bluuebunny/crossref_metadata_2025 huggingface dataset:
Distributed fiber‐optic temperature sensing for hydrologic systems
Authors: Selker John S. , Thévenaz Luc , Huwald Hendrik , Mallet Alfred , Luxemburg Wim , van de Giesen Nick , Stejskal Martin , Zeman Josef , Westhoff Martijn , Parlange Marc B.
Published: December 2006

Instruments for distributed fiber‐optic measurement of temperature are now available with temperature resolution of 0.01°C and spatial resolution of 1 m with temporal resolution of fractions of a minute along standard fiber‐optic cables used for communication with lengths of up to 30,000 m. We discuss the spectrum of fiber‐optic tools that may be employed to make these measurements, illuminating the potential and limitations of these methods in hydrologic science. There are trade‐offs between precision in temperature, temporal resolution, and spatial resolution, following the square root of the number of measurements made; thus brief, short measurements are less precise than measurements taken over longer spans in time and space. Five illustrative applications demonstrate configurations where the distributed temperature sensing (DTS) approach could be used: (1) lake bottom temperatures using existing communication cables, (2) temperature profile with depth in a 1400 m deep decommissioned mine shaft, (3) air‐snow interface temperature profile above a snow‐covered glacier, (4) air‐water interfacial temperature in a lake, and (5) temperature distribution along a first‐order stream. In examples 3 and 4 it is shown that by winding the fiber around a cylinder, vertical spatial resolution of millimeters can be achieved. These tools may be of exceptional utility in observing a broad range of hydrologic processes, including evaporation, infiltration, limnology, and the local and overall energy budget spanning scales from 0.003 to 30,000 m. This range of scales corresponds well with many of the areas of greatest opportunity for discovery in hydrologic science.
The interplay between host and viral factors in shaping the outcome of cytomegalovirus infection
Authors: Scalzo Anthony A , Corbett Alexandra J , Rawlinson William D , Scott Gillian M , Degli‐Esposti Mariapia A
Published: December 2006

Cytomegalovirus (CMV) remains a major human pathogen causing significant morbidity and mortality in immunosuppressed or immunoimmature individuals. Although significant advances have been made in dissecting out certain features of the host response to human CMV (HCMV) infection, the strict species specificity of CMVs means that most aspects of antiviral immunity are best assessed in animal models. The mouse model of murine CMV (MCMV) infection is an important tool for analysis of in vivo features of host–virus interactions and responses to antiviral drugs that are difficult to assess in humans. Important studies of the contribution of host resistance genes to infection outcome, interplays between innate and adaptive host immune responses, the contribution of virus immune evasion genes and genetic variation in these genes to the establishment of persistence and in vivo studies of resistance to antiviral drugs have benefited from the well‐developed MCMV model. In this review, we discuss recent advances in the immunobiology of host–CMV interactions that provide intriguing insights into the complex interplay between host and virus that ultimately facilitates viral persistence. We also discuss recent studies of genetic responses to antiviral therapy, particularly changes in DNA polymerase and protein kinase genes of MCMV and HCMV.
Acutely dysregulated, chronically disabled by the enemy within: T‐cell responses to HIV‐1 infection
Authors: Munier M L , Kelleher A D
Published: December 2006

Human immunodeficiency virus (HIV) infection causes chronic progressive immunodeficiency and immune dysregulaton. Although simple depletion of the major target of HIV infection, the CD4+ T cell, can explain much of the immunosuppression seen, there are multiple other factors contributing to the immune dysregulation. CD4+ T‐cell depletion induces a range of homeostatic mechanisms that contribute to immune activation and cell turnover, providing a milieu conducive to further viral replication and cell destruction, resulting in functional defects in various lymphoid organs. These changes are progressive and in turn compromise the homeostatic processes. Further, the infection, like any other viral infection, provokes an active immune response consisting of both CD4+ and CD8+ T‐cell responses. Both appear compromised, displaying aberrant memory cell production. While some of these defects result from viral variation and the chronicity of antigen presentation, other defects of memory cell production appear very early during the primary immune response limiting the viral specific T‐cell responses from the outset. This, combined with the ability of the virus to escape any successful immune responses, results in an attenuated immune response that eventually becomes exhausted, characterized by progressive deficits in T‐cell repertoire. Furthermore, negative regulatory mechanisms that normally control the immune response may be aberrantly invoked, perhaps directly by the virus, further compromising the efficacy of the immune response. Rational design of effective immunotherapies depends on a clear understanding of the processes compromising the immune response to HIV.
Microfluidic flow control on charged phospholipidpolymer interface
Authors: Xu Yan , Takai Madoka , Konno Tomohiro , Ishihara Kazuhiko
Published: December 2006

EOF was controlled in magnitude on a type of charged interface constructed by phospholipid polymers containing 2-methacryloyloxyethyl phosphorylcholine (MPC) units with a high tendency to suppress non-specific protein adsorption.
Woodward-Hoffmann rules in density functional theory: Initial hardness response
Authors: De Proft Frank , Ayers Paul W. , Fias Stijn , Geerlings Paul
Published: December 2006

