bluuebunny/crossref_metadata_2025 huggingface dataset:
Competition and cooperation between lattice-oriented growth and step-templated growth of aligned carbon nanotubes on sapphire
Authors: Ago Hiroki , Imamoto Kenta , Ishigami Naoki , Ohdo Ryota , Ikeda Ken-ichi , Tsuji Masaharu
Published: March 2007

The authors study the growth mechanism of single-walled carbon nanotubes (SWNTs) horizontally aligned on A-plane single crystal sapphire (112¯0) by making the controlled step/terrace structure. SWNT growth direction was sensitive to the surface geometry of the sapphire, and there was competition between two growth modes, lattice-oriented growth and step-templated growth. On the substrate with single-atomic steps, SWNTs aligned parallel to the [11¯00] direction as dominated by the lattice-oriented growth mode, while SWNTs aligned along the step edges when the double-atomic or higher steps were formed. Our findings have potential for the fabrication of designed architecture of SWNTs by combining these two growth modes.
Nanomesh fluidic filter using self-assembly of colloidal nanospheres and surface tension
Authors: Seo Young Ho
Published: March 2007

A simple and inexpensive method of fabricating a nanofluidic filter was developed by using self-assembly of colloidal nanospheres and surface tension. Colloid plug formed by surface tension in the microchannel was evaporated, then the nanospheres in a colloid were orderly stacked by capillary force. The porosity and mean pore size of the nanomesh membrane were 45.4% and 158nm, respectively. In the nanoindentation test with a spherical tip of 10μm radius, the nanomesh membranes withstood the maximum mechanical loading of 26.8±2.47mN, and the heat-treated membranes withstood 66.65±4.15mN.
Spontaneous charge transfer at organic-organic homointerfaces to establish thermodynamic equilibrium
Authors: Duhm S. , Glowatzki H. , Rabe J. P. , Koch N. , Johnson R. L.
Published: March 2007

The energy level alignment of α,ω-dihexylsexithienyl (DH6T) mono- and multilayers on tetrafluorotetracyanoquinodimethane (F4-TCNQ) precovered Ag(111) and polycrystalline Au substrates was investigated with ultraviolet photoelectron spectroscopy. For certain F4-TCNQ precoverages molecular level pinning at DH6T monolayer-multilayer homointerfaces was observed. The pinning behavior shows that thermodynamic equilibrium can be established across hexyl chains via charge transfer, indicating the limited use of these short alkyl chains for insulation in the field of molecular electronics.
Fabrication and device characteristics of Schottky-type bulk GaN-based “visible-blind” ultraviolet photodetectors
Authors: Zhou Yi , Ahyi Claude , Tin Chin-Che , Williams John , Park Minseo , Kim Dong-Joo , Cheng An-Jen , Wang Dake , Hanser Andrew , Preble Edward A. , Williams N. Mark , Evans Keith
Published: March 2007

The authors present the fabrication and characterization of vertical-geometry Schottky-type ultraviolet (UV) photodetectors based on a bulk n-GaN substrate. By using low temperature rapid thermal annealing of the semitransparent Schottky contacts (nickel with 7% vanadium), they obtained an ultralow dark current of 0.56pA at −10V reverse bias. A responsivity of ∼0.09A∕W at zero bias was measured for wavelength shorter than the absorption edge of GaN, and it was found to be independent of the incident power in the range measured (50mW∕m2–2.2kW∕m2). The devices are visible blind, with an UV/visible contrast of over six orders of magnitude. An open-circuit voltage of 0.3V was also obtained under a broadband UV illumination.
Study of self-diffraction process in photoconducting polymer-nematic liquid crystal hybrid structure
Authors: Mysliwiec Jaroslaw , Jarzab Dorota , Janus Krzysztof , Bartkiewicz Stanislaw
Published: March 2007

The authors present results of the measurements of self-diffraction process inside the nematic liquid crystal cell with a photoconducting polymeric layer poly(N-vinylcarbazole) doped with trinitrofluorenone molecules. The dynamics of diffraction grating fading process versus applied voltage and different Ar+ laser power has been studied. Three-step process of grating’s fading was observed, connected with the charge carrier generation and their mobility in the photoconducting polymer. Theoretical calculations assuming proposed mechanism responsible for the grating decay are in a very good agreement with experimental results.
Photoluminescence characterization of Zn1−xMgxO epitaxial thin films grown on ZnO by radical source molecular beam epitaxy
Authors: Shibata H. , Tampo H. , Matsubara K. , Yamada A. , Sakurai K. , Ishizuka S. , Niki S. , Sakai M.
Published: March 2007

The authors report that high-quality Zn1−xMgxO alloys are very brilliant light emitters, even more brilliant than ZnO, particularly in the high-temperature region; both the emission bandwidth and the oscillator strength of the photoluminescence from Zn1−xMgxO alloys increase remarkably with increasing Mg composition ratio x. The authors have revealed that the increase in the oscillator strength is mainly due to the increase in the activation energy required for the nonradiative recombination processes. Therefore, it is suggested that the localization of excitons, because of the compositional fluctuation, takes place in Zn1−xMgxO alloys and that the degree of the localization increases with increasing x.
High quality AlGaN solar-blind Schottky photodiodes fabricated on AIN/sapphire template
Authors: Jiang H. , Egawa T.
Published: March 2007

