bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of homogeneous condensation of small polyatomic systems in high pressure supersonic nozzle flows using Bhatnagar–Gross–Krook model
Authors: Kumar Rakesh , Levin Deborah A.
Published: April 2011

In the present work, we have simulated the homogeneous condensation of carbon dioxide and ethanol using the Bhatnagar–Gross–Krook based approach. In an earlier work of Gallagher-Rogers et al. [J. Thermophys. Heat Transfer 22, 695 (2008)], it was found that it was not possible to simulate condensation experiments of Wegener et al. [Phys. Fluids 15, 1869 (1972)] using the direct simulation Monte Carlo method. Therefore, in this work, we have used the statistical Bhatnagar–Gross–Krook approach, which was found to be numerically more efficient than direct simulation Monte Carlo method in our previous studies [Kumar et al., AIAA J. 48, 1531 (2010)], to model homogeneous condensation of two small polyatomic systems, carbon dioxide and ethanol. A new weighting scheme is developed in the Bhatnagar–Gross–Krook framework to reduce the computational load associated with the study of homogeneous condensation flows. The solutions obtained by the use of the new scheme are compared with those obtained by the baseline Bhatnagar–Gross–Krook condensation model (without the species weighting scheme) for the condensing flow of carbon dioxide in the stagnation pressure range of 1–5 bars. Use of the new weighting scheme in the present work makes the simulation of homogeneous condensation of ethanol possible. We obtain good agreement between our simulated predictions for homogeneous condensation of ethanol and experiments in terms of the point of condensation onset and the distribution of mass fraction of ethanol condensed along the nozzle centerline.
Integrated carbon fiber electrodes within hollow polymer microneedles for transdermal electrochemical sensing
Authors: Miller Philip R. , Gittard Shaun D. , Edwards Thayne L. , Lopez DeAnna M. , Xiao Xiaoyin , Wheeler David R. , Monteiro-Riviere Nancy A. , Brozik Susan M. , Polsky Ronen , Narayan Roger J.
Published: April 2011

In this study, carbon fiber electrodes were incorporated within a hollow microneedle array, which was fabricated using a digital micromirror device-based stereolithography instrument. Cell proliferation on the acrylate-based polymer used in microneedle fabrication was examined with human dermal fibroblasts and neonatal human epidermal keratinocytes. Studies involving full-thickness cadaveric porcine skin and trypan blue dye demonstrated that the hollow microneedles remained intact after puncturing the outermost layer of cadaveric porcine skin. The carbon fibers underwent chemical modification in order to enable detection of hydrogen peroxide and ascorbic acid; electrochemical measurements were demonstrated using integrated electrode-hollow microneedle devices.
Enhancement of the near-band-edge photoluminescence of ZnO nanowires: Important role of hydrogen incorporation versus plasmon resonances
Authors: Dev A. , Richters J. P. , Sartor J. , Kalt H. , Gutowski J. , Voss T.
Published: April 2011

We investigated the photoluminescence properties of ZnO nanowires coated with Au, Ag, and Pt nanoparticles deposited by dc sputtering. A strong enhancement of the near-band-edge emission was observed in all metal-coated samples but also if the samples were treated with Ar plasma without any nanoparticle deposition. High-resolution photoluminescence spectroscopy revealed hydrogen-donor-bound-exciton emission in all samples indicating unintentional hydrogen incorporation. A shorter decay time of the near-band-edge emission was observed in all cases. The results indicate that unintentional hydrogen incorporation plays a dominant role when metal deposition is performed by sputtering.
An experimental assembly for precise measurement of thermal accommodation coefficients
Authors: Trott Wayne M. , Castañeda Jaime N. , Torczynski John R. , Gallis Michael A. , Rader Daniel J.
Published: April 2011

An experimental apparatus has been developed to determine thermal accommodation coefficients for a variety of gas-surface combinations. Results are obtained primarily through measurement of the pressure dependence of the conductive heat flux between parallel plates separated by a gas-filled gap. Measured heat-flux data are used in a formula based on Direct Simulation Monte Carlo (DSMC) simulations to determine the coefficients. The assembly also features a complementary capability for measuring the variation in gas density between the plates using electron-beam fluorescence. Surface materials examined include 304 stainless steel, gold, aluminum, platinum, silicon, silicon nitride, and polysilicon. Effects of gas composition, surface roughness, and surface contamination have been investigated with this system; the behavior of gas mixtures has also been explored. Without special cleaning procedures, thermal accommodation coefficients for most materials and surface finishes were determined to be near 0.95, 0.85, and 0.45 for argon, nitrogen, and helium, respectively. Surface cleaning by in situ argon-plasma treatment reduced coefficient values by up to 0.10 for helium and by ∼0.05 for nitrogen and argon. Results for both single-species and gas-mixture experiments compare favorably to DSMC simulations.
A microfluidic device for simultaneous electrical and mechanical measurements on single cells
Authors: Chen Jian , Zheng Yi , Tan Qingyuan , Zhang Yan Liang , Li Jason , Geddie William R. , Jewett Michael A. S. , Sun Yu
Published: April 2011

