bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biodegradable poly(alkylene succinate) blends: Thermal behavior and miscibility study
Authors: Papageorgiou George Z. , Bikiaris Dimitrios N. 
Published: December 2005

AbstractNew binary blends composed of poly(ethylene succinate) and poly(propylene succinate) or poly(ethylene succinate) and poly(butylene succinate) were prepared. Both PESu/PPSu and PESu/PBSu systems belong to semicrystalline/semicrystalline pairs. The miscibility and crystallization behavior was investigated using differential scanning calorimetry (DSC), wide angle X‐ray diffraction (WAXD), and polarizing light microscopy (PLM). Blends of PESu and PPSu exhibited a single composition dependent glass transition temperature over the entire range of composition, indicating that the system is miscible. The melting point depression of the high melting temperature component, PESu, was analyzed according to the Nishi‐Wang equation. A negative polymer–polymer interaction parameter was obtained, indicating that the blends are thermodynamically miscible in the melt. The two components crystallized sequentially when the blends were cooled rapidly to a low temperature. DSC traces of PESu/PBSu blends after quenching showed two distinct composition dependent glass transition temperatures between those of the neat polymers, showing that the polymers are partially miscible. The amorphous PESu/PBSu blends in the intermediate compositions showed three cold‐crystallization peaks, indicating the influence of mixing. The crystallization rates of PBSu were reduced and those of PESu were increased. WAXD showed reduced crystallinity and peak broadening in the patterns of the blends of intermediate compositions, while no spherulites could be detected by PLM. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 584–597, 2006
Folding mechanism of β‐hairpins studied by replica exchange molecular simulations
Authors: Zhang Jian , Qin Meng , Wang Wei 
Published: December 2005

AbstractThe folding process of trpzip2 β‐hairpin is studied by the replica exchange molecular dynamics (REMD) and normal MD simulations, aiming to understand the folding mechanism of this unique small, stable, and fast folder, as well as to reveal the general principles in the folding of β‐hairpins. According to our simulations, the TS ensemble is mainly characterized by a largely formed turn and the interaction between the inner pair of hydrophobic core residues. The folding is a zipping up of hydrogen bonds. However, the nascent turn has to be stabilized by the partially formed hydrophobic core to cross the TS. Thus our folding picture is in essence a blend of hydrogen bond‐centric and hydrophobic core‐centric mechanism. Our simulations provide a direct evidence for a very recent experiment (Du et al., Proc Natl Acad Sci USA 2004;101:15915–15920), which suggests that the turn formation is the rate‐limiting step for β‐hairpin folding and the unfolding is mainly determined by the hydrophobic interactions. Besides, the relationship between hydrogen bond stabilities and their relative importance in folding are investigated. It is found that the hydrogen bonds with higher stabilities need not play more important roles in the folding process, and vice versa. Proteins 2006. © 2005 Wiley‐Liss, Inc.
A Statistical Investigation and Optimization of an Industrial Radiography Inspection Process for Aero‐engine Components
Authors: Wong W. K. , Ng S. H. , Xu K. 
Published: December 2005

AbstractObtaining a high‐quality radiographic image is imperative in a radiography inspection process as it improves the identification of flaws in aero‐engine parts, which in turn enhances the reliability and safety of aircrafts. Existing methods to improve the radiographic inspection process are ad hoc and rely heavily on the experiences of radiographers. The radiographic images obtained from X‐rays have dual conflicting quality features, contrast sensitivity and spatial resolution, and have to satisfy a density reading constraint. This paper investigates an industrial radiography inspection process using statistical design of experiments (DOE) and analysis to determine optimal design settings for the process. The investigation adapts from the standard response surface methodology (RSM) and provides a promising alternative to the current methods. It has several key features such as the sequential DOE to first determine the feasible region imposed by the film density constraint, a sliding‐level system design to handle the irregular region, and an optimization formulation to optimize the dual image quality responses simultaneously. It provides a systematic approach to analyzing processes with secondary response constraints, and provides a quantitative basis for selecting optimum process settings. To evaluate the effectiveness of the statistical models obtained for industrial radiography, the probability of detection methodology is used to compare the optimum process settings recommended. Copyright © 2005 John Wiley & Sons, Ltd.
Biased Reduced Sampling: Detectability of an Attribute and Estimation of Prevalence
Authors: Graves Todd , Hamada Michael 
Published: December 2005

