bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation between surface and buried InAs quantum dots
Authors: Liang B. L. , Wang Zh. M. , Mazur Yu. I. , Salamo G. J. , DeCuir Eric A. , Manasreh M. O.
Published: August 2006

The optical properties of uncapped InAs∕GaAs quantum dots sitting on multiple layers of buried quantum dots are investigated through a series of samples with a different number of buried quantum dot layers. Two photoluminescence peaks are observed, one from surface quantum dots and one from buried quantum dots. Close spatial and optical correlations between surface and buried quantum dots are demonstrated. Due to the carrier transfer from buried to surface quantum dots, the photoluminescence emission from surface quantum dots is significantly improved. As a result, the surface quantum dot–buried quantum dot sample shows potential for biological sensing.
Origin of cracking in nanoscale Cu∕Ta multilayers
Authors: Zhang G. P. , Zhu X. F. , Tan J. , Liu Y.
Published: August 2006

Cracking behaviors in nanoscale Cu∕Ta multilayers bonded to polyimide substrates have been investigated by uniaxial tensile tests. Experimental results show that cracks originate from the localized deformation regions associated with aligned grain boundaries. Microscopical observations suggest that the alignment of the grain boundaries is caused by local grain boundary sliding and grain rotation, which resulted in the in-plane and out-of-plane cooperative movements of the grains in the multilayers. From the localized damage regions, shear fracture in the through-thickness direction occurred in the nanoscale Cu∕Ta multilayer.
Two-dimensional particle-in-cell simulations of plasma cavitation and bursty Brillouin backscattering for nonrelativistic laser intensities
Authors: Riconda C. , Weber S. , Tikhonchuk V. T. , Adam J.-C. , Heron A.
Published: August 2006

Two-dimensional particle-in-cell simulations of laser-plasma interaction using a plane-wave geometry show strong bursty stimulated Brillouin backscattering, rapid filamentation, and subsequent plasma cavitation. It is shown that the cavitation is not induced by self-focusing. The electromagnetic fields below the plasma frequency that are excited are related to transient soliton-like structures. At the origin of these solitons is a three-wave decay process exciting new modes in the plasma. The cavitation is responsible for a strong local reduction of the reflectivity and goes along with an efficient but transient heating of the electrons. Once heating ceases, transmission starts to increase. Local as well as global average reflectivities attain a very low value due to strong plasma density variations brought about by the cavitation process. On the one hand, the simulations confirm the existence of a new mechanism of cavity and soliton formation in nonrelativistic laser-plasma interaction in two dimensions, which was shown to exist in one-dimensional simulations [S. Weber, C. Riconda, and V. T. Tikhonchuk, Phys. Rev. Lett. 94, 055005 (2005)]. On the other hand, new aspects are introduced inherently related to the additional degree of freedom.
Generalized coarse-grained model based on point multipole and Gay-Berne potentials
Authors: Golubkov Pavel A. , Ren Pengyu
Published: August 2006

This paper presents a general coarse-grained molecular mechanics model based on electric point multipole expansion and Gay-Berne [J. Chem. Phys. 74, 3316 (1981)] potential. Coarse graining of van der Waals potential is achieved by treating molecules as soft uniaxial ellipsoids interacting via a generalized anisotropic Gay-Berne function. The charge distribution is represented by point multipole expansion, including point charge, dipole, and quadrupole moments placed at the center of mass. The Gay-Berne and point multipole potentials are combined in the local reference frame defined by the inertial frame of the all-atom counterpart. The coarse-grained model has been applied to rigid-body molecular dynamics simulations of molecular liquids including benzene and methanol. The computational efficiency is improved by several orders of magnitude, while the results are in reasonable agreement with all-atom models and experimental data. We also discuss the implications of using point multipole for polar molecules capable of hydrogen bonding and the applicability of this model to a broad range of molecular systems including highly charged biopolymers.
Structure and conductivity of self-assembled films of gold nanoparticles
Authors: Pełka J. B. , Brust M. , Gierłowski P. , Paszkowicz W. , Schell N.
Published: August 2006

Self-assembled thin films of gold nanoparticles of 4–5nm, prepared on glass using aliphatic dithiols of different hydrocarbon chain lengths as interparticle linker molecules, have been studied by x-ray methods and dc conductivity. X-ray data revealed small spacer-dependent cluster size variations in the films. Conductivity, in the temperature range of 4.2–300K, showed a strong relation with spacer length, indicating that different mechanisms of conduction from metal-like through hopping to tunneling dominate, depending on temperature range and particle spacing. The results demonstrate that the electronic and optical properties of such films can be precisely controlled by interparticle distance.
Energy harvesting in silicon Raman amplifiers
Authors: Fathpour S. , Tsia K. K. , Jalali B.
Published: August 2006

Continuous-wave Raman amplification in silicon waveguides with negative electrical power dissipation is reported. It is shown that a p-n junction can simultaneously achieve carrier sweep-out leading to net continuous-wave gain and electrical power generation. The approach is also applicable to silicon Raman lasers and other third-order nonlinear optical devices.
Low writing field with large writing margin in toggle magnetic random access memories using synthetic antiferromagnet ferromagnetically coupled with soft magnetic layers
Authors: Fukumoto Yoshiyuki , Suzuki Tetsuhiro , Tahara Shuichi
Published: August 2006

