bluuebunny/crossref_metadata_2025 huggingface dataset:
Dielectric, ferroelectric, and pyroelectric characterization of Mn-doped 0.74Pb(Mg1/3Nb2/3)O3–0.26PbTiO3 crystals for infrared detection applications
Authors: Liu Linhua , Li Xiaobing , Wu Xiao , Wang Yaojin , Di Wenning , Lin Di , Zhao Xiangyong , Luo Haosu , Neumann Norbert
Published: November 2009

We investigated the dielectric, ferroelectric, and pyroelectric properties of Mn-doped 0.74Pb(Mg1/3Nb2/3)O3–0.26PbTiO3 crystals. Compared with pure PMN-0.26PT, Mn substitutions resulted in reduced dielectric loss and enhanced coercive field. Furthermore, the pyroelectric coefficient and detectivity figures of merits were enhanced to 17.2×10−4 C/m2 K and 40.2×10−5 Pa−1/2, respectively, which were the highest values so far reported among intrinsic pyroelectric materials with rhombohedral-tetragonal phase transition temperature greater than 90 °C. The specific detectivity of infrared detector based on Mn-doped crystals was 1.07×109 cm Hz1/2 W−1, and approximately doubles that of commercial LiTaO3 crystals-based, which makes them promising candidates for infrared detectors applications.
Direct imaging of doped fluorine in LaFeAsO1−xFx superconductor by atomic scale spectroscopy
Authors: Tohei Tetsuya , Mizoguchi Teruyasu , Hiramatsu Hidenori , Kamihara Yoichi , Hosono Hideo , Ikuhara Yuichi
Published: November 2009

We report direct observation of fluorine ion dopants in the recently discovered LaFeAsO1−xFx superconductor, where the doping is critical for the superconductivity. Employing spectroscopic imaging based on scanning transmission electron microscopy, the spatial distribution of the doped fluorine ions, which are invisible in Z-contrast imaging, is clearly visualized with atomic-scale resolution. The observation directly proves that fluorine substitutes into the oxygen site in the superconducting LaFeAsO1−xFx compound. Our results demonstrate the potential of the present method for revealing dopants undetectable by conventional microscopy imaging.
Homologous temperature dependence of global surface scaling behaviors of polycrystalline copper films
Authors: Yang J. J. , Liu B. , Wang Y. , Xu K. W.
Published: November 2009

A strategy integrating structure zone model with dynamic scaling theory was proposed to study the global surface dynamics of polycrystalline Cu films deposited at different homologous temperature Ts/Tm. The evolution of roughness exponent α and growth exponent β reveals a transition from random deposition to surface diffusion dominated smoothening in the lower Ts/Tm regime and then to rapid surface roughening in the higher Ts/Tm regime. In contrast to that of amorphous films, the distinct scaling behavior in higher Ts/Tm regime arises from the change of anisotropic mass transport mechanisms, which could be related to the texture evolution during growth.
Fiber laser generating switchable radially and azimuthally polarized beams with 140 mW output power at 1.6 μm wavelength
Authors: Zhou Renjie , Ibarra-Escamilla Baldemar , Haus Joseph W. , Powers Peter E. , Zhan Qiwen
Published: November 2009

We report a fiber laser design that is capable of producing switchable radially and azimuthally polarized beams at 1.6 μm. A c-cut calcite crystal within a three-lens telescope is inserted in the cavity of an erbium doped fiber laser design. Due to the axially symmetric birefringence of the calcite crystal, radially, and azimuthally polarized modes have spatially separated foci in the cavity. Switching between the radially and azimuthally polarized outputs can be achieved by simply translating one of the lenses of the telescope. Output power more than 135 mW for both polarizations has been obtained.
Dual-microring-resonator interference sensor
Authors: Yi Huaxiang , Citrin D. S. , Chen Yao , Zhou Zhiping
Published: November 2009

Dual-microring-resonator interference with the microrings on separate arms of a Mach–Zehnder interferometer is shown to provide the basis for high-performance sensors. The output spectrum, which depends on the overlap of the resonances of the two microring resonators, depends sensitively on the resonance shift of one of the microrings due to the presence of an analyte. The sensitivity and detection limit are obtained theoretically and found to be as large as 0.31 nm overlap resonance shift according to 2×10−6 refractive index units for Si-based sensors.
The Synthesis of 6-Substituted Methyl 1-O-Acetyl-3,4-anhydro-β-D-Tagatofuranosides. Regioselective Chlorination and Thioacetylation in the Presence of an Oxiran
Authors: Norton AK , Vonitzstein M
Published: November 2009

Methyl 1-O-acetyl-6-S-acetyl-3,4-anhydro-6-thio-β-D-tagatofuranoside (the 1-acetate of (2)) and methyl 1-O-acetyl-3,4-anhydro-6-chloro-6-deoxy-β-D-tagatofuranoside (the 1-acetate of (3)) have been prepared as fructose derivatives by treatment of methyl 3,4-anhydro-β-D-tagatofuranoside (1) with (p-dimethylaminophenyl ) diphenylphosphine/diisopropyl azodicarboxylate/thioacetic S-acid and (p- dimethylaminophenyl ) diphenylphosphine/tetrachloromethane respectively. The reactions proceed in good yield, under mild conditions, and are selective for the 6-hydroxy group. The oxiran ring is unaffected under these conditions.
The Allyl Group for Protection in Carbohydrate Chemistry. XXXI. Conversion of Allyl 2,6-Di-O-benzyl-α-D-galactopyranoside Into Allyl 2,6-Di-O-benzyl-α-D-glucopyranoside and 2,6-Di-O-benzyl-D-glucopyranose
Authors: Desai T , Gigg J , Gigg R
Published: November 2009

