bluuebunny/crossref_metadata_2025 huggingface dataset:
i‐RUBY: A novel software for quantitative analysis of highly accurate shotgun‐proteomics liquid chromatography/tandem mass spectrometry data obtained without stable‐isotope labeling of proteins
Authors: Wada Kazuya , Ogiwara Atsushi , Nagasaka Keiko , Tanaka Naoki , Komatsu Yasuhiko
Published: March 2011

We developed a novel software named i‐RUBY (identification‐Related qUantification‐Based strategY algorithm for liquid chromatography/tandem mass spectrometry (LC/MS/MS) data) that enables us to perform fully automatic ion current‐based spectral feature analysis of highly accurate data obtained by LC/MS/MS. At the 1st step, this software utilizes accurate peptide/protein identification information for peak detection and peak matching among measurements. Then, at the 2nd step, it picks yet unidentified peaks and matches them to the peaks identified at the 1st step by a linear interpolation algorithm. The analysis of human plasma externally spiked with a known amount of yeast alcohol dehydrogenase 1 showed a good linear relationship between the amount of protein spiked and the quantitative values obtained by i‐RUBY analysis. Experiment using human plasma digests spiked with a mixture of known amounts of synthetic peptides derived from two yeast proteins, alcohol dehydrogenase 1 and glucose‐6‐phospate isomerase, showed the expansion by the 2nd step of i‐RUBY of the lower quantification limits to 1/10 to 1/1000 of those reached only by identified peaks at the 1st step. Good correlations between the i‐RUBY results and the amount of proteins were confirmed by the analysis of real samples, i.e., sera of normal subjects and cancer patients, by comparing quantitative values of acute‐phase proteins obtained by i‐RUBY analysis of LC/MS/MS data with those obtained by an immunological method using Bio‐Plex. These results taken together show that i‐RUBY is a useful tool for obtaining dependable quantitative information from highly accurate shotgun‐proteomics LC/MS/MS data. Copyright © 2011 John Wiley & Sons, Ltd.
Nanoporous Elements in Microfluidics for Multiscale Manipulation of Bioparticles
Authors: Chen Grace D. , Fachin Fabio , Fernandez‐Suarez Marta , Wardle Brian L. , Toner Mehmet
Published: March 2011

Solid materials, such as silicon, glass, and polymers, dominate as structural elements in microsystems including microfluidics. Porous elements have been limited to membranes sandwiched between microchannel layers or polymer monoliths. This paper reports the use of micropatterned carbon‐nanotube forests confined inside microfluidic channels for mechanically and/or chemically capturing particles ranging over three orders of magnitude in size. Nanoparticles below the internanotube spacing (80 nm) of the forest can penetrate inside the forest and interact with the large surface area created by individual nanotubes. For larger particles (>80 nm), the ultrahigh porosity of the nanotube elements reduces the fluid boundary layer and enhances particle–structure interactions on the outer surface of the patterned nanoporous elements. Specific biomolecular recognition is demonstrated using cells (≈10 μm), bacteria (≈1 μm), and viral‐sized particles (≈40 nm) using both effects. This technology can provide unprecedented control of bioseparation processes to access bioparticles of interest, opening new pathways for both research and point‐of‐care diagnostics.
CFD Modelling and Analysis of Pulverized Coal Injection in Blast Furnace: An Overview
Authors: Shen Yansong , Yu Aibing , Zulli Paul
Published: March 2011

In order to understand the complicated phenomena of pulverized coal injection (PCI) process in blast furnace (BF), several mathematical models have been developed by the UNSW and BSR cooperation. These models are featuring from coal combustion in a pilot‐scale test rig, to coal combustion in a real BF, and then to coal/coke combustion in a real BF, respectively. This paper reviews these PCI models in aspects of model developments and model applicability. The model development is firstly discussed in terms of model formulation, their new features and geometry/regions considered. The model applicability is then discussed in terms of main findings followed by the model evaluation on their advantages and limitations. It is indicated that the three PCI models are all able to describe PCI operation qualitatively. The model of coal/coke combustion in a real BF is more reliable for simulating in‐furnace phenomena of PCI operation qualitatively and quantitatively. Such model gives a more reliable burnout prediction over the raceway surface, which could better represent the amount of unburnt char entering the coke bed. These models are useful for understanding the flow‐thermo‐chemical behaviours and then optimising the PCI operation in practice.
Performance analysis of multi‐stage interference cancellation for ultra‐wide band multiple‐access communication systems
Authors: Wen Jyh‐Horng , Hung Ho‐Lung
Published: March 2011

In this contribution, a novel particle swarm optimization (PSO)‐based multi‐user detector (MUD) aided time‐hopping ultra‐wide band (TH‐UWB) system has been investigated in the multi‐path channel model. In this approach, the PSO‐based MUD employs the output of the Rake receiver as its initial value to search for the best solution which results in a formulated optimization mechanism. By taking advantage of the heuristic values and the collective intelligence of PSO technique, the proposed detector offers almost the same bit error rate (BER) performance as the full‐search‐based optimum MUD does, while greatly reducing the potentially computational complexity. Simulation results have been provided to examine the evolutionary behavior and the detection performance of the proposed PSO‐based MUD in both the additive white Gaussian noise and the multi‐path fading channel. Copyright © 2011 John Wiley & Sons, Ltd.
Handsewn Versus Stapled Gastroduodenostomy in Patients with Gastric Cancer: Long‐Term Follow‐up of a Randomized Clinical Trial
Authors: Kim Taebong , Yu Wansik , Chung Hoyoung
Published: March 2011

Background

The role of circular staplers in gastroduodenostomy during subtotal gastrectomy for gastric cancer has not been defined clearly.

