bluuebunny/crossref_metadata_2025 huggingface dataset:
A pentacene ambipolar transistor: Experiment and theory
Authors: Schmechel Roland , Ahles Marcus , von Seggern Heinz
Published: October 2005

An ambipolar pentacene transistor with top-gold and top-calcium contacts has been realized by utilizing a parallactic shadow mask effect during vapor deposition. The pentacene deposited on top of a silicon dioxide gate insulator is doped by Ca at the pentacene/SiO2 interface in order to compensate electron traps. An equivalent circuit model based on a resistor-capacitor network has been developed to describe the basic electrical properties of the transistor. Shockley-like analytical expressions for the output and transfer characteristic, as well as an analytical expression for the potential and charge-carrier distribution in the channel, are derived under the assumption of a high electron-hole recombination probability. The model has been fitted to our experimental results and yields comparable mobilities for both holes and electrons in the order of 0.1cm2∕Vs. The increasing threshold voltages, with an increase in gate voltage, are discussed as an indication for trapped charge carriers within the insulator (SiO2).
A direct simulation Monte Carlo method for rarefied gas flows in the limit of small Mach number
Authors: Chun J. , Koch D. L.
Published: October 2005

Standard methods of simulating the mean velocity and mean force in a rarefied gas flow suffer from statistical errors associated with the random thermal motion of the gas molecules. The ratio of the statistical error to the mean velocity or force diverges in the limit of small Mach number, which is relevant to applications in aerosol science and microdevices. We present a novel extension of the direct-simulation Monte Carlo method in which the deviation from equilibrium is captured by noninteger weightings of the simulation gas particles, so that the mean velocity and force associated with the deviation from equilibrium can be computed without contamination by the thermal noise in the equilibrium state. The collision rules between simulation particles reproduce the changes in the gas velocity distribution function that would result from hard sphere intermolecular collisions. Because the collision rules produce new particles, particle splitting and recombination steps, which do not alter the velocity distribution function, must be introduced to maintain a finite number of particles and a finite maximum weighting per particle. The method is validated by comparing simulation results for pressure-driven flow in a channel and flow past a single sphere to corresponding solutions of the linearized Boltzmann equation. The method is then applied to obtain new results for the resistance to the relative motion of two spherical particles along their line of centers.
Comparison of morphology evolution of Ge(001) homoepitaxial films grown by pulsed laser deposition and molecular-beam epitaxy
Authors: Shin Byungha , Leonard John P. , McCamy James W. , Aziz Michael J.
Published: October 2005

Using a dual molecular-beam epitaxy (MBE)–pulsed laser deposition (PLD) ultrahigh vacuum chamber, we have conducted the first experiments under identical thermal, background, and surface preparation conditions to compare Ge(001) homoepitaxial growth morphology in PLD and MBE. We find that in PLD with low kinetic energy and in MBE the film morphology evolves in a similar fashion: initially irregularly shaped mounds form, followed by pyramidal mounds with edges of the square-base along the ⟨100⟩ directions; the film roughness and mound separation increase with film thickness. In PLD with high kinetic energy, well-defined pyramidal mounds are not observed and the morphology rather resembles that of an ion-etched Ge(001) surface. The areal feature density is higher for PLD films than for MBE films grown at the same average growth rate and temperature. Furthermore, the dependence upon film thickness of roughness and feature separation differ for PLD and MBE. We attribute these differences to the higher yield of defect generation by energetic species in PLD.
Magnetization reversal in diamond-shaped pseudo-spin-valve nanomagnets
Authors: Goolaup S. , Adeyeye A. O. , Singh N.
Published: October 2005

A systematic investigation of the magnetization reversal process of diamond-shaped Ni80Fe20(10nm)∕Cu(tCunm)∕Ni80Fe20(40nm) pseudo-spin-valve nanostructures is presented. The structures were fabricated on silicon substrate using deep ultraviolet lithography at 248 nm exposing wavelength. By carefully selecting two ferromagnetic layer thicknesses, with different reversal mechanisms, we have created a magnetic structure with unique magnetic properties. We observed that the magnetization reversal process of the spin valve is strongly influenced by the Cu spacer layer thickness. Our experimental results were substantiated with a three-dimensional micromagnetic simulation.
Suppression of oxidation in nickel germanosilicides by Pt incorporation
Authors: Rahman Md. Anisur , Osipowicz Thomas , Pey K. L. , Jin L. J. , Choi W. K. , Chi D. Z. , Antoniadis D. A. , Fitzgerald E. A. , Isaacson D. M.
Published: October 2005

The effect of oxidation of 10nm Ni∕Si0.75Ge0.25 and 10nm Ni(10at.%Pt)∕Si0.75Ge0.25 thin films at annealing temperatures ranging from 400to800°C has been studied in detail by Rutherford backscattering spectrometry analysis, cross-sectional transmission electron microscopy, energy dispersive x-ray, and sheet resistance measurements. It is observed that for the films without Pt incorporation, almost two-thirds of the germanosilicide is oxidized. The incorporation of a Pt(10at.%) into Ni not only dramatically reduces the oxidation of the germanosilicides, but also improves the interfacial roughness and morphology. The integral amount of oxygen found in the germanosilicide in the Ni(10at.%Pt)Si0.75Si0.25 films [(1.1±0.17)×1017at.∕cm2] is approximately four times less than that of NiSi0.75Si0.25 [(4.0±0.28)×1017at.∕cm2]. This result is explained in terms of the roles of the higher melting point and bond energy of PtSi in NiSi and NiGe, and much lower free energy of the formation of platinum oxide.
The anomalous “stiffness” of biphenydimethyldithiol
Authors: Feng D. Q. , Dowben P. A. , Rajesh R. , Redepenning J.
Published: October 2005