The authors report the high-performance AlGaN solar-blind Schottky photodiodes grown on AIN/sapphire templates by metal organic chemical vapor deposition. The devices exhibit dark current densities as low as 1.6×10−11A∕cm2 at −5V bias. The peak responsivity is 41mA∕W at 256nm in the photovoltaic mode, corresponding to a quantum efficiency of 20%. A sharp spectral response cutoff of more than two orders of magnitude by 300nm is observed under a low illumination intensity of 10nW∕cm2. The zero-bias resistance-area product of the device is found to be 5.0×1012Ωcm2, leading to an estimated detectivity of 7.0×1014cmHz1∕2∕W at 256nm.
Isotropic photonic magnetoresistance
Authors: Chau K. J. , Baron C. A. , Elezzabi A. Y.
Published: March 2007

The authors demonstrate isotropic photonic magnetoresistive behavior in the far-infrared transmission through ferromagnetic particle collections. Total suppression of the angular anisotropy, a fundamental characteristic of anisotropic magnetoresistance, is achieved in ensembles of highly porous, “cauliflower” shaped ferromagnetic particles. They reveal a morphological origin of the isotropic magnetic behavior using a phenomenological model in conjunction with three-dimensional calculations using Maxwell’s equations.
Dead-time optimized time-correlated photon counting instrument with synchronized, independent timing channels
Authors: Wahl Michael , Rahn Hans-Jürgen , Gregor Ingo , Erdmann Rainer , Enderlein Jörg
Published: March 2007

Time-correlated single photon counting is a powerful method for sensitive time-resolved fluorescence measurements down to the single molecule level. The method is based on the precisely timed registration of single photons of a fluorescence signal. Historically, its primary goal was the determination of fluorescence lifetimes upon optical excitation by a short light pulse. This goal is still important today and therefore has a strong influence on instrument design. However, modifications and extensions of the early designs allow for the recovery of much more information from the detected photons and enable entirely new applications. Here, we present a new instrument that captures single photon events on multiple synchronized channels with picosecond resolution and over virtually unlimited time spans. This is achieved by means of crystal-locked time digitizers with high resolution and very short dead time. Subsequent event processing in programmable logic permits classical histogramming as well as time tagging of individual photons and their streaming to the host computer. Through the latter, any algorithms and methods for the analysis of fluorescence dynamics can be implemented either in real time or offline. Instrument test results from single molecule applications will be presented.
Generalized phase-shifting interferometry with arbitrary unknown phase shifts: Direct wave-front reconstruction by blind phase shift extraction and its experimental verification
Authors: Xu X. F. , Cai L. Z. , Wang Y. R. , Yang X. L. , Meng X. F. , Dong G. Y. , Shen X. X. , Zhang H.
Published: March 2007

A simple wave-front reconstruction method by generalized phase-shifting interferometry (PSI) with arbitrary unknown phase shift between 0 and π for two adjacent frames is proposed. In this method the unknown phase shifts are extracted by a noniterative algorithm with the use of the interferograms and the intensities of object and reference waves, and then the original object field can be further obtained. This method is applicable for generalized PSI of any frame number N (N⩾2) and for both the amplitude and phase objects. Its effectiveness and accuracy are verified by both the computer simulations and optical experiments.
Realization of ultraviolet electroluminescence from ZnO homojunction with n-ZnO∕p-ZnO:As∕GaAs structure
Authors: Sun J. C. , Zhao J. Z. , Liang H. W. , Bian J. M. , Hu L. Z. , Zhang H. Q. , Liang X. P. , Liu W. F. , Du G. T.
Published: March 2007

ZnO homojunction light-emitting diode with n-ZnO∕p-ZnO:As∕GaAs structure is produced by metal organic chemical vapor deposition. The p-type ZnO:As film is obtained out of thermal diffusion of arsenic from GaAs substrate with subsequent thermal annealing at 550°C. The n-type layer is composed of unintentionally doped ZnO film. Desirable rectifying behavior is observed from the current-voltage curve of the ZnO p-n homojunction. Furthermore, two distinct electroluminescence bands centered at 3.2 and 2.5eV are obtained from the junction under forward bias at room temperature.
Growth of nonpolar AlN (112¯) and (11¯00) films on SiC substrates by flow-rate modulation epitaxy
Authors: Akasaka Tetsuya , Kobayashi Yasuyuki , Makimoto Toshiki
Published: March 2007

Nonpolar AlN (112¯0) and (11¯00) films were grown on SiC substrates by flow-rate modulation epitaxy (FME), wherein trimethylaluminum and NH3 were alternately supplied. FME provides both AlN (112¯0) and (11¯00) films with good crystallinity and smooth surfaces, whereas AlN (11¯00) films obtained by conventional metal-organic chemical vapor deposition exhibit poor crystallinity and rough surfaces with deep trenches consisting of (0001¯) and (11¯01) N-face microfacets. FME effectively eliminates these trenches, because the microfacets are unstable and have faster growth rates because of the enhanced migration of Al atoms in the absence of excess N surface coverage under the Al-rich condition.
Focal tunable liquid lens integrated with an electromagnetic actuator
Authors: Lee Seok Woo , Lee Seung S.
Published: March 2007