Allyl 2,6-di-O-benzyl-α-D-galactopyranoside was converted by tin-mediated alkylation into the 3-O-p-methoxybenzyl ether which gave the 4-O-mesyl derivative. Sodium benzoate in refluxing N,N-dimethylformamide converted the last compound into allyl 4-O-benzoyl-2,6-di-O-benzyl-3-O-p-methoxybenzyl-α-D-glucopyranoside in high yield. This was saponified and the product was treated with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone to give the required allyl 2,6-di-O-benzyl-α-D-glucopyranoside whose structure was confirmed by conversion into the known 2,3,4,6-tetra-O-benzyl-D-glucopyranose. Removal of the allyl group from allyl 2,6-di-O-benzyl-α-D-glucopyranoside by a standard procedure gave 2,6-di-O-benzyl-D-glucopyranose. Both of the title compounds are required as intermediates for the synthesis of analogues of the 'adenophostins'.
Reaction of 4,6-Dimethoxy-3-methylindole With Aromatic Aldehydes: a Simple Synthesis of Calix[3]indoles
Authors: Black DS , Craig DC , Kumar N
Published: November 2009

2,7:2,7:2,7-Linked calix [3] indoles (3a-d) have been prepared by the reaction of 4,6-dimethoxy-3-methylindole (1) and benzaldehydes with phosphoryl chloride or by a direct reaction of di (4,6-dimethoxy-3-methylindol-2-yl) phenylmethanes (2a-d) with phosphoryl chloride. An X-ray crystal structure determination of the macrocycle (3d) is reported. 4,6-Dimethoxy-3-methylindolemethanols (9) and (10) were prepared and reacted with phosphoryl chloride to study the mechanism of formation of the macrocycle.
A Tetrachloro Guest in a Molecular Box
Authors: Marjo CE , Bishop R , Craig DC , Scudder ML
Published: November 2009

The new lattice inclusion host exo-7,exo-15-dibromo-6,7,14,15-tetrahydro-6,14-methanocycloocta[1,2-b:5,6-b'] diquinoxaline (6) has been synthesized in three steps from bicyclo [3.3.1]nonane-2,6-dione and benzofurazan oxide. It preferentially forms crystalline inclusion compounds with small polyhaloalkane guest molecules, and the crystal structure of the 1,1,2,2-tetrachloroethane compound [(C21H14N4Br2)2.C2H2Cl4, Pbcn , a 11.663(2), b 13.195(3), c 27.444(5) Ǻ, Z 4, R 0.041] is described. The key characteristic of this compound is a series of molecular boxes in which the guest molecules reside. Construction of the six surrounding walls is achieved with the aromatic rings of just four host molecules, and the guest molecule occupies a fixed position within the box. The intermolecular forces resulting in formation of this novel inclusion structure are analysed in detail.
A New Approach to Some 1,6-Dideoxy 1,6-Epithio Sugars
Authors: Driguez H , Mcauliffe JC , Stick RV , Tilbrook DMG , Williams SJ
Published: November 2009

The treatment of hexopyranosyl bromides, also activated at C6 (Br, OTs, OMs), with H2S/HCONMe2 under basic conditions gives rise to 1,6-dideoxy 1,6-epithio sugars. One such sugar has been further transformed into the synthetically useful 3,4-anhydro-1,6-dideoxy-1,6-epithio-β-D-galactose. The treatment of this epoxide with sodium azide and with cyclohexylamine is described. An analogous treatment of one doubly activated hexopyranosyl bromide with sodium hydrogen selenide has led to a novel 1,6-dideoxy 1,6-episeleno sugar which displayed interesting n.m.r. spectra. Finally, in an attempt to prepare 1,6-dideoxy 1,6-epidithio sugars, a tetraalkylammonium tetrathiomolybdate reagent was found to be the reagent of choice for converting doubly activated hexopyranosyl bromides into 1,6-dideoxy 1,6-epithio sugars.
Conformational Analysis of Cyclohexane-1,2-diol Derivatives and MM3 Parameter Improvement
Authors: Rockwell GD , Grindley TB
Published: November 2009

The positions of the equilibria between the diequatorial and diaxial conformers of trans-1,2-dimethoxycyclohexane (2) and trans-2-methoxycyclohexanol (3) have been measured accurately by 13C n.m.r. spectroscopy at -80°C in a series of solvents ranging from non-polar pentane to highly polar methanol. The equilibria favour the diequatorial conformers under all conditions but the extent increases with solvent polarity and is greater for (3). Improved parameters for the OCCO torsional term in MM3 (94) have been developed (V1, V2, and V3, 3.0, -2.5, 1.25, respectively) by comparison with conformational data for (2) and 1,2-dimethoxyethane (1). Application of the modified parameters to a number of examples demonstrates marked improvement for ethers. These examples include 1,2-dimethoxypropane, for which n.m.r. spectra in (D12) cyclohexane have been analysed and those from the gas phase reevaluated. Lesser improvement was achieved for systems having intramolecular hydrogen bonding. Ab initio results for rotation about the C 5-C 6 bond in pyranosides are satisfactorily reproduced but experimental results favour the gg and tg rotamers over the tg rotamer considerably more than calculated.
Enolic Ortho Esters. VI. A New 'Pyranose→Cyclohexane' Transformation via 1,6-Dideoxy-1,1-ethylenedioxy-2,3,4-tri-O-methyl-D-xylo-hex-5-enopyranose
Authors: Bourke DG , Collins DJ , Hibberd AI , Mcleod MD
Published: November 2009