AbstractIn surveilling a population, detection of systems with an attribute of interest and estimation of the prevalence of the attribute in the population are two main goals. Due to cost constraints, only a subset of all components of sampled systems may be fully tested. Biasing the sampling to increase the probability of choosing a component with an attribute of interest ameliorates the impact of reduced sampling. In this paper, we consider the impact of biased reduced sampling on detection and propose an approach for estimating the prevalence of the attribute in the population which properly accounts for the biasing. The proposed method is illustrated with a simulated example. Copyright © 2005 John Wiley & Sons, Ltd.
Effect of reduction in endogenous dopamine on extrastriatal binding of [11C]FLB 457 in rat brain—An ex vivo study
Authors: Ahmad Rabia , Hirani Ella , Grasby Paul M. , Hume Susan P. 
Published: December 2005

AbstractCarbon‐11 labeled FLB 457 has been used successfully as a selective, high affinity PET ligand for the quantification of extrastriatal D2‐like receptors in man. This study was carried out in rats to investigate regional values for maximal binding and ED50(a measure of apparentKd) for the radioligand in vivo in control animals and in a group pretreated with the neuronal impulse flow inhibitor, γ‐butyrolactone. The aims were to obtain further information regarding the specific activity needed to ensure tracer kinetics and to investigate baseline occupancy by dopamine (DA), each relevant to optimal clinical use of the radioligand. RegionalBmaxvalues were consistent with the distribution of D2‐like receptors in rat brain. Of interest, 60% of the binding in cerebellum, often used as a low‐binding “reference region” for PET quantification, was saturable, withBmaxonly 2‐ to 3‐fold less than that in neocortex, hippocampus, and thalamus. ED50values were in the range 2–3 nmol/kg, confirming minimal receptor occupancy by the tracer in human PET, using high but achievable specific activities. In the majority of extrastriatal tissues, reduction in synaptic DA did not significantly decrease the apparentKd, except in cortical regions, where the extent of the effect suggested a low (∼10%), but measurable baseline receptor occupancy by DA. Synapse 59:162–172, 2006. © 2005 Wiley‐Liss, Inc.
A chamber system with automatic opening and closing for continuously measuring soil respiration based on an open‐flow dynamic method
Authors: Suh Sang‐Uk , Chun Young‐Moon , Chae Nam‐yi , Kim Joon , Lim Jong‐Hwan , Yokozawa Masayuki , Lee Mi‐Sun , Lee Jae‐Seok 
Published: December 2005

AbstractWe developed an automatic opening and closing chamber system (AOCC) based on an open‐flow dynamic method (open‐flow AOCC). The AOCC can be used during all four seasons, even at the surface of relatively deep snow. We compared the open‐flow AOCC with two closed dynamic methods [the AOCC configured as a closed dynamic system (closed dynamic AOCC) and the LI‐6400 system] under field conditions. The closed dynamic‐AOCC and LI‐6400 measurements were about 15.4% and 5.2% lower, respectively, than the values obtained with the open‐flow AOCC. There was a significant difference in soil respiration rate between the open‐flow AOCC and the closed dynamic AOCC system. In contrast, no significant difference in soil respiration rate was detected between the open‐flow AOCC and the LI‐6400 system. In the field, the open‐flow AOCC permitted continuous long‐term measurements under a range of temperature conditions and did a good job of reflecting the marked daily and seasonal variations in soil respiration as a function of soil temperature.
Short-term effects of enhanced treatment for depression in primary care: results from a randomized controlled trial
Authors: SMIT A. , KLUITER H. , CONRADI H. J. , MEER K. VAN DER , TIEMENS B. G. , JENNER J. A. , VAN OS T. W. D. P. , ORMEL J. 
Published: December 2005

Background. Depression is a highly prevalent, often recurring or persistent disorder. The majority of patients are initially seen and treated in primary care. Effective treatments are available, but possibilities for providing adequate follow-up care are often limited in this setting. This study assesses the effectiveness of primary-care-based enhanced treatment modalities on short-term patient outcomes.Method. In a randomized controlled trial we evaluated a psycho-educational self-management intervention. We included 267 adult patients meeting criteria for a DSM-IV diagnosis of major depressive disorder, assessed by a structured psychiatric interview. Patients were randomly assigned to: the Depression Recurrence Prevention (DRP) program (n=112); a combination of the DRP program with psychiatric consultation (PC+DRP, n=39); a combination with brief cognitive behavior therapy (CBT+DRP, n=44); and care as usual (CAU, n=72). Follow-up assessments were made at 3 months (response 90%) and 6 months (85%).Results. Patient acceptance of enhanced care was good. The mean duration of the index episode was 11 weeks (S.D.=9·78) and similar in CAU and enhanced care. Recovery rate after 6 months was 67% overall; 17% of all participants remained depressed for the entire 6-month period.Conclusion. Enhanced care did not result in better short-term outcomes. We found no evidence that the DRP program was more effective than CAU and no indications for added beneficial effects of either the psychiatric evaluation or the CBT treatment to the basic format of the DRP program. Observed depression treatment rates in CAU were high.
An evaluation of three diagnostic wind models (CALMET, MCSCIPUF, and SWIFT) with wind data from the Dipole Pride 26 field experiments
Authors: Cox Robert M. , Sontowski John , Dougherty Catherine M. 
Published: December 2005

AbstractThis paper describes the evaluation of three diagnostic wind models by direct comparison with wind field data. The models are the California Meteorological Model (CALMET), the Mass Consistent model (MCSCIPUF) associated with the Second Order Closure Integrated Puff (SCIPUFF) transport/dispersion model, and the Stationary Wind Field and Turbulence (SWIFT) model. The evaluation follows previous works by Chang, Franzese & Hanna, who compared the same three models, and by Bradley & Mazzola who evaluated SWIFT coupled with SCIPUFF. As with SWIFT, MCSCIPUF is incorporated in the Hazard Prediction and Assessment Capability (HPAC), while CALMET is linked with the California Puff model (CALPUFF), another transport and dispersion model. The Dipole Pride 26 (DP26) experiments, performed at the US Department of Energy (DOE) Nevada Test Site, are used as the source of the wind data. They provide a comprehensive set of meteorological data with wide‐ranging atmospheric stability conditions over a complex terrain. Model calculations were compared with measured data in two phases. The first phase uses complete sets of data from eight locations (the 8M phase) as model inputs, and thus tests the ability of the models to reproduce input conditions. In the second phase, five of the measured wind sites are withheld from input, and instead used for validation of model calculations (the 3M phase). In the first phase, the errors were found (with some exceptions) to be quite small. In the second phase, mean absolute errors were found to be of the order of 1ms−1 and 30°, with only small differences among models in terms of performance. Copyright © 2005 Royal Meteorological Society
An attempt to define the Road Climate Room
Authors: Almkvist Esben , Gustavsson Torbjörn , Bogren Jörgen 
Published: December 2005

AbstractSince the start of field station manufacturing approximately 25 years ago, the configuration of Road Weather Information System (RWIS) stations and the type of sensors used has changed very little. Little is known about the variation of climatic variables from the 2 m level, where instruments are normally placed, down to the road surface. The ‘Road Climate Room’ can be defined as the volume of air, road and surroundings influencing the conditions on the road. This study attempts to describe the Road Climate Room both theoretically and experimentally. Mobile measurements as well as a permanent station were used. At the permanent station detailed temperature measurements above and beside the road were made. These were related to other climatic variables such as wind, cloudiness, humidity and ground heat flux. The results show that the most important processes occur below the 10 cm level. The air column above this level is well represented by the 2 m level temperature sensor. For most situations the cooling of the air closest to the ground is much more intense in the vegetation than over the road. The temperature difference can be as large as 8°C and can be represented statistically with high determination by wind and cloudiness. The heat storage in the road is a key factor for keeping the temperature of the road high throughout a full diurnal cycle. The cold air in the vegetation can be considered as a potential source for cold air drainage onto the road surface in terrain where that is a problem. No advection affecting the road surface was observed at the permanent station. This suggests that the Road Climate Room can be defined as being well within the internal boundary layer of the road. The mobile measurements, however, show that advection from the surroundings is likely to have taken place, which makes the definition of the Road Climate Room more difficult. Further studies are needed to fully understand the complicated processes. Copyright © 2005 Royal Meteorological Society
Ridom TraceEdit: a DNA trace editor and viewer
Authors: Rothgänger Jörg , Weniger Markus , Weniger Thomas , Mellmann Alexander , Harmsen Dag 
Published: December 2005

Abstract
Summary: Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved.
Availability: TraceEdit is freely available via the Internet at . TraceEdit has been designed to operate on Windows, MacOS X and UNIX platforms.
Contact: info@ridom.de
HideNseek, a post-genome approach to locate transgenes exemplified in Arabidopsis thaliana
Authors: Yang Guojun , Hall Timothy C. 
Published: December 2005

Abstract
Summary: Determination of transgene location is essential for investigating the effects of position on transgene expression levels and facilitates cloning of the resident gene affected by insertion. Currently used PCR-based approaches for determination of transgene location are relatively complicated and often fail when the transgene is duplicated, rearranged or fragmented. HideNseek is a new bioinformatics tool that allows computation of transgene locations, provided that a suitable genomic restriction enzyme digestion profile is available. Since the new approach is not based on the terminal sequences of the transgene insert, it is less sensitive to transgene duplication, rearrangement or fragmentation. HideNseek has been tested experimentally and by in silico simulation. The experimental example provided here shows that this simple approach is feasible, permitting rapid location of transgenes with little bench work.
Availability: available on request from the authors.
Contact: tim@idmb.tamu.edu
Supplementary data: HideNseek input and output examples, experimental procedures and figures showing experimental results are provided as supplementary files: Supplementary material 1, 2, 3 and Supplementary figures (Figs 1 and 2), respectively. Supplementary data is available at Bioinformatics online.
SEAN: SNP prediction and display program utilizing EST sequence clusters
Authors: Huntley Derek , Baldo Angela , Johri Saurabh , Sergot Marek 
Published: December 2005

Abstract
Summary: SEAN is an application that predicts single nucleotide polymorphisms (SNPs) using multiple sequence alignments produced from expressed sequence tag (EST) clusters. The algorithm uses rules of sequence identity and SNP abundance to determine the quality of the prediction. A Java viewer is provided to display the EST alignments and predicted SNPs.
Availability: SEAN is freely available from
Contact: d.huntley@imperial.ac.uk
CMfinder—a covariance model based RNA motif finding algorithm
Authors: Yao Zizhen , Weinberg Zasha , Ruzzo Walter L. 
Published: December 2005

Abstract
Motivation: The recent discoveries of large numbers of non-coding RNAs and computational advances in genome-scale RNA search create a need for tools for automatic, high quality identification and characterization of conserved RNA motifs that can be readily used for database search. Previous tools fall short of this goal.
Results: CMfinder is a new tool to predict RNA motifs in unaligned sequences. It is an expectation maximization algorithm using covariance models for motif description, featuring novel integration of multiple techniques for effective search of motif space, and a Bayesian framework that blends mutual information-based and folding energy-based approaches to predict structure in a principled way.
Extensive tests show that our method works well on datasets with either low or high sequence similarity, is robust to inclusion of lengthy extraneous flanking sequence and/or completely unrelated sequences, and is reasonably fast and scalable. In testing on 19 known ncRNA families, including some difficult cases with poor sequence conservation and large indels, our method demonstrates excellent average per-base-pair accuracy—79% compared with at most 60% for alternative methods. More importantly, the resulting probabilistic model can be directly used for homology search, allowing iterative refinement of structural models based on additional homologs. We have used this approach to obtain highly accurate covariance models of known RNA motifs based on small numbers of related sequences, which identified homologs in deeply-diverged species.
Availability: Results and web server version are available at
Contact: yzizhen@cs.washington.edu
Supplementary information: Supplementary technical details are available at
Characterization of OCA2 cDNA in different porcine breeds and analysis of its potential effect on skin pigmentation in a red Iberian strain
Authors: Fernández A. , Silió L. , Rodríguez C. , Óvilo C. 
Published: December 2005

