bluuebunny/crossref_metadata_2025 huggingface dataset:
An index theorem for the stability of periodic travelling waves of Korteweg–de Vries type
Authors: Bronski Jared C. , Johnson Mathew A. , Kapitula Todd
Published: November 2011

We consider the stability of periodic travelling-wave solutions to a generalized Korteweg–de Vries (gKdV) equation and prove an index theorem relating the number of unstable and potentially unstable eigenvalues to geometric information on the classical mechanics of the travelling-wave ordinary differential equation. We illustrate this result with several examples, including the integrable KdV and modified KdV equations, the L2-critical KdV-4 equation that arises in the study of blow-up and the KdV-½ equation, which is an idealized model for plasmas.
Assessment of Urban Soundscapes
Authors: Marry Solène
Published: November 2011

This article presents the different tools for assessing soundscapes within urban public spaces and develops in particular the use of the sonic mind map. We will successively define the notions of sonic perception and representation, and sonic and spatial evaluation; we will approach the concept of soundscape and finally give details about the sonic mind-map tool. Through this tool, the soundscape of urban public spaces can be understood, not through speech analysis, but through spatial representations of memorised sonic ambiances.

Investigation results based among other things on sonic mind-map analyses explain the significance of sonic spatialisation and of the sound source distance in urban soundscape assessment. Using the sonic mind map to analyse the sonic representations associated with certain urban spaces seems to be relevant for researchers in space sciences or even for urban planners.
“Coolie work”: Sir Reginald Johnston at the School of Oriental Studies, 1931–1937
Authors: Bickers Robert A.
Published: November 2011

Surprisingly, the history of Chinese studies in Britain has received little academic attention. In fact, its development in the twentieth century, and its problems and lack of world standing actually tell us much about the background to Sino-British relations, and especially about the resources available to enable those interested, for professional, business, evangelical or plainly academic reasons, to understand China and the Chinese. British sinology in the interwar period, if discussed at all, is routinely condemned by historians. After 1949 China was closed off to outside contacts; not surprisingly, commentators thereafter look back jealously to the opportunities for close and frequent contact that were available before the revolution but which they saw as being apparently wasted. This common judgement does not, however, do full justice to the scale of the underlying problems, especially financial ones, faced by academic institutions that taught Chinese.
Long‐term changes in the thermospheric neutral winds over Arecibo: Climatology based on over three decades of Fabry‐Perot observations
Authors: Brum Christiano Garnett Marques , Tepley Craig A. , Fentzke Jonathan T. , Robles Eva , dos Santos Pedrina Terra , Gonzalez Sixto A.
Published: November 2011

We present a study of the climatology of thermospheric neutral wind (TNW) meridional and zonal components measured with the 630.0 nm nightglow Fabry‐Perot interferometer at the Arecibo Observatory from 1980 to 2010. We show and discuss the solar and geomagnetic dependencies as well as the long‐term trend of the TNW components and their variation over time and season. A main result of this study was the detection of a substantial seasonal and local time dependence of the response of the TNW to solar and geomagnetic activity. In addition, we found that there is a long‐term trend in the thermospheric neutral wind, which can be of a larger magnitude than the variation found in the seasonal, solar cycle, and geomagnetic activity influences. A major signature of this trend over the last 30 years was an increase in the meridional northward component up to 1.4 m s−1 yr−1 before midnight local time during the summer.
Mechanisms of summer intraseasonal sea surface temperature oscillations in the Bay of Bengal
Authors: Vinayachandran P. N. , Neema C. P. , Mathew Simi , Remya R.
Published: November 2011

Intraseasonal variations (ISV) of sea surface temperature (SST) in the Bay of Bengal (BoB) is highest in its northwestern part. An Indian Ocean model forced by QuikSCAT winds and climatological river discharge (QR run) reproduces ISV of SST, albeit with weaker magnitude. Air‐sea fluxes, in the presence of a shallow mixed layer, efficiently effect intraseasonal SST fluctuations. Warming during intraseasonal events is smaller (<1°C) for June ‐ July period and larger (1.5° to 2°C) during September, the latter due to a thinner mixed layer. To examine the effect of salinity on ISV, the model was run by artificially increasing the salinity (NORR run) and by decreasing it (MAHA10 run). In NORR, both rainfall and river discharge were switched off and in MAHA10 the discharge by river Mahanadi was increased tenfold. The spatial pattern of ISV as well as its periodicity was similar in QR, NORR and MAHA10. The ISV was stronger in NORR and weaker in MAHA10, compared to QR. In NORR, both intraseasonal warming and cooling were higher than in QR, the former due to reduced air‐sea heat loss as the mean SST was lower, and the latter due to enhanced subsurface processes resulting from weaker stratification. In MAHA10, both warming and cooling were lower than in QR, the former due to higher air‐sea heat loss owing to higher mean SST, and the latter due to weak subsurface processes resulting from stronger stratification. These model experiments suggest that salinity effects are crucial in determining amplitudes of intraseasonal SST variations in the BoB.
Central Pacific El Niño, the “subtropical bridge,” and Eurasian climate
Authors: Graf Hans‐F. , Zanchettin Davide
Published: November 2011