The authors propose free layer structures that can simultaneously reduce the writing field and enlarge the writing margin in toggle magnetic random access memories. In the free layers, two soft magnetic layers of NiFe and a synthetic antiferromagnet trilayer of NiFe∕Ru∕NiFe were ferromagnetically coupled through two ferromagnetic coupling layers (FCLs). The FCLs were composed of ultrathin Ta-based layers. As the coupling strength through the FCLs decreased, the spin-flop field (Hflop) decreased and the saturation field increased in these free layers, by which the Hflop could be freely decreased within the allowable range of its variation even for the 0.24-μm-wide bits.
Physiological and seed yield responses to water deficits among lentil genotypes from diverse origins
Authors: Shrestha R. , Turner Neil C. , Siddique K. H. M. , Turner D. W.
Published: August 2006

The effect of water deficits at 2 growth stages on the physiology and growth of lentil (Lens culinaris Medikus subsp. culinaris) genotypes bred/selected for 3 regions was examined in a glasshouse experiment. The water regimes imposed were: (i) a well-watered control, (ii) water withheld at flowering, from 72 to 93 days after sowing (DAS), and (iii) water withheld from podding (93 DAS) to maturity. The genotypes were a West Asian genotype released in Australia (Cassab), 2 South Asian Nepali cultivars (Khajura 2 and Simal), and 3 crossbreds between West Asian and South Asian parents (ILL 6829, ILL 7979, and ILL 7982). ILL 7979 and Simal had significantly greater total dry matter, water use, seed yield, number of pods and seeds per plant, and harvest index (HI) than the other genotypes under well-watered conditions. Water deficits reduced seed yield by up to 60% in the crossbreds and the South Asian cultivar, Simal. However, seed yield was increased by the water deficit at flowering and the water deficit at podding in the West Asian genotype, Cassab, and the South Asian genotype, Khajura 2, respectively. In the other genotypes, withholding water at flowering or podding reduced leaf area (48–55%), total dry matter (32–50%), flower production (22–55%), and number of pods and seeds (27–66%), with significantly higher flower drop and empty pods when water was withheld. The higher seed yield in Cassab and Khajura 2 when water was withheld was related to the production of more flowers and the maintenance of pod and seed set when they were re-watered after the period of water deficit.
When water was withheld during flowering, the West Asian genotype Cassab and the crossbred ILL 6829 used less water and hence maintained a high leaf water potential (ψleaf), whereas ψleaf decreased earlier to lower values in the crossbred ILL 7979 and the South Asian genotypes Khajura 2 and Simal. There were no significant differences in leaf net photosynthesis (PN), or stomatal conductance (gS), among genotypes during flowering and early podding, but PN and gS were reduced by 22–38 and 19–67%, respectively, when water was withheld. The lower ψleaf in ILL 7979, Simal, and Khajura 2 induced greater osmotic adjustment (OA) during the drying cycle at flowering, whereas there was no or little OA when water was withheld at podding. Variation in physiological traits (PN, gS, OA) under both watering regimes was not directly related to seed yield, but seed number was related to seed yield under both well-watered and water-deficit conditions.
The effect of mid- and late-pregnancy shearing of hoggets on lamb birthweight, weaning weight, survival rate, and wool follicle and fibre characteristics
Authors: Kenyon P. R. , Sherlock R. G. , Morris S. T. , Morel P. C. H.
Published: August 2006

Pregnancy shearing of mature ewes has been shown to influence lamb birthweight and sometimes lamb survival to weaning and wool follicle characteristics. However, the effects of shearing hoggets in mid- or late-pregnancy under New Zealand’s pastoral conditions have not been examined. This study was designed to determine the effects of mid- and late-pregnancy shearing on lambs born to Romney hoggets. Single-bearing hoggets were either shorn at average day 79 of pregnancy (n = 74), at average day 119 (n = 80), or left unshorn (n = 76) while their twin-bearing counterparts were either shorn at average day 79 of pregnancy (n = 18) or left unshorn (n = 12). Mid-pregnancy shearing was found to increase the birthweights of singles (by 0.32 kg, P < 0.05) in comparison with unshorn ewes; however, this relationship was not observed in twins. Neither mid- nor late-pregnancy shearing affected lamb survival to weaning. Singles born to late-pregnancy shorn ewes had whiter wool (P < 0.05) in comparison with lambs born to unshorn dams. Dam treatment had no other effects on follicle or wool characteristics. The results of this study indicate that mid-pregnancy shearing of hoggets can be used as a technique to increase birthweight in single lambs but not twin-born lambs. Pregnancy shearing had no effect on lamb survival rates to weaning, whereas shearing in late-pregnancy had minor effects on wool colour that would be unlikely to affect wool value in Romneys. Shearing in mid-pregnancy had no effect on either progeny follicle or wool characteristics.
On the control of bud release in macadamia (Macadamia integrifolia)
Authors: Olesen T. , Whalan K. , Muldoon S. , Robertson D. , Meyer R.
Published: August 2006

