bluuebunny/crossref_metadata_2025 huggingface dataset:
Generation of tumour‐necrosis‐factor‐α‐specific affibody1 molecules capable of blocking receptor binding in vitro
Authors: Jonsson Andreas , Wållberg Helena , Herne Nina , Ståhl Stefan , Frejd Fredrik Y.
Published: June 2009

Affibody molecules specific for human TNF‐α (tumour necrosis factor‐α) were selected by phage‐display technology from a library based on the 58‐residue Protein A‐derived Z domain. TNF‐α is a proinflammatory cytokine involved in several inflammatory diseases and, to this day, four TNF‐α‐blocking protein pharmaceuticals have been approved for clinical use. The phage selection generated 18 unique cysteine‐free affibody sequences of which 12 were chosen, after sequence cluster analysis, for characterization as proteins. Biosensor binding studies of the 12 Escherichia coli‐produced and IMAC (immobilized‐metal‐ion affinity chromatography)‐purified affibody molecules revealed three variants that demonstrated the strongest binding to human TNF‐α. These three affibody molecules were subjected to kinetic binding analysis and also tested for their binding to mouse, rat and pig TNF‐α. For ZTNF‐α:185, subnanomolar affinity (KD=0.1–0.5 nM) for human TNF‐α was demonstrated, as well as significant binding to TNF‐α from the other species. Furthermore, the binding site was found to overlap with the binding site for the TNF‐α receptor, since this interaction could be efficiently blocked by the ZTNF‐α:185 affibody. When investigating six dimeric affibody constructs with different linker lengths, and one trimeric construct, it was found that the inhibition of the TNF‐α binding to its receptor could be further improved by using dimers with extended linkers and/or a trimeric affibody construct. The potential implication of the results for the future design of affibody‐based reagents for the diagnosis of inflammation is discussed.
Analysis of phospholipids, sterols, and fatty acids in Taxus chinensis var. mairei cells in response to shear stress
Authors: Han Pei‐pei , Zhou Jian , Yuan Ying‐jin
Published: June 2009

Plant cell culture has been developed as an alternative method for the production of an anticancer drug, paclitaxel. However, the sensitivity of plant cells to shear stress has been one of the main obstacles to the scale‐up of the plant cell culture. To gain a better understanding of the mechanism of plant cells' response to hydrodynamic mechanical stress, lipid profiling of suspension‐cultured Taxus chinensis (Chinese yew) var. mairei cells under shear stress was carried out using liquid chromatography–tandem MS and gas chromatography–time‐of‐flight MS. T. chinensis var. mairei cells cultured in a Couette‐type shear reactor responded with an increase of cell membrane permeability compared with control cells, which indicated that the adaptation to shear stress altered membrane lipid composition. The main changes of lipid profiles in the shear‐stress‐induced cells were the following: (a) the total phospholipid content decreased, especially that of structural phospholipids such as phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine; (b) cells showed increased stigmasterol at the expense of sitosterol and campesterol; (c) the stigmasterol/phospholipid ratio increased; (d) the mono‐unsaturated‐fatty‐acid content increased; (e) the shear‐stress‐induced cells accumulated very‐long‐chain saturated fatty acids (C22:0, C23:0, C24:0 and C25:0). These findings suggested alterations in membrane composition and hinted at a possible molecular basis for the mechanotransduction processes induced by shear stress in T. chinensis var. mairei cells.
Origin of pyrimidine deoxyribonucleotide pools in perfused rat heart: implications for 3′-azido-3′-deoxythymidine-dependent cardiotoxicity
Authors: Morris Gerald W. , Iams Tyler A. , Slepchenko Kira G. , McKee Edward E.
Published: June 2009

In adult non-replicating tissues such as heart, demand for dNTPs (deoxynucleoside triphosphates) is low but essential for mitochondrial DNA replication and nuclear DNA repair. dNTPs may be synthesized from salvage of deoxyribonucleosides or by reduction of ribonucleotides. We have hypothesized that the cardiac mitochondrial toxicity of the nucleoside analogue AZT (3′-azido-3′-deoxythymidine; known as zidovudine) is caused by inhibition of thymidine kinase 2 of the salvage pathway and subsequent TTP pool depletion. The extent to which this hypothesis has merit depends on how much the heart relies on thymidine phosphorylation for maintenance of the TTP pool. In the present study, we used isotopic tracing to demonstrate that both TTP and dCTP are solely synthesized by phosphorylation of thymidine and deoxycytidine respectively, with no evidence for synthesis from other precursors. We have also shown that UTP and CTP are synthesized by phosphorylation of uridine and cytidine respectively, with no detectable role for the de novo pyrimidine synthesis pathway. Lastly, we have demonstrated that AZT decreased the TTP pool by 50% in 30 min of perfusion, while having no effect on other dNTPs. In summary, the present study demonstrated that adult rat heart has a limited mechanism for dCTP and TTP synthesis and thus these pools may be more sensitive than replicating cells to drugs such as AZT that affect the salvage pathway.
Ephrin-independent regulation of cell substrate adhesion by the EphB4 receptor
Authors: Noren Nicole K. , Yang Nai-Ying , Silldorff Morgan , Mutyala Ravi , Pasquale Elena B.
Published: June 2009