This study contributes to the discussion on possible effects of El Niño on North Atlantic/European regional climates. We use NCEP/NCAR reanalysis data to show how the two different types of El Niños (the central Pacific, or CP, and the east Pacific, or EP) result in remarkably different European winter temperature anomalies, specifically weak warming during EP and significant cooling during CP El Niños, the latter being associated with a negative phase of the winter North Atlantic Oscillation (NAO). Our results diverge from former suggestions addressing the weakened stratospheric polar vortex as the dominant factor contributing to the El Niño/NAO teleconnection. We propose a tropospheric bridge as the mechanism primarily responsible for the establishment of a negative NAO phase and of associated cold European winters. This mechanism includes the subtropical jet (STJ) waveguide being activated only during CP El Niños, when anomalous convective heating occurs near the edge of the Pacific warm pool. Under these conditions the STJ is enhanced by planetary wave flux divergence in the subtropical upper troposphere, providing favorable conditions for the propagation of a wave number 5 disturbance around the subtropical Northern Hemisphere. This wave contributes to weakening of the Azores High and, hence, to the negative NAO phase. As global warming scenarios project an increase in the frequency of CP El Niño events, the distinctive nature of this mechanism implies that the probability of cold European winters may increase as well in future decades.
Estimating 1992–2000 average active layer thickness on the Alaskan North Slope from remotely sensed surface subsidence
Authors: Liu Lin , Schaefer Kevin , Zhang Tingjun , Wahr John
Published: November 2011

The measurement of temporal changes in active layer thickness (ALT) is crucial to monitoring permafrost degradation in the Arctic. We develop a retrieval algorithm to estimate long‐term average ALT using thaw‐season surface subsidence derived from spaceborne interferometric synthetic aperture radar (InSAR) measurements. Our algorithm uses a model of vertical distribution of water content within the active layer accounting for soil texture, organic matter, and moisture. We determine the 1992–2000 average ALT for an 80 × 100 km study area of continuous permafrost on the North Slope of Alaska near Prudhoe Bay. We obtain an ALT of 30–50 cm over moist tundra areas, and a larger ALT of 50–80 cm over wet tundra areas. Our estimated ALT values match in situ measurements at Circumpolar Active Layer Monitoring (CALM) sites within uncertainties. Our results demonstrate that InSAR can provide ALT estimates over large areas at high spatial resolution.
Visualizing Cell Death in Experimental Focal Cerebral Ischemia: Promises, Problems, and Perspectives
Authors: Zille Marietta , Farr Tracy D , Przesdzing Ingo , Müller Jochen , Sommer Clemens , Dirnagl Ulrich , Wunder Andreas
Published: November 2011

One of the hallmarks of stroke pathophysiology is the widespread death of many different types of brain cells. As our understanding of the complex disease that is stroke has grown, it is now generally accepted that various different mechanisms can result in cell damage and eventual death. A plethora of techniques is available to identify various pathological features of cell death in stroke; each has its own drawbacks and pitfalls, and most are unable to distinguish between different types of cell death, which partially explains the widespread misuse of many terms. The purpose of this review is to summarize the standard histopathological and immunohistochemical techniques used to identify various pathological features of stroke. We then discuss how these methods should be properly interpreted on the basis of what they are showing, as well as advantages and disadvantages that require consideration. As there is much interest in the visualization of stroke using noninvasive imaging strategies, we also specifically discuss how these techniques can be interpreted within the context of cell death.
Sequential Activation of Hypoxia-Inducible Factor 1 and Specificity Protein 1 is Required for Hypoxia-Induced Transcriptional Stimulation of Abcc8
Authors: Woo Seung Kyoon , Kwon Min Seong , Geng Zhihua , Chen Zheng , Ivanov Alexander , Bhatta Sergei , Gerzanich Volodymyr , Simard J Marc
Published: November 2011

Cerebral ischemia causes increased transcription of sulfonylurea receptor 1 (SUR1), which forms SUR1-regulated NC(Ca-ATP) channels linked to cerebral edema. We tested the hypothesis that hypoxia is an initial signal that stimulates transcription of Abcc8, the gene encoding SUR1, via activation of hypoxia-inducible factor 1 (HIF1). In the brain microvascular endothelial cells, hypoxia increased SUR1 abundance and expression of functional SUR1-regulated NC(Ca-ATP) channels. Luciferase reporter activity driven by the Abcc8 promoter was increased by hypoxia and by coexpression of HIF1α. Surprisingly, a series of luciferase reporter assays studying the Abcc8 promoter revealed that binding sites for specificity protein 1 (Sp1), but not for HIF, were required for stimulation of Abcc8 transcription by HIF1α. Luciferase reporter assays studying Sp1 promoters of three species, and chromatin immunoprecipitation analysis in rats after cerebral ischemia, indicated that HIF binds to HIF-binding sites on the Sp1 promoter to stimulate transcription of the Sp1 gene. We conclude that sequential activation of two transcription factors, HIF and Sp1, is required to stimulate transcription of Abcc8 following cerebral ischemia. Sequential gene activation in cerebral ischemia provides a plausible molecular explanation for the prolonged treatment window observed for inhibition of the end-target gene product, SUR1, by glibenclamide.
Note: Fast and reliable fracture strain extraction technique applied to silicon at nanometer scale
Authors: Passi Vikram , Bhaskar Umesh , Pardoen Thomas , Sodervall Ulf , Nilsson Bengt , Petersson Goran , Hagberg Mats , Raskin Jean-Pierre
Published: November 2011

Simple fabrication process and extraction procedure to determine the fracture strain of monocrystalline silicon are demonstrated. Nanowires/nanoribbons in silicon are fabricated and subjected to uniaxial tensile stress along the complete length of the beams. Large strains up to 5% are measured for nanowires presenting a cross section of 50 nm × 50 nm and a length of 2.5 μm. An increase in fracture strain for silicon nanowires (NWs) with the downscaling of their volume is observed, highlighting the reduction of the defects probability as volume is decreased.
Molecular-beam study of the ammonia–noble gas systems: Characterization of the isotropic interaction and insights into the nature of the intermolecular potential
Authors: Pirani Fernando , Roncaratti Luiz F. , Belpassi Leonardo , Tarantelli Francesco , Cappelletti D.
Published: November 2011

