bluuebunny/crossref_metadata_2025 huggingface dataset:
Grain size effect on the dielectric nonlinearity of BaTiO3 ceramics
Authors: Fujii Ichiro , Ugorek Michael , Trolier-McKinstry Susan
Published: May 2010

The dielectric nonlinearity of BaTiO3 ceramics with grain sizes from 1.2 to 76 μm was investigated using the ac electric field dependence of the dielectric properties and the first order reversal curves (FORC) distribution. Defect dipoles in samples with large grains led to pinching of minor polarization-electric field hysteresis loops as well as a threshold field in the ac field dependence of the dielectric constant and loss. For samples with small grains, a sublinear ac field dependence was observed. The irreversible FORC distributions characterizing the responses showed two strong and narrow peaks for large-grained samples and a weak, broad peak centered near the origin for samples with small grains. As the grain size decreased, the reversible FORC distribution at zero-bias field increased. No grain size dependence of the reversible FORC distributions was observed at high dc electric fields. These results indicate that the grain size dependence of the small field dielectric constant is attributable to a domain wall contribution. Furthermore, the potential profile through which the domain walls travel changes from a landscape with shallow widely-spaced wells with deep local wells to one with deep widely-spaced wells with shallow local wells, as the grain size decreases.
Influence of background concentration induced field on the emission rate signatures of an electron trap in zinc oxide Schottky devices
Authors: Noor Hadia , Klason P. , Faraz S. M. , Nur O. , Wahab Q. , Willander M. , Asghar M.
Published: May 2010

Various well-known research groups have reported points defects in bulk zinc oxide (ZnO) [ND (intrinsic): 1014–1017 cm−3] naming oxygen vacancy, zinc interstitial, and/or zinc antisite having activation energy in the range of 0.32–0.22 eV below conduction band. The attribution is probably based on activation energy of the level which seems not to be plausible in accordance with Vincent et al., [J. Appl. Phys. 50, 5484 (1979)] who suggested that it was necessary to become vigilant before interpreting the data attained for a carrier trap using capacitance transient measurement of diodes having ND greater than 1015 cm−3. Accordingly the influence of background free-carrier concentration, ND induced field on the emission rate signatures of an electron point defect in ZnO Schottky devices has been investigated by means of deep level transient spectroscopy. A number of theoretical models were tried to correlate with the experimental data to ascertain the mechanism. Consequently Poole–Frenkel model based on Coulomb potential was found consistent. Based on these investigations the electron trap was attributed to Zn-related charged impurity. Qualitative measurements like current-voltage and capacitance-voltage measurements were also performed to support the results.
Stimulated Raman scattering of laser in heavily doped semiconductors
Authors: Kumar Pawan , Tripathi V. K.
Published: May 2010

An intense short pulse laser propagating through a heavily doped degenerate semiconductor, parametrically excites a free carrier space charge mode and back scattered electromagnetic mode via free carrier nonlinearity. Landau damping and collisional damping of the decay waves determine the threshold for the instability. Above the threshold, the growth rate scales as γ∼(v0/2c)(εLωω0)1/2, where v0 is the free carrier oscillatory velocity, c is the velocity of light in vacuum, εL is the lattice permittivity, ω is the frequency of the space charge mode, and ω0 is the pump frequency.
Stationary spiral waves in film flow over a spinning disk
Authors: Sisoev G. M. , Goldgof D. B. , Korzhova V. N.
Published: May 2010

Stationary spiral waves in liquid film flowing over a spinning disk have been observed in earlier experiments [H. Espig and R. Hoyle, “Waves in a thin liquid layer on a rotating disk,” J. Fluid Mech. 22, 671 (1965); A. F. Charwat et al., “The flow and stability of thin liquid films on a rotating disk,” J. Fluid Mech. 53, 227 (1972); G. Leneweit et al., “Surface instabilities of thin liquid film flow on a rotating disk,” Exp. Fluids 26, 75 (1999)]. In the framework of a mathematical model derived by the integral method, it is shown that the waves develop due to nonaxisymmetric liquid feeding onto the spinning disk, and the wave shapes are approximated by the Archimedean spirals, whose coefficients depend on the Eckman number. The dependence has been confirmed by experimental data from recorded videos.
Highly accurate deterministic lateral displacement device and its application to purification of fungal spores
Authors: Inglis David W. , Herman Nick , Vesey Graham
Published: May 2010

We have designed, built, and evaluated a microfluidic device that uses deterministic lateral displacement for size-based separation. The device achieves almost 100% purity and recovery in continuously sorting two, four, and six micrometer microspheres. We have applied this highly efficient device to the purification of fungal (Aspergillus) spores that are spherical (∼4 μm diameter) with a narrow size distribution. Such separation directly from culture using unfiltered A. niger suspensions is difficult due to a high level of debris. The device produces a two to three increase in the ratio of spores to debris as measured by light scatter in a flow cytometer. The procedure is feasible at densities up to 4.4×106 spores/ml. This is one of the first studies to apply microfluidic techniques to spore separations and has demonstrated that a passive separation system could significantly reduce the amount of debris in a suspension of fungal spores with virtually no loss of spore material.
Structural and electrical properties of fully strained (In,Ga)As field effect transistors with in situ deposited gate stacks
Authors: Marchiori C. , Kiewra E. , Fompeyrine J. , Gerl C. , Rossel C. , Richter M. , Locquet J.-P. , Smets T. , Sousa M. , Andersson C. , Webb D. J.
Published: May 2010

