bluuebunny/crossref_metadata_2025 huggingface dataset:
Theory of thermostatted inhomogeneous granular fluids: A self-consistent density functional description
Authors: Marini-Bettolo-Marconi Umberto , Tarazona Pedro , Cecconi Fabio
Published: April 2007

The authors present a study of the nonequilibrium statistical properties of a one dimensional hard-rod fluid dissipating energy via inelastic collisions and subject to the action of a Gaussian heat bath, simulating an external driving mechanism. They show that the description of the fluid based on the one-particle phase-space reduced distribution function, in principle necessary because of the presence of velocity dependent collisional dissipation, can be contracted to a simpler description in configurational space. Indeed, by means of a multiple-time-scale method the authors derive a self-consistent governing equation for the particle density distribution function. This equation is similar to the dynamic density functional equation employed in the study of colloids, but contains additional terms taking into account the inelastic nature of the fluid. Such terms cannot be derived from a Liapunov generating functional and contribute not only to the relaxational properties, but also to the nonequilibrium steady state properties. A validation of the theory against molecular dynamics simulations is presented in a series of cases, and good agreement is found.
Plasmonic effects and visible light diffraction in three-dimensional opal-metal photonic crystals
Authors: Akimov A. V. , Meluchev A. A. , Kurdyukov D. A. , Scherbakov A. V. , Holst A. , Golubev V. G.
Published: April 2007

The angular dependence of the reflectivity spectrum for visible light was measured in opal-metal (Ag and W) composites with a high filling factor. The diffraction patterns were observed at a wavelength essentially exceeding the period of a three-dimensional photonic structure. The authors offer a qualitative explanation based on the similarity between the experimental observations and those modified by the three-dimensional periodicity plasmonic effects in two-dimensional periodic structures with a subwavelength defect.
Kinetics of a semiflexible chain under external force
Authors: Nam Gi-moon , Lee Nam-Kyung
Published: April 2007

The kinetic properties of a semiflexible chain subject to an external force are investigated using scaling arguments and computer simulations. By monitoring the mean square displacements in principal axes, the authors found that the anisotropic dynamic fluctuations go through several distinct kinetic regimes characterized by two different exponents corresponding to transverse and longitudinal fluctuations. When a force is applied at one chain end, the tension propagates gradually to the other end, leading to nonuniform tension profiles. At short times, they observe sublinear relaxation of the mean square fluctuations in both longitudinal and transverse directions. At intermediate times, the kinetics is dominated by tension driven straightening with smaller kinetic exponents. Nonuniform tension profiles lead to the superlinear dependence of the longitudinal mean square displacement. In contrast, the late stage relaxation is diffusive again once the tension profile becomes uniform. The detailed tension profiles are reported for constant force measurement as well as constant pulling speed measurement.
Excited state dynamics of liquid water: Insight from the dissociation reaction following two-photon excitation
Authors: Elles Christopher G. , Shkrob Ilya A. , Crowell Robert A. , Bradforth Stephen E.
Published: April 2007

The authors use transient absorption spectroscopy to monitor the ionization and dissociation products following two-photon excitation of pure liquid water. The primary decay mechanism changes from dissociation at an excitation energy of 8.3eV to ionization at 12.4eV. The two channels occur with similar yield for an excitation energy of 9.3eV. For the lowest excitation energy, the transient absorption at 267nm probes the geminate recombination kinetics of the H and OH fragments, providing a window on the dissociation dynamics. Modeling the OH geminate recombination indicates that the dissociating H atoms have enough kinetic energy to escape the solvent cage and one or two additional solvent shells. The average initial separation of H and OH fragments is 0.7±0.2nm. Our observation suggests that the hydrogen bonding environment does not prevent direct dissociation of an O–H bond in the excited state. We discuss the implications of our measurement for the excited state dynamics of liquid water and explore the role of those dynamics in the ionization mechanism at low excitation energies.
Propagator for finite range potentials: The case of reflection
Authors: Cacciari Ilaria , Moretti Paolo
Published: April 2007

Following a previous study on the transmission propagator for a finite range potential, the problem of reflection is considered. It is found that the Laplace transform of the reflection propagator can be expressed in terms of the usual Fredholm determinant Δ and of a new similar determinant Γ, containing the peculiar characteristics of reflection. As an example, an array of delta potentials is considered. Moreover, a possible application to the calculation of quantum traversal time is shown.
Epitaxial integration of (0001) BiFeO3 with (0001) GaN
Authors: Tian W. , Vaithyanathan V. , Schlom D. G. , Zhan Q. , Yang S. Y. , Chu Y. H. , Ramesh R.
Published: April 2007

Epitaxial growth of (0001)-oriented BiFeO3 thin films on the (0001) surface of GaN has been realized using intervening epitaxial (111) SrTiO3∕(100) TiO2 buffer layers. The epitaxial BiFeO3 thin films have two in-plane orientations: [112¯0]BiFeO3‖[112¯0]GaN plus a twin variant related by a 180° in-plane rotation. BiFeO3 shows an out-of-plane remanent polarization of ∼90μC∕cm2, which is comparable to the remanent polarization of BiFeO3 prepared on (111) SrTiO3 single crystal substrates. The orientation of BiFeO3 realized on GaN provides the maximal out-of-plane polarization of BiFeO3, which is equivalent to a surface charge of 5×1014electrons∕cm2.
Al
N
∕
Al
Ga
N
∕
Ga
N
metal-insulator-semiconductor high-electron-mobility transistor on 4in. silicon substrate for high breakdown characteristics
Authors: Selvaraj S. Lawrence , Ito Tsuneo , Terada Yutaka , Egawa Takashi
Published: April 2007