We report new high resolution molecular beam experiments aimed at characterizing the intermolecular interaction in the NH3–Ng (Ng = He, Ne, Ar, Kr, Xe) weakly bound complexes. Integral cross section data are obtained over a sufficiently wide velocity range and with rotationally hot NH3 molecules to produce (except for the NH3–He case) a well resolved “glory” quantum interference pattern. Data analysis, carried out by employing a recently proposed potential model, allows unique information on the absolute scale of the intermolecular interaction to be obtained both at long range and at the equilibrium distance. An extensive and internally consistent comparison with the behavior of the corresponding Kr–Ng systems is exploited in order to identify those cases where an interaction component due to charge transfer effects provides an appreciable intermolecular bond stabilization that is clearly distinct from and must be added to the standard van der Waals plus induction picture. The results of the present investigation extend the phenomenology of perturbative charge transfer effects in gas phase complexes involving hydrogenated molecules.
Contrast agent-free sonoporation: The use of an ultrasonic standing wave microfluidic system for the delivery of pharmaceutical agents
Authors: Carugo Dario , Ankrett Dyan N. , Glynne-Jones Peter , Capretto Lorenzo , Boltryk Rosemary J. , Zhang Xunli , Townsend Paul A. , Hill Martyn
Published: November 2011

Sonoporation is a useful biophysical mechanism for facilitating the transmembrane delivery of therapeutic agents from the extracellular to the intracellular milieu. Conventionally, sonoporation is carried out in the presence of ultrasound contrast agents, which are known to greatly enhance transient poration of biological cell membranes. However, in vivo contrast agents have been observed to induce capillary rupture and haemorrhage due to endothelial cell damage and to greatly increase the potential for cell lysis in vitro. Here, we demonstrate sonoporation of cardiac myoblasts in the absence of contrast agent (CA-free sonoporation) using a low-cost ultrasound-microfluidic device. Within this device an ultrasonic standing wave was generated, allowing control over the position of the cells and the strength of the acoustic radiation forces. Real-time single-cell analysis and retrospective post-sonication analysis of insonated cardiac myoblasts showed that CA-free sonoporation induced transmembrane transfer of fluorescent probes (CMFDA and FITC-dextran) and that different mechanisms potentially contribute to membrane poration in the presence of an ultrasonic wave. Additionally, to the best of our knowledge, we have shown for the first time that sonoporation induces increased cell cytotoxicity as a consequence of CA-free ultrasound-facilitated uptake of pharmaceutical agents (doxorubicin, luteolin, and apigenin). The US-microfluidic device designed here provides an in vitro alternative to expensive and controversial in vivo models used for early stage drug discovery, and drug delivery programs and toxicity measurements.
Instability of nitrogen doped Sb2Te3 for phase change memory application
Authors: Li Xuelai , Rao Feng , Song Zhitang , Zhu Min , Liu Weili , Sun Zhimei
Published: November 2011

By means of experimental methods and ab initio total energy calculations, we have studied the stability and properties of nitrogen doped Sb2Te3 (NST). The NST film displayed a higher crystallization temperature and sheet resistance than undoped Sb2Te3 (ST) film. Nevertheless, the sheet resistance of the crystalline NST film unexpectedly increased as the temperature increased when the temperature was above 260 °C. The X-ray photoelectron spectroscopy (XPS) showed that the nitrogen concentration and the Sb-N bonds were decreasing as the annealing temperature increased, and no nitrogen existed in the NST when annealed at 300 °C for 5 min. Our theoretical calculations showed that the incorporation of nitrogen into crystalline Sb2Te3 was not energetically favorable, and the nitrogen atoms preferred forming chemical bonds with Sb atoms to Te atoms.
Cross talk by extensive domain wall motion in arrays of ferroelectric nanocapacitors
Authors: Kim Yunseok , Han Hee , Vrejoiu Ionela , Lee Woo , Hesse Dietrich , Alexe Marin
Published: November 2011

We report on extensive domain wall motion in ferroelectric nanocapacitor arrays investigated by piezoresponse force microscopy. Under a much longer or higher bias voltage pulse, compared to typical switching pulse conditions, domain walls start to propagate into the neighbouring capacitors initiating a significant cross-talk. The propagation paths and the propagated area into the neighbouring capacitors were always the same under repeated runs. The experimental and the simulated results show that the observed cross-talk is related to the capacitor parameters combined with local defects. The results can be helpful to test the reliability of nanoscale ferroelectric memory devices.
Suppression of scar formation in a murine burn wound model by the application of non-thermal plasma
Authors: Hoon Lee Dae , Lee Jae-Ok , Jeon Wonju , Choi Ihn-Geun , Kim Jun-Sub , Hoon Jeong Je , Kang Tae-Cheon , Hoon Seo Cheong
Published: November 2011

Suppression of hypertrophic scar generation in an animal model by treatment with plasma is reported. Contact burn following mechanical stretching was used to induce scar formation in mice. Exposure to the plasma tended to reduce the scar area more rapidly without affecting vitality. The treatment resulted in decreased vascularization in the scar tissue. Plasma-treated scars showed mild decrease in the thickness of hypertrophic tissues as shown by histological assessment. Finally, we showed that plasma treatment induced cell death and reactive oxygen species generation in hypertrophic scar fibroblast. All of the results support that plasma treatment can control scar generation.
Temperature dependence of current transport in Al/Al2O3 nanocomposite thin films
Authors: Liu Y. , Chen T. P. , Ding L. , Yang M. , Liu Z. , Wong J. I. , Fung S.
Published: November 2011

