bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequential waves of polyadenylation and deadenylation define a translation circuit that drives meiotic progression
Authors: Belloc Eulàlia , Piqué Maria , Méndez Raúl
Published: July 2008

The maternal mRNAs that drive meiotic progression in oocytes contain short poly(A) tails and it is only when these tails are elongated that translation takes place. Cytoplasmic polyadenylation requires two elements in the 3′-UTR (3′-untranslated region), the hexanucleotide AAUAAA and the CPE (cytoplasmic polyadenylation element), which also participates in the transport and localization, in a quiescent state, of its targets. However, not all CPE-containing mRNAs are activated at the same time during the cell cycle, and polyadenylation is temporally and spatially regulated during meiosis. We have recently deciphered a combinatorial code that can be used to qualitatively and quantitatively predict the translational behaviour of CPE-containing mRNAs. This code defines positive and negative feedback loops that generate waves of polyadenylation and deadenylation, creating a circuit of mRNA-specific translational regulation that drives meiotic progression.
RNA pseudoknots and the regulation of protein synthesis
Authors: Brierley Ian , Gilbert Robert J.C. , Pennell Simon
Published: July 2008

RNA pseudoknots are structural elements found in almost all classes of RNA. Pseudoknots form when a single-stranded region in the loop of a hairpin base-pairs with a stretch of complementary nucleotides elsewhere in the RNA chain. This simple folding strategy is capable of generating a large number of stable three-dimensional folds that display a diverse range of highly specific functions in a variety of biological processes. The present review focuses on pseudoknots that act in the regulation of protein synthesis using cellular and viral examples to illustrate their versatility. Emphasis is placed on structurally well-defined pseudoknots that play a role in internal ribosome entry, autoregulation of initiation, ribosomal frameshifting during elongation and trans-translation.
Contribution of internal initiation to translation of cellular mRNAs containing IRESs
Authors: Mardanova Eugenia S. , Zamchuk Ludmila A. , Ravin Nikolai V.
Published: July 2008

A broad range of cellular stresses lead to the inhibition of translation. Despite this, some cellular mRNAs are selectively translated under these conditions. It is widely supposed that cap-independent internal initiation may maintain efficient translation of particular cellular mRNAs under a variety of stresses and other special conditions when cap-dependent protein synthesis is impaired. However, in spite of a large number of reports focused on the investigation of the regulation of IRES (internal ribosome entry site) activity in different tissues and under various stresses, only rarely is the real efficiency of IRES-driven translation in comparison with cap-dependent translation evaluated. When precisely measured, the efficiencies of candidate IRESs in most cases appeared to be very low and not sufficient to compensate for the reduction of cap-dependent initiation under stresses. The usually low efficiency of internal initiation of translation is inconsistent with postulated biological roles of IRESs.
Dissection of a co-translational nascent chain separation event
Authors: Doronina Victoria A. , de Felipe Pablo , Wu Cheng , Sharma Pamila , Sachs Matthew S. , Ryan Martin D. , Brown Jeremy D.
Published: July 2008

Some RNA and protein sequences are capable of directing changes to the course of translation from that expected from the mRNA sequence, and this process is termed translational ‘recoding’. ‘CHYSEL’ peptides are ∼19-amino-acid sequences found in many viral genomes. When translated at internal portions of polypeptides, they yield co-translational separation of the nascent chain at their C-termini. We dissected the reaction promoted by CHYSEL sequences using yeast genetics and in vitro translation systems. Our results indicate that the reaction occurs within the peptidyltransferase centre of the ribosome where the nascent chain is hydrolytically released from tRNA despite the presence of further sense codons.
The emerging role of MS in structure elucidation of protein–nucleic acid complexes
Authors: Gordiyenko Yuliya , Robinson Carol V.
Published: July 2008

Developments in MS enable us to apply this technique to non-covalent complexes, defining their stoichiometry, subunit interactions and architectural organization. We illustrate the application of this non-covalent MS approach to uncovering the overall topological arrangements of subunits and interactions within RNA–protein complexes studied in our laboratory over the last 5 years. These studies exemplify the emerging role and potential of MS as a complementary structural biology methodology and demonstrate its unique niche in investigations of dynamic or heterogeneous protein–nucleic acid complexes, which are not accessible to classical high-resolution structural biology techniques.
Single-molecule micromanipulation studies of DNA and architectural proteins
Authors: Dame Remus Th.
Published: July 2008

Architectural proteins play a key role in the folding, organization and compaction of genomic DNA in all organisms. By bending, bridging or wrapping DNA, these proteins ensure that its effective volume is reduced sufficiently to fit inside the cell or a dedicated cellular organelle, the nucleus (in bacteria/archaea and in eukaryotes respectively). In addition, the properties of many of these proteins permit them to play specific roles as architectural cofactors in a large variety of DNA transactions. However, as architectural proteins often bind DNA with low sequence specificity and affinity, it is hard to investigate their interaction using biochemical ensemble techniques. Single-molecule micromanipulation approaches that probe the properties of DNA-binding proteins by pulling on individual protein–DNA complexes have, in this respect, proved to be a very powerful alternative. Besides revealing architectural properties, these approaches can also reveal unique parameters not accessible to biochemical approaches, such as the binding kinetics and unbinding forces of individual proteins.
Higher-throughput approaches to crystallization and crystal structure determination
Authors: Fogg Mark J. , Wilkinson Anthony J.
Published: July 2008

