bluuebunny/crossref_metadata_2025 huggingface dataset:
Comment on “Resonant dissociative electron transfer of the presolvated electron to CCl4 in liquid: Direct observation and lifetime of the CCl4∗− transition state” [J. Chem. Phys. 128, 041102 (2008)]
Authors: Müller Rolf
Published: July 2008

A recent paper [J. Chem. Phys.128, 041102 (2008)] reports resonant dissociative electron transfer (RDET) to CCl4 in liquid ethanol. Part of the motivation for this work was the proposed importance of RDET processes for stratospheric ozone chemistry via dissociative electron attachment (DEA) triggered by cosmic ray activity in the polar winter stratosphere. In the present comment, it is argued that the relevance of DEA-induced destruction of chlorofluorocarbons (CFCs) in the polar stratosphere as a possible pathway for rapid chemical ozone destruction should not be a motivation for studies of DEA on CFC molecules; no correlation is observed between polar chemical ozone loss and cosmic ray activity. In any event, the relevance of this process as a key mechanism for the formation of the ozone hole should be presented as an issue debated in the scientific literature rather than as an established scientific fact.
One-step growth and field emission properties of quasialigned TiO2 nanowire/carbon nanocone core-shell nanostructure arrays on Ti substrates
Authors: Huo Kaifu , Zhang Xuming , Hu Liangsheng , Sun Xianjiao , Fu Jijiang , Chu Paul K.
Published: July 2008

Quasialigned nanoarrays consisting of TiO2 nanowire cores and carbon nanocone shells have been produced directly on titanium foils via a simple one-step thermal reaction under acetone vapor at 850°C. The nanowire cores are single-crystalline rutile TiO2 with diameters of 15–20nm and the conical carbon shells are amorphous with gradually decreasing thicknesses from 200–300nm at the bases to 5–10nm at the tips. Disparity of precipitation and etching of carbon shell give rise to the conical shape. Such TiO2∕C nanocone arrays on a conducting substrate are a new member of the conical nanostructures and promising field electron emitters.
Influence of the hole filling fraction on the ultrasonic transmission through plates with subwavelength aperture arrays
Authors: Estrada Héctor , Candelas Pilar , Uris Antonio , Belmar Francisco , Meseguer Francisco , García de Abajo Francisco J.
Published: July 2008

We report on the large impact of the hole filling fraction on the ultrasonic transmission spectra of periodic subwavelength hole arrays. We demonstrate both theoretically and experimentally that transmission peaks become narrower as the filling fraction decreases. Our results are consistent in plates with different thickness values and provide a route map for the design of plates with tailored acoustic transmission profiles.
Compressive film stress in a thin, tensile heteroepitaxial film
Authors: Pao Chun-Wei , Srolovitz David J.
Published: July 2008

We performed atomistic scale simulations to simulate the heteroepitaxial growth of a film with a 0.62% tensile misfit strain and monitored the stress evolution. The calculated σftf is initially compressive but increases after the first monolayer is completed. We provide theoretical and simulation evidence that this effect is associated with surface stresses. These results demonstrate that wafer curvature measurements lead to unreliable predictions of film stresses when the film is very thin.
Conducting transition metal nitride thin films with tailored cell sizes: The case of δ-TixTa1−xN
Authors: Koutsokeras L. E. , Abadias G. , Lekka Ch. E. , Matenoglou G. M. , Anagnostopoulos D. F. , Evangelakis G. A. , Patsalas P.
Published: July 2008

We present results on the stability and tailoring of the cell size of conducting δ-TixTa1−xN obtained by film growth and ab initio calculations. Despite the limited solubility of Ta in Ti, we show that TiN and TaN are soluble due to the hybrization of the d and sp electrons of the metal and N, respectively, that stabilizes the ternary system to the rocksalt structure. The stress-free cell sizes follow the Vegard’s rule; nevertheless, process-dependent stresses expand the cell size of the as-grown films. The electronic properties of δ-TixTa1−xN films (ρ=180Ωcm) are similar to those of TiN and TaN.
Crystal growth and piezoelectricity of BaTiO3–CaTiO3 solid solution
Authors: Fu Desheng , Itoh Mitsuru , Koshihara Shin-ya
Published: July 2008

We report the crystal growth and piezoelectric properties of (1−x)BaTiO3–xCaTiO3. It is found that the perovskite structure is facilitated by incorporating small Ca into Ba site and single crystals for a wide composition range of 0.02⩽x⩽0.34 can be grown by the floating zone technique with a high rate of 20mm∕h. High values of piezoelectric coefficient (d33=180–310pC∕N) have been demonstrated for the single crystals as well as the biphasic polycrystals with composition close to the solid solution limit. These findings may stimulate further interests in the developments of lead-free piezoelectrics or optical devices.
A simple cold Ar plasma jet generated with a floating electrode at atmospheric pressure
Authors: Nie Qiu-Yue , Ren Chun-Sheng , Wang De-Zhen , Zhang Jia-Liang
Published: July 2008

An experimental study is presented of a cold atmospheric Ar plasma jet with distinct advantages of low-working voltage and high plasma stability. To effectively improve the performance of the jet, a pair of pin electrodes with one floating in the air is applied. Variation in the applied voltage and/or the Ar gas flow causes the transition of the jet plasma from ignition, through stable plume to an unstable stage. The characteristics of the jet discharge are also studied by means of the electrical and spectroscopic diagnosis.
Determination of internal parameters in blue InGaN laser diodes by the measurement of cavity-length dependent characteristics
Authors: Ryu H. Y. , Ha K. H. , Son J. K. , Lee S. N. , Paek H. S. , Jang T. , Sung Y. J. , Kim K. S. , Kim H. K. , Park Y. , Nam O. H.
Published: July 2008