In this work, Al/Al2O3 nanocomposite thin film is deposited on Si substrate by radio frequency sputtering to form a metal-insulator-semiconductor structure. It is found that the current conduction at low fields is greatly enhanced with temperature. The current increase can be attributed to the decrease in the tunneling resistance and/or the formation of some tunneling paths due to the release of some measurement-induced charges trapped in the thin film as a result of increase in the temperature. The current conduction evolves with a trend toward a three-dimensional transport as the temperature increases.
Flowery Ni Microcrystals Consisting of Star-shaped Nanorods: Facile Synthesis, Formation Mechanism and Magnetic Properties
Authors: Li Hao , Liao Jinyun , Jin Zhen , Zhang Xibin , Lu Xiuxian , Liang Jinjie , Feng Yufa , Yu Shiwen
Published: November 2011

Flowerlike Ni microcrystals composed of star-shaped Ni nanorods with a diameter of ~200 nm were fabricated by a facile chemical reduction process, in which ethylenediamine tetraacetic acid sodium (EDTA) was used as complexant to assist in the formation of the flowery shape of the sample. The products were characterized by X-ray diffractometer, scanning electron microscopy, energy-dispersive X-ray spectroscopy and superconducting quantum interference device magnetometer. Scanning electron microscopy images indicated the typical size of the flowery Ni microcrystals was 2–3 μm and the length of the star-shaped Ni nanorods was in the hundreds of nanometers up to micron scale. The X-ray diffraction pattern showed the Ni microcrystals were present in the face-centred cubic phase and magnetic measurement results demonstrated the greatly enhanced coercivity of the sample (168.5 Oe) at room temperature. Based on the evolution of the structure and the morphology of products with increasing reaction time, a possible formation mechanism was proposed to illustrate the growth of the flower-like Ni architecture.
pH-Dependent Assembly of Reduced Polyoxomolybdenum Phosphates Modified by MnII
Authors: Lu Jing , Liu Hou-Ting , Song Hao , Wang Su-Na , Wang Da-Qi , Zhang Xian-Xi
Published: November 2011

Three reduced polyoxomolybdenum(v) phosphates modified by MnII: (Hen)(H2en){Mn(H2O)[Mn0.5Mo6(HPO4)3(PO4)(OH)3O12]}·2H2O (1) (en = ethylenediamine), (en)(Hen)4{Mn(H2O)[MnMo12(H2PO4)3(HPO4)4(PO4)(OH)6O24]}·3.5H2O (2), and [H7(en)Mn2.5P4Mo6O31(H2O)3]·2.5H2O (3) were synthesized through the hydrothermal reaction at different pH values. Compound 1 exhibits a 3-D framework; each basic [Mn(P4Mo6O31)2] unit coordinates with eight MnII ions. Compound 2 contains two kinds of [Mn(P4Mo6O31)2] basic units, which are linked by MnII ions to form a 2-D network. For compound 3, each basic [Mn(P4Mo6O31)2] unit is modified by 12 MnII ions and exhibits a 3-D framework. It was established that the pH of the reaction and the amount of ethanediamine play very important roles in the assembly of polyoxometalate-based compounds. The pH value determines the electron density of polyoxometalate and the degree of en protonation, which affect the coordination ability of polyoxometalates and result in different structures. Compounds 1–3 display weak antiferromagnetic coupling.
Direct C - O Bond Activation Mediated by AcOH: A New Metal-Free Way for α-Functionalization of Ferrocene Alcohols
Authors: Jiang Ran , Chu Xue-Qiang , Xu Xiao-Ping , Wu Bin , Ji Shun-Jun
Published: November 2011

α-functionalization of ferrocenyl alcohols by direct C–O bond activation by indoles, active methylene compounds, electron-rich arenes, anilines, alcohols, and thiols in acetic acid is described. This protocol provides a relatively green and efficient combinatorial access to ferrocene derivatives in a metal-free manner.
Metal Binding by Water-Soluble Polychelates and Implications for Agriculture
Authors: Warrender Garry W. , Gilbert Robert G.
Published: November 2011

Means are developed to improve the metal ion delivery/remediation potential of polyacrylamides (PAMs), by incorporation of the co-monomer N-acryloyl-4-aminosalicylic acid. The polymers were synthesized by solution and inverse emulsion polymerization. The chemical binding of two soil micronutrients, Cu2+ and Fe3+, were investigated using atomic absorption spectroscopy. The modified PAM had an enhanced affinity for metal ions compared with conventional PAMs. This modified PAM has the potential as a delivery tool of plant micronutrients and stabilizers for agricultural soils undergoing intense irrigation. The same polymers may also provide a detoxifying effect in these applications where some micronutrient sources may be in excess and detrimental to productive agriculture.
Discovery of ortho-Carborane-Conjugated Triazines as Selective Topoisomerase I/II Inhibitors
Authors: Nakamura Hiroyuki , Shoji Atsushi , Takeuchi Ayano , Ban Hyun Seung , Lee Jong-Dae , Yamori Takao , Kang Sang Ook
Published: November 2011