Metal-oxide-semiconductor field-effect transistors (MOSFETs) were fabricated with amorphous Al2O3 and HfO2/SiOx–Si gate stacks, grown by molecular beam deposition. As and In oxides were observed at the Al2O3/In0.17Ga0.83As interface, whereas no oxides were detected on the Si-passivated In0.17Ga0.83As surface after HfO2 deposition. Traces of As were found in both gate stacks. Si-passivated MOSFETs, with a drain current of 2.8×103 μA/mm at Vg−Vt=2.0 V, Vd=1.0 V, Ion/Ioff=1×107, and inverse subthreshold slope of 98–120 mV/decade, show superior performance with respect to devices without Si interlayer.
Channel stress measurements of 45 nm node transistors with embedded silicon-germanium source and drain using ultraviolet Raman spectroscopy
Authors: Wong C. P. , Kasim J. , Liu J. P. , See A. , Shen Z. X.
Published: May 2010

We report the use of ultraviolet Raman spectroscopy to measure the average channel stress for 45 nm node transistors with embedded silicon-germanium (SiGe) source and drain. Direct probing of the channel for stress measurements was made possible by removing the polycrystalline silicon gate using a simple and cost-free approach. We demonstrate the feasibility of this method for measuring channel stress of dense transistor structures with varying pitch lengths, with ∼80 nm SiGe selectively grown in the source and drain regions.
The role of electric charge in microdroplets impacting on conducting surfaces
Authors: Deng Weiwei , Gomez Alessandro
Published: May 2010

A rich phenomenology is revealed by temporally resolved image sequences of electrically charged ethanol microdroplets impacting on a conductive surface at temperatures bracketing the liquid boiling point. Notable phenomena include the flattening of the sessile droplets with reduced contact angle, increased evaporation rates for substrate temperatures below the fluid boiling point, and the hindrance of droplet rebound at the Leidenfrost temperature. Scaling considerations are presented to rationalize the observed behavior and to generalize conclusions to a broader droplet size range.
Digital circuits using self-shunted Nb/NbxSi1−x/Nb Josephson junctions
Authors: Olaya David , Dresselhaus Paul D. , Benz Samuel P. , Herr Anna , Herr Quentin P. , Ioannidis Alexander G. , Miller Donald L. , Kleinsasser A. W.
Published: May 2010

Superconducting digital circuits based on Josephson junctions with amorphous niobium-silicon (a-NbSi) barriers have been designed, fabricated, and tested. Single-flux-quantum (SFQ) shift registers operated with ±30% bias margins, confirming junction reproducibility and uniformity. Static digital dividers operated up to 165 GHz for a single value of bias current, which was only marginally slower than circuits fabricated with externally shunted AlOx-barrier junctions having a comparable critical current density of 4.5 kA/cm2. In comparison, self-shunted a-NbSi junctions enabled a doubling in circuit density. This and their relatively thick 10 nm barriers could increase the yield of complex SFQ circuits.
Quantifying the interaction between large and small scales in wall-bounded turbulent flows: A note of caution
Authors: Schlatter Philipp , Örlü Ramis
Published: May 2010

Turbulent flow close to solid walls is dominated by an ensemble of fluctuations of large and small spatial scales. Recent work by Mathis et al. [J. Fluid Mech. 628, 311 (2009); Phys. Fluids 21, 111703 (2009)] introduced and used a decoupling procedure based on the Hilbert transformation applied to the filtered small-scale component of the fluctuating streamwise velocity. This method is employed as a robust tool to quantify a dominant amplitude modulation of the small scales by the large scales found in the outer part of the boundary layer. In the present study, however, we demonstrate by means of experimental and synthetic signals that the correlation coefficient used to quantify the amplitude modulation is related to the skewness of the original signal, and hence, for the Reynolds numbers considered here, may not be an independent tool to unambiguously detect or quantify the effect of large-scale amplitude modulation of the small scales.
Role of diffusion in two-dimensional bimolecular recombination
Authors: Nenashev A. V. , Jansson F. , Baranovskii S. D. , Österbacka R. , Dvurechenskii A. V. , Gebhard F.
Published: May 2010

Experiments on carrier recombination in two-dimensional organic structures are often interpreted in the frame of the Langevin model with taking into account only the drift of the charge carriers in their mutual electric field. While this approach is well justified for three-dimensional systems, it is in general not valid for two-dimensional structures where the contribution of diffusion can play a dominant role. We study the two-dimensional Langevin recombination theoretically and find the critical concentration below which diffusion cannot be neglected. For typical experimental conditions, neglecting the diffusion leads to an underestimation of the recombination rate by several times.
Triple-junction contribution to diffusion in nanocrystalline Si
Authors: Portavoce A. , Chow L. , Bernardini J.
Published: May 2010

The influence of triple-junctions on experimental Ge diffusion profiles (850–1000 °C) in nanocrystalline Si is investigated using three-dimensional finite element simulations. We found that triple-junction diffusion is not negligible in nanocrystalline Si made of 40 nm wide grains. Ge triple-junction diffusion coefficient follows the Arrhenius law 5.72×104 exp(−3.24 eV/kT)cm2 s−1. It is approximately 4.7×102 times higher than grain boundary diffusion coefficient, even though diffusion in triple-junction and in grain boundary exhibits similar activation energy.
Magnetopiezoelastic energy harvesting driven by random excitations
Authors: Litak G. , Friswell M. I. , Adhikari S.
Published: May 2010