Methods

A randomized clinical trial included patients with gastric cancer who underwent subtotal gastrectomy with either stapled (99 patients) or handsewn gastroduodenostomy (98 patients). The anastomosis time and postoperative outcomes in the two groups were compared.

Results

Performance of stapled gastroduodenostomy was significantly quicker than handsewn gastroduodenostomy. There were no significant differences between the groups in postoperative course, morbidity and mortality rates, survival rate, and recurrence pattern.

Conclusions

Stapled gastroduodenostomy with a circular stapler can reduce the anastomosis time with relative safety.
Some existence results on the exterior Dirichlet problem for the minimal hypersurface equation
Authors: do Espírito-Santo Nedir , Ripoll Jaime
Published: March 2011

It is proved the existence of solutions to the exterior Dirichlet problem for the minimal hypersurface equation in complete noncompact Riemannian manifolds either with negative sectional curvature and simply connected or with nonnegative Ricci curvature under a growth condition on the sectional curvature.
Well-posedness of a diffusive gyro-kinetic model
Authors: Hauray M. , Nouri A.
Published: March 2011

We study a finite Larmor radius model used to describe the ions distribution function in the core of a tokamak plasma, that consists in a gyro-kinetic transport equation coupled with an electro-neutrality equation. Since the last equation does not provide enough regularity on the electric potential, we introduce a simple linear collision operator adapted to the finite Larmor radius approximation. We next study the two-dimensional dynamics in the direction perpendicular to the magnetic field. Thanks to the smoothing effects of the collision and the gyro-average operators, we prove the global existence of solutions, as well as short time uniqueness and stability.

On étudie un modèle à rayon de Larmor fini décrivant la fonction de distribution des ions dans un plasma de coeur de tokamak. Il consiste en une équation de transport gyrocinétique couplée à une équation de quasi-neutralité. Lʼéquation de quasi-neutralité donnant peu de régularité au potentiel électrique, on introduit un opérateur de collisions linéaire adapté. On étudie alors la dynamique du système dans la direction perpendiculaire au champ magnétique. Lʼeffet régularisant des opérateurs de collisions et de gyro-moyenne permet de démontrer lʼexistence globale de solutions ainsi que leur unicité et stabilité locales en temps.
The instability of periodic surface gravity waves
Authors: DECONINCK BERNARD , OLIVERAS KATIE
Published: March 2011

Euler's equations describe the dynamics of gravity waves on the surface of an ideal fluid with arbitrary depth. In this paper, we discuss the stability of periodic travelling wave solutions to the full set of nonlinear equations via a non-local formulation of the water wave problem, modified from that of Ablowitz, Fokas & Musslimani (J. Fluid Mech., vol. 562, 2006, p. 313), restricted to a one-dimensional surface. Transforming the non-local formulation to a travelling coordinate frame, we obtain a new formulation for the stationary solutions in the travelling reference frame as a single equation for the surface in physical coordinates. We demonstrate that this equation can be used to numerically determine non-trivial travelling wave solutions by exploiting the bifurcation structure of this new equation. Specifically, we use the continuous dependence of the amplitude of the solutions on their propagation speed. Finally, we numerically examine the spectral stability of the periodic travelling wave solutions by extending Fourier–Floquet analysis to apply to the associated linear non-local problem. In addition to presenting the full spectrum of this linear stability problem, we recover past well-known results such as the Benjamin–Feir instability for waves in deep water. In shallow water, we find different instabilities. These shallow water instabilities are critically related to the wavelength of the perturbation and are difficult to find numerically. To address this problem, we propose a strategy to estimate a priori the location in the complex plane of the eigenvalues associated with the instability.
Effect of serum on the mitochondrial active area on developmental days 1 to 4 inin vitro-produced bovine embryos
Authors: Crocco M. , Alberio R.H. , Lauria L. , Mariano M.I.
Published: March 2011

Certain morphological changes at the subcellular level caused by the current techniques forin vitroembryo production seem to affect mitochondria. Many of these, including dysfunctional changes, have been associated with the presence of serum in the culture medium. Thus, the aim of the present work was to assess the mitochondrial dynamics occurring in embryos during the first 4 days of development, in order to analyze the most appropriate time for adding the serum. We used transmission electron microscopy (TEM) micrographs to calculate the embryo area occupied by the different morphological types of mitochondria, and analyzed them with Image Pro Plus analyzer. The results showed hooded mitochondria as the most representative type in 1- to 4-day-old embryos. Swollen, on-fusion, orthodox and vacuolated types were also present. When analyzed in embryos cultured without serum, the dynamics of the different mitochondrial types appeared to be similar, a fact that may provide evidence that the developmental changes control the mitochondrial dynamics, and that swollen mitochondria may not be completely inactive. In contrast, in culture medium supplemented with serum from estrous cows, we observed an increased area of hooded mitochondria by developmental day 4, a fact that may indicate an increased production of energy compared with previous days. According to these results, the bovine serum added to the culture medium seems not to be responsible for the functional changes in mitochondria.
Stenting of modified and classical Blalock–Taussig shunts – lessons learned from seven consecutive cases
Authors: Krasemann Thomas , Tzifa Aphrodite , Rosenthal Eric , Qureshi Shakeel A.
Published: March 2011

