bluuebunny/crossref_metadata_2025 huggingface dataset:
AW551984: a novel regulator of cardiomyogenesis in pluripotent embryonic cells
Authors: Yasuda Satoshi , Hasegawa Tetsuya , Hosono Tetsuji , Satoh Mitsutoshi , Watanabe Kei , Ono Kageyoshi , Shimizu Shunichi , Hayakawa Takao , Yamaguchi Teruhide , Suzuki Kazuhiro , Sato Yoji
Published: June 2011

An understanding of the mechanism that regulates the cardiac differentiation of pluripotent stem cells is necessary for the effective generation and expansion of cardiomyocytes as cell therapy products. In the present study, we have identified genes that modulate the cardiac differentiation of pluripotent embryonic cells. We isolated P19CL6 cell sublines that possess distinct properties in cardiomyogenesis and extracted 24 CMR (cardiomyogenesis-related candidate) genes correlated with cardiomyogenesis using a transcriptome analysis. Knockdown of the CMR genes by RNAi (RNA interference) revealed that 18 genes influence spontaneous contraction or transcript levels of cardiac marker genes in EC (embryonal carcinoma) cells. We also performed knockdown of the CMR genes in mouse ES (embryonic stem) cells and induced in vitro cardiac differentiation. Three CMR genes, AW551984, 2810405K02Rik (RIKEN cDNA 2810405K02 gene) and Cd302 (CD302 antigen), modulated the cardiac differentiation of both EC cells and ES cells. Depletion of AW551984 attenuated the expression of the early cardiac transcription factor Nkx2.5 (NK2 transcription factor related locus 5) without affecting transcript levels of pluripotency and early mesoderm marker genes during ES cell differentiation. Activation of Wnt/β-catenin signalling enhanced the expression of both AW551984 and Nkx2.5 in ES cells during embryoid body formation. Our findings indicate that AW551984 is a novel regulator of cardiomyogenesis from pluripotent embryonic cells, which links Wnt/β-catenin signalling to Nkx2.5 expression.
Why does mitochondrial complex I have so many subunits?
Authors: Hirst Judy
Published: June 2011

The prokaryotic and eukaryotic homologues of complex I (proton-pumping NADH:quinone oxidoreductase) perform the same function in energy transduction, but the eukaryotic enzymes are twice as big as their prokaryotic cousins, and comprise three times as many subunits. Fourteen core subunits are conserved in all complexes I, and are sufficient for catalysis – so why are the eukaryotic enzymes embellished by so many supernumerary or accessory subunits? In this issue of the Biochemical Journal, Angerer et al. have provided new evidence to suggest that the supernumerary subunits are important for enzyme stability. This commentary aims to put this suggestion into context.
Theoretical analysis of the intrinsic magnetic noise spectral density of magnetostrictive-piezoelectric laminated composites
Authors: Zhuang X. , Cordier C. , Saez S. , Lam Chok Sing M. , Dolabdjian C. , Gao J. , Li J. F. , Viehland D.
Published: June 2011

The equivalent magnetic noise spectral density level for long type magnetostrictive-piezoelectric laminated composites has been investigated by using a 1D equivalent circuit model, and exemplified for a longitudinal-transverse mode. The theoretical developments explain well our experimental results. The findings show that similar ultimate magnetic noise spectral noise density can be expected whether using either charge or voltage amplifier detection methods. The findings show that a volume effect and the dielectric loss factor of the piezoelectric layer are the dominant sources of the noise floor. Our findings show that the noise scales as 1/√f. The lowest equivalent noise floor value that has been observed is 10/√f pT/√Hz for f ≪ 10 kHz, with a white noise level of 100 fT/√Hz above 10 kHz.
Phase clustering in complex networks of delay-coupled oscillators
Authors: Pérez Toni , Eguíluz Víctor M. , Arenas Alex
Published: June 2011

We study the clusterization of phase oscillators coupled with delay in complex networks. For the case of diffusive oscillators, we formulate the equations relating the topology of the network and the phases and frequencies of the oscillators (functional response). We solve them exactly in directed networks for the case of perfect synchronization. We also compare the reliability of the solution of the linear system for non-linear couplings. Taking advantage of the form of the solution, we propose a frequency adaptation rule to achieve perfect synchronization. We also propose a mean-field theory for uncorrelated random networks that proves to be pretty accurate to predict phase synchronization in real topologies, as for example, the Caenorhabditis elegans or the autonomous systems connectivity.
Nonlinear evolution of two fast-particle-driven modes near the linear stability threshold
Authors: Zaleśny Jarosław , Galant Grzegorz , Lisak Mietek , Marczyński Sławomir , Berczyński Paweł , Gałkowski Andrzej , Berczyński Stefan
Published: June 2011

A system of two coupled integro-differential equations is derived and solved for the non-linear evolution of two waves excited by the resonant interaction with fast ions just above the linear instability threshold. The effects of a resonant particle source and classical relaxation processes represented by the Krook, diffusion, and dynamical friction collision operators are included in the model, which exhibits different nonlinear evolution regimes, mainly depending on the type of relaxation process that restores the unstable distribution function of fast ions. When the Krook collisions or diffusion dominate, the wave amplitude evolution is characterized by modulation and saturation. However, when the dynamical friction dominates, the wave amplitude is in the explosive regime. In addition, it is found that the finite separation in the phase velocities of the two modes weakens the interaction strength between the modes.
Tailoring the air plasma with a double laser pulse
Authors: Shneider M. N. , Zheltikov A. M. , Miles R. B.
Published: June 2011