The characteristics of blue InGaN single-quantum-well laser diodes (LDs) emitting at 445nm are investigated with varying cavity length of the LDs from 650to1450μm. From the measurement of cavity-length dependent slope efficiency, internal efficiency and internal loss of LD structures have been determined to be 0.89 and 10.5cm−1, respectively, indicating good quality of the LD structure. In addition, gain parameters have been extracted from the relation of threshold current density and cavity length. It is found that the internal parameters of blue LDs are comparable to those of violet LDs emitting at 405nm.
Multimode quantized thermal conductance tuned by external field in a quantum wire
Authors: Cao L. S. , Peng R. W. , Wang Mu
Published: July 2008

In this work, we propose an approach to realize field-dependent multimode quantized thermal conductance by introducing both harmonic and anharmonic couplings to a quantum wire. It is demonstrated theoretically that by stretching (or compressing) the wire, phononic band structures are tuned and multiple phononic channels are opened one by one. In this way, multiple-step quantized thermal conductance is realized. The research opens a way to manipulate heat transfer in mesoscopic phonon systems.
Real-time detection of airborne viruses on a mass-sensitive device
Authors: Lee Joonhyung , Jang Jaesung , Akin Demir , Savran Cagri A. , Bashir Rashid
Published: July 2008

We present real-time detection of airborne Vaccinia viruses using quartz crystal microbalance (QCM) in an integrated manner. Vaccinia viruses were aerosolized and neutralized using an electrospray aerosol generator, transported into the QCM chamber, and captured by a QCM crystal. The capture of the viruses on the QCM crystal resulted in frequency shifts proportional to the number of viruses. The capture rate varied linearly with the concentration of initial virus suspensions (8.5×108–8.5×1010particles∕ml) at flow rates of 2.0 and 1.1l∕min. This work demonstrates the general potential of mass sensitive detection of nanoscale biological entities in air.
O
2
(
a
Δ
1
g
)
production at atmospheric pressure by microdischarge
Authors: Sousa J. Santos , Bauville G. , Lacour B. , Puech V. , Touzeau M. , Pitchford L. C.
Published: July 2008

We report experimental results showing that singlet oxygen O2(aΔ1g) can be efficiently produced at atmospheric pressure in a three-electrode microcathode sustained discharge (MCSD) configuration. This configuration consists of a microhollow cathode discharge (MHCD) acting as a plasma cathode to sustain a stable glow discharge between the MHCD and a third planar electrode placed at a distance of 8 mm. Experiments were performed in He/O2/NO mixtures. O2(aΔ1g) number densities higher than 1016 cm−3 were measured in the MCSD afterglow at total flow rates up to 30 ln/mn, resulting in O2(aΔ1g) fluxes above 10 millimole per hour (mmol/h).
Synthesis and magnetic properties of Cu doped ZnO nanorods via radio frequency plasma deposition
Authors: Wu Z. F. , Wu X. M. , Zhuge L. J. , Chen X. M. , Wang X. F.
Published: July 2008

Well-aligned Cu doped ZnO nanorods were synthesized by simple radio frequency plasma deposition in the absence of extra catalysts. The synthesized nanorods having a typical average diameter of about 60nm, were about 700nm in length and well aligned along the normal direction of the substrate. Magnetic measurements indicate that the nanorods are ferromagnetic at room temperature. The presence of considerable oxygen vacancies in the nanorods does allow possible defect mediated mechanisms (e.g., bound magnetic polarons) for mediating exchange coupling of the dopant Cu ions resulting in room temperature ferromagnetism.
Magnetic-field-modulated terahertz absorption spectra of a quantum ring
Authors: Xie Yan , Chu Weidong , Duan Suqing
Published: July 2008

The magnetic-field-modulated terahertz absorption spectra of a real GaAs quantum ring (QR) are studied by calculating the photon-participated tunneling current through the QR. We find that the absorption of photons can lead to a reduction in the tunneling current and this manifests as dips in the current versus magnetic field curves. There exists a saturation value for the depth of the current dip, which is described by a simple formula. A full width at half maximum less than 10GHz can be reached for current dips induced by terahertz fields for Rabi frequencies smaller than 2.5GHz. Our study provides a possible way to realize tunable detection of terahertz fields.
Molecular orientation in diindenoperylene thin films deposited on polycrystalline gold
Authors: Casu M. B. , Biswas I. , Schuster B.-E. , Nagel M. , Nagel P. , Schuppler S. , Chassé T.
Published: July 2008

We present x-ray photoemission spectroscopy (XPS) and near-edge x-ray absorption fine structure spectroscopy measurements taken on diindenoperylene (DIP) thin films of different thicknesses deposited on polycrystalline gold. Our investigations show that DIP films present flat lying molecules in the first layer, while the angle between the molecular axis and the surface increases with thickness. By using XPS, we find evidence for Stranski–Krastanov growth mode.
High frequency columnar silicon microresonators for mass detection
Authors: Kehrbusch J. , Ilin E. A. , Hullin M. , Oesterschulze E.
Published: July 2008