In recent times, there has been a large increase in the number of protein structures deposited in the Protein Data Bank. Structural genomics initiatives have contributed to this expansion through their focus on high-throughput structural determination. This has fuelled advances in many of the techniques in the pipeline from gene to protein to crystal to structure. These include ligation-independent cloning methods, parallel purification systems, robotic crystallization devices and automated methods of crystal identification, data collection and, in some cases, structure solution. Some of these advances are described and discussed briefly with an emphasis on activities in the York Structural Biology Laboratory through its participation in the Structural Proteomics in Europe consortium.
Human tribbles homologue 2 is expressed in unstable regions of carotid plaques and regulates macrophage IL-10 in vitro
Authors: Deng Jingti , James Christian H. , Patel Lisa , Smith Alberto , Burnand Kevin G. , Rahmoune Hassan , Lamb Jonathan R. , Davis Bill
Published: July 2008

Mammalian orthologues of the Drosophila tribbles protein (Trb1, Trb2 and Trb3) are a recently described family of signalling molecules that regulate gene expression by modulation of protein kinase signalling pathways. In the present study, a screen for mRNA species specifically regulated in vulnerable regions of human atherosclerotic plaque demonstrated the up-regulation of both Trb1 and Trb2, the latter by more than 8-fold. In vitro experiments in primary human monocyte-derived macrophages showed that Trb2 expression was up-regulated by treatment with oxidized LDL (low-density lipoprotein), and that expression of recombinant Trb2 specifically reduced macrophage levels of IL-10 (interleukin-10) mRNA. Our results thus identify Trb2 as a highly regulated gene in vulnerable atherosclerotic lesions, and demonstrate inhibition of macrophage IL-10 biosynthesis as a potential pro-inflammatory consequence of high Trb2 expression, which may contribute to plaque instability.
Language and Literacy Connections for Children Who are African American
Authors: Connor Carol McDonald
Published: July 2008

Focusing on the links between language and literacy, this paper discusses possible reasons for the persistent reading skill gap between African American and White children. Three theories that describe the mechanisms through which the use of African American English (AAE) might affect literacy learning include (a) teacher bias against AAE, (b) the mismatch between the phonological and morphosyntactic structure of AAE and Standard or Mainstream American English (SAE), and (c) the linguistic flexibility theory, which suggests that it is not the mismatch per se that interferes with literacy learning, but rather students' limited linguistic flexibility. Thus, children who have strong linguistic flexibility are able to switch between the phonological and morphosyntactic structures of AAE and text SAE facilely, but children with weaker linguistic flexibility do not. Plus, a disproportionate number of African American children live in poverty. Thus, they tend to have weaker language and vocabulary skills (and, hence, less linguistic flexibility) when compared to their more affluent peers. By promoting teachers' understanding and sensitivity to students' AAE use and encouraging the use of more effective instructional strategies that are responsive to students' skills and areas of weakness, SLPs can work with teachers to help them understand ways to support African American children's language and literacy learning.
How Did the Doctor Decide? What SLPs Should Know About the Medical Diagnosis of Dementia
Authors: Smith Pamela A.
Published: July 2008

Even though the speech-language pathologist (SLP) does not assign a medical diagnosis, communication disorders professionals are responsible for the provision of screening and assessment of cognitive/linguistic skills in health-care environments. When a new patient is admitted with a diagnosis of Alzheimer's disease or another dementing condition, or when an existing patient seems to be exhibiting cognitive decline, the SLP should be aware of the procedures that the medical profession suggests for the assignment of this medical diagnosis. Furthermore, an awareness of the co-morbid conditions that can exacerbate cognitive impairments can guide the SLP in making appropriate referrals so that patients' cognitive abilities remain at their highest potential. The purpose of this article is to review the medical literature about the recommended practices for diagnosing Alzheimer's disease and other dementing conditions, to contrast the cognitive impairments that occur with some more common diseases and conditions, and to invite thoughtful reflection on the part of the SLP working with residents who have an Alzheimer's disease or other dementing diagnosis on a face sheet, a care plan, or a list of ICD-9 codes.
Vision and Perception Deficits Associated With Dementia
Authors: Robinson Monica
Published: July 2008

Sensory declines represent a broad category of normal age-related changes that can lead to diminished quality of life for the elderly individual, loss of independence, and increased costs for society as a whole (National Institute of Health, [NIH, 1999). As an individual ages, some of the most prevalent sensory losses are those related to vision and perception. According to the National Eye Institute (NEI, 2004), 3.3 million adult Americans have low vision or blindness and this figure is estimated to increase to 5.5 million by 2020. Vision deficits increase with age; sixty-nine percent of the population who are legally blind are those individuals 80 years old and older. Furthermore, as the population ages, so does the prevalence of multiple age-related diagnoses or conditions that effect vision and/or perception, such as diabetic retinopathy, cataracts, age-related macular degeneration, hemianopsia secondary to a stroke, and dementia.
The Inhibitory Effects of Carvedilol Against Arrhythmias Induced by Coronary Reperfusion in Anesthetized Rats
Authors: Takusagawa Masahiro , Komori Sadayoshi , Matsumura Kuniyoshi , Osada Mitsuru , Kohno Isao , Umetani Ken , Ishihara Tsukasa , Sawanobori Takao , Ijiri Hiroshi , Tamura Kohji
Published: July 2008

Background: Previous study has shown the antiarrhythmic effects of carvedilol on isolated rat hearts, but little is known about the mechanism of this protective action. This article examines the inhibitory effect of carvedilol against arrhythmias induced by reperfusion in anesthetized rats. In addition, the results are compared with those with propranolol, super oxide dismutase (SOD) plus catalase, and a combination of both in order to elucidate the mechanism of the protective actions.