This paper presents a microfluidic device for simultaneous mechanical and electrical characterization of single cells. The device performs two types of cellular characterization (impedance spectroscopy and micropipette aspiration) on a single chip to enable cell electrical and mechanical characterization. To investigate the performance of the device design, electrical and mechanical properties of MC-3T3 osteoblast cells were measured. Based on electrical models, membrane capacitance of MC-3T3 cells was determined to be 3.39±1.23 and 2.99±0.82 pF at the aspiration pressure of 50 and 100 Pa, respectively. Cytoplasm resistance values were 110.1±37.7 kΩ (50 Pa) and 145.2±44.3 kΩ (100 Pa). Aspiration length of cells was found to be 0.813±0.351 μm at 50 Pa and 1.771±0.623 μm at 100 Pa. Quantified Young’s modulus values were 377±189 Pa at 50 Pa and 344±156 Pa at 100 Pa. Experimental results demonstrate the device’s capability for characterizing both electrical and mechanical properties of single cells.
Spin-flip phenomena at the Co|graphene|Co interfaces
Authors: Li Baihai , Chen Liang , Pan Xiaoqing
Published: April 2011

In the present letter, we report phenomena at the Co|Graphene|Co interfaces based on first principles calculations. The nature of Co–C–Co and Co–graphene–Co atomic bonding at the interfaces were investigated by means of density of states, electron and spin density analysis. We show that the spins are antiferromagnetic coupled across the interface via the pd-π interactions between the Gr and Co layers, as exemplified by the superexchange mechanism. As a consequence, the spin injection efficiency at the Co|Graphene|Co interfaces and junctions will be reduced.
Metal-insulator transition without structural phase transition in V2O5 film
Authors: Kang Manil , Kim Inkoo , Kim Sok Won , Ryu Ji-Wook , Park Hyo Yeol
Published: April 2011

Spectroscopic ellipsometry and x-ray diffraction are used to investigate the metal-insulator transition in V2O5 films. Below and above Tc no significant change in the (001) peak is observed, but both n and k spectra undergo remarkable changes over the entire photon energy range. The SE and XRD results indicate that the V2O5 film undergoes a MIT without a structural phase transition near 280 °C. Further the MIT is confirmed by measurement of the resistance with temperature.
Ferroelectricity in the xAg2Nb4O11–(1−x)Na2Nb4O11 solid solution
Authors: Woodward David I. , Thomas Pam A.
Published: April 2011

Compositions in the (AgxNa1−x)2Nb4O11 solid solution have been prepared by a conventional solid state method. Composites containing Ag2Nb4O11 have been shown to be ferroelectric and the Curie temperature shown to decrease from 149 °C at x=1 to 62 °C at x=0.7. Room-temperature compositions with x≤0.7 are monoclinic, while those with x≥0.8 are rhombohedral with structures consistent with the relevant end members. At x=0.75, the structure was mainly rhombohedral but with coexistence of the monoclinic structure, indicating the proximity of a phase boundary.
Origin of exciton emissions from an AlN p-n junction light-emitting diode
Authors: Taniyasu Yoshitaka , Kasu Makoto
Published: April 2011

Exciton emissions from an AlN light-emitting diode with an improved emission efficiency of 1×10−4% were observed at 5.94 eV (208.7 nm) and 6.10 eV (203.2 nm) by current injection. The emission at 5.94 eV is attributed to an exciton emission originating from the crystal-field split off valence band (CH-exciton emission). Due to the large carrier-phonon interaction, the CH-exciton emission accompanies its phonon replicas. The emission at 6.10 eV is attributed to another exciton emission originating from heavy/light hole valence bands (HH/LH-exciton emission). From the emission energies, considering residual strain, the crystal-field splitting energy was determined to be −165 meV.
Elucidating the asymmetric behavior of the discharge in a dual magnetron sputter deposition system
Authors: Yusupov M. , Bultinck E. , Depla D. , Bogaerts A.
Published: April 2011

A magnetron discharge is characterized by drifts of the charged particles’ guiding center, caused by the magnetic field, in contrast to unmagnetized discharges. Because of these drifts, a pronounced asymmetry of the discharge can be observed in a dual magnetron setup. In this work, it is found that the shape of the discharge in a dual magnetron configuration depends on the magnetic field configuration. In a closed configuration, strong drifts were observed in one preferential direction, whereas in a mirror configuration the deflection of the discharge was not so pronounced. Our calculations confirm experimental observations.
An effective model of DNA like helicoidal structure: with length fluctuation nonlinearity
Authors: Tseytlin Y. M.
Published: April 2011

One of the natural helicoidal nanostructure, which thermomechanical features are studied carefully with the help of different mechanical models, is a DNA cell / molecule. Our study proves that the experimentally determined nonlinear fluctuations of the molecular length of DNA can be better understood by modeling the molecule as a helicoidal pretwisted nanostrip sensor with nonlinear function. The calculations presented here are in good agreement with the experimental data within 10%. Other used by many researchers mechanical models such as an elastic rod, wormlike chain (WLC), accordion bellows, or an elastic core wrapped with rigid wires do not show the possible variance nonlinearity of thermomechanical DNA molecular length fluctuations. We have found that the nonlinear variance of the length fluctuations is an intrinsic property of the micro-nano-sensors with helicoidal shape. This model allows us to estimate the persistence length and twist-stretch coupling of a DNA molecule as well. It also shows the molecule's overwinding possibility at initial stretching with correct numerical representation.
Solar cells based on the poly(N-vinylcarbazole): porphyrin: tris(8-hydroxyquinolinato) aluminium blend system*
Authors: Zhang Tian-Hui , Zhao Su-Ling , Piao Ling-Yu , Xu Zheng , Ju Si-Ting , Liu Xiao-Dong , Kong Chao , Xu Xu-Rong
Published: April 2011

