness. It is found that the intensity of the 2D peak is at a maximum when the incident photon is parallel to the scattered photon and at a minimum when these are perpendicular to each other. This effect has been explained on the basis of anisotropic photon scattering through the nodes at the K-point of the Brillouin zone in graphene during optical absorption.
A quasi-droplet optofluidic ring resonator laser using a micro-bubble
Authors: Lee Wonsuk , Sun Yuze , Li Hao , Reddy Karthik , Sumetsky Misha , Fan Xudong
Published: August 2011

Optofluidic ring resonator lasers based on micro-bubbles filled with liquid gain medium are demonstrated. Due to the sub-micron wall thickness of the micro-bubble, significant amount of the electric field resides inside the liquid. Consequently, micro-bubbles mimic the droplets in air that have 3-dimensional optical confinement, extremely high Q-factors, and versatility in handling liquids of different refractive index. Furthermore, they enable repetitive interrogation and easy directional laser emission out-coupling without evaporation or size/shape variations. The laser using Rhodamine 6G in methanol is achieved with a threshold of 300 nJ/mm2 and 5.3 μJ/mm2 for 1 mM and 10 μM in concentration, respectively.
An Exact Model of an Anisotropic Relativistic Sphere
Authors: Patel LK , Mehta NP
Published: August 2011

In this paper the field equations of general relativity are solved to obtain an exact solution for a static anisotropic fluid sphere. The solution is free from singularity and satisfies the necessary physical requirements. The physical 3-space of the solution is pseudo-spheroidal. The solution is matched at the boundary with the Schwarzschild exterior solution. Numerical estimates of various physical parameters are briefly discussed.
Comment on FTI Method and Transport Coefficient Definitions for Charged Particle Swarms in Gases
Authors: Robson RE
Published: August 2011

The kinetic theory of charged particle swarms in gases is based upon solution of the space and time dependent Boltzmann's equation for the phase space distribution function f(r, c, t). Hydrodynamic transport coefficients are defined in connection with a density gradient expansion (DGE) of f(r, c, t) and it is believed that these are the quantities measured in experiment. On the other hand, Ikuta and coworkers start with the spatially independent form of the Boltzmann equation, which they solve iteratively as in path-integral methods, and define transport coefficients in terms of the 'starting rate distribution', rather than f itself. Ikuta's procedure has come to be known as the 'flight time integral' (FTI) method and the discrepancies between numerical calculations based upon this and the more commonly known DGE procedure have generated a deal of controversy in recent times. The purpose of this paper is to point out that the respective definitions of the transverse diffusion coefficient DT coincide only for light swarm particles undergoing collisions for which the differential cross section is isotropic, and that the particular technique used for solving Boltzmann's equation, be it a path-integral or a multi-term method, has nothing to do with the numerical discrepancies which are observed when scattering is anisotropic. In particular, it is shown that Ikuta's definition of DT is inconsistent with even the well established result for constant collision frequency.
Chirality-dependent Plasma Density Profile Changes from Helicon Wave Ponderomotive Forces
Authors: Petržílka V , Dewar RL
Published: August 2011

It is shown that nonresonant helicon-wave-induced transport may result in significant changes in the plasma density radial profile; this is illustrated using parameters appropriate to the cylindrical experiment BASIL and the toroidal experiment SHEILA. Whereas m = +1 helicon waves induce an inward-directed transport and change the density profile to a more centrally peaked one with a higher density on the axis, m = −1 helicon waves induce an outward-directed transport velocity and change the density profile to a hollow one. This may be the clue to the puzzle as to why m = −1 helicon waves are frequently difficult or impossible to excite, as the plasma column is effectively blown off to the discharge chamber walls by the ponderomotive force density of the waves with this chirality (sense of rotation of the wavevector with respect to the axial or toroidal magnetic field).
Systematics of the Electroweak Plasma at Finite Temperature I
Authors: Smith BJK , Witte NS , Hines KC
Published: August 2011