In neonates and infants with a shunt-dependent pulmonary circulation, stenosis of the shunt needs to be treated aggressively to prevent a fatal outcome. We report the technique and outcome in seven consecutive neonates and infants with Blalock–Taussig shunt stenosis, who were treated with intraluminal stents. Stenting of classical or modified Blalock–Taussig shunts is technically feasible and can be used as a rescue procedure. Neointimal dissection is less likely compared with balloon angioplasty of the shunt alone.
Large‐Scale Experiments on Volcanic Processes
Authors: Valentine Greg A. , Bonadonna Costanza , Manzella Irene , Clarke Amanda , Dellino Pierfrancesco
Published: March 2011

Some of the least understood and most hazardous geologic processes involve complex multiphase flows, particularly those related to explosive volcanic eruptions. These phenomena inherently involve a wide range of characteristic length and time scales, as well as processes that are coupled across those scales in a range of flow regimes. For example, a pyroclastic density current's (pyroclastic flows and surges) behavior is governed in a complex way by the interactions between individual particles (∼10–4 to 101 meters, ∼10–1 to 101 seconds) and by turbulent mixing with surrounding air (∼10–2 to 102 meters, 1 to 102 seconds). Material properties within individual flows can vary over huge ranges; for example, when ascending magma interacts with groundwater in a volcanic conduit, the viscous melt and liquid water are transformed into brittle glass and steam.
A single point mutation in ricin A-chain increases toxin degradation and inhibits EDEM1-dependent ER retrotranslocation
Authors: Sokołowska Iwona , Wälchli Sébastien , Węgrzyn Grzegorz , Sandvig Kirsten , Słomińska-Wojewódzka Monika
Published: March 2011

Ricin is a potent plant cytotoxin composed of an A-chain [RTA (ricin A-chain)] connected by a disulfide bond to a cell binding lectin B-chain [RTB (ricin B-chain)]. After endocytic uptake, the toxin is transported retrogradely to the ER (endoplasmic reticulum) from where enzymatically active RTA is translocated to the cytosol. This transport is promoted by the EDEM1 (ER degradation-enhancing α-mannosidase I-like protein 1), which is also responsible for directing aberrant proteins for ERAD (ER-associated protein degradation). RTA contains a 12-residue hydrophobic C-terminal region that becomes exposed after reduction of ricin in the ER. This region, especially Pro250, plays a crucial role in ricin cytotoxicity. In the present study, we introduced a point mutation [P250A (substitution of Pro250 with alanine)] in the hydrophobic region of RTA to study the intracellular transport of the modified toxin. The introduced mutation alters the secondary structure of RTA into a more helical structure. Mutation P250A increases endosomal–lysosomal degradation of the toxin, as well as reducing its transport from the ER to the cytosol. Transport of modified RTA to the cytosol, in contrast to wild-type RTA, appears to be EDEM1-independent. Importantly, the interaction between EDEM1 and RTAP250A is reduced. This is the first reported evidence that EDEM1 protein recognition might be determined by the structure of the ERAD substrate.
The novel Nrf2-interacting factor KAP1 regulates susceptibility to oxidative stress by promoting the Nrf2-mediated cytoprotective response
Authors: Maruyama Atsushi , Nishikawa Keizo , Kawatani Yukie , Mimura Junsei , Hosoya Tomonori , Harada Nobuhiko , Yamamato Masayuki , Itoh Ken
Published: March 2011

The transcription factor Nrf2 (nuclear factor-erythroid 2-related factor 2) co-ordinately regulates ARE (antioxidant-response element)-mediated induction of cytoprotective genes in response to electrophiles and oxidative stress; however, the molecular mechanism controlling Nrf2-dependent gene expression is not fully understood. To identify factors that regulate Nrf2-dependent transcription, we searched for proteins that interact with the Nrf2-NT (N-terminal Nrf2 transactivation domain) by affinity purification from HeLa nuclear extracts. In the present study, we identified KAP1 [KRAB (Krüppel-associated box)-associated protein 1] as a novel Nrf2-NT-interacting protein. Pull-down analysis confirmed the interaction between KAP1 and Nrf2 in cultured cells and demonstrated that the N-terminal region of KAP1 binds to Nrf2-NT in vitro. Reporter assays showed that KAP1 facilitates Nrf2 transactivation activity in a dose-dependent manner. Furthermore, the induction of the Nrf2-dependent expression of HO-1 (haem oxygenase-1) and NQO1 [NAD(P)H quinone oxidoreductase 1] by DEM (diethyl maleate) was attenuated by KAP1 knockdown in NIH 3T3 fibroblasts. This finding established that KAP1 acts as a positive regulator of Nrf2. Although Nrf2 nuclear accumulation was unaffected by KAP1 knockdown, the ability of Nrf2 to bind to the regulatory region of HO-1 and NQO1 was reduced. Moreover, KAP1 knockdown enhanced the sensitivity of NIH 3T3 cells to tert-butylhydroquinone, H2O2 and diamide. These results support our contention that KAP1 participates in the oxidative stress response by maximizing Nrf2-dependent transcription.
Differentiation and characteristics of the enhanced green fluorescent protein gene transgenic goat neural stem cells cultured in attached and non‐attached plates
Authors: Zheng Yue‐Mao , Dang Yong‐Hui , Qiu Shuang , Qi Ying‐Pei , Xu Yong‐Ping , Sai Wu‐Jia‐Fu
Published: March 2011

