bluuebunny/crossref_metadata_2025 huggingface dataset:
Facile, nanoresolution translation setup for the growth of organic crystal meta-nitroaniline by Bridgman technique
Authors: Jayaprakasan M. , Kannan V. , Ganesh R. Bairava , Ramasamy P.
Published: May 2006

A nanoresolution translation setup for Bridgman technique was designed and employed for the growth of organic crystal meta-nitroaniline using stepper motor. Ultrasmooth and vibration-free translation was accomplished in microstepping mode. Linear translation of 40nm per microstep has been achieved. A potential molecular organic crystal meta-nitroaniline of 18mm diameter and 80mm length has been successfully grown with good optical quality. Ultraviolet-visible-near-infrared spectra showed excellent transmission from 1100to520nm. Etching studies reveal lower defect density.
Global hybrid simulations of energetic particle effects on the n=1 mode in tokamaks: Internal kink and fishbone instability
Authors: Fu G. Y. , Park W. , Strauss H. R. , Breslau J. , Chen J. , Jardin S. , Sugiyama L. E.
Published: May 2006

Global hybrid simulations of energetic particle effects on the n=1 internal kink mode have been carried out for tokamaks. For the International Thermonuclear Experimental Reactor (ITER) [ITER Physics Basis Editors et al., Nucl. Fusion 39, 2137 (1999)], it is shown that alpha particle effects are stabilizing for the internal kink mode. However, the elongation of ITER reduces the stabilization effects significantly. Nonlinear simulations of the precessional drift fishbone instability for circular tokamak plasmas show that the mode saturates due to flattening of the particle distribution function near the resonance region. The mode frequency chirps down rapidly as the flattening region expands radially outward. Fluid nonlinearity reduces the saturation level.
Dynamics of large-scale magnetically rotating arc plasmas
Authors: Xia Weidong , Li Lincun , Zhao Yuhan , Ma Qiang , Du Baihe , Chen Quan , Cheng Liang
Published: May 2006

Arc channels tend to shrink mainly due to the fact that the plasma conductivity naturally increases with its temperature. In this letter, we report a method of generating a large area homogeneous arc plasma at atmospheric pressure. The plasma generator consists of an 80mm diameter graphite anode chamber and an 18mm diameter concentric graphite cathode. A solenoid coil is used to produce a magnetic field along the electrode axis. In the chamber, the arc plasma is observed in various configurations and temporally and spatially evolves from a contractive column to diffuse plasma cloud which fills the entire chamber cross section.
In situ probing of magnetic parameter variations of nickel zinc ferrites during microwave H heating
Authors: Peelamedu R. D. , Dube D. C. , Lanagan M. T. , Agrawal D.
Published: May 2006

Changes in magnetic parameters of nickel zinc ferrite (NZF) ceramics have been monitored in situ during microwave H heating using an indigenous technique developed in the laboratory. The technique utilizes the concept based on combining a small measurement signal with a high power-processing signal, which permits a study on materials heated either in an electric or in a magnetic field of a TM103 single mode cavity. Coupling and decoupling of these two signals are suggested by the use of a simple arrangement. Experimental results obtained on various compositions of NZF ceramics up to 1200°C are presented. The results indicate that the higher zinc end compositions of the ferrites demonstrate the phenomenon of decrystallization under the influence of microwave H.
Measurement of local reactive and resistive photoresponse of a superconducting microwave device
Authors: Zhuravel Alexander P. , Anlage Steven M. , Ustinov Alexey V.
Published: May 2006

We propose and demonstrate a spatial partition method for the high-frequency photoresponse of superconducting devices correlated with inductive and resistive changes in microwave impedance. Using a laser scanning microscope, we show that resistive photoresponse is mainly produced by local defects at microstrip edges and by intergrain weak links formed in the high-temperature superconducting material at the boundary between individual twin-domain blocks. These defects are known to initiate nonlinear high-frequency response.
Experimental demonstration of a long-period grating based on the sampling theorem
Authors: Kwon Min-Suk , Cho Young-Bo , Shin Sang-Yung
Published: May 2006

We demonstrate experimentally the feasibility of a long-period grating whose index change pattern is in the form of sampling a raised-cosine function. We call such a grating a long-period grating based on the sampling theorem (LPGST). The LPGST is thermo-optically induced by an array of electrodes with individual widths. The array period is equal to the sampling period of 100μm, and the period of the sampled function is 395μm. A fabricated polymer long-period waveguide grating using the LPGST has a desired resonance band in its transmission spectrum, which is generated by the periodicity of the sampled function.
Special mechanism for dislocation nucleation in nanomaterials
Authors: Gutkin M. Yu. , Ovid’ko I. A.
Published: May 2006

A special mechanism of dislocation nucleation in deformed nanocrystalline materials (NCMs) is suggested and theoretically described. The mechanism represents nonlocal homogeneous nucleation of a nanoscale loop of “noncrystallographic” partial dislocation whose Burgers vector magnitude continuously grows during the nucleation process. It is shown that the special mechanism can effectively produce nanoscale loops of lattice and grain boundary dislocations in NCMs deformed at high mechanical stresses.
Definitive number of atoms on demand: Controlling the number of atoms in a few-atom magneto-optical trap
Authors: Yoon Seokchan , Choi Youngwoon , Park Sangbum , Kim Jaisoon , Lee Jai-Hyung , An Kyungwon
Published: May 2006