The cell growth inhibition profile of 2,4-(2-methyl-ortho-carboranyl)-4-(dimethylamino)-1,3,5-triazine (TAZ-6) was found to be similar to that of ICRF-193, a topoisomerase II inhibitor, as revealed by COMPARE analysis (correlation coefficient (r) = 0.724). Various mono- and di-ortho-carborane-substituted 1,3,5-triazines were synthesized based on the structure of TAZ-6 and tested for their ability to inhibit cell growth and the activities of topoisomerases I and II. Among the compounds synthesized, 3c, 4c, and 4f completely inhibited topoisomerase I activity without affecting topoisomerase II activity, whereas 3a and 3d completely inhibited topoisomerase II activity without affecting topoisomerase I activity, at 100 μM.
Seminal plasma enhances and accelerates progesterone-induced decidualisation of human endometrial stromal cells
Authors: Doyle U. , Sampson N. , Zenzmaier C. , Schwärzler P. , Berger P.
Published: November 2011

In preparation for embryo implantation, endometrial stromal cells (ESC) undergo differentiation, termed decidualisation. Enhancing endometrial decidualisation may overcome reduced endometrial receptivity, a major limiting factor in natural and assisted reproduction. To determine whether seminal plasma (SP) influences decidualisation, primary human ESC were treated with progesterone (P4, 50 ng mL–1) in the presence or absence of dialysed SP (0.5%) for 24 h or for up to 27 days to investigate immediate early effects or the effects of prolonged exposure, respectively. Combined SP and P4 treatment induced ESC morphological differentiation. Relative to control, P4 alone, and SP alone combined treatment with SP and P4 for 27 days significantly upregulated mRNA levels of the decidua-specific markers prolactin (PRL) and insulin-like growth factor binding protein 1 (IGFBP1). Consistently, PRL protein secretion was significantly increased over the course of 27 days combined SP and P4 treatment relative to control, P4 alone and SP alone. Likewise, IGFBP1 secretion was significantly greater relative to control and P4 alone over the course of 27 days. Thus, SP enhances and accelerates P4-mediated decidualisation of human ESC and may enhance endometrial receptivity.
Role of male novelty and familiarity in male-induced LH secretion in female sheep
Authors: de St Jorre T. Jorre , Hawken P. A. R. , Martin G. B.
Published: November 2011

Ewes supposedly need to be separated from rams before male stimuli can increase gonadotrophin secretion and induce ovulation. In the present study, we investigated the LH response of ewes to ‘novel’ and ‘familiar’ rams after varying periods of separation. In Experiment 1, ewes (n = 8 per treatment) were separated from familiar rams for 15 min or 1 month and then exposed to either familiar rams, novel rams or novel wethers. After 15 min or 1 month of separation, exposure to novel rams increased pulsatile LH secretion (P < 0.05) and induced an LH surge in all ewes whereas exposure to familiar rams or novel wethers had no effect on LH secretion (P > 0.1). After 1 month of separation, re-exposure to the same familiar rams increased pulsatile LH secretion (P < 0.05) in six of eight ewes, but only induced an LH surge in two of eight ewes. In Experiment 2, familiar rams were removed and returned after 15 min, 1 day or 17 days (n = 5 per treatment). None of these treatments affected LH secretion. We conclude that separation of ewes from rams is a prerequisite for familiar rams to increase LH secretion, but is not necessary if the rams are novel.
Discovery of deoxyceramides and diacylglycerols as CD1b scaffold lipids among diverse groove-blocking lipids of the human CD1 system
Authors: Huang Shouxiong , Cheng Tan-Yun , Young David C. , Layre Emilie , Madigan Cressida A. , Shires John , Cerundolo Vincenzo , Altman John D. , Moody D. Branch
Published: November 2011

Unlike the dominant role of one class II invariant chain peptide (CLIP) in blocking MHC class II, comparative lipidomics analysis shows that human cluster of differentiation (CD) proteins CD1a, CD1b, CD1c, and CD1d bind lipids corresponding to hundreds of diverse accurate mass retention time values. Although most ions were observed in association with several CD1 proteins, ligands binding selectively to one CD1 isoform allowed the study of how differing antigen-binding grooves influence lipid capture. Although the CD1b groove is distinguished by its unusually large volume (2,200 Å3) and the T′ tunnel, the average mass of compounds eluted from CD1b was similar to that of lipids from CD1 proteins with smaller grooves. Elution of small ligands from the large CD1b groove might be explained if two small lipids bind simultaneously in the groove. Crystal structures indicate that all CD1 proteins can capture one antigen with its hydrophilic head group exposed for T-cell recognition, but CD1b structures show scaffold lipids seated below the antigen. We found that ligands selectively associated with CD1b lacked the hydrophilic head group that is generally needed for antigen recognition but interferes with scaffold function. Furthermore, we identified the scaffolds as deoxyceramides and diacylglycerols and directly demonstrate a function in augmenting presentation of a small glycolipid antigen to T cells. Thus, unlike MHC class II, CD1 proteins capture highly diverse ligands in the secretory pathway. CD1b has a mechanism for presenting either two small or one large lipid, allowing presentation of antigens with an unusually broad range of chain lengths.
Hypermorphic mutation of the voltage-gated sodium channel encoding gene
Scn10a
causes a dramatic stimulus-dependent neurobehavioral phenotype
Authors: Blasius Amanda L. , Dubin Adrienne E. , Petrus Matt J. , Lim Byung-Kwan , Narezkina Anna , Criado José R. , Wills Derek N. , Xia Yu , Moresco Eva Marie Y. , Ehlers Cindy , Knowlton Kirk U. , Patapoutian Ardem , Beutler Bruce
Published: November 2011