Receptor tyrosine kinases of the Eph family become tyrosine phosphorylated and initiate signalling events upon binding of their ligands, the ephrins. Eph receptors such as EphA2 and EphB4 are highly expressed but poorly tyrosine phosphorylated in many types of cancer cells, suggesting a limited interaction with ephrin ligands. Nevertheless, decreasing the expression of these receptors affects the malignant properties of cancer cells, suggesting that Eph receptors may influence cancer cells independently of ephrin stimulation. Ligand-independent activities of Eph receptors in cancer, however, have not been demonstrated. By using siRNA (small interfering RNA) to downregulate EphB4 in MCF7 and MDA-MB-435 cancer cells, we found that EphB4 inhibits integrin-mediated cell substrate adhesion, spreading and migration, and reduces β1-integrin protein levels. Low expression of the EphB4 preferred ligand, ephrin-B2, and minimal contact between cells in these assays suggest that cell contact-dependent stimulation of EphB4 by the transmembrane ephrin-B2 ligand does not play a role in these effects. Indeed, inhibitors of ephrin-B2 binding to endogenous EphB4 did not influence cell substrate adhesion. Increasing EphB4 expression by transient transfection inhibited cell substrate adhesion, and this effect was also independent of ephrin stimulation because it was not affected by single amino acid mutations in EphB4 that impair ephrin binding. The overexpressed EphB4 was tyrosine phosphorylated, and we found that EphB4 kinase activity is important for inhibition of integrin-mediated adhesion, although several EphB4 tyrosine phosphorylation sites are dispensable. These findings demonstrate that EphB4 can affect cancer cell behaviour in an ephrin-independent manner.
Generation and functional characterization of a BCL10-inhibitory peptide that represses NF-κB activation
Authors: Marasco Daniela , Stilo Romania , Sandomenico Annamaria , Monti Simona Maria , Tizzano Barbara , de Capua Antonia , Varricchio Ettore , Liguoro Domenico , Zotti Tiziana , Formisano Silvestro , Ruvo Menotti , Vito Pasquale
Published: June 2009

The molecular complex containing BCL10 and CARMA [CARD (caspase recruitment domain)-containing MAGUK (membrane-associated guanylate kinase)] proteins has recently been identified as a key component in the signal transduction pathways that regulate activation of the transcription factor NF-κB (nuclear factor κB) in lymphoid and non-lymphoid cells. Assembly of complexes containing BCL10 and CARMA proteins relies on homophilic interactions established between the CARDs of these proteins. In order to identify BCL10-inhibitory peptides, we have established a method of assaying peptides derived from the CARD of BCL10 in binding competition assays of CARD–CARD self-association. By this procedure, a short peptide corresponding to amino acid residues 91–98 of BCL10 has been selected as an effective inhibitor of protein self-association. When tested in cell assays for its capacity to block NF-κB activation, this peptide represses activation of NF-κB mediated by BCL10, CARMA3 and PMA/ionomycin stimulation. Collectively, these results indicate that residues 91–98 of BCL10 are involved in BCL10 self-association and also participate in the interaction with external partners. We also show that blocking of the CARD of BCL10 may potentially be used for the treatment of pathological conditions associated with inappropriate NF-κB activation.
Recruitment of NAADP-sensitive acidic Ca2+ stores by glutamate
Authors: Pandey Vinita , Chuang Chia-Chen , Lewis Alexander M. , Aley Parvinder K. , Brailoiu Eugen , Dun Nae J. , Churchill Grant C. , Patel Sandip
Published: June 2009

NAADP (nicotinic acid–adenine dinucleotide phosphate) is an unusual second messenger thought to mobilize acidic Ca2+ stores, such as lysosomes or lysosome-like organelles, that are functionally coupled to the ER (endoplasmic reticulum). Although NAADP-sensitive Ca2+ stores have been described in neurons, the physiological cues that recruit them are not known. Here we show that in both hippocampal neurons and glia, extracellular application of glutamate, in the absence of external Ca2+, evoked cytosolic Ca2+ signals that were inhibited by preventing organelle acidification or following osmotic bursting of lysosomes. The sensitivity of both cell types to glutamate correlated well with lysosomal Ca2+ content. However, interfering with acidic compartments was largely without effect on the Ca2+ content of the ER or Ca2+ signals in response to ATP. Glutamate but not ATP elevated cellular NAADP levels. Our results provide evidence for the agonist-specific recruitment of NAADP-sensitive Ca2+ stores by glutamate. This links the actions of NAADP to a major neurotransmitter in the brain.
DNA damage signalling recruits RREB-1 to the p53 tumour suppressor promoter
Authors: Liu Hanshao , Hew Hoi Chin , Lu Zheng-Guang , Yamaguchi Tomoko , Miki Yoshio , Yoshida Kiyotsugu
Published: June 2009