The Woodward-Hoffmann rules for pericyclic reactions, a fundamental set of reactivity rules in organic chemistry, are formulated in the language of conceptual density functional theory (DFT). DFT provides an elegant framework to introduce chemical concepts and principles in a quantitative manner, partly because it is formulated without explicit reference to a wave function, on whose symmetry properties the Woodward-Hoffmann [J. Am. Chem. Soc. 87, 395 (1965)] rules are based. We have studied the initial chemical hardness response using a model reaction profile for two prototypical pericyclic reactions, the Diels-Alder cycloaddition of 1,3-butadiene to ethylene and the addition of ethylene to ethylene, both in the singlet ground state and in the first triplet excited state. For the reaction that is thermally allowed but photochemically forbidden, the initial hardness response is positive along the singlet reaction profile. (By contrast, for the triplet reaction profile, a negative hardness response is observed.) For the photochemically allowed, thermally forbidden reaction, the behavior of the chemical hardness along the initial stages of the singlet and triplet reaction profiles is reversed. This constitutes a first step in showing that chemical concepts from DFT can be invoked to explain results that would otherwise require invoking the phase of the wave function.
Thermoelectric power in very thin film thermocouples: Quantum size effects
Authors: Cattani M. , Salvadori M. C. , Vaz A. R. , Teixeira F. S. , Brown I. G.
Published: December 2006

The thermoelectric power SF of thin film thermocouples is related to the bulk thermopower Sbulk by ΔSF(t)=Sbulk−SF as a linear function of 1∕t when t⪢ℓ, where ℓ is the electron mean free path and t the film thickness. For these conditions quantum size effects (QSEs) are negligible. However, when t<ℓ QSEs become relevant. In recent work we have shown that for Pt∕Au thermocouples with film thickness t<ℓPt≈10nm, ΔSF(t)=0.194+26.7(1∕t)−93.6(1∕t)2+112.0(1∕t)3. Here we show that this nonlinear 1∕t behavior is due to QSE.
General continuum boundary conditions for miscible binary fluids from molecular dynamics simulations
Authors: Denniston Colin , Robbins Mark O.
Published: December 2006

Molecular dynamics simulations are used to explore the flow behavior and diffusion of miscible fluids near solid surfaces. The solid produces deviations from bulk fluid behavior that decay over a distance of the order of the fluid correlation length. Atomistic results are mapped onto two types of continuum model: Mesoscopic models that follow this decay and conventional sharp interface boundary conditions for the stress and velocity. The atomistic results, and mesoscopic models derived from them, are consistent with the conventional Marangoni stress boundary condition. However, there are deviations from the conventional Navier boundary condition that states that the slip velocity between wall and fluid is proportional to the strain rate. A general slip boundary condition is derived from the mesoscopic model that contains additional terms associated with the Marangoni stress and diffusion, and is shown to describe the atomistic simulations. The additional terms lead to strong flows when there is a concentration gradient. The potential for using this effect to make a nanomotor or pump is evaluated.
Pauli-Hamiltonian in the presence of minimal lengths
Authors: Nouicer Khireddine
Published: December 2006

We construct the Pauli-Hamiltonian on a space where the position and momentum operators obey generalized commutation relations leading to the appearance of a minimal length. Using the momentum space representation we determine exactly the energy eigenvalues and eigenfunctions for a charged particle of spin half moving under the action of a constant magnetic field. The thermal properties of the system in the regime of high temperatures are also investigated, showing a magnetic behavior in terms of the minimal length.
Two-state switching and dynamics in quantum dot two-section lasers
Authors: Markus A. , Rossetti M. , Calligari V. , Chek-Al-Kar D. , Chen J. X. , Fiore A. , Scollo R.
Published: December 2006

The electrical control of the lasing wavelength in two-section quantum dot lasers is investigated. By changing the optical loss in the absorber section, the control of the ground-state (GS) and excited-state (ES) lasing thresholds and output powers is achieved. Additionally, a complex self-pulsation dynamics with simultaneous oscillations of the GS and ES intensities is observed. The experimental results are well explained in the framework of a rate equation model.
Deoxyribonucleic acid hybridization acceleration by photovoltaic effect
Authors: Chen Chii-Chang , Ku Wei-Chi , Chiu Sung-Kay , Tzeng Chi-Meng
Published: December 2006

In this study, the authors show a method of enhancing the deoxyribonucleic acid (DNA) hybridization efficiency by exploiting the photovoltaic effect. The arrayed microchip is fabricated in a semiconductor wafer coated with metal thin films to immobilize the probe DNA. Hybridization between immobilized probe DNAs and fluorescent-labeled target DNA is performed under illumination by a laser. The photovoltaic effect induces positive charges on the surface of the microchip to attract negatively charged target DNAs toward the hybridization sites, increasing the hybridization rate by up to two orders of magnitude. The experimental results reveal that the method represents a cutting-edge solution to the problem of the time consuming microchip process.
DNA release from cationic liposome/DNA complexes by anionic lipids
Authors: Caracciolo Giulio , Pozzi Daniela , Caminiti Ruggero , Marchini Cristina , Montani Maura , Amici Augusto , Amenitsch Heinz
Published: December 2006