The voltage-gated sodium channel Na
v
1.8 is known to function in the transmission of pain signals induced by cold, heat, and mechanical stimuli. Sequence variants of human Na
v
1.8 have been linked to altered cardiac conduction. We identified an allele of
Scn10a
encoding the α-subunit of Na
v
1.8 among mice homozygous for
N
-ethyl-
N
-nitrosourea-induced mutations. The allele creates a dominant neurobehavioral phenotype termed
Possum
, characterized by transient whole-body tonic immobility induced by pinching the skin at the back of the neck (“scruffing”). The
Possum
mutation enhanced Na
v
1.8 sodium currents and neuronal excitability and heightened sensitivity of mutants to cold stimuli. Striking electroencephalographic changes were observed concomitant with the scruffing-induced behavioral change. In addition, electrocardiography demonstrated that
Possum
mice exhibited marked sinus bradycardia and R-R variability upon scruffing, abrogated by infusion of atropine. However, atropine failed to prevent or mitigate the tonic immobility response. Hyperactive sodium conduction via Na
v
1.8 thus leads to a complex neurobehavioral phenotype, which resembles catatonia in schizophrenic humans and tonic immobility in other mammals upon application of a discrete stimulus; no other form of mechanosensory stimulus could induce the immobility phenotype. Our data confirm the involvement of Na
v
1.8 in transducing pain initiated by cold and additionally implicate Na
v
1.8 in previously unknown functions in the central nervous system and heart.
Cross‐cultural comparison of ADHD symptoms among Japanese and US university students
Authors: Davis J. Mark , Takahashi Tomone , Shinoda Haruo , Gregg Noel
Published: November 2011

Problems related to attention, hyperactivity, and impulsiveness are known to impact social, academic, and vocational success. When the problems begin in childhood and lead to impaired functioning, the syndrome is identified as attention‐deficit/hyperactivity disorder (ADHD). Symptoms of the syndrome persist into adolescence and adulthood for many individuals, but less is known about characteristics of adults compared to children, especially adults attending university. Furthermore, there is little cross‐national and cross‐cultural research. This study compared DSM‐IV‐TR ADHD symptoms of US university students (N = 271) to Japanese peers (N = 712). Comparison of group means on a DSM‐IV‐TR‐based checklist indicated that Japanese students reported more problems with inattention (and overall ADHD symptoms) but not hyperactive–impulsive symptoms. Although differences were statistically significant, effect sizes were small, indicating that for practical purposes, the students reported similar levels of symptoms. Japanese students reported higher rates of meeting or exceeding symptom counts that comprise diagnostic criteria for ADHD, but differences were quite small. Using DSM‐IV‐TR thresholds, 5.70% of US students and 6.27% of Japanese students reported enough symptoms to meet the cut‐off for inattentive, hyperactive/impulsive, or combined type during childhood. With regard to recent problems, 2.66% of US students and 4.52% of Japanese students reported enough symptoms to meet the cut‐off for one of the three subtypes. Comparisons using other methods of calculating rates are also provided. This research adds to the limited knowledge of ADHD symptoms in university students across countries and it supports the view that ADHD is not merely a cultural construct. This study is among the first to identify potential attention problems in Japanese university students.
Construction of an extended library of adult male 3D models: rationale and results
Authors: Broggio D , Beurrier J , Bremaud M , Desbrée A , Farah J , Huet C , Franck D
Published: November 2011

In order to best cover the possible extent of heights and weights of male adults the construction of 25 whole body 3D models has been undertaken. Such a library is thought to be useful to specify the uncertainties and relevance of dosimetry calculations carried out with models representing individuals of average body heights and weights. Representative 3D models of Caucasian body types are selected in a commercial database according to their height and weight, and 3D models of the skeleton and internal organs are designed using another commercial dataset. A review of the literature enabled one to fix volume or mass target values for the skeleton, soft organs, skin and fat content of the selected individuals. The composition of the remainder tissue is fixed so that the weight of the voxel models equals the weight of the selected individuals. After mesh and NURBS modelling, volume adjustment of the selected body shapes and additional voxel-based work, 25 voxel models with 109 identified organs or tissue are obtained. Radiation transport calculations are carried out with some of the developed models to illustrate potential uses. The following points are discussed throughout this paper:

- justification of the fixed or obtained models’ features regarding available and relevant literature data;

- workflow and strategy for major modelling steps;

- advantages and drawbacks of the obtained library as compared with other works.

The construction hypotheses are explained and justified in detail since future calculation results obtained with this library will depend on them.
Defining fishing grounds with vessel monitoring system data
Authors: Jennings Simon , Lee Janette
Published: November 2011

Jennings, S., and Lee, J. 2012. Defining fishing grounds with vessel monitoring system data. – ICES Journal of Marine Science, 69: 51–63. Methods for defining fishing grounds to support marine spatial planning and management are developed, applied, and compared. The methods are broadly applicable and repeatable because they use vessel monitoring system (VMS) data that are archived and increasingly accessible. For several fleets at regional and national scales, an attempt is made to assess how the choice of criteria for defining grounds influences (i) size, shape, and location, (ii) overlap among grounds, and (iii) the extent to which annual and multi-annual patterns of fishing activity describe grounds used seasonally or by individual vessels. The results show that grounds defined by excluding infrequently fished margins (areas with <10% of total fishing activity) are typically 50% smaller than total fished area. However, landings weight or value (LWV) per unit activity can be higher at the margins, with 10% of activity usually accounting for 10–20% of LWV. The removal of fishing activity in the margins, as a consequence of regulation or fleet behaviour, would lead to disproportionately greater reductions in interactions with other fisheries, sectors, and the environment. Accessible high-resolution information on the “anatomy” of all fishing grounds would better inform debates on the allocation and the use of marine space and the integration of fisheries and environmental management.
Molecular Characterization of Pyraclostrobin Resistance and Structural Diversity of the Cytochrome b Gene in Botrytis cinerea from Apple
Authors: Yin Y. N. , Kim Y. K. , Xiao C. L.
Published: November 2011