Organic solar cells based on poly(N-vinylcarbazole) (PVK): porphyrin: tris (8-hydroxyquinolinato) aluminium (Alq3) blend p-n junction systems have been fabricated in this work. The roles of the different components in the blend system and of the amount of porphyrin have been investigated. The 5, 10, 15, 20-tetraphenylporphyrin (TPP) and 5, 10, 15, 20-tetra(o-chloro)phenylporphyrinato-copper (CuTClPP) are used in the solar cells. The results show that TPP is better than CuTCIPP in enhancing the performance of PVK:Alq3 solar cells. When the weight ratio of PVK:TPP:Alq3 is 1:1.5:1, the best performance of solar cell is obtained. The open circuit voltage (Voc) is 0.87 V, and the short circuit current (Jsc) is 17.5 μA·cm−2. In the ternary bulk hereojunction system, the device may be regarded as a cascade of three devices of PVK:TPP, TPP:Alq3 and PVK:Alq3. PVK, TPP and Alq3 can improve the hole mobility, light absorption intensity and electron mobility of the ternary bulk hereojunction system, respectively.
Estimation of the Bispectral Index by Anesthesiologists
Authors: Bottros Michael M. , Palanca Ben Julian A. , Mashour George A. , Patel Ami , Butler Catherine , Taylor Amanda , Lin Nan , Avidan Michael S.
Published: April 2011

Background

Processed electroencephalographic indices, such as the bispectral index (BIS), are potential adjuncts for assessing anesthetic depth. While BIS® monitors might aid anesthetic management, unprocessed or nonproprietary electroencephalographic data may be a rich source of information for clinicians. We hypothesized that anesthesiologists, after training in electroencephalography interpretation, could estimate the index of a reference BIS as accurately as a second BIS® monitor (twin BIS®) (Covidien Medical, Boulder, CO) when provided with clinical and electroencephalographic data.

Methods

Two sets of electrodes connected to two separate BIS® monitors were placed on the foreheads of 10 surgical patients undergoing general anesthesia. Electroencephalographic parameters, vital signs, and end-tidal anesthetic gas concentrations were recorded at prespecified time points, and were provided to two sets of anesthesiologists. Ten anesthesiologists received brief structured training in electroencephalograph interpretation and 10 were untrained. Although electroencephalographic waveforms and open-source processed electroencephalograph metrics were provided from the reference BIS®, both groups were blinded to BIS values and were asked to estimate BIS.

Results

The trained anesthesiologists averaged as close to or closer to the reference BIS® compared with the twin BIS® monitor for 34% of their BIS estimates versus 26% for the untrained anesthesiologists. Using linear mixed effects model analysis, there was a statistically significant difference between the trained and untrained anesthesiologists (P = 0.02), but no difference between the twin BIS® monitor and trained anesthesiologists (P = 0.9).

Conclusion

With limited electroencephalography training and access to clinical data, anesthesiologists can estimate the BIS almost as well as a second BIS® monitor. These results reinforce the potential utility of training anesthesia practitioners in unprocessed electroencephalogram interpretation.
Time-Lapse Imaging of Postimplantation Mouse Embryos
Authors: Garcia Monica D. , Udan Ryan S. , Hadjantonakis Anna-Katerina , Dickinson Mary E.
Published: April 2011

INTRODUCTION

Genetic manipulation methods allow fluorescent labeling of virtually any cell type or protein of interest in developing embryos, providing powerful insights into morphogenetic events at cellular and subcellular resolutions. The development of ex vivo embryo culture methods combined with high-resolution imaging provides a strong platform for observing morphogenetic events as they occur within the developing embryo. In this protocol, postimplantation mouse embryos are cultured directly on the microscope stage under conditions that carefully control temperature, humidity, and gas exchange. This permits time-lapse imaging of developing mouse embryos.
Megaselia abdita: Fixing and Devitellinizing Embryos: Figure 1.
Authors: Rafiqi Ab. Matteen , Lemke Steffen , Schmidt-Ott Urs
Published: April 2011

INTRODUCTION

This protocol describes a combined heat/formaldehyde fixation procedure, as well as a manual devitellinization procedure, for pregastrular Megaselia abdita embryos.
IgG Affinity Capture of TAP-tagged Protein Complexes from Cell Extracts: Affinity Purification Step 1
Authors: Link Andrew J. , Weaver Connie , Farley Adam
Published: April 2011

INTRODUCTION

One approach to identifying protein–protein interactions is the biochemical purification of a target protein from cells or tissues under nondenaturing conditions, followed by the mass spectrometric identification of the components of the purified protein complex. The combination of highly specific protein purification strategies and mass spectrometry has proven to be a very successful approach for identifying protein–protein interactions. The tandem affinity purification (TAP) affinity tag and purification method allows efficient recovery of proteins present at low cellular concentrations under native conditions. Expressing the target protein at its natural levels avoids the assembly of overexpressed proteins into nonphysiological complexes. This protocol describes the immunoglobulin G (IgG) affinity capture of TAP-tagged complexes. This procedure is followed by calmodulin affinity purification.
Affinity Capture of TAP-tagged Protein Complexes: Affinity Purification Step 2
Authors: Link Andrew J. , Weaver Connie , Farley Adam
Published: April 2011

INTRODUCTION

One approach to identifying protein–protein interactions is the biochemical purification of a target protein from cells or tissues under nondenaturing conditions, followed by the mass spectrometric identification of the components of the purified protein complex. The combination of highly specific protein purification strategies and mass spectrometry has proven to be a very successful approach for identifying protein–protein interactions. The tandem affinity purification (TAP) affinity tag and purification method allows efficient recovery of proteins present at low cellular concentrations under native conditions. Expressing the target protein at its natural levels avoids the assembly of overexpressed proteins into nonphysiological complexes. This protocol describes calmodulin affinity capture of the TAP-tagged complexes after immunoglobulin G (IgG) affinity purification has been performed. These complexes can then be analyzed by methods such as high-sensitivity liquid chromatography coupled with tandem mass spectrometry and/or multidimensional protein identification technology (MudPIT) analysis.
Imaging Gene Expression in Live Cells and Tissues
Authors: Hong Hao , Yang Yunan , Cai Weibo
Published: April 2011