This letter considers a nonlinear piezomagnetoelastic energy harvester driven by stationary Gaussian white noise. The increase in the energy generated by this device has been demonstrated for harmonic excitation with slowly varying frequency in simulation and validated by experiment. This paper considers the simulated response of this validated model to random base excitation and shows that the system exhibits a stochastic resonance. If the variance of the excitation were known then the device may be optimized to maximize the power harvested, even under random excitation.
Dependence of emission of terahertz radiation on geometrical parameters of dipole photoconductive antennas
Authors: Miyamaru Fumiaki , Saito Yu , Yamamoto Kohji , Furuya Takashi , Nishizawa Seizi , Tani Masahiko
Published: May 2010

The dependence of the emission spectrum of terahertz (THz) radiation on the geometrical parameters of the dipole antenna, and the relationship between these parameters and the temporal characteristics of the transient current that generate THz radiation, is reported. The emission intensity and the peak frequency strongly depend on these geometrical parameters. This dependence varies significantly with changes in the temporal characteristics of the transient current. We have also found that the emission efficiency can be increased by increasing the aspect ratio for the dipole.
Proposal for efficient generation of spin-polarized current in silicon
Authors: Castelano L. K. , Sham L. J.
Published: May 2010

We propose a spin-dependent resonant tunneling structure to efficiently inject spin-polarized current into silicon. By means of a heavily doped polycrystalline Si between the ferromagnetic metal and Si, the Schottky barrier resistance is reduced and consequently the tunneling current density is raised. The small Fermi sea of the charge carriers in Si focuses the tunneling electrons to the resonant spin states within a small region of transverse momentum in the ferromagnet which creates the spin polarization of the current.
Fluorination induced half metallicity in two-dimensional few zinc oxide layers
Authors: Chen Qian , Wang Jinlan , Zhu Liyan , Wang Shudong , Ding Feng
Published: May 2010

We systematically explore the stability, bonding characteristics, and electronic and magnetic properties of two-dimensional (2D) few zinc oxide layers (few-ZnOLs) with or without fluorination by using density functional theory approach. The pristine few-ZnOLs favor stable planar hexagonal structures, which stem from their unique bonding characteristics: The intralayer Zn–O interaction is dominated by covalent bonding while the interaction between layers is weak ionic bonding. Furthermore, we demonstrate that fluorination from one side turns the planar few-ZnOLs back to the wurtzitelike corrugated structure, which enhances the stability of the 2D ZnO films. The fluorinated few-ZnOLs are ferromagnets with magnetic moments as high as 0.84, 0.87, 0.89, and 0.72 μB per unit cell for the number of layers of N=1, 2, 3, and 4, respectively. Most interestingly, the fluorination can also turn few-ZnOLs from semiconductor into half metallicity with a half-metal gap up to 0.56 eV. These excellent electronic and magnetic properties may open 2D ZnO based materials great opportunity in future spintronics.
The impact of recent physiotherapy graduates in the workforce: a study of Curtin University entry-level physiotherapists 2000 - 2004
Authors: Mulcahy Amanda J. , Jones Sue , Strauss Geoff , Cooper Ian
Published: May 2010

Physiotherapy is the largest healthcare contributor after nursing and medicine and it is important to understand its employment characteristics. This study aimed to explore workforce trends for recent physiotherapy graduates, including satisfaction and motivating factors, and future career intentions. A self-administered questionnaire was provided to contactable entry-level physiotherapy graduates (2000–2004) from Curtin University. Of 256 respondents (62.9%), 76.5% were employed full-time. A total of 45% of physiotherapists worked in the public health system; 79.3% worked in cities; 92.2% were clinicians. Top salaries were earned by those completing more continuing professional development hours, working privately, in rural locations and males. A total of 65% (n = 118) of respondents believed they would leave physiotherapy within 10 years. The best aspects of working in physiotherapy were ‘helping people’, ‘flexibility’ and ‘working in a healthcare team’. Major areas for improvement were ‘remuneration’, ‘skill recognition’ and ‘marketing’. This study suggests serious implications for the future of the health; planning to avert shortages is essential.
What is known about the topic?Few recent studies have examined the extent to which physiotherapists may become dissatisfied and leave their professions, and much of the evidence is anecdotal.
What does the paper add?Through a self-administered survey, it was found that satisfaction with physiotherapy was indicated by 72.0% of respondents, with higher levels amongst rural workers, those completing more continuing professional development and senior physiotherapists.
What are the implications for practitioners?Health workforce planning must take into consideration that many graduates predicted a relatively short-term physiotherapy career. The most satisfied graduates were goal-oriented and developing a career path as evidenced by professional body membership, participation in more continuing professional development and working in a senior position.
Workforce education issues for international medical graduate specialists in anaesthesia
Authors: Higgins Niall S. , Taraporewalla Kersi , Steyn Michael , Brijball Rajesh , Watson Marcus
Published: May 2010