A simple but effective technological scheme for the fabrication of high frequency silicon columnar microresonators is presented. With the proposed technique the dimensions of the microresonators are controlled on a scale of at least 1μm. Characterization of the mechanical properties of silicon columns gave resonant frequencies of the lowest flexural mode of 3–7MHz with quality factors of up to 2500 in air and ∼8800 under vacuum condition. Columnar microresonators were operated as mass balance with a sensitivity of 1Hz∕fg. A mass detection limit of 25fg was deduced from experiments.
Ambipolar charge transport and electroluminescence properties of ZnO nanorods
Authors: Wong Chun-Yuen , Lai Lo-Ming , Leung Siu-Ling , Roy V. A. L. , Pun Edwin Yue-Bun
Published: July 2008

Hexagonal ZnO nanorod arrays have been prepared by a simple low-temperature ZnO-nanocrystal-assisted hydrothermal method. The photoluminescence spectrum of the ZnO nanorods features a weak band-edge emission at λmax∼3.3eV and a strong broad yellow emission at λmax∼2.17eV. Unlike the conventional reported n-type semiconducting property, our ZnO nanorods exhibit ambipolar charge transporting behavior. Using bottom contact field-effect transistor structure, the ZnO nanorods exhibit electron and hole mobilities up to 3.2 and 2.1cm2V−1s−1, respectively. Electroluminescence in the visible region from the nanorod-based device has also been demonstrated.
Room temperature continuous wave operation of quantum cascade lasers with 12.5% wall plug efficiency
Authors: Bai Y. , Slivken S. , Darvish S. R. , Razeghi M.
Published: July 2008

An InP based quantum cascade laser heterostructure emitting at 4.6μm was grown with gas-source molecular beam epitaxy. The wafer was processed into a conventional double-channel ridge waveguide geometry with ridge widths of 19.7 and 10.6μm without semi-insulating InP regrowth. An uncoated, narrow ridge device with a 4.8mm cavity length was epilayer down bonded to a diamond submount and exhibits 2.5W maximum output power with a wall plug efficiency of 12.5% at room temperature in continuous wave operation.
Simple Landau model of the RIV-RIII-RV rotator phases of alkanes
Authors: Mukherjee Prabir K.
Published: July 2008

Simple Landau-type free energy function is presented to describe the RIV-RIII-RV rotator phase sequence and the transitions between them. The order parameters necessary to describe the above rotator phase transitions are identified. Varying the coupling between the order parameters, the RIV-RIII and RIII-RV transitions occur. Available experimental results are consistent with our model.
Men's Attraction to Women's Bodies Changes Seasonally
Authors: Pawlowski Bogus∤aw , Sorokowski Piotr
Published: July 2008

Humans exhibit seasonal variation in hormone levels, behaviour, and perception. Here we show that men's assessments of women's attractiveness change also seasonally. In five seasons (from winter 2004 to winter 2005) 114 heterosexual men were asked to assess the attractiveness of the same stimuli: photos of a female with three different waist-to-hip ratios; photos of female breasts, and photos of average-looking faces of young women. For each season, the scores given to the stimuli of the same category (body shape, breast, and face) were combined. Friedman's test revealed significant changes for body shape and breast attractiveness assessments across the seasons, but no changes for face ratings. The highest scores for attractiveness were given in winter and the lowest in summer. We suggest that the observed seasonality is related to the well-known ‘contrast effect’. More frequent exposure to women's bodies in warmer seasons might increase men's attractiveness criteria for women's body shape and breasts.
Covert Detection of Attractiveness among the Neurologically Intact: Evidence from Skin-Conductance Responses
Authors: McDonald Paula R , Slater Alan M , Longmore Christopher A
Published: July 2008

Several studies have shown that participants, without a deficit in face recognition, give an increased skin conductance response (SCR) to familiar faces when presented subliminally, hence suggesting covert recognition of these faces. In the experiment presented here we manipulated familiarity and attractiveness and tested whether participants distinguished between faces for these variables when presented too fast to allow conscious recognition. Three sets of faces were presented: famous attractive; unfamiliar attractive; and unfamiliar less attractive. SCRs were the same for each category of faces whether presented subliminally or supraliminally, and were the same for attractive faces, whether famous or unfamiliar; however, SCRs differed between the attractive and less attractive faces. The findings support those of Stone et al (2001 Cognitive, Affective and Behavioral Neuroscience1 183–191) and suggest that higher SCRs to famous faces are not necessarily due to covert recognition, but may be a response to the positive affective valence of the stimuli.
Apparent Motion by Edge Discontinuities
Authors: Fantoni Carlo , Pinna Baingio
Published: July 2008

When the eyes move vertically across a jagged diamond, a local shift (LS) of edge discontinuities and a global shape distortion (GD) (ie expansion/contraction opposite to that expected by the aperture effect) are perceived. These phenomena cannot be accounted for by a local motion signals integration rule based either on the intersection of constraint lines or on the velocity vector summation. The threshold for GD perception and the salience of LS and GD (1 to 10 scale) were measured in two experiments by different methods and displays. In experiment 1 we induced GD through mimicking LS with a kinetic pattern constituted of a set of circular illusory apertures revealing drifting gratings. The point of subjective equality for compression/expansion was reached for gratings the linear extrapolations of which form an angle of 94.4°. In experiment 2 observers followed a dot moving along the vertical elongation axis of a static jagged diamond (with 70° or 90° angles), varying in the shape (triangular, wave, square), frequency, and amplitude of edge discontinuities. GD scores were correlated with LS scores that were inversely related to frequency/amplitude ratios of triangular edge discontinuities. Data are partially accounted for by averaging neighbouring local motion-capture vectors. Results prove that there are strong interrelations between phenomena in which visual motion affects visual localisation and phenomena involving apparent deformation of global shape.
Correspondence Matching in Long-Range Apparent Motion Precedes Featural Analysis
Authors: Prins Nicolaas
Published: July 2008