INTRODUCTION

Monitoring gene expression is crucial for studying the responses of gene therapy and clarifying gene function in various environments. Molecular imaging is a powerful tool for noninvasive visualization of gene expression. This article summarizes the current status of fluorescence and bioluminescence imaging (BLI) of gene expression in live cells and tissues, with the emphasis mainly on the early studies that pioneered the field. First, we describe fluorescence imaging of gene expression with a wide variety of fluorescent proteins. Next, we discuss the strategies for BLI of gene expression. Besides incorporating the reporter gene into the host DNA, mRNA-based BLI of gene expression is also briefly mentioned. Last, the construction of double- and triple-fusion reporter genes is presented. Because no single imaging modality is perfect and sufficient to obtain all of the necessary information for a given question, combinations of multiple molecular imaging modalities can offer synergistic advantages over any modality alone. Noninvasive optical imaging of gene expression has revolutionized biomedical research, and the progress made over the last decade should allow molecular imaging to play a major role in the field of gene therapy. For basic and preclinical research, optical imaging is indispensable for imaging gene expression. However, for clinical imaging of gene expression, positron emission tomography (PET) holds the greatest promise.
Live Imaging of Mouse Embryos
Authors: Garcia Monica D. , Udan Ryan S. , Hadjantonakis Anna-Katerina , Dickinson Mary E.
Published: April 2011

INTRODUCTION

The development of the mouse embryo is a dynamic process that requires the spatial and temporal coordination of multiple cell types as they migrate, proliferate, undergo apoptosis, and differentiate to form complex structures. However, the confined nature of embryos as they develop in utero limits our ability to observe these morphogenetic events in vivo. Previous work has used fixed samples and histological methods such as immunofluorescence or in situ hybridization to address expression or localization of a gene of interest within a developmental time line. However, such methods do not allow us to follow the complex, dynamic movements of individual cells as the embryo develops. Genetic manipulation methods now allow us to label virtually any cell type or protein of interest fluorescently, providing powerful insights into morphogenetic events at cellular and subcellular resolutions. The development of ex vivo embryo culture methods combined with high-resolution imaging now provides a strong platform for observing morphogenetic events as they occur within the developing embryo. In this article, we discuss the advantages of live embryo imaging for observing dynamic morphogenetic events in vivo.
Modernization of the small-angle neutron scattering spectrometer SANS-U by upgrade to a focusing SANS spectrometer
Authors: Iwase Hiroki , Endo Hitoshi , Katagiri Masaki , Shibayama Mitsuhiro
Published: April 2011

The small-angle neutron scattering spectrometer SANS-U at the research reactor (JRR-3) of the Japan Atomic Energy Agency, Tokai, Japan, has been successfully upgraded. This major upgrade was undertaken in order to install a high-resolution position-sensitive detector consisting of a cross-wired position-sensitive photomultiplier tube combined with a ZnS/6LiF scintillator on the SANS-U spectrometer. Without changing the total length of the spectrometer, the aim was to extend the accessible low-Qlimit (Qis the magnitude of the scattering vector) and to shorten the measurement time by employing focusing small-angle neutron scattering (FSANS). By using both spherical MgF2biconcave lenses and the new high-resolution position-sensitive detector, the accessible low-Qlimit was extended from 2.5 × 10−3to 3.8 × 10−4 Å−1. As a result, SANS-U can continuously cover a wideQrange from 3.8 × 10−4to 0.35 Å−1with a wavelength of 7 Å. FSANS can be utilized not only to improve the accessible low-Qlimit but also to increase the intensity of incident neutrons passing through the sample in the conventionalQrange from 2.5 × 10−3to 0.35 Å−1. The use of `high-intensity' FSANS also allowed a reduction of the measuring time by approximately 1/3.16 by increasing the incident neutron intensity.
Identification of de novo mutations and rare variants in hypoplastic left heart syndrome
Authors: Iascone M , Ciccone R , Galletti L , Marchetti D , Seddio F , Lincesso AR , Pezzoli L , Vetro A , Barachetti D , Boni L , Federici D , Soto AM , Comas JV , Ferrazzi P , Zuffardi O
Published: April 2011

Iascone M, Ciccone R, Galletti L, Marchetti D, Seddio F, Lincesso AR, Pezzoli L, Vetro A, Barachetti D, Boni L, Federici D, Soto AM, Comas JV, Ferrazzi P, Zuffardi O. Identification of de novo mutations and rare variants in hypoplastic left heart syndrome.