Hydrolysis of methyl 6-chloro-6-deoxy-2,3,4-tri-O-methyl-α-D-glucopyranoside (19b) and Swern oxidation of the resulting anomeric hemiacetals (20) gave 6-chloro-6-deoxy-2,3,4-tri-O-methyl-D-glucono-1,5-lactone (21), treatment of which with 1,2-bis( trimethylsilyloxy )ethane in the
presence of trimethylsilyl trifluoromethanesulfonate gave 6-chloro-1,6-dideoxy-1,1-ethylenedioxy-2,3,4-tri-O-methyl-D-glucopyranose (23a). Conversion of (23a) into the corresponding 6-iodo compound (23b) and treatment of this with 1,8-diazabicyclo[5.4.0]undec-7-ene afforded the enolic ortho ester 1,6-dideoxy-1,1-ethylenedioxy-2,3,4-tri-O-methyl-D-xylo-hex-5-enopyranose (26). Reaction of (26) with methylmagnesium iodide, or with titanium tetrachloride, gave (1R,6S,7R,8R,9S)-7,8,9-trimethoxy-6-methyl-2,5-dioxabicyclo[4.3.1]decan-1-ol (34), or (2S,3R,4R)-5,5-ethylenedioxy-2,3,4-trimethoxycyclohexanone (28), respectively.
Two size-selective mechanisms specifically trap bacteria-sized food particles in Caenorhabditis elegans
Authors: Fang-Yen Christopher , Avery Leon , Samuel Aravinthan D. T.
Published: November 2009

Caenorhabditis elegans
is a filter feeder: it draws bacteria suspended in liquid into its pharynx, traps the bacteria, and ejects the liquid. How pharyngeal pumping simultaneously transports and filters food particles has been poorly understood. Here, we use high-speed video microscopy to define the detailed workings of pharyngeal mechanics. The buccal cavity and metastomal flaps regulate the flow of dense bacterial suspensions and exclude excessively large particles from entering the pharynx. A complex sequence of contractions and relaxations transports food particles in two successive trap stages before passage into the terminal bulb and intestine. Filtering occurs at each trap as bacteria are concentrated in the central lumen while fluids are expelled radially through three apical channels. Experiments with microspheres show that the
C. elegans
pharynx, in combination with the buccal cavity, is tuned to specifically catch and transport particles of a size range corresponding to most soil bacteria.
Overexpression of the chromosomally encoded aminoglycoside acetyltransferase
eis
confers kanamycin resistance in
Mycobacterium tuberculosis
Authors: Zaunbrecher M. Analise , Sikes R. David , Metchock Beverly , Shinnick Thomas M. , Posey James E.
Published: November 2009

The emergence of multidrug-resistant (MDR) tuberculosis (TB) highlights the urgent need to understand the mechanisms of resistance to the drugs used to treat this disease. The aminoglycosides kanamycin and amikacin are important bactericidal drugs used to treat MDR TB, and resistance to one or both of these drugs is a defining characteristic of extensively drug-resistant TB. We identified mutations in the −10 and −35 promoter region of the
eis
gene, which encodes a previously uncharacterized aminoglycoside acetyltransferase. These mutations led to a 20–180-fold increase in the amount of
eis
leaderless mRNA transcript, with a corresponding increase in protein expression. Importantly, these promoter mutations conferred resistance to kanamycin [5 μg/mL < minimum inhibitory concentration (MIC) ≤40 μg/mL] but not to amikacin (MIC <4 μg/mL). Additionally, 80% of clinical isolates examined in this study that exhibited low-level kanamycin resistance harbored
eis
promoter mutations. These results have important clinical implications in that clinical isolates determined to be resistant to kanamycin may not be cross-resistant to amikacin, as is often assumed. Molecular detection of
eis
mutations should distinguish strains resistant to kanamycin and those resistant to kanamycin and amikacin. This may help avoid excluding a potentially effective drug from a treatment regimen for drug-resistant TB.
Nuclear HBx binds the HBV minichromosome and modifies the epigenetic regulation of cccDNA function
Authors: Belloni Laura , Pollicino Teresa , De Nicola Francesca , Guerrieri Francesca , Raffa Giuseppina , Fanciulli Maurizio , Raimondo Giovanni , Levrero Massimo
Published: November 2009

HBV cccDNA, the template for transcription of all viral mRNAs, accumulates in the nucleus of infected cells as a stable episome organized into minichromosomes by histones and non-histone viral and cellular proteins. Using a cccDNA-specific chromatin immunoprecipitation (ChIP)-based quantitative assay, we have previously shown that transcription of the HBV minichromosome is regulated by epigenetic changes of cccDNA-bound histones and that modulation of the acetylation status of cccDNA-bound H3/H4 histones impacts on HBV replication. We now show that the cellular histone acetyltransferases CBP, p300, and PCAF/GCN5, and the histone deacetylases HDAC1 and hSirt1 are all recruited in vivo onto the cccDNA. We also found that the HBx regulatory protein produced in HBV replicating cells is recruited onto the cccDNA minichromosome, and the kinetics of HBx recruitment on the cccDNA parallels the HBV replication. As expected, an HBV mutant that does not express HBx is impaired in its replication, and exogenously expressed HBx transcomplements the replication defects. p300 recruitment is severely impaired, and cccDNA-bound histones are rapidly hypoacetylated in cells replicating the HBx mutant, whereas the recruitment of the histone deacetylases hSirt1 and HDAC1 is increased and occurs at earlier times. Finally, HBx mutant cccDNA transcribes significantly less pgRNA. Altogether our results further support the existence of a complex network of epigenetic events that influence cccDNA function and HBV replication and identify an epigenetic mechanism (i.e., to prevent cccDNA deacetylation) by which HBx controls HBV replication.
Role of HIV membrane in neutralization by two broadly neutralizing antibodies
Authors: Alam S. Munir , Morelli Marco , Dennison S. Moses , Liao Hua-Xin , Zhang Ruijun , Xia Shi-Mao , Rits-Volloch Sophia , Sun Li , Harrison Stephen C. , Haynes Barton F. , Chen Bing
Published: November 2009