The authors found that recently developed multicomponent cationic liposome DNA complexes (lipoplexes) exhibit higher transfection efficiency with respect to usually employed binary lipoplexes in NIH 3T3 and A17 cell lines. Interaction of lipoplexes with anionic liposomes (model of cellular membranes) was investigated by synchrotron small angle x-ray diffraction. The authors used one-dimensional DNA packing density to estimate the molar fraction of DNA released from lipoplexes by anionic lipids.
Ge
∕
Hf
N
x
diffusion barrier for Cu metallization on Si
Authors: Rawal S. , Norton D. P. , Kim KeeChan , Anderson T. J. , McElwee-White L.
Published: December 2006

The properties of Ge∕HfNx have been investigated relative to its use as a diffusion barrier for Cu metallization. The Ge∕HfNx bilayer was grown on p-Si (001) substrates by reactive sputtering, followed by in situ deposition of Cu. Individually annealed films at different temperatures (400–700°C, 1h) were characterized for evidence of Cu transport through the barrier bilayer to the Si substrate. The annealed structures were characterized by x-ray diffraction, energy-dispersive spectroscopy, and high-resolution transmission electron microscopy. The results indicate superior diffusion barrier properties of Ge∕HfNx for Cu metallization on Si compared to that for HfNx (7nm).
Structure and photoluminescence properties of evaporated GeOx∕SiO2 multilayers
Authors: Ardyanian M. , Rinnert H. , Vergnat M.
Published: December 2006

Amorphous GeOx∕SiO2 multilayers were prepared by successive evaporations of GeO2 and SiO2 powders onto substrates maintained at 100°C. The evolution of the structure was investigated by x-ray reflectometry, transmission electron microscopy, infrared-absorption spectrometry and Raman spectrometry for annealing temperatures less than 800°C. These experiments allowed us to follow the phase decomposition of the GeOx alloy and to observe the appearance of amorphous and crystallized germanium aggregates. The evolution of the photoluminescence in the range of 0.8–2.2eV was correlated to the structure of the films.
Relevance of surface roughness to tungsten sputtering and carbon implantation
Authors: Bizyukov Ivan , Krieger Karl , Azarenkov Nikolay , Toussaint Udo v.
Published: December 2006

Tungsten sputtering and carbon layer growth by carbon ion bombardment has been investigated by experiments with thin W layers. Preparation of tungsten layers by magnetron deposition allows one to control the surface roughness by choosing appropriate substrates. The fluence dependent elemental composition of the bombarded surface has been studied in situ with ion beam analysis allowing separate measurements of the areal densities of tungsten and carbon atoms. In contrast to weight-loss measurements, this approach is much less affected by nonuniformities of the incident flux and therefore allows one to determine the dependency of the principal physics processes on input parameters with much higher accuracy. After bombardment, ex situ scanning electron microscopy has been used for the qualitative understanding of the evolution of the surface topography with increasing fluence. The experiments clearly show the influence of surface roughness, leading to increased tungsten sputter yields and strongly reduced carbon implantation rates. Comparison of the experimental results with simulations by the Monte Carlo code TRIDYN has verified the validity of the kinematic description for the interaction of carbon ions with mixed carbon-tungsten surfaces. At the same time, chemical effects, such as carbide formation, can be neglected in comparison with the contribution of surface roughness to the dynamics of sputtering and implantation.
Red to near-infrared electrophosphorescence from a platinum complex coordinated with 8-hydroxyquinoline
Authors: Yang Chang-Jian , Yi Chun , Xu Min , Wang Jiang-Huai , Liu Yan-Zhu , Gao Xi-Cun , Fu Ji-Wu
Published: December 2006

A platinum complex coordinated with 2-phenylpyridine and 8-hydroxyquinoline [(phpy)Pt(q)] was synthesized. When (phpy)Pt(q) was used as a guest emitting material in the electrophosphorescent devices, the emission starts at ∼600nm extending to the near-infrared region. The device with 40nm emitting layer of (phpy)Pt(q) doped into N, N′-dicarbazolyl-4, 4′-biphenyl (CBP) exhibits higher luminance and efficiency compared to the device with a layer of 20nm (phpy)Pt(q) doped into CBP combined with a layer of 20nm (phpy)Pt(q) doped into aluminum 8-hydroxyquinoline (Alq3) or a layer of 40nm (phpy)Pt(q) doped into Alq3.
Engineering electron and hole tunneling with asymmetric InAs quantum dot molecules
Authors: Bracker A. S. , Scheibner M. , Doty M. F. , Stinaff E. A. , Ponomarev I. V. , Kim J. C. , Whitman L. J. , Reinecke T. L. , Gammon D.
Published: December 2006

Most self-assembled quantum dot molecules are intrinsically asymmetric with inequivalent dots resulting from imperfect control of crystal growth. The authors have grown vertically aligned pairs of InAs∕GaAs quantum dots by molecular beam epitaxy, introducing intentional asymmetry that limits the influence of intrinsic growth fluctuations and allows selective tunneling of electrons or holes. They present a systemic investigation of tunneling energies over a wide range of interdot barrier thickness. The concepts discussed here provide an important tool for the systematic design and characterization of more complicated quantum dot nanostructures.
Photonuclear fission with quasimonoenergetic electron beams from laser wakefields
Authors: Reed S. A. , Chvykov V. , Kalintchenko G. , Matsuoka T. , Rousseau P. , Yanovsky V. , Vane C. R. , Beene J. R. , Stracener D. , Schultz D. R. , Maksimchuk A.
Published: December 2006