Al N ∕ Al Ga N ∕ Ga N metal-insulator-semiconductor high-electron-mobility transistors (MIS-HEMTs) grown on 4in. silicon substrate have been demonstrated. The heterostructure exhibited high sheet carrier density with small surface roughness. AlN∕AlGaN∕GaN MIS-HEMT exhibited maximum drain current density (IDSmax) of 361mA∕mm and maximum extrinsic transconductance (gmmax) of 152mS∕mm. Due to the increase of sheet carrier density, the 2DEG channel shifts towards the AlGaN/GaN interface resulting in positive shift of the threshold voltage (−2.6to−1.8V). Two orders of magnitude low gate leakage current and reduced drain current collapse with high breakdown voltage of 230V have been observed on AlN∕AlGaN∕GaN MIS-HEMTs.
Two-dimensional self-patterning of PbTiO3 on a Nb–SrTiO3 (001) surface using atomic force microscope lithography and hydrothermal epitaxy
Authors: Kim R. H. , Ahn W. S. , Han S. H. , Choi S. K.
Published: April 2007

Atomic force microscope (AFM) lithography and hydrothermal epitaxy processes were used to resolve issues related to aligning ferroelectric micro- and nanosized cell arrays through a bottom-up approach. A Nb-doped SrTiO3 (100) surface was transformed in two dimensions by applying bias using a conductive AFM tip. The locally transformed areas were etched out with an acidic solution. It was found that the PbTiO3 crystal nucleated and grew on the artificially aligned grooves preferentially during a hydrothermal epitaxial process. The self-patterned PbTiO3 cell had excellent piezoresponse hysteresis with ferroelectric properties suitable for the fabrication of micro- and nanosized ferroelectric devices.
‘Time-resolved and orientation-dependent electric-field-induced strains in lead zirconate titanate ceramics
Authors: Jones Jacob L. , Pramanick Abhijit , Nino Juan C. , Maziar Motahari S. , Üstündag Ersan , Daymond Mark R. , Oliver Edward C.
Published: April 2007

Electric-field-induced lattice strains in a tetragonal ferroelectric lead zirconate titanate bulk ceramic are characterized under application of subcoercive cyclic electric fields using neutron diffraction and a stroboscopic data collection technique. At a driving electric field equal to half of the coercive field, the field-induced lattice strains are found to be a function of orientation with the greatest electric-field-induced strain coefficient of 680pm∕V in crystal orientations such that the 211 pole is parallel to the electric field. A time dependence of the 111 strain was also observed. Suggestions as to the nature of these dependences are discussed.
Metal-enhanced fluorescence from copper substrates
Authors: Zhang Yongxia , Aslan Kadir , Previte Michael J. R. , Geddes Chris D.
Published: April 2007

In this letter, the authors report the observation of metal-enhanced fluorescence emission from fluorophores deposited on copper (Cu) substrates. Different thicknesses of Cu particulate films (from 1 to 5nm) were deposited onto glass slides using thermal vapor deposition. Fluorophores positioned in close proximity to the Cu films show fluorescence enhancement as a function of the Cu thickness increases, reaching a maximum (2.5-fold) at ≈3nm. The findings strongly suggest that surface plasmons from Cu can radiate and therefore enhance a fluorophore’s spectral properties, similar to observations reported for both silver and gold nanoparticle deposited substrates.
Basal-plane slip in InGaN∕GaN heterostructures in the presence of threading dislocations
Authors: Mei J. , Liu R. , Ponce F. A. , Omiya H. , Mukai T.
Published: April 2007

Basal-plane slip has been observed in InGaN∕GaN heterostructures containing a high density of threading dislocations. The InGaN epilayers were deposited on a GaN mesa structure grown by metal-organic chemical vapor deposition on (0001) sapphire substrates using conventional methods. The glide process starts at the edge of the mesas, generating misfit dislocation half loops with a Burger vector of 1∕3⟨112¯0⟩. The misfit dislocation propagation is shown to depend on the crystalline orientation of the mesa edge and results in relaxation of over 80% of the misfit strain. Pinning of the misfit dislocation loops by threading dislocations does not stop them from propagating into the layer. No reaction is observed between the dislocation loops and the threading dislocations. The number of dislocation loops and their propagation distance increase with the indium content of the InGaN epilayers, indicating that the process is driven by the misfit strain. As a result of plastic relaxation, InGaN epilayers are observed to expand outside the edge of the GaN mesa, forming a ledge. These observations suggest possible ways to overcome lattice mismatch with GaN in order to grow high quality InGaN films with high indium concentration.
Near-equilibrium polymorphic phase transformations in praseodymium under dynamic compression
Authors: Bastea Marina , Reisman D. B.
Published: April 2007

The authors report the first experimental observation of sequential, multiple polymorphic phase transformations occurring in praseodymium dynamically compressed using a ramp wave. The experiments also display the signatures of reverse transformations occurring upon pressure release and reveal the presence of small hysteresis loops. The results are in very good agreement with equilibrium hydrodynamic calculations performed using a thermodynamically consistent, multiphase equation of state for praseodymium, suggesting a near-equilibrium transformation behavior.
Tunable few-optical-cycle pulses with passive carrier-envelope phase stabilization from an optical parametric amplifier
Authors: Manzoni C. , Polli D. , Cirmi G. , Brida D. , De Silvestri S. , Cerullo G.
Published: April 2007