Methods and Materials: Ninety percent of the rats in the control group showed lethal ventricular fibrillation (VF). Carvedilol at the doses of 0.03, 0.1, and 0.3 mg/kg significantly reduced the incidence of lethal VF to 0%, 0%, and 10%, respectively ( P < .05). In contrast, propranolol at the doses of 0.3, 1.0, and 3.0 mg/kg and SOD (35,000 units/kg) plus catalase (400,000 units/kg) did not reduce the incidence of lethal VF (80%, 60%, 70%, and 70%, respectively). However, administration of a combination of propranolol (1.0 mg/kg) and SOD plus catalase completely inhibited the occurrence of lethal VF to 0% ( P < .05).

Conclusion: These results indicate that carvedilol has the inhibitory effect against reperfusion arrhythmias in rats and suggest that the mechanism of action of this compound is related to the combined effects of beta-blocking and antioxidant.
Captopril and L-Arginine Have a Synergistic Cardioprotective Effect in Ischemic-Reperfusion Injury in the Isolated Rat Heart
Authors: Greenberg Shai , Chemin Gil , Shapira Itzhak , George Jacob , Wollman Yoram , Laniado Shlomo , Keren Gad
Published: July 2008

Objectives: The present study was designed to evaluate the possible effect of the combined administration of both captopril (Cap) and L-arginine (L-a) in the isolated ischemic rat heart model.

Background: Recent studies suggest that L-arginine and angiotensin-converting enzyme (ACE) inhibitors possess independent cardioprotective effects in ischemic hearts. The pharmacological effect of the combination of both drugs has not yet been investigated in the ischemic myocardium.

Methods: Using the modified Langendorf model, rats were perfused with either Cap 360 μmol/L (n = 6) or (L-a) 3mmol/L (n = 6), both captopril and L-arginine (Cap+L-a) (n = 8), or saline control (Con) (n = 8). The study design included 30 minutes of perfusion, 30 minutes of global ischemia, and 30 minutes of reperfusion thereafter.

Results: Hearts treated with both Cap+L-a demonstrated an improved performance in all parameters. After 10 minutes of reperfusion, the Pmaxin the Cap+L-a group was 98 ± 8 mmHg ( P < .001), 59 ± 14 mmHg in the Cap group ( P < .02). and 44.3 ± 10 mmHg in the L-a group ( P = NS), compared with only 42 ± 8 mmHg in the control. After 10 minutes of reperfusion the dP/dtminwas: in the Cap+L-a group: -1,650 ± 223 mmHg/s ( P < .006); in the Cap group: -1,051 ± 302 mmHb/s ( P < .03); in the L-a group: -870 ± 131 mmHg/s ( P = NS), compared with only -487 ± 131 mmHb/s in the control. Coronary flow was significantly increased in all 3 groups: Cap+L-a group: 22.3 ± 1.5 mL/min ( P < .001); Cap group: 18 ± 1.6 mL/min ( P <.01); L-a group : 19.8 ± 0.9 mL/min ( P < .02), compared with 12.6 ± 0.9 mL/min in the Con group. Total NO level was significantly increased in the Cap+L-a group: 13.4 ± 2 μmol ( P < .03) vs. 6.1 ± 1 μmol for the L-a group. NO levels of both the Cap group and the Con group were beneath detectable values.

Conclusion: Combined administration of captopril and L-arginine has a synergistic, protective effect on heart function and coronary flow that may be mediated by enhanced NO production.
Cardioprotection Induced by AT1R Blockade After Reperfused Myocardial Infarction: Association With Regional Increase in AT2R, IP3R and PKCε Proteins and cGMP
Authors: Jugdutt Bodh I. , Yi Xu  , Balghith Mohammad , Moudgil Rohit , Menon Vijayan
Published: July 2008

Background: We hypothesized that the cardioprotective effect of angiotensin II (AngII) type 1 receptor (AT,R) blockade during in vivo ischemia-reperfusion (IR) might be associated with an increase in AngII type 2 receptor (AT2R) protein, as well as 1,4,5-inositol trisphosphate type 2 receptor (IP3R) and protein kinase Cε, (PKCε) proteins and cyclic guanosine 3',5' monophosphate (cGMP).

Methods and Results: We studied the effects of the AT1R blocker, candesartan, on in vivo left ventricular (LV) systolic and diastolic function and remodeling (echocardiogram/Doppler) and hemodynamics during canine reperfused anterior infarction (90-minute ischemia, 120-minute reperfusion), and ex vivo infarct size and AT1R/AT2R, IP3R, and PKCεproteins (immunoblots), and cGMP (enzyme immunoassay). Compared with controls, candesartan (1 mg/kg intravenously over 30-minute preischemia) inhibited the AngII pressor response, decreased preload and afterload, improved LV systolic and diastolic function, limited LV remodeling, decreased infarct size (55% vs 27% risk; P < .000003), markedly increased AT2R, IP3R, and PKCεproteins in the infarct zone, but not the AT,R protein, and increased infarct more than noninfarct cGMP.