Recent advancements in laser wakefield accelerators have resulted in the generation of low divergence, hundred MeV, quasimonoenergetic electron beams. The bremsstrahlung produced by these highly energetic electrons in heavy converters includes a large number of MeV γ rays that have been utilized to induce photofission in natural uranium. Analysis of the measured delayed γ emission demonstrates production of greater than 3×105 fission events per joule of laser energy, which is more than an order of magnitude greater than that previously achieved. Monte Carlo simulations model the generated bremsstrahlung spectrum and compare photofission yields as a function of target depth and incident electron energy.
Threading dislocation reduction by SiGeC domains in SiGe∕SiGeC heterostructure: Role of pure edge dislocations
Authors: Wong L. H. , Ferraris C. , Wong C. C. , Liu J. P.
Published: December 2006

The authors previously reported an unusual phenomenon of strain relaxation accompanied by a reduction in threading dislocation density (TDD) on a Si0.77Ge0.23 layer grown on top of alternating layers of Si0.77Ge0.23∕Si0.76Ge0.23C0.01 [Appl. Phys. Lett. 88, 041915 (2006)]. In this letter, the mechanism by which SiGeC domains, formed during annealing at 1000°C, assist in TDD annihilation process is further investigated. A g∙b analysis of transmission electron microscope images showed the formation of pure edge dislocations from the reaction of two 60° misfit dislocations, which glide and/or slip with the assistance of the localized interfacial strain of the SiGeC domains. TDD reduction in this structure is thus due to the annihilation of threading dislocation arms during misfit dislocation combination.
Estimation of minimum electron dose necessary to resolve molecular structure of deoxyribonucleic acid by phase transmission electron microscopy
Authors: Nomaguchi Tsunenori , Kimura Yoshihide , Takai Yoshizo
Published: December 2006

The minimum electron dose that is necessary to resolve the molecular structure of deoxyribonucleic acid (DNA) was estimated based on experimental measurements of information limits and simulated DNA images, considering conditions of a low electron dose. From these results, a dose of ∼400e∕Å2 was found to be necessary to achieve observation of DNA on a molecular scale under the present experimental setup. A DNA molecule was observed by a phase reconstruction method using through-focus images under the limited electron dose. In the reconstructed images, the helical structure and the intervals of the base pairs of DNA were partially resolved.
CdSe quantum dot microdisk laser
Authors: Renner Johannes , Worschech Lukas , Forchel Alfred , Mahapatra Suddhasatta , Brunner Karl
Published: December 2006

Laser emission from optically pumped CdSe quantum dots embedded in a ZnSe∕ZnMgSSe microdisk was observed at low temperatures. Laser thresholds below 20μW and spontaneous emission coupling β-factors exceeding 0.8 were determined. For different modes of the same microdisk cavity the laser threshold increases with higher mode energy, which the authors associate to a better coupling of larger quantum dots with the optical mode. Also the linewidth and energy shift of lasing modes as a function of pump power were analyzed.
Time evolution of the second-order nonlinearity layer in thermally poled optical fiber
Authors: An Honglin , Fleming Simon
Published: December 2006

Time evolution of the second-order nonlinearity induced in a single-hole D-shaped fiber thermally poled at 3.5kV and 320°C has been investigated with second-harmonic microscopy. It was found that the nonlinear layer moved towards the cathode with increasing poling time until it finally reached the cathode surface. The magnitude of the nonlinear coefficient first increased, saturated at ∼0.32pm∕V between 5 and 20min after poling, and then began to decrease for longer poling time. The nonlinearity remained large even when the nonlinearity layer reached the centerline between the two electrodes. In samples poled long enough (>45min), apart from the main nonlinearity layer at the cathode, weak second-order nonlinearity was also induced at the core-cladding interface sections that were nearly parallel to the poling direction.
A robust measure of food web intervality
Authors: Stouffer Daniel B. , Camacho Juan , Amaral Luís A. Nunes
Published: December 2006

Intervality of a food web is related to the number of trophic dimensions characterizing the niches in a community. We introduce here a mathematically robust measure for food web intervality. It has previously been noted that empirical food webs are not strictly interval; however, upon comparison to suitable null hypotheses, we conclude that empirical food webs actually do exhibit a strong bias toward contiguity of prey, that is, toward intervality. Further, our results strongly suggest that empirically observed species and their diets can be mapped onto a single dimension. This finding validates a critical assumption in the recently proposed static niche model and provides guidance for ongoing efforts to develop dynamic models of ecosystems.
Almost all human genes resulted from ancient duplication
Authors: Britten Roy J.
Published: December 2006

Results of protein sequence comparison at open criterion show a very large number of relationships that have, up to now, gone unreported. The relationships suggest many ancient events of gene duplication. It is well known that gene duplication has been a major process in the evolution of genomes. A collection of human genes that have known functions have been examined for a history of gene duplications detected by means of amino acid sequence similarity by using BLASTp with an expectation of two or less (open criterion). Because the collection of genes in build 35 includes sets of transcript variants, all genes of known function were collected, and only the longest transcription variant was included, yielding a 13,298-member library called KGMV (for known genes maximum variant). When all lengths of matches are accepted, >97% of human genes show significant matches to each other. Many form matches with a large number of other different proteins, showing that most genes are made up from parts of many others as a result of ancient events of duplication. To support the use of the open criterion, all of the members of the KGMV library were twice replaced with random protein sequences of the same length and average composition, and all were compared with each other with BLASTp at expectation two or less. The set of matches averaged 0.35% of that observed for the KGMV set of proteins.
Plasma membrane-associated proteins are clustered into islands attached to the cytoskeleton
Authors: Lillemeier Björn F. , Pfeiffer Janet R. , Surviladze Zurab , Wilson Bridget S. , Davis Mark M.
Published: December 2006