The aims of this study were (i) to determine whether NSCs (neural stem cells) could be isolated from the brain of embryonic day 98 fetal goat, (ii) to determine if these stem cells have the capability of multipotent differentiation following transfection with a reporter gene, EGFP (enhanced green fluorescent protein) and (iii) to study the characteristics of the stem cells cultured in attached and non‐attached plates. NSCs were isolated from embryonic day 98 fetal goat brain, transfected with EGFP gene using lipofection, and subcultured in attached and non‐attached plates respectively. The transgenic stem cells were induced to differentiate into osteogenic and endothelial cells in vitro respectively. Markers associated with undifferentiated NSCs and their differentiated cells were tested by RT—PCR (reverse transcription—PCR). The results demonstrated that stem cells could be isolated from embryonic day 98 fetal goat brain, and EGFP gene could be transfected into the cells. The transgenic NSCs were capable of self‐renewal, a defining property of stem cells, and were grown as free‐floating neurospheres in non‐attached plates. When the neurospheres were transferred and cultured in attached plates, cells migrate from the neurospheres and are grown as spindle cells. The stem cells were grown as quasi‐circular cells when the single stem cells were cultured in attached plates. Both the NSCs cultured in non‐attached and attached plates could express Hes1 (hairy and enhancer of split 1), Oct4 (octamer‐binding protein 4), Nanog, Sox2 [SRY (sex‐determining region Y)‐box 2] and Nestin, while following differentiation cells expressed markers for osteogenic cells (Osteocalcin+ and Osteonectin+) and endothelium (CD34+ and eNOS+). The results demonstrated that the goat EGFP gene transgenic NSCs have the capability of multipotent differentiation, which means that the transgenic NSCs may be useful in cell transplantation studies in future.
Esophageal Considerations After Spinal Cord Injury
Authors: Huffman Julie A.
Published: March 2011

Speech-Language Pathologists (SLPs) are frequently involved with patients after spinal cord injury due to the frequency of speech and swallowing problems. Any stage of swallowing can be adversely affected, and it is imperative that the SLP be aware that spinal cord injuries at various levels can produce a variety of deficits affecting oropharyngeal, esophageal, and many other functions. The SLP has a role in assessment and treatment of oropharyngeal dysphagia and also in recognizing how and when this injury should lead to screening and referral for disorders in the esophageal stage.
Walking through Doorways Causes Forgetting: Further Explorations
Authors: Radvansky Gabriel A. , Krawietz Sabine A. , Tamplin Andrea K.
Published: March 2011

Previous research using virtual environments has revealed a location-updating effect in which there is a decline in memory when people move from one location to another. Here we assess whether this effect reflects the influence of the experienced context, in terms of the degree of immersion of a person in an environment, as suggested by some work in spatial cognition, or by a shift in context. In Experiment 1, the degree of immersion was reduced by using smaller displays. In comparison, in Experiment 2 an actual, rather than a virtual, environment was used, to maximize immersion. Location-updating effects were observed under both of these conditions. In Experiment 3, the original encoding context was reinstated by having a person return to the original room in which objects were first encoded. However, inconsistent with an encoding specificity account, memory did not improve by reinstating this context. Finally, we did a further analysis of the results of this and previous experiments to assess the differential influence of foregrounding and retrieval interference. Overall, these data are interpreted in terms of the event horizon model of event cognition and memory.
Wide-angle and polarization-independent three-dimensional magnetic metamaterials with and without substrates
Authors: Chen Chun Hui , Qu Shao Bo , Wang Jia Fu , Ma Hua , Wang Jun , Zhao Jing Bo , Wang Xin Hua , Zhou Hang , Xu Zhuo
Published: March 2011

The sensitivities to incident angles and polarization states influence the usefulness of metamaterials in practical applications. In this paper, a three-dimensional magnetic metamaterial composed of connected symmetric split rings with dielectric substrates is proposed. Both simulation and experimental results show that it exhibits negative magnetic resonances under both normal and parallel incidences of electromagnetic waves. It is also insensitive to the incident angles and polarization states. Then based on this structure, a unit cell without substrates is presented. By alternatively arranging the unit cells in different ways, the combined structure exhibiting negative effective permeability at THz is almost insensitive to incident angles and polarization states. Thus, the proposed structures with and without substrates are the candidates to engineer three-dimensional metamaterials.
Large and highly reversible magnetic field-induced strains in textured Co1−xNixMnSi alloys at room temperature
Authors: Zhang C L , Zheng Y X , Xuan H C , Ma S C , Cao Q Q , Wang D H , Du Y W
Published: March 2011

The metamagnetic transition and magnetoelastic properties are investigated in transition-metal-based Co1−x
Ni
x
MnSi (0 < x < 0.03) alloys. Large low-field magnetostrains are observed in the Ni-doped CoMnSi alloys. Compared with some other metamagnetic materials with large magnetic field-induced strains, the present alloys show highly reversible magnetoelastic behaviour and have almost constant strain outputs around room temperature. These observations may shed light on developing transition-metal-based magnetostrictive materials.
Confocal spectroscopy of InGaN LED structures
Authors: Dobrovolskas D , Mickevičius J , Kuokštis E , Tamulaitis G , Shur M , Shatalov M , Yang J , Gaska R
Published: March 2011