We present a comprehensive model of plasma dynamics that enables a detailed understanding of the ways the air plasma induced in the atmosphere in the wake of a laser-induced filament can be controlled by an additional laser pulse. Our model self-consistently integrates plasma-kinetic, Navier−Stokes, electron heat conduction, and electron−vibration energy transfer equations, serving to reveal laser−plasma interaction regimes where the plasma lifetime can be substantially increased through an efficient control over plasma temperature, as well as suppression of attachment and recombination processes. The model is used to quantify the limitations on the length of uniform laser-filament heating due to the self-defocusing of laser radiation by the radial profile of electron density. The envisaged applications include sustaining plasma guides for long-distance transmission of microwaves, standoff detection of impurities and potentially hazardous agents, as well as lightning control and protection.
Spectroscopic diagnostics of plume rebound and shockwave dynamics of confined aluminum laser plasma plumes
Authors: Yeates P. , Kennedy E. T.
Published: June 2011

Generation and expansion dynamics of aluminum laser plasma plumes generated between parallel plates of varying separation (ΔZ = 2.0, 3.2, 4.0, and 5.6 mm), which confined plume expansion normal to the ablation surface, were diagnosed. Space and time resolved visible emission spectroscopy in the spectral range λ = 355-470 nm and time gated visible imaging were employed to record emission spectra and plume dynamics. Space and time resolved profiles of Ne (the electron density), Te (the electron temperature), and Tionz (the ionization temperature) were compared for different positions in the plasma plume. Significant modifications of the profiles of the above parameters were observed for plasma-surface collisions at the inner surface of the front plate, which formed a barrier to the free expansion of the plasma plume generated by the laser light on the surface of the back plate. Shockwave generation at the collision interface resulted in delayed compression of the low-density plasma plume near the inner ablation surface, at late stages in the plasma history. Upon exiting the cavity formed by the two plates, through an aperture in the front plate, the plasma plume underwent a second phase of free expansion.
Three-dimensional equilibria and transport in RFX-mod: A description using stellarator tools
Authors: Gobbin M. , Bonfiglio D. , Boozer A. H. , Cooper A. W. , Escande D. F. , Hirshman S. P. , Lore J. , Lorenzini R. , Marrelli L. , Martin P. , Martines E. , Momo B. , Pomphrey N. , Predebon I. , Puiatti M. E. , Sanchez R. , Spizzo G. , Spong D. A. , Terranova D. ,   RFX-mod Team
Published: June 2011

RFX-mod self-organized single helical axis (SHAx) states provide a unique opportunity to advance 3D fusion physics and establish a common knowledge basis in a parameter region not covered by stellarators and tokamaks. The VMEC code has been adapted to the reversed-field pinch (RFP) to model SHAx equilibria in fixed boundary mode with experimental measurements as constraint. The averaged particle diffusivity over the helical volume, estimated with the Monte Carlo code ORBIT, has a neoclassical-like dependence on collisionality and does not show the 1/ν trend of un-optimized stellarators. In particular, the helical region boundary, corresponding to an electron transport barrier with zero magnetic shear and improved confinement, has been investigated using numerical codes common to the stellarator community. In fact, the DKES/PENTA codes have been applied to RFP for local neoclassical transport computations, including radial electric field, to estimate thermal diffusion coefficients in the barrier region for typical RFX-mod temperature and density profiles. A comparison with power balance estimates shows that residual chaos due to secondary tearing modes and small-scale turbulence still contribute to drive anomalous transport in the barrier region.
Forward light scattering for highly sensitive detection of aggregation in crystallizing protein solutions
Authors: Wakamatsu Takashi
Published: June 2011

It is presented that a forward light scattering technique is highly sensitive to aggregation in crystallizing lysozyme solutions. Static light scattering in the crystallizing protein solutions has a characteristic radiation pattern that largely differs from that of small size silica particles dispersed in water. A method to evaluate aggregate formation was demonstrated from the dependence of forward light scattering on a precipitant concentration added to a lysozyme solution. These measurements provide possibilities for characterizing protein aggregation in crystallization process.
Dispersion corrections in the boron buckyball and nanotubes
Authors: Gunasinghe Rosi N. , Kah Cherno B. , Quarles Kregg D. , Wang Xiao-Qian
Published: June 2011

We have investigated structural and electronic properties of the B80 buckyball and boron nanotubes by means of dispersion-corrected density-functional calculations. Our analysis reveals the vibrational stability for the icosahedral B80 with the inclusion of dispersion corrections, in contrast to the instability to a tetrahedral B80 with puckered capping atoms from preceding density-functional theory calculations. Similarly, the dispersion-corrected density-functional calculations yield non-puckered boron nanotube conformations and an associated metallic state for zigzag tubes. Our study indicates that the incorporation of long-range dispersive interactions is particularly important to the structural and electronic properties of boron fullerenes and nanotubes.
Intermolecular vibrations and fast relaxations in supercooled ionic liquids
Authors: Ribeiro Mauro C. C.
Published: June 2011