Botrytis cinerea isolates obtained from apple orchards were screened for resistance to the quinone outside inhibitor (QoI) pyraclostrobin. Of the 220 isolates tested, 43 (19.5%) were resistant to pyraclostrobin. Analysis of partial sequences of the cytochrome b gene (cyt b) in five pyraclostrobin-resistant (PR) and five pyraclostrobin-sensitive (PS) isolates showed that PR isolates harbored the point mutation leading to the substitution of glycine by alanine at codon position 143 in cyt b (G143A). Two pairs of allele-specific primers were designed based on this point mutation, and allele-specific polymerase chain reaction analysis with these primers showed that all 73 PR isolates (including 30 collected from decayed apple fruit) harbored the G143A mutation but PS isolates did not. Six pairs of primers were designed to analyze the presence of various introns in cyt b. There were six types (I to VI) of cyt b present in 247 isolates of B. cinerea collected from various apple-production areas in Washington State. Of the 247 isolates, 23 had type I cyt b containing all four introns (Bcbi-67/68, Bcbi-131/132, Bcbi-143/144, and Bcbi-164), 176 had type II cyt b containing three introns (Bcbi-67/68, Bcbi-131/132, and Bcbi-164), six had type III cyt b containing two introns (Bcbi-67/68 and Bcbi-131/132), one had type IV cyt b containing two introns (Bcbi-131/132 and Bcbi-164), one had type V cyt b containing only the Bcbi-131/132 intron, and 40 had type VI cyt b containing no introns. This is the first report of types III to VI cyt b present in B. cinerea. All 73 PR isolates did not carry the Bcbi-143/144 intron in cyt b. Of the 247 isolates tested, >90% did not carry the Bcbi-143/144 intron in cyt b, suggesting that B. cinerea populations from apple pose a high inherent risk for the development of resistance to QoIs because the presence of this intron in cyt b prevents the occurrence of G143A-mediated resistance. Analysis of genetic background based on three microsatellite primers showed that PR isolates originated from different lineages, and there was no correlation between cyt b types (I, II, and III) and the genetic background of the isolates; however, isolates carrying type VI cyt b might originate from the same lineage.
Proinflammatory Stimuli Enhance Phagocytosis of Apoptotic Cells by Neutrophil Granulocytes
Authors: Hellberg Lars , Fuchs Sabrina , Gericke Christoph , Sarkar Arup , Behnen Martina , Solbach Werner , Laskay Tamás
Published: November 2011

Recently, we have reported that, in addition to macrophages, also neutrophil granulocytes can phagocytose apoptotic neutrophils. Based on this finding, we hypothesized that “cannibalistic” neutrophils at sites of acute infection/inflammation play a major role in the clearance of apoptotic neutrophils. Since at sites of infection/inflammation neutrophils are exposed to microbial constituents and proinflammatory cytokines, in the present study we analyzed the effect of TLR-ligands and cytokines on the ability of neutrophils to phagocytose apoptotic cellsin vitro. We observed that exposure to ligands of TLR2 (Malp2, Pam3CSK4), TLR4 (LPS), TLR7/TLR8 (R848), and TLR9 (ODN 2006) led to increased phagocytosis of apoptotic cells by neutrophils. In addition, proinflammatory cytokines such as TNF and GM-CSF strongly enhanced the uptake of apoptotic cells by neutrophils. These results support the hypothesis that neutrophils acquire the ability to phagocytose apoptotic cells at sites of acute infection/inflammation and thereby can contribute to the resolution of inflammation.
Maelstrom coordinates microtubule organization during Drosophila oogenesis through interaction with components of the MTOC
Authors: Sato Kaoru , Nishida Kazumichi M. , Shibuya Aoi , Siomi Mikiko C. , Siomi Haruhiko
Published: November 2011

The establishment of body axes in multicellular organisms requires accurate control of microtubule polarization. Mutations in Drosophila PIWI-interacting RNA (piRNA) pathway genes often disrupt the axes of the oocyte. This results from the activation of the DNA damage checkpoint factor Checkpoint kinase 2 (Chk2) due to transposon derepression. A piRNA pathway gene, maelstrom (mael), is critical for the establishment of oocyte polarity in the developing egg chamber during Drosophila oogenesis. We show that Mael forms complexes with microtubule-organizing center (MTOC) components, including Centrosomin, Mini spindles, and γTubulin. We also show that Mael colocalizes with αTubulin and γTubulin to centrosomes in dividing cyst cells and follicle cells. MTOC components mislocalize in mael mutant germarium and egg chambers, leading to centrosome migration defects. During oogenesis, the loss of mael affects oocyte determination and induces egg chamber fusion. Finally, we show that the axis specification defects in mael mutants are not suppressed by a mutation in mnk, which encodes a Chk2 homolog. These findings suggest a model in which Mael serves as a platform that nucleates other MTOC components to form a functional MTOC in early oocyte development, which is independent of Chk2 activation and DNA damage signaling.
Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase
Authors: Li Shuang , Duan Jingqi , Li Dandan , Yang Bing , Dong Mengqiu , Ye Keqiong
Published: November 2011