Transcriptional regulation of the p53 tumour suppressor gene plays an important role in the control of the expression of various target genes involved in the DNA damage response. However, the molecular basis of this regulation remains obscure. In the present study we demonstrate that RREB-1 (Ras-responsive-element-binding protein-1) efficiently binds to the p53 promoter via the p53 core promoter element and transactivates p53 expression. Silencing of RREB-1 significantly reduces p53 expression at both the mRNA and the protein levels. Notably, disruption of RREB-1-mediated p53 transcription suppresses the expression of the p53 target genes. We also show that, upon exposure to genotoxic stress, RREB-1 controls apoptosis in a p53-dependent manner. These findings provide evidence that RREB-1 participates in modulating p53 transcription in response to DNA damage.
Chronic fatigue syndrome: comments on deconditioning, blood volume and resulting cardiac function
Authors: Stewart Julian M.
Published: June 2009

Cardiovascular and autonomic dysfunction have been suggested to underlie the symptoms accompanying CFS (chronic fatigue syndrome). In the present issue of Clinical Science, Hurwitz and co-workers have investigated whether deficits were present in cardiac output and blood volume in a cohort of patients with CFS and if these were linked to illness severity and sedentary lifestyle. The results clearly demonstrate reduced cardiac stroke volume and cardiac output in more severely afflicted patients with CFS, which is primarily attributable to a measurable reduction in blood volume. Similar findings are observed in microgravity and bed rest deconditioning, in forms of orthostatic intolerance and, to a lesser extent, in sedentary people. The circulatory consequences of reduced cardiac output may help to account for many of the findings of the syndrome.
Phonological Milestones for African American English-Speaking Children Learning Mainstream American English as a Second Dialect
Authors: Pearson Barbara Z. , Velleman Shelley L. , Bryant Timothy J. , Charko Tiffany
Published: June 2009

Purpose

This study provides milestones for phonological development in African American English (AAE) speakers who are learning Mainstream American English (MAE) as a second dialect.

Method

The Dialect Sensitive Language Test (DSLT; H. Seymour, T. Roeper, & J. G. de Villiers, 2000) was administered to a nationwide sample of typically developing children ages 4 through 12: 537 speakers of AAE as a first dialect and 317 speakers of MAE as a first dialect. DSLT items tested all consonant segments and many clusters of MAE in initial and final position. The age at which each dialect group reached 90% criterion for each segment in each position was compared.

Results

Several phonetic elements that are contrastive between the dialects (i.e., differentiate the dialects) in word-finalposition were found to be similar in the 2 groups in word-initialposition. Only /ð/ was contrastive in both positions. We confirm the later acquisition of certain phonological segments and structures by AAE speakers compared to MAE speakers and report their earlier mastery of other elements of MAE phonology.

Conclusion

Both segmental and phonotactic development show different trajectories for AAE and MAE. Thus, initial diagnosis of impairment for AAE children should focus only on mastery of noncontrastive segments and structures that share a similar developmental profile for the 2 dialect groups.
Language, Mental State Vocabulary, and False Belief Understanding in Children With Cochlear Implants
Authors: Peters Kimberly , Remmel Ethan , Richards Debra
Published: June 2009

Purpose

This study examined false belief understanding and its predictors in school-age children who are deaf with cochlear implants and who use spoken language.

Method

False belief understanding was measured through an explanation-of-action task in 30 children between the ages of 3 and 12 years who used cochlear implants. Children told a wordless story from which expressive syntax and vocabulary scores were obtained. Scores on the false belief explanation task were then correlated with a variety of language and vocabulary variables, and regression analyses were completed to ascertain significant predictors of theory of mind (ToM) performance.

Results

Children’s false belief explanation of anomalous action was best predicted by age; general language ability; and spontaneous use of mental state vocabulary, specifically, cognitive vocabulary. Even the youngest children demonstrated awareness of others' mental states and made reference to them in explaining mistaken actions, supporting the assertion by M. Marschark, V. Green, G. Hindmarsh, and S. Walker (2000) that children who are deaf are not lacking a ToM.

Clinical Implications

Results of this study suggest that ToM maturation in deaf children might be facilitated by developing general spoken language skills as well as understanding and using cognitive and emotional language. These findings might also extend to children with normal hearing who are also at risk for ToM deficits (e.g., children on the autistic spectrum and children with pragmatic language delays).
Firms' contribution to open‐source software and the dominant user's skill
Authors: Jullien Nicolas , Zimmermann Jean‐Benoît
Published: June 2009

Abstract Free, libre or open‐source software (FLOSS) is nowadays produced not only by individual benevolent developers but, in a growing proportion, by firms that hire programmers for their own objectives of development in open source or for contributing to open‐source projects in the context of dedicated communities. A recent literature has focused on the question of the business models explaining how and why firms may draw benefits from such involvement and their connected activities. They can be considered as the building blocks of a new modus operandi of an industry, built on an alternative approach to intellectual property management. Its prospects will depend on both the firms' willingness to rally and its ability to compete with the traditional ‘proprietary’ approach. As a matter of fact, firms' involvement in FLOSS, while growing, remains very contrasted, depending on the nature of the products and the characteristics of the markets. This paper asks why for‐profit firms contribute to FLOSS development and why some firms contribute more than others. The common explanation is that FLOSS is often a complement to proprietary software (or hardware or services) that the for‐profit firm sells at a positive price. We present an alternative explanation based on the users' skill level. When users are skilled, opening the software is likely to result in a better product because the user base will contribute improvements (find bugs, write fixes and produce new features). We introduce the concept of the dominant user's skill and set up a theoretical model to better understand how it may condition the nature and outcome of the competition between a FLOSS firm and a proprietary firm. We discuss these results in the light of stylized facts drawn from recent trends in the software industry.
Employment relationships in knowledge‐based firms: Who should have power?
Authors: Panico Claudio
Published: June 2009