A few Rb85 atoms were trapped in a micron-size magneto-optical trap with a high quadrupole magnetic-field gradient and the number of atoms was precisely controlled by suppressing stochastic loading and loss events via real-time feedback on the magnetic-field gradient. The measured occupation probability of a single atom was as high as 99%. Atoms up to five were also trapped with high occupation probabilities. The present technique could be used to make a deterministic atom source.
Deep trench etching combining aluminum thermomigration and electrochemical silicon dissolution
Authors: Gautier G. , Ventura L. , Jérisian R. , Kouassi S. , Leborgne C. , Morillon B. , Roy M.
Published: May 2006

A micromachining technique for silicon deep anisotropic etching and isolating porous silicon structures is developed. This original method combines aluminum thermomigration and silicon electrochemical etching. In this way, we have generated high aspect ratio trenches and porous silicon isolating regions as well, through the entire thickness of the wafer. In order to evaluate our method, we performed etching rate measurements varying the current density. A maximum value of 22μm∕min has been already measured. The interest of the method in terms of cost and structures diversity is also justified.
Magnetoresistance switch effect in a multiferroic Fe3O4∕BaTiO3 bilayer
Authors: Ziese M. , Bollero A. , Panagiotopoulos I. , Moutis N.
Published: May 2006

Multiferroic bilayers composed of a magnetite (Fe3O4) and a BaTiO3 layer show nonlinear current-voltage characteristics in current perpendicular to plane configuration. The magnetoresistance of the bilayers is strongly bias dependent and can be switched from negative at low bias to positive at large bias. It is shown that these effects do not arise from charge-carrier modulation in the magnetite layer by an electric field effect. Therefore both the nonlinear transport characteristics and the switchable magnetoresistance are attributed to interfacial transport phenomena.
Artificial control of optical gain polarization by stacking quantum dot layers
Authors: Kita T. , Tamura N. , Wada O. , Sugawara M. , Nakata Y. , Ebe H. , Arakawa Y.
Published: May 2006

Polarization insensitivity of InAs∕GaAs quantum dot (QD) optical amplifier has been demonstrated by controlling the dot shape. The height of the QD has been controlled by stacking closely InAs islands to form a columnar QD. Room-temperature polarized amplified spontaneous emission from the columnar QDs has been investigated by using variable stripe-length method. With increasing the aspect ratio, transverse-magnetic-mode-dominant optical gain has been achieved. We obtained almost polarization insensitive optical gain for QDs with seven stacking layers.
In situ x-ray diffraction study of the thermal expansion of the ordered arrays of silver nanowires embedded in anodic alumina membranes
Authors: Xu Xi Jin , Fei Guang Tao , Yu Wen Hui , Chen Li , De Zhang Li , Ju Xin , Hao Xiao Peng , Wang Bao Yi
Published: May 2006

Thermal expansion of as-prepared and annealed ordered arrays of silver nanowires embedded in anodic alumina membranes (AAMs) was studied by in situ x-ray diffraction measurement in the temperature range from 25to800°C. The axial thermal expansion coefficient (TEC) for the as-prepared nanowires is 6.35×10−9∕°C and 6.02×10−6∕°C below and above 650°C, respectively. However, the TEC of the annealed sample turns from 2.32×10−6∕°Cto12.06×10−6∕°C when the temperature is above 350°C. The collective effects of the intrinsic expansion, surface pressure, the limit effect of AAM, and the vacancies incorporated into the silver lattice were responsible for the thermal expansion.
Acoustic charge transport in a n-i-n three terminal device
Authors: Cecchini Marco , De Simoni Giorgio , Piazza Vincenzo , Beltram Fabio , Beere H. E. , Ritchie D. A.
Published: May 2006

We present an unconventional scheme for acoustic charge transport devices based on a n-i-n lateral junction as electron injector. We show that surface acoustic waves (SAWs) are able to pick up electrons from a current flowing through the n-i-n junction and steer them towards the Ohmic output contact. Acoustic charge transport was studied at various temperatures, as a function of injector current, voltage bias, and SAW power. The possibility to modulate the acoustoelectric current by means of lateral in-plane gates is also discussed. The main advantage of our approach relies on the possibility to drive the n-i-n injector by means of both voltage and current sources, thus allowing to sample and process voltage and current signals.
Addition of NH3 to Al3O3−
Authors: Wyrwas Richard B. , Jarrold Caroline Chick , Das Ujjal , Raghavachari Krishnan
Published: May 2006

Recent computational studies on the addition of ammonia (NH3) to the Al3O3− cluster anion [A. Guevara-Garcia, A. Martinez, and J. V. Ortiz, J. Chem. Phys. 122, 214309 (2005)] have motivated experimental and additional computational studies, reported here. Al3O3− is observed to react with a single NH3 molecule to form the Al3O3NH3− ion in mass spectrometric studies. This is in contrast to similarly performed studies with water, in which the Al3O5H4− product was highly favored. However, the anion PE spectrum of the ammoniated species is very similar to that of Al3O4H2−. The adiabatic electron affinity of Al3O3NH3 is determined to be 2.35(5)eV. Based on comparison between the spectra and calculated electron affinities, it appears that NH3 adds dissociatively to Al3O3−, suggesting that the time for the Al3O3−∙NH3 complex to either overcome or tunnel through the barrier to proton transfer (which is higher for NH3 than for water) is short relative to the time for collisional cooling in the experiment.
Mechanically flexible thin-film transistors that use ultrathin ribbons of silicon derived from bulk wafers
Authors: Mack S. , Meitl M. A. , Baca A. J. , Zhu Z.-T. , Rogers J. A.
Published: May 2006