Macadamia (Macadamia integrifolia) is a recurrent flushing tree, with buds alternating between growth and quiescence. Here we report on factors governing bud release. We used staggered tip-pruning (equivalent to branch decapitation) to generate a range of trees with different flush maturities, but uniform maturity within any given canopy. We then tip-pruned the trees again to remove the most recent flush, and monitored the time taken for visible axillary bud emergence. New flushes appeared 9–16 days after tip-pruning. The slowest bud emergence was associated with flushes of intermediate maturity, approximately 7 weeks old. Overall, the variation in bud emergence was most closely related to the growth rate of the most recent flush at the time of pruning, and not related to the levels of stored carbohydrates.
Voltage-dependent conformational changes in human Ca
2+
- and voltage-activated K
+
channel, revealed by voltage-clamp fluorometry
Authors: Savalli Nicoletta , Kondratiev Andrei , Toro Ligia , Olcese Riccardo
Published: August 2006

Large conductance voltage- and Ca
2+
-activated K
+
(BK
Ca
) channels regulate important physiological processes such as neurotransmitter release and vascular tone. BK
Ca
channels possess a voltage sensor mainly represented by the S4 transmembrane domain. Changes in membrane potential displace the voltage sensor, producing a conformational change that leads to channel opening. By site-directed fluorescent labeling of residues in the S3–S4 region and by using voltage clamp fluorometry, we have resolved the conformational changes the channel undergoes during activation. The voltage dependence of these conformational changes (detected as changes in fluorescence emission, fluorescence vs. voltage curves) always preceded the channel activation curves, as expected for protein rearrangements associated to the movement of the voltage sensor. Extremely slow conformational changes were revealed by fluorescent labeling of position 202, elicited by a mutual interaction of the fluorophore with the adjacent tryptophan 203.
The structure of the endoribonuclease XendoU: From small nucleolar RNA processing to severe acute respiratory syndrome coronavirus replication
Authors: Renzi Fabiana , Caffarelli Elisa , Laneve Pietro , Bozzoni Irene , Brunori Maurizio , Vallone Beatrice
Published: August 2006

Small nucleolar RNAs (snoRNAs) play a key role in eukaryotic ribosome biogenesis. In most cases, snoRNAs are encoded in introns and are released through the splicing reaction. Some snoRNAs are, instead, produced by an alternative pathway consisting of endonucleolytic processing of pre-mRNA. XendoU, the endoribonuclease responsible for this activity, is a U-specific, metal-dependent enzyme that releases products with 2′–3′ cyclic phosphate termini. XendoU is broadly conserved among eukaryotes, and it is a genetic marker of nidoviruses, including the severe acute respiratory syndrome coronavirus, where it is essential for replication and transcription. We have determined by crystallography the structure of XendoU that, by refined search methodologies, appears to display a unique fold. Based on sequence conservation, mutagenesis, and docking simulations, we have identified the active site. The conserved structural determinants of this site may provide a framework for attempting to design antiviral drugs to interfere with the infectious nidovirus life cycle.
Follicle-stimulating hormone/cAMP regulation of aromatase gene expression requires β-catenin
Authors: Parakh Tehnaz N. , Hernandez Jennifer A. , Grammer Jean C. , Weck Jennifer , Hunzicker-Dunn Mary , Zeleznik Anthony J. , Nilson John H.
Published: August 2006

Estrogens profoundly influence the physiology and pathology of reproductive and other tissues. Consequently, emphasis has been placed on delineating the mechanisms underlying regulation of estrogen levels. Circulating levels of estradiol in women are controlled by follicle-stimulating hormone (FSH), which regulates transcription of the aromatase gene (CYP19A1) in ovarian granulosa cells. Previous studies have focused on two downstream effectors of the FSH signal, cAMP and the orphan nuclear receptor steroidogenic factor-1 (NR5A1). In this report, we present evidence for β-catenin (CTNNB1) as an essential transcriptional regulator ofCYP19A1. FSH induction of select steroidogenic enzyme mRNAs, includingCyp19a1, is enhanced by β-catenin. Additionally, β-catenin is present in transcription complexes assembled on the endogenous gonad-specificCYP19A1promoter, as evidenced by chromatin immunoprecipitation assays. Transient expression and RNAi studies demonstrate that FSH- and cAMP-dependent regulation of this promoter is sensitive to alterations in the level of β-catenin. The stimulatory effect of β-catenin is mediated through functional interactions with steroidogenic factor-1 that involve four acidic residues within its ligand-binding domain, mutation of which attenuates FSH/cAMP-inducedCyp19a1mRNA accumulation. Together, these data demonstrate that β-catenin is essential for FSH/cAMP-regulated gene expression in the ovary, identifying a central and previously unappreciated role for β-catenin in estrogen biosynthesis, and a potential broader role in other aspects of follicular maturation.
Resonance Raman spectroscopy of chloroperoxidase compound II provides direct evidence for the existence of an iron(IV)–hydroxide
Authors: Stone Kari L. , Behan Rachel K. , Green Michael T.
Published: August 2006