International medical graduate (IMG) specialists in anaesthesia need education to be part of the assessment process for pre-registration college fellowship. Fellowship of the anaesthetic college is required in Australia for registration as a specialist in this field. Marked differences exist between local trainees and IMG specialists in terms of training, stakes of the exam and isolation of practice. We have examined the reasons for the low pass rate for IMG specialists compared to the local trainees in the Australian and New Zealand College of Anaesthetists (ANZCA) final fellowship examinations. We also offer an IMG specialists’ view of this perceived problem. It highlights their difficulties in obtaining adequate supervision and education. What is known about the topic?There has been a worldwide shortage of doctors over the last decade. In Australia this shortage has been attributed to government policy in the 1990s limiting the number of medical school places. Other factors that may have contributed to this shortage are changes in the practice of medicine, increasing specialisation, growth in population and patterns of population settlement at the coastal fringes of Australia. The use of international medical graduates and reliance on them is associated with several problems and challenges. A key factor relates to their performance at a standard acceptable to the country. What does the paper add?This paper offers an examination of the issues that present to IMG specialists located at rural and remote areas of Australia. The global aim of this study is to understand the workforce education issues that present to IMG specialists as a basis for supporting this group, having migrated to Australia, to better prepare for assessment of their practice in this country. Results of a survey of IMG specialists in Anaesthesia are included to contribute to an overall view. It highlights their understanding of the issues that present when preparing for specialist assessments. What are the implications for practitioners?This information will be useful for policy practitioners who determine critical elements that influence workforce planning and education support. Decision makers will be able to make more informed decisions on the need to integrate education into planning for workforce efficiencies. There are currently no published data explaining why the pass rate for IMG specialist in anaesthesia is so different from local trainees and this paper also offers a viewpoint of present issues from those who are attempting these examinations.
Modelling the physical oceanography of the D'Entrecasteaux Channel and the Huon Estuary, south-eastern Tasmania
Authors: Herzfeld M. , Andrewartha J. , Sakov P.
Published: May 2010

A three-dimensional primitive-equation hydrodynamic model was applied to the Huon Estuary and D'Entrecasteaux Channel in south-eastern Tasmania to characterise the physical oceanography of the coupled system. Model results verify that the Huon Estuary behaves as a salt-wedge estuary, and can be considered the driver for residual circulation for the system; the bottom water enters the southern channel and is directed up-estuary in the form of a salt wedge, to be entrained into the surface layer along its length, whereas freshwater downstream flow is returned to the channel. The D'Entrecasteaux Channel behaves as a ROFI (Regions of Freshwater Influence) regime, where buoyancy owing to the freshwater inflow stabilises the water column, in competition with mixing processes. The ROFI is influenced by rotation, resulting in a flow predominantly directed northward in the channel, with only a small percentage exiting the southern boundary under the influence of northerly winds. The connectivity of the region is largely influenced by the residual circulation, where the northern channel exhibits poor connectivity with the rest of the system, whereas the southern channel and Huon are relatively well connected throughout. Flushing analysis and particle tracking show the flushing time for the whole region to be ∼20–26 days.
Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation
Authors: Salomonis Nathan , Schlieve Christopher R. , Pereira Laura , Wahlquist Christine , Colas Alexandre , Zambon Alexander C. , Vranizan Karen , Spindler Matthew J. , Pico Alexander R. , Cline Melissa S. , Clark Tyson A. , Williams Alan , Blume John E. , Samal Eva , Mercola Mark , Merrill Bradley J. , Conklin Bruce R.
Published: May 2010

Two major goals of regenerative medicine are to reproducibly transform adult somatic cells into a pluripotent state and to control their differentiation into specific cell fates. Progress toward these goals would be greatly helped by obtaining a complete picture of the RNA isoforms produced by these cells due to alternative splicing (AS) and alternative promoter selection (APS). To investigate the roles of AS and APS, reciprocal exon–exon junctions were interrogated on a genome-wide scale in differentiating mouse embryonic stem (ES) cells with a prototype Affymetrix microarray. Using a recently released open-source software package named AltAnalyze, we identified 144 genes for 170 putative isoform variants, the majority (67%) of which were predicted to alter protein sequence and domain composition. Verified alternative exons were largely associated with pathways of Wnt signaling and cell-cycle control, and most were conserved between mouse and human. To examine the functional impact of AS, we characterized isoforms for two genes. As predicted by AltAnalyze, we found that alternative isoforms of the gene Serca2 were targeted by distinct microRNAs (miRNA-200b, miRNA-214), suggesting a critical role for AS in cardiac development. Analysis of the Wnt transcription factor Tcf3, using selective knockdown of an ES cell-enriched and characterized isoform, revealed several distinct targets for transcriptional repression (Stmn2, Ccnd2, Atf3, Klf4, Nodal, and Jun) as well as distinct differentiation outcomes in ES cells. The findings herein illustrate a critical role for AS in the specification of ES cells with differentiation, and highlight the utility of global functional analyses of AS.
Adults with dyslexia are impaired in categorizing speech and nonspeech sounds on the basis of temporal cues
Authors: Vandermosten Maaike , Boets Bart , Luts Heleen , Poelmans Hanne , Golestani Narly , Wouters Jan , Ghesquière Pol
Published: May 2010