In this letter, a focal tunable liquid lens using a large deformable polydimethylsiloxane (PDMS) membrane is integrated with an electromagnetic microactuator for uniform pressure on the membrane by a fabrication process of PDMS compatible with conventional micromachining processes. The fabricated device is characterized by surface profiling and optical observations. A rectangular PDMS membrane of 3mm in width for actuation shows that the maximum displacement is 51.4μm when the current is 30mA. In the optical observations, the image is blurred when the applied current is varied. From the result, it was found that the device changes the focal length.
Two-photon passive electro-optic upconversion in a GaAs∕AlGaAs heterostructure device
Authors: Zhao Lai , Thompson Pete , Faleev N. N. , Prather D. W. , Appelbaum Ian
Published: March 2007

A semiconductor heterostructure device that requires no external power source to upconvert two low-energy photons into one higher-energy photon is proposed. This passive device is fabricated in the AlGaAs∕GaAs material system and it is used to demonstrate photon upconversion from 808to710nm at room temperature.
Room temperature pulsed laser deposited indium gallium zinc oxide channel based transparent thin film transistors
Authors: Suresh Arun , Wellenius Patrick , Dhawan Anuj , Muth John
Published: March 2007

Indium gallium zinc oxide deposited by pulsed laser deposition at room temperature was used as a channel layer to fabricate transparent thin film transistors with good electrical characteristics: field effect mobility of 11cm2V−1s−1 and subthreshold voltage swing of 0.20V∕decade. By varying the oxygen partial pressure during deposition the conductivity of the channel was controlled to give a low off-current of ∼10pA and a drain current on/off ratio of ∼5×107. Changing the channel layer thickness was a viable way to vary the threshold voltage. The effect of the gate dielectric on the electrical behavior was also explored.
High peak-power (10.5W) GaInAs∕AlGaAsSb quantum-cascade lasers emitting at λ∼3.6–3.8μm
Authors: Yang Quankui , Manz Christian , Bronner Wolfgang , Lehmann Nico , Fuchs Frank , Köhler Klaus , Wagner Joachim
Published: March 2007

High peak-power operation of quaternary-barrier GaInAs∕AlGaAsSb quantum-cascade lasers emitting at λ∼3.6–3.8μm is reported. With as-cleaved facets, the lasers (18μm×2.7mm) emit a maximum peak power of 8.2W per facet at 77K. When applying a high-reflection coating to the back facet, a maximum peak power emitted from the front facet of 10.5W at 77K has been obtained for an 18μm×2.0mm device. The lasers operate in pulsed mode up to 340K, and their emission wavelength shifts from 3.65μm at 77Kto3.79μm at 300K.
Spectral and spatial single mode emission from a photonic crystal distributed feedback laser
Authors: Hofmann H. , Scherer H. , Deubert S. , Kamp M. , Forchel A.
Published: March 2007

The authors report on the fabrication and characterization of photonic crystal distributed feedback lasers, which are a generalization of distributed feedback and angled distributed feedback lasers. Spectral and spatial mode selection is provided by a two-dimensional, rectangular lattice of etched air holes that is tilted relatively to the cleaved facets. InGaAs∕AlGaAs laser layers emitting around 1μm were used for the fabrication of the devices. The laser emits at a single wavelength with a side mode suppression ratio of 50dB. The emission is concentrated in a narrow far field, indicating that a coherent mode is formed over the entire width of the device.
Intergovernmental Relations and International Urban Strategies: Constraints and Opportunities in Multilevel Polities
Authors: Kübler Daniel , Piliutyte Jolita
Published: March 2007

The authors analyse the influence of intergovernmental relations on international urban strategies. They build on the general premise that institutional settings shape actor behaviour, both as constraints and as opportunities. First, they focus on the influence of domestic intergovernmental patterns on the international activities of cities. It is found that the political status of city governments with respect to higher government levels, the strength of regional governments within a national intergovernmental system, and city-regional dynamics, are all factors that shape international urban strategies—in terms both of their orientation and of their coherence. Second, concerning the relationship between international urban strategies and intergovernmental processes linked to European integration, it is found that both ‘download’ and ‘upload’ Europeanisation create a pattern of institutional constraints and opportunities that push cities—especially secondary cities—towards active participation in European networks and the development of a clear international profile.
Partnership for Success—Community-Based Economic Development: A Case Study of Ngolowindo Cooperative, Malawi
Authors: Hill T R , Nel E L , Illgner P
Published: March 2007

Africa has a disproportionate share of the world's poorest countries and within this context economically weak states generally lack the ability to provide the ideal level of support and opportunities for their citizens. This paper examines how, in Malawi, a community-based economic development initiative, with the aid of a supportive NGO, has significantly improved rural livelihoods and facilitated market access in the formal market economy. Active government and NGO support for small scale irrigation farming coupled with their encouragement of community development led to the emergence of the Ngolowindo agricultural cooperative which serves as a useful model and example of locality-based development in Africa. After providing a context for the study in terms of both contextual literature and details specific to the Malawian context, the paper examines how the cooperative emerged, how it operates, what role the supporting NGO plays, and how products are sold. The study concludes with an overview of key findings and an examination of the lessons for local development in Africa.
The Legacies of the Dead: Commemorating the Troubles in Northern Ireland
Authors: Graham Brian , Whelan Yvonne
Published: March 2007