Induction of effective antibody responses against HIV-1 infection remains an elusive goal for vaccine development. Progress may require in-depth understanding of the molecular mechanisms of neutralization by monoclonal antibodies. We have analyzed the molecular actions of two rare, broadly neutralizing, human monoclonal antibodies, 4E10 and 2F5, which target the transiently exposed epitopes in the membrane proximal external region (MPER) of HIV-1 gp41 envelope during viral entry. Both have long CDR H3 loops with a hydrophobic surface facing away from the peptide epitope. We find that the hydrophobic residues of 4E10 mediate a reversible attachment to the viral membrane and that they are essential for neutralization, but not for interaction with gp41. We propose that these antibodies associate with the viral membrane in a required first step and are thereby poised to capture the transient gp41 fusion intermediate. These results bear directly on strategies for rational design of HIV-1 envelope immunogens.
Localization of mRNAs coding for peroxisomal proteins in the yeast, Saccharomyces cerevisiae
Authors: Zipor Gadi , Haim-Vilmovsky Liora , Gelin-Licht Rita , Gadir Noga , Brocard Cecile , Gerst Jeffrey E.
Published: November 2009

Targeted mRNA trafficking and local translation may play a significant role in controlling protein localization. Here we examined for the first time the localization of all (≈50) mRNAs encoding peroxisomal proteins (mPPs) involved in peroxisome biogenesis and function. By using the bacteriophage MS2-CP RNA-binding protein (RBP) fused to multiple copies of GFP, we demonstrated that >40 endogenously expressed mPPs tagged with the MS2 aptamer form fluorescent RNA granules in vivo. The use of different RFP-tagged organellar markers revealed 3 basic patterns of mPP granule localization: to peroxisomes, to the endoplasmic reticulum (ER), and nonperoxisomal. Twelve mPPs (i.e.,
PEX1
,
PEX5
,
PEX8
,
PEX11–15
,
DCI1
,
NPY1
,
PCS60
, and
POX1
) had a high percentage (52%–80%) of mRNA colocalization with peroxisomes. Thirteen mPPs (i.e.,
AAT2
,
PEX6
,
MDH3
,
PEX28
, etc.) showed a low percentage (30%–42%) of colocalization, and 1 mPP (
PEX3
) preferentially localized to the ER. The mPPs of the nonperoxisomal pattern (i.e.,
GPD1
,
PCD1
,
PEX7
) showed ≪30% colocalization. mPP association with the peroxisome or ER was verified using cell fractionation and RT-PCR analysis. A model mPP,
PEX14
mRNA, was found to be in close association with peroxisomes throughout the cell cycle, with its localization depending in part on the 3′-UTR, initiation of translation, and the Puf5 RBP. The different patterns of mPP localization observed suggest that multiple mechanisms involved in mRNA localization and translation may play roles in the importation of protein into peroxisomes.
Single molecule detection of direct, homologous, DNA/DNA pairing
Authors: Danilowicz C. , Lee C. H. , Kim K. , Hatch K. , Coljee V. W. , Kleckner N. , Prentiss M.
Published: November 2009

Using a parallel single molecule magnetic tweezers assay we demonstrate homologous pairing of two double-stranded (ds) DNA molecules in the absence of proteins, divalent metal ions, crowding agents, or free DNA ends. Pairing is accurate and rapid under physiological conditions of temperature and monovalent salt, even at DNA molecule concentrations orders of magnitude below those found in vivo, and in the presence of a large excess of nonspecific competitor DNA. Crowding agents further increase the reaction rate. Pairing is readily detected between regions of homology of 5 kb or more. Detected pairs are stable against thermal forces and shear forces up to 10 pN. These results strongly suggest that direct recognition of homology between chemically intact B-DNA molecules should be possible in vivo. The robustness of the observed signal raises the possibility that pairing might even be the “default” option, limited to desired situations by specific features. Protein-independent homologous pairing of intact dsDNA has been predicted theoretically, but further studies are needed to determine whether existing theories fit sequence length, temperature, and salt dependencies described here.
Viscosity of glass-forming liquids
Authors: Mauro John C. , Yue Yuanzheng , Ellison Adam J. , Gupta Prabhat K. , Allan Douglas C.
Published: November 2009

The low-temperature dynamics of ultraviscous liquids hold the key to understanding the nature of glass transition and relaxation phenomena, including the potential existence of an ideal thermodynamic glass transition. Unfortunately, existing viscosity models, such as the Vogel–Fulcher–Tammann (VFT) and Avramov–Milchev (AM) equations, exhibit systematic error when extrapolating to low temperatures. We present a model offering an improved description of the viscosity–temperature relationship for both inorganic and organic liquids using the same number of parameters as VFT and AM. The model has a clear physical foundation based on the temperature dependence of configurational entropy, and it offers an accurate prediction of low-temperature isokoms without any singularity at finite temperature. Our results cast doubt on the existence of a Kauzmann entropy catastrophe and associated ideal glass transition.
Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest
Authors: Sheehan Timothy F. , Legault Christopher M. , King Timothy L. , Spidle Adrian P.
Published: November 2009