Photoluminescence of InGaN structures for green light-emitting diodes (LEDs) with multiple quantum wells as an active medium was studied with spatial and spectral resolution using confocal microscopy. Bright spots of ∼200 nm diameter were observed. Emission from these bright areas was up to 8 times more intense than from the rest of the sample surface and the band peak position in these areas was blueshifted with respect to the band position in the background surface of lower photoluminescence intensity. The data on emission properties in bright and dark areas and the dependence of these properties on the excitation power density were interpreted by assuming inhomogeneous distribution of defects acting as nonradiative recombination centres.
Dielectric breakdown in AlOx tunnelling barriers
Authors: Schaefer D M , Fichtner P F P , Carara M , Schelp L F , Dorneles L S
Published: March 2011

We studied the dielectric breakdown in tunnelling barriers produced by plasma-assisted oxidation of an aluminium surface. The barrier mean height, thickness and the effective tunnelling area were extracted from current versus voltage curves measured at room temperature. The effective tunnelling area ranged from 10−10 to 10−5 cm2, corresponding to less than 1% of the geometrical surface of the samples. The estimated electrical field to breakdown agreed with predictions from thermochemical models, and decreased exponentially with the effective tunnelling area.
Investigation of the dielectric and piezoelectric properties of ReCa4O(BO3)3 crystals
Authors: Yu Fapeng , Zhang Shujun , Zhao Xian , Guo Shiyi , Duan Xiulan , Yuan Duorong , Shrout Thomas R
Published: March 2011

Piezoelectric ReCa4O(BO3)3 (ReCOB, Re: rare earth) crystals, including ErCOB, SmCOB, PrCOB and LaCOB, were successfully grown by the Czochralski (Cz) method. The dielectric constants were determined to be
,
and
for ErCOB,
,
and
for SmCOB,
,
and
for PrCOB,
,
and
for LaCOB, respectively. The electromechanical coupling factors k
26 and piezoelectric coefficients d
26 were found to be 18.5% (7.6 pC N−1), 27.0% (12.7 pC N−1), 31.5% (15.8 pC N−1) and 25.0% (11.8 pC N−1) for ErCOB, SmCOB, PrCOB and LaCOB crystals, respectively. The dielectric and piezoelectric properties as a function of Re3+ ion radius were studied, with maximum values being observed in the PrCOB crystals, due to the similar ion radius of Pr3+ and Ca2+. The relationship between the structure and dielectric/piezoelectric properties of ReCOB crystals was explored, to further optimize the dielectric and piezoelectric properties in ReCOB series crystals.
Mg doping of GaN by molecular beam epitaxy
Authors: Lieten R R , Motsnyi V , Zhang L , Cheng K , Leys M , Degroote S , Buchowicz G , Dubon O , Borghs G
Published: March 2011

We present a systematic study on the influence of growth conditions on the incorporation and activation of Mg in GaN layers grown by plasma-assisted molecular beam epitaxy. We show that high quality p-type GaN layers can be obtained on GaN-on-silicon templates. The Mg incorporation and the electrical properties have been investigated as a function of growth temperature, Ga : N flux ratio and Mg : Ga flux ratio. It was found that the incorporation of Mg and the electrical properties are highly sensitive to the Ga : N flux ratio. The highest hole mobility and lowest resistivity were achieved for slightly Ga-rich conditions. In addition to an optimal Ga : N ratio, an optimum Mg : Ga flux ratio was also observed at around 1%. We observed a clear Mg flux window for p-type doping of GaN : 0.31% < Mg : Ga < 5.0%. A lowest resistivity of 0.98 Ω cm was obtained for optimized growth conditions. The p-type GaN layer then showed a hole concentration of 4.3 × 1017 cm−3 and a mobility of 15 cm2 V−1 s−1. Temperature-dependent Hall effect measurements indicate an acceptor depth in these samples of 100 meV for a hole concentration of 5.5 × 1017 cm−3. The corresponding Mg concentration is 5 × 1019 cm−3, indicating approximately 1% activation at room temperature. In addition to continuous growth of Mg-doped GaN layers we also investigated different modulated growth procedures. We show that a modulated growth procedure has only limited influence on Mg doping at a growth temperature of 800 °C or higher. This result is thus in contrast to previously reported GaN : Mg doping at much lower growth temperatures of 500 °C.
Kinesin-5, a mitotic microtubule-associated motor protein, modulates neuronal migration
Authors: Falnikar Aditi , Tole Shubha , Baas Peter W.
Published: March 2011

Kinesin-5 (also called Eg5 or kif11) is a homotetrameric motor protein that functions by modulating microtubule (MT)–MT interactions. In the case of mitosis, kinesin-5 slows the rate of separation of the half-spindles. In the case of the axon, kinesin-5 limits the frequency of transport of short MTs, and also limits the rate of axonal growth. Here we show that experimental inhibition of kinesin-5 in cultured migratory neurons results in a faster but more randomly moving neuron with a shorter leading process. As is the case with axons of stationary neurons, short MT transport frequency is notably enhanced in the leading process of the migratory neuron when kinesin-5 is inhibited. Conversely, overexpression of kinesin-5, both in culture and in developing cerebral cortex, causes migration to slow and even cease. Regions of anti-parallel MT organization behind the centrosome were shown to be especially rich in kinesin-5, implicating these regions as potential sites where kinesin-5 forces may be especially relevant. We posit that kinesin-5 acts as a “brake” on MT–MT interactions that modulates the advance of the entire MT apparatus. In so doing, kinesin-5 regulates the rate and directionality of neuronal migration and possibly the cessation of migration when the neuron reaches its destination.
Decreased Interleukin‐10 Secretion by Peripheral Blood Mononuclear Cells in Children With Irritable Bowel Syndrome
Authors: Hua Man‐Chin , Lai Ming‐Wei , Kuo Ming‐Ling , Yao Tsung‐Chieh , Huang Jing‐Long , Chen Shu‐Mei
Published: March 2011

Background and Aims:

The aim of the present study was to evaluate proinflammatory and anti‐inflammatory cytokine levels in children with irritable bowel syndrome (IBS).