The authors report on a scheme for the generation of few-optical-cycle pulses broadly tunable in the visible with passively stabilized carrier-envelope phase (CEP). The system starts with an infrared optical parametric amplifier in which both pump and seed are derived from an amplified, non-CEP-stabilized Ti:sapphire laser. The passively stabilized idler beam is then spectrally broadened through white-light generation and seeds a blue-pumped noncollinear optical parametric amplifier. The system produces few-optical-cycle pulses tunable from 500to800nm, with energy up to 5μJ and 0.23rad rms CEP fluctuations.
Heat-to-electricity thermoacoustic-magnetohydrodynamic conversion
Authors: Castrejón-Pita A. A. , Huelsz G.
Published: April 2007

A design for the conversion of heat into electricity is proposed. The conversion is based on the combined effects of a thermoacoustic prime mover coupled to a magnetohydrodynamic generator where different working fluids can be optimally chosen for each process. The results of preliminary experiments are presented.
Surface steps lead to heterogeneous contact mechanics and facilitate dislocation nucleation in nanoindentation
Authors: Ravi Shankar M.
Published: April 2007

In this letter the author examines the consequences of a very small surface step on the mechanics of contact in indentation using linear continuum elasticity. Surface steps are shown to lead to a loss of contact in the vicinity of the surface steps as well as a singular contact pressure distribution. This singularity exists for any finite surface step height and leads to shear stress concentration in the bulk material that declines in proportion to the inverse of distance from the surface step. This concentration facilitates the nucleation of dislocations and lowers the threshold for onset of plasticity in nanoindentation.
Interfacial strengthening by soft phase in lamellar microstructure of TiAl alloys
Authors: Zhu Hanliang , Maruyama K. , Seo D. Y. , Au P.
Published: April 2007

The authors report a mechanism of interfacial strengthening during creep deformation of fully lamellar TiAl alloys. In the lamellar microstructure of TiAl alloys, the α2 phase or the β phase is softer than the γ phase at elevated temperature. Conventionally, the creep resistance increases with decreasing the volume fraction of the soft phases. However, the lamellar interfaces of γ∕α2 or γ∕β retard the motion of dislocations during creep, causing a great strengthening, and thus the creep resistance increases with increasing the amount of the phase interfaces. In this study, a physically based model is developed to explain the strengthening behavior of the soft phases in lamellar TiAl alloys.
Cathodoluminescence studies of carrier concentration dependence for the electron-irradiation effects in p-GaN
Authors: Lopatiuk-Tirpak O. , Chernyak L. , Wang Y. L. , Ren F. , Pearton S. J. , Gartsman K. , Feldman Y.
Published: April 2007

Electron-irradiation increase of nonequilibrium carrier lifetime was studied as a function of hole concentration in Mg-doped GaN. Temperature-dependent cathodoluminescence (CL) studies yielded activation energies of 344, 326, 237, and 197meV for samples with hole concentrations of 2×1016, 9×1016, 3×1018, and 7×1018cm−3, respectively. The systematic decay of activation energy with carrier concentration was found to be consistent with Mg acceptors, indicating the involvement of the latter levels in irradiation-induced lifetime changes.
Hysteresis of pentacene thin-film transistors and inverters with cross-linked poly(4-vinylphenol) gate dielectrics
Authors: Lim Sang Chul , Kim Seong Hyun , Koo Jae Bon , Lee Jung Hun , Ku Chan Hoe , Yang Yong Suk , Zyung Taehyoung
Published: April 2007

The authors report the effects of hydroxyl groups (OH bonds) on the electrical reliabilities of pentacene organic thin-film transistors (OTFTs) with poly-4-vinylphenol (PVP) gate dielectrics. PVP gate dielectric films mixed with different concentrations of methylated poly(melamine-co-formaldehyde) (MMF) were fabricated, and experiments on the hysteresis behavior of the OTFT device were conducted. Pentacene TFTs with the PVP (MMF 0wt.%) exhibited a large hysteresis, while in the PVP (MMF 125wt.%), nearly no hysteresis was observed. Large hysteresis observed in OTFT devices was confirmed to be strongly related to the hydroxyl groups existing inside of the polymeric dielectrics and could reduced by the decrease of OH group.
An Efficient and Green Procedure for the Preparation of 2-{2-[N′-(2-Hydroxybenzylidene)hydrazino]thiazol-4-yl}phenols
Authors: Kamble Vinod T. , Davane Bhaskar S. , Chavan Sanjay A. , Bhosale Raghunath B.
Published: April 2007

An efficient and convenient approach for the synthesis of thiazole derivatives from α-halo ketones, thiosemicarbazide, and o-hydroxybenzaldehydes in poly(ethylene glycol) (PEG-400) is described. The preparation procedure presented is operationally simple and environmentally benign. Some of the major advantages of this procedure are high yields and ease of operation.
Uncatalyzed Reactions in Aqueous Media: Three-Component, One-Pot, Clean Synthesis of Tetrahydrobenzo[b]pyran Derivatives
Authors: Bandgar Sunita B. , Bandgar Babasaheb P. , Korbad Balaji L. , Totre Jalinder V. , Patil Sachin
Published: April 2007

The synthesis of various tetrahydrobenzo[b]pyran derivatives has been carried out by means of an uncatalyzed, three-component, one-pot clean condensation of aromatic aldehydes, reactive methylene compounds, and dimidone in aqueous medium. Simple workup, and mild and neutral conditions that give quantitative yields of products in pure form, are the attractive features of this method.
Synthesis and Copper(I) Complexation of 3,6-Di(2-pyridyl)pyridazine and 2,2′-Bipyridine Ligands Functionalized with a Dangling Iridium(III) Complex
Authors: Marin Veronica , Hoogenboom Richard , Moore Brian , Holder Elisabeth , Schubert Ulrich S.
Published: April 2007