Sheehan, T. F., Legault, C. M., King, T. L., and Spidle, A. P. 2010. Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest. – ICES Journal of Marine Science, 67: 537–550. A multistock Atlantic salmon (Salmo salar) fishery operates off the coast of West Greenland and harvests fish of North American and European origin. Annual landings peaked in 1971 at 2700 t, but declined to 22 t in 2003. Biological data are collected to characterize the catch and its stock composition. Multilocus genotypes, generated via microsatellite DNA analysis, are used to derive statistics on continent of origin and less accurate finer-scale assignments. We developed a probabilistic-based genetic assignment (PGA) model to estimate the contribution of salmon from individual North American rivers in the 2000–2003 West Greenland catch. Uncertainty associated with finer-scale assignments is addressed by incorporating estimated misclassification rates and by reporting results as distributions generated via Monte Carlo resampling. US-origin fish represented ∼1% (by number) of the salmon harvested at West Greenland during the years 2000–2003. The resulting loss of spawners to this stock complex was approximately half the estimated adult returns in 2001, but was below 4% in the other 3 years. This is the first attempt to partition the US component of the West Greenland mixed-stock fishery to its finer parts. The approach can be used to identify the effects of fishing on individual stocks within any multistock complex where genetic samples of known origin are available.
The biogeography of introgression in the critically endangered African monkey
Rungwecebus kipunji
Authors: Roberts Trina E. , Davenport Tim R. B. , Hildebrandt Kyndall B. P. , Jones Trevor , Stanley William T. , Sargis Eric J. , Olson Link E.
Published: November 2009

In the four years since its original description, the taxonomy of the kipunji (
Rungwecebus kipunji
), a geographically restricted and critically endangered African monkey, has been the subject of much debate, and recent research suggesting that the first voucher specimen of
Rungwecebus
has baboon mitochondrial DNA has intensified the controversy. We show that
Rungwecebus
from a second region of Tanzania has a distinct mitochondrial haplotype that is basal to a clade containing all
Papio
species and the original
Rungwecebus
voucher, supporting the placement of
Rungwecebus
as the sister taxon of
Papio
and its status as a separate genus. We suggest that the
Rungwecebus
population in the Southern Highlands has experienced geographically localized mitochondrial DNA introgression from
Papio
, while the Ndundulu population retains the true
Rungwecebus
mitochondrial genome.
Social influences of competition on impulsive choices in domestic chicks
Authors: Amita Hidetoshi , Kawamori Ai , Matsushima Toshiya
Published: November 2009

Social factors involved in the control of impulsiveness were examined in domestic chicks. In binary choices between a large/long-delay option (LL) and a small/short-delay alternative (SS), chicks that had been competitively trained in groups of three individuals showed fewer choices of LL than did those trained in isolation (experiment 1), suggesting that competition causes impulsive choice. In experiment 2, in order to identify the critical factor involved, we tested the effects of
perceived competition
(coincident feeding without interruption) and
scrounging
(gaining food without pecking bead) separately. To examine the effects of risk/noise that individual chicks experienced in competition, the food amount varied randomly in trials according to a binomial distribution around the expected mean.
Perceived competition
primarily contributed to the influence on the impulsive choice, whereas the contribution of
scrounging
was weaker. Collection risk did not explain the social influences since the
perceived competition
was not accompanied by actual interruption of the delayed food reward. The risk owing to variable food
per se
did not cause impulsive choices. Coincident foraging during competition is thought to play a critical role.
On the Poincaré–Hill cycle map of rotational random walk: locating the stochastic limit cycle in a reversible Schnakenberg model
Authors: Vellela Melissa , Qian Hong
Published: November 2009

Recent studies on stochastic oscillations mostly focus on the power spectral analysis. However, the power spectrum yields information only on the frequency of oscillation and cannot differentiate between a stable limit cycle and a stable focus. The cycle flux, introduced by Hill (Hill 1989
Free energy transduction and biochemical cycle kinetics
), is a quantitative measure of the net movement over a closed path, but it is impractical to compute for all possible cycles in systems with a large state space. Through simple examples, we introduce concepts used to quantify stochastic oscillation, such as the cycle flux, the Hill–Qian stochastic circulation and rotation number. We introduce a novel device, the Poincaré–Hill cycle map (PHCM), which combines the concept of Hill’s cycle flux with the Poincaré map from nonlinear dynamics. Applying the PHCM to a reversible extension of an oscillatory chemical system, the Schnakenberg model, reveals stable oscillations outside the Hopf bifurcation region in which the deterministic system contains a limit cycle. Bistable behaviour is found on the small volume scale with high probabilities around both the fixed point and the limit cycle. Convergence to the deterministic system is found in the thermodynamic limit.
Matchgate and space-bounded quantum computations are equivalent
Authors: Jozsa Richard , Kraus Barbara , Miyake Akimasa , Watrous John
Published: November 2009

Matchgates are an especially multiflorous class of two-qubit nearest-neighbour quantum gates, defined by a set of algebraic constraints. They occur for example in the theory of perfect matchings of graphs, non-interacting fermions and one-dimensional spin chains. We show that the computational power of circuits of matchgates is equivalent to that of space-bounded quantum computation with unitary gates, with space restricted to being logarithmic in the width of the matchgate circuit. In particular, for the conventional setting of polynomial-sized (logarithmic-space generated) families of matchgate circuits, known to be classically simulatable, we characterize their power as coinciding with polynomial-time and logarithmic-space-bounded universal unitary quantum computation.
A glance beyond the quantum model
Authors: Navascués Miguel , Wunderlich Harald
Published: November 2009

One of the most important problems in physics is to reconcile quantum mechanics with general relativity, and some authors have suggested that this may be realized at the expense of having to drop the quantum formalism in favour of a more general theory. Here, we propose a mechanism to make general claims on the microscopic structure of the Universe by postulating that any post-quantum theory should recover classical physics in the macroscopic limit. We use this mechanism to bound the strength of correlations between distant observers in any physical theory. Although several quantum limits are recovered, such as the set of two-point quantum correlators, our results suggest that there exist plausible microscopic theories of Nature that predict correlations impossible to reproduce in any quantum mechanical system.
Evolving graphs: dynamical models, inverse problems and propagation
Authors: Grindrod Peter , Higham Desmond J.
Published: November 2009