It has been suggested that correspondence matching in long-range motion is mediated by a perceptually high-level, ‘intelligent’ system. This suggestion is based on findings that long-range motion can be perceived between stimuli that could not be detected by lower-level motion mechanisms acting on Fourier motion energy, and that correspondence matching is affected by featural similarities between motion tokens that would be invisible to low-level (Fourier) motion detectors. Here, the effects of spatial-frequency content, color, and binocular disparity on correspondence matching are investigated. It is shown that the effects of featural matches between motion tokens develop only over time and lag behind the effects of the relative proximity between motion tokens in the retinal projection. This suggests that correspondence matching in long-range apparent motion is mediated by a mechanism which acts initially on the retinal coordinates of the motion tokens only, but may be biased to favor matching tokens that are featurally similar through a slower top–down influence by higher-level processes.
A Novel Piezoelectric Immunosensor for CA125 Using a Hydroxyapatite/Chitosan Nanocomposite-Based Biomolecular Immobilization Method
Authors: Ding Yanjun , Liu Jia , Jin Xiaoyong , Shen Guoli , Yu Ruqin
Published: July 2008

The ideal immobilization methods that are suitable for binding immunoactive materials with high efficiency onto a sensing surface are the key target to pursue in current biosensor design. In the present paper, the formation of a hydroxyapatite/chitosan (HA/CS) hybrid nanocomposite is described and a general design strategy for immunosensing platforms is proposed on the basis of HA/CS nanocomposite and nanogold particle adsorption of antibodies. A quartz crystal microbalance used as a model transducer and the detection performances of the resulting immunosensor were investigated by using the immuno-system of CA125, an important indicator in the diagnosis of clinical cancers. The hybrid nanocomposite was characterized by scanning electron microscopy and transmission electron microscopy measurements. The frequency response characteristics for the processes of immobilization and immunoreaction of anchored anti-CA125 antibodies were studied in detail. It was found that the developed sensing interface has some advantages, such as activation-free immobilization and high antigen-binding activities of antibodies. The as-prepared immunosensor can allow the determination of CA125 in the concentration range 15.3–440.0 U mL–1. Such an interface design with the hybrid nanocomposite could be tailored as a new alternative used for biosensor design.
A Novel Copper Cyanide Complex with a Layered Structure
Authors: Liu Xi , Guo Guo-Cong
Published: July 2008

The solvothermal reaction of copper(i) cyanide with 18-crown-6 (18C-6) in anhydrous acetonitrile and further diffusion with ether leads to a novel copper cyanide complex Cu(CN)(CH3CN)·0.5(18C-6) with a rare layered structure that exhibits complex violet luminescence originating from different layers.
Electrochemical Reduction of Cinnamonitrile in the Presence of Carbon Dioxide: Synthesis of Cyano- and Phenyl-Substituted Propionic Acids
Authors: Wang Huan , Lin Mei-Yu , Zhang Kai , Li Su-Jiao , Lu Jia-Xing
Published: July 2008

Cyano- and phenyl-substituted propionic acids were synthesized simply and efficiently by electrocarboxylation of cinnamonitrile in undivided cells using the non-noble metal nickel as cathode and magnesium as the anode. The radical anion generated by the electroreduction of cinnamonitrile in the absence of CO2 is involved in several competitive reactions that lead to the formation of linear hydrodimers, cyclic hydrodimers, saturated dihydro products, and glutaronitrile derivatives. While under 101.325 kPa of CO2, the electrocarboxylation could easily be carried out in the absence of additional catalysts, and with good yield (84.8%). The influence of various synthetic parameters, such as the nature of the electrode, the working potential, the concentration, and the temperature, on the electrocarboxylation reaction was investigated.
Genomic markers for malignant progression in pulmonary adenocarcinoma with bronchioloalveolar features
Authors: Aviel-Ronen Sarit , Coe Bradley P. , Lau Suzanne K. , da Cunha Santos Gilda , Zhu Chang-Qi , Strumpf Dan , Jurisica Igor , Lam Wan L. , Tsao Ming-Sound
Published: July 2008

Bronchioloalveolar carcinoma (BAC), a subtype of lung adenocarcinoma (ADC) without stromal, vascular, or pleural invasion, is considered an
in situ
tumor with a 100% survival rate. However, the histological criteria for invasion remain controversial. BAC-like areas may accompany otherwise invasive adenocarcinoma, referred to as mixed type adenocarcinoma with BAC features (AWBF). AWBF are considered to evolve from BAC, representing a paradigm for malignant progression in ADC. However, the supporting molecular evidence remains forthcoming. Here, we have studied the genomic changes of BAC and AWBF by array comparative genomic hybridization (CGH). We used submegabase-resolution tiling set array CGH to compare the genomic profiles of 14 BAC or BAC with focal area suspicious for invasion with those of 15 AWBF. Threshold-filtering and frequency-scoring analysis found that genomic profiles of noninvasive and focally invasive BAC are indistinguishable and show fewer aberrations than tumor cells in BAC-like areas of AWBF. These aberrations occurred mainly at the subtelomeric chromosomal regions. Increased genomic alterations were noted between BAC-like and invasive areas of AWBF. We identified 113 genes that best differentiated BAC from AWBF and were considered candidate marker genes for tumor invasion and progression. Correlative gene expression analyses demonstrated a high percentage of them to be poor prognosis markers in early stage ADC. Quantitative PCR also validated the amplification and overexpression of
PDCD6
and
TERT
on chromosome 5p and the prognostic significance of
PDCD6
in early stage ADC patients. We identified candidate genes that may be responsible for and are potential markers for malignant progression in AWBF.
Conceptual knowledge increases infants' memory capacity
Authors: Feigenson Lisa , Halberda Justin
Published: July 2008