Short-time dynamics of ionic liquids has been investigated by low-frequency Raman spectroscopy (4 < ω < 100 cm−1) within the supercooled liquid range. Raman spectra are reported for ionic liquids with the same anion, bis(trifluoromethylsulfonyl)imide, and different cations: 1-butyl-3-methylimidazolium, 1-hexyl-3-methylimidazolium, 1-butyl-1-methylpiperidinium, trimethylbutylammonium, and tributylmethylammonium. It is shown that low-frequency Raman spectroscopy provides similar results as optical Kerr effect (OKE) spectroscopy, which has been used to study intermolecular vibrations in ionic liquids. The comparison of ionic liquids containing aromatic and non-aromatic cations identifies the characteristic feature in Raman spectra usually assigned to librational motion of the imidazolium ring. The strength of the fast relaxations (quasi-elastic scattering, QES) and the intermolecular vibrational contribution (boson peak) of ionic liquids with non-aromatic cations are significantly lower than imidazolium ionic liquids. A correlation length assigned to the boson peak vibrations was estimated from the frequency of the maximum of the boson peak and experimental data of sound velocity. The correlation length related to the boson peak (∼19 Å) does not change with the length of the alkyl chain in imidazolium cations, in contrast to the position of the first-sharp diffraction peak observed in neutron and X-ray scattering measurements of ionic liquids. The rate of change of the QES intensity in the supercooled liquid range is compared with data of excess entropy, free volume, and mean-squared displacement recently reported for ionic liquids. The temperature dependence of the QES intensity in ionic liquids illustrates relationships between short-time dynamics and long-time structural relaxation that have been proposed for glass-forming liquids.
Characterization of a microwave frequency resonator via a nearby quantum dot
Authors: Frey T. , Leek P. J. , Beck M. , Ensslin K. , Wallraff A. , Ihn T.
Published: June 2011

We present measurements of a hybrid system consisting of a microwave transmission-line resonator and a lateral quantum dot defined on a GaAs heterostructure. The two subsystems are separately characterized and their interaction is studied by monitoring the electrical conductance through the quantum dot. The presence of a strong microwave field in the resonator is found to reduce the resonant conductance through the quantum dot and is attributed to electron heating and modulation of the dot potential. We use this interaction to demonstrate a measurement of the resonator transmission spectrum using the quantum dot.
Introduction to Focus Issue: Synchronization and Cascading Processes in Complex Networks
Authors: Nishikawa Takashi
Published: June 2011

The study of collective dynamics in complex networks has emerged as a next frontier in the science of networks. This Focus Issue presents the latest developments on this exciting front, focusing in particular on synchronous and cascading dynamics, which are ubiquitous forms of network dynamics found in a wide range of physical, biological, social, and technological systems.
Characterization of Fe-doped In-Sb-Te (Fe: 10 at.%) material with individual electrical-phase-change and magnetic properties
Authors: Lee Young Mi , Dung Dang Duc , Cho Sunglae , Jung Min Sang , Choi Duck Kyun , Ahn Docheon , Kim Min Kyu , Kim Jae-Young , Jung Min-Cherl
Published: June 2011

We propose a new electrical-phase-change magnetic material, namely Fe-doped In-Sb-Te (FIST), for possible non-volatile multi-bit memory applications. FIST was formed by typical co-sputter method with Fe 10 at.% doping in In3Sb1Te2. FIST offers the electrical-phase-change and magnetic properties by way of the change of In 4d chemical bonding density and embedded Fe nanoclusters with the size of 4∼5 nm, respectively. It maintained the amorphous phase on the electrical-phase-change. Chemical state of In was only changed to increase the density of In-In chemical bonding during the electrical-phase-change without Fe nanoclusters contribution. Also, the magnetic property by Fe nanoclusters was not changed by the electrical-phase-change. On this basis, we propose the FIST material with the individual electrical-phase-change and magnetic properties for the multi-bit nonvolatile memory materials.
Diverse two-cysteine photocycles in phytochromes and cyanobacteriochromes
Authors: Rockwell Nathan C. , Martin Shelley S. , Feoktistova Kateryna , Lagarias J. Clark
Published: June 2011

Phytochromes are well-known as photoactive red- and near IR-absorbing chromoproteins with cysteine-linked linear tetrapyrrole (bilin) prosthetic groups. Phytochrome photoswitching regulates adaptive responses to light in both photosynthetic and nonphotosynthetic organisms. Exclusively found in cyanobacteria, the related cyanobacteriochrome (CBCR) sensors extend the photosensory range of the phytochrome superfamily to shorter wavelengths of visible light. Blue/green light sensing by a well-studied subfamily of CBCRs proceeds via a photolabile thioether linkage to a second cysteine fully conserved in this subfamily. In the present study, we show that dual-cysteine photosensors have repeatedly evolved in cyanobacteria via insertion of a second cysteine at different positions within the bilin-binding GAF domain (cGMP-specific phosphodiesterases, cyanobacterial adenylate cyclases, and formate hydrogen lyase transcription activator FhlA) shared by CBCRs and phytochromes. Such sensors exhibit a diverse range of photocycles, yet all share ground-state absorbance of near-UV to blue light and a common mechanism of light perception: reversible photoisomerization of the bilin 15,16 double bond. Using site-directed mutagenesis, chemical modification and spectroscopy to characterize novel dual-cysteine photosensors from the cyanobacterium
Nostoc punctiforme
ATCC 29133, we establish that this spectral diversity can be tuned by varying the light-dependent stability of the second thioether linkage. We also show that such behavior can be engineered into the conventional phytochrome Cph1 from
Synechocystis
sp. PCC6803. Dual-cysteine photosensors thus allow the phytochrome superfamily in cyanobacteria to sense the full solar spectrum at the earth surface from near infrared to near ultraviolet.
Rac1/osmosensing scaffold for MEKK3 contributes via phospholipase C-γ1 to activation of the osmoprotective transcription factor NFAT5
Authors: Zhou Xiaoming , Izumi Yuichiro , Burg Maurice B. , Ferraris Joan D.
Published: June 2011