Although much evidence suggests that the plasma membrane of eukaryotic cells is not homogenous, the precise architecture of this important structure has not been clear. Here we use transmission electron microscopy of plasma membrane sheets and specific probes to show that most or all plasma membrane-associated proteins are clustered in cholesterol-enriched domains (“islands”) that are separated by “protein-free” and cholesterol-low membrane. These islands are further divided into subregions, as shown by the localization of “raft” and “non-raft” markers to specific areas. Abundant actin staining and inhibitor studies show that these structures are connected to the cytoskeleton and at least partially depend on it for their formation and/or maintenance.
Existence of an operative pathway from the endoplasmic reticulum to the immature poxvirus membrane
Authors: Husain Matloob , Weisberg Andrea S. , Moss Bernard
Published: December 2006

In thin sections of cells infected with vaccinia virus or other poxviruses, the viral membrane is first discerned as a crescent or circle lacking obvious continuity with a cellular organelle, presenting an appearance of
de novo
membrane biogenesis. This notion, which many consider heretical, is nevertheless consistent with the absence of a signature of endoplasmic reticulum (ER) trafficking, such as signal peptide cleavage or glycosylation, in any of the numerous viral membrane proteins. The purpose of this study was to determine whether an operative pathway exists between the ER and the immature virion membrane. We showed that the highly conserved A9 viral membrane protein was inserted into the ER of uninfected cells with the same topology as in viral membranes. Next, we found that replacement of the nonessential cytoplasmic tail of A9 with one containing COPII-binding sites reduced incorporation of the modified A9 into viral membranes and led to its accumulation in the Golgi apparatus, implying that A9 was inserted into the ER and then diverted from its natural path. Most importantly, we demonstrated cleavage of a heterologous signal peptide fused to the N-terminal region of A9 and localized the truncated protein in immature and mature virions. Additionally, immunoelectron micrographs showed A9 in tubules containing protein disulfide isomerase, an ER lumenal protein, near immature viral membranes. The present data provide strong evidence for an operative pathway from ER domains within the virus factory to the viral membrane.
Transgenic analysis of Dlx regulation in fish tooth development reveals evolutionary retention of enhancer function despite organ loss
Authors: Jackman William R. , Stock David W.
Published: December 2006

It has been considered a “law” that a lost structure cannot reappear in evolution. The common explanation, that genes required for the development of the lost structure degrade by mutation, remains largely theoretical, however. Additionally, the extent to which this mechanism applies to systems of repeated parts, where individual modules are likely to exhibit few unique aspects of genetic control, is unclear. We investigated reversibility of evolution in one such system, the vertebrate dentition, using as a model loss of oral teeth in cypriniform fishes, which include the zebrafish. This evolutionary event, which occurred >50 million years ago, has not been reversed despite subsequent diversification of feeding modes and retention of pharyngeal teeth. We asked whether the cis-regulatory region of a gene whose expression loss parallels cypriniform tooth loss, Dlx2b, retains the capacity for expression in oral teeth. We first created a zebrafish reporter transgenic line that recapitulates endogenous
dlx2b
expression. We then showed that this zebrafish construct drives reporter expression in oral teeth of the related characiform
Astyanax mexicanus
. This result, along with our finding that Dlx genes are required for normal tooth development, suggests that changes in trans-acting regulators of these genes were responsible for loss of cypriniform oral teeth. Preservation of oral enhancer function unused for >50 million years could be the result of pleiotropic function in the pharyngeal dentition. If enhancers of other genes in the tooth developmental pathway are similarly preserved, teeth lost from specific regions may be relatively easy to reacquire in evolution.
Orchestration of lymphocyte chemotaxis by mitochondrial dynamics
Authors: Campello Silvia , Lacalle Rosa Ana , Bettella Monica , Mañes Santos , Scorrano Luca , Viola Antonella
Published: December 2006

Lymphocyte traffic is required to maintain homeostasis and perform appropriate immunological reactions. To migrate into inflamed tissues, lymphocytes must acquire spatial and functional asymmetries. Mitochondria are highly dynamic organelles that distribute in the cytoplasm to meet specific cellular needs, but whether this is essential to lymphocyte functions is unknown. We show that mitochondria specifically concentrate at the uropod during lymphocyte migration by a process involving rearrangements of their shape. Mitochondrial fission facilitates relocation of the organelles and promotes lymphocyte chemotaxis, whereas mitochondrial fusion inhibits both processes. Our data substantiate a new role for mitochondrial dynamics and suggest that mitochondria redistribution is required to regulate the motor of migrating cells.
Dynamic imaging of dendritic cell extension into the small bowel lumen in response to epithelial cell TLR engagement
Authors: Chieppa Marcello , Rescigno Maria , Huang Alex Y.C. , Germain Ronald N.
Published: December 2006

