bluuebunny/crossref_metadata_2025 huggingface dataset:
Raman intensity enhancement in silicon-on-insulator substrates by laser deflection at atomic force microscopy tips and particles
Authors: Georgi Carsten , Hecker Michael , Zschech Ehrenfried
Published: April 2007

It is shown that Raman intensities of bulk and film in silicon-on-insulator substrates strongly depend on the incident angle of the exciting laser. In a backscattering geometry with perpendicular laser incidence, deflection at particles or atomic force microscopy tips can thereby lead to a selective enhancement of the film signal, which can be misinterpreted as surface/tip enhanced Raman scattering. The authors report strong enhancement effects by scattering at dielectric particles on silicon-on-insulator and silicon substrates as well as smaller effects for deflection at tips. In evaluating field enhancements on such substrates, this must be considered.
Carbon nanotube cantilevers on self-aligned copper silicide nanobeams
Authors: Parajuli Omkar , Kumar Nitin , Kipp Dylan , Hahm Jong-in
Published: April 2007

In this letter, the authors describe both a growth method for self-aligning copper silicide (Cu3Si) nanobeams and their use as active catalysts for carbon nanotube (CNT) synthesis via chemical vapor deposition. In the unique geometry of these useful structures, CNT cantilevers are anchored firmly to the Cu3Si nanobeams. The resulting CNT-Cu3Si structures may improve accuracy and reliability of CNT applications in nanoelectromechanical systems.
Fluorine effects on the dipole structures of the Al2O3 thin films and characterization by spectroscopic ellipsometry
Authors: Lai Chao Sung , Fan Kung Ming , Peng Hsing Kan , Lin Shian Jyh , Lee Chung Yuan , Ai Chi Fong
Published: April 2007

Fluorine-terminated chemical bonds and dipole structures within an Al2O3 layer were investigated in this study. Spectroscopic ellipsometry (SE) was employed to estimate the characteristics of fluorinated Al2O3. The parameters S0 and λ0 extracted from SE were analyzed to detect the influence of F-terminated bonding. Al–O bonds were replaced by the Al–F bonds after fluorine was implanted on the silicon substrate. A physical model of dipole structures was proposed explaining the F incorporation phenomenon.
Size dependence of optical eigenmodes in photonic quantum dots prepared by conformal deposition method
Authors: Chen San , Qian Bo , Chen Kunji , Zhang Xiangao , Xu Jun , Ma Zhongyuan , Li Wei , Huang Xinfan
Published: April 2007

An approach was proposed to achieve Si-based three-dimensional optical microcavities, in which photons were confined by Bragg reflectors in all dimensions instead of the lateral confinement by using total internal reflection. Size-dependent photonic energy modes were observed when the lateral size is changed from 4.5to1.5μm. With decreasing lateral size the modes shift to higher energies, and the splitting between the modes increases which indicates that the three-dimensional optical microcavity looks like photonic quantum dots. The observed discrete optical eigenmodes show a quantitative agreement with numerical calculations of quantized photon states in photonic quantum dots.
Air-coupled excitation of rocking motion of individual microspheres on surfaces
Authors: Murthy Peri M. D. , Cetinkaya Cetin
Published: April 2007

In current study, it is demonstrated that the rocking motion of a single microsphere can be excited by means of impulsive acoustic fields generated by air-coupled transduction and the transient response of the particle can be detected optically. Such observation indicates the existence of rolling moment resistance of particle-surface adhesion bonds. A set of experiments were conducted for measuring the rocking resonance frequency of a microsphere on a flat substrate. The waveforms corresponding to the transient out-of-plane displacement of the rocking particle are used to extract the work of adhesion of the bond between the particle and substrate. Some of the frequency responses of the particles exhibited small shifts in their peak frequencies, which are away from their resonance frequencies, when compared to those of the base motion. These shifts are attributed to the viscoelastic damping effect due to capillary water meniscus formation in the adhesion bond of the particle-substrate system.
Electric preconcentration and detection of latex beads with interdigitated electrodes
Authors: de la Rica Roberto , Fernández-Sánchez César , Baldi Antonio
Published: April 2007

Latex beads are adhered to the surface of a chip containing polycrystalline silicon interdigitated electrodes by positive dielectrophoresis. The presence of the microparticles induces a change in the distribution of the electric fields and currents that can be detected by measuring either the conductance or the capacitance at the electrode terminals. This combination of actuation and detection with a single device is proposed as a suitable system applicable to biosensing.
Structural characterization of the Co2FeZ (Z=Al, Si, Ga, and Ge) Heusler compounds by x-ray diffraction and extended x-ray absorption fine structure spectroscopy
Authors: Balke Benjamin , Wurmehl Sabine , Fecher Gerhard H. , Felser Claudia , Alves Maria C. M. , Bernardi Fabiano , Morais Jonder
Published: April 2007

This work reports on the structure of Fe containing, Co2-based Heusler compounds that are suitable for magnetoelectronic applications. The compounds Co2FeZ (where Z=Al, Si, Ga, and Ge) were investigated using the x-ray diffraction (XRD) and extended x-ray absorption fine structure (EXAFS) techniques. Using XRD, it was shown conclusively that Co2FeAl crystallizes in the B2 structure whereas Co2FeSi crystallizes in the L21 structure. For compounds containing Ga or Ge, the XRD technique cannot be used to easily distinguish between the two structures. For this reason, the EXAFS technique was used to elucidate the structure of these two compounds. Analysis of the EXAFS data indicated that both compounds crystallize in the L21 structure.
How do nanometer scale dislocation traces evolve in the stress anomaly domain of intermetallics?
Authors: Coupeau Christophe , Bonneville Joël
Published: April 2007