The combination of multiple metal complexes into single heterometallic architectures is of interest to study energy and electron transfer processes. In this contribution, the synthesis and characterization of iridium(iii) complexes with pendant dipyridyl–pyridazine and bipyridine moieties are reported. The successful coupling of an amino-functional mixed ligand IrIII complex was performed by a carbamate linkage using carbonyl-diimidazole-activated ligands. Characterization by 1H NMR spectroscopy, MALDI-TOFMS, and elemental analysis proved the purity of the synthesized complexes. Further, the complexation of these ligands with copper(i) ions and the effect of complexation on the phosphorescence of the IrIII complex are discussed, whereby model complexation studies were performed to further understand the observed quenching behaviour.
Biomimetic Preparation of the Racemic Modifications of the Stilbenolignan Aiphanol and Three Congeners
Authors: Chand Satish , Banwell Martin G.
Published: April 2007

A chromatographically separable mixture of the racemic modification, (±)-1, of the stilbenolignan (–)-aiphanol and congeners (±)-2–4 has been generated by a silver(I)-mediated and potentially biomimetic oxidative coupling of piceatannol (5) with sinapic alcohol (6).
New taxa of 'leafless' Tetratheca (Elaeocarpaceae, formerly Tremandraceae) from Western Australia.
Authors: Butcher Ryonen
Published: April 2007

The relationships among rare ‘leafless’ species of Tetratheca Sm. occurring on banded ironstone ranges near Koolyanobbing, Western Australia, and allied, unclassified, populations from Eneabba, Newdegate and the Die Hardy Range have been assessed by molecular characters. These findings, in conjunction with morphological investigations, have identified a new species and two new subspecies from within the ‘T. aphylla group’ and these are formally described here. Tetratheca nephelioides R.Butcher, is geographically restricted to the Eneabba area and has close morphological affinity to T. aphylla F.Muell. Tetratheca aphylla subsp. megacarpa R.Butcher, is restricted to the Newdegate area, some 300 km south of the only known populations of T. aphylla subsp. aphylla in the Helena and Aurora Range. Tetratheca paynterae Alford subsp. cremnobata R.Butcher is restricted to the Die Hardy Range, c. 10 km north-east of the only known population of T. paynterae subsp. paynterae at ‘Windarling’. All of these taxa are recognised as Declared Rare Flora. In the process of updating the existing key to ‘leafless’ species of Tetratheca to include these new taxa, two additional new species were identified from within collections of T. nuda Lindl. These are described here as T. angulata R.Butcher and T. applanata R.Butcher. Images and distribution maps for all taxa are provided.
Evidence for convergent evolution among phylogenetically distant rare species of Tetratheca (Elaeocarpaceae, formerly Tremandraceae) from Western Australia
Authors: Butcher Ryonen , Byrne Margaret , Crayn Darren M.
Published: April 2007

Morphological and molecular investigations of taxon relationships among rare species of Tetratheca Sm. occurring near Koolyanobbing, Western Australia, have confirmed the distinctness of T. aphylla F.Muell., T. harperi F.Muell. and T. paynterae Alford and identified three new rare taxa from collections affiliated with T. aphylla and T. paynterae. The recognition of these taxa at specific and sub-specific ranks is based on their different degrees of morphological and molecular divergence, combined with geographic disjunction. Cladistic analysis of nrDNA internal transcribed spacer and cpDNA trnL-trnF sequences from a range of Tetratheca species from Western Australia and the eastern states indicates that T. aphylla, T. harperi and T. paynterae belong to three separate evolutionary lineages and that the endemism displayed among these taxa to small, disjunct ranges within the same geographic area, is a result of in situ speciation due to historical fragmentation. These results exemplify the extremely high conservation value of the Yilgarn banded ironstone ranges. The superficial similarity among the study taxa in having a ‘leafless’ habit can be seen to be adaptive convergence in response to the marginal and semi-arid environments in which they occur, and this character is highly homoplastic within the genus.
Akt1 governs breast cancer progression
in vivo
Authors: Ju Xiaoming , Katiyar Sanjay , Wang Chenguang , Liu Manran , Jiao Xuanmao , Li Shengwen , Zhou Jie , Turner Jacob , Lisanti Michael P. , Russell Robert G. , Mueller Susette C. , Ojeifo John , Chen William S. , Hay Nissim , Pestell Richard G.
Published: April 2007

The serine threonine kinase
Akt1
has been implicated in the control of cellular metabolism, survival and growth. Here, disruption of the ubiquitously expressed member of the
Akt
family of genes,
Akt1
, in the mouse demonstrates a requirement for
Akt1
in ErbB2-induced mammary tumorigenesis.
Akt1 deficiency
delayed tumor growth and reduced lung metastases, correlating with a reduction in phosphorylation of the
Akt1
target, tuberous sclerosis 2 (TSC2) at Ser-939.
Akt1
-deficient mammary epithelial tumor cells (MEC) were reduced in size and proliferative capacity, with reduced cyclin D1 and p27
KIP1
abundance.
Akt1
deficiency abrogated the oncogene-induced changes in polarization of MEC in three-dimensional culture and reverted oncogene-induced relocalization of the phosphorylated ezrin–radixin–moesin proteins.
Akt1
increased MEC migration across an endothelial cell barrier, enhancing the persistence of migratory directionality. An unbiased proteomic analysis demonstrated
Akt1
mediated MEC migration through paracrine signaling via induction of expression and secretion of CXCL16 and MIP1γ.
Akt1
governs MEC polarity, migratory directionality and breast cancer onset induced by ErbB2
in vivo
.
Negative regulation of the RIG-I signaling by the ubiquitin ligase RNF125
Authors: Arimoto Kei-ichiro , Takahashi Hitoshi , Hishiki Takayuki , Konishi Hideyuki , Fujita Takashi , Shimotohno Kunitada
Published: April 2007