Separate reports that hypertonicity activates p38 via a Rac1–OSM–MEKK3–MKK3–p38 pathway and that p38α contributes to activation of TonEBP/OREBP led us to the hypothesis that Rac1 might activate TonEBP/OREBP via p38. The present studies examine that possibility. High NaCl is hypertonic. We find that siRNA knockdown of Rac1 reduces high NaCl-induced increase of TonEBP/OREBP transcriptional activity (by reducing its transactivating activity but not its nuclear localization). Similarly, siRNA knockdown of osmosensing scaffold for MEKK3 (OSM) also reduces high NaCl-dependent TonEBP/OREBP transcriptional and transactivating activities. Simultaneous siRNA knockdown of Rac1 and OSM is not additive in reduction of TonEBP/OREBP transcriptional activity, indicating a common pathway. However, siRNA knockdown of MKK3 does not reduce TonEBP/OREBP transcriptional activity, although siRNA knockdown of MKK6 does. Nevertheless, the effect of Rac1 on TonEBP/OREBP is also independent of MKK6 because it occurs in MKK6-null cells. Furthermore, we find that siRNA knockdown of Rac1 or OSM actually increases activity (phosphorylation) of p38, rather than decreasing it, as previously reported. Thus, the effect of Rac1 on TonEBP/OREBP is independent of p38. We find instead that phospholipase C-γ1 (PLC-γ1) is involved. When transfected into PLC-γ1–null mouse embryonic fibroblast cells, catalytically active Rac1 does not increase TonEBP/OREBP transcriptional activity unless PLC-γ1 is reconstituted. Similarly, dominant-negative Rac1 also does not inhibit TonEBP/OREBP in PLC-γ1–null cells unless PLC-γ1 is reconstituted. We conclude that Rac1/OSM supports TonEBP/OREBP activity and that this activity is mediated via PLC-γ1, not p38.
Functional synthetic
Antennapedia
genes and the dual roles of YPWM motif and linker size in transcriptional activation and repression
Authors: Papadopoulos Dimitrios K. , Reséndez-Pérez Diana , Cárdenas-Chávez Diana L. , Villanueva-Segura Karina , Canales-del-Castillo Ricardo , Felix Daniel A. , Fünfschilling Raphael , Gehring Walter J.
Published: June 2011

Segmental identity along the anteroposterior axis of bilateral animals is specified by
Hox
genes. These genes encode transcription factors, harboring the conserved homeodomain and, generally, a YPWM motif, which binds Hox cofactors and increases Hox transcriptional specificity in vivo. Here we derive synthetic
Drosophila Antennapedia
genes, consisting only of the YPWM motif and homeodomain, and investigate their functional role throughout development. Synthetic peptides and full-length Antennapedia proteins cause head-to-thorax transformations in the embryo, as well as antenna-to-tarsus and eye-to-wing transformations in the adult, thus converting the entire head to a mesothorax. This conversion is achieved by repression of genes required for head and antennal development and ectopic activation of genes promoting thoracic and tarsal fates, respectively. Synthetic Antennapedia peptides bind DNA specifically and interact with Extradenticle and Bric-à-brac interacting protein 2 cofactors in vitro and ex vivo. Substitution of the YPWM motif by alanines abolishes Antennapedia homeotic function, whereas substitution of YPWM by the WRPW repressor motif, which binds the transcriptional corepressor Groucho, allows all proteins to act as repressors only. Finally, naturally occurring variations in the size of the linker between the homeodomain and YPWM motif enhance Antennapedia repressive or activating efficiency, emphasizing the importance of linker size, rather than sequence, for specificity. Our results clearly show that synthetic
Antennapedia
genes are functional in vivo and therefore provide powerful tools for synthetic biology. Moreover, the YPWM motif is necessary—whereas the entire N terminus of the protein is dispensable—for
Antennapedia
homeotic function, indicating its dual role in transcriptional activation and repression by recruiting either coactivators or corepressors.
Determinants of local and migratory movements of Great Lakes double-crested cormorants
Authors: Guillaumet Alban , Dorr Brian , Wang Guiming , Taylor Jimmy D. , Chipman Richard B. , Scherr Heidi , Bowman Jeff , Abraham Kenneth F. , Doyle Terry J. , Cranker Elizabeth
Published: June 2011