The yield stress of Ni3Al intermetallic compounds exhibits positive temperature dependence. These compounds are used as the reinforcing phase of superalloys for aerospace and aeronautic applications. The proposed models based on cross-slip events from primary octahedral to cube slip planes explain this phenomenon either by dislocation velocity or mobile dislocation density effects. In situ atomic force microscopy observations of Ni3(Al,Hf) single crystals under increasing strain are reported. The fine slip line structure provides a direct evidence of a permanent locking of mobile dislocations in the yield stress anomaly domain.
Annealing effects on interfacial electronic structures and photoexcitation kinetics of regioregular poly(3-hexylthiophene) film on gold
Authors: Sohn Youngku , Stuckless J. Todd
Published: April 2007

The authors have studied annealing effects on the interfacial electronic structures and long-lived photoexcitation kinetics of poly(3-hexylthiophene-2,5-diyl) (P3HT) on gold, in comparison with poly[2-methoxy-5-(2′-ethyl-hexyloxy)-1,4-phenylene vinylene], using two-photon photoemission spectroscopy. Their studies show dramatic annealing effects on the two-photon photoemission yield and the kinetics of long-lived photoexcitations of P3HT. The interfacial electronic structures also strongly depend on the thermal annealing condition. Upon annealing P3HT, the photoemission yield is enhanced by two orders of magnitude, and the work function decreases by 1.0eV.
Specific heat capacity of a single component adsorbent-adsorbate system
Authors: Chakraborty A. , Saha B. B. , Koyama S. , Ng K. C.
Published: April 2007

A thermodynamic framework for calculating the specific heat capacity (Cp) of a single component adsorbent+adsorbate system has been derived and developed using the classical thermodynamics, and these are essential for the design of adsorption processes. The derived formulation of the Cp is compared with the experimentally measured Cp of adsorbent+adsorbate systems. The purpose of this letter is to fill up the information gap with respect to the state of adsorbed phase to dispel the confusion as to what is the actual state of the adsorbed phase.
Coarse molecular-dynamics analysis of stress-induced structural transitions in crystals
Authors: Amat Miguel A. , Kevrekidis Ioannis G. , Maroudas Dimitrios
Published: April 2007

We present a coarse molecular-dynamics approach for the study of stress-induced structural transformations in crystals at finite temperatures. The method relies on proper choice of a coarse variable (order parameter, observable), which parametrizes the changes in effective free energy during the transformation. Results are reported for bcc-to-hcp lattice transitions under pressure. We explore coarse-variable space to reconstruct an effective free-energy landscape quantifying the relative stability of different metastable basins and locate the onset, at a critical pressure, of the bcc-to-hcp transformation.
Investigation of water evolution and transport in fuel cells with high resolution synchrotron x-ray radiography
Authors: Manke I. , Hartnig Ch. , Grünerbel M. , Lehnert W. , Kardjilov N. , Haibel A. , Hilger A. , Banhart J. , Riesemeier H.
Published: April 2007

The authors report on in situ investigations of liquid water evolution and transport in an undisturbed operating fuel cell at the microscopic level. Synchrotron x-ray radiography enhances the spatial resolution by two orders of magnitude compared to the state-of-the-art techniques in this field. The primary spots of liquid water formation, their growth, and transport inside the porous gas diffusion material were analyzed; correlations between operating conditions and the dynamics of droplet formation are described. Previous findings from modeling and simulation approaches are confirmed and the applicability for the description of in situ processes of a recently proposed model has been proven.
Efficient generation of coherent acoustic phonons in (111) InGaAs∕GaAs multiple quantum wells through piezoelectric effects
Authors: Wen Yu-Chieh , Chou Li-Chang , Lin Hao-Hsiung , Gusev Vitalyi , Lin Kung-Hsuan , Sun Chi-Kuang
Published: April 2007

The authors demonstrate the generation of coherent acoustic phonons in (111)-strained InGaAs∕GaAs multiple quantum wells through piezoelectric coupling by an optical pump-probe technique. Dependence of the induced strain amplitude on the photocarrier density reveals that coherent acoustic phonons can be efficiently excited by the piezoelectric effect with an unscreened built-in electric field. Under high fluence excitation, the generation of coherent acoustic phonons saturates. The experimental results are supported by a macroscopic theoretical model. No backward Raman signal and no zone-folded phonon modes were observed in this low impedance-mismatch and finite-period heterostructure.
Epitaxial growth of lead zirconium titanate thin films on Ag buffered Si substrates using rf sputtering
Authors: Wang Chun , Laughlin David E. , Kryder Mark H.
Published: April 2007