Retinoic acid-inducible gene I (
RIG-I
) plays a pivotal role in the regulation of cytokine production induced by pathogens. The RIG-I also augments the production of IFN and other cytokines via an amplification circuit. Because the production of cytokines is closely controlled, up- and down-regulation of RIG-I signaling also needs strict regulation. The mechanism of this regulation, however, remains elusive. Here, we found that RIG-I undergoes proteasomal degradation after conjugation to ubiquitin by RNF125. Further, RNF125 conjugates ubiquitin to MDA5, a family protein of RIG-I as well as IPS-1, which is also a downstream protein of RIG-I signaling that results in suppressing the functions of these proteins. Because RNF125 is enhanced by IFN, these functions constitute a negative regulatory loop circuit for IFN production.
Adult-onset pulmonary fibrosis caused by mutations in telomerase
Authors: Tsakiri Kalliopi D. , Cronkhite Jennifer T. , Kuan Phillip J. , Xing Chao , Raghu Ganesh , Weissler Jonathan C. , Rosenblatt Randall L. , Shay Jerry W. , Garcia Christine Kim
Published: April 2007

Idiopathic pulmonary fibrosis (IPF) is an adult-onset, lethal, scarring lung disease of unknown etiology. Some individuals with IPF have a familial disorder that segregates as a dominant trait with incomplete penetrance. Here we used linkage to map the disease gene in two families to chromosome 5. Sequencing a candidate gene within the interval,
TERT
, revealed a missense mutation and a frameshift mutation that cosegregated with pulmonary disease in the two families.
TERT
encodes telomerase reverse transcriptase, which together with the RNA component of telomerase (
TERC
), is required to maintain telomere integrity. Sequencing the probands of 44 additional unrelated families and 44 sporadic cases of interstitial lung disease revealed five other mutations in
TERT
. A heterozygous mutation in
TERC
also was found in one family. Heterozygous carriers of all of the mutations in
TERT
or
TERC
had shorter telomeres than age-matched family members without the mutations. Thus, mutations in
TERT
or
TERC
that result in telomere shortening over time confer a dramatic increase in susceptibility to adult-onset IPF.
Sacred bounds on rational resolution of violent political conflict
Authors: Ginges Jeremy , Atran Scott , Medin Douglas , Shikaki Khalil
Published: April 2007

We report a series of experiments carried out with Palestinian and Israeli participants showing that violent opposition to compromise over issues considered sacred is (
i
) increased by offering material incentives to compromise but (
ii
) decreased when the adversary makes symbolic compromises over their own sacred values. These results demonstrate some of the unique properties of reasoning and decision-making over sacred values. We show that the use of material incentives to promote the peaceful resolution of political and cultural conflicts may backfire when adversaries treat contested issues as sacred values.
The generation of influenza outbreaks by a network of host immune responses against a limited set of antigenic types
Authors: Recker Mario , Pybus Oliver G. , Nee Sean , Gupta Sunetra
Published: April 2007

It is commonly believed that influenza epidemics arise through the incremental accumulation of viral mutations, culminating in a novel antigenic type that is able to escape host immunity. Successive epidemic strains therefore become increasingly antigenically distant from a founding strain. Here, we present an alternative explanation where, because of functional constraints on the defining epitopes, the virus population is characterized by a limited set of antigenic types, all of which may be continuously generated by mutation from preexisting strains and other processes. Under these circumstances, influenza outbreaks arise as a consequence of host immune selection in a manner that is independent of the mode and tempo of viral mutation. By contrast with existing paradigms, antigenic distance between epidemic strains does not necessarily accumulate with time in our model, and it is the changing profile of host population immunity that creates the conditions for the emergence of the next influenza strain rather than the mutational capabilities of the virus.
Nitric oxide mediates prostaglandins' deleterious effect on lipopolysaccharide-triggered murine fetal resorption
Authors: Aisemberg J. , Vercelli C. , Billi S. , Ribeiro M. L. , Ogando D. , Meiss R. , McCann S. M. , Rettori V. , Franchi A. M.
Published: April 2007

Genital tract bacterial infections could induce abortion and are some of the most common complications of pregnancy; however, the mechanisms remain unclear. We investigated the role of prostaglandins (PGs) in the mechanism of bacterial lipopolysaccharide (LPS)-induced pregnancy loss in a mouse model, and we hypothesized that PGs might play a central role in this action. LPS increased PG production in the uterus and decidua from early pregnant mice and stimulated cyclooxygenase (COX)-II mRNA and protein expression in the decidua but not in the uterus. We also observed that COX inhibitors prevented embryonic resorption (ER). To study the possible interaction between nitric oxide (NO) and PGs, we administered aminoguanidine, an inducible NO synthase inhibitor. NO inhibited basal PGE and PGF2αproduction in the decidua but activated their uterine synthesis and COX-II mRNA expression under septic conditions. A NO donor (S-nitroso-N-acetylpenicillamine) produced 100% ER and increased PG levels in the uterus and decidua. LPS-stimulated protein nitration was higher in the uterus than in the decidua. Quercetin, a peroxynitrite scavenger, did not reverse LPS-induced ER. Our results suggest that in a model of septic abortion characterized by increased PG levels, NO might nitrate and thus inhibit COX catalytic activity. ER prevention by COX inhibitors adds a possible clinical application to early pregnancy complications due to infections.
Protein Arms in the Kinetochore-Microtubule Interface of the Yeast DASH Complex
Authors: Miranda JJ L. , King David S. , Harrison Stephen C.
Published: April 2007