Applications such as neuroscience, telecommunication, online social networking, transport and retail trading give rise to connectivity patterns that change over time. In this work, we address the resulting need for network models and computational algorithms that deal with dynamic links. We introduce a new class of evolving range-dependent random graphs that gives a tractable framework for modelling and simulation. We develop a spectral algorithm for calibrating a set of edge ranges from a sequence of network snapshots and give a proof of principle illustration on some neuroscience data. We also show how the model can be used computationally and analytically to investigate the scenario where an evolutionary process, such as an epidemic, takes place on an evolving network. This allows us to study the cumulative effect of two distinct types of dynamics.
A new transitional sauropodomorph dinosaur from the Early Jurassic of South Africa and the evolution of sauropod feeding and quadrupedalism
Authors: Yates Adam M. , Bonnan Matthew F. , Neveling Johann , Chinsamy Anusuya , Blackbeard Marc G.
Published: November 2009

Aardonyx celestaegen. et sp. nov. is described from the upper Elliot Formation (Early Jurassic) of South Africa. It can be diagnosed by autapomorphies of the skull, particularly the jaws, cervical column, forearm and pes. It is found to be the sister group of a clade of obligatory quadrupedal sauropodomorphs (Melanorosaurus+ Sauropoda) and thus lies at the heart of the basal sauropodomorph–sauropod transition. The narrow jaws ofA. celestaeretain a pointed symphysis but appear to have lacked fleshy cheeks. Broad, U-shaped jaws were previously thought to have evolved prior to the loss of gape-restricting cheeks. However, the narrow jaws ofA. celestaeretain a pointed symphysis but appear to have lacked fleshy cheeks, demonstrating unappreciated homoplasy in the evolution of the sauropod bulk-browsing apparatus. The limbs ofA. celestaeindicate that it retained a habitual bipedal gait although incipient characters associated with the pronation of the manus and the adoption of a quadrupedal gait are evident through geometric morphometric analysis (using thin-plate splines) of the ulna and femur. Cursorial ability appears to have been reduced and the weight bearing axis of the pes shifted to a medial, entaxonic position, falsifying the hypothesis that entaxony evolved in sauropods only after an obligate quadrupedal gait had been adopted.
Damped trophic cascades driven by fishing in model marine ecosystems
Authors: Andersen K. H. , Pedersen M.
Published: November 2009

The largest perturbation on upper trophic levels of many marine ecosystems stems from fishing. The reaction of the ecosystem goes beyond the trophic levels directly targeted by the fishery. This reaction has been described either as a change in slope of the overall size spectrum or as a trophic cascade triggered by the removal of top predators. Here we use a novel size- and trait-based model to explore how marine ecosystems might react to perturbations from different types of fishing pressure. The model explicitly resolves the whole life history of fish, from larvae to adults. The results show that fishing does not change the overall slope of the size spectrum, but depletes the largest individuals and induces trophic cascades. A trophic cascade can propagate both up and down in trophic levels driven by a combination of changes in predation mortality and food limitation. The cascade is damped as it comes further away from the perturbed trophic level. Fishing on several trophic levels leads to a disappearance of the signature of the trophic cascade. Differences in fishing patterns among ecosystems might influence whether a trophic cascade is observed.
Evidence of a general 2/3-power law of scaling leaf nitrogen to phosphorus among major plant groups and biomes
Authors: Reich Peter B. , Oleksyn Jacek , Wright Ian J. , Niklas Karl J. , Hedin Lars , Elser James J.
Published: November 2009

Scaling relations among plant traits are both cause and consequence of processes at organ-to-ecosystem scales. The relationship between leaf nitrogen and phosphorus is of particular interest, as both elements are essential for plant metabolism; their limited availabilities often constrain plant growth, and general relations between the two have been documented. Herein, we use a comprehensive dataset of more than 9300 observations of approximately 2500 species from 70 countries to examine the scaling of leaf nitrogen to phosphorus within and across taxonomical groups and biomes. Power law exponents derived from log–log scaling relations were near 2/3 for all observations pooled, for angiosperms and gymnosperms globally, and for angiosperms grouped by biomes, major functional groups, orders or families. The uniform 2/3 scaling of leaf nitrogen to leaf phosphorus exists along a parallel continuum of rising nitrogen, phosphorus, specific leaf area, photosynthesis and growth, as predicted by stoichiometric theory which posits that plants with high growth rates require both high allocation of phosphorus-rich RNA and a high metabolic rate to support the energy demands of macromolecular synthesis. The generality of this finding supports the view that this stoichiometric scaling relationship and the mechanisms that underpin it are foundational components of the living world. Additionally, although abundant variance exists within broad constraints, these results also support the idea that surprisingly simple rules regulate leaf form and function in terrestrial ecosystems.
Methylenetetrahydrofolate reductase polymorphisms, serum methylenetetrahydrofolate reductase levels, and risk of childhood acute lymphoblastic leukemia in a Chinese population
Authors: Tong Na , Fang Yongjun , Li Jie , Wang Meilin , Lu Qin , Wang Shizhi , Tian Yuanyuan , Rong Liucheng , Sun Jielin , Xu Jianfeng , Zhang Zhengdong
Published: November 2009

(Cancer Sci 2010; 101: 782–786)