Adults can expand their limited working memory capacity by using stored conceptual knowledge to chunk items into interrelated units. For example, adults are better at remembering the letter string PBSBBCCNN after parsing it into three smaller units: the television acronyms PBS, BBC, and CNN. Is this chunking a learned strategy acquired through instruction? We explored the origins of this ability by asking whether untrained infants can use conceptual knowledge to increase memory. In the absence of any grouping cues, 14-month-old infants can track only three hidden objects at once, demonstrating the standard limit of working memory. In four experiments we show that infants can surpass this limit when given perceptual, conceptual, linguistic, or spatial cues to parse larger arrays into smaller units that are more efficiently stored in memory. This work offers evidence of memory expansion based on conceptual knowledge in untrained, preverbal subjects. Our findings demonstrate that without instruction, and in the absence of robust language, a fundamental memory computation is available throughout the lifespan, years before the development of explicit metamemorial strategies.
A βα-barrel built by the combination of fragments from different folds
Authors: Bharat Tanmay A. M. , Eisenbeis Simone , Zeth Kornelius , Höcker Birte
Published: July 2008

Combinatorial assembly of protein domains plays an important role in the evolution of proteins. There is also evidence that protein domains have come together from stable subdomains. This concept of modular assembly could be used to construct new well folded proteins from stable protein fragments. Here, we report the construction of a chimeric protein from parts of a (βα)
8
-barrel enzyme from histidine biosynthesis pathway (HisF) and a protein of the (βα)
5
-flavodoxin-like fold (CheY) from
Thermotoga maritima
that share a high structural similarity. We expected this construct to fold into a full (βα)
8
-barrel. Our results show that the chimeric protein is a stable monomer that unfolds with high cooperativity. Its three-dimensional structure, which was solved to 3.1 Å resolution by x-ray crystallography, confirms a barrel-like fold in which the overall structures of the parent proteins are highly conserved. The structure further reveals a ninth strand in the barrel, which is formed by residues from the HisF C terminus and an attached tag. This strand invades between β-strand 1 and 2 of the CheY part closing a gap in the structure that might be due to a suboptimal fit between the fragments. Thus, by a combination of parts from two different folds and a small arbitrary fragment, we created a well folded and stable protein.
A pathogenic dyskerin mutation impairs proliferation and activates a DNA damage response independent of telomere length in mice
Authors: Gu Bai-Wei , Bessler Monica , Mason Philip J.
Published: July 2008

Telomeres are nucleoprotein structures that cap the ends of chromosomes, protecting them from exonucleases and distinguishing them from double-stranded breaks. Their integrity is maintained by telomerase, an enzyme consisting of a reverse transcriptase, TERT and an RNA template,
TERC
, and other components, including the pseudouridine synthase, dyskerin, the product of the
DKC1
gene. When telomeres become critically short, a p53-dependent pathway causing cell cycle arrest is induced that can lead to senescence, apoptosis, or, rarely to genomic instability and transformation. The same pathway is induced in response to DNA damage.
DKC1
mutations in the disease dyskeratosis congenita are thought to act via this mechanism, causing growth defects in proliferative tissues through telomere shortening. Here, we show that pathogenic mutations in mouse
Dkc1
cause a growth disadvantage and an enhanced DNA damage response in the context of telomeres of normal length. We show by genetic experiments that the growth disadvantage, detected by disparities in X-inactivation patterns in female heterozygotes, depends on telomerase. Hemizygous male mutant cells showed a strikingly enhanced DNA damage response via the ATM/p53 pathway after treatment with etoposide with a significant number of DNA damage foci colocalizing with telomeres in cytological preparations. We conclude that dyskerin mutations cause slow growth independently of telomere shortening and that this slow growth is the result of the induction of DNA damage. Thus, dyskerin interacts with telomerase and affects telomere maintenance independently of telomere length.
Widespread spatial integration in primary somatosensory cortex
Authors: Reed Jamie L. , Pouget Pierre , Qi Hui-Xin , Zhou Zhiyi , Bernard Melanie R. , Burish Mark J. , Haitas John , Bonds A. B. , Kaas Jon H.
Published: July 2008

