bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mesenchymal Stem Cell Injection Induces Cardiac Nerve Sprouting and Increased Tenascin Expression in a Swine Model of Myocardial Infarction
Authors: Pak Hui‐Nam , Qayyum Mohammed , Kim Dave T. , Hamabe Akira , Miyauchi Yasushi , Lill Michael C. , Frantzen Malkar , Takizawa Kaname , Chen Lan S. , Fishbein Michael C. , Sharifi Behrooz G. , Chen Peng‐Sheng , Makkar Raj 
Published: July 2003

Introduction: Mesenchymal stem cell (MSC) transplantation is a promising technique to improve cardiac function. Whether MSC can increase cardiac nerve density and contribute to the improved cardiac function is unclear. Methods and Results: Anterior wall myocardial infarction was created in 16 swine. One month later, 6 swine were given MSC and fresh bone marrow (BM) into infarcted myocardium (MSC group). Four swine were given fresh BM only (BM group), and 6 swine were given culture media (MI‐only group). The swine were sacrificed 95.8 ± 3.5 days after MI. Six normal swine were used as control. Immunocytochemical staining was performed using antibodies against growth‐associated protein 43 (GAP43), tyrosine hydroxylase (TH), and three subtypes of tenascin (R, C, and X). Five fields per slide were counted for nerve density. The results show the following. (1) There were more GAP43‐positive nerves in the MSC group than in the BM, MI‐only, or Control group (P < 0.0001). TH staining showed higher nerve densities in the MSC group than in the MI‐only (P < 0.01) or Control group (P < 0.0001) in the atria. (2) There were more sympathetic (TH‐positive) nerves in myocardium distant from infarct than in the peri‐infarct area (P < 0.05). (3) Optical intensity and color analyses showed significantly higher tenascin R and tenascin C expression in the MSC and BM groups than in the MI‐only or Control group (P < 0.01). Conclusion: MSC injected with BM into swine infarct results in overexpression of cardiac tenascin, increased the magnitude of cardiac nerve sprouting in both atria and ventricles, and increased the magnitude of atrial sympathetic hyperinnervation 2 months after injection. (J Cardiovasc Electrophysiol, Vol. 14, pp. 841‐848, August 2003)
The Atrial Pacing Peri-ablation for Paroxysmal Atrial Fibrillation (PA3) Study
Authors: Gillis A. M. 
Published: July 2003

Abstract
The Canadian Atrial Pacing Peri-Ablation for Paroxysmal Atrial Fibrillation Study tested the hypotheses that atrial pacing prevents paroxysmal atrial fibrillation (PAF) in patients without symptomatic bradycardia and that DDDR pacing is more likely to prevent PAF following total atrioventricular (AV) node ablation compared to VDD pacing. Patients with PAF who were refractory to or intolerant of antiarrhythmic drug therapy received a Medtronic Thera DR pacemaker 3 months prior to a planned total AV node ablation. Patients were randomized to atrial pacing or no pacing therapy. The time to first recurrence of sustained PAF was the primary study outcome event. Following AV node ablation, patients were randomized to the DDDR or VDD mode in a crossover study design. Patients were followed in each mode for 6 months. The time course of PAF recurrence was compared for each pacing mode.
New normalization methods for cDNA microarray data
Authors: Wilson D.L. , Buckley M.J. , Helliwell C.A. , Wilson I.W. 
Published: July 2003

Abstract
Motivation: The focus of this paper is on two new normalization methods for cDNA microarrays. After the image analysis has been performed on a microarray and before differentially expressed genes can be detected, some form of normalization must be applied to the microarrays. Normalization removes biases towards one or other of the fluorescent dyes used to label each mRNA sample allowing for proper evaluation of differential gene expression.
Results: The two normalization methods that we present here build on previously described non-linear normalization techniques. We extend these techniques by firstly introducing a normalization method that deals with smooth spatial trends in intensity across microarrays, an important issue that must be dealt with. Secondly we deal with normalization of a new type of cDNA microarray experiment that is coming into prevalence, the small scale specialty or ‘boutique’ array, where large proportions of the genes on the microarrays are expected to be highly differentially expressed.
Availability: The normalization methods described in this paper are available via http://www.pi.csiro.au/gena/ in a software suite called tRMA: tools for R Microarray Analysis upon request of the authors. Images and data used in this paper are also available via the same link.
Contact: dwilson@gmp.usyd.edu.au
* To whom correspondence should be addressed.
Increased coverage obtained by combination of methods for
protein sequence database searching
Authors: Webber Caleb , Barton Geoffrey J. 
Published: July 2003