Abstract This paper investigates the relationship between an employer and a knowledge worker when an arrangement is set ex‐ante to affect the relative bargaining position in the ex‐post negotiation. Specifically, we study what drives the employer's decision to endow the worker with the rights to control the deployment of valuable resources when this choice affects the worker's bargaining power in the negotiation. Our analysis highlights how different informational asymmetries impact on the employer's problem of designing the employment contract to be offered to the worker.
Nonlinear time series analysis of knee and ankle kinematics during side by side treadmill walking
Authors: Nessler Jeff A. , De Leone Charles J. , Gilliland Sara
Published: June 2009

Nonlinear time series analysis was used to estimate maximal Lyapunov exponents of select ankle and knee kinematics during three different conditions of treadmill walking: independent, side by side, and side by side with forced synchronization of stepping. Stride to stride variability was significantly increased for the condition in which individuals walked side by side and synchronized unintentionally when compared to the conditions of forced synchronization and independent walking. In addition, standard deviations of three kinematic variables of lower extremity movement were significantly increased during the condition in which unintentional synchronization occurred. No relationship was found between standard deviation and estimates of maximal Lyapunov exponents. An increase in kinematic variability during side by side walking for nonimpaired individuals who are not at risk of falling suggests that variability in certain aspects of performance might be indicative of a healthy system. Modeling this variability for an impaired individual to imitate may have beneficial effects on locomotor function. These results may therefore have implications for the rehabilitation of gait in humans by suggesting that a different functional outcome might be achieved by practicing side by side walking as opposed to more commonly used strategies involving independent walking.
Dynamic stability and phase resetting during biped gait
Authors: Nomura Taishin , Kawa Kazuyoshi , Suzuki Yasuyuki , Nakanishi Masao , Yamasaki Taiga
Published: June 2009

Dynamic stability during periodic biped gait in humans and in a humanoid robot is considered. Here gait systems of human neuromusculoskeletal system and a humanoid are simply modeled while keeping their mechanical properties plausible. We prescribe periodic gait trajectories in terms of joint angles of the models as a function of time. The equations of motion of the models are then constrained by one of the prescribed gait trajectories to obtain types of periodically forced nonlinear dynamical systems. Simulated gait of the models may or may not fall down during gait, since the constraints are made only for joint angles of limbs but not for the motion of the body trunk. The equations of motion can exhibit a limit cycle solution (or an oscillatory solution that can be considered as a limit cycle practically) for each selected gait trajectory, if an initial condition is set appropriately. We analyze the stability of the limit cycle in terms of Poincaré maps and the basin of attraction of the limit cycle in order to examine how the stability depends on the prescribed trajectory. Moreover, the phase resetting of gait rhythm in response to external force perturbation is modeled. Since we always prescribe a gait trajectory in this study, reacting gait trajectories during the phase resetting are also prescribed. We show that an optimally prescribed reacting gait trajectory with an appropriate amount of the phase resetting can increase the gait stability. Neural mechanisms for generation and modulation of the gait trajectories are discussed.
The time-delayed inverted pendulum: Implications for human balance control
Authors: Milton John , Cabrera Juan Luis , Ohira Toru , Tajima Shigeru , Tonosaki Yukinori , Eurich Christian W. , Campbell Sue Ann
Published: June 2009

The inverted pendulum is frequently used as a starting point for discussions of how human balance is maintained during standing and locomotion. Here we examine three experimental paradigms of time-delayed balance control: (1) mechanical inverted time-delayed pendulum, (2) stick balancing at the fingertip, and (3) human postural sway during quiet standing. Measurements of the transfer function (mechanical stick balancing) and the two-point correlation function (Hurst exponent) for the movements of the fingertip (real stick balancing) and the fluctuations in the center of pressure (postural sway) demonstrate that the upright fixed point is unstable in all three paradigms. These observations imply that the balanced state represents a more complex and bounded time-dependent state than a fixed-point attractor. Although mathematical models indicate that a sufficient condition for instability is for the time delay to make a corrective movement, τn, be greater than a critical delay τc that is proportional to the length of the pendulum, this condition is satisfied only in the case of human stick balancing at the fingertip. Thus it is suggested that a common cause of instability in all three paradigms stems from the difficulty of controlling both the angle of the inverted pendulum and the position of the controller simultaneously using time-delayed feedback. Considerations of the problematic nature of control in the presence of delay and random perturbations (“noise”) suggest that neural control for the upright position likely resembles an adaptive-type controller in which the displacement angle is allowed to drift for small displacements with active corrections made only when θ exceeds a threshold. This mechanism draws attention to an overlooked type of passive control that arises from the interplay between retarded variables and noise.
Neuromechanical tuning of nonlinear postural control dynamics
Authors: Ting Lena H. , van Antwerp Keith W. , Scrivens Jevin E. , McKay J. Lucas , Welch Torrence D. J. , Bingham Jeffrey T. , DeWeerth Stephen P.
Published: June 2009