This letter introduces a type of thin-film transistor that uses aligned arrays of thin (submicron) ribbons of single-crystal silicon created by lithographic patterning and anisotropic etching of bulk silicon (111) wafers. Devices that incorporate such ribbons printed onto thin plastic substrates show good electrical properties and mechanical flexibility. Effective device mobilities, as evaluated in the linear regime, were as high as 360cm2V−1s−1, and on/off ratios were >103. These results may represent important steps toward a low-cost approach to large-area, high-performance, mechanically flexible electronic systems for structural health monitors, sensors, displays, and other applications.
Experimental determination of the local geometry around In and In–C complexes in Si
Authors: d’Acapito F. , Shimizu Y. , Scalese S. , Italia M. , Alippi P. , Grasso S.
Published: May 2006

The electrical properties of dopants in Si are of primary importance for the realization of electronic devices. Indium represents a promising p-type dopant whose electrical properties are improved by codoping with C. From theoretical studies In and C are expected to pair in the Si matrix in order to lower the strain energy. In this contribution we provide the first direct experimental determination of the sites of In and In–C complexes in Si.
Fractional quasi-phase-matching by Fresnel birefringence
Authors: Haidar Riad
Published: May 2006

In order to reach the optical parametric oscillation in an isotropic semiconductor, it is of prime importance to enhance the nonlinear conversion efficiency per crystal length unity. In this letter, we describe the concept of fractional quasi-phase-matching which is theoretically shown to provide very high conversion yield, close to those of perfectly phase matched scenarios. The conceptual design in the case of second-harmonic generation is presented, along with predicted performances.
A unique strategy for mRNA cap methylation used by vesicular stomatitis virus
Authors: Li Jianrong , Wang Jennifer T. , Whelan Sean P. J.
Published: May 2006

Nonsegmented negative-sense (nsNS) RNA viruses typically replicate within the host cell cytoplasm and do not have access to the host mRNA capping machinery. These viruses have evolved a unique mechanism for mRNA cap formation in that the guanylyltransferase transfers GDP rather than GMP onto the 5′ end of the RNA. Working with vesicular stomatitis virus (VSV), a prototype nsNS RNA virus, we now provide genetic and biochemical evidence that its mRNA cap methylase activities are also unique. Using recombinant VSV, we determined the function in mRNA cap methylation of a predicted binding site in the polymerase for the methyl donor,
S
-adenosyl-
l
-methionine. We found that amino acid substitutions to this site disrupted methylation at the guanine-N-7 (G-N-7) position or at both the G-N-7 and ribose-2′-O (2′-O) positions of the mRNA cap. These studies provide genetic evidence that the two methylase activities share an
S
-adenosyl-
l
-methionine-binding site and show that, in contrast to other cap methylation reactions, methylation of the G-N-7 position is not required for 2′-O methylation. These findings suggest that VSV evolved an unusual strategy of mRNA cap methylation that may be shared by other nsNS RNA viruses.
Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor
Authors: Velicer Gregory J. , Raddatz Günter , Keller Heike , Deiss Silvia , Lanz Christa , Dinkelacker Iris , Schuster Stephan C.
Published: May 2006

Precise characterization of the mutation histories of evolutionary lineages is crucial for understanding the evolutionary process, yet mutation identification has been constrained by traditional techniques. We sought to identify all accumulated mutations in an experimentally evolved lineage of the cooperative bacterium
Myxococcus xanthus
, which constructs fruiting bodies by a process of social multicellular development in response to starvation. This lineage had undergone two major transitions in social phenotype: from an ancestral cooperator to a socially defective cheater, and from the cheater to a competitively dominant cooperator that re-evolved social and developmental proficiency. The 9.14-Mb genome of the evolved, dominant cooperator (strain “PX”) was sequenced to ≈19-fold coverage by using recent “sequencing-by-synthesis” technology and partially sequenced (≈45%) by using capillary technology. The resulting data revealed 15 single-nucleotide mutations relative to the laboratory ancestor of PX after the two phases of experimental evolution but no evidence of duplications, transpositions, or multiple-base deletions. No mutations were identified by capillary sequencing beyond those found by pyrosequencing, resulting in a high probability that all mutations were discovered. Seven errors in the reference strain previously sequenced by the Sanger approach were revealed, as were five mutational differences between two distinct laboratory stocks of the reference strain. A single mutation responsible for the restoration of development in strain PX was identified, whereas 14 mutations occurred during the prior phase of experimental evolution. These results provide insight into the genetic basis of two large adaptive transitions in a social bacterium.
Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms
Authors: Wagoner Jason A. , Baker Nathan A.
Published: May 2006

Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating the need for expensive sampling. Our previous work has demonstrated that Poisson-Boltzmann methods are capable of faithfully reproducing polar explicit solvent forces for dilute protein systems; however, the popular solvent-accessible surface area model was shown to be incapable of accurately describing nonpolar solvation forces at atomic-length scales. Therefore, alternate continuum methods are needed to reproduce nonpolar interactions at the atomic scale. In the present work, we address this issue by supplementing the solvent-accessible surface area model with additional volume and dispersion integral terms suggested by scaled particle models and Weeks–Chandler–Andersen theory, respectively. This more complete nonpolar implicit solvent model shows very good agreement with explicit solvent results and suggests that, although often overlooked, the inclusion of appropriate dispersion and volume terms are essential for an accurate implicit solvent description of atomic-scale nonpolar forces.
Dynamic fragility of oceanic coral reef ecosystems
Authors: Graham Nicholas A. J. , Wilson Shaun K. , Jennings Simon , Polunin Nicholas V. C. , Bijoux Jude P. , Robinson Jan
Published: May 2006

As one of the most diverse and productive ecosystems known, and one of the first ecosystems to exhibit major climate-warming impacts (coral bleaching), coral reefs have drawn much scientific attention to what may prove to be their Achilles heel, the thermal sensitivity of reef-building corals. Here we show that climate change-driven loss of live coral, and ultimately structural complexity, in the Seychelles results in local extinctions, substantial reductions in species richness, reduced taxonomic distinctness, and a loss of species within key functional groups of reef fish. The importance of deteriorating physical structure to these patterns demonstrates the longer-term impacts of bleaching on reefs and raises questions over the potential for recovery. We suggest that isolated reef systems may be more susceptible to climate change, despite escaping many of the stressors impacting continental reefs.
Effects of surface tethering on protein folding mechanisms
Authors: Friedel Miriam , Baumketner Andrij , Shea Joan-Emma
Published: May 2006

The folding mechanisms of proteins are increasingly being probed through single-molecule experiments in which the protein is immobilized on a surface. Nevertheless, a clear understanding of how the surface might affect folding, and whether or not it changes folding from its bulk behavior, is lacking. In this work, we use molecular dynamics simulations of a model β-barrel protein tethered to a surface to systematically investigate how the surface impacts folding. In the bulk, this protein folds in a three-state manner through a compact intermediate state, and its transition state (TS) has a well formed hydrophobic core. Upon tethering, we find that folding rates and stability are impacted differently by the surface, with dependencies on both the length and location of the tether. Significant changes in folding times are observed for tether points that do not alter the folding temperature. Tethering also locally enhances the formation of structure for residues proximal to the tether point. We find that neither the folding mechanism nor the TS of this protein are altered if the tether is in a fully structured or completely unstructured region of the TS. By contrast, tethering in a partially structured region of the TS leads to dramatic changes. For one such tether point, the intermediate present in bulk folding is eliminated, leading to a two-state folding process with a heterogeneous, highly unstructured TS ensemble. These results have implications for both the design of single-molecule experiments and biotechnological applications of tethered proteins.
Attachment of capsular polysaccharide to the cell wall of
Streptococcus pneumoniae
type 2 is required for invasive disease
Authors: Morona Judy K. , Morona Renato , Paton James C.
Published: May 2006

The capacity of
Streptococcus pneumoniae
to produce capsular polysaccharide (CPS) is essential for virulence. The CPS biosynthesis proteins CpsB, CpsC, and CpsD function to regulate CPS production via tyrosine phosphorylation of CpsD. This mechanism of regulating CPS production is important for enabling
S. pneumoniae
to cause invasive disease. Here, we identify mutations affecting the attachment of CPS to the cell wall. These mutations were located in
cpsC
, such that CpsC functioned independently from CpsD tyrosine phosphorylation. These mutants produced WT levels of CPS, but were unable to cause bacteremia in mice after intranasal challenge. This finding suggests that cell-wall attachment of CPS is essential for invasive pneumococcal disease; production of WT levels of CPS alone is not sufficient. We also show that
cpsB
mutants, which lack the phosphotyrosine-protein phosphatase, produced less CPS than the WT strain, but attached substantially more CPS to their cell wall. Thus, the phosphorylated form of CpsD promotes attachment of CPS to the cell wall.
Structural and functional recovery from early monocular deprivation in adult rats
Authors: Pizzorusso Tommaso , Medini Paolo , Landi Silvia , Baldini Sara , Berardi Nicoletta , Maffei Lamberto
Published: May 2006

Visual deficits caused by abnormal visual experience during development are hard to recover in adult animals. Removal of chondroitin sulfate proteoglycans from the mature extracellular matrix with chondroitinase ABC promotes plasticity in the adult visual cortex. We tested whether chondroitinase ABC treatment of adult rats facilitates anatomical, functional, and behavioral recovery from the effects of a period of monocular deprivation initiated during the critical period for monocular deprivation. We found that chondroitinase ABC treatment coupled with reverse lid-suturing causes a complete recovery of ocular dominance, visual acuity, and dendritic spine density in adult rats. Thus, manipulations of the extracellular matrix can be used to promote functional recovery in the adult cortex.
Processes of copy-number change in human DNA: The dynamics of α-globin gene deletion
Authors: Lam Kwan-Wood G. , Jeffreys Alec J.
Published: May 2006