The Belfast Agreement of 1998, which initiated the so-called Peace Process in Northern Ireland, was fashioned so as to avoid creating mechanisms for addressing the legacy of the past, not least the commemoration of the fatalities of the Troubles which began in 1969. In this paper we explore, first, the role of the past and practices of commemoration in unagreed societies such as Northern Ireland in which consensus appears an unlikely proposition, the focus being on inclusion and exclusion and on the role of the contested nature of a hierarchical victimhood in commemoration. Second, the discussion engages with a succession of interconnected ideas that define the spatiality and landscapes of commemoration and considers the practices and spatialization of commemorating the Troubles within the grounded reality of everyday life and within the pragmatism of politics in Northern Ireland. We argue that processes of remembering and forgetting the dead of the Troubles point, at best, to a democracy shaped by ‘conflictual consensus’, in which the contested heritage of victimhood both constitutes an important resource in ethnonationalist and ethnosectarian politics and undermines the consociational Belfast Agreement and its attempt to elide the burdens of the past.
Bats under a hot tin roof: comparing the microclimate of eastern cave bat (Vespadelus troughtoni) roosts in a shed and cave overhangs
Authors: Law B. S. , Chidel M.
Published: March 2007

We compared the microclimate experienced by maternity groups of eastern cave bats (Vespadelus troughtoni) in northern New South Wales between roosts in overhang caves versus a nearby maternity roost beneath the corrugated iron roof of a farm shed. The shed’s microclimate differed dramatically from that of the caves. Caves provided well-buffered microclimate conditions, which were cooler and more humid than ambient conditions during the day, but were warmer and less humid than ambient at night. Early summer temperatures remained between 20 and 25°C in the maternity caves. In contrast, the microclimate at the shed was not buffered, with conditions varying enormously over a 24-h period, being hotter than ambient during the day (mean = 30°C, maximum = 40°C in the middle of the day), and similar to ambient at night (mean = 18°C at dawn). Rather than selecting thermal stability, lactating females selected warm, but variable, diurnal temperatures in the shed, presumably to sustain lactation. Under this situation, we estimated considerable energetic savings by roosting in the shed (27–35%, assuming normothermia) compared with that for caves, and even higher savings if bats were torpid in the mornings and passively rewarmed later (60–69%). Lactating bats therefore presumably traded-off the cost of leaving juveniles behind in a cool roost at night with these energetic benefits. In late autumn bats continued to roost in the shed with day temperatures rising above 30°C, compared with unoccupied caves, which were considerably cooler at this time (~20°C). Clarification of the estimated energy savings and the possible costs in terms of milk production requires further research to measure concurrently body temperatures, roost temperature and energy expenditure, together with juvenile growth in different types of roosts.
The role of mantle ultrapotassic fluids in diamond formation
Authors: Palyanov Yuri N. , Shatsky Vladislav S. , Sobolev Nikolay V. , Sokol Alexander G.
Published: March 2007

Analysis of data on micro- and nano-inclusions in mantle-derived and metamorphic diamonds shows that, to a first approximation, diamond-forming medium can be considered as a specific ultrapotassic, carbonate/chloride/silicate/water fluid. In the present work, the processes and mechanisms of diamond crystallization were experimentally studied at 7.5 GPa, within the temperature range of 1,400–1,800°C, with different compositions of melts and fluids in the KCl/K
2
CO
3
/H
2
O/C system. It has been established that, at constant pressure, temperature, and run duration, the mechanisms of diamond nucleation, degree of graphite-to-diamond transformation, and formation of metastable graphite are governed chiefly by the composition of the fluids and melts. The experimental data suggest that the evolution of the composition of deep-seated ultrapotassic fluids/melts is a crucial factor of diamond formation in mantle and ultrahigh-pressure metamorphic processes.
Global patterns and determinants of vascular plant diversity
Authors: Kreft Holger , Jetz Walter
Published: March 2007

Plants, with an estimated 300,000 species, provide crucial primary production and ecosystem structure. To date, our quantitative understanding of diversity gradients of megadiverse clades such as plants has been hampered by the paucity of distribution data. Here, we investigate the global-scale species-richness pattern of vascular plants and examine its environmental and potential historical determinants. Across 1,032 geographic regions worldwide, potential evapotranspiration, the number of wet days per year, and measurements of topographical and habitat heterogeneity emerge as core predictors of species richness. After accounting for environmental effects, the residual differences across the major floristic kingdoms are minor, with the exception of the uniquely diverse Cape Region, highlighting the important role of historical contingencies. Notably, the South African Cape region contains more than twice as many species as expected by the global environmental model, confirming its uniquely evolved flora. A combined multipredictor model explains ≈70% of the global variation in species richness and fully accounts for the enigmatic latitudinal gradient in species richness. The models illustrate the geographic interplay of different environmental predictors of species richness. Our findings highlight that different hypotheses about the causes of diversity gradients are not mutually exclusive, but likely act synergistically with water–energy dynamics playing a dominant role. The presented geostatistical approach is likely to prove instrumental for identifying richness patterns of the many other taxa without single-species distribution data that still escape our understanding.
Mania-like behavior induced by disruption of
CLOCK
Authors: Roybal Kole , Theobold David , Graham Ami , DiNieri Jennifer A. , Russo Scott J. , Krishnan Vaishnav , Chakravarty Sumana , Peevey Joseph , Oehrlein Nathan , Birnbaum Shari , Vitaterna Martha H. , Orsulak Paul , Takahashi Joseph S. , Nestler Eric J. , Carlezon William A. , McClung Colleen A.
Published: March 2007