Tactile discrimination depends on integration of information from the discrete receptive fields (RFs) of peripheral sensory afferents. Because this information is processed over a hierarchy of subcortical nuclei and cortical areas, the integration likely occurs at multiple levels. The current study presents results indicating that neurons across most of the extent of the hand representation in monkey primary somatosensory cortex (area 3b) interact, even when these neurons have separate RFs. We obtained simultaneous recordings by using a 100-electrode array implanted in the hand representation of primary somatosensory cortex of two anesthetized owl monkeys. During a series of 0.5-s skin indentations with single or dual probes, the distance between electrodes from which neurons with synchronized spike times were recorded exceeded 2 mm. The results provide evidence that stimuli on different parts of the hand influence the degree of synchronous firing among a large population of neurons. Because spike synchrony potentiates the activation of commonly targeted neurons, synchronous neural activity in primary somatosensory cortex can contribute to discrimination of complex tactile stimuli.
Sterols in a unicellular relative of the metazoans
Authors: Kodner Robin B. , Summons Roger E. , Pearson Ann , King Nicole , Knoll Andrew H.
Published: July 2008

Molecular clocks suggest that animals originated well before they first appear as macroscopic fossils, but geologic tests of these hypotheses have been elusive. A rare steroid hydrocarbon, 24-isopropylcholestane, has been hypothesized to be a biomarker for sponges or their immediate ancestors because of its relatively high abundance in pre-Ediacaran to Early Cambrian sedimentary rocks and oils. Biolipid precursors of this sterane have been reported to be prominent in several demosponges. Whether 24-isopropylcholestane can be interpreted as a sponge (and, hence, animal) biomarker, and so provide clues about early metazoan history, depends on an understanding of the distribution of sterol biosynthesis among animals and their protistan relatives. Accordingly, we characterized the sterol profile of the choanoflagellate
Monosiga brevicollis
, a representative of the unicellular sister group of animals.
M. brevicollis
does not produce a candidate sterol precursor for 24-isopropylcholestane under our experimental growth conditions. It does, however, produce a number of other sterols, and comparative genomics confirms its biosynthetic potential to produce the full suite of compounds recovered. Consistent with the phylogenetic position of choanoflagellates, the sterol profile and biosynthetic pathway of
M. brevicollis
display characteristics of both fungal and poriferan sterol biosynthesis. This is an example in which genomic and biochemical information have been used together to investigate the taxonomic specificity of a fossil biomarker.
The FHA domain proteins DAWDLE in
Arabidopsis
and SNIP1 in humans act in small RNA biogenesis
Authors: Yu Bin , Bi Liu , Zheng Binglian , Ji Lijuan , Chevalier David , Agarwal Manu , Ramachandran Vanitharani , Li Wanxiang , Lagrange Thierry , Walker John C. , Chen Xuemei
Published: July 2008

Proteins containing the forkhead-associated domain (FHA) are known to act in biological processes such as DNA damage repair, protein degradation, and signal transduction. Here we report that DAWDLE (DDL), an FHA domain-containing protein in
Arabidopsis
, acts in the biogenesis of miRNAs and endogenous siRNAs. Unlike mutants of genes known to participate in the processing of miRNA precursors, such as
dcl1
,
hyponastic leaves1
, and
serrate
,
ddl
mutants show reduced levels of pri-miRNAs as well as mature miRNAs. Promoter activity of
MIR
genes, however, is not affected by
ddl
mutations. DDL is an RNA binding protein and is able to interact with DCL1. In addition, we found that SNIP1, the human homolog of DDL, is involved in miRNA biogenesis and interacts with Drosha. Therefore, we uncovered an evolutionarily conserved factor in miRNA biogenesis. We propose that DDL participates in miRNA biogenesis by facilitating DCL1 to access or recognize pri-miRNAs.
Structure of UL18, a peptide-binding viral MHC mimic, bound to a host inhibitory receptor
Authors: Yang Zhiru , Bjorkman Pamela J.
Published: July 2008

UL18 is a human cytomegalovirus class I MHC (MHCI) homolog that binds the host inhibitory receptor LIR-1 and the only known viral MHC homolog that presents peptides. The 2.2-Å structure of a LIR-1/UL18/peptide complex reveals increased contacts and optimal surface complementarity in the LIR-1/UL18 interface compared with LIR/MHCI interfaces, resulting in a >1,000-fold higher affinity. Despite sharing only ≈25% sequence identity, UL18's structure and peptide binding are surprisingly similar to host MHCI. The crystal structure suggests that most of the UL18 surface, except where LIR-1 and the host-derived light chain bind, is covered by carbohydrates attached to 13 potential N-glycosylation sites, thereby preventing access to bound peptide and association with most MHCI-binding proteins. The LIR-1/UL18 structure demonstrates how a viral protein evolves from its host ancestor to impede unwanted interactions while preserving and improving its receptor-binding site.
Knowledge-Based Urban Development: The Local Economic Development Path of Brisbane, Australia
Authors: Yigitcanlar Tan , Velibeyoglu Koray
Published: July 2008

Knowledge-based development strategies play an important role in supporting local economic development of cities in the knowledge era. This paper investigates local knowledge-based urban development policies of Brisbane, Australia in its long journey to become a competitive knowledge city. The paper examines Brisbane's recent progress towards establishing knowledge community precincts that are critical creative urban environments to attract and retain global investment and talent. This paper also discusses major challenges Brisbane is experiencing during the implementation of its state- and city-wide knowledge-based urban development strategies.
Quantitative analysis of autophagy-related protein stoichiometry by fluorescence microscopy
Authors: Geng Jiefei , Baba Misuzu , Nair Usha , Klionsky Daniel J.
Published: July 2008