The yeast DASH complex is a heterodecameric component of the kinetochore necessary for accurate chromosome segregation. DASH forms closed rings around microtubules with a large gap between the DASH ring and the microtubule cylinder. We characterized the microtubule-binding properties of limited proteolysis products and subcomplexes of DASH, thus identifying candidate polypeptide extensions involved in establishing the DASH-microtubule interface. The acidic C-terminal extensions of tubulin subunits are not essential for DASH binding. We also measured the molecular mass of DASH rings on microtubules with scanning transmission electron microscopy and found that approximately 25 DASH heterodecamers assemble to form each ring. Dynamic association and relocation of multiple flexible appendages of DASH may allow the kinetochore to translate along the microtubule surface.
Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec data
Authors: Park Yuhyun , Downing Sean R. , Kim Dohyun , Hahn William C. , Li Cheng , Kantoff Philip W. , Wei L.J.
Published: April 2007

Motivation: Analysis of high-throughput proteomic/genomic data, in particular, surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) data and microarray data, has led to a multitude of techniques aimed at identifying potential biomarkers. Most of the statistical techniques for comparing two groups are based on qualitative measures such as P-value. A quantitative way such as interval estimation for the contrasts of two groups is more appealing.

Results: We have devised a simultaneous confidence bands method capable of detecting potential biomarkers, while controlling for overall confidence coverage level, in high-dimensional datasets that discriminate two treatment groups using a permutation scheme. For example, for the SELDI-TOF MS data, we deal with the entire spectrum simultaneously and construct (1 − α) confidence bands for the mean differences between groups. Furthermore, peaks were identified based on the maximal differences between the groups as determined by the confidence bands. The analysis method herein described gives both qualitative (P-value) and quantitative data (magnitude of difference). The Clinical Proteomics Programs Databank's ovarian cancer dataset and data from in-house samples containing known spiked-in proteins were analyzed. We were able to identify potential biomarkers similar to those described in previous analysis of the ovarian cancer data, however, while these markers are highly significant between cancer and normal groups, our analysis indicated the absolute difference between the two groups was minimal. In addition, we found additional markers than those previously described with greater differences in average intensities. The proposed confidence bands method successfully detected the spiked-in peaks, as well as, secondary peaks generated by adducts and double-charged species. We also illustrate our method utilizing paired gene expression data from a prostate cancer microarray experiment by constructing confidence bands for the fold changes between cancer and normal samples.

Availability: R-package, ‘seie.zip’ (license: GNU GPL), is publiclly available at http://research2.dfci.harvard.edu/dfci/MS_spike-in_data/

Contact:  parkyuhyun@gmail.com

Supplementary information: For supplementary data, please refer to Bioinformatics online.
TOPD/FMTS: a new software to compare phylogenetic trees
Authors: Puigbò Pere , Garcia-Vallvé Santiago , McInerney James O.
Published: April 2007

Summary: TOPD/FMTS has been developed to evaluate similarities and differences between phylogenetic trees. The software implements several new algorithms (including the Disagree method that returns the taxa, that disagree between two trees and the Nodal method that compares two trees using nodal information) and several previously described methods (such as the Partition method, Triplets or Quartets) to compare phylogenetic trees. One of the novelties of this software is that the FMTS (From Multiple to Single) program allows the comparison of trees that contain both orthologs and paralogs. Each option is also complemented with a randomization analysis to test the null hypothesis that the similarity between two trees is not better than chance expectation.

Availability: The Perl source code of TOPD/FMTS is available at http://genomes.urv.es/topd.

Contact:  ppuigbo@urv.cat

Supplementary information: A complete tutorial and several examples of how to use the software have been included on the home page of the application.
GENOME: a rapid coalescent-based whole genome simulator
Authors: Liang Liming , Zöllner Sebastian , Abecasis Gonçalo R.
Published: April 2007

Summary: GENOME proposes a rapid coalescent-based approach to simulate whole genome data. In addition to features of standard coalescent simulators, the program allows for recombination rates to vary along the genome and for flexible population histories. Within small regions, we have evaluated samples simulated by GENOME to verify that GENOME provides the expected LD patterns and frequency spectra. The program can be used to study the sampling properties of any statistic for a whole genome study.

Availability: The program and C++ source code are available online at http://www.sph.umich.edu/csg/liang/genome/

Contact:  lianglim@umich.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
How Does Open‐Mouth Breathing Influence Upper Airway Anatomy?
Authors: Lee Seung Hoon , Choi Ji Ho , Shin Chol , Lee Heung Man , Kwon Soon Young , Lee Sang Hag
Published: April 2007

Objectives/Hypothesis: Open‐mouth breathing during sleep may increase the severity of obstructive sleep apnea (OSA) and complicate nasal continuous positive airway pressure (CPAP) therapy in patients with OSA. The aim of this study was to assess the effect of open‐mouth breathing on upper airway anatomy using lateral cephalometry and fiberoptic nasopharyngoscopy.

Study Design: This was a cross‐sectional study.

