bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extraction of fluorescent cell puncta by adaptive fuzzy segmentation
Authors: Pham Tuan D. , Crane Denis I. , Tran Tuan H. , Nguyen Tam H. 
Published: April 2004

Abstract
Motivation: The discrimination and measurement of fluorescent-labeled vesicles using microscopic analysis of fixed cells presents a challenge for biologists interested in quantifying the abundance, size and distribution of such vesicles in normal and abnormal cellular situations. In the specific application reported here, we were interested in quantifying changes to the population of a major organelle, the peroxisome, in cells from normal control patients and from patients with a defect in peroxisome biogenesis. In the latter, peroxisomes are present as larger vesicular structures with a more restricted cytoplasmic distribution. Existing image processing methods for extracting fluorescent cell puncta do not provide useful results and therefore, there is a need to develop some new approaches for dealing with such a task effectively.
Results: We present an effective implementation of the fuzzy c-means algorithm for extracting puncta (spots), representing fluorescent-labeled peroxisomes, which are subject to low contrast. We make use of the quadtree partition to enhance the fuzzy c-means based segmentation and to disregard regions which contain no target objects (peroxisomes) in order to minimize considerable time taken by the iterative process of the fuzzy c-means algorithm. We finally isolate touching peroxisomes by an aspect-ratio criterion. The proposed approach has been applied to extract peroxisomes contained in several sets of color images and the results are superior to those obtained from a number of standard techniques for spot extraction.
Availability: Image data and computer codes written in Matlab are available upon request from the first author.
Bio-Mirror project for public bio-data distribution
Authors: Gilbert Don , Ugawa Yoshihiro , Buchhorn Markus , Wee Tan Tin , Mizushima Akira , Kim Hyunchul , Chon Kilnam , Weon Seyeon , Ma Juncai , Ichiyanagi Yoshihiro , Liou Der-Ming , Keretho Somnuk , Napis Suhaimi 
Published: April 2004

Abstract
Summary: Timely worldwide distribution of biosequence and bioinformatics data depends on high performance networking and advances in Internet transport methods. The Bio-Mirror project focuses on providing up-to-date distribution of this rapidly growing and changing data. It offers FTP, Web and Rsync access to many high-volume databanks from several sites around the world. Experiments with data grids and other methods offer future improvements in biology data distribution.
Availability: http://www.bio-mirror.net/
Design and implementation of a mosquito database through an entomological ontology
Authors: Koum Guillaume , Yekel Augustin , Ndifon Bengyella , Simard Frédéric 
Published: April 2004

Abstract
Summary: There have been constant changes in the biology and behavior of the vector and parasite involved in the transmission of malaria. There is limited interest in developing new technologies and procedures for controlling the underlying factors of this threat, which poses an enormous challenge to health systems. To understand the various vector species and their interrelations is of prime importance in understanding the transmission mechanisms of malaria in order to react efficiently. To attain this objective, we have used an ontological approach to producing a database that we consider to be our own contribution in helping to control malaria vectors if eradication has been unsuccessful in the previous control campaign.
A database for management of gene expression data in situ
Authors: Poustelnikova Ekaterina , Pisarev Andrei , Blagov Maxim , Samsonova Maria , Reinitz John 
Published: April 2004

Abstract
Motivation: To create a spatiotemporal atlas of Drosophila segmentation gene expression at cellular resolution.
Results: The expression of segmentation genes plays a crucial role in the establishment of the Drosophila body plan. Using the IBM DB2 Relational Database Management System we have designed and implemented the FlyEx database. FlyEx contains 2832 images of 14 segmentation gene expression patterns obtained from 954 embryos and 2 073 662 quantitative data records. The averaged data is available for most of segmentation genes at eight time points. FlyEx supports operations on images of gene expression patterns. The database can be used to examine the quality of data, analyze the dynamics of formation of segmentation gene expression domains, as well as estimate the variability of gene expression patterns. We also provide the capability to download data of interest.
Availability: http://urchin.spbcas.ru/flyex, http://flyex.ams.sunysb.edu/flyex
SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome
Authors: Dolinsky T. J. , Burgers P. M. J. , Karplus K. , Baker N. A. 
Published: April 2004