Although organic adsorbates and thin films are generally regarded as “soft” materials, the effective Debye temperature, indicative of the dynamic motion of lattice normal to the surface, can be very high. For biphenyldimethyldithiol, the effective Debye temperature, determined from core level photoemission from the all carbon arene rings, is comparable to that of graphite. We associate this rigidity to the stiffness of the benzene rings, and the ordering in the molecular thin film. Measurements on the sulfur of poly(hexylthiophene) show that sulfur in an arene ring is less dominated by soft modes than the pendant sulfur of biphenyldimethyldithiol on the time scale of photoemission.
Controlled transition between parametric and Raman oscillations in ultrahigh-Q silica toroidal microcavities
Authors: Min Bumki , Yang Lan , Vahala Kerry
Published: October 2005

A controllable and reversible transition between parametric and Raman oscillations in an ultrahigh-Q silica toroidal microcavity is experimentally demonstrated and theoretically analyzed. By direct change of cavity loading and indirect adjustment of frequency detuning, parametric and/or Raman oscillation can be accessed selectively without modification of cavity geometry in a toroidal microcavity with a large enough aspect ratio. Based on an effective cavity gain theory, this transition is analyzed in terms of cavity loading and frequency detuning leading to a better understanding of the combined effects of parametric and Raman processes in silica microcavities.
Room-temperature InAlAs∕InGaAs∕InP planar resonant tunneling-coupled transistor
Authors: Moon Jeong S. , Rajavel Rajesh , Bui Steven , Wong Danny , Chow David H.
Published: October 2005

We report an experimental demonstration of room-temperature InAlAs∕InGaAs∕InP planar two-dimensional to two-dimensional resonant tunneling-coupled transistors, in which the tunneling characteristics such as negative differential resistance and peak current are controlled by a surface Schottky gate similar to the state-of-the-art high-electron-mobility transistors (HEMT) with high gain. The tunneling peak voltage was modulated linearly with the Schottky gate voltage with a ratio of nearly unity. Functionality of the device can also be switched between HEMT and tunneling transistor mode. The fabrication process is fully compatible with conventional HEMT processes, offering a fully integrable and scalable tunneling transistor technology.
Angle-dependent photovoltaic effect in Al–Si multilayers
Authors: Kyarad A. , Lengfellner H.
Published: October 2005

Al–Si multilayer stacks have been prepared by an alloying process from aluminum and silicon platelets. Irradiation of a stack with infrared to visible laser radiation generates photovoltaic signals depending on the angle of incidence of the laser beam with respect to the layer planes, with zero signal and a polarity reversal for beam and layers in parallel. Results are explained in terms of photoactive layers connected in series and symmetrically aligned along the stack axis. For light beams inclined with respect to the layer planes, asymmetry is introduced by fractional shadowing of photoactive regions due to the intransparent metallic layers.
( La 0.8 , Sr 0.2 ) MnO 3 ∕ Ti -metal foil substrate heterostructure effects on the ferroelectric and piezoelectric properties of lead zirconate titanate thin films
Authors: Es-Souni M. , Piorra A. , Habouti S. , Kumar S. Rudra , Faupel F.
Published: October 2005

The ferroelectric and piezoelectric properties of lead zirconate titanate thin films deposited on a (La0.8,Sr0.2)MnO3(LSMO)∕Ti-metal foil heterostructure are reported. The results are compared to those of films of similar thickness deposited on platinized silicon substrate. It is shown that the films deposited on LSMO∕Ti are characterized by square ferroelectric and piezoelectric hysteresis loops with high remnant polarization and strain of 26μC∕cm2 and 0.8%, respectively. The effective piezoelectric strain constant, d33, obtained for films deposited on platinized silicon amounts to 103pm∕V. The piezoelectric behavior of the film deposited on LSMO∕Ti is analyzed in terms of a unimorph bending actuator. The extracted effective piezoelectric strain constant, d33, amounts to approximately 600pm∕V.
Damage formation and annealing at low temperatures in ion implanted ZnO
Authors: Lorenz K. , Alves E. , Wendler E. , Bilani O. , Wesch W. , Hayes M.
Published: October 2005

N, Ar, and Er ions were implanted into ZnO at 15 K within a large fluence range. The Rutherford backscattering technique in the channeling mode was used to study in situ the damage built-up in the Zn sublattice at 15 K. Several stages in the damage formation were observed. From the linear increase of the damage for low implantation fluences, an upper limit of the Zn displacement energy of 65 eV could be estimated for [0001] oriented ZnO. Annealing measurements below room temperature show a significant recovery of the lattice starting at temperatures between 80 and 130 K for a sample implanted with low Er fluence. Samples with higher damage levels do not reveal any damage recovery up to room temperature, pointing to the formation of stable defect complexes.
Effects of ZrO2 additions on the dielectric properties of CaCu3Ti4O12
Authors: Patterson Eric A. , Kwon Seunghwa , Huang Chien-Chih , Cann David P.
Published: October 2005

The dielectric spectra of CaCu3Ti4O12 is characterized by a large permittivity (εr>10000) with only a weak dependence on temperature over the temperature range 200–400 K. In this work, doping with 0.1–1.0 wt % ZrO2 has been shown to dramatically reduce the dielectric loss. At 0.5 wt % ZrO2,tanδ remains below 0.05 over the frequency range 50 Hz–30 kHz and is just 0.065 at 100 kHz. While there is some diminution of the permittivity (εr≈5000 at 10 kHz) Zr-doped ceramics, exhibited very little bias dependence (ΔC∕C0<1.0% up to 40 V). In summary, results suggest that ZrO2 doping is an effective method for maintaining a high permittivity and low loss over a broad range in temperature, bias, and frequency.
Tuning the ferromagnetic properties of hydrogenated GaMnAs
Authors: Thevenard L. , Largeau L. , Mauguin O. , Lemaître A. , Theys B.
Published: October 2005