Abstract
Motivation: Sequence alignment methods that compare two sequences (pairwise methods) are important tools for the detection of biological sequence relationships. In genome annotation, multiple methods are often run and agreement between methods taken as confirmation. In this paper, we assess the advantages of combining search methods by comparing seven pairwise alignment methods, including three local dynamic programming algorithms (PRSS, SSEARCH and SCANPS), two global dynamic programming algorithms (GSRCH and AMPS) and two heuristic approximations (BLAST and FASTA), individually and by pairwise intersection and union of their result lists at equal p-value cut-offs.
Results: When applied singly, the dynamic programming methods SCANPS and SSEARCH gave significantly better coverage (p=0.01) compared to AMPS, GSRCH, PRSS, BLAST and FASTA.
Results ranked by BLAST p-values gave significantly better coverage compared to ranking by BLAST e-values.
Of 56 combinations of eight methods considered, 19 gave significant increases in coverage at low error compared to the parent methods at an equal p-value cutoff.
The union of results by BLAST (p-value) and FASTA at an equal p-value cutoff gave significantly better coverage than either method individually.
The best overall performance was obtained from the intersection of the results from SSEARCH and the GSRCH62 global alignment method. At an error level of five false positives, this combination found 444 true positives, a significant 12.4% increase over SSEARCH applied alone.
Contact: geoff@compbio.dundee.ac.uk
* To whom correspondence should be addressed.
MeKE: discovering the functions of gene products
from biomedical literature via sentence alignment
Authors: Chiang Jung-Hsien , Yu Hsu-Chun 
Published: July 2003

Abstract
Motivation: Research on roles of gene products in cells is accumulating and changing rapidly, but most of the results are still reported in text form and are not directly accessible by computers. To expedite the progress of functional bioinformatics, it is, therefore, important to efficiently process large amounts of biomedical literature and transform the knowledge extracted into a structured format usable by biologists and medical researchers. Our aim was to develop an intelligent text-mining system that will extract from biomedical documents knowledge about the functions of gene products and thus facilitate computing with function.
Results: We have developed an ontology-based text-mining system to efficiently extract from biomedical literature knowledge about the functions of gene products. We also propose methods of sentence alignment and sentence classification to discover the functions of gene products discussed in digital texts.
Availability: http://ismp.csie.ncku.edu.tw/~yuhc/meke/
Contact: jchiang@mail.ncku.edu.tw
* To whom correspondence should be addressed.
The binding interface
database (BID): a compilation
of amino acid hot spots in protein interfaces
Authors: Fischer T. B. , Arunachalam K. V. , Bailey D. , Mangual V. , Bakhru S. , Russo R. , Huang D. , Paczkowski M. , Lalchandani V. , Ramachandra C. , Ellison B. , Galer S. , Shapley J. , Fuentes E. , Tsai J. 
Published: July 2003

Abstract
Summary: To make information about protein interactive function easily accessible, we are mining the primary scientific literature for detailed data about protein interfaces. The Binding Interface Database (BID) organizes the vast amount of protein interaction information into tables, graphical contact maps and descriptive functional profiles. Currently data on 170 interacting protein pairs are available with over 1300 mutations described.
Availability: The BID database is freely available at http://tsailab.org/BID/ To have your protein of interest entered, contact Tiffany Fischer (tiffbrink@neo.tamu.edu) or Jerry Tsai at the email below
Contact: JerryTsai@TAMU.edu
* To whom correspondence should be addressed.
Alignment of BLAST high-scoring segment pairs
based on the longest increasing subsequence algorithm
Authors: Zhang Hongyu 
Published: July 2003