This paper provides a systematic treatment of the finite temperature field theory which will be required for the subsequent calculation in detail (given in the second paper in this series) of the linear response properties of the electroweak plasma at finite temperature at the one-loop level in the R{ gauge. Following a brief summary of the path integral formalism in field theory, the finite temperature theory is introduced with emphasis on the relevant Feynman rules and Matsubara sums. The polarisation tensor for the electroweak plasma is calculated by analysing the appropriate Feynman diagrams. The contributions to the one-loop polarization tensor are calculated for the tadpole, loop and balloon diagrams in a form suitable for the subsequent investigation of electroweak plasma properties.
Short-range Correlation Effect on p?p Elastic Scattering with the Composite Model
Authors: A Hassan Mohamed , El-Aziz R Yousef Abd , SA Hassan Samia
Published: August 2011

Using a representation of the quark distribution inside the proton, where a short-range correlation between quarks is considered, we can describe the p-p elastic scattering differential cross section with experimental agreement in the range 0 :::; q2 :::; 10 (GeV/ c)2. Evaluations of the proton core and quark radii are obtained. From our analysis, we see that the suggested configuration of quarks inside the proton can be considered as a nearly realistic distribution even with a non-relativistic wavefunction.
Renormalised Perturbation Theory of Resonant Multiphoton Ionisation
Authors: Unnikrishnan K
Published: August 2011

Perturbation theory of multiphoton ionisation due to a classical electromagnetic field is modified to allow for intermediate resonances with bound states. Complex energies, generally associated with resonances, do not enter into this formalism. For a monochromatic field of frequency u, a constant ionisation rate can then be defined unambiguously and only such continuum states are excited which correspond to the absorption of energy in integral multiples of hu. As an application, differential and total cross sections for the two-photon ionisation of hydrogen, for frequencies below the n = 3 resonance region, are obtained in closed form. Existing data for generalised cross sections, calculated numerically using the complex coordinate method, are in good agreement with the present results. Finally, the mean fractional ionisation resulting from a pulse of finite duration is estimated on the basis of the associated power spectrum. For short pulses, the time dependence of ionisation exhibits a departure from that expected of a time-independent rate.
Hamiltonian Maps for Heliac Magnetic Islands
Authors: Davidson MG , Dewar RL , Gardner HJ , Howard J
Published: August 2011

Magnetic islands in toroidal heliac stellarator vacuum fields are explored with Hamiltonian chaos theory and the associated area-preserving maps. Magnetic field line island chains are examined first analytically, with perturbation theory, and then numerically to produce Poincaré sections, which are compared with H−1 Heliac stellarator puncture plot diagrams. Rotational transform profiles are chosen to permit the comparison of twist map and nontwist map predictions with field line behaviour computed by a field line tracing computer program and observed experimentally.
Extending KNIME for next-generation sequencing data analysis
Authors: Jagla Bernd , Wiswedel Bernd , Coppée Jean-Yves
Published: August 2011

Summary: KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis and exploration platform. We present here new functionality and workflows that open the door to performing next-generation sequencing analysis using the KNIME framework.

Availability: All sources and compiled code are available via the KNIME update mechanism. Example workflows and descriptions are available through http://tech.knime.org/community/next-generation-sequencing.

Contact:  bernd.jagla@pasteur.fr

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Spatial clustering of protein binding sites for template based protein docking
Authors: Ghoorah Anisah W. , Devignes Marie-Dominique , Smaïl-Tabbone Malika , Ritchie David W.
Published: August 2011

Motivation: In recent years, much structural information on protein domains and their pair-wise interactions has been made available in public databases. However, it is not yet clear how best to use this information to discover general rules or interaction patterns about structural protein–protein interactions. Improving our ability to detect and exploit structural interaction patterns will help to provide a better 3D picture of the known protein interactome, and will help to guide docking-based predictions of the 3D structures of unsolved protein complexes.