Abstract
Summary: SPrCY is a web-accessible database which provides comparison of structure prediction results for the Saccharomyces cerevisiae genome. This web service offers the ability to search, analyze and compare the yeast structural predictions from sequence-only (Superfamily, PDBAA BLAST and Pfam) and sequence-structure-based (SAM-T02, 3D-PSSM, mGenTHREADER) methods.
Availability: The service is freely available via web at http://agave.wustl.edu/yeast/
PedSplit: pedigree management for stratified analysis
Authors: Lanktree M. B. , VanderBeek L. , Macciardi F. M. , Kennedy J. L. 
Published: April 2004

Abstract
Summary: PedSplit facilitates pedigree management for gene–gene interaction and sex specific tests for increased homogeneity within subgroups. PedSplit also provides a simple approach for calculating haplotype relative risk and generating internal ‘controls’.
Availability: Executables, C++ source code and documentation for PedSplit can be downloaded from http://www.pharmacogenetics.ca in the links and software section.
BioMercator: integrating genetic maps and QTL towards discovery of candidate genes
Authors: Arcade Anne , Labourdette Aymeric , Falque Matthieu , Mangin Brigitte , Chardon Fabien , Charcosset Alain , Joets Johann 
Published: April 2004

Abstract
Summary: Breeding programs face the challenge of integrating information from genomics and from quantitative trait loci (QTL) analysis in order to identify genomic sequences controlling the variation of important traits. Despite the development of integrative databases, building a consensus map of genes, QTL and other loci gathered from multiple maps remains a manual and tedious task. Nevertheless, this is a critical step to reveal co-locations between genes and QTL. Another important matter is to determine whether QTL linked to same traits or related ones is detected in independent experiments and located in the same region, and represents a single locus or not. Statistical tools such as meta-analysis can be used to answer this question. BioMercator has been developed to automate map compilation and QTL meta-analysis, and to visualize co-locations between genes and QTL through a graphical interface.
Availability: Available upon request (http://moulon/~bioinfo/BioMercator/). Free of charge for academic use.
Arby: automatic protein structure prediction using profile–profile alignment and confidence measures
Authors: von Öhsen Niklas , Sommer Ingolf , Zimmer Ralf , Lengauer Thomas 
Published: April 2004

Abstract
Motivation: Arby is a new server for protein structure prediction that combines several homology-based methods for predicting the three-dimensional structure of a protein, given its sequence. The methods used include a threading approach, which makes use of structural information, and a profile–profile alignment approach that incorporates secondary structure predictions. The combination of the different methods with the help of empirically derived confidence measures affords reliable template selection.
Results: According to the recent CAFASP3 experiment, the server is one of the most sensitive methods for predicting the structure of single domain proteins. The quality of template selection is assessed using a fold-recognition experiment.
Availability: The Arby server is available through the portal of the Helmholtz Network for Bioinformatics at http://www.hnbioinfo.de under the protein structure category.
TRMP: a database of therapeutically relevant multiple pathways
Authors: Zheng C. J. , Zhou H. , Xie B. , Han L. Y. , Yap C. W. , Chen Y. Z. 
Published: April 2004

Abstract
Summary: Disease processes often involve crosstalks between proteins in different pathways. Different proteins have been used as separate therapeutic targets for the same disease. Synergetic targeting of multiple targets has been explored in combination therapy of a number of diseases. Potential harmful interactions of multiple targeting have also been closely studied. To facilitate mechanistic study of drug actions and a more comprehensive understanding the relationship between different targets of the same disease, it is useful to develop a database of known therapeutically relevant multiple pathways (TRMPs). Information about non-target proteins and natural small molecules involved in these pathways also provides useful hint for searching new therapeutic targets and facilitate the understanding of how therapeutic targets interact with other molecules in performing specific tasks. The TRMPs database is designed to provide information about such multiple pathways along with related therapeutic targets, corresponding drugs/ligands, targeted disease conditions, constituent individual pathways, structural and functional information about each protein in the pathways. Cross links to other databases are also introduced to facilitate the access of information about individual pathways and proteins.
Availability: This database can be accessed at http://bidd.nus.edu.sg/group/trmp/trmp.asp and it currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions together with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name.
Supplementary information: http://bidd.nus.edu.sg/group/trmp/sm.pdf
Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys
Authors: Susko Edward , Roger Andrew J. 
Published: April 2004