Abstract
Motivation:The popular BLAST algorithm is based on a local similarity search strategy, so its high-scoring segment pairs (HSPs) do not have global alignment information. When scientists use BLAST to search for a target protein or DNA sequence in a huge database like the human genome map, the existence of repeated fragments, homologues or pseudogenes in the genome often makes the BLAST result filled with redundant HSPs. Therefore, we need a computational strategy to alleviate this problem.
Results: In the gene discovery group of Celera Genomics, I developed a two-step method, i.e. a BLAST step plus an LIS step, to align thousands of cDNA and protein sequences into the human genome map. The LIS step is based on a mature computational algorithm, Longest Increasing Subsequence (LIS) algorithm. The idea is to use the LIS algorithm to find the longest series of consecutive HSPs in the BLAST output. Such a BLAST+LIS strategy can be used as an independent alignment tool or as a complementary tool for other alignment programs like Sim4 and GenWise. It can also work as a general purpose BLAST result processor in all sorts of BLAST searches. Two examples from Celera were shown in this paper.
Contact: me@hongyu.org
* Present address: Ceres Inc., 3007 Malibu Canyon Road, Malibu, CA 90265, USA.
GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the
identification of T-DNA insertion mutants in Arabidopsis
thaliana
Authors: Li Yong , Rosso Mario G. , Strizhov Nicolai , Viehoever Prisca , Weisshaar Bernd 
Published: July 2003

Abstract
Summary: GABI-Kat SimpleSearch is a database of flanking sequence tags (FSTs) of T-DNA mutagenized Arabidopsis thaliana lines that were generated by the GABI-Kat project. Sequences flanking the T-DNA insertion sites were aligned to the A.thaliana genome sequence, annotated with information about the FST, the insertion site and the line from which the FST was derived. A web interface permits text-based as well as sequence-based searches for relevant insertions. GABI-Kat SimpleSearch aims to help biologists to quickly find T-DNA insertion mutants for their research.
Availability: http://www.mpiz-koeln.mpg.de/GABI-Kat/
Contact: weisshaa@mpiz-koeln.mpg.de
* To whom correspondence should be addressed.
† Present address: Max Planck Unit for Structural Molecular Biology, Notkestrasse 85, D-22607 Hamburg, Germany.
‡ Present address: Bielefeld University, Faculty of Biology, PO Box, D-33501 Bielefeld, Germany.
The connectivity structure, giant strong component
and centrality of metabolic networks
Authors: Ma Hong-Wu , Zeng An-Ping 
Published: July 2003

Abstract
Motivation:Structural and functional analysis of genome-based large-scale metabolic networks is important for understanding the design principles and regulation of the metabolism at a system level. The metabolic network is conventionally considered to be highly integrated and very complex. A rational reduction of the metabolic network to its core structure and a deeper understanding of its functional modules are important.
Results: In this work, we show that the metabolites in a metabolic network are far from fully connected. A connectivity structure consisting of four major subsets of metabolites and reactions, i.e. a fully connected sub-network, a substrate subset, a product subset and an isolated subset is found to exist in metabolic networks of 65 fully sequenced organisms. The largest fully connected part of a metabolic network, called ‘the giant strong component (GSC)’, represents the most complicated part and the core of the network and has the feature of scale-free networks. The average path length of the whole network is primarily determined by that of the GSC. For most of the organisms, GSC normally contains less than one-third of the nodes of the network. This connectivity structure is very similar to the‘ bow-tie’ structure of World Wide Web. Our results indicate that the bow-tie structure may be common for large-scale directed networks. More importantly, the uncovered structure feature makes a structural and functional analysis of large-scale metabolic network more amenable. As shown in this work, comparing the closeness centrality of the nodes in the GSC can identify the most central metabolites of a metabolic network. To quantitatively characterize the overall connection structure of the GSC we introduced the term ‘overall closeness centralization index (OCCI)’. OCCI correlates well with the average path length of the GSC and is a useful parameter for a system-level comparison of metabolic networks of different organisms.
Contact: aze@gbf.de
Supplementary Information: http://genome.gbf.de/bioinformatics/
* To whom correspondence should be addressed.
Computational analysis of stop codon readthrough in D.melanogaster
Authors: Sato Misaki , Umeki Hitomi , Saito Rintaro , Kanai Akio , Tomita Masaru 
Published: July 2003