Postural control may be an ideal physiological motor task for elucidating general questions about the organization, diversity, flexibility, and variability of biological motor behaviors using nonlinear dynamical analysis techniques. Rather than presenting “problems” to the nervous system, the redundancy of biological systems and variability in their behaviors may actually be exploited to allow for the flexible achievement of multiple and concurrent task-level goals associated with movement. Such variability may reflect the constant “tuning” of neuromechanical elements and their interactions for movement control. The problem faced by researchers is that there is no one-to-one mapping between the task goal and the coordination of the underlying elements. We review recent and ongoing research in postural control with the goal of identifying common mechanisms underlying variability in postural control, coordination of multiple postural strategies, and transitions between them. We present a delayed-feedback model used to characterize the variability observed in muscle coordination patterns during postural responses to perturbation. We emphasize the significance of delays in physiological postural systems, requiring the modulation and coordination of both the instantaneous, “passive” response to perturbations as well as the delayed, “active” responses to perturbations. The challenge for future research lies in understanding the mechanisms and principles underlying neuromechanical tuning of and transitions between the diversity of postural behaviors. Here we describe some of our recent and ongoing studies aimed at understanding variability in postural control using physical robotic systems, human experiments, dimensional analysis, and computational models that could be enhanced from a nonlinear dynamics approach.
N-derived signals in the x-ray photoelectron spectra of N-doped anatase TiO2
Authors: Yu Y. P. , Xing X. J. , Xu L. M. , Wu S. X. , Li S. W.
Published: June 2009

The plasma-assisted molecular beam epitaxial anatase TiO2−xNx (x<0.3) films were chosen to investigate the N-derived variation in the x-ray photoelectron spectroscopy (XPS). With increasing nitrogen concentration, the small chemical shift and the shoulder of the main peak emerge in the N 1s, O 1s, or Ti 2p3/2 core level spectra. In combination with the experimental results obtained from x-ray diffraction and atomic force microscopy, the variations in the spectra could be ascribed to the microstructural distortion. This distortion, induced by the N3− substitution for lattice O2−, could slightly decrease the average ionicity of the Ti–O (or N) bonds. In addition, the other N 1s features (at 399.8 and 401.8 eV) and the oxygen vacancy are also discussed. For the N-doped TiO2, this work introduces a correlation between the microstructural properties and the XPS signals.
Neuromechanical considerations for incorporating rhythmic arm movement in the rehabilitation of walking
Authors: Klimstra Marc D. , Thomas Evan , Stoloff Rebecca H. , Ferris Daniel P. , Zehr E. Paul
Published: June 2009

We have extensively used arm cycling to study the neural control of rhythmic movements such as arm swing during walking. Recently rhythmic movement of the arms has also been shown to enhance and shape muscle activity in the legs. However, restricted information is available concerning the conditions necessary to maximally alter lumbar spinal cord excitability. Knowledge on the neuromechanics of a task can assist in the determination of the type, level, and timing of neural signals, yet arm swing during walking and arm cycling have not received a detailed neuromechanical comparison. The purpose of this research was to provide a combined neural and mechanical measurement approach that could be used to assist in the determination of the necessary and sufficient conditions for arm movement to assist in lower limb rehabilitation after stroke and spinal cord injury. Subjects performed three rhythmic arm movement tasks: (1) cycling (cycle); (2) swinging while standing (swing); and (3) swinging while treadmill walking (walk). We hypothesized that any difference in neural control between tasks (i.e., pattern of muscle activity) would reflect changes in the mechanical constraints unique to each task. Three-dimensional kinematics were collected simultaneously with force measurement at the hand and electromyography from the arms and trunk. All data were appropriately segmented to allow a comparison between and across conditions and were normalized and averaged to 100% movement cycle based on shoulder excursion. Separate mathematical principal components analysis of kinematic and neural variables was performed to determine common task features and muscle synergies. The results highlight important neural and mechanical features that distinguish differences between tasks. For example, there are considerable differences in the anatomical positions of the arms during each task, which relate to the moments experienced about the elbow and shoulder. Also, there are differences between tasks in elbow flexion/extension kinematics alongside differential muscle activation profiles. As well, mechanical assistance and constraints during all tasks could affect muscle recruitment and the functional role of muscles. Overall, despite neural and mechanical differences, the results are consistent with conserved common central motor control mechanisms operational for cycle, walk, and swing but appropriately sculpted to demands unique to each task. However, changing the mechanical parameters could affect the role of afferent feedback altering neural control and the coupling to the lower limbs.
Control entropy identifies differential changes in complexity of walking and running gait patterns with increasing speed in highly trained runners
Authors: McGregor Stephen J. , Busa Michael A. , Skufca Joseph , Yaggie James A. , Bollt Erik M.
Published: June 2009