Hydrogenation and posthydrogenation annealings have been used as a very efficient tool to tune the hole density over a wide range, at fixed magnetic moment concentration, in thin GaMnAs layers. Reduction of the hole density resulted in strong modifications of their ferromagnetic properties. In particular, we observed in magnetotransport experiments the decrease of the Curie temperature, along with modifications of the magnetic anisotropy, a behavior consistent with the mean-field theory.
Emission properties of an organic light-emitting diode patterned by a photoinduced autostructuration process
Authors: Hubert C. , Fiorini-Debuisschert C. , Hassiaoui I. , Rocha L. , Raimond P. , Nunzi J.-M.
Published: October 2005

The photoluminescence properties of a periodically structured organic light-emitting diode are presented. Patterning is achieved using an original single-step autostructuration technique based on photoinduced effects in azo-polymer films. We show that single beam laser irradiation can lead to the induction of regular two-dimensional surface relief gratings. The waveguide properties of these microstructures as well as their effect on the emission properties of a light-emitting material are studied. We demonstrate a new straightforward technique to improve external light emission efficiency by outcoupling part of the light that was initially guided into the different diode layers.
Observation of ice nucleation in acoustically levitated water drops
Authors: Lü Y. J. , Xie W. J. , Wei B.
Published: October 2005

The supercooling and nucleation of acoustically levitated water drops were investigated at two different sound pressure levels (SPL). These water drops were supercooled by 13to16K at the low SPL of 160.6dB, whereas their supercoolings varied from 5to11K at the high SPL of 164.4dB. The maximum supercooling obtained in the experiments is 32K. Statistical analyses based on the classical nucleation theory reveal that the occurrence of ice nucleation in water drops is mainly confined to the surface region under acoustic levitation conditions and the enlargement of drop surface area caused by the acoustic radiation pressure reduces water supercoolability remarkably. A comparison of the nucleation rates at the two SPLs indicates that the sound pressure can strengthen the surface-dominated nucleation of water drops. The acoustic stream around levitated water drops and the cavitation effect associated with ultrasonic field are the main factors that induce surface-dominated nucleation.
Ferroelectric domain structure in epitaxial BiFeO3 films
Authors: Zavaliche F. , Das R. R. , Kim D. M. , Eom C. B. , Yang S. Y. , Shafer P. , Ramesh R.
Published: October 2005

Piezoelectric force microscopy is employed to study the ferroelectric domain structure in a 600nm thick epitaxial BiFeO3 film. In the as-grown film, a mosaic-like domain structure is observed. Scans taken with the cantilever pointing along the principal crystallographic directions enabled us to reconstruct the polarization direction. By combining the perpendicular and in-plane piezoresponse data, we found that the ferroelectric domain structure is mainly described by four polarization directions. These directions point oppositely along two body diagonals, which form an angle of ∼71°. The other variants are also occasionally observed.
Glutathione S-transferase and aluminum toxicity in maize
Authors: Cançado Geraldo M. A. , De Rosa Vicente E. , Fernandez Jorge H. , Maron Lyza G. , Jorge Renato A. , Menossi Marcelo
Published: October 2005

Aluminum (Al) toxicity induces changes in the expression of several genes, some of which are involved in plant responses to oxidative stress. Using mRNA differential display, we identified a maize Al-inducible cDNA encoding a glutathione S-transferase (GST). The gene was named GST27.2 owing to its homology to the maize gene GST27, which is known to be induced by xenobiotics. GST27.2 is present in the maize genome as a single copy and analysis of its expression pattern revealed that the gene is expressed mainly in the root tip. Expression was up-regulated in response to various Al and Cd concentrations in both Al-tolerant and Al-sensitive maize lines. Consistent with its role in plants, phylogenetic analysis of theta-type GSTs revealed that GST27.2 belongs to a group of proteins that respond to different stresses. Finally, structural analysis of the polypeptide chain indicates that the two amino acids that differ between GST27.2 and GST27 (E102K and P123L) could be responsible for alterations in activity and / or specificity. Together, these results suggest that GST27.2 may play an important part in plant defenses against Al toxicity.
Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in
Arabidopsis thaliana
Authors: Duchêne Anne-Marie , Giritch Anatoli , Hoffmann Beate , Cognat Valérie , Lancelin Dominique , Peeters Nemo M. , Zaepfel Marlyse , Maréchal-Drouard Laurence , Small Ian D.
Published: October 2005

In plants, protein synthesis occurs in the cytosol, mitochondria, and plastids. Each compartment requires a full set of tRNAs and aminoacyl-tRNA synthetases. We have undertaken a systematic analysis of the targeting of organellar aminoacyl-tRNA synthetases in the model plant
Arabidopsis thaliana
. Dual targeting appeared to be a general rule. Among the 24 identified organellar aminoacyl-tRNA synthetases (aaRSs), 15 (and probably 17) are shared between mitochondria and plastids, and 5 are shared between cytosol and mitochondria (one of these aaRSs being present also in chloroplasts). Only two were shown to be uniquely chloroplastic and none to be uniquely mitochondrial. Moreover, there are no examples where the three aaRS genes originating from the three ancestral genomes still coexist. These results indicate that extensive exchange of aaRSs has occurred during evolution and that many are now shared between two or even three compartments. The findings have important implications for studies of the translation machinery in plants and on protein targeting and gene transfer in general.
Integration and evolution of the cichlid mandible: The molecular basis of alternate feeding strategies
Authors: Albertson R. Craig , Streelman J. Todd , Kocher Thomas D. , Yelick Pamela C.
Published: October 2005