Hypoplastic left heart syndrome (HLHS) is one of the most severe congenital heart malformations, characterized by underdevelopment of the structures in the left heart–aorta complex. The majority of cases are sporadic. Although multiple genetic loci have been tentatively implicated in HLHS, no gene or pathway seems to be specifically associated with the disease. To elucidate the genetic basis of HLHS, we analyzed 53 well‐characterized patients with isolated HLHS using an integrated genomic approach that combined DNA sequencing of five candidate genes (NKX2‐5, NOTCH1, HAND1, FOXC2 and FOXL1) and genome‐wide screening by high‐resolution array comparative genomic hybridization. In 30 patients, we identified two novel de novo mutations in NOTCH1, 23 rare patients inherited gene variants in NOTCH1, FOXC2 and FOXL1, and 33 rare patients mostly inherited copy‐number variants. Some of the identified variations coexisted in the same patient. The biological significance of such rare variations is unknown, but our findings strengthen the role of NOTCH pathway in cardiac valve development, indicating that HLHS is, at least in part, a ‘valve’ disease. This is the first report of de novo mutations associated with isolated HLHS. Moreover, the coexistence of multiple rare variants suggests in some cases a cumulative effect, as shown for other complex disease.
Urinary angiotensin‐converting enzyme 2 in patients with CKD
Authors: MIZUIRI SONOO , AOKI TOSHIYUKI , HEMMI HIROMICHI , ARITA MICHITSUNE , SAKAI KEN , AIKAWA ATSUSHI
Published: April 2011

Aim:  Angiotensin‐converting enzyme 2 (ACE2) is a type I membrane protein that antagonizes the action of angiotensin II. Because of the need for invasive kidney biopsy, little is known about the role of renal ACE2 in human kidney diseases. The authors studied if urinary ACE2 could provide a novel clue to renal ACE2 in chronic kidney disease (CKD).

Methods:  Subjects were 190 patients with CKD including 38 patients with diabetic nephropathy and 36 healthy subjects. Parameters were urinary ACE2 by enzyme‐linked immunosorbent assay, blood pressure, casual plasma glucose, proteinuria, microalbuminuria, serum creatinine and estimated glomerular filtration rate. Urine and serum samples were also subjected to western blotting of ACE2.

Results:  Western blotting confirmed increased urinary ACE2 levels in patients with CKD. Urinary ACE2 was significantly higher in patients with CKD than healthy subjects (median 9.64 (interquartile range, 4.41–16.89) vs 1.50 (0.40–2.33) mg/g·creatinine, P < 0.001) and in patients with diabetic nephropathy than patients without diabetic nephropathy (median 13.16 (interquartile range 6.81–18.70) vs 8.90 (4.19–16.67) mg/g·creatinine, P < 0.05). No significant difference in urinary ACE2 was observed by the use of angiotensin‐converting enzyme inhibitor and angiotensin receptor blocker.

Conclusion:  Urinary ACE2 could be used as a non‐invasive marker to understand the role of renal ACE2 in CKD.
Gene acquisition, duplication and metabolic specification: the evolution of fungal methylisocitrate lyases
Authors: Müller Sebastian , Fleck Christian B. , Wilson Duncan , Hummert Christian , Hube Bernhard , Brock Matthias
Published: April 2011

Gene duplication represents an evolutionary mechanism for expanding metabolic potential. Here we analysed the evolutionary relatedness of isocitrate and methylisocitrate lyases, which are key enzymes of the glyoxylate and methylcitrate cycle respectively. Phylogenetic analyses imply that ancient eukaryotes acquired an isocitrate lyase gene from a prokaryotic source, but it was lost in some eukaryotic lineages. However, protists, oomycetes and most fungi maintained this gene and successfully integrated the corresponding enzyme into the glyoxylate cycle. A second gene, encoding a highly related enzyme, is present in fungi, but absent from other eukaryotes. This methylisocitrate lyase is specifically involved in propionyl‐CoA degradation via the methylcitrate cycle. Although bacteria possess methylisocitrate lyases with a structural fold similar to that of isocitrate lyases, their sequence identity to fungal methylisocitrate lyases is low. Phylogenetic analyses imply that fungal methylisocitrate lyases arose from gene duplication of an ancient isocitrate lyase gene from the basidiomycete lineage. Mutagenesis of active‐site residues of a bacterial and fungal isocitrate lyase, which have been predicted to direct the substrate specificity of iso‐ and methylisocitrate lyases, experimentally confirmed the possibility of direct evolution of methylisocitrate lyases from isocitrate lyases. Thus, gene duplication has increased the metabolic capacity of fungi.
Whole‐genome expression analysis reveals a role for death‐related genes in stress acclimation of the diatom Thalassiosira pseudonana
Authors: Thamatrakoln Kimberlee , Korenovska Olga , Niheu A. Kalani , Bidle Kay D.
Published: April 2011

Low iron (Fe) availability critically limits diatom distribution and productivity in vast regions of the modern ocean, such as open‐ocean, high nutrient low chlorophyll areas and coastal regimes characterized as Fe limitation ‘mosaics’. While unique strategies of Fe uptake and storage confer competitive advantages to pennate diatoms, the molecular determinants of low Fe acclimation are largely unknown in centric diatoms. We combined genome‐wide and targeted comparative transcriptomic analysis with diagnostic biochemistry and in vivo cell staining as a platform to identify the suite of genes involved in acclimation to Fe and associated oxidative stress in Thalassiosira pseudonana. A total of 1312 genes, nearly 12% of the total genome content, responded to Fe starvation in growing cells characterized by low photosynthetic efficiency and enhanced oxidative stress, caspase activity and metacaspase expression. While 82% of the most highly upregulated genes were also represented in EST libraries derived from diverse diatoms grown under various stress conditions (e.g. silicon, CO2 and nitrogen limitation), our analysis suggests that T. pseudonana mounts a unique molecular response to Fe starvation that includes a number of genes distinct from those of the model pennate diatom, Phaeodactylum tricornutum, which diverged ∼90 million years ago. Homologues to ∼50% of the upregulated genes were also identified in a metatranscriptome of eukaryotic phytoplankton communities from a chronically Fe‐limited region in the Northeast Pacific. Furthermore, we provide experimental evidence that a subset of putative death‐related genes participate in the cellular acclimation to low Fe and associated oxidative damage, suggesting that they co‐evolved with other metabolic pathways and play adaptive roles in the success of diatoms.
CD4+ and CD8+ T‐lymphocyte scores cannot reliably predict progression in patients with benign prostatic hyperplasia
Authors: Lamb Alastair D. , Qadan Motaz , Roberts Simon , Timlin Hannah , Vowler Sarah L. , Campbell Fiona M. , Grigor Ken , Bartlett John M. S. , McNeill S. Alan
Published: April 2011