Circadian rhythms and the genes that make up the molecular clock have long been implicated in bipolar disorder. Genetic evidence in bipolar patients suggests that the central transcriptional activator of molecular rhythms, CLOCK, may be particularly important. However, the exact role of this gene in the development of this disorder remains unclear. Here we show that mice carrying a mutation in the
Clock
gene display an overall behavioral profile that is strikingly similar to human mania, including hyperactivity, decreased sleep, lowered depression-like behavior, lower anxiety, and an increase in the reward value for cocaine, sucrose, and medial forebrain bundle stimulation. Chronic administration of the mood stabilizer lithium returns many of these behavioral responses to wild-type levels. In addition, the
Clock
mutant mice have an increase in dopaminergic activity in the ventral tegmental area, and their behavioral abnormalities are rescued by expressing a functional CLOCK protein via viral-mediated gene transfer specifically in the ventral tegmental area. These findings establish the
Clock
mutant mice as a previously unrecognized model of human mania and reveal an important role for CLOCK in the dopaminergic system in regulating behavior and mood.
Directing macromolecular conformation through halogen bonds
Authors: Voth Andrea Regier , Hays Franklin A. , Ho P. Shing
Published: March 2007

The halogen bond, a noncovalent interaction involving polarizable chlorine, bromine, or iodine molecular substituents, is now being exploited to control the assembly of small molecules in the design of supramolecular complexes and new materials. We demonstrate that a halogen bond formed between a brominated uracil and phosphate oxygen can be engineered to direct the conformation of a biological molecule, in this case to define the conformational isomer of a four-stranded DNA junction when placed in direct competition against a classic hydrogen bond. As a result, this bromine interaction is estimated to be ≈2–5 kcal/mol stronger than the analogous hydrogen bond in this environment, depending on the geometry of the halogen bond. This study helps to establish halogen bonding as a potential tool for the rational design and construction of molecular materials with DNA and other biological macromolecules.
Identification of a new intrinsically timed developmental checkpoint that reprograms key hematopoietic stem cell properties
Authors: Bowie Michelle B. , Kent David G. , Dykstra Brad , McKnight Kristen D. , McCaffrey Lindsay , Hoodless Pamela A. , Eaves Connie J.
Published: March 2007

Hematopoietic stem cells (HSCs) execute self-renewal divisions throughout fetal and adult life, although some of their properties do alter. Here we analyzed the magnitude and timing of changes in the self-renewal properties and differentiated cell outputs of transplanted HSCs obtained from different sources during development. We also assessed the expression of several “stem cell” genes in corresponding populations of highly purified HSCs. Fetal and adult HSCs displayed marked differences in their self-renewal, differentiated cell output, and gene expression properties, with persistence of a fetal phenotype until 3 weeks after birth. Then, 1 week later, the HSCs became functionally indistinguishable from adult HSCs. The same schedule of changes in HSC properties occurred when HSCs from fetal or 3-week-old donors were transplanted into adult recipients. These findings point to the existence of a previously unrecognized, intrinsically regulated master switch that effects a developmental change in key HSC properties.
Enhancements and modifications of primer design program Primer3
Authors: Koressaar Triinu , Remm Maido
Published: March 2007

Summary: The determination of annealing temperature is a critical step in PCR design. This parameter is typically derived from the melting temperature of the PCR primers, so for successful PCR work it is important to determine the melting temperature of primer accurately. We introduced several enhancements in the widely used primer design program Primer3. The improvements include a formula for calculating melting temperature and a salt correction formula. Also, the new version can take into account the effects of divalent cations, which are included in most PCR buffers. Another modification enables using lowercase masked template sequences for primer design.

Availability: Features described in this article have been implemented into the development code of Primer3 and will be available in future versions (version 1.1 and newer) of Primer3. Also, a modified version is compiled under the name of mPrimer3 which is distributed independently. The web-based version of mPrimer3 is available at http://bioinfo.ebc.ee/mprimer3/ and the binary code is freely downloadable from the URL http://bioinfo.ebc.ee/download/.

Contact:  maido.remm@ut.ee
RETRACTED: Analysis and prediction of β-turn types using multinomial logistic regression and artificial neural network
Authors: Mehdi Poursheikhali Asgary , Parviz Abdolmaleki , Anoshirvan Kazemnejad , Samad Jahandidehs
Published: March 2007

Motivation

So far various statistical and machine learning techniques applied for prediction of β-turns. The majority of these techniques have been only focused on the prediction of β-turn location in proteins. We developed a hybrid approach for analysis and prediction of different types of β-turn.

Results

A two-stage hybrid model developed to predict the β-turn types I, II, IV and VIII. Multinomial logistic regression was initially used for the first time to select significant parameters in prediction of β-turn types using a self-consistency test procedure. The extracted parameters were consisted of 80 amino acid positional occurrences and 20 amino acid percentages in β-turn sequence. The most significant parameters were then selected using multinomial logistic regression model. Among these, the occurrences of glutamine, histidine, glutamic acid and arginine, respectively, in positions i, i+1, i+2 and i+3 of β-turn sequence had an overall relationship with 5 β-turn types. A neural network model was then constructed and fed by the parameters selected by multinomial logistic regression to build a hybrid predictor. The networks have been trained and tested on a non-homologous dataset of 565 protein chains by nine fold cross-validation. It has been observed that the hybrid model gives a Matthews correlation coefficient (MCC) of 0.473 and 0.124, respectively, for β-turn types II and VIII which are best among previously reported results. Our model also distinguished the different types of β-turn in the embedded binary logit comparisons which have not carried out so far.