Conclusions: The overall results suggest that cardioprotective effects of AT1R blockade on acute IR injury might involve AT2R activation and downstream signaling via IP3R, PKCε, and cGMP.
Observations of neutral depletion and plasma acceleration in a flowing high-power argon helicon plasma
Authors: Denning C. Mark , Wiebold Matt , Scharer John E.
Published: July 2008

Neutral depletion effects are observed in a steady-state flowing argon helicon plasma with a magnetic nozzle for high rf input powers (up to 3kW). Noninvasive diagnostics including 105GHz microwave interferometry and optical spectroscopy with collisional-radiative modeling are used to measure the electron density (ne), electron temperature (Te), and neutral density (nn). A region of weak neutral depletion is observed upstream of the antenna where increasing rf power leads to increased electron density (up to ne=1.6×1013cm−3) while Te remains essentially constant and low (1.7–2.0eV). The downstream region exhibits profound neutral depletion (maximum 92% line-averaged ionization), where Te rises linearly with increasing rf power (up to 4.9eV) and ne remains constrained (below 6.5×1012cm−3). Flux considerations indicate accelerated plasma flow (Mach 0.24) through the antenna region due to an axial pressure gradient with reduced collisional drag from neutral depletion.
Wave properties of coating for skin friction reduction
Authors: Kulik Victor M. , Lee Inwon , Chun H. H.
Published: July 2008

Toward the understanding of the drag reduction mechanism, theoretical as well as experimental investigations have been made of the wave properties of compliant coatings such as the wave velocity and the decay parameters. The compliant coating consisted of a homogeneous layer of viscoelastic material attached to a rigid substrate. Based on two-dimensional elastic wave analysis, wave properties such as the dispersion of wave velocity, the ratio between the amplitudes of two wave components, and decay characteristics have been calculated as a function of Poisson’s ratio σ and the loss tangent μ. It was found that the wave parameters are strongly affected by Poisson’s ratio σ. A new experimental technique is devised for direct measurement of the wave parameters of the coating. The wave velocity and the rate of decay were measured based on the amplitude and phase of coating deformation with varying distances from the excitation point. Two kinds of silicon rubber were tested in the frequency range from 500 to 1200Hz. Comparison of the present two-dimensional model with the conventional local deformation model was made. Two conditions (time factor and space factor) for drag reduction were drawn to maximize the interaction between the coating and the turbulent flow. These conditions suggest a certain optimum region in the coordinates of the flow velocity and the coating thickness.
The coupled electric field effects on localized surface plasmon resonance in nanoparticle arrays
Authors: Yin Shaoyun , Deng Qiling , Luo Xiangang , Du Chunlei , Zhang Yudong
Published: July 2008

When a metal nanoparticle exhibits its unique dipole plasmon resonance, optical properties can be treated by considering a point dipole. Here we established a strong correlation between the surface-plasmon-induced coupled electric field in nanoparticle arrays and the extinction peak shifts. The model provides an effective way to explain the peak shifts caused by variation of the array structures. The extinction peak shifts of a one-dimensional silver cylinder array with different interparticle distances were predicted, and the results are in good agreement with those obtained by the discrete dipole approximation.
Cylindrical cloak with axial permittivity/permeability spatially invariant
Authors: Luo Yu , Zhang Jingjing , Chen Hongsheng , Xi Sheng , Wu Bae-Ian
Published: July 2008

In order to reduce the difficulties in the experimental realizations of the cloak but still keep good performance of invisibility, we proposed a perfect cylindrical invisibility cloak with spatially invariant axial material parameters. The advantage of this kind of cloak is that only ρ and φ components of μ (or ε) are spatially variant, which makes it possible to realize perfect invisibility with two-dimensional metamaterials. The effects of perturbations of the parameters on the performance of this cloak are quantitatively analyzed by scattering theory. Our work provides a simple and feasible solution to the experimental realization of cloaks with ideal parameters.
Finite system size effects in the interfacial dynamics of binary liquid films
Authors: Thakre Amol K. , Padding J. T. , den Otter W. K. , Briels W. J.
Published: July 2008

We study the relaxation dynamics of capillary waves in the interface between two confined liquid layers by means of molecular dynamics simulations. We measure the autocorrelations of the interfacial Fourier modes and find that the finite thickness of the liquid layers leads to a marked increase of the relaxation times as compared to the case of fluid layers of infinite depth. The simulation results are in good agreement with a theoretical first-order perturbation derivation, which starts from the overdamped Stokes’ equation. The theory also takes into account an interfacial friction, but the difference with no-slip interfacial conditions is small. When the walls are sheared, it is found that the relaxation times of modes perpendicular to the flow are unaffected. Modes along the flow direction are relatively unaffected as long as the equilibrium relaxation time is sufficiently short compared to the rate of deformation. We discuss the consequences for experiments on thin layers and on ultralow surface tension fluids, as well as computer simulations.
Flexible high gain complementary inverter using n-ZnO and p-pentacene channels on polyethersulfone substrate
Authors: Oh Min Suk , Choi Wonjun , Lee Kimoon , Hwang D. K. , Im Seongil
Published: July 2008

We report on the fabrication of complementary inverters that have ZnO and pentacene as n-type and p-type channels on a polyethersulfone substrate operating under 7V. Patterned Al and AlOx thin film were deposited at room temperature on the plastic as a common gate electrode and dielectric, respectively. After initial gate instability between ZnO channel and AlOx dielectric was controlled, our n-type thin-film transistors (TFTs) displayed quite a similar drain current level to that of p-type TFTs. Our flexible complementary device showed much high voltage gain of ∼100 even under a bent condition (56mm radius of curvature). Our complementary inverter also demonstrates a promising dynamic behavior of ∼20ms.
A modification of the laser detonation-type hyperthermal oxygen atom beam source for a long-term operation
Authors: Kinoshita Hiroshi , Yamamoto Shunsuke , Yatani Hideaki , Ohmae Nobuo
Published: July 2008