Regularity statistics have been previously applied to walking gait measures in the hope of gaining insight into the complexity of gait under different conditions and in different populations. Traditional regularity statistics are subject to the requirement of stationarity, a limitation for examining changes in complexity under dynamic conditions such as exhaustive exercise. Using a novel measure, control entropy (CE), applied to triaxial continuous accelerometry, we report changes in complexity of walking and running during increasing speeds up to exhaustion in highly trained runners. We further apply Karhunen–Loeve analysis in a new and novel way to the patterns of CE responses in each of the three axes to identify dominant modes of CE responses in the vertical, mediolateral, and anterior/posterior planes. The differential CE responses observed between the different axes in this select population provide insight into the constraints of walking and running in those who may have optimized locomotion. Future comparisons between athletes, healthy untrained, and clinical populations using this approach may help elucidate differences between optimized and diseased locomotor control.
Positive feedback regulation results in spatial clustering and fast spreading of active signaling molecules on a cell membrane
Authors: Das Jayajit , Kardar Mehran , Chakraborty Arup K.
Published: June 2009

Positive feedback regulation is ubiquitous in cell signaling networks, often leading to binary outcomes in response to graded stimuli. However, the role of such feedbacks in clustering, and in spatial spreading of activated molecules, has come to be appreciated only recently. We focus on the latter, using a simple model developed in the context of Ras activation with competing negative and positive feedback mechanisms. We find that positive feedback, in the presence of slow diffusion, results in clustering of activated molecules on the plasma membrane, and rapid spatial spreading as the front of the cluster propagates with a constant velocity (dependent on the feedback strength). The advancing fronts of the clusters of the activated species are rough, with scaling consistent with the Kardar–Parisi–Zhang equation in one dimension. Our minimal model is general enough to describe signal transduction in a wide variety of biological networks where activity in the membrane-proximal region is subject to feedback regulation.
On the reliability of the Bhatnagar–Gross–Krook collision model in weakly ionized plasmas
Authors: Else D. , Kompaneets R. , Vladimirov S. V.
Published: June 2009

The ion velocity distribution in weakly ionized plasma with mobility-limited ion flow driven by an electric field is studied numerically, with the assumption that the charge exchange is the dominant mechanism of ion scattering. The calculations are performed using the realistic constant mean free path model and the results are compared with those given by the constant mean free time (Bhatnagar–Gross–Krook) model. The comparison shows that in the regime where the flow velocity is less than or comparable with the thermal velocity of neutrals the two models yield quite similar velocity distributions. Nevertheless, even in this regime, there are quantitative differences that might be important for certain cases. The implications for theoretical investigations in dusty plasmas are discussed.
Magnetic and structural properties of ion nitrided stainless steel
Authors: Basso R. L. O. , Pimentel V. L. , Weber S. , Marcos G. , Czerwiec T. , Baumvol I. J. R. , Figueroa C. A.
Published: June 2009

The magnetic properties and crystalline structure of expanded austenite obtained by ion beam nitriding of AISI 316 steel are investigated. Magnetic force microscopy reveals that the nitrogen expanded austenite has two different layers, an outermost ferromagnetic layer and a paramagnetic layer beneath it. Superimposing the nitrogen concentration profile determined by secondary neutral mass spectrometry and the magnetic force microscopy image, one can see that the paramagnetic-ferromagnetic transition takes place at the inflection point of the nitrogen concentration profile at about 14±2 N at. %. Conventional and glancing angle x-ray diffraction suggests that nitrogen could occupy first tetrahedral interstitial positions (nitrogen-poor paramagnetic phase) and then, after saturation of Cr traps, octahedral interstitial positions (nitrogen-rich ferromagnetic phase). The ferromagnetic-paramagnetic transition is seen to be governed by Cr (traps)–N interactions.
Asymmetric electrical properties of fork a-Si:H thin-film transistor and its application to flat panel displays
Authors: Lee Hojin , Yoo Geonwook , Yoo Juhn-Seok , Kanicki Jerzy
Published: June 2009

Inverted stagger hydrogenated amorphous silicon (a-Si:H) fork-shaped thin-film transistors (TFTs) were fabricated with a five-photomask process used in the processing of the active-matrix liquid crystal displays (AM-LCDs). We investigated the asymmetric electrical characteristics of a fork-shaped a-Si:H TFT under different bias conditions. To extract the electrical device parameters, we developed asymmetric geometrical factors. Current-voltage measurements indicate that the ON-OFF current ratio of fork TFT can be enhanced significantly by choosing the outer electrode as the drain, while the field-effect mobility and threshold voltage have the identical values when different drain bias conditions are used. Finally, we developed concepts of its possible application to AM-LCDs.
Analytic dynamics of the Morse oscillator derived by semiclassical closures
Authors: Heatwole Eric M. , Prezhdo Oleg V.
Published: June 2009

The quantized Hamilton dynamics methodology [O. V. Prezhdo and Y. V. Pereverzev, J. Chem. Phys. 113, 6557 (2000)] is applied to the dynamics of the Morse potential using the SU(2) ladder operators. A number of closed analytic approximations are derived in the Heisenberg representation by performing semiclassical closures and using both exact and approximate correspondence between the ladder and position-momentum variables. In particular, analytic solutions are given for the exact classical dynamics of the Morse potential as well as a second-order semiclassical approximation to the quantum dynamics. The analytic approximations are illustrated with the O–H stretch of water and a Xe–Xe dimer. The results are extended further to coupled Morse oscillators representing a linear triatomic molecule. The reported analytic expressions can be used to accelerate classical molecular dynamics simulations of systems containing Morse interactions and to capture quantum-mechanical effects.
Nanostructured solid-state hybrid photovoltaic cells fabricated by electrostatic layer-by-layer deposition
Authors: Kniprath Rolf , McLeskey James T. , Rabe Jürgen P. , Kirstein Stefan
Published: June 2009