Developmental dyslexia is characterized by severe reading and spelling difficulties that are persistent and resistant to the usual didactic measures and remedial efforts. It is well established that a major cause of these problems lies in poorly specified representations of speech sounds. One hypothesis states that this phonological deficit results from a more fundamental deficit in auditory processing. Despite substantial research effort, the specific nature of these auditory problems remains debated. A first controversy concerns the speech specificity of the auditory processing problems: Can they be reduced to more basic auditory processing, or are they specific to the perception of speech sounds? A second topic of debate concerns the extent to which the auditory problems are specific to the processing of rapidly changing temporal information or whether they encompass a broader range of complex spectro-temporal processing. By applying a balanced design with stimuli that were adequately controlled for acoustic complexity, we show that adults with dyslexia are specifically impaired at categorizing speech and nonspeech sounds that differ in terms of rapidly changing acoustic cues (i.e., temporal cues), but that they perform adequately when categorizing steady-state speech and nonspeech sounds. Thus, we show that individuals with dyslexia have an auditory temporal processing deficit that is not speech-specific.
Activin A, a product of fetal Leydig cells, is a unique paracrine regulator of Sertoli cell proliferation and fetal testis cord expansion
Authors: Archambeault Denise R. , Yao Humphrey Hung-Chang
Published: May 2010

Formation of tubular structures relies upon complex interactions between adjacent epithelium and mesenchyme. In the embryonic testes, dramatic compartmentalization leads to the formation of testis cords (epithelium) and the surrounding interstitium (mesenchyme). Sertoli cells, the epithelial cell type within testis cords, produce signaling molecules to orchestrate testis cord formation. The interstitial fetal Leydig cells, however, are thought only to masculinize the embryo and are not known to be involved in testis cord morphogenesis. Contrary to this notion, we have identified activin A, a member of the TGF-β protein superfamily, as a product of the murine fetal Leydig cells that acts directly upon Sertoli cells to promote their proliferation during late embryogenesis. Genetic disruption of activin βA, the gene encoding activin A, specifically in fetal Leydig cells resulted in a failure of fetal testis cord elongation and expansion due to decreased Sertoli cell proliferation. Conditional inactivation ofSmad4, the central component of TGF-β signaling, in Sertoli cells led to testis cord dysgenesis and proliferative defects similar to those of Leydig cell-specific activin βA knockout testes. These results indicate that activin A is the major TGF-β protein that acts directly on Sertoli cells. Testicular dysgenesis in activin βA andSmad4conditional knockout embryos persists into adulthood, leading to low sperm production and abnormal testicular histology. Our findings challenge the paradigm that fetal testis development is solely under the control of Sertoli cells, by uncovering an active and essential role of fetal Leydig cells during testis cord morphogenesis.
Entropy driven self-assembly of nonamphiphilic colloidal membranes
Authors: Barry Edward , Dogic Zvonimir
Published: May 2010

We demonstrate that homogeneous monodisperse rods in the presence of attractive interactions assemble into equilibrium 2D fluid-like membranes composed of a one-rod length thick monolayer of aligned rods. Unique features of our system allow us to simultaneously investigate properties of these membranes at both continuum and molecular lengthscales. Analysis of thermal fluctuations at continuum lengthscales yields the membranes’ lateral compressibility and bending rigidity and demonstrates that the properties of colloidal membranes are comparable to those of traditional lipid bilayers. Fluctuations at molecular lengthscales, in which single rods protrude from the membrane surface, are directly measured by comparing the positions of individual fluorescently labeled rods within a membrane to that of the membrane’s continuum conformation. As two membranes approach each other in suspension, protrusion fluctuations are suppressed leading to effective repulsive interactions. Motivated by these observations, we propose an entropic mechanism that explains the stability of colloidal membranes and offers a general design principle for the self-assembly of 2D nanostructured materials from rod-like molecules.
A circadian-regulated gene,
Nocturnin
, promotes adipogenesis by stimulating PPAR-γ nuclear translocation
Authors: Kawai Masanobu , Green Carla B. , Lecka-Czernik Beata , Douris Nicholas , Gilbert Misty R. , Kojima Shihoko , Ackert-Bicknell Cheryl , Garg Neha , Horowitz Mark C. , Adamo Martin L. , Clemmons David R. , Rosen Clifford J.
Published: May 2010

Nocturnin (NOC) is a circadian-regulated protein related to the yeast family of transcription factors involved in the cellular response to nutrient status. In mammals, NOC functions as a deadenylase but lacks a transcriptional activation domain. It is highly expressed in bone-marrow stromal cells (BMSCs), hepatocytes, and adipocytes. In BMSCs exposed to the PPAR-γ (peroxisome proliferator-activated receptor-γ) agonist rosiglitazone,
Noc
expression was enhanced 30-fold. Previously, we reported that
Noc
−/−
mice had low body temperature, were protected from diet-induced obesity, and most importantly exhibited absence of
Pparg
circadian rhythmicity on a high-fat diet. Consistent with its role in influencing BMSCs allocation,
Noc
−/−
mice have reduced bone marrow adiposity and high bone mass. In that same vein, NOC overexpression enhances adipogenesis in 3T3-L1 cells but negatively regulates osteogenesis in MC3T3-E1 cells. NOC and a mutated form, which lacks deadenylase activity, bind to PPAR-γ and markedly enhance PPAR-γ transcriptional activity. Both WT and mutant NOC facilitate nuclear translocation of PPAR-γ. Importantly, NOC-mediated nuclear translocation of PPAR-γ is blocked by a short peptide fragment of NOC that inhibits its physical interaction with PPAR-γ. The inhibitory effect of this NOC-peptide was partially reversed by rosiglitazone, suggesting that effect of NOC on PPAR-γ nuclear translocation may be independent of ligand-mediated PPAR-γ activation. In sum,
Noc
plays a unique role in the regulation of mesenchymal stem-cell lineage allocation by modulating PPAR-γ activity through nuclear translocation. These data illustrate a unique mechanism whereby a nutrient-responsive gene influences BMSCs differentiation, adipogenesis, and ultimately body composition.
Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T
Authors: Tachiwana Hiroaki , Kagawa Wataru , Osakabe Akihisa , Kawaguchi Koichiro , Shiga Tatsuya , Hayashi-Takanaka Yoko , Kimura Hiroshi , Kurumizaka Hitoshi
Published: May 2010