Epitaxial lead zirconium titanate (PZT) (001) thin films with a Pt bottom electrode were deposited by rf sputtering onto Si(001) single crystal substrates with a Ag buffer layer. Both PZT(20∕80) and PZT(53∕47) samples were shown to consist of a single perovskite phase and to have the (001) orientation. The orientation relationship was determined to be PZT(001)[110]‖Pt(001)[110]‖Ag(001)[110]‖Si(001)[110]. The microstructure of the multilayer was studied using transmission electron microscopy (TEM). The electron diffraction pattern confirmed the epitaxial relationship between each layer. The measured remanent polarization Pr and coercive field Ec of the PZT(20∕80) thin film were 26μC∕cm2 and 110kV∕cm, respectively. For PZT(53∕47), Pr was 10μC∕cm2 and Ec was 80kV∕cm.
Defect-driven gain bistability in neutron damaged, silicon bipolar transistors
Authors: Fleming R. M. , Seager C. H. , Lang D. V. , Bielejec E. , Campbell J. M.
Published: April 2007

Using deep level transient spectroscopy, the authors have measured the defect spectrum in the collector of a n-p-n bipolar transistor following fast neutron irradiation as well as the gain on the same device. They show that a slow change observed in both the gain and deep level traps in the n-type collector at 300K are bistable. The transistor gain and the defects can be returned to the postirradiation condition by forward bias at room temperature, i.e., by operating the transistor (gain) or injection through the base-collector diode (defect spectrum).
Magnetic and electrical properties of Sm1−xNdxCd intermetallics
Authors: Li G. F. , Su J. R. , Zhu C. F.
Published: April 2007

The dc magnetization and resistivity of polycrystalline Sm1−xNdxCd (x=0,0.02,0.04,0.06,0.08,0.10) have been measured from 8K to room temperature. A magnetic compensation temperature (Tcomp), where the spin magnetization equals to the antiparallel orbital one, was observed for x⩾0.06 in the ordered state. Tcomp increases with increasing Nd content, and reaches 105K for x=0.10. This Tcomp is higher than that observed in Sm1−xGdxAl2 series.
Dynamical stability of the hardest known oxide and the cubic solar material: TiO2
Authors: Kim D. Y. , de Almeida J. S. , Koči L. , Ahuja R.
Published: April 2007

The authors have studied dynamical stability of different polymorphs of TiO2 using ab initio phonon calculations based on density functional theory in conjunction with force-constant method. Rutile TiO2 was found stable at ambient pressure, but unstable at high pressure. The calculated Raman frequency and phonon density of states (PDOS) of rutile TiO2 are in a good agreement with experiment. Concerning two cubic phases (solar materials), fluorite stabilized under pressure, whereas pyrite showed instability throughout the whole pressure range. Furthermore, the PDOS of cotunnite (the hardest known oxide) phase confirmed that it exists at high pressure and can be quenched down to a low pressure limit.
Design of semiconductor CdSe core ZnS∕CdS multishell quantum dots for multiphoton applications
Authors: Fu Y. , Han T.-T. , Ågren H. , Lin L. , Chen P. , Liu Y. , Tang G.-Q. , Wu J. , Yue Y. , Dai N.
Published: April 2007

Optical properties of colloidal II-VI semiconductor CdSe cores with ZnS and CdS multishell quantum dots (QDs) have been studied by experimental characterization and theoretical analysis. Due to the large number of energy states densely compacted in both conduction and valence bands of the quantum dots, strong interband and intraband optical couplings are induced by the multiphoton excitation, implicating an efficient fluorescence of such II-VI-based core-multishell CdSe QDs. This fact in combination with the advantage of the size tolerance of II-VI QDs with respect to the narrow fluorescence bandwidth make these systems excellent candidates for applications using fluorescence induced by multiphoton excitation.
Raman properties of gold nanoparticle-decorated individual carbon nanotubes
Authors: Assmus Tilman , Balasubramanian Kannan , Burghard Marko , Kern Klaus , Scolari Matteo , Fu Nan , Myalitsin Anton , Mews Alf
Published: April 2007

Single-wall carbon nanotubes decorated by gold nanoparticles with sizes of a few tens of nanometers were investigated by confocal Raman microscopy. It was found that individual nanoparticles impart a sizable Raman enhancement exceeding one order of magnitude, without appreciably interfering with polarization dependent Raman measurements. By contrast, cavity effects within small nanoparticle agglomerates resulted in a 20-fold stronger enhancement and significant distortions of the polarization characteristic.
Cutoff wavelength of Hg1−xCdxTe epilayers by infrared photoreflectance spectroscopy
Authors: Shao Jun , Lü Xiang , Lu Wei , Yue Fangyu , Huang Wei , Li Ning , Wu Jun , He Li , Chu Junhao
Published: April 2007

A comparative study of cutoff wavelength is performed by photocurrent (PC), transmission, and infrared photoreflectance (PR) spectroscopies on arsenic-doped Hg1−xCdxTe molecular beam epitaxial layers in the midinfrared spectral region. It is illustrated that (i) a shorter cutoff wavelength of PC response may be predicted by either the band gap or the energy of the half-maximum transmission and (ii) the main PR peak is coincident energetically to that of the third-derivative maximum of the PC spectrum. The mechanism behind is discussed with the aid of photoluminescence measurements. The results indicate that the infrared PR spectroscopy may serve as a contactless alternative to the PC spectroscopy for predicting the cutoff wavelength of narrow-gap HgCdTe epilayers reliably.
The successful eradication of introduced roof rats (Rattus rattus) from Buck Island using diphacinone, followed by an irruption of house mice (Mus musculus)
Authors: Witmer Gary W. , Boyd Frank , Hillis-Starr Zandy
Published: April 2007