Cells lining the gastrointestinal tract serve as both a barrier to and a pathway for infectious agent entry. Dendritic cells (DCs) present in the lamina propria under the columnar villus epithelium of the small bowel extend processes across this epithelium and capture bacteria, but previous studies provided limited information on the nature of the stimuli, receptors, and signaling events involved in promoting this phenomenon. Here, we use immunohistochemical as well as dynamic explant and intravital two-photon imaging to investigate this issue. Analysis of CD11c–enhanced green fluorescent protein (EGFP) or major histocompatibility complex CII-EGFP mice revealed that the number of trans-epithelial DC extensions, many with an unusual “balloon” shape, varies along the length of the small bowel. High numbers of such extensions were found in the proximal jejunum, but only a few were present in the terminal ileum. The extensions in the terminal ileum markedly increased upon the introduction of invasive or noninvasive Salmonella organisms, and chimeric mouse studies revealed the key role of MyD88-dependent Toll-like receptor (TLR) signaling by nonhematopoietic (epithelial) elements in the DC extension response. Collectively, these findings support a model in which epithelial cell TLR signaling upon exposure to microbial stimuli induces active DC sampling of the gut lumen at sites distant from organized lymphoid tissues.
cBrother: relaxing parental tree assumptions for Bayesian recombination detection
Authors: Fang Fang , Ding Jing , Minin Vladimir N. , Suchard Marc A. , Dorman Karin S.
Published: December 2006

Summary: Bayesian multiple change-point models accurately detect recombination in molecular sequence data. Previous Java-based implementations assume a fixed topology for the representative parental data. cBrother is a novel C language implementation that capitalizes on reduced computational time to relax the fixed tree assumption. We show that cBrother is 19 times faster than its predecessor and the fixed tree assumption can influence estimates of recombination in a medically-relevant dataset.

Availability: cBrother can be freely downloaded from and can be compiled on Linux, Macintosh and Windows operating systems. Online documentation and a tutorial are also available at the site.

Contact:  kdorman@iastate.edu
AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps
Authors: Derrien Thomas , André Catherine , Galibert Francis , Hitte Christophe
Published: December 2006

AutoGRAPH is an interactive web server for automatic multi-species comparative genomics analyses based on personal datasets or pre-inserted public datasets. This program automatically identifies conserved segments (CS) and breakpoint regions, assesses the conservation of marker/gene order between organisms, constructs synteny maps for two to three species and generates high-quality, interactive displays facilitating the identification of chromosomal rearrangements. AutoGRAPH can also be used for the integration and comparison of several types of genomic resources (meiotic maps, radiation hybrid maps and genome sequences) for a single species, making AutoGRAPH a versatile tool for comparative genomics analysis.

Availability:  

Contact:  hitte@univ-rennes1.fr

Supplementary information: A description of the algorithm and additional information are available at
Copper Deficiency Misdiagnosed as Postpolio Syndrome
Authors: Sorenson Eric J
Published: December 2006

Symptoms of progressive weakness and pain after years of stability are common in survivors of paralytic poliomyelitis. These symptoms been coined the postpolio syndrome. In the majority of patients, this condition is stable and benign. Here, a case of copper deficiency as a result of excessive zinc supplementation is presented, mimicking the post polio syndrome. This case highlights the importance of a thorough medical history and evaluation in polio survivors when they present with new progressive deficits. Postpolio syndrome remains a diagnosis of exclusion and is a benign entity in most patients. Common and atypical features of the postpolio syndrome are reviewed. In the appropriate clinical setting, a diagnosis of copper deficiency should be considered and may be confirmed with the proper serologic testing.
Low Dose of Cyclosporine in Myasthenia Gravis
Authors: Souayah Nizar , Khella Sami L
Published: December 2006

Objective:

To determine if a low dose of cyclosporine is effective adjuvant therapy in the treatment of myasthenia gravis (MG).

Methods:

We added cyclosporine-A (Cs-A) at a low dose (mean 1.95 mg/kg/day and range of 0.84-3.8 mg/kg/day) to the immunosuppressive regimen of 12 patients with severe MG and followed them for a mean period of 40 months.

Results:

A statistically significant reduction in myasthenic severity was seen after 12 months of cyclosporine therapy. Three patients went into complete remission (no medication required). A substantial and statistically significant reduction in the dose of prednisone was seen in 5 patients who were previously receiving prednisone therapy. Mild adverse effects that resolved with dose reduction were seen in 3 patients.

Conclusion:

Preliminarily, we conclude that low-dose cyclosporine (less than 4 mg/kg/day) may be effective in myasthenia gravis with fewer adverse effects and is well tolerated for long-term therapy.
High-Frequency Chest Wall Oscillation Therapy in Amyotrophic Lateral Sclerosis
Authors: Jackson Carlayne E , Moore Dan H , Kittrell Pamela , Ensrud Erik
Published: December 2006

Objectives:

To evaluate the effectiveness of high-frequency chest wall oscillation (HFCWO) therapy in patients with amyotrophic lateral sclerosis (ALS).

Methods:

A retrospective chart review was performed of 18 patients receiving HFCWO therapy. Data was obtained pre-treatment and post-treatment including ALS Functional Rating Scale-Revised (ALSFRS-R), forced vital capacity (FVC), maximal inspiratory pressure (MIP), peak cough expiratory flow (PCEF), and daytime oximetry.