A histone H3 variant, H3T, is highly expressed in the testis, suggesting that it may play an important role in the chromatin reorganization required for meiosis and/or spermatogenesis. In the present study, we found that the nucleosome containing human H3T is significantly unstable both in vitro and in vivo, as compared to the conventional nucleosome containing H3.1. The crystal structure of the H3T nucleosome revealed structural differences in the H3T regions on both ends of the central α2 helix, as compared to those of H3.1. The H3T-specific residues (Met71 and Val111) are the source of the structural differences observed between H3T and H3.1. A mutational analysis revealed that these residues are responsible for the reduced stability of the H3T-containing nucleosome. These physical and structural properties of the H3T-containing nucleosome may provide the basis of chromatin reorganization during spermatogenesis.
One SUMO is sufficient to silence the dimeric potassium channel K2P1
Authors: Plant Leigh D. , Dementieva Irina S. , Kollewe Astrid , Olikara Sonia , Marks Jeremy D. , Goldstein Steve A. N.
Published: May 2010

Small ubiquitin modifier 1 (SUMO1) is shown to regulate K2P1 background channels in the plasma membrane (PM) of live mammalian cells. Confocal microscopy reveals native SUMO1, SAE1, and Ubc9 (the enzymes that activate and conjugate SUMO1) at PM where SUMO1 and expressed human K2P1 are demonstrated to colocalize. Silent K2P1 channels in excised PM patches are activated by SUMO isopeptidase (SENP1) and resilenced by SUMO1. K2P1-Lys274 is crucial: when mutated to Gln, Arg, Glu, Asp, Cys, or Ala, the channels are constitutively active and insensitive to SUMO1 and SENP1. Tandem mass spectrometry confirms conjugation of SUMO1 to the ε-amino group of Lys274 in vitro. FRET microscopy shows that assembly of K2P1 and SUMO1 requires Lys274. Single-particle TIRF microscopy shows that wild-type channels in PM have two K2P1 subunits and assemble with two SUMO1 monomers. Although channels engineered with one Lys274 site carry just one SUMO1 they are activated and silenced by SENP1 and SUMO1 like wild-type channels.
Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1
Authors: Ren Yi , Seo Hyuk-Soo , Blobel Günter , Hoelz André
Published: May 2010

The export of mRNAs is a multistep process, involving the packaging of mRNAs into messenger ribonucleoprotein particles (mRNPs), their transport through nuclear pore complexes, and mRNP remodeling events prior to translation. Ribonucleic acid export 1 (Rae1) and Nup98 are evolutionarily conserved mRNA export factors that are targeted by the vesicular stomatitis virus matrix protein to inhibit host cell nuclear export. Here, we present the crystal structure of human Rae1 in complex with the Gle2-binding sequence (GLEBS) of Nup98 at 1.65 Å resolution. Rae1 forms a seven-bladed β-propeller with several extensive surface loops. The Nup98 GLEBS motif forms an ≈50-Å-long hairpin that binds with its C-terminal arm to an essentially invariant hydrophobic surface that extends over the entire top face of the Rae1 β-propeller. The C-terminal arm of the GLEBS hairpin is necessary and sufficient for Rae1 binding, and we identify a tandem glutamate element in this arm as critical for complex formation. The Rae1•Nup98
GLEBS
surface features an additional conserved patch with a positive electrostatic potential, and we demonstrate that the complex possesses single-stranded RNA-binding capability. Together, these data suggest that the Rae1•Nup98 complex directly binds to the mRNP at several stages of the mRNA export pathway.
DNA polymerase η lacking the ubiquitin-binding domain promotes replicative lesion bypass in humans cells
Authors: Acharya Narottam , Yoon Jung-Hoon , Hurwitz Jerard , Prakash Louise , Prakash Satya
Published: May 2010