The United States National Park Service and the United States Wildlife Services made a planned and sustained effort to eradicate the introduced roof rats (Rattus rattus) from Buck Island Reef National Monument in the Caribbean Sea during 1998–2000. The rats were causing substantial damage to a variety of the 80-ha island’s floral and faunal resources. An island-wide grid of elevated bait stations containing anticoagulant (0.005% diphacinone; 50 ppm) rodenticide bait blocks were used to eradicate the rats. The bait stations were modified several times to assure ready access by rats while minimising access by non-target animals, especially crabs and birds. Numerous post-project trapping sessions over six years resulted in no rat captures, suggesting that, indeed, the rats had been eradicated from the island. No non-target losses resulting from the baiting program were observed by field personnel, but they noted what appeared to be a recovery of some of the island’s floral and faunal resources. There have been no depredations of endangered sea turtle nests since the eradication. Post-project monitoring sessions revealed the presence of a growing house mouse (Mus musculus) population on the island. The threats posed by, and potential management strategies for, this introduced pest species are being investigated. This is the first successful rat eradication on a sizable island, using diphacinone bait blocks with a unique, elevated bait-station system. Diphacinone can provide an alternative to the highly toxic brodifacoum and may help reduce non-target hazards in some situations, although several applications are generally required.
Recovery of the red-finned blue-eye: an endangered fish from springs of the Great Artesian Basin
Authors: Fairfax R. , Fensham R. , Wager R. , Brooks S. , Webb A. , Unmack P.
Published: April 2007

The red-finned blue-eye (Scaturiginichthys vermeilipinnis) is endemic to a single complex of springs emanating from the Great Artesian Basin, Australia. The species has been recorded as naturally occurring in eight separate very shallow (generally <20 mm) springs, with a combined wetland area of ~0.3 ha. Since its discovery in 1990, five red-finned blue-eye (RFBE) populations have been lost and subsequent colonisation has occurred in two spring wetlands. Current population size is estimated at <3000 individuals. Artesian bores have reduced aquifer pressure, standing water levels and spring-flows in the district. There is evidence of spatial separation within the spring pools where RFBE and the introduced fish gambusia (Gambusia holbrooki) co-occur, although both species are forced together when seasonal extremes affect spring size and water temperature. Gambusia was present in four of the five springs where RFBE populations have been lost. Four out of the five remaining subpopulations of RFBE are Gambusia free. Circumstantial evidence suggests that gambusia is a major threat to red-finned blue-eyes. The impact of Gambusia is probably exacerbated by domestic stock (cattle and sheep), feral goats and pigs that utilise the springs and can negatively affect water quality and flow patterns. Three attempts to translocate RFBE to apparently suitable springs elsewhere within the complex have failed. Opportunities to mitigate threats are discussed, along with directions for future research to improve management of this extremely threatened fish and habitat.
A monomeric G protein-coupled receptor isolated in a high-density lipoprotein particle efficiently activates its G protein
Authors: Whorton Matthew R. , Bokoch Michael P. , Rasmussen Søren G. F. , Huang Bo , Zare Richard N. , Kobilka Brian , Sunahara Roger K.
Published: April 2007

G protein-coupled receptors (GPCRs) respond to a diverse array of ligands, mediating cellular responses to hormones and neurotransmitters, as well as the senses of smell and taste. The structures of the GPCR rhodopsin and several G proteins have been determined by x-ray crystallography, yet the organization of the signaling complex between GPCRs and G proteins is poorly understood. The observations that some GPCRs are obligate heterodimers, and that many GPCRs form both homo- and heterodimers, has led to speculation that GPCR dimers may be required for efficient activation of G proteins. However, technical limitations have precluded a definitive analysis of G protein coupling to monomeric GPCRs in a biochemically defined and membrane-bound system. Here we demonstrate that a prototypical GPCR, the β2-adrenergic receptor (β2AR), can be incorporated into a reconstituted high-density lipoprotein (rHDL) phospholipid bilayer particle together with the stimulatory heterotrimeric G protein, Gs. Single-molecule fluorescence imaging and FRET analysis demonstrate that a single β2AR is incorporated per rHDL particle. The monomeric β2AR efficiently activates Gs and displays GTP-sensitive allosteric ligand-binding properties. These data suggest that a monomeric receptor in a lipid bilayer is the minimal functional unit necessary for signaling, and that the cooperativity of agonist binding is due to G protein association with a receptor monomer and not receptor oligomerization.
Characterization of a UBC13 kinase in
Plasmodium falciparum
Authors: Philip Nisha , Haystead Timothy A.
Published: April 2007