We investigated how individual strategies combine with demographic and ecological factors to determine local and migratory movements in the double-crested cormorants (Phalacrocorax auritus). One hundred and forty-five cormorants were captured from 14 nesting colonies across the Great Lakes area and fitted with satellite transmitters. We first tested the hypotheses that sexual segregation, density-dependent effects, and the intensity of management operations influenced home range size during the breeding season. The influence of these factors appeared to be limited in part due to random variability in foraging and dispersal decisions at individual and colony levels. We also designed a statistical framework to investigate the degree and determinants of migratory connectivity. Our analyses revealed a significant migratory connectivity in cormorants, although we also observed a nonnegligible amount of individual variability and flexibility. Our data were most consistent with the existence of a migratory divide across the Great Lakes, with western populations using mainly the Mississippi Flyway and eastern populations the Atlantic Flyway. Previous and current studies suggest that the divide cannot be explained by past divergence in isolation, a way to diminish travel cost, or the Appalachians constituting an ecological barrier per se but is rather the consequence of the distribution of suitable stopover and nonbreeding areas. However, a parallel migration system and no migratory divide could not be entirely ruled out with present data.
Epidural Analgesia Is Associated with Improved Health Outcomes of Surgical Patients with Chronic Obstructive Pulmonary Disease
Authors: van Lier Felix , van der Geest Patrick J. , Hoeks Sanne E. , van Gestel Yvette R. B. M. , Hol Jaap W. , Sin Don D. , Stolker Robert Jan , Poldermans Don
Published: June 2011

Background

Patients with chronic obstructive pulmonary disease (COPD) have increased postoperative morbidity and mortality. Epidural analgesia (EDA) improves postoperative outcome but may worsen postoperative lung function. It is unknown whether patients with COPD benefit from EDA. The objective of this study was to determine whether patients with COPD undergoing major abdominal surgery benefit from EDA in addition to general anesthesia.

Methods

This cohort study included 541 consecutive patients with COPD who underwent major abdominal surgery between 1995 and 2007 at a university medical center. Propensity scores estimating the probability of receiving EDA were used in multivariate correction. The primary outcome was postoperative pneumonia and 30-day mortality.

Results

There were 324 patients (60%) who received EDA in addition to general anesthesia. The incidence of postoperative pneumonia (16% vs. 11%; P = 0.08) and 30-day mortality (9% vs. 5%; P = 0.03) was lower in patients who received EDA. After correction EDA was associated with improved outcome for postoperative pneumonia (OR 0.5; 95% CI: 0.3-0.9; P = 0.03). The strongest preventive effect was seen in patients with the most severe type of COPD.

Conclusion

This study provides evidence that in patients with COPD who are scheduled for major abdominal surgery, epidural analgesia decreases postoperative pulmonary complications.
An Evaluation of the Role of Gene Expression in the Prediction and Diagnosis of Ventilator-associated Pneumonia
Authors: Textoris Julien , Loriod Béatrice , Benayoun Laurent , Gourraud Pierre-Antoine , Puthier Denis , Albanèse Jacques , Mantz Jean , Martin Claude , Nguyen Catherine , Leone Marc
Published: June 2011

Background

The SepsiChip project explored transcriptional modulation associated with ventilator-associated pneumonia (VAP) in patients admitted to the intensive care unit for trauma. Genome-wide expression analysis may help to identify potential diagnostic markers for diseases. The current study examined the changes in blood transcriptome during VAP.

Methods

The authors prospectively included 165 trauma patients, and 41 developed VAP. Whole blood samples were collected at admission and at VAP. To predict VAP, the admission samples were compared by microarray in patients who did or did not develop VAP. To identify diagnosis markers, paired samples of 35 patients who developed VAP were analyzed. Using NanoString (Seattle, WA), the results were confirmed in the patients who developed VAP. Trauma patients who did not develop VAP served as controls to eliminate a time effect.

Results

The injury severity scores of the patients who did or did not develop VAP were 36 and 29, respectively. No predictive biomarker was identified. For patients who developed VAP, a transcriptional signature was identified between the two sampling times. However, this signature was a generalized pattern related to trauma, independent of the infectious process. Genes involved in the proinflammatory response were down-regulated in the patients who developed VAP, but this difference was not statistically significant.

Conclusions

In contrast to clinical assessment, transcriptional analysis of whole blood samples cannot predict or diagnose VAP in trauma patients. Differentiating infection from inflammation seems challenging.
No Clinical or Electrophysiologic Evidence of Nerve Injury after Intraneural Injection during Sciatic Popliteal Block
Authors: Sala-Blanch Xavier , López Ana M. , Pomés Jaume , Valls-Sole Josep , García Ana I. , Hadzic Admir
Published: June 2011

Background

Intraneural injection during nerve-stimulator-guided sciatic block at the popliteal fossa may be a common occurrence. Although intraneural injections have not resulted in clinically detectable neurologic injury in small studies in human subjects, intraneural injections result in postinjection inflammation in animal models. This study used clinical, imaging, and electrophysiologic measures to evaluate the occurrence of any subclinical neurologic injury in patients with intraneural injection during sciatic popliteal block.

Methods

Twenty patients undergoing popliteal block were enrolled; 17 patients completed the study protocol. After tibial nerve response was achieved by nerve stimulation (0.3-0.5 mA; 2 Hz; 0.1 ms), 20 ml mixture of mepivacaine (1.25%) and radiopaque contrast (2 ml) were injected. Location and spread of the injectant were assessed by ultrasound measurements of the sciatic nerve area before and after injection, and by computed tomography. In addition to clinical neurologic evaluations, serial electrophysiologic studies (nerve conduction and late response studies using predefined criteria) were performed at baseline and at 1 week and 3 weeks after the block for signs of subclinical neurologic dysfunction.