In yeast, ∼31 autophagy-related (Atg) proteins have been identified. Most of them reside at the phagophore assembly site (PAS), although the function of the PAS mostly remains unclear. One reason for the latter is the lack of stoichiometric information regarding the Atg proteins at this site. We report the application of fluorescence microscopy to study the amount of Atg proteins at the PAS. We find that an increase in the amount of Atg11 at the PAS enhances the recruitment of Atg8 and Atg9 to this site and facilitates the formation of more cytoplasm-to-vacuole targeting vesicles. In response to autophagy induction, the amount of most Atg proteins remains unchanged at the PAS, whereas we see an enhanced recruitment of Atg8 and 9 at this site. During autophagy, the amount of Atg8 at the PAS showed a periodic change, indicating the formation of autophagosomes. Application of this method and further analysis will provide more insight into the functions of Atg proteins.
Avidity maturation of memory CD8 T cells is limited by self-antigen expression
Authors: Turner Michael J. , Jellison Evan R. , Lingenheld Elizabeth G. , Puddington Lynn , Lefrançois Leo
Published: July 2008

Immune tolerance to self-antigens is a complex process that utilizes multiple mechanisms working in concert to maintain homeostasis and prevent autoimmunity. We developed a system that revealed a population of self-specific CD8 T cells within the endogenous T cell repertoire. Immunization of ovalbumin (OVA)-expressing transgenic mice with recombinant viruses expressing OVA-peptide variants induced self-reactive T cells in vivo that matured into memory T cells able to respond to secondary infection. However, whereas the avidity of memory cells in normal mice increased dramatically with repeated immunizations, avidity maturation was limited for self-specific CD8 T cells. Despite decreased avidity, such memory cells afforded protection against infection, but did not induce overt autoimmunity. Further, up-regulation of self-antigen expression in dendritic cells using an inducible system promoted programmed death-1 expression, but not clonal expansion of preexisting memory cells. Thus, the self-reactive T cell repertoire is controlled by overlapping mechanisms influenced by antigen dose.
Antibiotic Exposure and Room Contamination Among Patients Colonized With Vancomycin-Resistant Enterococci
Authors: Drees Marci , Snydman David R. , Schmid Christopher H. , Barefoot Laurie , Hansjosten Karen , Vue Padade M. , Cronin Michel , Nasraway Stanley A. , Golan Yoav
Published: July 2008

Objective.

To determine whether total and antianaerobic antibiotic exposure increases the risk of room contamination among vancomycin-resistant enterococci (VRE)–colonized patients.

Design And Setting.

A 14-month study in 2 intensive care units at an academic tertiary care hospital in Boston, Massachusetts.

Patients.

All patients who acquired VRE or were VRE-colonized on admission and who had environmental cultures performed.

Methods.

We performed weekly environmental cultures (2 sites per room) and considered a room to be contaminated if there was a VRE-positive environmental culture during the patient's stay. We determined risk factors for room contamination by use of the Cox proportional hazards model.

Results.

Of 142 VRE-colonized patients, 35 (25%) had an associated VRE-positive environmental culture. Patients who contaminated their rooms were more likely to have diarrhea than those who did not contaminate their rooms (23 [66%] of 35 vs 41 [38%] of 107;P= .005) and more likely to have received antibiotics while VRE colonized (33 [94%] of 35 vs 86 [80%] of 107;P= .02). There was no significant difference in room contamination rates between patients exposed to antianaerobic regimens and patients exposed to nonantianaerobic regimens or between patients with and patients without diarrhea, but patients without any antibiotic exposure were unlikely to contaminate their rooms. Diarrhea and antibiotic use were strongly confounded; although two-thirds of room contamination occurred in rooms of patients with diarrhea, nearly all of these patients received antibiotics. In multivariable analysis, higher mean colonization pressure in the ICU increased the risk of room contamination (adjusted hazard ratio per 10% increase, 1.44 [95% confidence interval, 1.04–2.04]), whereas no antibiotic use during VRE colonization was protective (adjusted hazard ratio, 0.21 [95% confidence interval, 0.05–0.89]).

Conclusions.

Room contamination with VRE was associated with increased mean colonization pressure in the ICU and diarrhea in the VRE-colonized patient, whereas no use of any antibiotics during VRE colonization was protective.
Controlled Trial Measuring the Effect of a Feedback Intervention on Hand Hygiene Compliance in a Step-Down Unit
Authors: Marra Alexandre R. , D'Arco Cláudia , Bravim Bruno de Arruda , Martino Marinês Dalla Valle , Correa Luci , Silva Cláudia Vallone , Lamblet Luiz Carlos R. , Junior Moacyr Silva , Lima Gisele de , Guastelli Luciana Reis , Barbosa Luciana , Santos Oscar Fernando Pavão dos , Edmond Michael B.
Published: July 2008

Objective.

To evaluate hand hygiene compliance in 2 adult step-down units (SDUs).

Design.

A 6-month (from March to September 2007), controlled trial comparing 2 SDUs, one with a feedback intervention program (ie, the intervention unit) and one without (ie, the control unit).

Setting.

Two 20-bed SDUs at a tertiary care private hospital.

Methods.

Hand hygiene episodes were measured by electronic recording devices and periodic observational surveys. In the intervention unit, feedback was provided by the SDU nurse manager, who explained twice a week to the healthcare workers the goals and targets for the process measures.

Results.