Protein kinases are generally recognized as attractive drug targets to treat a variety of human diseases. Recent analysis of the
Plasmodium falciparum
kinome identified several kinases that are entirely unique to
Plasmodium
species. The specific functions and targets of most of these enzymes remain largely unknown. Here, we have identified a
P. falciparum
kinase (PfPK9/PF13_0085 ORF) that does not cluster with any of the typical eukaryotic protein kinases. PfPK9 protein expression was induced ≈18 h after red blood cell infection, and was mainly localized to the parasitophorous vacuolar membrane as well as the cytosol. Recombinant PfPK9 autophosphorylated
in vitro
and specifically phosphorylated the exogenous substrate histone H1, indicating that it is catalytically active. Phosphopeptide mapping studies showed that autophosphorylation occurred at three residues: T082, T265, and T269. We identified a
P. falciparum
homolog of the E2 ubiquitin-conjugating enzyme 13 (UBC13) as an endogenous substrate for PfPK9. PfPK9 phosphorylated UBC13 at S106, a highly conserved residue among eukaryotic E2s, and suppressed its ubiquitin-conjugating activity. Our findings not only describe a previously uncharacterized
Plasmodium
kinase and its likely
in vivo
target, but also suggest that modulation of UBC13 activity by phosphorylation may be a common regulatory mechanism in eukaryotes.
Multiple molecular evidences for a living mammalian fossil
Authors: Huchon Dorothée , Chevret Pascale , Jordan Ursula , Kilpatrick C. William , Ranwez Vincent , Jenkins Paulina D. , Brosius Jürgen , Schmitz Jürgen
Published: April 2007

Laonastes aenigmamus
is an enigmatic rodent first described in 2005. Molecular and morphological data suggested that it is the sole representative of a new mammalian family, the Laonastidae, and a member of the Hystricognathi. However, the validity of this family is controversial because fossil-based phylogenetic analyses suggest that
Laonastes
is a surviving member of the Diatomyidae, a family considered to have been extinct for 11 million years. According to these data,
Laonastes
and Diatomyidae are the sister clade of extant Ctenodactylidae (i.e., gundies) and do not belong to the Hystricognathi. To solve the phylogenetic position of
Laonastes
, we conducted a large-scale molecular phylogeny of rodents. The analysis includes representatives of all major rodent taxonomic groups and was based on 5.5 kb of sequence data from four nuclear and two mitochondrial genes. To further validate the obtained results, a short interspersed element insertion analysis including 11 informative loci was also performed. Our molecular data based on sequence and short interspersed element analyses unambiguously placed
Laonastes
as a sister clade of gundies. All alternative hypotheses were significantly rejected based on Shimodaira–Hasegawa tests, supporting the idea that
Laonastes
does not belong to the Hystricognathi. Molecular dating analysis also supports an ancient divergence, ≈44 Mya ago, between Ctenodactylidae and
Laonastes
. These combined analyses support the hypothesis that
Laonastes
is indeed a living fossil. Protection of this surviving species would conserve an ancient mammalian family.
Pigeons combine compass and landmark guidance in familiar route navigation
Authors: Biro Dora , Freeman Robin , Meade Jessica , Roberts Stephen , Guilford Tim
Published: April 2007

How do birds orient over familiar terrain? In the best studied avian species, the homing pigeon (
Columba livia
), two apparently independent primary mechanisms are currently debated: either memorized visual landmarks provide homeward guidance directly, or birds rely on a compass to home from familiar locations. Using miniature Global Positioning System tracking technology and clock-shift procedures, we set sun-compass and landmark information in conflict, showing that experienced birds can accurately complete their memorized routes by using landmarks alone. Nevertheless, we also find that route following is often consistently offset in the expected compass direction, faithfully reproducing the shape of the track, but in parallel. Thus, we demonstrate conditions under which compass orientation and landmark guidance must be combined into a system of simultaneous or oscillating dual control.
Political polarization
Authors: Dixit Avinash K. , Weibull Jörgen W.
Published: April 2007

Failures of government policies often provoke opposite reactions from citizens; some call for a reversal of the policy, whereas others favor its continuation in stronger form. We offer an explanation of such polarization, based on a natural bimodality of preferences in political and economic contexts and consistent with Bayesian rationality.
European early modern humans and the fate of the Neandertals
Authors: Trinkaus Erik
Published: April 2007

A consideration of the morphological aspects of the earliest modern humans in Europe (more than ≈33,000 B.P.) and the subsequent Gravettian human remains indicates that they possess an anatomical pattern congruent with the autapomorphic (derived) morphology of the earliest (Middle Paleolithic) African modern humans. However, they exhibit a variable suite of features that are either distinctive Neandertal traits and/or plesiomorphic (ancestral) aspects that had been lost among the African Middle Paleolithic modern humans. These features include aspects of neurocranial shape, basicranial external morphology, mandibular ramal and symphyseal form, dental morphology and size, and anteroposterior dental proportions, as well as aspects of the clavicles, scapulae, metacarpals, and appendicular proportions. The ubiquitous and variable presence of these morphological features in the European earlier modern human samples can only be parsimoniously explained as a product of modest levels of assimilation of Neandertals into early modern human populations as the latter dispersed across Europe. This interpretation is in agreement with current analyses of recent and past human molecular data.
Functional evaluation of domain–domain interactions and human protein interaction networks
Authors: Schlicker Andreas , Huthmacher Carola , Ramírez Fidel , Lengauer Thomas , Albrecht Mario
Published: April 2007

Motivation: Large amounts of protein and domain interaction data are being produced by experimental high-throughput techniques and computational approaches. To gain insight into the value of the provided data, we used our new similarity measure based on the Gene Ontology (GO) to evaluate the molecular functions and biological processes of interacting proteins or domains. The applied measure particularly addresses the frequent annotation of proteins or domains with multiple GO terms.

Results: Using our similarity measure, we compare predicted domain–domain and human protein–protein interactions with experimentally derived interactions. The results show that our similarity measure is of significant benefit in quality assessment and confidence ranking of domain and protein networks. We also derive useful confidence score thresholds for dividing domain interaction predictions into subsets of low and high confidence.