We report direct evidence for the existence of an iron(IV)–hydroxide. Resonance Raman measurements on chloroperoxidase compound II (CPO-II) reveal an isotope (
18
O and
2
H)-sensitive band at ν
Fe–O
= 565 cm
−1
. Preparation of CPO-II in H
2
O using H
2
18
O
2
results in a red-shift of 22 cm
−1
, while preparation of CPO-II in
2
H
2
O using H
2
O
2
results in a red-shift of 13 cm
−1
. These values are in good agreement with the isotopic shifts predicted (23 and 12 cm
−1
, respectively) for an Fe–OH harmonic oscillator. The measured Fe–O stretching frequency is also in good agreement with the 1.82-Å Fe–O bond reported for CPO-II. A Badger’s rule analysis of this distance provides an Fe–O stretching frequency of ν
Badger
= 563 cm
−1
. We also present X-band electron nuclear double resonance (ENDOR) data for cryoreduced CPO-II. Cryogenic reduction (77 K) of the EPR-silent Fe(IV)OH center in CPO-II results in an EPR-active Fe(III)OH species with a strongly coupled (13.4 MHz) exchangeable proton. Based on comparisons with alkaline myoglobin, we assign this resonance to the hydroxide proton of cryoreduced CPO-II.
Nature designs tough collagen: Explaining the nanostructure of collagen fibrils
Authors: Buehler Markus J.
Published: August 2006

Collagen is a protein material with superior mechanical properties. It consists of collagen fibrils composed of a staggered array of ultra-long tropocollagen (TC) molecules. Theoretical and molecular modeling suggests that this natural design of collagen fibrils maximizes the strength and provides large energy dissipation during deformation, thus creating a tough and robust material. We find that the mechanics of collagen fibrils can be understood quantitatively in terms of two critical molecular length scales χ
S
and χ
R
that characterize when (
i
) deformation changes from homogeneous intermolecular shear to propagation of slip pulses and when (
ii
) covalent bonds within TC molecules begin to fracture, leading to brittle-like failure. The ratio χ
S
/χ
R
indicates which mechanism dominates deformation. Our modeling rigorously links the chemical properties of individual TC molecules to the macroscopic mechanical response of fibrils. The results help to explain why collagen fibers found in nature consist of TC molecules with lengths in the proximity of 300 nm and advance the understanding how collagen diseases that change intermolecular adhesion properties influence mechanical properties.
West Nile virus in complex with the Fab fragment of a neutralizing monoclonal antibody
Authors: Kaufmann Bärbel , Nybakken Grant E. , Chipman Paul R. , Zhang Wei , Diamond Michael S. , Fremont Daved H. , Kuhn Richard J. , Rossmann Michael G.
Published: August 2006

Flaviviruses, such as West Nile virus (WNV), are significant human pathogens. The humoral immune response plays an important role in the control of flavivirus infection and disease. The structure of WNV complexed with the Fab fragment of the strongly neutralizing mAb E16 was determined to 14.5-Å resolution with cryo-electron microscopy. E16, an antibody with therapeutic potential, binds to domain III of the WNV envelope glycoprotein. Because of steric hindrance, Fab E16 binds to only 120 of the 180 possible binding sites on the viral surface. Fitting of the previously determined x-ray structure of the Fab–domain III complex into the cryo-electron microscopy density required a change of the elbow angle between the variable and constant domains of the Fab. The structure suggests that the E16 antibody neutralizes WNV by blocking the initial rearrangement of the E glycoprotein before fusion with a cellular membrane.
Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy
Authors: Heugen U. , Schwaab G. , Bründermann E. , Heyden M. , Yu X. , Leitner D. M. , Havenith M.
Published: August 2006

The dynamics of water surrounding a solute is of fundamental importance in chemistry and biology. The properties of water molecules near the surface of a bio-molecule have been the subject of numerous, sometimes controversial experimental and theoretical studies, with some suggesting the existence of rather rigid water structures around carbohydrates and proteins [Pal, S. K., Peon, J., Bagchi, B. & Zewail A. H. (2002)
J. Phys. Chem. B
106, 12376–12395]. Hydrogen bond rearrangement in water occurs on the picosecond time scale, so relevant experiments must access these times. Here, we show that terahertz spectroscopy can directly investigate hydration layers. By a precise measurement of absorption coefficients between 2.3 THz and 2.9 THz we could determine the size and the characteristics of the hydration shell. The hydration layer around a carbohydrate (lactose) is determined to extend to 5.13 ± 0.24 Å from the surface corresponding to ≈123 water molecules beyond the first solvation shell. Accompanying molecular modeling calculations support this result and provide a microscopic visualization. Terahertz spectroscopy is shown to probe the collective modes in the water network. The observed increase of the terahertz absorption of the water in the hydration layer is explained in terms of coherent oscillations of the hydration water and solute. Simulations also reveal a slowing down of the hydrogen bond rearrangement dynamics for water molecules near lactose, which occur on the picosecond time scale. The present study demonstrates that terahertz spectroscopy is a sensitive tool to detect solute-induced changes in the water network.
Monitoring molecular dynamics using coherent electrons from high harmonic generation
Authors: Wagner Nicholas L. , Wüest Andrea , Christov Ivan P. , Popmintchev Tenio , Zhou Xibin , Murnane Margaret M. , Kapteyn Henry C.
Published: August 2006