A total of 117,579 hand hygiene episodes were recorded in the intervention unit, and a total of 110,718 were recorded in the control unit (P= .63). There was no significant difference in the amount of chlorhexidine used in the intervention and control units (34.0 vs 26.7 L per 1,000 patient-days;P= .36) or the amount of alcohol gel used (72.5 vs 70.7 L per 1,000 patient-days;P= .93). However, in both units, healthcare workers used alcohol gel more frequently than chlorhexidine (143.2 vs 60.7 L per 1,000 patient-days;P< .001). Nosocomial infection rates in the intervention and control units, respectively, were as follows: for bloodstream infection, 3.5 and 0.79 infections per 1,000 catheter-days (P= .18); for urinary tract infection, 15.8 and 15.7 infections per 1,000 catheter-days (P= .99); and for tracheostomy-associated pneumonia, 10.7 and 5.1 infections per 1,000 device-days (P= . 13). There were no cases of infection with vancomycin-resistant enterococci and only a single case of infection with methicillin-resistantStaphylococcus aureus(in the control unit).

Conclusions.

The feedback intervention regarding hand hygiene had no significant effect on the rate of compliance. Other measures must be used to increase and sustain the rate of hand hygiene compliance.
Potential Economic Impact of Hospital-Acquired Infections in Uninsured Patients: A Preliminary Investigation
Authors: Thompson Jess , Jefferson Julie , Mermel Leonard A.
Published: July 2008

We studied uninsured patients admitted to Rhode Island Hospital from January 1 through June 30, 2005, and from January 1 through June 30, 2006. The mean total hospital charge for an uninsured patient with a hospital-acquired infection was $18,487; for those without such an infection, it was $4,951 (P < .001). Multivariable linear regression revealed that a hospital-acquired infection accounted for 11.8 excess hospital days (P = .001). Length of stay was the only independent variable associated with total excess hospital charges.
Artificial neural network for prediction of antigenic activity for a major conformational epitope in the hepatitis C virus NS3 protein
Authors: Lara James , Wohlhueter Robert M. , Dimitrova Zoya , Khudyakov Yury E.
Published: July 2008

Motivation: Insufficient knowledge of general principles for accurate quantitative inference of biological properties from sequences is a major obstacle in the rationale design of proteins with predetermined activities. Due to this deficiency, protein engineering frequently relies on the use of computational approaches focused on the identification of quantitative structure–activity relationship (SAR) for each specific task. In the current article, a computational model was developed to define SAR for a major conformational antigenic epitope of the hepatitis C virus (HCV) non-structural protein 3 (NS3) in order to facilitate a rationale design of HCV antigens with improved diagnostically relevant properties.

Results: We present an artificial neural network (ANN) model that connects changes in the antigenic properties and structure of HCV NS3 recombinant proteins representing all 6 HCV genotypes. The ANN performed quantitative predictions of the enzyme immunoassay (EIA) Signal/Cutoff (S/Co) profiles from sequence information alone with 89.8% accuracy. Amino acid positions and physicochemical factors strongly associated with the HCV NS3 antigenic properties were identified. The positions most significantly contributing to the model were mapped on the NS3 3D structure. The location of these positions validates the major associations found by the ANN model between antigenicity and structure of the HCV NS3 proteins.

Availability: Matlab code is available at the following URL address: http://bio-ai.myeweb.net/box_widget.html

Contact:  jlara@cdc.gov; yek0@cdc.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
The influence of mesoscale porosity on cortical bone anisotropy. Investigations via asymptotic homogenization
Authors: Parnell William J , Grimal Quentin
Published: July 2008

Recently, the mesoscale of cortical bone has been given particular attention in association with novel experimental techniques such as nanoindentation, micro-computed X-ray tomography and quantitative scanning acoustic microscopy (SAM). A need has emerged for reliable mathematical models to interpret the related microscopic and mesoscopic data in terms of effective elastic properties. In this work, a new model of cortical bone elasticity is developed and used to assess the influence of mesoscale porosity on the induced anisotropy of the material. Only the largest pores (Haversian canals and resorption cavities), characteristic of the mesoscale, are considered. The input parameters of the model are derived from typical mesoscale experimental data (e.g. SAM data). We use the method of asymptotic homogenization to determine the local effective elastic properties by modelling the propagation of low-frequency elastic waves through an idealized material that models the local mesostructure. We use a novel solution of the cell problem developed by Parnell & Abrahams. This solution is stable for the physiological range of variation of mesoscopic porosity and elasticity found in bone. Results are computed efficiently (in seconds) and the solutions can be implemented easily by other workers. Parametric studies are performed in order to assess the influence of mesoscopic porosity, the assumptions regarding the material
inside
the mesoscale pores (drained or undrained bone) and the shape of pores. Results are shown to be in good qualitative agreement with existing schemes and we describe the potential of the scheme for future use in modelling more complex microstructures for cortical bone. In particular, the scheme is shown to be a useful tool with which to predict the qualitative changes in anisotropy due to variations in the structure at the mesoscale.
Dynamics of haemopoiesis across mammals
Authors: Dingli David , Traulsen Arne , Pacheco Jorge M
Published: July 2008

Haemopoiesis is a fundamental physiologic process found in many animals. Among mammals, the diversity in size and function required suitable adaptations of this process. In this work, we use allometric principles to determine whether this required a change in the basic architecture of haemopoiesis. We show that it is possible to express both the number and rate with which haemopoietic stem cells replicate as well as total marrow output across all mammals as a function of adult mass. This unified view, which is compatible with the existing data, suggests that there was no need for major adaptations in the architecture of haemopoiesis across mammals.