Patients and Methods:

Thirty‐five children with IBS (17 diarrhea‐predominant, 7 constipation‐predominant, and 11 mixed type) and 25 healthy children as healthy controls (HCs) were enrolled. All of the participants completed a questionnaire recording the duration, severity, and associated academic and social influences. Peripheral blood mononuclear cells were isolated and cultured for 24 hours with and without 1 or 5 ng/mL Escherichia coli lipopolysaccharide (LPS). Cytokine production including tumor necrosis factor‐α (TNF‐α), interleukin (IL)‐6, and IL‐10 was measured using enzyme‐linked immunosorbent assays.

Results:

Children with IBS revealed lower baseline and significantly lower IL‐10 levels after LPS stimulation compared with HCs (P = 0.001). Although not to a significant level, TNF‐α and IL‐6 levels were higher in children with IBS compared with HCs. The IL‐10 levels in patients with IBS with strong pain intensity were lower both in baseline and under 1 ng/mL LPS stimulation. The levels became significantly lower under 5 ng/mL LPS stimulation compared with those experiencing mild and moderate pain intensity (P = 0.025).

Conclusions:

Our study suggests that children with IBS tend to produce lower amounts of the anti‐inflammatory cytokine IL‐10 at baseline and after LPS stimulation, implying that defects in immune modulation may contribute to IBS in children.
Does Reflux Monitoring With Multichannel Intraluminal Impedance Change Clinical Decision Making?
Authors: Rosen Rachel , Hart Kristen , Nurko Samuel
Published: March 2011

Objectives:

Multichannel intraluminal impedance with pH (pH‐MII) has become the criterion standard test for the evaluation of gastroesophageal reflux disease, but it is not clear whether the results of this test change clinical decision making. The goal of the present study was to determine the differences in clinical decision making by attending physicians based on the pH probe results versus MII results.

Methods:

We conducted a prospective study in which physicians were initially given pH probe results and asked how they would change the patient's clinical management based on these results. Physicians were then given the MII results and asked how their management would change. Physicians then were asked whether they believed MII affected their clinical decision making overall.

Results:

pH probe results changed clinical management 40% of the time and MII results changed clinical management an additional 22% of the time. Clinical decision making was not influenced by the performance of pH‐MII on or off acid suppression. The escalation of acid suppression therapy was the main management change that occurred based on the pH‐MII results.

Conclusions:

The addition of MII to the standard pH probe resulted in a change in management in approximately 25% of the patients, suggesting that there may be a role for pH‐MII in clinical practice.
Comparative complete genome analysis of dengue virus type 3 circulating in India between 2003 and 2008
Authors: Sharma Shashi , Dash Paban Kumar , Agarwal Surekha , Shukla Jyoti , Parida M. M. , Rao P. V. L.
Published: March 2011

Dengue is endemic in most parts of the tropics including India. So far, complete genome information for Indian dengue isolates is not available. In the present study, we characterized the genome of three dengue type 3 viruses isolated from India. The genomes of all three viruses were found to be 10 707 bp long with an ORF encoding 3390 aa. Extensive molecular phylogenetic analysis based on comparison of the complete genome and envelope gene classified the recent Indian viruses into genotype III (lineage III), revealing a shift of lineage from lineage V. The sequence analysis revealed several non-conservative changes in major structural proteins. This study clearly indicates that the genotype III (lineage III) dengue type 3 viruses have been continuously circulating in major parts of India since 2003 and are responsible for the recent major outbreaks all over India. This is the first extensive study on complete genome analysis of dengue type 3 viruses in India.
An amino acid substitution (V3I) in the Japanese encephalitis virus NS4A protein increases its virulence in mice, but not its growth rate in vitro
Authors: Yamaguchi Yukie , Nukui Yoko , Tajima Shigeru , Nerome Reiko , Kato Fumihiro , Watanabe Haruo , Takasaki Tomohiko , Kurane Ichiro
Published: March 2011

Our previous studies have shown that the Japanese encephalitis virus (JEV) strain Mie/40/2004 is the most virulent of the strains isolated by us in Japan from 2002 to 2004. Comparison of the amino acid sequence of Mie/40/2004 with those of low-virulence strains revealed that an isoleucine residue at position 3 of the Mie/40/2004 NS4A protein may increase viral pathogenicity. A recombinant virus with a single valine-to-isoleucine substitution (V3I) at position 3 in the low-virulence Mie/41/2002 background (rJEV-Mie41-NS4AV3I) exhibited increased virulence in mice compared with the Mie/41/2002 parent strain. The V3I mutation did not affect virus growth in several cell lines. These results demonstrate that the isoleucine at position 3 in the NS4A protein of Mie/40/2004 is responsible for its high virulence in vivo. This is the first report to show that an amino acid substitution in a flavivirus NS4A protein alters viral pathogenicity in mice.
Antibodies to a new viral citrullinated peptide, VCP2: fine specificity and correlation with anti-cyclic citrullinated peptide (CCP) and anti-VCP1 antibodies
Authors: Pratesi F , Tommasi C , Anzilotti C , Puxeddu I , Sardano E , Di Colo G , Migliorini P
Published: March 2011