We report a previously undescribed spectroscopic probe that makes use of electrons rescattered during the process of high-order harmonic generation. We excite coherent vibrations in SF
6
using impulsive stimulated Raman scattering with a short laser pulse. A second, more intense laser pulse generates high-order harmonics of the fundamental laser, at wavelengths of ≈20–50 nm. The high-order harmonic yield is observed to oscillate, at frequencies corresponding to all of the Raman-active modes of SF
6
, with an asymmetric mode most visible. The data also show evidence of relaxation dynamics after impulsive excitation of the molecule. Theoretical modeling indicates that the high harmonic yield should be modulated by both Raman and infrared-active vibrational modes. Our results indicate that high harmonic generation is a very sensitive probe of vibrational dynamics and may yield more information simultaneously than conventional ultrafast spectroscopic techniques. Because the de Broglie wavelength of the recolliding electron is on the order of interatomic distances, i.e., ≈1.5 Å, small changes in the shape of the molecule lead to large changes in the high harmonic yield. This work therefore demonstrates a previously undescribed spectroscopic technique for probing ultrafast internal dynamics in molecules and, in particular, on the chemically important ground-state potential surface.
TAF4 nucleates a core subcomplex of TFIID and mediates activated transcription from a TATA-less promoter
Authors: Wright Kevin J. , Marr Michael T. , Tjian Robert
Published: August 2006

Activator-dependent recruitment of TFIID initiates formation of the transcriptional preinitiation complex. TFIID binds core promoter DNA elements and directs the assembly of other general transcription factors, leading to binding of RNA polymerase II and activation of RNA synthesis. How TATA box-binding protein (TBP) and the TBP-associated factors (TAFs) are assembled into a functional TFIID complex with promoter recognition and coactivator activities
in vivo
remains unknown. Here, we use RNAi to knock down specific TFIID subunits in
Drosophila
tissue culture cells to determine which subunits are most critical for maintaining stability of TFIID
in vivo
. Contrary to expectations, we find that TAF4 rather than TBP or TAF1 plays the most critical role in maintaining stability of the complex. Our analysis also indicates that TAF5, TAF6, TAF9, and TAF12 play key roles in stability of the complex, whereas TBP, TAF1, TAF2, and TAF11 contribute very little to complex stability. Based on our results, we propose that holo-TFIID comprises a stable core subcomplex containing TAF4, TAF5, TAF6, TAF9, and TAF12 decorated with peripheral subunits TAF1, TAF2, TAF11, and TBP. Our initial functional studies indicate a specific and significant role for TAF1 and TAF4 in mediating transcription from a TATA-less, downstream core promoter element (DPE)-containing promoter, whereas a TATA-containing, DPE-less promoter was far less dependent on these subunits. In contrast to both TAF1 and TAF4, RNAi knockdown of TAF5 had little effect on transcription from either class of promoter. These studies significantly alter previous models for the assembly, structure, and function of TFIID.
HiRes—a tool for comprehensive assessment and interpretation of metabolomic data
Authors: Zhao Qi , Stoyanova Radka , Du Shuyan , Sajda Paul , Brown Truman R.
Published: August 2006

Summary: The increasing role of metabolomics in system biology is driving the development of tools for comprehensive analysis of high-resolution NMR spectral datasets. This task is quite challenging since unlike the datasets resulting from other ‘omics’, a substantial preprocessing of the data is needed to allow successful identification of spectral patterns associated with relevant biological variability. HiRes is a unique stand-alone software tool that combines standard NMR spectral processing functionalities with techniques for multi-spectral dataset analysis, such as principal component analysis and non-negative matrix factorization. In addition, HiRes contains extensive abilities for data cleansing, such as baseline correction, solvent peak suppression, removal of frequency shifts owing to experimental conditions as well as auxiliary information management. Integration of these components together with multivariate analytical procedures makes HiRes very capable of addressing the challenges for assessment and interpretation of large metabolomic datasets, greatly simplifying this otherwise lengthy and difficult process and assuring optimal information retrieval.

Availability:  HiRes is freely available for research purposes at

Contact:  qz2106@columbia.edu
A large quantity of novel human antisense transcripts detected by LongSAGE
Authors: Ge Xijin , Wu Qingfa , Jung Yong-Chul , Chen Jun , Wang San Ming
Published: August 2006

Motivation: Taking advantage of the high sensitivity and specificity of LongSAGE tag for transcript detection and genome mapping, we analyzed the 632 813 unique human LongSAGE tags deposited in public databases to identify novel human antisense transcripts.

Results: Our study identified 45 321 tags that match the antisense strand of 9804 known mRNA sequences, 6606 of which contain antisense ESTs and 3198 are mapped only by SAGE tags. Quantitative analysis showed that the detected antisense transcripts are present at levels lower than their counterpart sense transcripts. Experimental results confirmed the presence of antisense transcripts detected by the antisense tags. We also constructed an antisense tag database that can be used to identify the antisense SAGE tags originated from the antisense strand of known mRNA sequences included in the RefSeq database.

Conclusions: Our study highlights the benefits of exploring SAGE data for comprehensive identification of human antisense transcripts and demonstrates the prevalence of antisense transcripts in the human genome.

Contact:  swang1@northwestern.edu

Supplementary information:  Supplementary data are available at Bioinformatics online
ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting
Authors: Bekaert Michaël , Atkins John F , Baranov Pavel V
Published: August 2006

Summary: Correct annotation of genes encoding release factors in bacterial genomes is often complicated by utilization of +1 programmed ribosomal frameshifting during synthesis of release factor 2, RF2. In the absence of robust computational approaches for predicting ribosomal frameshifting, the success of proper annotation depends on annotators' familiarity with this phenomenon. Here we describe a novel computer tool that allows automatic discrimination of genes encoding class-I bacterial release factors, RF1, RF2 and RFH. Most usefully, this program identifies and automatically annotates +1 frameshifting in RF2 encoding genes. Comparison of ARFA performance with existing annotations of bacterial genomes revealed that only 20% of RF2 genes utilizing ribosomal frameshifting during their expression are annotated correctly.