Methylenetetrahydrofolate reductase (MTHFR), involved in DNA methylation and nucleotide synthesis, is thought to be associated with a decreased risk of adult and childhood acute lymphoblastic leukemia (ALL). Accumulating evidence has indicated that two common genetic variants, C677T and A1298C, are associated with cancer risk. We hypothesized that these two variants were associated with childhood ALL susceptibility and influence serum MTHFR levels. We genotyped these two polymorphisms and detected MTHFR levels in a case–control study of 361 cases and 508 controls. Compared with the 677CC and 677CC/CT genotypes, the 677TT genotype was associated with a statistically significantly decreased risk of childhood ALL (odds ratio = 0.53, 95% confidence interval = 0.32–0.88, and odds ratio = 0.55, 95% confidence interval = 0.35–0.88, respectively). In addition, a pronounced reduced risk of ALL was observed among low‐risk ALL and B‐phenotype ALL. Moreover, the mean serum MTHFR level was 8.01 ng/mL (±4.38) in cases and 9.27 ng/mL (±4.80) in controls (P < 0.001). MTHFR levels in subjects with 677TT genotype was significantly higher than those with 677CC genotype (P = 0.010) or 677CT genotype (P = 0.043) in controls. In conclusion, our results provide evidence that the MTHFR polymorphisms might contribute to reduced childhood ALL risk in this population.
Review article: the clinical management of congenital chloride diarrhoea
Authors: WEDENOJA S. , HÖGLUND P. , HOLMBERG C.
Published: November 2009

Aliment Pharmacol Ther 31, 477–485

Background  Congenital chloride diarrhoea in a newborn is a medical emergency, requiring early diagnostics and treatment to prevent severe dehydration and infant mortality. While most of the 250 cases reported arise from Finland, Poland and Arab countries, single cases with this autosomal recessive disorder appear worldwide. Such congenital chloride diarrhoea rarity makes diagnosis difficult. Life‐long salt substitution with NaCl and KCl stabilizes fluid, electrolyte and acid‐base balance diagnosis. When properly treated, the long‐term outcome is favourable.

Aim To summarize data on congenital chloride diarrhoea diagnosis, pathophysiology and treatment, and to provide guidelines for both acute and long‐term management of congenital chloride diarrhoea.

Methods  Data are based on MEDLINE search for ‘chloride diarrhoea’, in addition to clinical experience in the treatment of the largest known series of patients.

Results  Treatment of congenital chloride diarrhoea involves (i) life‐long salt substitution; (ii) management of acute dehydration and hypokalaemia during gastroenteritis or other infections; and (iii) recognition and treatment of other manifestations of the disease, such as intestinal inflammation, renal impairment and male subfertility.

Conclusions  This review summarizes data on congenital chloride diarrhoea and provides guidelines for treatment. After being a mostly paediatric problem, adult patients constitute a rare challenge for gastroenterologists worldwide.
A20 is an early responding negative regulator of Toll-like receptor 5 signalling in intestinal epithelial cells during inflammation
Authors: Oshima N , Ishihara S , Rumi M A K , Aziz M M , Mishima Y , Kadota C , Moriyama I , Ishimura N , Amano Y , Kinoshita Y
Published: November 2009

Several negative regulatory mechanisms control Toll-like receptor (TLR)-mediated inflammatory responses and restore immune system balance, including the zinc-finger protein A20, a negative regulator of TLR signalling that inhibits nuclear factor kappa B (NF-κB) activity. In the present study, we investigated TLR-5-mediated A20 expression and its role in intestinal epithelial cells (IECs) during inflammation. HCT-15 and HT-29 cells were stimulated with flagellin, then the expressions of A20, interleukin-1 receptor-associated kinase (IRAK-M) and Tollip were evaluated using RNase protection assay. Furthermore, experimental colitis was induced in tlr4-deficient CH3/HeJ mice by administration of dextran sodium sulphate (DSS), then flagellin was injected anally, and the colonic expression of A20 was examined by real-time polymerase chain reaction (PCR) and immunohistochemistry. To confirm flagellin-induced expression of A20, we employed an organ culture system. The role of A20 in flagellin-induced tolerance induction was evaluated in vitro, using a gene knock-down method targeting A20. A20 expression increased rapidly and peaked at 1 h after flagellin stimulation in cultured IECs, then declined gradually to the basal level. In vivo, anal injection of flagellin induced epithelial expression of A20 in injured colonic tissue, whereas flagellin did not cause a significant increase in A20 expression in non-injured normal tissue, which was also confirmed in vitro using the organ culture system. Gene knock-down using A20 siRNA did not influence tolerance induced by restimulation with flagellin. A20 is an early response negative regulator of TLR-5 signalling in IECs that functions during intestinal inflammation. Our results provide new insights into the negative feedback regulation of TLR-5 signalling that maintains the innate immune system in the gut.
Anti-transglutaminase antibodies in non-coeliac children suffering from infectious diseases
Authors: Ferrara F , Quaglia S , Caputo I , Esposito C , Lepretti M , Pastore S , Giorgi R , Martelossi S , Dal Molin G , Di Toro N , Ventura A , Not T
Published: November 2009

Anti-transglutaminase antibodies are the diagnostic markers of coeliac disease. A role is suggested for infectious agents in the production of anti-transglutaminase antibodies. The aim was to measure positive anti-transglutaminase antibody levels in children with infectious diseases and to compare immunological and biological characteristics of the anti-transglutaminase antibodies derived from these children with that from coeliac patients. Two hundred and twenty-two children suffering from infectious diseases were enrolled prospectively along with seven biopsy-proven coeliacs. Serum samples were tested for anti-transglutaminase antibodies and anti-endomysium antibodies; positive samples were tested for coeliac-related human leucocyte antigen (HLA)-DQ2/8 and anti-viral antibodies. Purified anti-transglutaminase antibodies from the two study groups were tested for urea-dependent avidity, and their ability to induce cytoskeletal rearrangement and to modulate cell-cycle in Caco-2 cells, using phalloidin staining and bromodeoxyuridine incorporation assays, respectively. Nine of 222 children (4%) tested positive to anti-transglutaminase, one of whom also tested positive for anti-endomysium antibodies. This patient was positive for HLA-DQ2 and was diagnosed as coeliac following intestinal biopsy. Of the eight remaining children, two were positive for HLA-DQ8. Levels of anti-transglutaminase returned to normal in all subjects, despite a gluten-containing diet. Purified anti-transglutaminase of the two study groups induced actin rearrangements and cell-cycle progression. During an infectious disease, anti-transglutaminase antibodies can be produced temporarily and independently of gluten. The infection-triggered anti-transglutaminase antibodies have the same biological properties as that of the coeliacs, with the same in-vivo potential for damage.
Benefit of short‐term iodide supplementation to antithyroid drug treatment of thyrotoxicosis due to Graves’ disease
Authors: Takata Kazuna , Amino Nobuyuki , Kubota Sumihisa , Sasaki Ichiro , Nishihara Eijun , Kudo Takumi , Ito Mitsuru , Fukata Shuji , Miyauchi Akira
Published: November 2009