Results: This article presents KBDOCK, a 3D database approach for spatially clustering protein binding sites and for performing template-based (knowledge-based) protein docking. KBDOCK combines residue contact information from the 3DID database with the Pfam protein domain family classification together with coordinate data from the Protein Data Bank. This allows the 3D configurations of all known hetero domain–domain interactions to be superposed and clustered for each Pfam family. We find that most Pfam domain families have up to four hetero binding sites, and over 60% of all domain families have just one hetero binding site. The utility of this approach for template-based docking is demonstrated using 73 complexes from the Protein Docking Benchmark. Overall, up to 45 out of 73 complexes may be modelled by direct homology to existing domain interfaces, and key binding site information is found for 24 of the 28 remaining complexes. These results show that KBDOCK can often provide useful information for predicting the structures of unknown protein complexes.

Availability:  http://kbdock.loria.fr/

Contact:  Dave.Ritchie@inria.fr

Supplementary Information:  Supplementary data are available at Bioinformatics online.
iMod: multipurpose normal mode analysis in internal coordinates
Authors: Lopéz-Blanco José Ramón , Garzón José Ignacio , Chacón Pablo
Published: August 2011

Motivation: Dynamic simulations of systems with biologically relevant sizes and time scales are critical for understanding macromolecular functioning. Coarse-grained representations combined with normal mode analysis (NMA) have been established as an alternative to atomistic simulations. The versatility and efficiency of current approaches normally based on Cartesian coordinates can be greatly enhanced with internal coordinates (IC).

Results: Here, we present a new versatile tool chest to explore conformational flexibility of both protein and nucleic acid structures using NMA in IC. Consideration of dihedral angles as variables reduces the computational cost and non-physical distortions of classical Cartesian NMA methods. Our proposed framework operates at different coarse-grained levels and offers an efficient framework to conduct NMA-based conformational studies, including standard vibrational analysis, Monte-Carlo simulations or pathway exploration. Examples of these approaches are shown to demonstrate its applicability, robustness and efficiency.

Contact:  pablo@chaconlab.org

Supplementary Information:  Supplementary data are available at Bioinformatics online.
The Shareholder Voice: British and American Accents, 1890–1965
Authors: Rutterford Janette
Published: August 2011

This article discusses the interaction between directors and small shareholders who made up the majority of names on the share ledgers of many companies in both the UK and the USA. It is concerned with the period 1890–1965 and concentrates on the management/shareholder relationship in the context of the annual general meeting and shareholder activism. I argue that there were significant differences between shareholder activism in the UK and the USA, due to the difference in relative numbers of the shareholders themselves, to legal and geographic differences, to corporate culture, and to the earlier diffusion of shareholding in the UK compared to the USA. UK shareholders concentrated their interventions on management issues, as well as some social and labor matters. US shareholders, mostly through so-called ‘corporate gadflies’, concentrated their efforts on corporate governance issues, some of which were already enshrined in UK company law and practice.
Golden Perspective: Application of Laser‐Generated Gold Nanoparticle Conjugates in Reproductive Biology
Authors: Barchanski A , Taylor U , Klein S , Petersen S , Rath D , Barcikowski S
Published: August 2011

Contents

The current demand for female calves has grown rapidly and controlling the sex of offspring provides an economically flexible management for the livestock producer. The only functioning method of efficiently producing separate populations of X and Y sperm in mammals is based on relative DNA differentiation by high‐speed flow cytometry. In this context, gold nanoparticles conjugated to sex chromosome‐specific moieties display promising application as novel fluorophor‐alternative for the high‐throughput screening, since they feature no photo bleaching, high quantum yield, good biocompatibility and the possibility of non‐destructive membrane penetration. Especially, gold nanoparticles fabricated by pulsed laser ablation are in the recent focus of interest, due to excellent biocompatibility, fabrication‐dependent, tuneable particle size as well as surface charge and ease of (bio)‐functionalization with a remarkably strong ligand binding. For the purpose of our studies functionalized gold nanoparticles may be used as novel markers for sex‐sorting of mammalian sperm and, depending on the selected probe, also for the selection of sperm with heritable DNA‐sequences interesting for animal breeding.