Ectopic recombination between locally repeated DNA sequences is of fundamental importance in the evolution of gene families, generating copy-number variation in human DNA and often leading to pathological rearrangements. Despite its importance, little is known about the dynamics and processes of these unequal crossovers and the degree to which meiotic recombination plays a role in instability. We address this issue by using as a highly informative system the duplicated α-globin genes in which ectopic recombination can lead to gene deletions, often very prevalent in populations affected by malaria, as well as reduplications. Here we show that spontaneous deletions can be accessed directly in genomic DNA by using single-DNA-molecule methods. These deletions proved to be remarkably common in both blood and sperm. Somatic deletions arise by a strictly intrachromosomal pathway of homologous exchange that also operates in the germ line and can generate mutational mosaicism, whereas sperm deletions frequently involve recombinational interactions between homologous chromosomes that most likely occur at meiosis. Ectopic recombination frequencies show surprisingly little requirement for long, identical homology blocks shared by paralogous sequences, and exchanges can occur even between short regions of sequence identity. Finally, direct knowledge of germ-line deletion rates can give insights into the fitness of individuals with these α-globin gene deletions, providing a new approach to investigating historical levels of selection operating in human populations.
The AAA ATPase p97 links peptide
N
-glycanase to the endoplasmic reticulum-associated E3 ligase autocrine motility factor receptor
Authors: Li Guangtao , Zhao Gang , Zhou Xiaoke , Schindelin Hermann , Lennarz William J.
Published: May 2006

Mouse peptide
N
-glycanase (mPNGase) cleaves the
N
-glycan chain from misfolded glycoproteins and glycopeptides. Previously, several proteins were found to directly interact with mPNGase; among them, both mHR23B and mS4 were found to link mPNGase to the proteasome. In this study, we found that the cytoplasmic protein mp97 participates in the formation of a ternary complex containing mouse autocrine motility factor receptor (mAMFR), mp97, and mPNGase. This assemblage recruits the cytosolic mPNGase close to the endoplasmic reticulum (ER) membrane, where the retrotranslocation of misfolded glycoproteins is thought to occur. In addition to the ER membrane-associated E3 ligase mAMFR, a cytosolic protein mY33K, containing both UBA and UBX domains, was found to also directly interact with mp97. Thus, a complex containing five proteins, mAMFR, mY33K, mp97, mPNGase, and mHR23B, is formed in close proximity to the ER membrane and serves to couple the activities of retrotranslocation, ubiquitination, and deglycosylation and, thereby, route misfolded glycoproteins to the proteasome.
Efficient gene delivery to pancreatic islets with ultrasonic microbubble destruction technology
Authors: Chen Shuyuan , Ding Jia-huan , Bekeredjian Raffi , Yang Bing-zhi , Shohet Ralph V. , Johnston Stephen A. , Hohmeier Hans E. , Newgard Christopher B. , Grayburn Paul A.
Published: May 2006

This study describes a method of gene delivery to pancreatic islets of adult, living animals by ultrasound targeted microbubble destruction (UTMD). The technique involves incorporation of plasmids into the phospholipid shell of gas-filled microbubbles, which are then infused into rats and destroyed within the pancreatic microcirculation with ultrasound. Specific delivery of genes to islet beta cells by UTMD was achieved by using a plasmid containing a rat insulin 1 promoter (RIP), and reporter gene expression was regulated appropriately by glucose in animals that received a RIP–luciferase plasmid. To demonstrate biological efficacy, we used UTMD to deliver RIP–human insulin and RIP–hexokinase I plasmids to islets of adult rats. Delivery of the former plasmid resulted in clear increases in circulating human C-peptide and decreased blood glucose levels, whereas delivery of the latter plasmid resulted in a clear increase in hexokinase I protein expression in islets, increased insulin levels in blood, and decreased circulating glucose levels. We conclude that UTMD allows relatively noninvasive delivery of genes to pancreatic islets with an efficiency sufficient to modulate beta cell function in adult animals.
Anomalous levels of Cl
−
transporters in the hippocampal subiculum from temporal lobe epilepsy patients make GABA excitatory
Authors: Palma E. , Amici M. , Sobrero F. , Spinelli G. , Di Angelantonio S. , Ragozzino D. , Mascia A. , Scoppetta C. , Esposito V. , Miledi R. , Eusebi F.
Published: May 2006

The mRNA levels of NKCC1, an inwardly directed Na
+
, K
+
-2Cl
−
cotransporter that facilitates the accumulation of intracellular Cl
−
, and of KCC2, an outwardly directed K
+
-Cl
−
cotransporter that extrudes Cl
−
, were studied in surgically resected brain specimens from drug-resistant temporal lobe (TL) epilepsy (TLE) patients. Quantitative RT-PCR analyses of the mRNAs extracted from the human TLE-associated brain regions revealed an up-regulation of NKCC1 mRNA and a down-regulation of KCC2 mRNA in the hippocampal subiculum, compared with the hippocampus proper or the TL neocortex, suggesting an abnormal transcription of Cl
−
transporters in the TLE subiculum. In parallel experiments, cell membranes isolated from the same TLE-associated brain regions were injected into
Xenopus
oocytes that rapidly incorporated human GABA
A
receptors into their surface membrane. The GABA currents elicited in oocytes injected with membranes from the subiculum had a more depolarized reversal potential (
E
GABA
) compared with the hippocampus proper or the neocortex. The NKCC1 blocker bumetanide or a temperature decrease of 10°C shifted the GABA-current
E
GABA
more negative in oocytes injected with membranes from TLE hippocampal subiculum, matching the
E
GABA
of TL neocortex-injected oocytes. We conclude that the anomalous expression of both Cl
−
transporters, KCC1 and NKCC2, in TLE hippocampal subiculum probably causes altered Cl
−
transport in the “epileptic” neurons, as revealed in the microtransplanted
Xenopus
oocytes, and renders GABA aberrantly “exciting,” a feature that may contribute to the precipitation of epileptic seizures.
Foxp3
+
CD25
+
regulatory T cells specific for a neo-self-antigen develop at the double-positive thymic stage
Authors: Cabarrocas Julie , Cassan Cécile , Magnusson Fay , Piaggio Eliane , Mars Lennart , Derbinski Jens , Kyewski Bruno , Gross David-Alexandre , Salomon Benoit L. , Khazaie Khashayarsha , Saoudi Abdelhadi , Liblau Roland S.
Published: May 2006