Abstract
Motivation: Expressed sequence tag (EST) surveys are an efficient way to characterize large numbers of genes from an organism. The rate of gene discovery in an EST survey depends on the degree of redundancy of the cDNA libraries from which sequences are obtained. However, few statistical methods have been developed to assess and compare redundancies of various libraries from preliminary EST surveys.
Results: We consider statistics for the comparison of EST libraries based upon the frequencies with which genes occur in subsamples of reads. These measures are useful in determining which one of several libraries is more likely to yield new genes in future reads and what proportion of additional reads one might want to take from the libraries in order to be likely to obtain new genes. One approach is to compare single sample measures that have been successfully used in species estimation problems, such as coverage of a library, defined as the proportion of the library that is represented in the given sample of reads. Another single library measure is an estimate of the expected number of additional genes that will be found in a new sample of reads. We also propose statistics that jointly use data from all the libraries. Analogous formulas for coverage and the expected numbers of new genes are presented. These measures consider coverage in a single library based upon reads from all libraries and similarly, the expected numbers of new genes that will be discovered by taking reads from all libraries with fixed proportions. Together, the statistics presented provide useful comparative measures for the libraries that can be used to guide sampling from each of the libraries to maximize the rate of gene discovery.
Finally, we present tests for whether genes are equally represented or expressed in a set of libraries. Binomial and χ2 tests are presented for gene-by-gene comparisons of expression. Overall tests of the equality of proportional representation are presented and multiple comparisons issues are addressed. These methods can be used to evaluate changes in gene expression reflected in the composition of EST libraries prepared from different tissue types or cells exposed to different environmental conditions.
Availability: Software will be made available at http://www.mathstat.dal.ca/~tsusko
p53 gene status and expression of p53, MDM2, and p14ARF proteins in ameloblastomas
Authors: Kumamoto Hiroyuki , Izutsu Takashi , Ohki Kousuke , Takahashi Nobuhiro , Ooya Kiyoshi 
Published: April 2004

Background:  To clarify the roles of the p53–MDM2–p14ARF cell cycle regulation system in oncogenesis and cytodifferentiation of odontogenic tumors, p53 gene status and expression of p53, MDM2, and p14ARF proteins was analyzed in ameloblastomas as well as tooth germs.Methods:  Paraffin sections of 16 tooth germs and 46 benign and 5 malignant ameloblastomas were examined immunohistochemically for the expression of p53, MDM2, and p14ARF proteins. Frozen tissue samples of 10 benign ameloblastomas and 1 malignant (metastasizing) ameloblastoma were analyzed by direct DNA sequencing to detect p53 gene alteration.Results:  Immunohistochemical reactivity for p53 was detected in 2 of 13 tooth germs, 13 of 29 ameloblastomas, and 5 of 5 malignant ameloblastomas, and the expression ratio of p53 in tooth germs was significantly lower than those in benign and malignant ameloblastomas. Direct DNA sequencing showed no alteration of p53 gene exons 5–8 in any sample of 10 benign ameloblastomas and 1 metastasizing ameloblastoma. Expression of MDM2 and p14ARF was detected in all samples of normal and neoplastic odontogenic epithelium, and the expression ratios in tooth germs tended to be lower than those in benign and malignant ameloblastomas. In ameloblastomas, expression of p53, MDM2, and p14ARF was significantly higher in plexiform cases than in follicular cases. Markedly decreased reactivity for p53, MDM2, and p14ARF was detected in keratinizing and granular cells in ameloblastoma subtypes. Basal cell ameloblastoma showed slightly higher reactivity for p53, MDM2, and p14ARF as compared with other subtypes.Conclusion:  Elevated expression of p53, MDM2, and p14ARF in benign and malignant ameloblastomas suggests that alteration of the p53–MDM2–p14ARF cascade is involved in oncogenesis and/of malignant transformation of odontogenic epithelium. p53 gene status implied that p53 mutation might play a minor role in neoplastic changes of odontogenic epithelium. Immunoreactivity for p53, MDM2, and p14ARF in ameloblastoma variants suggests that these factors might be associated with tissue structuring and cytodifferentiation of ameloblastomas.
Identity of TUNEL‐positive cells in the oral buccal epithelium of normal mucosa and lichen lesions
Authors: Karatsaidis Andreas , Schreurs Olav , Axéll Tony , Helgeland Kristen , Schenck Karl 
Published: April 2004