Availability: The PHP based web interface of ARFA and the source code are located at

Contact:  baranov@genetics.utah.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Few crucial links assure checkpoint efficiency in the yeast cell-cycle network
Authors: Stoll Gautier , Rougemont Jacques , Naef Félix
Published: August 2006

Motivation: The ability of cells to complete mitosis with high fidelity relies on elaborate checkpoint mechanisms. We study S- and M-phase checkpoint responses in silico in the budding yeast with a stochastic dynamical model for the cell-cycle. We aim to provide an unbiased functional classification of network interactions that reflect the contribution of each link to checkpoint efficiency in the presence of cellular fluctuations.

Results: We developed an algorithm BNetDyn to compute stochastic dynamical trajectories for an input gene network and its structural perturbations. User specified output measures like the mutual information between trigger and output nodes are then evaluated on the stationary state of the Markov process. Systematic perturbations of the yeast cell-cycle model by Li et al. classify each link according to its effect on checkpoint efficiencies and stabilities of the main cell-cycle phases. This points to the crosstalk in the cascades downstream of the SBF/MBF transcription activator complexes as determinant for checkpoint optimality; a finding that consistently reflects recent experiments. Finally our stochastic analysis emphasizes how dynamical stability in the yeast cell-cycle network crucially relies on backward inhibitory circuits next to forward induction.

Availability: C++ source code and network models can be downloaded at

Contact:  felix.naef@isrec.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
COPA—cancer outlier profile analysis
Authors: MacDonald James W. , Ghosh Debashis
Published: August 2006

Summary: Chromosomal translocations are common in cancer, and in some cases may be causal in the progression of the disease. Using microarrays, in which the expression of thousands of genes are simultaneously measured, could potentially allow one to detect recurrent translocations for a particular cancer type. Standard statistical tests, such as the t-test are not suited for detecting these translocations, but a simple test based on robust centering and scaling of the data to help detect outlier samples, followed by a search for pairs of samples with mutually exclusive outliers, may be used to find genes involved in recurrent translocations. We have implemented this method, termed Cancer Outlier Profile Analysis (COPA) in an R package (that we call the copa package), and show its applicability on a publicly available dataset.

Availability:  

Contact:  jmacdon@med.umich.edu
A Liquid Chromatography-Mass Spectrometry-Based Metabolome Database for Tomato
Authors: Moco Sofia , Bino Raoul J. , Vorst Oscar , Verhoeven Harrie A. , de Groot Joost , van Beek Teris A. , Vervoort Jacques , de Vos C.H. Ric
Published: August 2006

For the description of the metabolome of an organism, the development of common metabolite databases is of utmost importance. Here we present the Metabolome Tomato Database (MoTo DB), a metabolite database dedicated to liquid chromatography-mass spectrometry (LC-MS)- based metabolomics of tomato fruit (Solanum lycopersicum). A reproducible analytical approach consisting of reversed-phase LC coupled to quadrupole time-of-flight MS and photodiode array detection (PDA) was developed for large-scale detection and identification of mainly semipolar metabolites in plants and for the incorporation of the tomato fruit metabolite data into the MoTo DB. Chromatograms were processed using software tools for mass signal extraction and alignment, and intensity-dependent accurate mass calculation. The detected masses were assigned by matching their accurate mass signals with tomato compounds reported in literature and complemented, as much as possible, by PDA and MS/MS information, as well as by using reference compounds. Several novel compounds not previously reported for tomato fruit were identified in this manner and added to the database. The MoTo DB is available at http://appliedbioinformatics.wur.nl and contains all information so far assembled using this LC-PDA-quadrupole time-of-flight MS platform, including retention times, calculated accurate masses, PDA spectra, MS/MS fragments, and literature references. Unbiased metabolic profiling and comparison of peel and flesh tissues from tomato fruits validated the applicability of the MoTo DB, revealing that all flavonoids and α-tomatine were specifically present in the peel, while several other alkaloids and some particular phenylpropanoids were mainly present in the flesh tissue.
Genome-Wide Analysis of Basic/Helix-Loop-Helix Transcription Factor Family in Rice and Arabidopsis
Authors: Li Xiaoxing , Duan Xuepeng , Jiang Haixiong , Sun Yujin , Tang Yuanping , Yuan Zheng , Guo Jingkang , Liang Wanqi , Chen Liang , Yin Jingyuan , Ma Hong , Wang Jian , Zhang Dabing
Published: August 2006

The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes. They are known to play important roles in the specification of tissue types in animals. On the other hand, few plant bHLH proteins have been studied functionally. Recent completion of whole genome sequences of model plants Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) allows genome-wide analysis and comparison of the bHLH family in flowering plants. We have identified 167 bHLH genes in the rice genome, and their phylogenetic analysis indicates that they form well-supported clades, which are defined as subfamilies. In addition, sequence analysis of potential DNA-binding activity, the sequence motifs outside the bHLH domain, and the conservation of intron/exon structural patterns further support the evolutionary relationships among these proteins. The genome distribution of rice bHLH genes strongly supports the hypothesis that genome-wide and tandem duplication contributed to the expansion of the bHLH gene family, consistent with the birth-and-death theory of gene family evolution. Bioinformatics analysis suggests that rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs. In addition, similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs.
Consensus by Democracy. Using Meta-Analyses of Microarray and Genomic Data to Model the Cold Acclimation Signaling Pathway in Arabidopsis
Authors: Benedict Catherine , Geisler Matt , Trygg Johan , Huner Norman , Hurry Vaughan
Published: August 2006