Abstract
Motivation: Readthrough is an unusual process in which a stop codon is misread or skipped. Recently it has been shown that some translation is regulated by the readthrough reactions although the complete mechanism is not clear. Therefore, the discovery of ‘readthrough genes’ is important for further investigation of their cellular roles, which may provide additional insights into the mechanism of translational regulation.
Results: We constructed a system that lists candidates of readthrough genes based on the existence of a ‘protein motif’ at the 3′ untranslated region (UTR). Using this system, we extracted 85 candidates from 4082 nucleic acid sequences of Drosophila melanogaster in GenBank database. The sequences of these candidates had a slightly more stable secondary structure and different base preferences compared to the non-candidates. As these features are known to have an effect on readthrough events, we would like to suggest that these candidates contain actual readthrough genes.
Availability: Source code of the system is available upon request.
Contact: rsaito@sfc.keio.ac.jp
* To whom correspondence should be addressed.
Scaffolding speech and writing in the primary classroom: a consideration of work with literature and science pupil groups in the USA and UK
Authors: Warwick Paul , Maloch Beth 
Published: July 2003

AbstractIn considering scaffolding as it is enacted across two disciplines – literacy and science – the focus of this paper is specifically on issues related to teacher scaffolding of pupils' learning in these areas. Features of scaffolding in action are drawn out that reflect a concern with developing a principled approach to instruction and learning. The three notions around which the paper pivots are: scaffolding theprocessesof learning in classroom; the importance of this type of scaffolding for independent learning; and the idea of appropriateness as it relates to the level of scaffolding employed by the teacher. The strategies used by teachers to encourage groups of pupils to adopt and use ways of thinking appropriate to the subject context are explored, and this is linked toMercer's (2000)conception of the Intermental Developmental Zone, which explored how the concepts of scaffolding and the Zone of Proximal Development (Vygotsky, 1978) might be extended to group contexts, rather than dyadic ones. Some consideration is given to how individual pupils may conceive of the teacher's structuring of thinking as scaffold or straitjacket.
Gender and the Family in Pre‐industrial Europe
Authors: Rigby S. H. 
Published: July 2003

P. Fleming, Family and Household in Medieval EnglandA. Lynn Martin, Alcohol, Sex and Gender in Late Medieval and Early Modern EuropeN. J. Menuge (ed.), Medieval Women and the LawP. Skinner, Women in Medieval Italian Society, 500–1200F. A. Underhill, For Her Good Estates: The Life of Elizabeth de Burgh
Discrepancies between Mothers' and Fathers' Perceptions of Sons' and Daughters' Problem Behaviour: A Longitudinal Analysis of Parent‐Adolescent Agreement on Internalising and Externalising Problem Behaviour
Authors: Seiffge‐Krenke Inge , Kollmar Frank 
Published: July 2003

One hundred and ninety‐eight adolescents and their mothers (N= 189) and fathers (N= 136) participated in a 4‐year longitudinal study. Adolescent problem behaviour was assessed by the Youth Self‐Report (YSR) and the Child Behavior Checklist (CBCL). In addition, parental stress and marital adjustment were determined.Results showed that mothers and fathers showed high agreement, especially about their daughters, whereas parents and adolescents showed little agreement. Agreement was higher for internalising than for externalising behaviours. In general, adolescents reported more symptomatology than their parents did. However, mothers' ratings of their children's behaviours were significantly correlated with adolescents' self‐ratings, but fathers' ratings were not. Statistical tests of correlations showed that mothers experiencing stress caused by marital problems perceived more problem behaviours in their children. Fathers' perceptions were relatively unaffected by personal adjustment. However, poor marital adjustment perceived by both parents showed a significant negative relation to adolescent externalising problem behaviour.
Being Canadian
Authors: Kymlicka Will 
Published: July 2003