Background:  In situ detection of DNA fragmentation by TdT (terminal deoxynucleotidyl transferase)‐mediated dUTP nick end labeling (TUNEL) is a widely used technique to identify apoptotic cells in the terminal phases of cell death. Several studies have shown that there are statistically increased numbers of TUNEL+ cells within the epithelium of oral lichen (OL). It was suggested that this indicates an increased rate of apoptosis among basal and suprabasal keratinocytes in OL epithelium. The aim of this study was to identify the TUNEL+ cells in the epithelium of erythematous (ERY) OL and normal oral mucosa (NOM).Methods:  Sections of biopsies from NOM and ERY OL were processed for TUNEL combined with immunostaining for pan‐cytokeratin or for cell markers specifically expressed by different leukocytes.Results:  In NOM, TUNEL+ keratinocytes were almost exclusively seen in the outermost epithelial layers. This labeling was absent in ERY OL. In the basal and lower spinous layers, more TUNEL+ cell nuclei were seen in ERY OL as compared with NOM, in accordance with previous studies. The present observations show, however, that only very few of these cells were keratinocytes, but rather were CD4+ lymphocytes and CD68+ macrophages. There was no difference between the numbers of TUNEL+ keratinocytes in basal and lower spinous layers in ERY OL and NOM epithelium. No intraepithelial CD8+ lymphocytes, Langerhans cells, or mast cells were found to be TUNEL+.Conclusion:  The findings indicate that the pathologic changes in ERY OL epithelium cannot be explained by increased prevalence of terminal keratinocyte cell death identified by TUNEL.
The histopathology of syphilis of the oral mucosa
Authors: Barrett A. W. , Villarroel Dorrego M. , Hodgson T. A. , Porter S. R. , Hopper C. , Argiriadou A. S. , Speight P. M. 
Published: April 2004

Background:  Reported cases of syphilis in the United States, Europe and elsewhere are increasing in number. Clinical manifestations are protean, and oral biopsies may be taken where the diagnosis is unsuspected, but data on the histopathology of oral mucosal syphilis are sparse.Methods:  The histopathology of five oral lesions in patients with serologically proven syphilis was reviewed.Results:  There were two cases of primary syphilis, one secondary and two tertiary. Epithelial hyperplasia was present in three cases, and was pseudocarcinomatous in one case of primary syphilis, and psoriasiform in the secondary lesion, where heaped‐up epithelium surrounded a defined crater covered by flatter epithelium. Plasma cell (primary and secondary disease) and granulomatous (tertiary) infiltrates were prominent. Other features observed were endarteritis (5/5), plasma cell neuritis (3/5) and spirochetes (4/5).Conclusions:  Although no single microscopic feature is specific, a diagnosis of syphilis should be considered where there is unusual epithelial hyperplasia, granulomatous or plasma cell‐predominant chronic inflammation, endarteritis and neuritis.
Oral submucous fibrosis: a case‐control study in Chennai, South India
Authors: Ranganathan K. , Devi M. Uma , Joshua Elizabeth , Kirankumar K. , Saraswathi T. R. 
Published: April 2004