It has been an impedimental problem, for the laser detonation-type atom beam generator, that a poppet in the pulsed supersonic valve is rapidly eroded by the irradiation of powerful laser light and high temperature plasma. In order to operate the atom beam source for a long duration, a modification was made to hide the poppet from direct irradiation of laser and plasma. The alteration of device configuration resulted in great improvement in endurance of poppet more than 300 000 repetitions. Morphology of a polyimide film exposed to approximately 200 000 pulses of hyperthermal oxygen atom beam showed a shaglike carpet structure, which is a characteristic to that exposed to energetic oxygen atoms. A flux of the oxygen atom beam was estimated to be 5×1014 atoms/cm2/pulse at a location of 30 cm away from the nozzle throat.
Invited Review Article: Accurate and fast nanopositioning with piezoelectric tube scanners: Emerging trends and future challenges
Authors: Moheimani S. O. Reza
Published: July 2008

Piezoelectric tube scanners have emerged as the most widely used nanopositioning technology in modern scanning probe microscopes. Despite their impressive properties, their fast and accurate operations are hindered due to complications such as scan induced mechanical vibrations, hysteresis nonlinearity, creep, and thermal drift. This paper presents an overview of emerging innovative solutions inspired from recent advances in fields such as smart structures, feedback control, and advanced estimation aimed at maximizing positioning precision and bandwidth of piezoelectric tube scanners. The paper presents a thorough survey of the related literature and contains suggestions for future research prospects.
Subpicoliter droplet generation based on a nozzle-free acoustic transducer
Authors: Lee Chuang-Yuan , Pang Wei , Yu Hongyu , Kim Eun Sok
Published: July 2008

This letter reports picoliter liquid droplet generation using an orifice-free acoustic ejector operating at its harmonic frequencies. For an acoustic ejector working at the thickness-mode resonance, the droplet size is primarily determined by the acoustic wavelength, which is proportional to the piezoelectric substrate thickness. In our design, we do not need to lap the bulk piezoelectric lead zirconate titanate (PZT) substrate or deposit high temperature processing PZT thin film, but we use harmonic frequencies of the bulk form to reduce the wavelength. The fabricated acoustic ejector with a size of 1200×1200μm2 has been shown to be very effective up to the ninth harmonic (180MHz), continuously ejecting ∼10μm diameter droplets, corresponding to droplet volumes as small as 0.5pl.
Reduction in the reset current in a resistive random access memory consisting of NiOx brought about by reducing a parasitic capacitance
Authors: Kinoshita K. , Tsunoda K. , Sato Y. , Noshiro H. , Yagaki S. , Aoki M. , Sugiyama Y.
Published: July 2008

The dependence of the relationship between the reset current Ireset and the compliance current Icomp (Ireset-Icomp characteristic) of a Pt∕NiOx∕Pt structure on the parasitic capacitance between the Pt∕NiOx∕Pt structure and a current limiter C was measured for Icomp<1mA. It was clarified that C deviated the Ireset-Icomp characteristic from the ideal linear relationship expected for C=0 and Ireset saturated at higher Icomp for larger C. This is attributed to a transient current flowing through C when the forming or set transitions occurred. The relationship of Ireset≈Icomp was maintained down to Icomp=150μA in the 1T1R cell with very small C.
Heat diffusion across magnetic islands and ergodized plasma regions in realistic tokamak geometry
Authors: Hölzl M. , Günter S. ,   ASDEX Upgrade Team
Published: July 2008

Heat diffusion in magnetized plasmas is investigated numerically for tokamak geometry and realistic plasma parameters. Heat transport across single and overlapping magnetic islands is studied. As an application, the influence of an (n+1,m+1) helical perturbation onto the temperature perturbation caused by an (n,m) neoclassical tearing mode is examined. It is shown that the resulting ergodization of the magnetic field structure is able to reduce the resonant bootstrap current perturbation of a neoclassical tearing mode. This might explain the drop in the mode amplitude observed in the frequently interrupted regime. Furthermore, the influence of edge ergodization as generated by external perturbation coils onto the electron temperature is studied. It is shown that ergodization of the plasma boundary can decrease the pedestal temperature gradient significantly. This effect might be one element in the mitigation effects of edge-localized modes achieved by external resonant perturbation fields.
Between microdroplets and microfluidics: Unbreakable liquid/liquid interfaces at a junction of hydrophilic microchannels
Authors: Shinohara Kyosuke , Yokoyama Yuto , Torii Toru , Okamoto Koji
Published: July 2008

The intermediate state between microdroplets and microfluidics in two immiscible fluids is described. It was found that Y-shaped two-phase flow is formed with a stable liquid/liquid interface at a cross junction in a hydrophilic microchannel. A velocity vector map, obtained by microparticle image velocimetry, reveals the Y-shaped flow consists of aqueous phase flow along the edge of the channel and an acrylate monomer phase flow penetrating the center. The transition from the Y-shaped flow to other flow patterns can be characterized by a state diagram that depends on the capillary number and the Weber number of each injecting phase.
Enhancement of fluorescence intensity from an immunoassay chip using high-aspect-ratio nanopillars fabricated by nanoimprinting
Authors: Kuwabara Kosuke , Ogino Masahiko , Ando Takashi , Miyauchi Akihiro
Published: July 2008

High-aspect-ratio structures (nanopillars) were used to enhance the fluorescence intensity of immunoassay chips. Nanoimprinting with elongation phenomenon was applied to fabricate polystyrene nanopillars. Human alpha fetoprotein was detected by a fluorescence immunoassay protocol. Fluorescence intensities were evaluated for areas with nanopillars of different surface areas. The area with nanopillars of 95nm diameter and 4.1μm height showed fluorescence intensity 34 times higher than that of flat areas.
Multigigabit 1.3μm GaNAsSb∕GaAs Photodetectors
Authors: Fedderwitz S. , Stöhr A. , Yoon S. F. , Tan K. H. , Weiß M. , Loke W. K. , Poloczek A. , Wicaksono S. , Jäger D.
Published: July 2008