Contact:  mario.albrecht@mpi-inf.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Acupuncture Research: Strategies for Clinical Evaluation: Workshop Report, York, July 5–8, 2006
Authors: Hopwood Val , MacPherson Hugh
Published: April 2007

This report summarizes a ground‐breaking workshop on the strategic direction of acupuncture research which was held in York in early July 2006. Three days were spent discussing the history, the philosophy and the practicalities of researching acupuncture. Attending the workshop were an international group of researchers with varied backgrounds, including acupuncturists, physicians, physiotherapists, sociologists and anthropologists. Supported by the Medical Research Council′s Health Services Research Collaboration, Elsevier and others, this workshop was an opportunity to brainstorm the issues and to the concerns in the field and set out directions for research that would tackle some of the major challenges facing the acupuncture research community.
DDOMAIN: Dividing structures into domains using a normalized domain–domain interaction profile
Authors: Zhou Hongyi , Xue Bin , Zhou Yaoqi
Published: April 2007

Dividing protein structures into domains is proven useful for more accurate structural and functional characterization of proteins. Here, we develop a method, called DDOMAIN, that divides structure into DOMAINs using a normalized contact‐based domain–domain interaction profile. Results of DDOMAIN are compared to AUTHORS annotations (domain definitions are given by the authors who solved protein structures), as well as to popular SCOP and CATH annotations by human experts and automatic programs. DDOMAIN's automatic annotations are most consistent with the AUTHORS annotations (90% agreement in number of domains and 88% agreement in both number of domains and at least 85% overlap in domain assignment of residues) if its three adjustable parameters are trained by the AUTHORS annotations. By comparison, the agreement is 83% (81% with at least 85% overlap criterion) between SCOP‐trained DDOMAIN and SCOP annotations and 77% (73%) between CATH‐trained DDOMAIN and CATH annotations. The agreement between DDOMAIN and AUTHORS annotations goes beyond single‐domain proteins (97%, 82%, and 56% for single‐, two‐, and three‐domain proteins, respectively). For an “easy” data set of proteins whose CATH and SCOP annotations agree with each other in number of domains, the agreement is 90% (89%) between “easy‐set”‐trained DDOMAIN and CATH/SCOP annotations. The consistency between SCOP‐trained DDOMAIN and SCOP annotations is superior to two other recently developed, SCOP‐trained, automatic methods PDP (protein domain parser), and DomainParser 2. We also tested a simple consensus method made of PDP, DomainParser 2, and DDOMAIN and a different version of DDOMAIN based on a more sophisticated statistical energy function. The DDOMAIN server and its executable are available in the services section on http://sparks.informatics.iupui.edu.
A bacterial two‐hybrid system based on the twin‐arginine transporter pathway of E. coli
Authors: Strauch Eva‐Maria , Georgiou George
Published: April 2007

We have developed a bacterial two‐hybrid system for the detection of interacting proteins that capitalizes on the folding quality control mechanism of the Twin Arginine Transporter (Tat) pathway. The Tat export pathway is responsible for the membrane translocation of folded proteins, including proteins consisting of more than one polypeptide, only one of which contains a signal peptide (“hitchhiker export”). Here, one protein (bait) is expressed as a fusion to a Tat signal peptide, whereas the second protein (prey) is fused to a protein reporter that can confer a phenotype only after export into the bacterial periplasmic space. Since the prey–reporter fusion lacks a signal peptide, it can only be exported as a complex with the bait–signal peptide fusion that is capable of targeting the Tat translocon. Using maltose‐binding protein as a reporter, clones expressing interacting proteins can be grown on maltose minimal media or on MacConkey plates. In addition, we introduce the use of the cysteine disulfide oxidase DsbA as a reporter. Export of a signal peptide–prey:bait–DsbA complex into the periplasm allows complementation of dsbA− mutants and restores the formation of active alkaline phosphatase, which in turn can be detected by a chromogenic assay.
Cell‐free complements in vivo expression of the E. coli membrane proteome
Authors: Savage David F. , Anderson Corey L. , Robles‐Colmenares Yaneth , Newby Zachary E. , Stroud Robert M.
Published: April 2007

Reconstituted cell‐free (CF) protein expression systems hold the promise of overcoming the traditional barriers associated with in vivo systems. This is particularly true for membrane proteins, which are often cytotoxic and due to the nature of the membrane, difficult to work with. To evaluate the potential of cell‐free expression, we cloned 120 membrane proteins from E. coli and compared their expression profiles in both an E. coli in vivo system and an E. coli‐derived cell‐free system. Our results indicate CF is a more robust system and we were able to express 63% of the targets in CF, compared to 44% in vivo. To benchmark the quality of CF produced protein, five target membrane proteins were purified and their homogeneity assayed by gel filtration chromatography. Finally, to demonstrate the ease of amino acid labeling with CF, a novel membrane protein was substituted with selenomethionine, purified, and shown to have 100% incorporation of the unnatural amino acid. We conclude that CF is a novel, robust expression system capable of expressing more proteins than an in vivo system and suitable for production of membrane proteins at the milligram level.
The FliK protein and flagellar hook‐length control
Authors: Waters Richard C. , O'Toole Paul W. , Ryan Kieran A.
Published: April 2007