Anti-citrullinated protein/peptide antibodies (ACPA) are a hallmark of rheumatoid arthritis (RA) and can be measured using different citrullinated substrates. In this paper we describe a new viral citrullinated peptide – VCP2 – derived from the Epstein–Barr virus-encoded protein EBNA-2 and analyse its potential as substrate for ACPA detection. Analysing sera from 100 RA patients and 306 controls, anti-VCP2 immunoglobulin (Ig)G were found in 66% of RA sera, IgM in 46% and IgA in 39%, compared with less than 3% of control sera. Anti-VCP2 IgG was associated with erosive arthritis, the presence of rheumatoid factor and anti-VCP1 and anti-cyclic citrullinated peptide (CCP) antibodies. Anti-VCP2 antibodies were detected in 1% and anti-VCP1 antibodies in 4% of CCP-negative RA sera; conversely, 3% of the VCP-negative sera were CCP-positive. Taken together, these data suggest that VCP2 could offer a valuable tool for ACPA detection. Inhibition assays showed that two non-overlapping epitopes – a citrulline–glycine stretch shared between VCP1 and VCP2 and the N-terminal portion of the VCP2 sequence – were targeted by anti-VCP2 antibodies. Moreover, in some RA sera that tested positive in CCP and VCP2 assays, preincubation with VCP2 inhibited binding to CCP, whereas in other sera the binding was unaffected. Thus, the reactivity with more than one ACPA substrate might be due in some RA patients to antibody populations with different specificities, and in others to cross-reactive antibody populations. Finally, affinity-purified anti-VCP2 antibodies immunoprecipitated deiminated Epstein–Barr virus nuclear antigen (EBNA-2) from an EBNA-2-transfected cell line, suggesting that viral sequences may be involved in the generation of the ACPA response.
Evidence for the innate immune response as a correlate of protection in human immunodeficiency virus (HIV)-1 highly exposed seronegative subjects (HESN)
Authors: Tomescu C , Abdulhaqq S , Montaner L J
Published: March 2011

The description of highly exposed individuals who remain seronegative (HESN) despite repeated exposure to human immunodeficiency virus (HIV)-1 has heightened interest in identifying potential mechanisms of HIV-1 resistance. HIV-specific humoral and T cell-mediated responses have been identified routinely in HESN subjects, although it remains unknown if these responses are a definitive cause of protection or merely a marker for exposure. Approximately half of HESN lack any detectible HIV-specific adaptive immune responses, suggesting that other mechanisms of protection from HIV-1 infection also probably exist. In support of the innate immune response as a mechanism of resistance, increased natural killer (NK) cell activity has been correlated with protection from infection in several high-risk cohorts of HESN subjects, including intravenous drug users, HIV-1 discordant couples and perinatally exposed infants. Inheritance of protective NK KIR3DL1high and KIR3DS1 receptor alleles have also been observed to be over-represented in a high-risk cohort of HESN intravenous drug users and HESN partners of HIV-1-infected subjects. Other intrinsic mechanisms of innate immune protection correlated with resistance in HESN subjects include heightened dendritic cell responses and increased secretion of anti-viral factors such as β-chemokines, small anti-viral factors and defensins. This review will highlight the most current evidence in HESN subjects supporting the role of epithelial microenvironment and the innate immune system in sustaining resistance against HIV-1 infection. We will argue that as a front-line defence the innate immune response determines the threshold of infectivity that HIV-1 must overcome to establish a productive infection.
Quantitative immunohistochemical fingerprinting of adhesion/growth‐regulatory galectins in salivary gland tumours: divergent profiles with diagnostic potential
Authors: Remmelink Myriam , de Leval Laurence , Decaestecker Christine , Duray Anaelle , Crompot Emerence , Sirtaine Nicolas , André Sabine , Kaltner Herbert , Leroy Xavier , Gabius Hans‐Joachim , Saussez Sven
Published: March 2011

Remmelink M, de Leval L, Decaestecker C, Duray A, Crompot E, Sirtaine N, André S, Kaltner H, Leroy X, Gabius H‐J & Saussez S (2011) Histopathology 58, 543–556 Quantitative immunohistochemical fingerprinting of adhesion/growth‐regulatory galectins in salivary gland tumours: divergent profiles with diagnostic potential

Aims:  This study tests the hypothesis that histopathological fingerprinting of galectins, which are emerging multifunctional effectors in cell sociology, could refine the differential diagnosis of salivary tumours.