Results

Sixteen injections (94%, 95% CI: 71-100%) met criteria for an intraneural injection. Postinjection nerve area on ultrasound increased by 45% (95% CI: 29-58%), P < 0.001. Computed tomography demonstrated fascicular separation in 70% (95% CI: 44-90%), air within the nerve in 29% (95% CI: 10-56%), contrast along bifurcations in 65% (95% CI: 38-86%), and concentric contrast layers in 100% (95% CI: 84-100%). Neither clinical nor electrophysiologic studies detected neurologic dysfunction indicating injury to the nerve.

Conclusions

Nerve-stimulator-guided sciatic block at the popliteal fossa often results in intraneural injection that may not lead to clinical or electrophysiologic nerve injury.
Noisy human neighbours affect where urban monkeys live
Authors: Duarte Marina H. L. , Vecci Marco A. , Hirsch André , Young Robert J.
Published: June 2011

Urban areas and many natural habitats are being dominated by a new selection pressure: anthropogenic noise. The ongoing expansion of urban areas, roads and airports throughout the world makes the noise almost omnipresent. Urbanization and the increase of noise levels form a major threat to living conditions in and around cities. Insight into the behavioural strategies of urban survivors may explain the sensitivity of other species to urban selection pressures. Here, we show that urban black-tufted marmosets (
Callithrix penicillata
) living in noisy urban areas may select their home-range based primarily on ambient noise level. We have tested the hypothesis that the noise from vehicular traffic and visitors in an urban park in Brazil influences the use of home-range (space) by urban marmosets. Marmosets even avoided noisy areas with high food availability. In addition, they systematically preferred the quieter areas even with dynamic changes in the acoustic landscape of the park between weekdays and Sundays (no observations were made on Saturdays). These data provide evidence that the use of home-range by wild animals can be affected by a potential aversive stimulus such as noise pollution.
Controlling molecular transport through nanopores
Authors: Keyser Ulrich F.
Published: June 2011

Nanopores are emerging as powerful tools for the detection and identification of macromolecules in aqueous solution. In this review, we discuss the recent development of active and passive controls over molecular transport through nanopores with emphasis on biosensing applications. We give an overview of the solutions developed to enhance the sensitivity and specificity of the resistive-pulse technique based on biological and solid-state nanopores.
Surface wettability of plasma SiO

x

:H nanocoating-induced endothelial cells' migration and the associated FAK-Rho GTPases signalling pathways
Authors: Shen Yang , Wang Guixue , Huang Xianliang , Zhang Qin , Wu Jiang , Tang Chaojun , Yu Qingsong , Liu Xiaoheng
Published: June 2011

Vascular endothelial cell (EC) adhesion and migration are essential processes in re-endothelialization of implanted biomaterials. There is no clear relationship and mechanism between EC adhesion and migration behaviour on surfaces with varying wettabilities. As model substrates, plasma SiO

x

:H nanocoatings with well-controlled surface wettability (with water contact angles in the range of 98.5 ± 2.3° to 26.3 ± 4.0°) were used in this study to investigate the effects of surface wettability on cell adhesion/migration and associated protein expressions in FAK-Rho GTPases signalling pathways. It was found that EC adhesion/migration showed opposite behaviour on the hydrophilic and hydrophobic surfaces (i.e. hydrophobic surfaces promoted EC migration but were anti-adhesions). The number of adherent ECs showed a maximum on hydrophilic surfaces, while cells adhered to hydrophobic surfaces exhibited a tendency for cell migration. The focal adhesion kinase (FAK) inhibitor targeting the Y-397 site of FAK could significantly inhibit cell adhesion/migration, suggesting that EC adhesion and migration on surfaces with different wettabilities involve (
p
)FAK and its downstream signalling pathways. Western blot results suggested that the FAK-Rho GTPases signalling pathways were correlative to EC migration on hydrophobic plasma SiO

x

:H surfaces, but uncertain to hydrophilic surfaces. This work demonstrated that surface wettability could induce cellular behaviours that were associated with different cellular signalling events.
An extended thermodynamic model of transient heat conduction at sub-continuum scales
Authors: Lebon G. , Machrafi H. , Grmela M. , Dubois Ch.
Published: June 2011

A thermodynamic description of transient heat conduction at small length and timescales is proposed. It is based on extended irreversible thermodynamics and the main feature of this formalism is to elevate the heat flux vector to the status of independent variable at the same level as the classical variable, the temperature. The present model assumes the coexistence of two kinds of heat carriers: diffusive and ballistic phonons. The behaviour of the diffusive phonons is governed by a Cattaneo-type equation to take into account the high-frequency phenomena generally present at nanoscales. To include non-local effects that are dominant in nanostructures, it is assumed that the ballistic carriers are obeying a Guyer–Krumhansl relation. The model is applied to the problem of transient heat conduction through a thin nanofilm. The numerical results are compared with those provided by Fourier, Cattaneo and other recent models.
Testing the adjustable threshold model for intruder recognition on
Myrmica
ants in the context of a social parasite
Authors: Fürst Matthias A. , Durey Maëlle , Nash David R.
Published: June 2011