The bacterial flagellum is a highly complex prokaryotic organelle. It is the motor that drives bacterial motility, and despite the large amount of energy required to make and operate flagella, motile organisms have a strong adaptive advantage. Flagellar biogenesis is both complex and highly coordinated and it typically involves at least three two‐component systems. Part of the flagellum is a type III secretion system, and it is via this structure that flagellar components are exported. The assembly of a flagellum occurs in a number of stages, and the “checkpoint control” protein FliK functions in this process by detecting when the flagellar hook substructure has reached its optimal length. FliK then terminates hook export and assembly and transmits a signal to begin filament export, the final stage in flagellar biosynthesis. As yet the exact mechanism of how FliK achieves this is not known. Here we review what is known of the FliK protein and discuss the evidence for and against the various hypotheses that have been proposed in recent years to explain how FliK controls hook length, FliK as a molecular ruler, the measuring cup theory, the role of the FliK N terminus, the infrequent molecular ruler theory, and the molecular clock theory.
Endozoochory varies with ecological scale and context
Authors: Anne Bråthen Kari , T. González Victoria , Iversen Marianne , Killengreen Siw , T. Ravolainen Virve , A. Ims Rolf , G. Yoccoz Nigel
Published: April 2007

Several studies on endozoochory have established large herbivores as important for seed dispersal, yet no studies have evaluated how endozoochory is dependent on ecological scale and context. Here we address effects of reindeer density on endozoochory in a hierarchical, multi‐scale study, encompassing several ecological contexts.

We found reindeer density effects on endozoochory to vary with spatial scale. Higher reindeer densities at the level of landscape areas, as indexed through faeces abundance, were related to both less species and lower abundance of emerging plants from faeces. In contrast, there was no effect of higher reindeer densities at the level of herding districts (i.e. large scale assemblages of landscapes). Lack of consistency between scales reflects ecological hierarchy, indicating that reindeer density effects on endozoochory best matches at the scale of landscapes.

Pasture seed plant composition was only partly an important ecological factor. That is, ericoid species, the dominating plants in the pastures, were also the most abundant seed plants found to emerge from the faeces. However, most herbaceous seed plant species in the pastures were not emerging from the faeces and the few that emerged were positively related to the site fertility and altitude of the pasture.

Studies addressing endozoochory of ruminants are typically concerned with seed plants, whereas in this study we also found indications of that diaspores of ferns are viable after passing the digestive tract of large herbivores. Vascular spore plants were even more abundant in the faeces than were vascular seed plants.

Results from this study demonstrate that reindeer may counteract a potentially negative impact on seed limitation from their grazing by returning viable seeds in their faeces. However, in Finnmark, northern Norway, this effect is only marginal, relates only to a very few species and individuals and shows ecological scale and context dependence.
Faulting, seismic‐stratigraphic architecture and Late Quaternary evolution of the Gulf of Alkyonides Basin–East Gulf of Corinth, Central Greece
Authors: Sakellariou D. , Lykousis V. , Alexandri S. , Kaberi H. , Rousakis G. , Nomikou P. , Georgiou P. , Ballas D.
Published: April 2007

Swath bathymetry, single‐channel seismic profiling, gravity and box coring, 210Pb down‐core radiochemical analyses and sequence stratigraphic analysis in the Gulf of Alkyonides yielded new data on the evolution of the easternmost part of the Gulf of Corinth. Three fault segments, the South Strava, West Alkyonides and East Alkyonides faults, dipping 45, 30 and 45°, respectively, northwards, form the southern tectonic boundary of the Alkyonides Basin. Two 45° southwards dipping segments, the Domvrena and Germeno Faults, form the northern tectonic margin. The Alkyonides Basin architecture is the result of a complex interaction between fault dynamics and the effects of changes in climate and sea/lake level. Chrono‐stratigraphic interpretation of the seismic stratigraphy through correlation of the successive seismic packages with lowstands and highstands of the Late Quaternary indicates that the evolution of the basin started 0.40–0.45 Ma BP and can be divided in two stages. Subsidence of the basin floor during the early stage was uniform across the basin and the mean sedimentation rate was 1.0 m kyear−1. Vertical slip acceleration on the southern tectonic margin since 0.13 Ma BP resulted in the present asymmetric character of the basin. Subsidence concentrated close to the southern margin and sedimentation rate increased to 1.4 m kyear−1 in the newly formed depocentre of the basin. Actual (last 100 year) sedimentation rates were calculated to >2 mm year−1, but are significantly influenced by the presence of episodic gravity flow deposits. Total vertical displacement of 1.1 km is estimated between the subsiding Alkyonides Basin floor and the uplifting Megara Basin since the onset of basin subsidence at a mean rate of 2.4–2.75 m kyear−1, recorded on the East Alkyonides Fault. Gravity coring in the Strava Graben and in the lower northern margin of Alkyonides Basin proved the presence of whitish to olive grey laminated mud below thin marine sediments. Aragonite crystals and absence of the marine coccolithophora Emiliania huxleyi indicate sedimentation in lacustrine environment during the last lowstand glacial interval.
The size–grain hypothesis: do macroarthropods see a fractal world?
Authors: KASPARI MICHAEL , WEISER MICHAEL
Published: April 2007

Abstract1. In the size–grain hypothesis (a) long legs allow walking organisms to step over gaps and pores in substrate but prohibit them from entering those gaps; (b) the world is more rugose for small organisms; and (c) the relative cost of long legs increases as organisms grow smaller. The hypothesis predicts a positive allometry of leg length ( = massbwhereb> 0.33 of isometry), a pattern that robustly holds for ants.