The whole-genome response of Arabidopsis (Arabidopsis thaliana) exposed to different types and durations of abiotic stress has now been described by a wealth of publicly available microarray data. When combined with studies of how gene expression is affected in mutant and transgenic Arabidopsis with altered ability to transduce the low temperature signal, these data can be used to test the interactions between various low temperature-associated transcription factors and their regulons. We quantized a collection of Affymetrix microarray data so that each gene in a particular regulon could vote on whether a cis-element found in its promoter conferred induction (+1), repression (−1), or no transcriptional change (0) during cold stress. By statistically comparing these election results with the voting behavior of all genes on the same gene chip, we verified the bioactivity of novel cis-elements and defined whether they were inductive or repressive. Using in silico mutagenesis we identified functional binding consensus variants for the transcription factors studied. Our results suggest that the previously identified ICEr1 (induction of CBF expression region 1) consensus does not correlate with cold gene induction, while the ICEr3/ICEr4 consensuses identified using our algorithms are present in regulons of genes that were induced coordinate with observed ICE1 transcript accumulation and temporally preceding genes containing the dehydration response element. Statistical analysis of overlap and cis-element enrichment in the ICE1, CBF2, ZAT12, HOS9, and PHYA regulons enabled us to construct a regulatory network supported by multiple lines of evidence that can be used for future hypothesis testing.
Three Years Later: A Follow‐Up Study of Parents' Assessments of Their Children's Competencies1
Authors: Räty Hannu , Kasanen Kati , Honkalampi Kirsi
Published: August 2006

The present study is a follow‐up of one that was designed to examine the changes that have occurred in parents' views of a child's competencies during the child's first 3 years of school. Parents with a university education (N=180) and a vocational education (N=249) were asked to assess their children's competencies in domains representing school subjects and abilities in preschool and at the end of the 1st and 3rd school years. The findings indicated that parents' initial optimistic views had prevailed. Furthermore, our findings on the gender‐ and education‐dependent differences suggested that the underlying social psychological organization of parental assessments already has taken shape by the time the child enters school.
An Examination of Goal Orientation Profiles Using Cluster Analysis and Their Relationships With Dispositional Characteristics and Motivational Response Patterns
Authors: Fortunato Vincent J. , Goldblatt Andrew M.
Published: August 2006

Goal orientation is a multidimensional construct widely examined by social, organizational, educational, and sports psychology researchers. However, despite theoretical perspectives indicating that individuals can adopt or manifest more than one goal orientation simultaneously, researchers traditionally examine relationships between the goal orientation dimensions and outcome variables of interest independently. In contrast, this study was designed to examine whether individuals can be sorted into meaningful goal orientation profiles based on their scores on measures of learning, performance–approach, and performance–avoidance goal orientation, and the relationships between the resulting profiles and various dispositional and motivational variables. Our results indicated that a 4‐profile solution best fit our data and that the 4 profiles differed uniquely across our dependent variables.
Impact of comorbid autism spectrum disorders on stimulant response in children with attention deficit hyperactivity disorder: a retrospective and prospective effectiveness study
Authors: Santosh P. J. , Baird G. , Pityaratstian N. , Tavare E. , Gringras P.
Published: August 2006

Background  In the recent past, psychiatrists and paediatricians have avoided prescribing stimulant medication, such as methylphenidate and dexamphetamine to patients with autism spectrum disorders (ASD) because of both doubts about efficacy and concern that these medications make stereotypies worse. Recently, a number of small trials have suggested that methyphenidate does have a role in the management of hyperactivity in children with autistic spectrum disorders.

Methods  Children with ASD and attention deficit hyperactivity disorder (ADHD), and children with ADHD without ASD received standard treatment with methyphenidate from one specialist centre. A combination of standardized and novel outcome tools was used to allow both an exploratory retrospective study of 174 children and then a prospective study of a further 52 children to be carried out.

Results  After treatment with stimulants, the subjects in both groups showed statistically significant improvements in target symptoms of ‘hyperactivity’, ‘impulsivity’, ‘inattention’, ‘oppositionality’, ‘aggression’ and ‘intermittent explosive rage’. The Clinical Global Impression‐Improvement and efficacy index measures also improved in each group. In both the retrospective and the prospective studies, there was no statistically significant difference in the degree of improvements between each group. Importantly, neither tics nor repetitive behaviours worsened in either group. Children in the ‘ADHD‐only’ group who were prescribed stimulants experienced significant ‘nausea’, ‘giddiness’, ‘headaches’ and ‘sleep difficulties’, whereas sleep difficulties were the only side effect that emerged in children in the ASD with ADHD group.