OBJECTIVE

To determine whether the density of CD4+ and CD8+ T‐lymphocytes in a transrectal ultrasonography (TRUS) biopsy of the prostate can be used to predict the progression of lower urinary tract symptoms (LUTS) in benign prostatic hyperplasia (BPH).

PATIENTS AND METHODS

In total, 100 patients were randomly selected from a pool of patients with histologically proven, benign TRUS biopsy specimens. There were seven full years of follow‐up available. Clinical data were recorded, including prostate volume, International Prostate Symptom Score (IPSS), prostate‐specific antigen, urine flow rate, postvoid residual urine volume and previous prostate surgery. Markers of disease progression included the subsequent development of acute urinary retention (AUR), ≥4 point rise in IPSS, prescription of medical therapy (α‐blocker or 5‐α‐reductase inhibitor) and bladder outlet surgery. Four patients’ specimens were unsuitable for analysis. Biopsy sections from 96 patients were immunohistochemically stained for the presence of CD4+ and CD8+ T‐lymphocytes and the density of infiltrate was assessed using random field sampling and point counting.

RESULTS

Some 29% of patients (28/96) did not have BPH at the time of biopsy. Of all patients, 41% (39/96) progressed, 10% of whom (4/39) did not have BPH at the time of biopsy. A further 10% (10/96) developed AUR, 7% (7/96) had a ≥4 point rise in IPSS, 33% (32/96) required medical therapy for BPH and 11% (11/96) required bladder outlet surgery. There was low correlation between CD4+ and CD8+ densities in paired sections. CD4+ and CD8+ densities did not provide any significant predictive function in the progression of BPH, nor was their any predictive association noted between CD4+ and CD8+ scores and the development of prostate cancer. Sub‐analysis did show that a threshold mean of ≥1.35 CD8+ cells per field predicted progression to AUR with a sensitivity of 60% (95% confidence interval, CI, 26.2–87.8), specificity of 73.3% (95% CI 62.6–82.2) but a positive predictive value of 20.6% (95% CI 8.0–39.7). CD4+ infiltrate density suggested a trend to general progression but without statistical significance.

CONCLUSION

The present study, despite certain trends, shows no evidence for an association between CD4+ and CD8+ T‐lymphocytes and the progression of LUTS in BPH.
Allomorphy, autonomous morphology and phonological conditioning in the history of the Daco‐Romance present and subjunctive
Authors: Maiden Martin
Published: April 2011

Daco‐Romance dialects inherited the effects of two distinct sound changes which coincidentally gave rise to almost identical distributional patterns of alternation in the inflectional paradigm of the verb. Once the original phonological conditioning of the alternants (apparently) ceased to operate, what was left was a frequently encountered yet ‘nonsensical’ pattern of paradigmatic distribution, irreducible to any coherent common set of morphosyntactic features. It appears to have been, in the terminology of Aronoff, ‘morphomic’. Drawing on a large body of historical and comparative dialectological data, I chart the history of this apparently morphomic pattern. For much of the history of Daco‐Romance, it constitutes a kind of leitmotiv of paradigmatic organisation, practically inviolable in its distribution and providing a recurrent distributional model for novel types of alternation, unconnected with the original sound change. Yet, in relatively recent times, the distributional coherence has collapsed in apparent chaos. My analysis of these diachronic facts will suggest that there are morphological phenomena which may properly be seen as morphomic while also retaining elements of extramorphological, phonological conditioning.
Overlapping dual ERP responses to low cloze probability sentence continuations
Authors: Delong Katherine A. , Urbach Thomas P. , Groppe David M. , Kutas Marta
Published: April 2011

In 2005, DeLong, Urbach, and Kutas took advantage of the a/an English indefinite article phonological alternation and the sensitivities of the N400 ERP component to show that readers can neurally preactivate individual words of a sentence (including nouns and their prenominal indefinite articles) in a graded fashion with a likelihood estimated from the words' offline probabilities as sentence continuations. Here we report an additional finding from that study: a prolonged ERP frontal positivity to less probable noun continuations. We suggest that this positivity is consistent with hypotheses that additional neural processing may be invoked when highly expected continuations are not encountered in the input and speculate briefly on possible functional correlates.
Estimation of soil organic carbon stock and its spatial distribution in the Republic of Ireland
Authors: Xu X. , Liu W. , Zhang C. , Kiely G.
Published: April 2011