We report on the fabrication of hybrid organic/inorganic photovoltaic cells utilizing layer-by-layer deposition of water-soluble polyions and nanocrystals. A bulk heterojunction structure was created consisting of alternating layers of the p-conductive polythiophene derivative poly[2-(3-thienyl)-ethoxy-4-butylsulfonate] and n-conductive TiO2 nanoparticles. We fabricated working devices with the heterostructure sandwiched between suitable charge carrier blocking layers and conducting oxide and metal electrodes, respectively. We analyzed the influence of the thickness and nanostructure of the active layer on the cell performance and characterized the devices in terms of static and transient current response with respect to illumination and voltage conditions. We observed reproducible and stable photovoltaic behavior with photovoltages of up to 0.9 V.
Investigation of spectra unfolded for a filtered x-ray diode array with improved smoothness
Authors: Li Jing , Huang Xian-Bin , Zhang Si-Qun , Yang Li-Bing , Xie Wei-Ping , Pu Yi-Kang
Published: June 2009

An unfolding algorithm using parabolic B-splines to smoothly reconstruct the soft x-ray spectra from the measurements of a filtered x-ray diode array is proposed. This array has been fabricated for the study of the soft x ray emitted by Z-pinch plasma. Unfolding results show that for the simulated noise-free blackbody spectra with temperature ranging from 20 to 250 eV, both the spectra and the total power are accurately recovered. Typical experimental waveforms along with the unfolded spectra and total power of x rays are presented. Possible defects due to the adoption of parabolic B-splines instead of conventionally used histograms are discussed.
Microcanonical analysis of adsorption of homopolymer chain on a surface
Authors: Chen Tao , Wang Lei , Lin Xiangsong , Liu Yuan , Liang Haojun
Published: June 2009

The adsorption process of a homopolymer chain nongrafted on an attractive surface is numerically investigated using replica-exchange multicanonical Monte Carlo simulation. Based on the microcanonical analysis, the microcanonical entropy in the adsorption transition shows convex features. Correspondingly, with the coexistence of two phases, negative specific heat is also observed in the region, implying first-orderlike transition. The origin of the negative specific heat is due to the nonextensitivity of the energy in the system. This adsorption process has some similarities to the nucleation and growth mechanism in the crystalline process. Further study reveals that the transition type, either first- or second-orderlike, during chain adsorption is strongly dependent on the chain length, interactions among segments, whether chain grafted on the surface, and force upon segments imposed by surface.
Influences of streaming potential on cross stream migration of flexible polymer molecules in nanochannel flows
Authors: Das Tamal , Das Siddhartha , Chakraborty Suman
Published: June 2009

We execute augmented Brownian dynamics (BD) simulation studies to show that the migration of flexible polyelectrolyte chains through nanochannels may be strongly governed by a complicated interplay between the electroviscous effects, near-wall interaction mechanisms, and diffusophoretic transport due to thermal gradients prevailing in the system. We further illustrate that in presence of mutually opposing pressure-driven and electro-osmotic transport and with an optimal choice of the ratio of the strength of these two flow fields, the electroviscous effects may turn out to be immensely consequential in strengthening the effective confinement of the polyelectrolyte. This, in turn may permit in achieving important biophysical feats that are otherwise obtainable only through significantly reduced nanochannel dimensions.
The influence of shape on the glassy dynamics of hard nonspherical particle fluids. I. Dynamic crossover and elasticity
Authors: Tripathy Mukta , Schweizer Kenneth S.
Published: June 2009

We extend and apply the center-of-mass version of the microscopic naïve mode coupling theory to study the ideal kinetic glass transition of dense fluids and suspensions composed of broad families of one-, two-, and three- dimensional hard nonspherical particles. A kinetic arrest diagram is constructed which indicates a dynamical crossover or onset of activated barrier hopping controlled transport. We find (quasi-) one-dimensional rods and rings form ideal glasses at the lowest volume fractions which decrease strongly with aspect ratio. Two-dimensional disks form ideal glasses at intermediate volume fractions which decrease slowly with the number of particles comprising the planar objects. Compact three-dimensional cluster particles exhibit a subtle nonmonotonic variation of the onset volume fraction that depends on their detailed shape, surface corrugation, and intraparticle interstitial volume. A strong correlation between the ideal kinetic arrest volume fraction and dimensionless compressibility (amplitude of density fluctuations) is predicted. The elastic shear modulus (transient localization length) grows (decreases) exponentially with volume fraction in a manner that becomes stronger as particle dimensionality increases.
The influence of shape on the glassy dynamics of hard nonspherical particle fluids. II. Barriers, relaxation, fragility, kinetic vitrification, and universality
Authors: Tripathy Mukta , Schweizer Kenneth S.
Published: June 2009