Results:

Daytime oximetry increased for 8 of 18 patients. None of the other measures changed significantly over the 3 months, although the change in slope of FVC, MIP, and PCEF following initiation of treatment suggested a reduction in the rate of decline of each measure. A patient survey revealed that 92% felt better after therapy and that their breathing was easier. Of patients, 85% agreed that it was easier to clear airways and that it had improved their quality of life.

Conclusions:

HFCWO appears to be an effective tool for airway secretion management in ALS patients and may also have an impact in improving daytime oxygen saturation.
Duchenne Muscular Dystrophy: An Update, Part I
Authors: Palmieri Beniamino , Sblendorio Valeriana
Published: December 2006

Although the cloning of the dystrophin gene has led to major advances in the knowledge of the genetic, molecular basis of Duchenne Muscular Dystrophy (DMD), Becker Muscular Dystrophy (BMD), and other muscular dystrophies, with mutations of genes encoding the dystrophin-associated glycoprotein complex (DGC), effective therapies are still lacking. This review reports some of the most promising pharmacological, molecular, and cellular approaches to DMD/BMD. Altogether, these exciting developments are just puzzling work hypothesis whose clinical developments are on the way.
Amyotrophic Lateral Sclerosis Presenting With a Clivus Mass and Dysarthria
Authors: Maragakis Nicholas J , Pardo Andrea C
Published: December 2006

A patient developed dysarthria and was found to have fibrous dysplasia of the clivus accompanied by cranial nerve impingement, particularly the hypoglossal canal. The dysarthria progressed to more severe bulbar dysfunction and a subsequent diagnosis of amyotrophic lateral sclerosis. This case highlights a discussion of the potential influences of focal lesions on the site of symptom onset in this neurodegenerative disease.
Purification of soluble and active RaxH, a transmembrane histidine protein kinase from Xanthomonas oryzae pv. oryzae required for AvrXa21 activity
Authors: STOLOV AVITAL , VALVERDE ANGEL , RONALD PAMELA , BURDMAN SAUL
Published: December 2006

The RaxHR two‐component regulatory system (TCS) of the rice pathogen Xanthomonas oryzae pv. oryzae is required for AvrXa21 activity. RaxH is a typical transmembrane histidine protein kinase (HK), whereas RaxR is its concomitant response regulator (RR). Here, we report the isolation of soluble, active amounts of recombinant His‐tagged full‐length RaxH and RaxR following growth of Escherichia coli over‐expressing strains in the presence of sorbitol and glycine betaine. Full‐length His‐RaxH showed similar autophosphorylation activities to that of a truncated version of the protein (His‐t‐RaxH), lacking the N‐terminal transmembrane region. Transphosphorylation assays revealed that only full‐length RaxH was able to induce phosphorylation of His‐RaxR, indicating that the N‐terminal region of RaxH may be required for transphosphorylation of RaxR. Using site‐directed mutagenesis we also demonstrated that residues histidine 222 in RaxH and aspartate 51 in RaxR are essential for phosphorylation activities of these proteins. Utilization of compatible solutes may be widely applied for purification of soluble, active recombinant transmembrane proteins, and in particular for purification of transmembrane HKs.
Disease resistance to bacterial pathogens affected by the amount of ferredoxin‐I protein in plants
Authors: HUANG HSIANG‐EN , GER MANG‐JYE , CHEN CHAO‐YING , PANDEY AJAY‐KUMAR , YIP MEI‐KUEN , CHOU HUNG‐WEN , FENG TENG‐YUNG
Published: December 2006

Ferredoxin‐I (Fd‐I) is a fundamental protein that is involved in several metabolic pathways. The amount of Fd‐I found in plants is generally regulated by environmental stress, including biotic and abiotic events. In this study, the correlation between quantity of Fd‐I and plant disease resistance was investigated. Fd‐I levels were increased by inoculation with Pseudomonas syringae pv. syringae but were reduced by Erwinia carotovora ssp. carotovora. Transgenic tobacco over‐expressing Fd‐I with the sense sweet pepper Fd‐I gene (pflp) was resistant to E. carotovora ssp. carotovora and the saprophytic bacterium P. fluorescens. By contrast, transgenic tobacco with reduced total Fd‐I and the antisense pflp gene was susceptible to E. carotovora ssp. carotovora and P. fluorescens. Both of these transgenic tobaccos were resistant to P. syringae pv. syringae. By contrast, the mutated E. carotovora ssp. carotovora, with a defective harpin protein, was able to invade the sense‐pflp transgenic tobacco as well as the non‐transgenic tobacco. An in vitro kinase assay revealed that harpin could activate unidentified kinases to phosphorylate PFLP. These results demonstrate that Fd‐I plays an important role in the disease defence mechanism.
Costs of caring for a child with cancer: a questionnaire survey
Authors: Eiser C. , Upton P.
Published: December 2006

Background  Current therapies for childhood cancer have resulted in improved survival rates. However, this has been achieved at considerable price to families, with financial costs including additional expenditure and loss of earnings having been described. The impact of these extra costs for UK families and the extent to which help from charities and government benefits is able to alleviate this is unknown.