Conclusions  Both studies presented here support previous findings from smaller studies that show children with autism and ADHD can respond as well to stimulants as children with ADHD alone. Although randomized controlled trials remain the gold standard for efficacy studies, systems like this that allow clinicians to continue rigorous and consistent monitoring for many years have a valuable role to play. Furthermore, such monitoring systems which now exist electronically can easily accumulate large data sets and reveal details about long‐term effectiveness and long‐term side effects of medication that are unlikely to be discovered in short‐term trials.
Families in a state of flux: the experience of grandparents in autism spectrum disorder
Authors: Margetts J. K. , Le Couteur A. , Croom S.
Published: August 2006

Background  The experience of being a grandparent of a grandchild with autism spectrum disorder (ASD) is a previously under‐researched area. This study sets out to examine the grandparents’ own perspective in an exploratory way using a qualitative approach to answer the question, ‘What is the experience like?’

Method  A qualitative research project, using a purposive sampling technique and semi‐structured interviews to examine the experiences of six grandparents of children with ASD diagnosed by a specialist team in a second opinion Tier 4 Child and Adolescent Mental Health Service.

Results  The experiences of the grandparents were characterized by three Key Themes which emerged from the interviews: (1) The Parental Bond (protective bonding towards grandchild and adult child); (2) Striving for Answers (searching for meaning); (3) Keeping Intact (holding the family together).

Conclusion  The study suggests some interesting insights and confirms the need for more attention to this area. A key question raised by the study is how a child‐focused multidisciplinary team can embrace its role in delivering a family‐centred service. The clinical implications of this project have led to a change of practice in the specialist team. Further research would be appropriate to investigate the therapeutic effectiveness and cost effectiveness of involving grandparents as part of the assessment process.
Socioeconomic determinants of health related quality of life in childhood and adolescence: results from a European study
Authors: Spencer Nick
Published: August 2006

.
 
Von Rueden, U.,
Gosch, A.,
Rajmil, L.,
Bisegger, C.,
Ravens‐Sieberer, U.
,

(
2006
)

,
60
,
130
–
135
.

Study objective  The objective of this study was to investigate the impact of two different socio‐economic status (SES) measures on child and adolescent self‐reported health‐related quality of life (HRQoL). The European KIDSCREEN project aims at simultaneous developing, testing and implementing a generic HRQoL instrument.

Design and setting  The pilot version of the questionnaire was applied in school surveys to students from 8 to 18 years of age, as well as to their parents, together with such determinants of health status as two SES indicators, the parental educational status and the number of material goods in the family (family affluence scale).

Participants  Students from seven European countries: 754 children (39.8%; mean: 9.8 years), and 1142 adolescents (60.2%; mean: 14.1 years), as well as their respective parents.

Main results  In children, a higher parental educational status was found to have a significant positive impact on the KIDSCREEN dimensions: physical well‐being, psychological well‐being, moods and emotions, bullying and perceived financial resources. Increased risk of low HRQoL was detected for adolescents in connection with their physical well‐being. Family wealth plays a part for children’s physical well‐being, parent relations and home life, and perceived financial resources. For adolescents, family wealth furthermore predicts HRQoL on all KIDSCREEN dimensions.

Conclusions  There is evidence to suggest that exposure to low parental educational status may result in a decreased HRQoL in childhood, whereas reduced access to material (and thereby social) resources may lead to a lower HRQoL especially in adolescence.
Findings in older children with abusive head injury: does shaken‐child syndrome exist?
Authors: Reading Richard
Published: August 2006

Salehi‐Had, H.,
Brandt, J.D.,
Rosas, A.J. &
Rogers, K.K.
(
2006
)

,
117
,
e1039
–
e1044
.
doi:10.1542/peds.2005‐0811
.
Spatial QRS‐T angle: association with diabetes and left ventricular performance
Authors: Voulgari Ch. , Tentolouris N. , Moyssakis I. , Dilaveris P. , Gialafos E. , Papadogiannis D. , Votteas V. , Cokkinos D. V. , Stefanadis Ch. , Katsilambros N.
Published: August 2006

Background  The spatial QRS‐T angle obtained by vectorcardiography is a combined measurement of the electrical activity of the heart and predicts cardiovascular morbidity and mortality. Disturbances in repolarization and depolarization are common in diabetes. No data, however, exist on the effect of diabetes on QRS‐T angle. In this study we examined differences in QRS‐T angle between type 2 diabetic and non‐diabetic subjects; in addition, the potential relationship between QRS‐T angle and left ventricular performance as well as glycaemic control were also examined.

Patients and methods  A total of 74 subjects with type 2 diabetes and 74 non‐diabetic individuals, matched for age and sex with the diabetic subjects were examined. All subjects were free of clinically apparent macrovascular complications. Spatial vectorcardiogaphic descriptors of ventricular depolarization and repolarization were reconstructed from the 12‐electrocardiographic leads using a computer‐based electrocardiogram. Left ventricular mass and performance were measured using M‐mode and Doppler echocardiography.

Results  QRS‐T angle values were higher (by almost 2‐fold) in the diabetic in comparison with the non‐diabetic subjects (P < 0·001). After multivariate adjustment, QRS‐T angle was independently associated with age (P = 0·01), HbA1c (P = 0·003), and low‐density lipoprotein cholesterol levels (P = 0·04) in the non‐diabetic, and with HbA1c (P = 0·03) as well as Tei index (P = 0·003) in the diabetic subjects.

Conclusions  The spatial QRS‐T angle is high in subjects with type 2 diabetes and is associated with glycaemic control and left ventricular performance. The prognostic importance of the higher spQRS‐T angle values in subjects with diabetes remains to be evaluated in prospective studies.