Social insect colonies are like fortresses, well protected and rich in shared stored resources. This makes them ideal targets for exploitation by predators, parasites and competitors. Colonies of
Myrmica rubra
ants are sometimes exploited by the parasitic butterfly
Maculinea alcon
.
Maculinea alcon
gains access to the ants' nests by mimicking their cuticular hydrocarbon recognition cues, which allows the parasites to blend in with their host ants.
Myrmica rubra
may be particularly susceptible to exploitation in this fashion as it has large, polydomous colonies with many queens and a very viscous population structure. We studied the mutual aggressive behaviour of
My. rubra
colonies based on predictions for recognition effectiveness. Three hypotheses were tested: first, that aggression increases with distance (geographical, genetic and chemical); second, that the more queens present in a colony and therefore the less-related workers within a colony, the less aggressively they will behave; and that colonies facing parasitism will be more aggressive than colonies experiencing less parasite pressure. Our results confirm all these predictions, supporting flexible aggression behaviour in
Myrmica
ants depending on context.
Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development
Authors: Pal Sharmistha , Gupta Ravi , Kim Hyunsoo , Wickramasinghe Priyankara , Baubet Valérie , Showe Louise C. , Dahmane Nadia , Davuluri Ramana V.
Published: June 2011

Despite our growing knowledge that many mammalian genes generate multiple transcript variants that may encode functionally distinct protein isoforms, the transcriptomes of various tissues and their developmental stages are poorly defined. Identifying the transcriptome and its regulation in a cell/tissue is the key to deciphering the cell/tissue-specific functions of a gene. We built a genome-wide inventory of noncoding and protein-coding transcripts (transcriptomes), their promoters (promoteromes) and histone modification states (epigenomes) for developing, and adult cerebella using integrative massive-parallel sequencing and bioinformatics approach. The data consists of 61,525 (12,796 novel) distinct mRNAs transcribed by 29,589 (4792 novel) promoters corresponding to 15,669 protein-coding and 7624 noncoding genes. Importantly, our results show that the transcript variants from a gene are predominantly generated using alternative transcriptional rather than splicing mechanisms, highlighting alternative promoters and transcriptional terminations as major sources of transcriptome diversity. Moreover, H3K4me3, and not H3K27me3, defined the use of alternative promoters, and we identified a combinatorial role of H3K4me3 and H3K27me3 in regulating the expression of transcripts, including transcript variants of a gene during development. We observed a strong bias of both H3K4me3 and H3K27me3 for CpG-rich promoters and an exponential relationship between their enrichment and corresponding transcript expression. Furthermore, the majority of genes associated with neurological diseases expressed multiple transcripts through alternative promoters, and we demonstrated aberrant use of alternative promoters in medulloblastoma, cancer arising in the cerebellum. The transcriptomes of developing and adult cerebella presented in this study emphasize the importance of analyzing gene regulation and function at the isoform level.
Exploring Collections of Tagged Text for Literary Scholarship
Authors: Correll M. , Witmore M. , Gleicher M.
Published: June 2011

Modern literary scholars must combine access to vast collections of text with the traditional close analysis of their field. In this paper, we discuss the design and development of tools to support this work. Based on analysis of the needs of literary scholars, we constructed a suite of visualization tools for the analysis of large collections of tagged text (i.e. text where one or more words have been annotated as belonging to a specific category). These tools unite the aspects of the scholars’ work: large scale overview tools help to identify corpus‐wide statistical patterns while fine scale analysis tools assist in finding specific details that support these observations. We designed visual tools that support and integrate these levels of analysis. The result is the first tool suite that can support the multilevel text analysis performed by scholars, combining standard visual elements with novel methods for selecting individual texts and identifying represenative passages in them.
Semantic‐Preserving Word Clouds by Seam Carving
Authors: Wu Yingcai , Provan Thomas , Wei Furu , Liu Shixia , Ma Kwan‐Liu
Published: June 2011

Word clouds are proliferating on the Internet and have received much attention in visual analytics. Although word clouds can help users understand the major content of a document collection quickly, their ability to visually compare documents is limited. This paper introduces a new method to create semantic‐preserving word clouds by leveraging tailored seam carving, a well‐established content‐aware image resizing operator. The method can optimize a word cloud layout by removing a left‐to‐right or top‐to‐bottom seam iteratively and gracefully from the layout. Each seam is a connected path of low energy regions determined by a Gaussian‐based energy function. With seam carving, we can pack the word cloud compactly and effectively, while preserving its overall semantic structure. Furthermore, we design a set of interactive visualization techniques for the created word clouds to facilitate visual text analysis and comparison. Case studies are conducted to demonstrate the effectiveness and usefulness of our techniques.
A User Study of Visualization Effectiveness Using EEG and Cognitive Load
Authors: Anderson E. W. , Potter K. C. , Matzen L. E. , Shepherd J. F. , Preston G. A. , Silva C. T.
Published: June 2011

Effectively evaluating visualization techniques is a difficult task often assessed through feedback from user studies and expert evaluations. This work presents an alternative approach to visualization evaluation in which brain activity is passively recorded using electroencephalography (EEG). These measurements are used to compare different visualization techniques in terms of the burden they place on a viewer's cognitive resources. In this paper, EEG signals and response times are recorded while users interpret different representations of data distributions. This information is processed to provide insight into the cognitive load imposed on the viewer. This paper describes the design of the user study performed, the extraction of cognitive load measures from EEG data, and how those measures are used to quantitatively evaluate the effectiveness of visualizations.
Dynamic Insets for Context‐Aware Graph Navigation
Authors: Ghani S. , Riche N. Henry , Elmqvist N.
Published: June 2011