Data scarcity often prevents the estimate of regional (or national) scale soil organic carbon (SOC) stock and its spatial distribution. This study attempts to overcome the data limitations by combining two existing Irish soil databases [SoilC and national soil database (NSD)] at the national scale, to create an improved estimate of the national SOC stock. Representative regression models between the near‐surface SOC concentration and those of deeper depths, and between SOC concentration and bulk density (BD) were developed based on the SoilC database. These regression models were then applied to the NSD derived SOC concentration map, resulting in an improved SOC stock and spatial distribution map for the top 10 cm, 30 cm and 50 cm depths. Western Ireland, particularly coastal areas, was found to have higher SOC densities than eastern Ireland, corresponding to the spatial distribution of peatland. We estimated the national SOC stock at 383 ± 38 Tg for the near‐surface of 0–10 cm depth; 1016 ± 118 Tg for 0–30 cm depth; and 1474 ± 181 Tg for 0–50 cm depth.
Antagonism of the antithrombotic and anti‐atherosclerotic actions of aspirin by rofecoxib in the cholesterol‐fed rabbit
Authors: Kaber G , Kaiser B , Baumgärtel‐Allekotte D , Rauch BH , Noßmann S , Heim KH , Weber AA , Nagy N , Fischer JW , Schrör K
Published: April 2011

BACKGROUND AND PURPOSE Most patients at elevated cardiovascular risk receive long‐term aspirin (ASA) anti‐platelet treatment. The present study specifically addresses the pharmacological interactions between selective COX‐2 inhibitors and ASA and the possible consequences for the thrombotic risk during long‐term treatment.

EXPERIMENTAL APPROACH New Zealand white rabbits were fed a standard laboratory diet supplemented with 1% cholesterol (CON) for 12 weeks. Age‐matched control rabbits were fed the same standard diet without addition of cholesterol (SD). Rabbits were randomly assigned to one of the following groups: rofecoxib (ROFE, 25 mg·kg−1, bid), acetylsalicylic acid (ASA, 5 mg·kg−1, bid) or a combination of both (ASA + ROFE). At the end of the feeding period, the severity of atherosclerotic plaque formation was assessed in the aorta. Thrombus formation was assessed in the left carotid artery using a modified Folts procedure.

KEY RESULTS Treatment of cholesterol‐fed rabbits with ASA significantly reduced plaque formation. This reduction in lesion size was not observed in animals treated with the combination of rofecoxib and ASA. In the modified Folts model, treatment with either rofecoxib or ASA increased the total blood flow above that of untreated animals. This increase was statistically significant in the case of ASA, while cotreatment with rofecoxib abolished this ASA effect completely and reduced the total flow rate to the levels seen in untreated hypercholesterolaemic controls.

CONCLUSIONS COX‐2 inhibition by rofecoxib attenuates the antithrombotic and anti‐atherosclerotic effects of ASA during long‐term treatment in cholesterol‐fed rabbits.
The endocannabinoid system as a key mediator during liver diseases: new insights and therapeutic openings
Authors: Mallat A , Teixeira‐Clerc F , Deveaux V , Manin S , Lotersztajn S
Published: April 2011

Chronic liver diseases represent a major health problem due to cirrhosis and its complications. During the last decade, endocannabinoids and their receptors have emerged as major regulators of several pathophysiological aspects associated with chronic liver disease progression. Hence, hepatic cannabinoid receptor 2 (CB2) receptors display beneficial effects on alcoholic fatty liver, hepatic inflammation, liver injury, regeneration and fibrosis. Cannabinoid receptor 1 (CB1) receptors have been implicated in the pathogenesis of several lesions such as alcoholic and metabolic steatosis, liver fibrogenesis, or circulatory failure associated with cirrhosis. Although the development of CB1 antagonists has recently been suspended due to the high incidence of central side effects, preliminary preclinical data obtained with peripherally restricted CB1 antagonists give real hopes in the development of active CB1 molecules devoid of central adverse effects. CB2‐selective molecules may also offer novel perspectives for the treatment of liver diseases, and their clinical development is clearly awaited. Whether combined treatment with a peripherally restricted CB1 antagonist and a CB2 agonist might result in an increased therapeutic potential will warrant further investigation.

LINKED ARTICLES This article is part of a themed issue on Cannabinoids in Biology and Medicine. To view the other articles in this issue visit http://dx.doi.org/10.1111/bph.2011.163.issue‐7
Natriuretic peptide receptor‐3 underpins the disparate regulation of endothelial and vascular smooth muscle cell proliferation by C‐type natriuretic peptide
Authors: Khambata Rayomand S , Panayiotou Catherine M , Hobbs Adrian J
Published: April 2011

BACKGROUND AND PURPOSE C‐type natriuretic peptide (CNP) is an endothelium‐derived vasorelaxant, exerting anti‐atherogenic actions in the vasculature and salvaging the myocardium from ischaemic injury. The cytoprotective effects of CNP are mediated in part via the Gi‐coupled natriuretic peptide receptor (NPR)3. As GPCRs are well‐known to control cell proliferation, we investigated if NPR3 activation underlies effects of CNP on endothelial and vascular smooth muscle cell mitogenesis.

EXPERIMENTAL APPROACH Proliferation of human umbilical vein endothelial cells (HUVEC), rat aortic smooth muscle cells (RAoSMC) and endothelial and vascular smooth muscle cells from NPR3 knockout (KO) mice was investigated in vitro.

KEY RESULTS CNP (1 pM–1 µM) facilitated HUVEC proliferation and inhibited RAoSMC growth concentration‐dependently. The pro‐ and anti‐mitogenic effects of CNP were blocked by the NPR3 antagonist M372049 (10 µM) and the extracellular signal‐regulated kinase (ERK) 1/2 inhibitor PD98059 (30 µM) and were absent in cells from NPR3 KO mice. Activation of ERK 1/2 by CNP was inhibited by Pertussis toxin (100 ng·mL−1) and M372049 (10 µM). In HUVEC, ERK 1/2 activation enhanced expression of the cell cycle promoter, cyclin D1, whereas in RAoSMC, ERK 1/2 activation increased expression of the cell cycle inhibitors p21waf1/cip1 and p27kip1.