African cichlid fishes have repeatedly evolved highly specialized modes of feeding through adaptations of their oral jaws. Here, we explore the molecular genetic basis of the opening and closing lever mechanisms of the cichlid lower jaw, which have traditionally been used to describe the mechanics of feeding behavior in bony fishes. Quantitative genetic analyses demonstrate that the opening and closing mechanisms are genetically modular and therefore free to evolve independently.
Bmp4
(
bone morphogenetic protein 4
) is one of two loci that segregate with the mechanical advantage of closing and that together account for >30% of the phenotypic variance in this trait. Species-specific differences in jaw shape are obvious early in cichlid larval development and are correlated with patterns of
bmp4
expression in the mandibular primordium. When
bmp4
is overexpressed in the obligate suction feeder
Danio rerio
, mandibular morphology exhibits specific transformations of opening and closing lever ratios. We conclude that patterns of morphological integration of the cichlid jaw reflect a balance among conflicting functional demands. Further, we demonstrate that
bmp4
has the potential to alter mandibular morphology in a way that mimics adaptive variation among fish species.
Adhesion controls bacterial actin polymerization-based movement
Authors: Soo Frederick S. , Theriot Julie A.
Published: October 2005

As part of its infectious life cycle, the bacterial pathogen
Listeria monocytogenes
propels itself through the host-cell cytoplasm by triggering the polymerization of host-cell actin near the bacterial surface, harnessing the activity of several cytoskeletal proteins used during actin-based cell crawling. To distinguish among several classes of biophysical models of actin-based bacterial movement, we used a high-throughput tracking technique to record the movement of many individual bacteria during temperature shifts. The speed of each bacterium varied strongly with temperature, closely following the Arrhenius rate law. Among bacteria, the prefactor
A
of the Arrhenius dependence unexpectedly varied exponentially with apparent activation energy,
E
a
, over a wide range (8–21 kcal/mol), reminiscent of the “rate compensation effect” of classical catalytic reactions. Average
E
a
were increased for mutant bacteria deficient in binding Ena/VASP proteins and bacteria moving in diluted extract. These two effects were additive. The observed temperature and rate compensation effects are consistent with a class of simple kinetic models in which the bacterium advances through the thermally driven, cooperative breakage of groups of adhesive bonds on its surface. The estimated number of coupled adhesive bonds
N
on the bacterial surface varies between 10 and 40 bonds. In contrast to other models, this model correctly predicts an experimentally observed negative correlation between bacterial speed and actin gel density. The idea that speed depends on adhesion, rather than polymerization, suggests several alternative mechanisms by which known cytoskeletal regulatory proteins could control cellular movement.
Mouse lackingCOUP-TFIIas an animal model of Bochdalek-type congenital diaphragmatic hernia
Authors: You Li-Ru , Takamoto Norio , Yu Cheng-Tai , Tanaka Toshiya , Kodama Tatsuhiko , DeMayo Francesco J. , Tsai Sophia Y. , Tsai Ming-Jer
Published: October 2005

Congenital diaphragmatic hernia (CDH), a life-threatening anomaly, is a major cause of pediatric mortality. Although the disease was described >350 years ago, the etiology of CDH is poorly understood. Here, we show that tissue-specific null mutants ofCOUP-TFIIexhibit Bochdalek-type CDH, the most common form of CDH.COUP-TFII, a member of orphan nuclear receptors, is expressed in regions critical for the formation of the diaphragm during embryonic development. Ablation ofCOUP-TFIIin the foregut mesenchyme, including the posthepatic mesenchymal plate (PHMP), results in the malformation of the diaphragm and the failure of appropriate attachment of the PHMP to the body wall. Thus, both the stomach and liver enter the thoracic cavity, leading to lung hypoplasia and neonatal death. Recently a minimally deleted region for CDH has been identified on chromosome 15q26.1-26.2 by CGH array and FISH analysis.COUP-TFIIis one of the four known genes residing within this critical region. Our finding suggests thatCOUP-TFIIis a likely contributor to the formation of CDH in individuals with 15q deletions, and it may also be a potential contributor to some other Bochdalek-type of CDH.
Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2
Authors: Young Juan I. , Hong Eugene P. , Castle John C. , Crespo-Barreto Juan , Bowman Aaron B. , Rose Matthew F. , Kang Dongcheul , Richman Ron , Johnson Jason M. , Berget Susan , Zoghbi Huda Y.
Published: October 2005

Rett syndrome (RTT) is a postnatal neurodevelopmental disorder characterized by the loss of acquired motor and language skills, autistic features, and unusual stereotyped movements. RTT is caused by mutations in the X-linked gene encoding methyl-CpG binding protein 2 (MeCP2). Mutations in
MECP2
cause a variety of neurodevelopmental disorders including X-linked mental retardation, psychiatric disorders, and some cases of autism. Although MeCP2 was identified as a methylation-dependent transcriptional repressor, transcriptional profiling of RNAs from mice lacking MeCP2 did not reveal significant gene expression changes, suggesting that MeCP2 does not simply function as a global repressor. Changes in expression of a few genes have been observed, but these alterations do not explain the full spectrum of Rett-like phenotypes, raising the possibility that additional MeCP2 functions play a role in pathogenesis. In this study, we show that MeCP2 interacts with the RNA-binding protein Y box-binding protein 1 and regulates splicing of reporter minigenes. Importantly, we found aberrant alternative splicing patterns in a mouse model of RTT. Thus, we uncovered a previously uncharacterized function of MeCP2 that involves regulation of splicing, in addition to its role as a transcriptional repressor.
Formation of apoptosome is initiated by cytochrome
c
-induced dATP hydrolysis and subsequent nucleotide exchange on Apaf-1
Authors: Kim Hyun-Eui , Du Fenghe , Fang Min , Wang Xiaodong
Published: October 2005