Methods: Lateral cephalometry and fiberoptic nasopharyngoscopy were carried out on 28 subjects with a mean age of 36.7 years. We compared the effect of the mouth being open or closed on the results in lateral cephalometry (pharyngeal length, distance between the mandible and hyoid bone [MP‐H], angles from the sella‐nasion to mandibular points A and B [SNA, SNB, respectively], retropalatal, retroglossal, and hypopharyngeal distance) and fiberoptic nasopharyngoscopy (retropalatal and retroglossal cross‐sectional area).

Results: On lateral cephalometric measurements, retropalatal distance (P = .000), retroglossal distance (P = .000), and MP‐H (P = .002) were lower with mouth open, and pharyngeal length (P = .000) was greater. However, there were no significant differences in SNA and hypopharyngeal distance. On fiberoptic nasopharyngoscopy, retropalatal (P = .005) and retroglossal (P = .000) cross‐sectional areas were significantly reduced with the mouth open.

Conclusions: Open‐mouth breathing is associated with reduction of the retropalatal and retroglossal areas, lengthening of the pharynx and shortening of the MP‐H in the upper airway. We suggest that knowledge of these anatomic changes improves our understanding of the increase of OSA severity and the low adherence to nasal CPAP therapy in mouth breathers.
Evolution of Mild Obstructive Sleep Apnea after Different Treatments
Authors: Sahlman Johanna , Pukkila Matti , Seppä Juha , Tuomilehto Henri
Published: April 2007

Study Objectives: To evaluate the prognosis of mild obstructive sleep apnea in relation to different treatment modalities.

Study Design: An open, retrospective, longitudinal follow‐up study.

Methods: Fifty adult patients diagnosed and treated for mild obstructive sleep apnea at the Department of Otorhinolaryngology at Kuopio University Hospital between 1998 and 2004 had a control polysomnography in 2005. The changes in apnea‐hypopnea index (AHI) were observed in untreated (n = 28), operative (n = 11), and continuous positive airway pressure (n = 11) treatment groups at a long‐term follow‐up visit.

Results: The mean follow‐up period was 4 (range, 1.3–9.0; SD, 1.9) years. The untreated patients had a statistically significant increase in AHI (13.3, SD 18.3) at the follow‐up. Half of these patients developed a moderate or severe degree of sleep apnea, and only 11% were cured. In patients who were treated with continuous positive airway pressure, the degree of obstructive sleep apnea became worse in 64% of cases, and in 27% of patients, the AHI returned to normal (<5). The degree of obstructive sleep apnea in operated patients deteriorated only in 18%, and in 27% of the patients, the AHI returned to normal (<5).

Conclusions: Mild obstructive sleep apnea has a natural tendency to worsen with time. Active treatment of mild obstructive sleep apnea appears, therefore, to be advisable.
EFFECT OF A TREMOLITIC TALC IN WHITEWARE BODIES*
Authors: Hagar Donald
Published: April 2007

Abstract

This paper describes the use of a specific type of tale in wall‐tile bodies and explains the effect of various percentages on shrinkage, absorption, modulus of rupture, moisture expansion, and resistance to delayed crazing. The data indicate the effects of talc with various combinations of wall‐tile body ingredients and the compositions and heat treatment of greatest potential resistance to crazing.
THE USE OF PENETRATING RADIATIONS IN THE MEASUREMENT OF THE POROSITY OF REFRACTORY BRICK*
Authors: Austin J. B.
Published: April 2007

Abstract

The possibility of using the absorption of X‐rays or γ‐rays in a refractory brick as a measure of porosity has been tested experimentally for both kinds of radiation. It is found that the method is entirely practical in either case and when the necessary apparatus is set up it should yield results, with much less effort, better than those now obtained by the displacement method. Gamma‐rays from radium appear to have some advantages over X‐rays.
LOADING DEVICE FOR LOAD‐TEST FURNACE*
Authors: Carruthers John L.
Published: April 2007

Abstract

A loading device for use in making the standard load test on refractory brick is described. It consists of two steel shafts plus added weights, mounted in a simple steel frame to provide true direct vertical loads on the two test samples. Illustrations showing details of construction are included.
EFFECT OF CLAYS ON THE OPACITY OF WHITE ENAMEL FOR SHEET STEEL*
Authors: Danielson R. R.
Published: April 2007

The various means for developing the maximum covering power of enamels are very important. This investigation brings out the marked effect on the opacity of different clays used for suspending cover enamels. This may be equivalent to at least 5% in the reflectance, as measured by the reflectometer. Where suspension and opacity are both important, a blend of clays may be used, one of which may have excellent suspension while the other imparts opacity to the enamel.
PLASTIC FLOW IN A NEARLY DRY CLAY BODY*
Authors: THIEMECKE H.
Published: April 2007

A method for determining the moisture content at which a plastic body becomes elastic is given. Results of tests made on an earthenware body indicate the transition to have taken place at approximately 12.8% water content. With decreased water content of the body the yield values decreased, the deformation per unit stress beyond the yield value pressures decreased, the total deformation at ultimate failure decreased, and the ultimate failure pressures increased.
A METHOD AND APPARATUS FOR STUDYING THE PHYSICAL PROPERTIES OF VITREOUS ENAMELS ON STEEL*
Authors: Rosenberg J. E. , Langerman A.
Published: April 2007

Abstract

A method has been devised for studying the physical properties of the fused enamel containing the mill additions by firing it onto a split‐steel ring and studying the changes in the radius of the ring and stresses produced due to the difference in the coefficient of thermal expansion of the enamel and the steel.
SOME EXPERIMENTS IN THE DEVELOPMENT OF A SAND‐ABRASION MACHINE*
Authors: Spencer‐Strong G. H.
Published: April 2007