Availability

Available on request from the authors.
iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations
Authors: Huang Liang-Tsung , Gromiha M. Michael , Ho Shinn-Ying
Published: March 2007

Summary: We have developed a web server, iPTREE-STAB for discriminating the stability of proteins (stabilizing or destabilizing) and predicting their stability changes (ΔΔG) upon single amino acid substitutions from amino acid sequence. The discrimination and prediction are mainly based on decision tree coupled with adaptive boosting algorithm, and classification and regression tree, respectively, using three neighboring residues of the mutant site along N- and C-terminals. Our method showed an accuracy of 82% for discriminating the stabilizing and destabilizing mutants, and a correlation of 0.70 for predicting protein stability changes upon mutations.

Availability:  http://bioinformatics.myweb.hinet.net/iptree.htm

Contact:  michael-gromiha@aist.go.jp

Supplementary information: Dataset and other details are given.
Structure of PICK1 and other PDZ domains obtained with the help of self‐binding C‐terminal extensions
Authors: Elkins Jonathan M. , Papagrigoriou Evangelos , Berridge Georgina , Yang Xiaowen , Phillips Claire , Gileadi Carina , Savitsky Pavel , Doyle Declan A.
Published: March 2007

PDZ domains are protein–protein interaction modules that generally bind to the C termini of their target proteins. The C‐terminal four amino acids of a prospective binding partner of a PDZ domain are typically the determinants of binding specificity. In an effort to determine the structures of a number of PDZ domains we have included appropriate four residue extensions on the C termini of PDZ domain truncation mutants, designed for self‐binding. Multiple truncations of each PDZ domain were generated. The four residue extensions, which represent known specificity sequences of the target PDZ domains and cover both class I and II motifs, form intermolecular contacts in the expected manner for the interactions of PDZ domains with protein C termini for both classes. We present the structures of eight unique PDZ domains crystallized using this approach and focus on four which provide information on selectivity (PICK1 and the third PDZ domain of DLG2), binding site flexibility (the third PDZ domain of MPDZ), and peptide–domain interactions (MPDZ 12th PDZ domain). Analysis of our results shows a clear improvement in the chances of obtaining PDZ domain crystals by using this approach compared to similar truncations of the PDZ domains without the C‐terminal four residue extensions.
Structure of M11L: A myxoma virus structural homolog of the apoptosis inhibitor, Bcl‐2
Authors: Douglas Andrew E. , Corbett Kevin D. , Berger James M. , McFadden Grant , Handel Tracy M.
Published: March 2007

Apoptosis of virally infected cells is an innate host mechanism used to prevent viral spread. However, viruses have evolved a number of proteins that function to modulate the apoptotic cascades and thereby favor productive viral replication. One such antiapoptotic protein, myxoma virus M11L, has been shown to inhibit mitochondrial‐dependent apoptosis by binding to and blocking the two executioner proteins Bak and Bax. Since M11L has no obvious sequence homology with Bcl‐2 or Bcl‐xL, the normal cellular inhibitors for Bak and Bax, and the structure of M11L has not been solved, the mode of binding to Bak and Bax is not known. In order to understand how M11L functions, the crystal structure of M11L was solved to 2.91 Å. Despite the lack of sequence similarity, M11L is a structural homolog of Bcl‐2. Studies using a peptide derived from Bak indicate that M11L binds to Bak with a similar affinity (4.9 ± 0.3 μM) to the published binding affinities of Bcl‐2 and Bcl‐xL to the same peptide (12.7 μM and 0.5 μM, respectively), indicating that M11L inhibits apoptosis by mimicking and competing with host proteins for the binding of Bak and Bax. The structure provides important insight into how myxoma virus and other poxviruses facilitate viral dissemination by inhibiting mitochondrial dependent apoptosis.
Low plasma levels of the protein pro‐LL‐37 as an early indication of severe disease in patients with chronic neutropenia
Authors: Karlsson Jenny , Carlsson Göran , Ramme Kim Göransdotter , Hägglund Hans , Fadeel Bengt , Nordenskjöld Magnus , Henter Jan‐Inge , Palmblad Jan , Pütsep Katrin , Andersson Mats
Published: March 2007

Chronic neutropenia comprises several different diseases that vary in degree of severity and management. We analysed the levels of the neutrophil‐derived protein pro‐LL‐37 in plasma of patients with chronic neutropenia to assess whether it could be used to differentiate different categories of chronic neutropenia. All patients with severe congenital neutropenia were pro‐LL‐37 deficient. This was in contrast to patients with autoimmune or idiopathic neutropenia, who exhibited normal pro‐LL‐37 levels while patients with cyclic neutropenia displayed an oscillation of pro‐LL‐37 in plasma. Plasma levels of pro‐LL‐37 may thus prove useful for differential diagnosis of chronic neutropenia.
Management of acute graft‐versus‐host disease
Authors: Bacigalupo Andrea
Published: March 2007