Box H/ACA ribonucleoprotein particles (RNPs) mediate pseudouridine synthesis, ribosome formation, and telomere maintenance. The structure of eukaryotic H/ACA RNPs remains poorly understood. We reconstituted functionalSaccharomyces cerevisiaeH/ACA RNPs with recombinant proteins Cbf5, Nop10, Gar1, and Nhp2 and a two-hairpin H/ACA RNA; determined the crystal structure of a Cbf5, Nop10, and Gar1 ternary complex at 1.9 Å resolution; and analyzed the structure–function relationship of the yeast complex. Although eukaryotic H/ACA RNAs have a conserved two-hairpin structure, isolated single-hairpin RNAs are also active in guiding pseudouridylation. Nhp2, unlike its archaeal counterpart, is largely dispensable for the activity, reflecting a functional adaptation of eukaryotic H/ACA RNPs to the variable RNA structure that Nhp2 binds. The N-terminal extension of Cbf5, a hot spot for dyskeratosis congenita mutation, forms an extra structural layer on the PUA domain. Gar1 is distinguished from the assembly factor Naf1 by containing a C-terminal extension that controls substrate turnover and the Gar1–Naf1 exchange during H/ACA RNP maturation. Our results reveal significant novel features of eukaryotic H/ACA RNPs.
A master CLOCK hard at work brings rhythm to the transcriptome: Figure 1.
Authors: Edery Isaac
Published: November 2011

In this issue of Genes & Development, Abruzzi et al. (pp. 2374–2386) use chromatin immunoprecipitation (ChIP) tiling array assays (ChIP–chip) to show that physical interactions between circadian (≅24-h) clock machineries and genomes are more widespread than previously thought and provide novel insights into how clocks drive daily rhythms in global gene expression.
Gene Expression and Metabolite Profiling of Developing Highbush Blueberry Fruit Indicates Transcriptional Regulation of Flavonoid Metabolism and Activation of Abscisic Acid Metabolism
Authors: Zifkin Michael , Jin Alena , Ozga Jocelyn A. , Zaharia L. Irina , Schernthaner Johann P. , Gesell Andreas , Abrams Suzanne R. , Kennedy James A. , Constabel C. Peter
Published: November 2011

Highbush blueberry (Vaccinium corymbosum) fruits contain substantial quantities of flavonoids, which are implicated in a wide range of health benefits. Although the flavonoid constituents of ripe blueberries are known, the molecular genetics underlying their biosynthesis, localization, and changes that occur during development have not been investigated. Two expressed sequence tag libraries from ripening blueberry fruit were constructed as a resource for gene identification and quantitative real-time reverse transcription-polymerase chain reaction primer design. Gene expression profiling by quantitative real-time reverse transcription-polymerase chain reaction showed that flavonoid biosynthetic transcript abundance followed a tightly regulated biphasic pattern, and transcript profiles were consistent with the abundance of the three major classes of flavonoids. Proanthocyanidins (PAs) and corresponding biosynthetic transcripts encoding anthocyanidin reductase and leucoanthocyanidin reductase were most concentrated in young fruit and localized predominantly to the inner fruit tissue containing the seeds and placentae. Mean PA polymer length was seven to 8.5 subunits, linked predominantly via B-type linkages, and was relatively constant throughout development. Flavonol accumulation and localization patterns were similar to those of the PAs, and the B-ring hydroxylation pattern of both was correlated with flavonoid-3′-hydroxylase transcript abundance. By contrast, anthocyanins accumulated late in maturation, which coincided with a peak in flavonoid-3-O-glycosyltransferase and flavonoid-3′5′-hydroxylase transcripts. Transcripts of VcMYBPA1, which likely encodes an R2R3-MYB transcriptional regulator of PA synthesis, were prominent in both phases of development. Furthermore, the initiation of ripening was accompanied by a substantial rise in abscisic acid, a growth regulator that may be an important component of the ripening process and contribute to the regulation of blueberry flavonoid biosynthesis.
Novel pathway of centrosome amplification that does not require DNA lesions
Authors: Tsuda Masataka , Tanaka Masakazu , Mushiake Masatoshi , Takahashi Jun , Tanaka Koji , Watase Joji , Fujisawa Jun‐Ichi , Miwa Masanao
Published: November 2011

Centrosome amplification (also known as centrosome overduplication) is common in cancer cells and can be induced by DNA damaging agents. However, the mechanism and significance of centrosome amplification during carcinogenesis or after DNA damage are not clear. Previously, we showed that centrosome amplification could be induced by 3‐aminobenzamide (3‐AB), an inhibitor of poly(ADP‐ribose) polymerases (PARPs) in mouse embryonic fibroblasts. In this paper, we determined if the effect of 3‐AB on centrosome amplification was dependent on DNA damage in CHO‐K1 cells. We used the well‐known mutagen/carcinogen N‐methyl‐N’‐nitro‐N‐nitrosoguanidine (MNNG). Ten micromolar MNNG and 10 mM 3‐AB induced significant centrosome amplification in 18.1 ± 1.1% and 19.4 ± 1.8% of CHO‐K1 cells, respectively, compared to 7.0 ± 0.5% of untreated CHO‐K1 cells. AG14361, another potent inhibitor of PARPs, also induced centrosome amplification. We then used γ‐H2AX analysis and alkaline comet assays to show that 10 μM MNNG induced a significant number of DNA lesions and cell cycle arrest at the G2/M phase. However, 10 mM 3‐AB neither induced DNA lesions nor altered cell cycle progression. In the umu test, 10 μM MNNG was mutagenic, but 10 mM 3‐AB was not. In addition, 10 μM MNNG induced significant accumulation of ataxia telangiectasia mutated protein in the nuclei, but 10 mM 3‐AB did not. Thus, we found no association between apparent DNA lesions and centrosome amplification after 3‐AB treatment. Therefore, we propose the presence of a novel pathway for centrosome amplification that does not necessarily require DNA lesions but involves regulation of epigenetic changes or post‐translational modifications including polyADP‐ribosylation. (Cancer Sci 2012; 103: 191–196)