Maintaining both overview and detail while navigating in graphs, such as road networks, airline route maps, or social networks, is difficult, especially when targets of interest are located far apart. We present a navigation technique called Dynamic Insets that provides context awareness for graph navigation. Dynamic insets utilize the topological structure of the network to draw a visual inset for off‐screen nodes that shows a portion of the surrounding area for links leaving the edge of the screen. We implement dynamic insets for general graph navigation as well as geographical maps. We also present results from a set of user studies that show that our technique is more efficient than most of the existing techniques for graph navigation in different networks.
Assisted Descriptor Selection Based on Visual Comparative Data Analysis
Authors: Bremm Sebastian , von Landesberger Tatiana , Bernard Jürgen , Schreck Tobias
Published: June 2011

Exploration and selection of data descriptors representing objects using a set of features are important components in many data analysis tasks. Usually, for a given dataset, an optimal data description does not exist, as the suitable data representation is strongly use case dependent. Many solutions for selecting a suitable data description have been proposed. In most instances, they require data labels and often are black box approaches. Non‐expert users have difficulties to comprehend the coherency of input, parameters, and output of these algorithms. Alternative approaches, interactive systems for visual feature selection, overburden the user with an overwhelming set of options and data views. Therefore, it is essential to offer the users a guidance in this analytical process. In this paper, we present a novel system for data description selection, which facilitates the user's access to the data analysis process. As finding of suitable data description consists of several steps, we support the user with guidance. Our system combines automatic data analysis with interactive visualizations. By this, the system provides a recommendation for suitable data descriptor selections. It supports the comparison of data descriptors with differing dimensionality for unlabeled data. We propose specialized scores and interactive views for descriptor comparison. The visualization techniques are scatterplot‐based and grid‐based. For the latter case, we apply Self‐Organizing Maps as adaptive grids which are well suited for large multi‐dimensional data sets. As an example, we demonstrate the usability of our system on a real‐world biochemical application.
Structural Decomposition Trees
Authors: Engel D. , Rosenbaum R. , Hamann B. , Hagen H.
Published: June 2011

Researchers and analysts in modern industrial and academic environments are faced with a daunting amount of multi‐dimensional data. While there has been significant development in the areas of data mining and knowledge discovery, there is still the need for improved visualizations and generic solutions. The state‐of‐the‐art in visual analytics and exploratory data visualization is to incorporate more profound analysis methods while focusing on fast interactive abilities. The common trend in these scenarios is to either visualize an abstraction of the data set or to better utilize screen‐space.

This paper presents a novel technique that combines clustering, dimension reduction and multi‐dimensional data representation to form a multivariate data visualization that incorporates both detail and overview. This amalgamation counters the individual drawbacks of common projection and multi‐dimensional data visualization techniques, namely ambiguity and clutter. A specific clustering criterion is used to decompose a multi‐dimensional data set into a hierarchical tree structure. This decomposition is embedded in a novel Dimensional Anchor visualization through the use of a weighted linear dimension reduction technique. The resulting Structural Decomposition Tree (SDT) provides not only an insight of the data set's inherent structure, but also conveys detailed coordinate value information. Further, fast and intuitive interaction techniques are explored in order to guide the user in highlighting, brushing, and filtering of the data.
Probabilistic Marching Cubes
Authors: Pöthkow Kai , Weber Britta , Hege Hans‐Christian
Published: June 2011

In this paper we revisit the computation and visualization of equivalents to isocontours in uncertain scalar fields. We model uncertainty by discrete random fields and, in contrast to previous methods, also take arbitrary spatial correlations into account. Starting with joint distributions of the random variables associated to the sample locations, we compute level crossing probabilities for cells of the sample grid. This corresponds to computing the probabilities that the well‐known symmetry‐reduced marching cubes cases occur in random field realizations. For Gaussian random fields, only marginal density functions that correspond to the vertices of the considered cell need to be integrated. We compute the integrals for each cell in the sample grid using a Monte Carlo method. The probabilistic ansatz does not suffer from degenerate cases that usually require case distinctions and solutions of ill‐conditioned problems. Applications in 2D and 3D, both to synthetic and real data from ensemble simulations in climate research, illustrate the influence of spatial correlations on the spatial distribution of uncertain isocontours.
Visualizing the Positional and Geometrical Variability of Isosurfaces in Uncertain Scalar Fields
Authors: Pfaffelmoser Tobias , Reitinger Matthias , Westermann Rüdiger
Published: June 2011

We present a novel approach for visualizing the positional and geometrical variability of isosurfaces in uncertain 3D scalar fields. Our approach extends recent work by Pöthkow and Hege [PH10] in that it accounts for correlations in the data to determine more reliable isosurface crossing probabilities. We introduce an incremental update‐scheme that allows integrating the probability computation into front‐to‐back volume ray‐casting efficiently. Our method accounts for homogeneous and anisotropic correlations, and it determines for each sampling interval along a ray the probability of crossing an isosurface for the first time. To visualize the positional and geometrical uncertainty even under viewing directions parallel to the surface normal, we propose a new color mapping scheme based on the approximate spatial deviation of possible surface points from the mean surface. The additional use of saturation enables to distinguish between areas of high and low statistical dependence. Experimental results confirm the effectiveness of our approach for the visualization of uncertainty related to position and shape of convex and concave isosurface structures.