Acute graft‐versus‐host disease (GvHD) is a frequent complication of allogeneic haemopoietic stem cell transplantation (HSCT) and donor lymphocyte infusions (DLI). Its incidence and severity depends on several factors, such as prophylaxis method, donor/recipient matching, intensity of the conditioning regimen and composition of the graft. Significant progress has been made in recent years in understanding the pathogenesis of the disease, and some of these advances have been translated into clinical trials. First‐line treatment of acute GvHD is based on corticosteroids, and produce sustained responses in 50–80% of patients depending on the initial severity. Non‐responders are offered second‐line therapy, with combinations of immunosuppressive agents, but 1‐year survival is 30% in most large trials. New strategies explored include infusion of expanded mesenchymal stem cells (MSC), down regulation of antigen‐presenting cells (APC) and suicide gene transduced T cells. Acute GvHD is complicated by severe immunodeficiency causing life‐threatening infections. To date, GvHD has not been differentiated from the graft‐versus‐leukaemia effect. The present review will discuss some of these aspects.
Protein Z/Z‐dependent protease inhibitor (PZ/ZPI) anticoagulant system and thrombosis
Authors: Corral Javier , González‐Conejero Rocio , Hernández‐Espinosa David , Vicente Vicente
Published: March 2007

A new anticoagulant system involving a serpin has been recently characterised. The protein Z/Z‐dependent protease inhibitor (PZ/ZPI) system inhibits activated factors X, XI and IX by different mechanisms. By homology with other anticoagulant systems (antithrombin or the protein C/protein S), deficiency of the serpin (ZPI) or its cofactor (PZ) might imbalance the haemostatic system with thrombotic consequences. Evidence supports the in vivo anticoagulant role of this complex and the thrombotic consequences of its deficiency. Non‐sense variations of the ZPI (W303X and R67X) have been associated with increased risk of venous thrombosis. Moreover, PZ deficient mice carrying the FV Leiden have a thrombotic phenotype. Finally, some reports suggest that PZ deficiency might increase the risk of thrombosis. However, other studies question the thrombotic relevance of both ZPI and PZ deficiencies. This system could play a redundant role in haemostasis that explains the conflicting results on its thrombotic potential, which might be exacerbated in combination with other prothrombotic factors.
Parenting programmes: a systematic review and synthesis of qualitative research
Authors: Kane G. A. , Wood V. A. , Barlow J.
Published: March 2007

Background  Parenting programmes are at the heart of intervention strategies for parents of children with emotional and behaviour problems. Systematic reviews and meta‐analyses of randomized controlled trials have indicated that such programmes can improve many aspects of family life. However, there is currently a dearth of information concerning what it is that makes parenting programmes meaningful and helpful to parents. The aim of this paper was to examine parents' experience and perceptions of parenting programmes using the meta‐ethnographic method, in order to sensitize policymakers and practitioners to the key factors that parents perceive to be of value.

Methods  Systematic searches of a number of electronic databases were undertaken using key search terms. Critical appraisal of included studies was conducted using standardized criteria, and the reports were synthesized using meta‐ethnographic methods.

Results  Six reports were purposefully selected and critically appraised independently by two reviewers. Two were excluded. Based on the remaining four papers, five key concepts were identified as important when planning and delivering parenting programmes. A lines‐of‐argument synthesis was developed which suggests that the acquisition of knowledge, skills and understanding, together with feelings of acceptance and support from other parents in the parenting group, enabled parents to regain control and feel more able to cope. This led to a reduction in feelings of guilt and social isolation, increased empathy with their children and confidence in dealing with their behaviour.

Conclusion  This evaluation provides an indication of the components that parents perceive to be necessary in the provision of parenting programmes, independent of the particular type of programme being provided. It may therefore aid policymakers in decisions about which programmes to provide.
Interleukin‐6, tumour necrosis factor‐alpha and insulin relationships to body composition, metabolism and resting energy expenditure in a migrant Asian Indian population
Authors: Rush Elaine C. , Plank Lindsay D. , Yajnik Chittaranjan S.
Published: March 2007

Objective  Systemic inflammation and insulin resistance may play important roles in the pathogenesis of obesity‐related diseases for which migrant Asian Indians are at particularly high risk. We examined relationships between markers of insulin resistance and inflammation, resting energy expenditure (REE), and body composition.

Design and methods  Measurements were made of total and regional body composition, including regional fat mass (FM) and appendicular skeletal muscle mass (ASMM) by dual‐energy X‐ray absorptiometry (DXA), REE by indirect calorimetry and fasting interleukin (IL)‐6, tumour necrosis factor (TNF)‐α, glucose and insulin, in 79 healthy Asian Indians (38F, 41M; age 30–49 years) from urban Auckland, New Zealand. Beta‐cell function (HOMA B%) and insulin sensitivity (HOMA S%) were derived using homeostatic model assessment.

Results  Men had a more central distribution of body fat than women. REE was strongly correlated with IL‐6 concentrations in men but not in women. In both sexes, IL‐6 was associated positively with percentage body fat and HOMA B% and inversely with ASMM and HOMA S%. Insulin increased and HOMA S% decreased with increasing waist‐to‐hip ratio and abdominal‐to‐thigh fat ratio in men but not in women. TNF‐α was not significantly associated with any of the variables examined.