Apoptosis in metazoans is executed by a group of intracellular proteases named caspases. One of the caspase-activating pathways in mammals is initiated by the release of cytochrome
c
from mitochondria to cytosol, where it binds to Apaf-1 to form a procaspase-9-activating heptameric protein complex named apoptosome. We report here the reconstitution of this pathway with purified recombinant Apaf-1, procaspase-9, procaspase-3, and cytochrome
c
from horse heart. Apaf-1 contains a dATP as a cofactor. Cytochrome
c
binding to Apaf-1 induces hydrolysis of dATP to dADP, which is subsequently replaced by exogenous dATP. The dATP hydrolysis and exchange on Apaf-1 are two required steps for apoptosome formation.
The eukaryotic initiation factor (eIF) 5 HEAT domain mediates multifactor assembly and scanning with distinct interfaces to eIF1, eIF2, eIF3, and eIF4G
Authors: Yamamoto Yasufumi , Singh Chingakham Ranjit , Marintchev Assen , Hall Nathan S. , Hannig Ernest M. , Wagner Gerhard , Asano Katsura
Published: October 2005

Eukaryotic translation initiation factor (eIF) 5 is crucial for the assembly of the eukaryotic preinitiation complex. This activity is mediated by the ability of its C-terminal HEAT domain to interact with eIF1, eIF2, and eIF3 in the multifactor complex and with eIF4G in the 48S complex. However, the binding sites for these factors on eIF5–C-terminal domain (CTD) have not been known. Here we present a homology model for eIF5-CTD based on the HEAT domain of eIF2Bε. We show that the binding site for eIF2β is located in a surface area containing aromatic and acidic residues (aromatic/acidic boxes), that the binding sites for eIF1 and eIF3c are located in a conserved surface region of basic residues, and that eIF4G binds eIF5-CTD at an interface overlapping with the acidic area. Mutations in these distinct eIF5 surface areas impair
GCN4
translational control by disrupting preinitiation complex interactions. These results indicate that the eIF5 HEAT domain is a critical nucleation core for preinitiation complex assembly and function.
Building native protein conformation from highly approximate backbone torsion angles
Authors: Gong Haipeng , Fleming Patrick J. , Rose George D.
Published: October 2005

Reconstructing a protein in three dimensions from its backbone torsion angles is an ongoing challenge because minor inaccuracies in these angles produce major errors in the structure. As a familiar example, a small change in an elbow angle causes a large displacement at the end of your arm, the longer the arm, the larger the displacement. Even accurate knowledge of the backbone torsions φ and Ψ is insufficient, owing to the small, but cumulative, deviations from ideality in backbone planarity, which, if ignored, also lead to major errors in the structure. Against this background, we conducted a computational experiment to assess whether protein conformation can be determined from highly approximate backbone torsion angles, the kind of information that is now obtained readily from NMR. Specifically, backbone torsion angles were taken from proteins of known structure and mapped into 60° × 60° grid squares, called mesostates. Side-chain atoms beyond the β -carbon were discarded. A mesostate representation of the protein backbone was then used to extract likely candidates from a fragment library of mesostate pentamers, followed by Monte Carlo-based fragment-assembly simulations to identify stable conformations compatible with the given mesostate sequence. Only three simple energy terms were used to gauge stability: molecular compaction, soft-sphere repulsion, and hydrogen bonding. For the six representative proteins described here, stable conformers can be partitioned into a remarkably small number of topologically distinct clusters. Among these, the native topology is found with high frequency and can be identified as the cluster with the most favorable energy.
Validation of the Spanish version of the physical activity questionnaire used in the Nurses' Health Study and the Health Professionals' Follow-up Study
Authors: Martínez-González Miguel Angel , López-Fontana Constanza , Varo José Javier , Sánchez-Villegas Almudena , Martinez J Alfredo
Published: October 2005

Objective

The objective of this analysis was to test the validity of the estimates of energy expenditure and sedentary lifestyle obtained through a self-administered questionnaire of physical activity for Spanish-speaking people adapted from US questionnaires (Nurses' Health Study and Health Professionals' Follow-up Study) using a triaxial accelerometer (RT3 Triaxial Research Tracker) as the reference.

Design and setting: Validation study, calculating the non-parametric correlation coefficients between the level of physical activity and sedentary lifestyle collected by the self-administered questionnaire and the triaxial accelerometer measurements. Percentage of misclassification and kappa coefficients were also calculated.

Subjects

The study population consisted of a sample of 40 obese women who were participants of the SUN (Seguimiento Universidad de Navarra) project (a prospective cohort study among Spanish university alumni). They were selected because of their peculiar metabolic characteristics, in the search for a sub-optimal scenario for validity.

Results

Physical activity during leisure time (estimated as MET-h week-1) derived from the self-administered questionnaire moderately correlated with kcal day-1 assessed through the accelerometer (Spearman's ρ = 0.507, 95% confidence interval (CI) 0.232, 0.707). The Spearman correlation between the ratio of sedentary lifestyle to physical activity obtained through the questionnaire and the direct estimation (RT3) was -0.578 (95% CI -0.754, -0.325). The kappa index was 0.25 (P = 0.002) when assessing the cross-classification into quintiles and 0.41 for the dichotomous estimation of a sedentary lifestyle. Only 2.5% of participants were misclassified by the questionnaire more than two quintiles apart from the estimates of the RT3.