Thymus-derived regulatory T cells (Tregs) expressing CD4, CD25, and the transcription factor Foxp3 play major roles in preventing autoimmunity. The Treg population is enriched in T cells expressing high-avidity self-reactive T cell receptors, and thymic epithelial cells expressing self-antigens (Ag) have been implicated in their induction and/or selection. However, the thymic selection events leading to Treg lineage commitment remain unclear. We followed the thymic development of self-Ag-specific Tregs in double-transgenic mice coexpressing a neo-self-Ag, hemagglutinin (HA) under the control of a neural tissue-specific promoter, and a transgenic class II-restricted T cell antigen receptor specific for HA111-119. Our data show that the promiscuous expression of the HA transgene in thymic epithelial cells is involved in the selective induction and/or expansion of HA-specific Foxp3
+
Treg thymic precursors as early as the double-positive stage.
WNK1 kinase isoform switch regulates renal potassium excretion
Authors: Wade James B. , Fang Liang , Liu Jie , Li Dimin , Yang Chao-Ling , Subramanya Arohan R. , Maouyo Djikolngar , Mason Amanda , Ellison David H. , Welling Paul A.
Published: May 2006

Members of the WNK family of serine/threonine kinases have been implicated as important modulators of salt homeostasis, regulating the balance between renal sodium reabsorption and potassium excretion. Gain-of-expression mutations in the WNK1 gene uncouple Na
+
and K
+
balance and cause a familial disorder of diminished renal potassium excretion, excessive sodium retention, and hypertension (pseudohypoaldosteronism type II or Gordon’s syndrome). Alternative splicing of the WNK1 gene produces a kidney-specific short form of WNK1 (KS-WNK1) and a more ubiquitous long form (L-WNK1), but it is not clear how either of these isoforms influence renal potassium excretion. Here we demonstrate that KS-WNK1 and L-WNK1 converge in a pathway to regulate the renal outer-medullary K
+
channel, Kir1.1. Reconstitution studies in
Xenopus
oocytes reveal that L-WNK1 significantly inhibits Kir1.1 by reducing cell surface localization of the channel. A catalytically inactive L-WNK1 mutant has no inhibitory effect on Kir1.1, indicating that channel inhibition depends on kinase activity. KS-WNK1, lacking an intact kinase domain, does not directly alter Kir1.1. Instead, KS-WNK1 negatively regulates L-WNK1 to release Kir1.1 from inhibition. Acute dietary potassium loading increases the relative abundance of KS-WNK1 to L-WNK1 transcript and protein in the kidney, indicating that physiologic up-regulation of Kir1.1 activity involves a WNK1 isoform switch and KS-WNK1-mediated release from L-WNK1 inhibition. Thus, these observations provide evidence for the physiological regulation of Na
+
and K
+
balance by a kinase isoform switch mechanism.
Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset
Authors: Liu X. , Sivaganesan S. , Yeung K. Y. , Guo J. , Bumgarner R. E. , Medvedovic Mario
Published: May 2006

Motivation: Identifying groups of co-regulated genes by monitoring their expression over various experimental conditions is complicated by the fact that such co-regulation is condition-specific. Ignoring the context-specific nature of co-regulation significantly reduces the ability of clustering procedures to detect co-expressed genes due to additional ‘noise’ introduced by non-informative measurements.

Results: We have developed a novel Bayesian hierarchical model and corresponding computational algorithms for clustering gene expression profiles across diverse experimental conditions and studies that accounts for context-specificity of gene expression patterns. The model is based on the Bayesian infinite mixtures framework and does not require a priori specification of the number of clusters. We demonstrate that explicit modeling of context-specificity results in increased accuracy of the cluster analysis by examining the specificity and sensitivity of clusters in microarray data. We also demonstrate that probabilities of co-expression derived from the posterior distribution of clusterings are valid estimates of statistical significance of created clusters.

Availability: The open-source package gimm is available at

Contact: Mario.Medvedovic@uc.edu

Supplementary information:
Independent component analysis-based penalized discriminant method for tumor classification using gene expression data
Authors: Huang De-Shuang , Zheng Chun-Hou
Published: May 2006

Motivation: Microarrays are capable of determining the expression levels of thousands of genes simultaneously. One important application of gene expression data is classification of samples into categories. In combination with classification methods, this technology can be useful to support clinical management decisions for individual patients, e.g. in oncology. Standard statistic methodologies in classification or prediction do not work well when the number of variables p (genes) far too exceeds the number of samples n. So, modification of existing statistical methodologies or development of new methodologies is needed for the analysis of microarray data.