Abstract

A simple and comparatively inexpensive apparatus for determining the relative abrasion resistance of enamels is described. Abrasion is obtained by fixing the specimen in the path of a stream of sand, propelled by a rapidly revolving disk. The severity of the abrasive action is dependent upon the particle size of the abrasive. Data are given as to the comparative resistance both to severe and mild abrasion of several enamel types.
THE PLASTICITY OF FINELY GROUND MINERALS WITH WATER*
Authors: Wilson Earl O.
Published: April 2007

Abstract

A study is made of the plasticity of finely ground minerals in water. For this purpose a machine was developed to give quantitatively the factors making up plasticity. It is shown that the particle shape is an important factor governing plasticity.
THE PACKING OF PARTICLES: EMPIRICAL EQUATIONS FOR INTERMEDIATE DIAMETER RATIOS*
Authors: Westman A. E. R.
Published: April 2007

Abstract

An empirical equation was developed which could be used for representing the packing characteristics of systems consisting of mixtures of particles of two sizes. Application to data previously published gave a definite indication of a relation between the parameter of the equation and the diameter ratio of the particles.
THE USE OF PYROPHYLLITE IN WALL‐TILE BODIES*
Authors: Sproat Ira E.
Published: April 2007

Abstract

The use of pyrophyllite in tile bodies is discussed. A statement of the place and character of the geological formation is made. The properties and thermal reactions of pyrophyllite are stated. The advantages gained by the use of pyrophyllite are decreased crazing, increased firing range, less fire‐cracking, less warpage, and less die wear. Data and literature citations are given.
THE EFFECT OF ALUMINA UPON THE CHEMICAL DURABILITY OF SAND‐SODA‐LIME GLASSES*
Authors: Lyle A. K. , Horak William , Sharp Donald E.
Published: April 2007

Abstract

The chemical durabilities of 25 glasses, with and without alumina, were determined by a powder method. From the data obtained a formula was derived for calculating the chemical durability of sand‐soda‐lime glasses containing alumina. The introduction of 1.5 to 2.5% alumina improves the chemical durability, the greatest benefit occurring when the alumina is one‐eighth the soda content.
KINETICS OF SOME REACTIONS OF INTEREST TO CERAMISTS* The Disintegration of Blast‐Furnace Linings Due to Carbon Deposition†
Authors: Furnas C. C.
Published: April 2007

Abstract

The reaction has a maximum rate between 450°C and 500°C. Experimental work showed that commercial fire brick could be completely shattered by the reaction in a few hours. Firing brick in reducing atmosphere reduces the rate of deposition.
THE IMPACT ABRASION‐HARDNESS OF CERTAIN MINERALS AND CERAMIC PRODUCTS*
Authors: Milligan Lowell H.
Published: April 2007

Abstract

Impact abrasion was produced by an accurately controlled blast of “standard Ottawa quartz sand.” The “abrasion‐hardness” of various glasses, minerals, hotel chinaware, porcelains, abrasive, refractory, and miscellaneous materials was thus determined in comparison with plate glass which was chosen as a standard. A relationship between crystallographic orientation and abrasion‐hardness was demonstrated in the case of feldspar and quartz crystals. A Brazilian quartz crystal was found to have trigonal and not hexagonal abrasion‐hardness symmetry. The hardness of hotel chinaware and of porcelains tested ranged from 3.2 to 7, with the surface skin on one sillimanite‐type porcelain giving the high value of 34 (plate‐glass standard = 1.00). Crystalline α‐alumina gave a value of about 40, and silicon carbide about 400. Experiments with abrading grains other than quartz sand showed that corresponding hardness values for such hard materials as crystalline a‐alumina and silicon carbide come much closer together when hard artificial abrasive grains are used for the blasting.
THE FREEZING OF PYROMETRIC CONES*
Authors: Rea R. F. , Shaw M. C.
Published: April 2007

Abstract

Pyrometric cones are sometimes subjected to atmospheric or firing conditions which cause a misbehavior known as “freezing.” Under such conditions, the cone may not come down until a higher temperature, sometimes two or three cones higher, is reached. Definite conclusions have not yet been reached as to the cause of this action. Through petrographic and X‐ray analysis, however, certain definite ideas have been formulated which have served as a basis for the development of a series of nonfreezing cones. These cones have been used under conditions where freezing is ordinarily produced and were found to act normally, recording the true heat work.
FOURIER ANALYSIS OF X‐RAY PATTERNS OF VITREOUS SiO2 AND B2O2*
Authors: Warren B. E. , Krutter H. , Morningstar O.
Published: April 2007

Abstract

The X‐ray scattering curves for vitreous SiO2 and B2O2 are obtained in a vacuum camera, using monochromatic Mo and Cu radiation. A Fourier analysis of the scattering curve gives directly a curve representing the distribution of neighboring atoms about any one atom. For SiO2, the distribution curve establishes definitely the tetrahedral silicon‐oxygen network. The distribution curve for B2O3 indicates a triangular coordination, each boron surrounded by three oxygens, and each oxygen shared between two borons. The interatomic distances which are found are in good agreement with the values found in crystalline silicates and borates. The importance of the new Fourier method of analysis of glass diffraction patterns is emphasized by the fact that the distribution curves which are obtained are unique, no assumptions as to structure being involved.
SIZE DETERMINATION WITH THE HAEMACYTOMETER*
Authors: Amberg C. R.
Published: April 2007

Abstract

The article describes a quick microscope method for determining the average particle size of ground materials under 200‐mesh in size. The method is an adaptation of the blood‐count cell or haemacytometer.