Objective  Combined treatment with anti‐thyroid drugs (ATDs) and potassium iodide (KI) has been used only for severe thyrotoxicosis or as a pretreatment before urgent thyroidectomy in patients with Graves’ disease. We compared methimazole (MMI) treatment with MMI + KI treatment in terms of rapid normalization of thyroid hormones during the early phase and examined the later induction of disease remission.

Design and patients  A total of 134 untreated patients with Graves’ disease were randomly assigned to one of four regimens: Group 1, MMI 30 mg; Group 2, MMI 30 mg + KI; Group 3, MMI 15 mg and Group 4, MMI 15 mg + KI. For easy handling, KI tablets were used instead of saturated solution of KI. KI was discontinued when patients showed normal free thyroxine (FT4) levels but MMI was continued with a tapering dosage until remission. Remission rate was examined during a 4‐ to 5‐year observation.

Measurements  Serum FT4, FT3 and TSH were measured by chemiluminescent immunoassays. TSH receptor antibody (TRAb) was assayed with TRAb‐ELISA. Goitre size was estimated by ultrasonography.

Results  After 2 weeks of treatment, normal FT4 was observed in 29% of patients in Group 1 and 59% (P < 0·05) of patients in Group 2. Furthermore, normal FT4 after 2 weeks of treatment was observed in 27% of patients in Group 3 and 54% (P < 0·05) of patients in Group 4. Similarly, FT3 normalized more rapidly in Groups 2 and 4 than in Groups 1 and 3. None of the patients showed an increase in thyroid hormones or aggravation of disease during combined treatment with MMI and KI. The remission rates in Groups 1, 2, 3 and 4 were 34%, 44%, 33% and 51%, respectively, and were higher in the groups receiving combined therapy but differences among four groups did not reach significance.

Conclusions  Combined treatment with MMI and KI improved the short‐term control of Graves’ hyperthyroidism and was not associated with worsening hyperthyroidism or induction of thionamide resistance.
What is the optimal therapy for young males with hypogonadotropic hypogonadism?
Authors: Han T. S. , Bouloux P. M. G.
Published: November 2009

Hypogonadotropic hypogonadism (HH), consequent to congenital or acquired disorders of the hypothalamic–pituitary axis, presents as absent/delayed/arrested sexual maturation and infertility. Optimal management includes: (a) confirmation of the diagnosis and prognosis, (b) timing and choice of therapeutic intervention and (c) consideration of future fertility prospects. Therapy is usually initiated with testosterone to induce development of secondary sexual characteristics, taking the patient (often diagnosed late) through puberty. Monitoring of the impact of the condition on long‐term health and psychosocial function is necessary. Treatment is likely to be life‐long, requiring regular monitoring for its optimization and avoidance of adverse responses. Induction of spermatogenesis requires either pulsatile gonadotropin releasing hormone (GnRH) or gonadotropin administration. Gonadotropins can be self‐administered subcutaneously and are not inferior to the more costly GnRH. ‘Reversible genetic hypogonadotropic hypogonadism’ is a recently described entity which has implications for the long‐term management of patients with HH.
Multiplex ligation‐dependent probe amplification (MLPA) screening for exon copy number variation in the calcium sensing receptor gene: no large rearrangements identified in patients with calcium metabolic disorders
Authors: Nissen Peter H. , Christensen Signe E. , Wallace Andrew , Heickendorff Lene , Brixen Kim , Mosekilde Leif
Published: November 2009

Background  Mutation screening of the CASR by DNA sequencing is commonly used in the diagnosis of disorders of calcium metabolism, such as familial hypocalciuric hypercalcaemia (FHH). Exon copy number variation is not detected by currently used molecular genetic screening methods, and might be a genetic cause of inherited forms of hyper‐ or hypocalcaemia caused by the CASR.

Objective  We wanted to further evaluate possible genetic causes for disorders of calcium metabolism, by investigating the prevalence of exon copy number variations, such as large deletions or duplications of the CASR.

Patients and methods  The study included 257 patient samples referred to our laboratory for molecular genetic analysis of the CASR gene. A total of 245 were patients suspected to have FHH, while the remaining 12 samples represent patients with a phenotype of idiopathic hypocalcaemia/hypoparathyroidism. All samples were previously found negative for CASR mutations. Multiplex ligation‐dependent probe amplification was used to screen the patients for exon copy number variations.

Results  All exons were amplified with mean normalised ratios between 0·98 and 1·06. We did not identify any exon copy number variation in the CASR. Bioinformatic analyses revealed that the CASR gene contains 52% repeated elements, of which approximately 6% consist of Alu elements.

Conclusions  The present study indicates that including CASR MLPA analysis as a routine part of the diagnostic setup is not necessary, but could still be of interest in cases with a clear family history and no evidence of missense mutations in the CASR gene.