Results: This paper proposes a new method for tumor classification using gene expression data. In this method, we first employ independent component analysis to model the gene expression data, then apply optimal scoring algorithm to classify them. Further speaking, this approach can first make full use of the high-order statistical information contained in the gene expression data. Second, this approach also employs regularized regression models to handle the situation of large numbers of correlated predictor variables. Finally, the predictive models are developed for classifying tumors based on the entire gene expression profile. To show the validity of the proposed method, we apply it to classify four DNA microarray datasets involving various human normal and tumor tissue samples. The experimental results show that the method is efficient and feasible.

Availability: Matlab scripts are available on request.

Contact:  dshuang@iim.ac.cn
A model diagram layout extension for SBML
Authors: Gauges Ralph , Rost Ursula , Sahle Sven , Wegner Katja
Published: May 2006

Motivation: Since the knowledge about processes in living cells is increasing, modelling and simulation techniques are used to get new insights into these complex processes. During the last few years, the SBML file format has gained in popularity and support as a means of exchanging model data between the different modelling and simulation tools. In addition to specifying the model as a set of equations, many modern modelling tools allow the user to create and to interact with the model in the form of a reaction graph. Unfortunately, the SBML file format does not provide for the storage of this graph data along with the mathematical description of the model.

Results: Therefore, we developed an extension to the SBML file format that makes it possible to store such layout information which describes position and size of objects in the graphical representation.

Availability: The complete specification can be found on ( (SBML Layout Extension documentation, 2005). Additionally, a complete implementation exists as part of libSBML (2006, ).

Contact:  Ralph.Gauges@eml-r.villa-bosch.de

Supplementary information: Supplementary data are available on Bioinformatics online.
Male dominance determines female egg laying rate in crickets
Authors: Bretman Amanda , Rodríguez-Muñoz Rolando , Tregenza Tom
Published: May 2006

A key prediction of theories of differential allocation and sexual conflict is that male phenotype will affect resource allocation by females. Females may adaptively increase investment in offspring when mated to high quality males to enhance the quality of their offspring, or males may vary in their ability to manipulate female investment post-mating. Males are known to be able to influence female reproductive investment, but the male traits underlying this ability have been little studied in taxa other than birds. We investigated the relationship between male dominance and female oviposition rate in two separate experiments using the field cricket,
Gryllus bimaculatus
. In both experiments, females mated to more dominant (but not larger) males laid more eggs. This reveals that either females allocate more effort to reproduction after mating with a dominant male or that dominance status is associated with male ability to manipulate their mates. This is the first evidence that dominance, rather than male attractiveness, has a post-copulatory effect on reproductive investment by females.
Neimark–Sacker bifurcations in a non-standard numerical scheme for a class of positivity-preserving ODEs
Authors: Alexander Murray E , Summers Arthur R , Moghadas Seyed M
Published: May 2006

We discuss the nature of Neimark–Sacker bifurcations occurring in a non-standard numerical scheme, for a class of positivity-preserving systems of ordinary differential equations (ODEs) which undergoes a corresponding Hopf bifurcation. Extending previous work (Alexander & Moghadas 2005aElectron. J. Diff. Eqn. Conf.12, 9–19), it is shown that the type of Neimark–Sacker bifurcation (supercritical or subcritical) may be affected by the integration time-step. The general form of the scheme in the vicinity of a fixed point is given, from which the expression for the first Lyapunov coefficient for two-dimensional systems, valid for arbitrary time-step, is explicitly derived. The analysis shows that this coefficient undergoes anshift with respect to the corresponding coefficient of the original ODE. This could lead to a type of bifurcation which differs from the corresponding Hopf bifurcation in the ODE, due to changes in the sign of the first Lyapunov coefficient asvaries. This is especially problematic in the vicinity of certain types of degenerate Hopf bifurcation, at which this coefficient may vanish. We also present a general method to eliminate the possibleshift in the bifurcation parameter of the scheme; however, the first Lyapunov coefficient may still be subjected to anshift, leading to a possibly erroneous type of bifurcation. Examples are given to illustrate the theoretical results of the paper with applications to mathematical biology.
Dynamics of an axisymmetric body spinning on a horizontal surface. IV. Stability of steady spin states and the ‘rising egg’ phenomenon for convex axisymmetric bodies
Authors: Branicki M , Shimomura Y
Published: May 2006

Following part III in the series, the linear stability of previously identified steady states is analysed for a general convex axisymmetric body spinning on the horizontal plane in order to determine spin orientations leading to the ‘rising egg’ phenomenon. The viscous friction law is assumed between the body and the plane, which is linear in the velocity of the point of contact and allows for analytical treatment of the problem. In the analysis, the emphasis is put on the relationship between the geometrical structure of interconnected structures of non-isolated fixed-points, representing the steady-spin states in the system phase space, and their stability properties. It is shown that the rising egg phenomenon, discussed initially in part I for the flip-symmetric geometry of a uniform spheroid, occurs in a much broader class of spinning axisymmetric bodies. It is also shown that for some geometries, the steady spin configurations of minimum potential energy are always stable, contrary to the flip-symmetric case, so that even a rapid spin does not cause the centre-of-mass to rise. Particular attention is focused on a spheroid with displaced centre-of-mass and the tippe-top.
The
N
-vortex problem on a rotating sphere. II. Heterogeneous Platonic solid equilibria
Authors: Jamaloodeen Mohamed I , Newton Paul K
Published: May 2006