CONCLUSIONS AND IMPLICATIONS A facet of the vasoprotective profile of CNP is mediated via NPR3‐dependent ERK 1/2 phosphorylation, resulting in augmented endothelial cell proliferation and inhibition of vascular smooth muscle growth. This pathway may offer an innovative approach to reversing the endothelial damage and vascular smooth muscle hyperplasia that characterize many vascular disorders.
Endogenous peptide YY and neuropeptide Y inhibit colonic ion transport, contractility and transit differentially via Y1 and Y2 receptors
Authors: Tough IR , Forbes S , Tolhurst R , Ellis M , Herzog H , Bornstein JC , Cox HM
Published: April 2011

BACKGROUND AND PURPOSE Peptide YY (PYY) and neuropeptide Y (NPY) activate Y receptors, targets under consideration as treatments for diarrhoea and other intestinal disorders. We investigated the gastrointestinal consequences of selective PYY or NPY ablation on mucosal ion transport, smooth muscle activity and transit using wild‐type, single and double peptide knockout mice, comparing mucosal responses with those from human colon.

EXPERIMENTAL APPROACH Mucosae were pretreated with a Y1 (BIBO3304) or Y2 (BIIE0246) receptor antagonist and changes in short‐circuit current recorded. Colonic transit and colonic migrating motor complexes (CMMCs) were assessed in vitro and upper gastrointestinal and colonic transit measured in vivo.

KEY RESULTS Y receptor antagonists revealed tonic Y1 and Y2 receptor‐mediated antisecretory effects in human and wild‐type mouse colon mucosae. In both, Y1 tone was epithelial while Y2 tone was neuronal. Y1 tone was reduced 90% in PYY−/− mucosa but unchanged in NPY−/− tissue. Y2 tone was partially reduced in NPY−/− or PYY−/− mucosae and abolished in tetrodotoxin‐pretreated PYY−/− tissue. Y1 and Y2 tone were absent in NPYPYY−/− tissue. Colonic transit was inhibited by Y1 blockade and increased by Y2 antagonism indicating tonic Y1 excitation and Y2 inhibition respectively. Upper GI transit was increased in PYY−/− mice only. Y2 blockade reduced CMMC frequency in isolated mouse colon.

CONCLUSIONS AND IMPLICATIONS Endogenous PYY and NPY induced significant mucosal antisecretory tone mediated by Y1 and Y2 receptors, via similar mechanisms in human and mouse colon mucosa. Both peptides contributed to tonic Y2‐receptor‐mediated inhibition of colonic transit in vitro but only PYY attenuated upper GI transit.
Numerical Simulation of the Flow Field Within the Aortic Arch During Cardiac Assist
Authors: Filipovic Nenad , Schima Heinrich
Published: April 2011

In recent years, artificial heart devices have been implanted in a considerable number of patients with terminal cardiac failure for bridge to transplantation and even destination therapy. These devices provide either pulsatile or continuous blood flow. To determine eventual physiological effects of these different types of flow on the aorta, a computational fluid dynamics model of the aorta and its thoracic branches was implemented. Pulsatile and continuous flow fields were calculated by implementing a comprehensive computational framework with a stabilized finite element method. The computed results revealed that the pulsatile pump support results in a lower mean shear stress and higher oscillatory shear stress index than the continuous pump support. The flow patterns for the pulsatile pump support above the closed aortic valves show a similar washout as for the continuous pump support. In summary, from the flow pattern simulation there was no particular preference for either pulsatile or continuous devices.
The Long‐Term Effect of Insomnia on Primary Headaches: A Prospective Population‐Based Cohort Study (HUNT‐2 and HUNT‐3)
Authors: Ødegård Siv S. , Sand Trond , Engstrøm Morten , Stovner Lars J. , Zwart John‐Anker , Hagen Knut
Published: April 2011

(Headache 2011;51:570‐580)

Objective.— Few prospective studies have evaluated the relationship between insomnia and headache. We aimed to analyze the influence of insomnia at baseline on the risk for headache 11 years later.

Methods.— This longitudinal cohort study included subjects who participated in 2 consecutive surveys of the Nord‐Trøndelag Health Study (HUNT‐2 and HUNT‐3). Among the invited individuals aged 20 years or more in HUNT‐2 (n = 92,566) and HUNT‐3 (n = 94,194), a total of 26,197 completed the headache section of both surveys. A proxy insomnia diagnosis based on DSM‐IV at baseline and ICDH‐2‐based headache diagnoses at follow‐up were derived from questionnaires. Headache‐free individuals in HUNT‐2 (n = 15,268) were selected for analysis. The relative risks (RRs) for headache in insomniacs were calculated with logistic regression.

Results.— The presence of baseline insomnia was associated with a 40% increased risk for headache in HUNT‐3 (RR = 1.4, 95% CI = 1.2‐1.7). Similar results were found for tension‐type headache (TTH), migraine, and non‐classified headache. Subjects with insomnia‐related working disability had a 60% increased headache risk (RR = 1.6, 95% CI = 1.3‐2.1). The RR was larger for migraine (RR = 2.0, 95% CI = 1.3‐3.1) than for TTH (RR = 1.5, 95% CI = 1.1‐2.1). Insomnia at baseline was related to headache frequency at follow‐up for both migraine (P trend = 0.02) and TTH (P trend < 0.001).

Conclusion.— In headache‐free subjects, insomnia was associated with an increased risk of headache 11 years later. The association was particularly strong for chronic headache.