Conclusions

The moderate values obtained for correlation in a sub-optimal scenario for validity and the low percentage of extreme misclassification suggest the validity of the questionnaire to assess physical activity in Spanish-speaking women aged 20–50 years.
Evaluation of the Carcinogenic Potential of Clofibrate in the p53+/− Mouse
Authors: Torrey Carla E. , Campbell James A. , Hoivik Debie J. , Miller Richard T. , Allen Jane S. , Mann Peter C. , Selinger Krzysztof , Rickert Douglas , Savina Paul M. , Santostefano Michael J.
Published: October 2005

This study was conducted as part of International Life Sciences Institute (ILSI) program to evaluate the carcinogenic potential of clofibrate, a nongenotoxic, peroxisome proliferator-activated receptor (PPAR) α agonist, following oral administration to p53+ /− heterozygous mice for a minimum of 26 weeks. p-Cresidine, a urinary bladder carcinogen, was given orally at 400 mg/kg/day as a positive control. Initial clofibrate doses were 50, 250, and 400 mg/kg/day for males and 50, 200, and 500 mg/kg/day for females. Due to unexpected mortality during the first week of dosing, clofibrate doses were lowered to 25, 75, and 100 mg/kg/day for males and 25, 75, and 125 mg/kg/day for females. Clinical signs and mortality were greater in p53+ /− than wild-type (WT) mice. With the exception of liver weights, no marked differences in any other parameters either between the sexes or between WT and p53+ /− mice were noted. Moderate increases in liver weights noted in WT males given 100 mg/kg/day clofibrate were not associated with any microscopic changes. No neoplastic response was observed in p53+ /−mice after 6 months of exposure to clofibrate at doses up to 100 mg/kg/day for males and 125 mg/kg/day for females. Transitional-cell hyperplasia and carcinoma of the urinary bladder were noted in both sexes given p-cresidine, demonstrating that the p53+ /− mouse responded to a known mouse carcinogen as expected. Clofibrate produced non-neoplastic findings in the adrenals, pancreas, and prostate, whereas p-cresidine affected the kidney, liver, pancreas, and spleen.
Cusp size bounds from singular surfaces in hyperbolic 3-manifolds
Authors: Adams C. , Colestock A. , Fowler J. , Gillam W. , Katerman E.
Published: October 2005

Singular maps of surfaces into a hyperbolic 3-manifold are utilized to find upper bounds on meridian length,

ℓ
\ell

-curve length and maximal cusp volume for the manifold. This allows a proof of the fact that there exist hyperbolic knots with arbitrarily small cusp density and that every closed orientable 3-manifold contains a knot whose complement is hyperbolic with maximal cusp volume less than or equal to 9. We also find particular upper bounds on meridian length,

ℓ
\ell

-curve length and maximal cusp volume for hyperbolic knots in

S

3

\mathbb {S}^3

depending on crossing number. Particular improved bounds are obtained for alternating knots.
Surfaces of general type with 𝑝_{𝑔}=𝑞=1,𝐾²=8 and bicanonical map of degree 2
Authors: Polizzi Francesco
Published: October 2005

We classify the minimal algebraic surfaces of general type with

p
g

=
q
=
1
,

K
2

=
8

p_g=q=1, \; K^2=8

and bicanonical map of degree

2
2

. It will turn out that they are isogenous to a product of curves, i.e. if

S
S

is such a surface, then there exist two smooth curves

C
,

F

C, \; F

and a finite group

G
G

acting freely on

C
×
F

C \times F

such that

S
=
(
C
×
F
)

/

G

S = (C \times F)/G

. We describe the

C
,

F

C, \; F

and

G
G

that occur. In particular the curve

C
C

is a hyperelliptic-bielliptic curve of genus

3
3

, and the bicanonical map

ϕ
\phi

of

S
S

is composed with the involution

σ
\sigma

induced on

S
S

by

τ
×
i
d
:
C
×
F
⟶
C
×
F

\tau \times id: C \times F \longrightarrow C \times F

, where

τ
\tau

is the hyperelliptic involution of

C
C

. In this way we obtain three families of surfaces with

p
g

=
q
=
1
,

K
2

=
8

p_g=q=1, \; K^2=8

which yield the first-known examples of surfaces with these invariants. We compute their dimension and we show that they are three generically smooth, irreducible components of the moduli space

M

\mathcal {M}

of surfaces with

p
g

=
q
=
1
,

K
2

=
8

p_g=q=1, \; K^2=8

. Moreover, we give an alternative description of these surfaces as double covers of the plane, recovering a construction proposed by Du Val.
Isovariant Borsuk-Ulam results for pseudofree circle actions and their converse
Authors: Nagasaki Ikumitsu
Published: October 2005

In this paper we shall study the existence of an

S
1

S^1

-isovariant map from a rational homology sphere

M
M

with pseudofree action to a representation sphere

S
W

SW

. We first show some isovariant Borsuk-Ulam type results. Next we shall consider the converse of those results and show that there exists an

S
1

S^1

-isovariant map from

M
M

to

S
W

SW

under suitable conditions.
On meromorphic functions with finite logarithmic order
Authors: Chern Peter
Published: October 2005