The Rad6-Rad18 mediated monoubiquitylation of proliferating cell nuclear antigen (PCNA) at lys 164 plays a crucial role in promoting the access of translesion synthesis (TLS) DNA polymerases (Pols) to PCNA in the replication fork stalled at a lesion site. Although a number of genetic and biochemical observations have provided strong evidence that TLS Pols bind PCNA at its interdomain connector loop (IDCL) via their PCNA-interacting protein (PIP) domain, a more recent proposal formulates that TLS Pols bind PCNA at two sites, to the IDCL via their PIP domain and to lys-164 linked ubiquitin (Ub) via their ubiquitin-binding domain. To ascertain the relative contributions of the PIP and Ub-binding zinc finger (UBZ) domains of human Polη in TLS, we have determined whether the C-terminal truncations of hPolη that contain the PIP1 domain but lack the UBZ and PIP2 domains can still function in TLS in human cells. Our observations that such C-terminally truncated proteins promote efficient TLS opposite a
cis-syn
TT dimer and confer a high degree of UV resistance to XPV cells provide unambiguous evidence that the binding of PCNA via its PIP domain is essential as well as sufficient for providing hPolη the ability to carry out TLS in human cells.
Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing
Authors: Xie Weibo , Feng Qi , Yu Huihui , Huang Xuehui , Zhao Qiang , Xing Yongzhong , Yu Sibin , Han Bin , Zhang Qifa
Published: May 2010

Bar-coded multiplexed sequencing approaches based on new-generation sequencing technologies provide capacity to sequence a mapping population in a single sequencing run. However, such approaches usually generate low-coverage and error-prone sequences for each line in a population. Thus, it is a significant challenge to genotype individual lines in a population for linkage map construction based on low-coverage sequences without the availability of high-quality genotype data of the parental lines. In this paper, we report a method for constructing ultrahigh-density linkage maps composed of high-quality single-nucleotide polymorphisms (SNPs) based on low-coverage sequences of recombinant inbred lines. First, all potential SNPs were identified to obtain drafts of parental genotypes using a maximum parsimonious inference of recombination, making maximum use of SNP information found in the entire population. Second, high-quality SNPs were identified by filtering out low-quality ones by permutations involving resampling of windows of SNPs followed by Bayesian inference. Third, lines in the mapping population were genotyped using the high-quality SNPs assisted by a hidden Markov model. With 0.05× genome sequence per line, an ultrahigh-density linkage map composed of bins of high-quality SNPs using 238 recombinant inbred lines derived from a cross between two rice varieties was constructed. Using this map, a quantitative trait locus for grain width (
GW5
) was localized to its presumed genomic region in a bin of 200 kb, confirming the accuracy and quality of the map. This method is generally applicable in genetic map construction with low-coverage sequence data.
The role of UDP-Glc:glycoprotein glucosyltransferase 1 in the maturation of an obligate substrate prosaposin
Authors: Pearse Bradley R. , Tamura Taku , Sunryd Johan C. , Grabowski Gregory A. , Kaufman Randal J. , Hebert Daniel N.
Published: May 2010

An endoplasmic reticulum (ER) quality control system assists in efficient folding and disposal of misfolded proteins. N-linked glycans are critical in these events because their composition dictates interactions with molecular chaperones. UDP-glucose:glycoprotein glucosyltransferase 1 (UGT1) is a key quality control factor of the ER. It adds glucoses to N-linked glycans of nonglucosylated substrates that fail a quality control test, supporting additional rounds of chaperone binding and ER retention. How UGT1 functions in its native environment is poorly understood. The role of UGT1 in the maturation of glycoproteins at basal expression levels was analyzed. Prosaposin was identified as a prominent endogenous UGT1 substrate. A dramatic decrease in the secretion of prosaposin was observed in ugt1−/− cells with prosaposin localized to large juxtanuclear aggresome-like inclusions, which is indicative of its misfolding and the essential role that UGT1 plays in its proper maturation. A model is proposed that explains how UGT1 may aid in the folding of sequential domain–containing proteins such as prosaposin.
BCL6 is critical for the development of a diverse primary B cell repertoire
Authors: Duy Cihangir , Yu J. Jessica , Nahar Rahul , Swaminathan Srividya , Kweon Soo-Mi , Polo Jose M. , Valls Ester , Klemm Lars , Shojaee Seyedmehdi , Cerchietti Leandro , Schuh Wolfgang , Jäck Hans-Martin , Hurtz Christian , Ramezani-Rad Parham , Herzog Sebastian , Jumaa Hassan , Koeffler H. Phillip , de Alborán Ignacio Moreno , Melnick Ari M. , Ye B. Hilda , Müschen Markus
Published: May 2010

BCL6 protects germinal center (GC) B cells against DNA damage–induced apoptosis during somatic hypermutation and class-switch recombination. Although expression of BCL6 was not found in early IL-7–dependent B cell precursors, we report that IL-7Rα–Stat5 signaling negatively regulates BCL6. Upon productive VH-DJH gene rearrangement and expression of a μ heavy chain, however, activation of pre–B cell receptor signaling strongly induces BCL6 expression, whereas IL-7Rα–Stat5 signaling is attenuated. At the transition from IL-7–dependent to –independent stages of B cell development, BCL6 is activated, reaches expression levels resembling those in GC B cells, and protects pre–B cells from DNA damage–induced apoptosis during immunoglobulin (Ig) light chain gene recombination. In the absence of BCL6, DNA breaks during Ig light chain gene rearrangement lead to excessive up-regulation of Arf and p53. As a consequence, the pool of new bone marrow immature B cells is markedly reduced in size and clonal diversity. We conclude that negative regulation of Arf by BCL6 is required for pre–B cell self-renewal and the formation of a diverse polyclonal B cell repertoire.
Differences in the Epidemiological Characteristics and Clinical Outcomes of Pandemic (H1N1) 2009 Influenza, Compared with Seasonal Influenza
Authors: Shiley Kevin T. , Nadolski Gregory , Mickus Timothy , Fishman Neil O. , Lautenbach Ebbing
Published: May 2010

Background.