AbstractThis article is one of a series commissioned byGovernment and Oppositionexploring identity politics in several national and international contexts. Most discussions of ‘the Canadian identity’ focus on how ‘being Canadian’ relates to various sub-state group identities, such as Québécois, Aboriginal or immigrant identities. There is often said to be a distinctly Canadian model of reconciling national identity with sub-group identities. I argue that the Canadian model of accommodating identities is not unique, but rather reflects broader trends throughout the West. I also suggest that an equally important but neglected part of ‘being Canadian’ is the external dimension i.e., how Canadians relate to the wides world.
Gray-Scale Nonlinear Shape Normalization Method for Handwritten Oriental Character Recognition
Authors: Kim Sang-Yup , Lee Seong-Whan 
Published: July 2003

In general, nonlinear shape normalization methods for binary images have been used in order to compensate for the shape distortions of handwritten characters. However, in most document image analysis and recognition systems, a gray-scale image is first captured and digitized using a scanner or a video camera, then a binary image is extracted from the original gray-scale image using a certain extraction technique. This binarization process may remove some useful information of character images such as topological features, and introduce noises to character background. These errors are accumulated in nonlinear shape normalization step and transferred to the following feature extraction or recognition step. They may eventually cause incorrect recognition results. In this paper, we propose nonlinear shape normalization methods for gray-scale handwritten Oriental characters in order to minimize the loss of information caused by binarization and compensate for the shape distortions of characters. Two-dimensional linear interpolation technique has been extended to nonlinear space and the extended interpolation technique has been adopted in the proposed methods to enhance the quality of normalized images. In order to verify the efficiency of the proposed methods, the recognition rate, the processing time and the computational complexity of the proposed algorithms have been considered. The experimental results demonstrate that the proposed methods are efficient not only to compensate for the shape distortions of handwritten Oriental characters but also to maintain the information in gray-scale Oriental characters.
Texture Classification with Single- and Multiresolution Co-Occurrence Maps
Authors: Valkealahti Kimmo , Oja Erkki 
Published: July 2003

We have developed methods for the classification of textures with multidimensional co-occurrence histograms. Gray levels of several pixels with a given spatial arrangement are first compressed linearly and the resulting multidimensional vectors are quantized using the self-organizing map. Histograms of quantized vectors are classified by matching them with precomputed texture model histograms.In the present study, a multiple resolution technique in linear compression of pixel values is evaluated. The multiple resolution linear compression was made with a local wavelet transform. The vectors were quantized with the tree-structured variant of the self-organizing map. In the tree-structured self-organizing map, the quantization error is reduced, in comparison to the traditional tree-structured codebook, by limited lateral searches in topologically-ordered neighborhoods. The performance of multiresolution texture histograms was compared with single-resolution histograms. The histogram method was compared with three well-established methods: co-occurrence matrices, Gaussian Markov random fields, and multiresolution Gabor energies. The results for a set of natural textures showed that the performance of single- and multiresolution texture histograms was similar. Thus, the benefit of multiresolution analysis was overridden by the multidimensionality of our texture models. Our method gave significantly higher classification accuracies than the three other methods.
Edge Detection
Authors: Vitulano S. , Ruberto C. Di , Nappi M. 
Published: July 2003

The paper describes a technique called ISE for image segmentation using entropy. The relation between the entropy of an image domain and the entropy of its subdomains is explored as a uniformity predicate. Such entropy is obtained from the analysis of the image histogram associating a Gaussian distribution to the maximum frequency of gray levels. In order to implement the model, we have introduced a well-known technique of Problem Solving. In our model, the most important roles are played by the Evaluation Function (EF) and the Control Strategy. The EF is related to the ratio between the entropy of one region or zone of the picture and the entropy of the entire picture, while the Control Strategy determines the optimal path in the search tree (quadtree) so that the nodes in the optimal path have minimal entropy. The paper shows some comparisons between ISE and classical edge detection techniques.