Methods and results:  We applied non‐crossreactive polyclonal antibodies against galectin‐1 (Gal‐1), galectin‐3 (Gal‐3), galectin‐7 (Gal‐7) and galectin‐8 (Gal‐8) for immunohistochemical analysis of salivary gland tumours (72 cases with benign disease and 39 cases with malignancy) and 29 control specimens. The principal positivity of cases, the site of signal presence and the quantitative parameters concerning percentage of positive cells and labelling intensity were determined. Acinic cell and adenoid cystic carcinomas (specifically tubular and cribriform types) shared the expression signature of Gal‐1, Gal‐3 and Gal‐8 presence combined with Gal‐7 absence. Mucoepidermoid carcinomas presented a unique profile based on cytoplasmic Gal‐1, Gal‐3, Gal‐7 and Gal‐8 localization in the intermediate cells. Adenomas were separable from malignancy by a consistent decrease in the labelling index (LI) for Gal‐7 and Gal‐8 (LI Gal‐7, P < 10−6; LI Gal‐8, P = 0.001). When present, staining for the tumour suppressor p16INK4a coincided with Gal‐1 presence.

Conclusions:  Expression profiling of the four tested galectins in salivary gland tumours revealed non‐uniform staining patterns with discriminatory potential based on intracellular localization and quantitative aspects.
Reviewing studies with diverse designs: the development and evaluation of a new tool
Authors: Sirriyeh Reema , Lawton Rebecca , Gardner Peter , Armitage Gerry
Published: March 2011

Rationale, aims & objective  Tools for the assessment of the quality of research studies tend to be specific to a particular research design (e.g. randomized controlled trials, or qualitative interviews). This makes it difficult to assess the quality of a body of research that addresses the same or a similar research question but using different approaches. The aim of this paper is to describe the development and preliminary evaluation of a quality assessment tool that can be applied to a methodologically diverse set of research articles.

Methods  The 16‐item quality assessment tool (QATSDD) was assessed to determine its reliability and validity when used by health services researchers in the disciplines of psychology, sociology and nursing. Qualitative feedback was also gathered from mixed‐methods health researchers regarding the comprehension, content, perceived value and usability of the tool.

Results  Reference to existing widely used quality assessment tools and experts in systematic review confirmed that the components of the tool represented the construct of ‘good research technique’ being assessed. Face validity was subsequently established through feedback from a sample of nine health researchers. Inter‐rater reliability was established through substantial agreement between three reviewers when applying the tool to a set of three research papers (κ = 71.5%), and good to substantial agreement between their scores at time 1 and after a 6‐week interval at time 2 confirmed test–retest reliability.

Conclusions  The QATSDD shows good reliability and validity for use in the quality assessment of a diversity of studies, and may be an extremely useful tool for reviewers to standardize and increase the rigour of their assessments in reviews of the published papers which include qualitative and quantitative work.
Impact of light quality on leaf and shoot hydraulic properties: a case study in silver birch (Betula pendula)
Authors: SELLIN ARNE , SACK LAWREN , ÕUNAPUU EELE , KARUSION ANNIKA
Published: March 2011

Responses of leaf and shoot hydraulic conductance to light quality were examined on shoots of silver birch (Betula pendula), cut from lower (‘shade position’) and upper thirds of the crowns (‘sun position’) of trees growing in a natural temperate forest stand. Hydraulic conductances of leaf blades (Klb), petioles (KP) and branches (i.e. leafless stem; KB) were determined using a high pressure flow meter in steady state mode. The shoots were exposed to photosynthetic photon flux density of 200–250 µmol m−2 s−1 using white, blue or red light. Klb depended significantly on both light quality and canopy position (P < 0.001), KB on canopy position (P < 0.001) and exposure time (P = 0.014), and none of the three factors had effect on KP. The highest values of Klb were recorded under the blue light (3.63 and 3.13 × 10−4 kg m−2 MPa−1 s−1 for the sun and shade leaves, respectively), intermediate values under white light (3.37 and 2.46 × 10−4 kg m−2 MPa−1 s−1, respectively) and lowest values under red light (2.83 and 2.02 × 10−4 kg m−2 MPa−1 s−1, respectively). Light quality has an important impact on leaf hydraulic properties, independently of light intensity or of total light energy, and the specific light receptors involved in this response require identification. Given that natural canopy shade depletes blue and red light, Klb may be decreased both by reduced fluence and shifts in light spectra, indicating the need for studies of the natural heterogeneity of Klb within and under canopies, and its impacts on gas exchange.
Oxidation–reduction and reactive oxygen species homeostasis in mutant plants with respiratory chain complex I dysfunction
Authors: JUSZCZUK IZABELA M. , SZAL BOŻENA , RYCHTER ANNA M.
Published: March 2011

Mutations in a mitochondrial or nuclear gene encoding respiratory chain complex I subunits lead to decreased or a total absence of complex I activity. Plant mutants with altered or lost complex I activity adapt their respiratory metabolism by inducing alternative pathways of the respiratory chain and changing energy metabolism. Apparently, complex I is a crucial component of the oxidation–reduction (redox) regulatory system in photosynthetic cells, and alternative NAD(P)H dehydrogenases of the mitochondrial electron transport chain (mtETC) cannot fully compensate for its impairment. In most cases, dysfunction of complex I is associated with lowered or unchanged hydrogen peroxide (H2O2) concentrations, but increased superoxide (O2‐) levels. Higher production of reactive oxygen species (ROS) by mitochondria in the mosaic (MSC16) cucumber mutant may be related to retrograde signalling. Different effects of complex I dysfunction on H2O2 and O2‐ levels in described mutants might result from diverse regulation of processes involved in H2O2 and O2‐ production. Often, dysfunction of complex I did not lead to oxidative stress, but increased the capacity of the antioxidative system and enhanced stress tolerance. The new cellular homeostasis in mutants with dysfunction of complex I allows growth and development, reflecting the plasticity of plant metabolism.