We describe a new method of constructing point vortex equilibria on a sphere made-up of
N
vortices with different strengths. Such equilibria, called
heterogeneous equilibria
, are obtained for the five Platonic solid configurations, hence for

. The method is based on calculating a basis set for the nullspace of a matrix obtained by enforcing the necessary and sufficient condition that the mutual distances between each pair of vortices remain constant. By symmetries inherent in the Platonic solid configurations, this matrix is reduced for each case and we call the dimension of the nullspace the
degree of heterogeneity
of the structure. For the tetrahedron (
N
=4) and octahedron (
N
=6), the degree of heterogeneity is 4 and 6, respectively, hence we are free to choose each of the vortex strengths independently. For the cube (
N
=8), the degree of heterogeneity is 5, for the icosahedron (
N
=12) it is 7, while for the dodecahedron (
N
=20) it is 4. Thus, the entire set of equilibria based on the Platonic solid configurations is obtained, including substructures associated with each configuration constructed by taking different linear combinations of the basis elements.
The influence of fibril organization on the mechanical behaviour of articular cartilage
Authors: Lei Fulin , Szeri Andras Z
Published: May 2006

The paper presents a three-dimensional microstructural model that was developed to study both equilibrium and time-dependent mechanical behaviour of articular cartilage. The model is based on consolidation theory and makes use of the structure and the mechanical properties of tissue components. Fibrils provide tensile stiffness in this model, whose geometric orientation is described by distribution functions that can be changed freely, making the model applicable to any particular fibril configuration. The model is capable of quantitatively predicting equilibrium properties of the different tests using a single set of model parameters, and explains the anomaly that small compressive modulus and small Poisson's ratio are observed in unconfined compression while tension is governed by large tensile modulus and large Poisson's ratio.
Demographic structure and pathogen dynamics on the network of livestock movements in Great Britain
Authors: Kao R.R , Danon L , Green D.M , Kiss I.Z
Published: May 2006

Using a novel interpretation of dynamic networks, we analyse the network of livestock movements in Great Britain in order to determine the risk of a large epidemic of foot-and-mouth disease (FMD). This network is exceptionally well characterized, as there are legal requirements that the date, source, destination and number of animals be recorded and held on central databases. We identify a percolation threshold in the structure of the livestock network, indicating that, while there is little possibility of a national epidemic of FMD in winter when the catastrophic 2001 epidemic began, there remains a risk in late summer or early autumn. These predictions are corroborated by a non-parametric simulation in which the movements of livestock in 2003 and 2004 are replayed as they occurred. Despite the risk, we show that the network displays small-world properties which can be exploited to target surveillance and control and drastically reduce this risk.
A basal ceratopsian with transitional features from the Late Jurassic of northwestern China
Authors: Xu Xing , Forster Catherine A , Clark James M , Mo Jinyou
Published: May 2006

Although the Ceratopsia and Pachycephalosauria, two major ornithischian groups, are united as the Marginocephalia, few synapomorphies have been identified due to their highly specialized body-plans. Several studies have linked the Heterodontosauridae with either the Ceratopsia or Marginocephalia, but evidence for these relationships is weak, leading most recent studies to consider the Heterodontosauridae as the basal member of another major ornithischian radiation, the Ornithopoda. Here, we report on a new basal ceratopsian dinosaur,Yinlong downsigen. et. sp. nov., from the Late Jurassic upper part of the Shishugou Formation of Xinjiang, China. This new ceratopsian displays a series of features transitional between more derived ceratopsians and other ornithischians, shares numerous derived similarities with both the heterodontosaurids and pachycephalosaurians and provides strong evidence supporting a monophyletic Marginocephalia and its close relationship to the Heterodontosauridae. Character distributions along the marginocephalian lineage reveal that, compared to the bipedal Pachycephalosauria, which retained a primitive post-cranial body-plan, the dominantly quadrupedal ceratopsians lost many marginocephalian features and evolved their own characters early in their evolution.
Signal content of red facial coloration in female mandrills (
Mandrillus sphinx
)
Authors: Setchell Joanna M , Jean Wickings E , Knapp Leslie A
Published: May 2006

Studies of secondary sexual ornamentation and its maintenance by sexual selection tend to focus on males; however, females may also possess showy ornaments. For example, female mandrills possess facial coloration that ranges from black to bright pink. We used fortnightly photographs of 52 semi-free-ranging females aged above 3 years over 19 months to evaluate whether colour conveys information concerning female competitive ability, reproductive quality, age or reproductive status. Colour was not related to female rank or quality (body mass index, age at first birth or mean inter-birth interval); however, colour did increase significantly with age and primiparous females were darker than multiparous females. Colour may therefore signal reproductive quality, as younger females are less fertile and produce smaller offspring. Colour was brighter during the follicular phase than during the luteal phase, suggesting that it may signal fertility. Colour also varied across gestation and peaked at four and eight weeks post-parturition, suggesting that it may signal approaching parturition and lactation. Future studies should examine the relationship between colour and the menstrual cycle in more detail, the hormonal basis of female colour, and determine experimentally whether mandrills of both sexes attend to differences in colour between and within females.