We report on the fabrication of high-speed GaNAsSb photodetector for multigigabit operation at 1.3μm wavelength. The 2μm thick bulk GaNAsSb photoabsorption layer contains 3.3% of N and 8% of Sb, resulting in optical band gap of ∼0.9eV suitable for near infrared operation up to wavelengths of about 1380nm. By using the bulk photoabsorption layer, we have fabricated GaNAsSb photodetector with high dc responsivity of 0.12A∕W at 1.3μm wavelength. The photodetector exhibits 3dB cutoff frequency at 1.3μm wavelength of 4.5GHz. Furthermore, 5Gb∕s fiber-optic transmission at 1.3μm wavelength is demonstrated using the GaNAsSb photodetector.
High-numerical-aperture-based virtual point detectors for photoacoustic tomography
Authors: Li Changhui , Wang Lihong V.
Published: July 2008

The focal point of a high-numerical-aperture (NA) ultrasonic transducer can be used as a virtual point detector. This virtual point detector detects omnidirectionally over a wide acceptance angle. It also combines a large active transducer surface and a small effective virtual detector size. Thus the sensitivity is high compared with that of a real point detector, and the aperture effect is small compared with that of a finite size transducer. We present two kinds of high-NA-based virtual point detectors and their successful application in photoacoustic tomography. They can also be applied in other ultrasound-related fields.
Nuf, a Rab11 effector, maintains cytokinetic furrow integrity by promoting local actin polymerization
Authors: Cao Jian , Albertson Roger , Riggs Blake , Field Christine M. , Sullivan William
Published: July 2008

Plasma membrane ingression during cytokinesis involves both actin remodeling and vesicle-mediated membrane addition. Vesicle-based membrane delivery from the recycling endosome (RE) has an essential but ill-defined involvement in cytokinesis. In the Drosophila melanogaster early embryo, Nuf (Nuclear fallout), a Rab11 effector which is essential for RE function, is required for F-actin and membrane integrity during furrow ingression. We find that in nuf mutant embryos, an initial loss of F-actin at the furrow is followed by loss of the associated furrow membrane. Wild-type embryos treated with Latrunculin A or Rho inhibitor display similar defects. Drug- or Rho-GTP–induced increase of actin polymerization or genetically mediated decrease of actin depolymerization suppresses the nuf mutant F-actin and membrane defects. We also find that RhoGEF2 does not properly localize at the furrow in nuf mutant embryos and that RhoGEF2–Rho1 pathway components show strong specific genetic interactions with Nuf. We propose a model in which RE-derived vesicles promote furrow integrity by regulating the rate of actin polymerization through the RhoGEF2–Rho1 pathway.
Phosphatidylinositol 4,5-bisphosphate regulates SNARE-dependent membrane fusion
Authors: James Declan J. , Khodthong Chuenchanok , Kowalchyk Judith A. , Martin Thomas F.J.
Published: July 2008

Phosphatidylinositol 4,5-bisphosphate (PI 4,5-P2) on the plasma membrane is essential for vesicle exocytosis but its role in membrane fusion has not been determined. Here, we quantify the concentration of PI 4,5-P2 as ∼6 mol% in the cytoplasmic leaflet of plasma membrane microdomains at sites of docked vesicles. At this concentration of PI 4,5-P2 soluble NSF attachment protein receptor (SNARE)–dependent liposome fusion is inhibited. Inhibition by PI 4,5-P2 likely results from its intrinsic positive curvature–promoting properties that inhibit formation of high negative curvature membrane fusion intermediates. Mutation of juxtamembrane basic residues in the plasma membrane SNARE syntaxin-1 increase inhibition by PI 4,5-P2, suggesting that syntaxin sequesters PI 4,5-P2 to alleviate inhibition. To define an essential rather than inhibitory role for PI 4,5-P2, we test a PI 4,5-P2–binding priming factor required for vesicle exocytosis. Ca2+-dependent activator protein for secretion promotes increased rates of SNARE-dependent fusion that are PI 4,5-P2 dependent. These results indicate that PI 4,5-P2 regulates fusion both as a fusion restraint that syntaxin-1 alleviates and as an essential cofactor that recruits protein priming factors to facilitate SNARE-dependent fusion.
Spindle checkpoint activation at meiosis I advances anaphase II onset via meiosis-specific APC/C regulation
Authors: Yamamoto Ayumu , Kitamura Kenji , Hihara Daisuke , Hirose Yukinobu , Katsuyama Satoshi , Hiraoka Yasushi
Published: July 2008

During mitosis, the spindle assembly checkpoint (SAC) inhibits the Cdc20-activated anaphase-promoting complex/cyclosome (APC/CCdc20), which promotes protein degradation, and delays anaphase onset to ensure accurate chromosome segregation. However, the SAC function in meiotic anaphase regulation is poorly understood. Here, we examined the SAC function in fission yeast meiosis. As in mitosis, a SAC factor, Mad2, delayed anaphase onset via Slp1 (fission yeast Cdc20) when chromosomes attach to the spindle improperly. However, when the SAC delayed anaphase I, the interval between meiosis I and II shortened. Furthermore, anaphase onset was advanced and the SAC effect was reduced at meiosis II. The advancement of anaphase onset depended on a meiosis-specific, Cdc20-related factor, Fzr1/Mfr1, which contributed to anaphase cyclin decline and anaphase onset and was inefficiently inhibited by the SAC. Our findings show that impacts of SAC activation are not confined to a single division at meiosis due to meiosis-specific APC/C regulation, which has probably been evolved for execution of two meiotic divisions.
Risk Factors for Methicillin-ResistantStaphylococcus aureusSurgical Site Infection
Authors: Harbarth Stephan , Huttner Benedikt , Gervaz Pascal , Fankhauser Carolina , Chraiti Marie-Noelle , Schrenzel Jacques , Licker Marc , Pittet Didier
Published: July 2008