By using a slow growth scale, the logarithmic order, with which to measure the growth of functions, we obtain basic results on the value distribution of a class of meromorphic functions of zero order.
Constant mean curvature surfaces in 𝑀²×𝐑
Authors: Hoffman David , de Lira Jorge , Rosenberg Harold
Published: October 2005

The subject of this paper is properly embedded

H
−

H-

surfaces in Riemannian three manifolds of the form

M
2

×

R

M^2\times \mathbf {R}

, where

M
2

M^2

is a complete Riemannian surface. When

M
2

=

R

2

M^2={\mathbf R}^2

, we are in the classical domain of

H
−

H-

surfaces in

R

3

{\mathbf R}^3

. In general, we will make some assumptions about

M
2

M^2

in order to prove stronger results, or to show the effects of curvature bounds in

M
2

M^2

on the behavior of

H
−

H-

surfaces in

M
2

×

R

M^2\times \mathbf {R}

.
The Thioredoxin System Protects Ribosomes against Stress-induced Aggregation
Authors: Rand Jonathan D. , Grant Chris M.
Published: October 2005

We previously showed that thioredoxins are required for dithiothreitol (DTT) tolerance, suggesting they maintain redox homeostasis in response to both oxidative and reductive stress conditions. In this present study, we screened the complete set of viable deletion strains in Saccharomyces cerevisiae for sensitivity to DTT to identify cell functions involved in resistance to reductive stress. We identified 195 mutants, whose gene products are localized throughout the cell. DTT-sensitive mutants were distributed among most major biological processes, but they particularly affected gene expression, metabolism, and the secretory pathway. Strikingly, a mutant lacking TSA1, encoding a peroxiredoxin, showed a similar sensitivity to DTT as a thioredoxin mutant. Epistasis analysis indicated that thioredoxins function upstream of Tsa1 in providing tolerance to DTT. Our data show that the chaperone function of Tsa1, rather than its peroxidase function, is required for this activity. Cells lacking TSA1 were found to accumulate aggregated proteins, and this was exacerbated by exposure to DTT. Analysis of the protein aggregates revealed that they are predominantly composed of ribosomal proteins. Furthermore, aggregation was found to correlate with an inhibition of translation initiation. We propose that Tsa1 normally functions to chaperone misassembled ribosomal proteins, preventing the toxicity that arises from their aggregation.
Phosphatidylinositol 3-Phosphate Indirectly Activates KCa3.1 via 14 Amino Acids in the Carboxy Terminus of KCa3.1
Authors: Srivastava Shekhar , Choudhury Papiya , Li Zhai , Liu GongXin , Nadkarni Vivek , Ko Kyung , Coetzee William A. , Skolnik Edward Y.
Published: October 2005

KCa3.1 is an intermediate conductance Ca2+-activated K+channel that is expressed predominantly in hematopoietic cells, smooth muscle cells, and epithelia where it functions to regulate membrane potential, Ca2+influx, cell volume, and chloride secretion. We recently found that the KCa3.1 channel also specifically requires phosphatidylinositol-3 phosphate [PI(3)P] for channel activity and is inhibited by myotubularin-related protein 6 (MTMR6), a PI(3)P phosphatase. We now show that PI(3)P indirectly activates KCa3.1. Unlike KCa3.1 channels, the related KCa2.1, KCa2.2, or KCa2.3 channels do not require PI(3)P for activity, suggesting that the KCa3.1 channel has evolved a unique means of regulation that is critical for its biological function. By making chimeric channels between KCa3.1 and KCa2.3, we identified a stretch of 14 amino acids in the carboxy-terminal calmodulin binding domain of KCa3.1 that is sufficient to confer regulation of KCa2.3 by PI(3)P. However, mutation of a single potential phosphorylation site in these 14 amino acids did not affect channel activity. These data together suggest that PI(3)P and these 14 amino acids regulate KCa3.1 channel activity by recruiting an as yet to be defined regulatory subunit that is required for Ca2+gating of KCa3.1.
Unique Suppression of Prostaglandin H Synthase-2 Expression by Inhibition of Histone Deacetylation, Specifically in Human Amnion but Not Adjacent Choriodecidua
Authors: Mitchell Murray D.
Published: October 2005

The key molecular regulatory mechanisms that govern and coordinate the molecular alterations that underpin the process of human labor remain incompletely understood although enhanced intrauterine prostaglandin production is known to be requisite. Studies from cancer tissues have indicated that at least one key enzyme of prostaglandin biosynthesis can have its activity severely reduced by increased histone deacetylation and enhanced DNA methylation status. We have advanced the hypothesis that similar regulation may occur in intrauterine tissues during pregnancy to prevent inadvertent activation of this powerful initiating signal by dampening responses to premature activation by agents such as cytokines. Our studies have shown that responsiveness of amnion, a key intrauterine tissue, to interleukin-1β is abrogated by inhibition of histone deacetylation, whereas PGDH amounts were increased basally. The findings do integrate well with others concerning progesterone (inhibitory) actions such that a decrease in the level of histone acetylation in human gestational tissues near term might herald a coordinated series of events that all result in a positive drive for parturition. Hence, a new level of regulatory action and potential therapeutic targets for pathologies such as preterm labor can flow from these findings.
Cortical Recruitment and Nuclear–Cytoplasmic Shuttling of Scd5p, a Protein Phosphatase-1-targeting Protein Involved in Actin Organization and Endocytosis
Authors: Chang Ji Suk , Henry Kenneth , Geli María Isabel , Lemmon Sandra K.
Published: October 2005