We extend and apply the nonlinear Langevin equation theory of activated barrier hopping dynamics in glassy fluids and colloidal suspensions to study broad families of one-, two-, and three-dimensional hard nonspherical particles. Beyond the ideal kinetic arrest volume fraction, entropic barriers emerge with heights (alpha relaxation times, inverse diffusion constants) that increase nonlinearly (nonexponentially) with volume fraction and in a manner that becomes stronger with particle dimensionality. Partial collapse of the volume fraction dependence of barrier heights and reduced relaxation times of different particle shapes within a fixed dimensionality class are achieved based on a difference volume fraction variable that quantifies the distance from the ideal mode coupling theory dynamic crossover. However, the barrier, alpha relaxation time, and self-diffusion constant results of all shapes are remarkably well collapsed onto a single universal master curve based on a theoretically motivated coupling constant which quantifies the renormalized mean square force on a tagged particle. The latter is determined mainly by the square of the intermolecular site-site contact value of the pair correlation function, thereby providing an explicit microscopic connection between local packing, binary collisions, and slow dynamics. A large variation of the dynamic fragility with particle shape is found with compact cluster particles being the most fragile. A kinetic glass transition map is constructed that is relevant to vitrification of laboratory colloidal suspensions. The possible relevance of the hard particle results for understanding the dynamic fragility of thermal van der Waals liquids is discussed.
Ultrafast release and capture of carriers in InGaAs/GaAs quantum dots observed by time-resolved terahertz spectroscopy
Authors: Porte H. P. , Uhd Jepsen P. , Daghestani N. , Rafailov E. U. , Turchinovich D.
Published: June 2009

We observe ultrafast release and capture of charge carriers in InGaAs/GaAs quantum dots in a room-temperature optical pump-terahertz probe experiment sensitive to the population dynamics of conducting states. In case of resonant excitation of the quantum dot ground state, the maximum conductivity is achieved at approximately 35 ps after photoexcitation, which is assigned to release of carriers from the quantum dots. When exciting carriers into the conduction band of the barriers, depletion of the conductivity via carrier capture into the quantum dots with a few picosecond pump fluence-dependent time constant was observed.
Direct evidence for Sb as a Zn site impurity in ZnO
Authors: Wahl U. , Correia J. G. , Mendonça T. , Decoster S.
Published: June 2009

The lattice location of ion implanted antimony in zinc oxide has been determined by means of β− emission channeling from the radioactive S124b isotope. Following 30 keV implantation of S124b into a single-crystalline ZnO sample to a fluence of 1×1014 cm−2, the angular-dependent emission rate of β− particles around several crystallographic directions was measured with a position-sensitive Si detector. The majority of Sb was found to occupy Zn sites, with the possible fraction on O sites being at maximum 5%–6%.
Proton heating by parallel Alfvén wave cascade
Authors: Yoon P. H. , Fang T.-M.
Published: June 2009

In a recent series of papers, the present authors developed a kinetic theory for low-frequency turbulence propagating parallel to the ambient magnetic field. Making use of this theory, it was shown that low-frequency Alfvénic turbulence may cascade to ion-cyclotron frequency range and beyond by nonlinear three-wave decay processes. The significance of such a finding is that it may lead to the proton heating by cyclotron resonance. However, the actual proton heating process was not demonstrated. The present paper complements the previous works by including the proton heating in the discussion. It is found that the left-hand circularly polarized Alfvén-cyclotron turbulence leads to a moderate heating of the protons in the perpendicular direction and cooling in the parallel direction. It is also found that ion-acoustic turbulence is generated by the decay instability process. Finally, the heating rate is shown to increase in inverse proportion to the time scale of the wave source.
Temperature dependences of photoluminescence and electroluminescence spectra in light-emitting diodes
Authors: Li Lian , Li Ping , Wen Yumei , Wen Jing , Zhu Yong
Published: June 2009

The temperature influence on the luminescence characteristics of light-emitting diodes (LEDs) is investigated to reveal the connection of photoluminescence (PL) with photon absorption and electroluminescence (EL) through current injection. By inspecting the PL and EL spectra at identical injection intensities, it has been found that the normalized spectra in PL and EL exhibit obvious similarities in shape and apparent differences in spectral characteristic values. Furthermore, the differences are found to originate from the junction temperatures in diverse injection modes. The observations are conducted on AlGaInP red LED chips.
200 mW type I GaSb-based laser diodes operating at 3 μm: Role of waveguide width
Authors: Hosoda Takashi , Kipshidze Gela , Shterengas Leon , Suchalkin Sergey , Belenky Gregory
Published: June 2009

Laser diodes based on AlInGaAsSb/InGaAsSb heterostructures with different waveguide widths were designed and fabricated. The decrease in the waveguide width from 1470 to 470 nm led to the improvement of the device performance. Lasers with 470 nm quinternary waveguides demonstrated 200 mW continuous wave output power at room temperature.
Measuring the profile of the emission zone in polymeric organic light-emitting diodes
Authors: Gather Malte C. , Flämmich Michael , Danz Norbert , Michaelis Dirk , Meerholz Klaus
Published: June 2009

The profile of the emission zone (PEZ) in the emissive layer (EML) of polymeric organic light-emitting diodes (OLEDs) is determined by fitting the measured electroluminescence spectrum of the device with a series of simulated spectra that correspond to different emitter locations. The studied OLEDs are based on two different blue-emitting conjugated polymers. In one case, the PEZ is confined to a 10 nm thin sheet at the anode indicating electron dominated current in the EML. In OLEDs based on the other emitter, the PEZ spreads over the entire EML.