Background: Oral submucous fibrosis (OSF) is a pre‐cancerous condition caused by the use of areca nut in various forms. There are very few published reports on areca nut use and OSF from Chennai, South India.Methods: A hospital‐based case‐control study on habits and OSF was performed in Chennai over a 3‐year period. A total of 185 consecutive patients with OSF were matched with age‐ and sex‐matched controls. History was recorded in a pre‐determined format by qualified dental surgeons.Results: The male to female ratio of OSF cases was 9.9 : 1. All areca nut products were associated with OSF, with the risk being greatest for pan masala. The duration of the habit was more significant than the frequency of the chewing habit.Conclusion: The present study confirms the strong association between areca nut use and OSF and the increasing use of pan masala.
Depressive symptoms in Asian TMD patients and their association with non‐specific physical symptoms reporting
Authors: Yap Adrian U. J. , Chua E. K. , Tan Keson B. C. 
Published: April 2004

Background:  The expression of depression in Asian temporomandibular disorder (TMD) patients may differ from that of their Caucasian counterparts. This study examined the prevalence of depressive symptoms and their association with non‐specific physical symptoms (NPSs) reporting in Asian patients.Methods:  Two hundred and fifty‐five Asian TMD patients (68 males; 187 females) with a mean age of 33.0 years were selected for this study. Research diagnostic criteria (RDC)/TMD history questionnaire was input directly into computers by patients using the NUS TMDv.1.1 software. Symptom Checklist 90 (SCL‐90) depression and NPS scales were generated online and automatically archived for statistical analysis. Data were subjected to ANOVA/Scheffe's test and Pearson's correlation at significance level 0.05 and 0.01, respectively.Results:  43.1 and 50.6% of the patients scored moderate‐to‐severe on the depression and NPS scales, respectively. The percentage of patients with diffuse physical symptoms remained high (45.5%), even after pain items were excluded from the computation. NPS scores ranged from 0.34 to 1.64, while depression scores ranged from 0.27 to 1.21. A significant and positive correlation (r = 0.74) was observed between depression and NPS scores.Conclusions:  The prevalence of depressive symptoms and NPSs was lower in Asian TMD patients. Psychological distress experienced by female Asian TMD patients was comparable to their male counterparts. Results also suggest that depressive symptomatology is associated with the reporting of multiple NPSs.
Prevalence of oral mucosal lesions in alcohol misusers in south London
Authors: Harris C. K. , Warnakulasuriya K. A. A. S. , Cooper D. J. , Peters T. J. , Gelbier S. 
Published: April 2004

Background:  Information on alcohol‐associated oral mucosal lesions (OMLs) and conditions is meagre. A prevalence survey among alcohol misusers in south London was therefore undertaken.Methods:  Six hundred and ninety‐three subjects (388 alcohol misusers and 305 alcohol + substance abuse) attending several clinical care facilities in south London between 1994 and 1999 were interviewed on their alcohol and drug habits. A comprehensive oral mucosal examination was performed, and soft tissue lesions found were classified by the clinical criteria of Axéll.Results:  Mean age of the sample was 40.5 years. The majority was white (92.6%); of the whites, 29.9% were Celts (i.e. Irish, Scots resident in London). Many subjects reported misusing more than one type of beverage. Two hundred and twenty‐seven OMLs were found in 195 subjects (28.1%). The highest prevalences were found for frictional keratosis (8.8%), scar tissue of the lips (4.8%) and candidiasis (3.8%). Angular cheilitis was present in 21 subjects (3.0%). The alcohol‐related OMLs detected were three white patches compatible with a diagnosis of leukoplakia and one treated oral carcinoma. No erythroplakias were detected. The differences in prevalence of mucosal lesions in the two groups were not significant (χ2 = 2.18; P = 0.14). The prevalence of tobacco smoking was high in both study groups. OMLs were found with all four types of beverages consumed, and there was little variation by the units per week consumed. Concurrent use of substances and alcohol did not make a significant difference to the prevalence of OML. In the logistic regression analysis, minority ethnic groups (Black or Asian), smokers, those with a body mass index (BMI) under 20 and beer drinkers had an increased risk of an OML in this group of alcohol misusers.Conclusions:  In comparison with previous oral mucosal screening programmes undertaken in several settings in the UK, the present study has yielded a higher prevalence of oral mucosal diseases and conditions in this risk population. There are several ways in which alcohol could contribute to these detected oral lesions, either directly or indirectly.