Methods  Questionnaires concerning income, expenditure, employment and financial support were completed by 145 parents, recruited from three United Kingdom Children’s Cancer Study Group treatment centres.

Results  Parents’ responses highlighted increased expenditure related mainly to travel to treatment centres. The majority of families (55%) had spent between £50–100 in the past week over and above pre‐illness expenditure, with a further 18% spending more than £100. Many parents (mainly mothers) had either given up or reduced outside employment in order to care for their child and this was associated with further financial problems for 42.7% of families. Despite help from charities and government benefits for the majority of families, extra costs were associated with money worries for 68.3% of families.

Conclusions  Although families are offered timely information about their entitlement to benefits, financial problems are incurred by families of a child with cancer partly because legislation prevents benefits being claimed for the first 3 months of a child’s illness – the time when expenses are still at their highest. Furthermore, because benefits are backdated only to the point at which the claim was made, families do not recoup all their costs. Waiving of the 84‐day wait period for children undergoing chemotherapy and radiotherapy, and the introduction of weekly bridging payments while a Disability Living Allowance claim is being assessed, would ameliorate this problem and so improve the treatment experience for families.
Antigen‐specific immunoglobulin E+ B cells are preferentially localized within germinal centres
Authors: Kelly Kathleen A. , Butch Anthony W.
Published: December 2006

Allergen‐specific immunoglobulin E (IgE) mediates immediate‐type hypersensitivity reactions and plays a central role in allergic diseases. Although antigen‐driven B‐cell maturation and isotype switching occur within germinal centres (GCs), the role of GCs in IgE production is poorly understood. In view of this, we investigated the development of IgE‐expressing cells within GCs in response to an extensively characterized antigen, 2‐phenyloxazolone (phOx). The phOx‐specific IgE‐expressing cells localized within GCs 7 days after immunization, and peaked in number on day 11. Surprisingly, very few IgE‐positive cells were found in the T‐cell areas of the lymph node. Flow cytometric studies confirmed that IgE was expressed by B cells and was not the result of trapping by follicular dendritic cells. The specificity of the antibody response was confirmed by microdissection and reverse transcription‐polymerase chain reaction using phOx‐specific IgE primers. IgE‐positive cells were primarily found within GCs while, in contrast, many IgG1‐positive cells could also be detected outside GCs in the T‐cell areas. Taken together, these data highlight the importance of GCs in the production of antigen‐specific IgE antibody.
Compatible genetic and ecological estimates of dispersal rates in insect (Coenagrion mercuriale: Odonata: Zygoptera) populations: analysis of ‘neighbourhood size’ using a more precise estimator
Authors: WATTS PHILLIP C. , ROUSSET FRANÇOIS , SACCHERI ILIK J. , LEBLOIS RAPHAËL , KEMP STEPHEN J. , THOMPSON DAVID J.
Published: December 2006

Genetic and demographic estimates of dispersal are often thought to be inconsistent. In this study, we use the damselfly Coenagrion mercuriale (Odonata: Zygoptera) as a model to evaluate directly the relationship between estimates of dispersal rate measured during capture–mark–recapture fieldwork with those made from the spatial pattern of genetic markers in linear and two‐dimensional habitats. We estimate the ‘neighbourhood size’ (Nb) — the product of the mean axial dispersal rate between parent and offspring and the population density — by a previously described technique, here called the regression method. Because C. mercuriale is less philopatric than species investigated previously by the regression method we evaluate a refined estimator that may be more applicable for relatively mobile species. Results from simulations and empirical data sets reveal that the new estimator performs better under most situations, except when dispersal is very localized relative to population density. Analysis of the C. mercuriale data extends previous results which demonstrated that demographic and genetic estimates of Nb by the regression method are equivalent to within a factor of two at local scales where genetic estimates are less affected by habitat heterogeneity, stochastic processes and/or differential selective regimes. The corollary is that with a little insight into a species’ ecology the pattern of spatial genetic structure provides quantitative information on dispersal rates and/or population densities that has real value for conservation management.
Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching
Authors: UNDERWOOD J. N. , SMITH L. D. , VAN OPPEN M. J. H. , GILMOUR J. P.
Published: December 2006

Understanding the pattern of connectivity among populations is crucial for the development of realistic and spatially explicit population models in marine systems. Here we analysed variation at eight microsatellite loci to assess the genetic structure and to infer patterns of larval dispersal for a brooding coral,Seriatopora hystrix, at an isolated system of reefs in northern Western Australia. Spatial autocorrelation analyses show that populations are locally subdivided, and that the majority of larvae recruit to within 100 m of their natal colony. Further, a combination ofF‐ andR‐ statistics showed significant differentiation at larger spatial scales (2–60 km) between sites, and this pattern was clearly not associated with distance. However, Bayesian analysis demonstrated that recruitment has been supplemented by less frequent but recent input of larvae from outside the local area; 2–6% of colonies were excluded from the site at which they were sampled. Individual assignments of these migrants to the most likely populations suggest that the majority of migrants were produced at the only site that was not decimated by a recent and catastrophic coral bleaching event. Furthermore, the only site that recovered to prebleaching levels received most of these immigrants. We conclude that the genetic structure of this brooding coral reflects its highly opportunistic life history, in which prolific, philopatric recruitment is occasionally supplemented by exogenously produced larvae.