There are limited data comparing the clinical presentations, comorbidities, and outcomes of patients with infections due to seasonal influenza with patients with infections due to pandemic (H1N1) 2009 influenza.

Objective.

To compare the epidemiological characteristics and outcomes of pandemic (H1N1) 2009 influenza with those of seasonal influenza.

Methods.

A cross-sectional study was conducted among patients who received diagnoses during emergency department and inpatient encounters at 2 affiliated academic medical centers in Philadelphia, Pennsylvania. Cases of seasonal influenza during the period November 1, 2005, through June 1, 2008, and cases of pandemic influenza during the period from May 1, 2009, through August 7, 2009, were identified retrospectively.

Results.

Forty-nine cases of pandemic influenza and 503 cases of seasonal influenza were identified. Patients with pandemic H1N1 were younger (median age, 29 years) than patients with seasonal influenza (median age, 59 years) (P<.001). More patients with pandemic H1N1 (35 [71%] of 49) were African American, compared with patients with seasonal influenza (267 [53%] of 503;P= .02). Several symptoms were more common among patients with pandemic influenza infections than among patients with seasonal influenza infections: cough (98% vs 83%;P= .007), myalgias (71% vs 46%;P= .001), and pleuritic chest pain (45% vs 15%;P< .001). Pregnancy was the only comorbidity that occurred significantly more often in the pandemic influenza group than in the seasonal influenza group (16% vs 1%;P< .001). There were no significant differences in frequencies of deaths of hospitalized patients, intensive care unit admission, or length of hospitalization between groups.

Conclusion.

Other than pregnancy, there were few clinically important differences between infections due to seasonal influenza and those due to pandemic influenza. The greater rate of lower respiratory tract symptoms in pandemic cases might serve to differentiate pandemic influenza from seasonal influenza.
Outbreak of Adenovirus Type 4 Infection in a Long-Term Care Facility for the Elderly
Authors: Kandel Ruth , Srinivasan Arjun , D'Agata Erika M. C. , Lu Xiaoyan , Erdman Dean , Jhung Michael
Published: May 2010

An outbreak of acute respiratory disease due to human adenovirus and a resulting increase in mortality occurred in a long-term care facility for the elderly. By use of viral culture and polymerase chain reaction, not a rapid antigen test, the virus was detected. Human adenovirus infection can occur in elderly individuals, but detection by rapid antigen testing may be limited.
Integrative platform to translate gene sets to networks
Authors: Laakso Marko , Hautaniemi Sampsa
Published: May 2010

Summary: We have implemented a computational platform (Moksiskaan) that integrates pathway, protein–protein interaction, genome and literature mining data to result in comprehensive networks for a list of genes or proteins. Moksiskaan is able to generate hypothetical pathways for these genes or proteins as well as estimate their activation statuses using regulation information in pathway repositories. An automatically generated result document provides a detailed description of the query genes, biological processes and drug targets. Moksiskaan networks can be downloaded to Cytoscape for further analysis. To demonstrate the utility of Moksiskaan, we use gene microarray and clinical data from >200 glioblastoma multiforme primary tumor samples and translate the resulting set of 124 survival-associated genes to a network.

Availability and Implementation: Moksiskaan and user guide are freely available under GNU General Public License at http://csbi.ltdk.helsinki.fi/moksiskaan/

Contact:  Sampsa.Hautaniemi@Helsinki.FI

Supplementary information:  Supplementary data are available at Bioinformatics online.
The male reproductive strategy of a deep-sea squid: sperm allocation, continuous production, and long-term storage of spermatophores in Histioteuthis miranda
Authors: Hoving Hendrik Jan T. , Lipiński Marek R. , Dam Lammertjan
Published: May 2010

Hoving, H. J. T., Lipiński, M. R., and Dam, L. 2010. The male reproductive strategy of a deep-sea squid: sperm allocation, continuous production, and long-term storage of spermatophores in Histioteuthis miranda. – ICES Journal of Marine Science, 67: 1478–1486. Squid are semelparous organisms. Much of what we know about squid reproduction relates to females, because few studies have addressed males and, although males are similarly challenged by semelparity, it remains virtually unknown what tactics squid have evolved to allocate sperm to spermatophores. The male reproductive strategy of the deep-sea squid Histioteuthis miranda was examined by describing the male reproductive anatomy, which appears unique among cephalopods, and by quantifying spermatophore production and sperm allocation. The species produces and stores spermatophores over a considerable period of continuous somatic growth. Body size and spermatophore length (SpL) are positively correlated, and the size difference between spermatophores stored by a single individual was up to 270%. Individuals had between 136 and 2276 spermatophores inside their reproductive system, and spermatophores may be stored for as long as 4.5 months. The relationship between SpL and the mass of sperm per spermatophore was polynomial, demonstrating that larger spermatophores did not necessarily contain more sperm. The unique male morphology and the continuous production and long-term storage of spermatophores in H. miranda seem to allow the species to increase the window in which reproduction can take place, a strategy that may be valuable in the deep-sea environment.