We prospectively evaluated 46 possible risk factors for methicillin-resistantStaphylococcus aureus(MRSA) surgical site infection (SSI) among patients with MRSA carriage in a large intervention study. Of 6,130 study patients, 68 (1.1%) developed MRSA SSI, which occurred a median of 14 days after surgery. Risk factors associated with MRSA SSI were receipt of emergency surgery, presence of comorbid condition, receipt of immunosuppressive therapy, receipt of contaminated surgery, and a surgical duration longer than the 75th percentile. MRSA carriage on admission did not predict MRSA SSI.
Reprocessing and Reuse of Single-Use Medical Devices Used During Hemodynamic Procedures in Brazil: A Widespread and Largely Overlooked Problem
Authors: Amarante Jorge M. Buchdid , Toscano Cristiana M. , Pearson Michele L. , Roth Virginia , Jarvis William R. , Levin Anna S.
Published: July 2008

Background.

Several medical devices used during hemodynamic procedures, particularly angiographic diagnostic and therapeutic cardiac catheters, are manufactured for single use only. However, reprocessing and reuse of these devices has been reported, to determine the frequency of reuse and reprocessing of single-use medical devices used during hemodynamic procedures in Brazil and to evaluate how reprocessing is performed.

Design.

National survey, conducted from December 1999 to July 2001.

Methods.

Most of the institutions affiliated with the Brazilian Society of Hemodynamic and Interventional Cardiology were surveyed by use of a questionnaire sent in the mail.

Results.

The questionnaire response rate was 50% (119 of 240 institutions). Of the 119 institutions that responded, 116 (97%) reported reuse of single-use devices used during hemodynamic procedures, and only 26 (22%) reported use of a standardized reprocessing protocol. Cleaning, flushing, rinsing, drying, sterilizing and packaging methods varied greatly and were mostly inadequate. Criteria for discarding reused devices varied widely. Of the 119 institutions that responded, 80 (67%) reported having a surveillance system for adverse events associated with the reuse of medical devices, although most of these institutions did not routinely review the data, and only 38 (32%) described a training program for the personnel who reprocessed single-use devices.

Conclusions.

The reuse of single-use devices used during hemodynamic procedures was very frequent in hospitals in Brazil. Basic guidance on how to reuse and reprocess single-use medical devices is urgently needed, because, despite the lack of studies to support reusing and reprocessing single-use medical devices, such devices are necessary in limited-resource areas in which these practices are current.
Generalized Cauchy difference equations. II
Authors: Ebanks Bruce
Published: July 2008

The main result is an improvement of previous results on the equation\[<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="f left-parenthesis x right-parenthesis plus f left-parenthesis y right-parenthesis minus f left-parenthesis x plus y right-parenthesis equals g left-bracket phi left-parenthesis x right-parenthesis plus phi left-parenthesis y right-parenthesis minus phi left-parenthesis x plus y right-parenthesis right-bracket">f(x)+f(y)−f(x+y)=g[ϕ(x)+ϕ(y)−ϕ(x+y)]f(x)+f(y)-f(x+y)=g[\phi (x)+\phi (y)-\phi (x+y)]\]for a given functionϕ\phi. We find its general solution assuming only continuous differentiability and local nonlinearity ofϕ\phi. We also provide new results about the more general equation\[f(x)+f(y)−f(x+y)=g(H(x,y))f(x)+f(y)-f(x+y)=g(H(x,y))\]for a given functionHH. Previous uniqueness results required strong regularity assumptions on a particular solutionf0,g0f_{0},g_{0}. Here we weaken the assumptions onf0,g0f_{0},g_{0}considerably and find all solutions under slightly stronger regularity assumptions onHH.
Gradient estimates for a nonlinear parabolic equation on Riemannian manifolds
Authors: Yang Yunyan
Published: July 2008

Let

(
M
,
g
)

(M,g)

be a complete noncompact Riemannian manifold. In this paper, we derive a local gradient estimate for positive solutions to a simple nonlinear parabolic equation
\[

∂
u

∂
t

=
Δ
u
+
a
u
log
⁡
u
+
b
u

\frac {\partial u}{\partial t}=\Delta u+au\log u+bu

\]
on

M
×
[
0
,
+
∞
)

M\times [0,+\infty )

, where

a
a

,

b
b

are two real constants. This equation is closely related to the gradient Ricci soliton. We extend the result of L. Ma (Journal of Functional Analysis 241 (2006) 374-382).
Acoustic determination of early stages of intravascular blood coagulation
Authors: Uzlova Svetlana G , Guria Konstantin G , Guria Georgy Th
Published: July 2008

The blood coagulation system (BCS) is a complex biological system playing a principal role in the maintenance of haemostasis. Insufficient activity of the BCS may lead to bleeding and blood loss (e.g. in the case of haemophilia). On the other hand, excessive activity may cause intravascular blood coagulation, thromboses and embolization. Most of the methods currently used for BCS monitoring suffer from the major disadvantage of being invasive. The purpose of the present work is to demonstrate the feasibility of using ultrasonic methods for non-invasive registration of the early stages of blood coagulation processes in intensive flows. With this purpose, a special experimental set-up was designed, facilitating the simultaneous detection of optical and acoustic signals during the clotting process. It was shown that (i) as microemboli appear in the flow during the early stage of blood coagulation, the intensity of the Doppler signal increases twofold, and (ii) microemboli formation in the early stages of blood clotting always reveals itself through an acoustic contrast. Both of these effects are well defined, so we hope that they may be used for non-invasive BCS monitoring in clinical practice.
Use of a serum‐based antifungal susceptibility assay to predict the in vivo efficacy of novel echinocandin compounds
Authors: Maki Katsuyuki , Matsumoto Satoru , Watabe Etsuko , Iguchi Yumi , Tomishima Masaki , Ohki Hidenori , Yamada Akira , Ikeda Fumiaki , Tawara Shuichi , Mutoh Seitaro
Published: July 2008

In vitro susceptibility assays of antifungal activity do not always accurately predict in vivo efficacy. As well as having a clear clinical importance, the ability to predict efficacy is also essential for effective screening of novel drug compounds. Initial screening of novel compounds must often be based on in vitro data. The present report describes the use of serum‐MIC, an in vitro test of antifungal susceptibility, to accurately predict in vivo efficacy of echinocandin drugs in a mouse model of disseminated candidiasis. The basis of the serum‐MIC method was to measure the inhibitory activity of a test compound against Candida albicans hyphal growth in the presence of pooled mouse serum. For 13 previously uncharacterized echinocandin compounds, as well as for the known echinocandin drugs, micafungin and caspofungin, serum‐MIC determinations were shown to give better correlation to efficacy in the animal model than conventional, CLSI standard, in vitro antifungal susceptibility tests. The most accurate prediction of efficacy was obtained when the serum‐MIC was adjusted in relation to the serum concentration at 30 min post‐treatment. Furthermore, when the efficacy of micafungin was determined by measuring C. albicans kidney burden in the mouse model of infection, the adjusted serum‐MIC consistently reflected the effective serum concentrations. Our data indicate that determination of serum‐MIC values will facilitate prediction of the in vivo potency of new antifungal compounds such as novel echinocandins.
Characterization of rat β‐glucan receptor dectin‐1
Authors: Kato Yuya , Adachi Yoshiyuki , Ohno Naohito
Published: July 2008

Dectin‐1 is a small C‐type lectin receptor for fungal cell wall β‐glucan. Its homologues in some species, including mouse and human, have been characterized, and their importance in antifungal immunity has also been clarified. However, its homologue in the rat has not yet been identified. In this study, DNA/amino acid sequences of rat dectin‐1 were analyzed by rapid amplification of cDNA ends. The sequence of rat dectin‐1 was found to be highly homologous to that of the mouse. It possesses essential motifs for the recognition of β‐glucan and signal transduction. However, the position of the start codon in the detected sequence was not conserved, and its cytoplasmic tail was shorter than that observed in other species. Similar to mouse dectin‐1, two major isoforms of rat dectin‐1 that were generated by alternative splicing were identified: a full‐length isoform and a shorter isoform deficient in the stalk domain. It was also demonstrated that rat dectin‐1 is capable of binding fungal β‐glucan and activating nuclear factor‐kappa B via Syk and the CARD9/Bcl10‐mediated pathway. These results suggest that rat dectin‐1 also plays essential roles in immune responses against fungi.
Human mediator kinase subunit CDK11 plays a negative role in viral activator VP16‐dependent transcriptional regulation
Authors: Tsutsui Taiki , Umemura Hiroyasu , Tanaka Aki , Mizuki Fumitaka , Hirose Yutaka , Ohkuma Yoshiaki
Published: July 2008

Mediator is an essential transcriptional cofactor of RNA polymerase II (Pol II) in eukaryotes. This cofactor is a large complex containing up to 30 subunits and consisting of four modules: head, middle, tail, and CDK/Cyclin. Generally, Mediator connects transcriptional regulators, cofactors, chromatin regulators, and chromatin remodellers, with the pre‐initiation complex to provide a platform for the assembly of these factors. Many previous studies have revealed that CDK8, a subunit of the CDK/Cyclin module, is one of the key subunits mediating the pivotal roles of Mediator in transcriptional regulation. In addition to CDK8, CDK11 is conserved among vertebrates as a Mediator subunit and closely resembles CDK8. While the role of CDK8 has been studied extensively, little is known of the role of CDK11 in Mediator. We purified human CDK11 (hCDK11)‐containing protein complexes from an epitope‐tagged hCDK11‐expressing HeLa cell line and found that hCDK11 could independently form Mediator complexes devoid of human CDK8 (hCDK8). To investigate the in vivo transcriptional activity of the complex, we employed a luciferase assay. Although hCDK11 has nearly 80% amino acid sequence identity to hCDK8, siRNA‐knockdown study revealed that hCDK8 and hCDK11 possess opposing functions in viral activator VP16‐dependent transcriptional regulation.
Some aspects of the geology of Svalbard
Authors: Fookes Peter G.
Published: July 2008

Svalbard has exceptional geological diversity within a relatively small area. The islands are situated between 76°N and 81°N, longitude 10°E and 35°E, with a total land area of some 63 000 km2, about twice the size of Belgium. Around 60 per cent is covered by glaciers. It is one of the few places in the world where stratigraphical sections representing much of the Earth's history are relatively easily accessible for study.