2. Toward testing for leg length allometries in other taxa, arthropods were extracted from the Panama leaf litter and measured. Three common taxa (spiders, diplopods, Coleoptera) yieldedbs that exceeded 0.33 while three others (Acarina, Pseudoscorpiones, and Collembola) did not. The exponentbtended to increase (P =0.06,n= 7) with an arthropod taxon’s average body mass.

3. Since leg length in cursorial organisms tends toward isometry in very small and very large taxa (i.e. mammals) this suggests that the size–grain hypothesis may best apply at a transition zone of intermediate body mass: the macroarthropods.

4. Body length was a robust predictor of mass in all groups despite variation in shape.
Bioactive glass particles of narrow size range for the treatment of oral bone defects: a 1–24 month experiment with several materials and particle sizes and size ranges
Authors: SCHEPERS E.J.G. , DUCHEYNE P.
Published: April 2007

summary
The aim of this study was to evaluate bone growth around bioactive glass particles in bone defects in comparison to hydroxylapatite particles. The bioactive glass particles were implanted in the partial edentulous jaws of Beagle dogs in two different compositions and several sizes and size ranges. After 1, 2, 3, 6, 12 and 24 months the samples were harvested and processed for undecalcified sectioning. Histological analysis showed a superior response of the bioactive glass particles of composition A and narrow size range (300‐355 μm). Besides extensive osteoconductive properties, the bone repair was also stimulated by bone growth in the internally eroded particles. The data demonstrate conclusively that the well known corrosion reactions of the bioactive glass lead to the formation of protective pouches. In these protective pouches formation of new bone is detected without this bone being connected to the bone tissue outside the particles. These islands of newly formed bone tissue function as nuclei for further bone growth and enhance the repair of the defect.
An investigation of potential desensitizing agents in the dentine disc model: a scanning electron microscopy study
Authors: LING T.Y.Y. , GILLAM D.G. , BARBER P.M. , MORDAN N.J. , CRITCHELL J.
Published: April 2007

summary
Cervical dentine sensitivity (CDS) may be defined as pain arising from exposed dentine. The prefix cervical indicates the location of the sensitivity and/or its subsequent treatment. Currently the most accepted mechanism of intradental nerve activation associated with dentine sensitivity appears to be hydrodynamic in nature. The concept of tubule occlusion as a method of dentine desensitization is a logical conclusion of the hydrodynamic theory. The authors employed the dentine disc model, qualitative scanning electron microscopy (SEM) and X‐ray microanalysis to investigate whether selected desensitizing agents occlude dentinal tubule orifices. Strict control procedures have been used together with various methods of application to apply these agents to human dentine discs. SEM was used to examine the degree of deposit left by the various agents on disc surfaces and X‐ray microanalysis was employed to characterize the elemental composition of the deposit. Analysis of selected agents, both prior to and after application on dentine discs was performed for comparative purposes. The degree of retention of the surface deposit upon rotation with saliva supernatant for 6 h was also studied. The results of this study indicated that ferric oxalate, the active ingredient of Sensodyne Sealant®, which produced initial crystal‐like structures, occluding almost all the tubule orifices was superior to potassium oxalate (Butler Protect®). Of the over‐the‐counter (OTC) desensitizing products tested, both silica‐ and calcium‐based abrasive components were observed both on the surface and within the tubules, indicating a certain degree of therapeutic potential for these two components. These findings suggest that certain desensitizing agents have tubule occluding properties as observed in this in vitro system which, in turn, may indicate a therapeutic potential in vivo.
The influence of acupuncture on salivary flow rates in healthy subjects
Authors: DAWIDSON I. , BLOM M. , LUNDEBERG T. , ANGMAR‐MÅNSSON B.
Published: April 2007

summary
This Study investigated the influence of acupuncture stimulation on the salivary secretion of eight healthy subjects. The salivary flow of each subject was measured before, during and after every acupuncture session. The unstimulated, chewing‐stimulated and citric acid‐stimulated flows were investigated, in combination with manual and electrically stimulated acupuncture. The results showed a significant increase of the unstimulated salivary flow both during and after the manual acupuncture stimulation as compared to baseline levels. There was no effect on the unstimulated salivary flow with electro‐acupuncture. The stimulated salivary flow was not affected by manual acupuncture, while the electrically stimulated acupuncture led to a significant decrease of the chewing‐stimulated salivary flow. The improvement of the unstimulated salivary secretion in healthy subjects was in accordance with our previous findings in xerostomic patients. It is possible that the salivary secretion is influenced by the augmented release of neuropeptides caused by acupuncture. Some neuro‐peptides have been shown to affect salivary secretion as well as capillary blood flow.
Vibration transmission across the temporomandibular joint
Authors: PRINZ J. F.
Published: April 2007

summary
A non‐invasive method of assessing the status of the temporomandibular joint is presented. The method involves placing a computer‐controlled vibrator against a lower incisor, and microphones over the temporal bones. The amplitude of the signal transmitted is shown to be a function of the input frequency, the position of the mandible and the loading on the joint.