Scd5p regulates endocytosis and cortical actin organization as a targeting subunit for the Ser/Thr protein phosphatase-1 (PP1) in yeast. To identify localization signals in Scd5p required for cell surface recruitment, visualization of GFP-tagged Scd5 truncations and deletions was performed. Scd5p contains a PP1 binding site, a 3-repeat region of 20 amino acids (3R), and a 9-repeat region of 12 amino acids (9R). We found that the 9R is critical for cortical localization of Scd5p, but cortical recruitment is not essential for Scd5p's function in actin organization and endocytosis. We propose that Scd5p can target PP1 to endocytic factors in the cytoplasm that have been disassembled and/or inactivated by phosphorylation. We also found that Scd5p undergoes nuclear-cytoplasmic shuttling in a Crm1p-dependent manner. Scd5p-ΔCT lacking the 9R region and its nuclear export signal (NES) accumulates in the nucleus, causing cortical actin and endocytic defects. Cytoplasmic localization and function of Scd5p-ΔCT is restored by NES addition. However, removal of Scd5p's nuclear localization signal prevents nuclear entry, but endocytosis and actin organization remain relatively normal. These results indicate that nuclear-cytoplasmic shuttling is not required for regulation of Scd5p's cortical function and suggest that Scd5p has an independent nuclear function.
Large-scale prokaryotic gene prediction and comparison to genome annotation
Authors: Nielsen Pernille , Krogh Anders
Published: October 2005

Motivation: Prokaryotic genomes are sequenced and annotated at an increasing rate. The methods of annotation vary between sequencing groups. It makes genome comparison difficult and may lead to propagation of errors when questionable assignments are adapted from one genome to another. Genome comparison either on a large or small scale would be facilitated by using a single standard for annotation, which incorporates a transparency of why an open reading frame (ORF) is considered to be a gene.

Results: A total of 143 prokaryotic genomes were scored with an updated version of the prokaryotic genefinder EasyGene. Comparison of the GenBank and RefSeq annotations with the EasyGene predictions reveals that in some genomes up to ∼60% of the genes may have been annotated with a wrong start codon, especially in the GC-rich genomes. The fractional difference between annotated and predicted confirms that too many short genes are annotated in numerous organisms. Furthermore, genes might be missing in the annotation of some of the genomes. We predict 41 of 143 genomes to be over-annotated by >5%, meaning that too many ORFs are annotated as genes. We also predict that 12 of 143 genomes are under-annotated. These results are based on the difference between the number of annotated genes not found by EasyGene and the number of predicted genes that are not annotated in GenBank.

We argue that the average performance of our standardized and fully automated method is slightly better than the annotation.

Availability: The EasyGene 1.2 predictions and statistics can be accessed at

Contact:  pern@binf.ku.dk
GSMA: software implementation of the genome search meta-analysis method
Authors: Pardi Fabio , Levinson Douglas F. , Lewis Cathryn M.
Published: October 2005

Meta-analysis can be used to pool results of genome-wide linkage scans. This is of great value in complex diseases, where replication of linked regions occurs infrequently. The genome search meta-analysis (GSMA) method is widely used for this analysis, and a computer program is now available to implement the GSMA.

Availability:  

Contact:  Cathryn.lewis@genetics.kcl.ac.uk
ISER: selection of differentially expressed genes from DNA array data by non-linear data transformations and local fitting
Authors: Drummond R. D. , Pinheiro A. , Rocha C. S. , Menossi M.
Published: October 2005

Summary: This report describes an algorithm (intensity-dependent selection of expression ratios or ISER) developed to analyse DNA array data by optimizing the selection of genes with the most significant variations in expression amongst two RNA samples. The algorithm is designed for use when little or no replication of array hybridizations is available.

Availability: ISER is written in R language, and its code and on-line version are freely available at

Contact:  menossi@unicamp.br

Supplementary information:
Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens
Authors: Huang Yu-Cheng , Chang Chun-Fan , Chan Chen-hsiung , Yeh Tze-Jung , Chang Ya-Chun , Chen Chaur-Chin , Kao Cheng-Yan
Published: October 2005

Motivation: Differential detection on symptom-related pathogens (SRP) is critical for fast identification and accurate control against epidemic diseases. Conventional polymerase chain reaction (PCR) requires a large number of unique primers to amplify selected SRP target sequences. With multiple-use primers (mu-primers), multiple targets can be amplified and detected in one PCR experiment under standard reaction condition and reduced detection complexity. However, the time complexity of designing mu-primers with the best heuristic method available is too vast. We have formulated minimum-set mu-primer design problem as a set covering problem (SCP), and used modified compact genetic algorithm (MCGA) to solve this problem optimally and efficiently. We have also proposed new strategies of primer/probe design algorithm (PDA) on combining both minimum-set (MS) mu-primers and unique (UniQ) probes. Designed primer/probe set by PDA-MS/UniQ can amplify multiple genes simultaneously upon physical presence with minimum-set mu-primer amplification (MMA) before intended differential detection with probes-array hybridization (PAH) on the selected target set of SRP.

Results: The proposed PDA-MS/UniQ method pursues a much smaller number of primers set compared with conventional PCR. In the simulation experiment for amplifying 12 669 target sequences, the performance of our method with 68% reduction on required mu-primers number seems to be superior to the compared heuristic approaches in both computation efficiency and reduction percentage. Our integrated PDA-MS/UniQ method is applied to the differential detection on 9 plant viruses from 4 genera with MMA and PAH of 11 mu-primers instead of 18 unique ones in conventional PCR while amplifying overall 9 target sequences. The results of wet lab experiments with integrated MMA-PAH system have successfully validated the specificity and sensitivity of the primers/probes designed with our integrated PDA-MS/UniQ method.

Contact:  cykao@csie.ntu.edu.tw

Supplementary information: