bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computer-aided design of nano-filter construction using DNA self-assembly
Authors: Mohammadzadegan Reza , Mohabatkar Hassan 
Published: November 2006

Abstract
Computer-aided design plays a fundamental role in both top-down and bottom-up nano-system fabrication. This paper presents a bottom-up nano-filter patterning process based on DNA self-assembly. In this study we designed a new method to construct fully designed nano-filters with the pores between 5 nm and 9 nm in diameter. Our calculations illustrated that by constructing such a nano-filter we would be able to separate many molecules.
Recovery after coronary artery bypass grafting: Patients’ and health professionals’ views of the hospital experience
Authors: Dunckley Maria , Ellard David , Quinn Tom , Barlow Julie 
Published: November 2006

Background Increasing access to revascularisation procedures is a key aspect of a National Service Framework. Coronary artery bypass grafting (CABG) is effective in relieving symptoms and reducing mortality but some patients do not report an improved quality of life or experience a good recovery. Aims To describe the recovery trajectory after CABG and identify facilitators and barriers to recovery. Methods Semi-structured interviews were conducted with 11 patients who had previously undergone elective, isolated, first-time CABG and with 10 health professionals experienced in caring for these patients. Results Thematic analysis identified the following themes: definition and timeline of recovery, preparation for surgery including information provision, attitude to surgery and confidence in staff, clinical factors and the in-patient experience. The key finding is the different recovery trajectory between patients with severe versus mild pre-operative symptoms; patients with few pre-CABG symptoms reported a much longer recovery time. Conclusions This study has provided insights into the barriers and facilitators to recovery after CABG and the processes involved. Findings have indicated areas where health professionals can intervene to aid patients’ long-term recovery and thereby maximise the benefits of CABG.
A review of records from follow-up visits for immigrant and Swedish patients at a heart failure clinic
Authors: Hedemalm Azar , Schaufelberger Maria , Ekman Inger 
Published: November 2006

Today, nearly 20% of the Swedish population originates from multiethnic backgrounds. Patients’ symptom expressions, adherence to health regimens, and communication with health-care professionals have been shown to be related to their ethnic and cultural backgrounds. Purpose To describe documented care of immigrant patients and matched Swedish patients at a heart failure clinic. Method Journal audit of records of 25 immigrant and 25 matched Swedish patients with HF included from the patient registration database at the hospital where they were cared for. Results In the immigrant group, significantly fewer clinical parameters were assessed during their visits and fewer patients were scheduled for follow-up visits. Analyses revealed that some of the items recommended in the European Society of Cardiology guidelines for non-pharmacological HF care were overlooked for both of the groups. Conclusions We found that medication adjustments and information about the condition and treatment were fairly similarly documented between Swedish and immigrant patients while significantly fewer clinical measurements and follow-up visits were documented for the immigrant group.
Electronic reverse auction configuration and its impact on buyer price and supplier perceptions of opportunism: A laboratory experiment
Authors: Carter Craig R. , Stevens Cynthia Kay 
Published: November 2006

AbstractBuying organizations are increasingly using electronic reverse auctions (eRAs) to source from suppliers. However, recent quasi‐experimental and field research has suggested that the use of this sourcing technique can create perceptions of opportunism among participating suppliers. Yet from the buyer's perspective, online reverse auctions can yield lower purchase prices. Given the many ways in which to configure on‐line auctions, we extend existing research by using a laboratory experiment to investigate how different reverse auction configurations jointly influence bid price and suppliers’ perceptions of buyer opportunism.Our findings suggest that supplier bid prices decrease over time as they participate in more eRAs, regardless of the configuration of auction parameters. However, the combination of rank (versus price) visibility, high (versus low) supplier need to win a contract, and six (versus three) competitors was significantly more effective than other combinations of variables in immediately reducing bid prices. The data also indicated that when suppliers’ bids dropped substantially across auctions, their perceptions of opportunism increased. Notably, auction parameter combinations such as price visibility, three competitors, and low need for the contract yielded comparably low bids by the third auction, without any increases in perceived buyer opportunism.
Dung, diet, and the paleoenvironment of the extinct shrub-ox (Euceratherium Collinum) on the Colorado Plateau, USA
Authors: Kropf Manny , Mead Jim I. , Scott Anderson R. 
Published: November 2006

AbstractFossil remains of Euceratherium collinum (extinct shrub-ox) have been found throughout North America, including the Grand Canyon. Recent finds from the Escalante River Basin in southern Utah further extend the animal's range into the heart of the Colorado Plateau. E. collinum teeth and a metapodial condyle (foot bone) have been recovered in association with large distinctively shaped dung pellets, a morphology similar to a ‘Hershey's Kiss’ (HK), from a late Pleistocene dung layer in Bechan Cave. HK dung pellets have also been recovered from other alcoves in the Escalante River Basin including Willow and Fortymile canyons. Detailed analyses of the HK pellets confirmed them to be E. collinum and indicate a browser-type diet dominated (> 95%) by trees and shrubs: Artemisia tridentata (big sagebrush), Acacia sp. (acacia), Quercus (oak), and Chrysothamnus (rabbit brush). The retrieval of spring and fall pollen suggests E. collinum was a year-round resident in the Escalante River Basin.
The dynamics of strong turbulence at free surfaces. Part 2. Free-surface boundary conditions
Authors: BROCCHINI M. , PEREGRINE D. H. 
Published: November 2006

Strong turbulence at a water–air free surface can lead to splashing and a disconnected
surface as in a breaking wave. Averaging to obtain boundary conditions for such flows
first requires equations of motion for the two-phase region. These are derived using an
integral method, then averaged conservation equations for mass and momentum are
obtained along with an equation for the turbulent kinetic energy in which extra work
terms appear. These extra terms include both the mean pressure and the mean rate
of strain and have similarities to those for a compressible fluid. Boundary conditions
appropriate for use with averaged equations in the body of the water are obtained
by integrating across the two-phase surface layer.A number of ‘new’ terms arise for which closure expressions must be found for
practical use. Our knowledge of the properties of strong turbulence at a free surface
is insufficient to make such closures. However, preliminary discussions are given for
two simplified cases in order to stimulate further experimental and theoretical studies.Much of the turbulence in a spilling breaker originates from its foot where turbulent
water meets undisturbed water. A discussion of averaging at the foot of a breaker
gives parameters that may serve to measure the ‘strength’ of a breaker.
Application of a simple likelihood ratio approximant to protein sequence classification
Authors: Kaján László , Kertész-Farkas Attila , Franklin Dino , Ivanova Neli , Kocsor András , Pongor Sándor 
Published: November 2006

Abstract
Motivation: Likelihood ratio approximants (LRA) have been widely used for model comparison in statistics. The present study was undertaken in order to explore their utility as a scoring (ranking) function in the classification of protein sequences.
Results: We used a simple LRA-based on the maximal similarity (or minimal distance) scores of the two top ranking sequence classes. The scoring methods (Smith–Waterman, BLAST, local alignment kernel and compression based distances) were compared on datasets designed to test sequence similarities between proteins distantly related in terms of structure or evolution. It was found that LRA-based scoring can significantly outperform simple scoring methods.
Contact: pongor@icgeb.org.
Supplementary information: .
ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes
Authors: Loots Gabriela , Ovcharenko Ivan 
Published: November 2006

AbstractMotivation: Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish and fugu genomes. It is freely accessible at .Contact: ovcharenko1@llnl.govSupplementary information: Supplementary Data are available at Bioinformatics online.
Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes
Authors: Barker Daniel , Meade Andrew , Pagel Mark 
Published: November 2006

AbstractMotivation: We compare phylogenetic approaches for inferring functional gene links. The approaches detect independent instances of the correlated gain and loss of pairs of genes from species' genomes. We investigate the effect on results of basing evidence of correlations on two phylogenetic approaches, Dollo parsminony and maximum likelihood (ML). We further examine the effect of constraining the ML model by fixing the rate of gene gain at a low value, rather than estimating it from the data.Results: We detect correlated evolution among a test set of pairs of yeast (Saccharomyces cerevisiae) genes, with a case study of 21 eukaryotic genomes and test data derived from known yeast protein complexes. If the rate at which genes are gained is constrained to be low, ML achieves by far the best results at detecting known functional links. The model then has fewer parameters but it is more realistic by preventing genes from being gained more than once.Availability: BayesTraits by M. Pagel and A. Meade, and a script to configure and repeatedly launch it by D. Barker and M. Pagel, are available atContact: m.pagel@rdg.ac.ukSupplementary information: Supplementary Data are available at Bioinformatics online.
An RNA conformational shift in recent H5N1 influenza A viruses
Authors: Gultyaev Alexander P. , Heus Hans A. , Olsthoorn René C. L. 
Published: November 2006

AbstractRecent outbreaks of avian influenza are being caused by unusually virulent H5N1 strains. It is unknown what makes these recent H5N1 strains more aggressive than previously circulating strains. Here, we have compared more than 3000 RNA sequences of segment 8 of type A influenza viruses and found a unique single nucleotide substitution typically associated with recent H5N1 strains. By phylogenetic analysis, biochemical and biophysical experiments, we demonstrate that this substitution dramatically affects the equilibrium between a hairpin and a pseudoknot conformation near the 3′ splice-site of the NS gene. This conformational shift may have consequences for splicing regulation of segment 8 mRNA. Our data suggest that besides changes at the protein level, changes in RNA secondary structure should be seriously considered when attempting to explain influenza virus evolution.Contact: olsthoor@chem.leidenuniv.nlSupplementary information: Supplementary data is available here.
Computing the maximum similarity bi-clusters of gene expression data
Authors: Liu Xiaowen , Wang Lusheng 
Published: November 2006

AbstractMotivations: Bi-clustering is an important approach in microarray data analysis. The underlying bases for using bi-clustering in the analysis of gene expression data are (1) similar genes may exhibit similar behaviors only under a subset of conditions, not all conditions, (2) genes may participate in more than one function, resulting in one regulation pattern in one context and a different pattern in another. Using bi-clustering algorithms, one can obtain sets of genes that are co-regulated under subsets of conditions.Results: We develop a polynomial time algorithm to find an optimal bi-cluster with the maximum similarity score. To our knowledge, this is the first formulation for bi-cluster problems that admits a polynomial time algorithm for optimal solutions. The algorithm works for a special case, where the bi-clusters are approximately squares. We then extend the algorithm to handle various kinds of other cases. Experiments on simulation data and real data show that the new algorithms outperform most of the existing methods in many cases. Our new algorithms have the following advantages: (1) no discretization procedure is required, (2) performs well for overlapping bi-clusters and (3) works well for additive bi-clusters.Availability: The software is available at .Contact: lwang@cs.cityu.edu.hkSupplementary information: The Supplementary Data is available at .
New technology for transfusion safety
Authors: Dzik Walter H. 
Published: November 2006

SummaryHemovigilance programs from around the world document that the greatest risk to recipients of blood transfusion is human error, resulting in transfusion of the incorrect blood component. Errors in transfusion care have strong parallels with errors in medication administration. Errors often result from ‘lapse’ or ‘slip’ mistakes in which details of patient identification are overlooked. Three areas of transfusion are focal points for improved care: the labelling of the patient's pre‐transfusion sample, the decision to transfuse and the final bedside check designed to prevent mis‐transfusion. Both barcodes and radio‐frequency identification technology, each ideally suited to matching alpha‐numeric identifiers, are being implemented in order to improve performance sample labelling and the bedside check. The decision to transfuse should ultimately be enhanced through the use of nanotechnology sensors, computerised order entry and decision support systems. Obstacles to the deployment of new technology include resistance to change, confusion regarding the best technology, and uncertainty regarding the return‐on‐investment. By focusing on overall transfusion safety, deploying validated systems appropriate for both medication and blood administration, thoughtful integration of technology into bedside practice and demonstration of improved performance, the application of new technologies will improve care for patients in need of transfusion therapy.
Quantitative misorientation characteristics of interphase boundaries in composites
Authors: SZTWIERTNIA K. , FARYNA M. , SAWINA G. 
Published: November 2006

SummarySpecific crystallographic correlations between neighbouring grains in composites were established by the use of selected area electron diffraction in the transmission electron microscope. However, it was the development of orientation mapping techniques that made it possible to obtain a quantitative description of the distribution of boundaries between the grains of both the same phase and different phases. This study shows that orientation topography measurements made by electron backscatter diffraction in the scanning electron microscope allowed determination of the crystallographic relationships between grains of different phases. An alumina‐based composite with a content of 10 vol% tungsten carbide was chosen for investigations. Misorientation distribution functions were calculated to describe the distribution density of misorientations with respect to the nearest neighbouring measured point located in the grain of the second phase. The analysis of misorientation distribution functions permitted the evaluation of preferences for some special crystallographic correlations between the grains of composite matrix and inclusions as well as shares of interphase boundaries characterized by those correlations.
Microstructural changes of CM186LC single‐crystal superalloy during creep deformation at 750 °C
Authors: DUBIEL B. , CZYRSKA‐FILEMONOWICZ A. 
Published: November 2006

SummaryThe microstructure of creep‐tested CM186LC Ni‐base single‐crystal alloy was studied to assess its suitability for use in the gas turbine environment. Creep tests were conducted at 750 °C and at stresses of 560 and 675 MPa up to 11 440 h. The microstructure of fractured and terminated specimens was investigated by light microscopy, scanning electron microscopy and analytical transmission electron microscopy. Microstructural analysis revealed the differences in the microstructure of creep‐tested CM186LC depending on the stress applied during creep at 750 °C.
Transmission electron microscopy investigations of AZ91 alloy deformed by equal‐channel angular pressing
Authors: BRASZCZYŃSKA‐MALIK K. N. , LITYŃSKA L. , BALIGA W. 
Published: November 2006

SummaryThe microstructure of transverse and longitudinal sections of a commercial AZ91 alloy processed by equal‐channel angular pressing was examined by transmission electron microscopy. A high dislocation density and large number of deformation twins were observed in the investigated material. The {102}matrix ‖ {012}twin twinning system was determined by selection area diffraction patterns obtained from the twin and matrix. Transmission electron microscopy analyses also revealed that the twins interacted with each other and pile‐ups of dislocations occurred near the twin boundary.
Structural analysis and intergranular corrosion tests of AISI 316L steel
Authors: STONAWSKÁ Z. , SVOBODA M. , SOZAŃSKA M. , KŘÍSTKOVÁ M. , SOJKA J. , DAGBERT C. , HYSPECKÁ L. 
Published: November 2006

SummaryPure AISI 316L steel is investigated after solution heat treatment (1050 °C/H2O) and structural sensitization (650 °C). Two quite different intergranular corrosion tests are used to determine the degree of structural sensitization due to the precipitation of secondary phases along the grain boundaries (mainly the M23C6 and σ‐phase): the oxalic acid etch test and the electrochemical potentio‐kinetic reactivation test. Generally, the dissolution of chromium‐rich carbides (M23C6) is provoked by oxalic acid etch tests, whereas the chromium‐depleted zones, in the vicinity of chromium‐rich carbides (M23C6), are attacked by electrochemical potentio‐kinetic reactivation tests. Both intergranular corrosion tests are used to determine the maximum degree of structural sensitization. Thus structural analysis by carbon replicas reveals the Laves phase, and both the M23C6 and (Cr,Mo)x(Fe,Ni)y phases. The results of intergranular corrosion tests are related to the findings of the structural analysis.
The effect of an Ni–Cr protective layer on cyclic oxidation of Ti3Al
Authors: CVIJOVIĆ I. , JOVANOVIĆ M. T. , VASILJEVIĆ‐RADOVIĆ D. , PERUŠKO D. 
Published: November 2006

SummaryThe effect of an 80Ni−20Cr (at.%) metallic coating on the cyclic oxidation behaviour of a Ti3Al‐based alloy with the composition Ti−25Al−11Nb (at.%) was investigated in this study. Cyclic oxidation tests were carried out in air at 600 °C and 900 °C for 120 h. For one cycle test, the specimens were held for 24 h at test temperature and then furnace‐cooled to room temperature. The oxidation rate was determined by plotting the mass gain per unit surface area of the specimen vs. exposure time. The morphology and composition of the oxidation products were characterized on the cross‐section of the specimens by scanning electron microscopy, energy‐dispersive X‐ray spectroscopy and atomic force microscopy. The oxidation scale forms during exposure at both 600 °C and 900 °C. TiO2 is the main oxide component, whereas the Al2O3 layer appears only discontinuously. The remarkable improvement in oxidation resistance at 900 °C was attributed to the chemical composition and structure of the scale formed on the 80Ni−20Cr coating.
Pretreatment plasma fibrinogen level correlates with tumor progression and metastasis in patients with squamous cell carcinoma of the esophagus
Authors: Takeuchi Hiroya , Ikeuchi Shunji , Kitagawa Yuko , Shimada Atsushi , Oishi Takashi , Isobe Yoh , Kubochi Kiyoshi , Kitajima Masaki , Matsumoto Sumio 
Published: November 2006

AbstractBackground:  Hypercoagulation has been reported to be associated with tumor progression and a poor prognosis in various carcinomas. In this study, we examined fibrinogen levels in pretreated patients with esophageal squamous cell carcinoma (ESCC) and assessed its correlation with clinicopathological factors and prognosis in patients with ESCC.Methods:  Pretreatment fibrinogen levels were examined prior to surgery or other treatments (e.g. endoscopic mucosal resection and chemoradiotherapy [CRT]) in 105 patients with primary ESCC. We investigated the association of fibrinogen levels with clinicopathological background factors and the survival of ESCC patients.Results:  The plasma fibrinogen concentration (PFC) ranged from 209.4 to 781.6 mg/dL. Pretreatment PFC correlated significantly with the depth of invasion (T factor). There also existed a significant correlation between higher fibrinogen levels and lymph node metastasis (N factor) and distant organ metastasis. Patients with a higher fibrinogen level experienced a significantly worse overall survival (P = 0.006). Fibrinogen levels strongly correlated with platelet counts, white blood cell counts and tumor length. Pretreatment PFC were observed to have a significant correlation with CRT responsiveness in ESCC patients in stages II and III (P = 0.005).Conclusion:  This study revealed that higher levels of fibrinogen correlated with tumor progression, metastasis and poor responsiveness to CRT in ESCC patients.