Conclusion  Relationships between body fat distribution and HOMA S% were strongly sex dependent and may indicate a greater propensity for development of the metabolic syndrome among male Asian Indians than females in the age group examined.
The analgesic efficacy of lidocaine/prilocaine (EMLA) cream during fine‐needle aspiration biopsy of thyroid nodules
Authors: Gursoy Alptekin , Ertugrul Derun Taner , Sahin Mustafa , Tutuncu Neslihan Bascil , Demirer Asli Nar , Demirag Nilgun Guvener
Published: March 2007

Objective  Pain is one of the few drawbacks of fine‐needle aspiration biopsy (FNAB) in patients with nodular thyroid disease (NTD). Lidocaine/prilocaine cream, an eutectic mixture of local anaesthetics (EMLA), is a frequently used topical anaesthetic. Despite its well‐documented efficacy for the relief of pain associated with other cutaneous procedures that involve needle insertion, the analgesic role of EMLA has not been previously reported in patients with NTD who are undergoing FNAB. The aim of this study was to determine the analgesic efficacy of EMLA for FNAB‐associated pain in patients with NTD.

Design  Double‐blind, placebo‐controlled clinical trial.

Patients  The study was conducted at a thyroid outpatient clinic. We studied 99 patients with NTD.

Measurements  Patients with NTD were allocated to receive either 2·5 g of EMLA (n = 50) or placebo (n = 49) 60 min before ultrasonographically guided FNAB. A series of four biopsies of each nodule was performed. Patients rated pain associated with the procedure according to a 100‐mm visual analogue scale (VAS), an 11‐point numeric rating scale (NRS), and 4‐category verbal rating scale (VRS).

Results  When the EMLA group was compared with the placebo group, there were no significant differences with respect to age, sex, thyroid volume, nodule size or nodule site. Significant differences were noted in the pain ratings of the two groups according to all three pain scales. When the effectiveness of EMLA was compared with that of placebo, the mean VAS score was 25·0 ± 22·3 mm vs. 40·0 ± 30·5 mm (P = 0·006) and the mean NRS score was 2·9 ± 2·3 points vs. 4·0 ± 2·6 points (P = 0·02). The absolute numbers according to VRS score in each group was also significantly different (P = 0·01). Although our sample size was small, the data suggest that FNAB‐associated pain was sex‐related and that women were significantly more sensitive than were men (P = 0·003 for VAS score and P = 0·001 for NRS score). No adverse effects from the use of EMLA were reported.

Conclusions  To our knowledge, this is the first study demonstrating that a topical anaesthetic, EMLA, provides an effective and noninvasive analgesia during the FNAB of NTD.
Relative adrenal insufficiency: an identifiable entity in nonseptic critically ill patients?
Authors: De Jong Margriet F. C. , Beishuizen Albertus , Spijkstra Jan‐Jaap , Girbes Armand R. J. , Groeneveld A. B. Johan
Published: March 2007

Objective  To determine whether relative adrenal insufficiency (RAI) can be identified in nonseptic hypotensive patients in the intensive care unit (ICU).

Design  Retrospective study in a medical–surgical ICU of a university hospital.

Patients  One hundred and seventy‐two nonseptic ICU patients (51% after trauma or surgery), who underwent a short 250 µg ACTH test because of > 6 h hypotension or vasopressor/inotropic therapy.

Measurements  On the test day, the Simplified Acute Physiology Score II (SAPS II) and Sequential Organ Failure Assessment (SOFA) score were calculated to estimate disease severity. The ICU mortality until day 28 was recorded. Best discriminative levels of baseline cortisol, increases and peaks were established using receiver operating characteristic curves. These and corticosteroid treatment (in n = 112, 65%), among other variables, were examined by multiple logistic regression and Cox proportional hazard regression analyses to find independent predictors of ICU mortality until day 28.

Results  ICU mortality until day 28 was 23%. Nonsurvivors had higher SAPS II and SOFA scores. Baseline cortisol levels correlated directly with albumin levels and SAPS II. In the multivariate analyses, a cortisol baseline > 475 nmol/l and cortisol increase < 200 nmol/l predicted mortality, largely dependent on disease severity but independent of albumin levels. Corticosteroid (hydrocortisone) treatment was not associated with an improved outcome, regardless of the ACTH test results.

Conclusion  In nonseptic hypotensive ICU patients, a low cortisol/ACTH response and treatment with corticosteroids do not contribute to mortality prediction by severity of disease. The data thus argue against RAI identifiable by cortisol/ACTH testing and necessitating corticosteroid substitution treatment in these patients.
The speed of ecological speciation
Authors: HENDRY ANDREW P. , NOSIL PATRIK , RIESEBERG LOREN H.
Published: March 2007

Adaptation can occur on ecological time‐scales (contemporary evolution) and adaptive divergence can cause reproductive isolation (ecological speciation). From the intersection of these two premises follows the prediction that reproductive isolation can evolve on ecological time‐scales. We explore this possibility in theory and in nature. Finding few relevant studies, we examine each in some detail.

Theory: Several models have demonstrated that ecological differences can drive the evolution of partial reproductive barriers in dozens to hundreds of generations. Barriers likely to evolve quickly include dispersal rate, habitat preference and selection against migrants/hybrids.

Plants: Adjacent populations adapting to different fertilizer treatments or to mine tailings can develop reproductive barriers within at least 100 generations. These barriers include differences in flowering time and selection against migrants/hybrids.

Invertebrates: Populations on native and introduced host plants can manifest reproductive barriers in dozens to hundreds of generations. These barriers include local host preference and selection against migrants/hybrids.

Vertebrates: Salmon adapting to divergent breeding environments can show restricted gene flow within at least 14 generations. Birds evolving different migratory routes can mate assortatively within at least 10–20 generations. Hybrid sculpins can become isolated from their ancestral species within at least 20–200 generations.

Ecological speciation can commence within dozens of generations. How far it goes is an important question for future research.