SummaryAlthough the function of the OCA2 gene product has not been totally clarified, variation in OCA2 has been associated with skin and hair pigmentation in human and mouse. However, its contribution to skin colour in domestic species has not been reported. In this study, cDNA and intron 9 sequences of the porcine OCA2 gene have been characterized in several pig populations. The cDNA sequence alignment of 20 animals from eight porcine populations allowed the identification of 10 single nucleotide polymorphisms (SNPs); five of the 10 SNPs were non‐synonymous. The intron 9 sequence alignment of 12 animals belonging to four pig populations revealed four additional SNPs. Skin colour variation was analysed in a red strain of Iberian pigs with segregation of three SNPs forming two OCA2 intragenic haplotypes. Results from this study provide evidence of a suggestive dominant effect of haplotypes on colour intensity and indicate an important contribution of additive polygenic effects (h2 = 0.56 ± 0.21) to the variance of this trait.
Autoantibodies to thrombin directed against both of its cryptic exosites
Authors: Mollica Luigina , Preston Roger J.S. , Chion Alain Chan Kwo , Lees Steve J. , Collins Peter , Lewis Sarah , Lane David A. 
Published: December 2005

SummaryImmunoglobulin G (IgG) anti‐thrombin autoantibodies (ATA) were purified from the plasma of a patient referred for haematological investigation because of bleeding for 24 h following a dental extraction. The ATA did not inhibit the catalytic activity of thrombin against a chromogenic substrate, suggesting that they did not interact with the active site of thrombin. The ATA did, however, prolong the time required to generate thrombin in plasma, suggesting that they inhibited factor V and factor VIII activation. Surface plasmon resonance (SPR) was used to demonstrate that ATA bound to thrombin with high affinity. Competition of thrombin‐ATA binding, using known thrombin exosite I and II ligands (hirudin, thrombomodulin and heparin), demonstrated that ATA bound to both thrombin exosites. Thrombin residues that are important for ATA binding were identified using a library of 53 recombinant thrombin variants encompassing alanine substitutions of 78 surface‐exposed residues. They were H66, R68, R70 and Y71 in exosite I, and R89, R93, E94, R98, R245 and K248 in exosite II. ATA bound predominantly to exosite II. They did not bind to prothrombin, illustrating the cryptic nature of both exosites exposed and presented as potential antigens following prothrombin conversion to thrombin.
Do habitat models accurately predict the depth distribution of pelagic fishes?
Authors: WARD PETER J. , MYERS RANSOM A. 
Published: December 2005

AbstractHabitat models are used to correct estimates of fish abundance derived from pelagic longline fishing gear. They combine information on hook depth with the species’ preferences for ambient environmental conditions to adjust the gear's catchability. We compare depth distributions of bigeye tuna (Thunnus obesus) catch predicted by a habitat model with distributions derived from data collected by observers on longliners in the tropical Pacific Ocean. Our analyses show that the habitat model does not accurately predict the depth distribution of bigeye tuna; its predictions are worse than those from models that assume no effect of depth on catches. Statistical models provided superior fits to the observed depth distribution. The poor performance of the habitat model is probably due to (1) problems in estimating hook depth, (2) fine‐scale variations in environmental conditions, (3) incomplete knowledge of habitat preferences and (4) differences between the distribution of bigeye tuna and their vulnerability to longline gear.