bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein Kinase C Activation Upregulates Intercellular Adhesion of α-Catenin–negative Human Colon Cancer Cell Variants via Induction of Desmosomes
Authors: Hengel Jolanda van , Gohon Lionel , Bruyneel Erik , Vermeulen Stefan , Cornelissen Maria , Mareel Marc , Roy Frans van 
Published: July 2002

The α-catenin molecule links E-cadherin/ β-catenin or E-cadherin/plakoglobin complexes to the actin cytoskeleton. We studied several invasive human colon carcinoma cell lines lacking α-catenin. They showed a solitary and rounded morphotype that correlated with increased invasiveness. These round cell variants acquired a more normal epithelial phenotype upon transfection with an α-catenin expression plasmid, but also upon treatment with the protein kinase C (PKC) activator 12-O-tetradecanoyl-phorbol-13-acetate (TPA). Video registrations showed that the cells started to establish elaborated intercellular junctions within 30 min after addition of TPA. Interestingly, this normalizing TPA effect was not associated with α-catenin induction. Classical and confocal immunofluorescence showed only minor TPA-induced changes in E-cadherin staining. In contrast, desmosomal and tight junctional proteins were dramatically rearranged, with a conversion from cytoplasmic clusters to obvious concentration at cell–cell contacts and exposition at the exterior cell surface. Electron microscopical observations revealed the TPA-induced appearance of typical desmosomal plaques. TPA-restored cell–cell adhesion was E-cadherin dependent as demonstrated by a blocking antibody in a cell aggregation assay. Addition of an antibody against the extracellular part of desmoglein-2 blocked the TPA effect, too. Remarkably, the combination of anti–E-cadherin and anti-desmoglein antibodies synergistically inhibited the TPA effect.
Our studies show that it is possible to bypass the need for normal α-catenin expression to establish tight intercellular adhesion by epithelial cells. Apparently, the underlying mechanism comprises upregulation of desmosomes and tight junctions by activation of the PKC signaling pathway, whereas E-cadherin remains essential for basic cell–cell adhesion, even in the absence of α-catenin.
Control of Neuronal Size Homeostasis by Trophic Factor–mediated Coupling of Protein Degradation to Protein Synthesis
Authors: Franklin James L. , Johnson Eugene M. 
Published: July 2002

We demonstrate that NGF couples the rate of degradation of long-lived proteins in sympathetic neurons to the rate of protein synthesis. Inhibiting protein synthesis rate by a specific percentage caused an almost equivalent percentage reduction in the degradation rate of long-lived proteins, indicating nearly 1:1 coupling between the two processes. The rate of degradation of short-lived proteins was unaffected by suppressing protein synthesis. Included in the pool of proteins that had increased half-lives when protein synthesis was inhibited were actin and tubulin. Both of these proteins, which had half-lives of several days, exhibited no degradation over a 3-d period when protein synthesis was completely suppressed. The half-lives of seven other long-lived proteins were quantified and found to increase by 84–225% when protein synthesis was completely blocked.
Degradation–synthesis coupling protected cells from protein loss during periods of decreased synthesis. The rate of protein synthesis greatly decreased and coupling between degradation and synthesis was lost after removal of NGF. Uncoupling resulted in net loss of cellular protein and somatic atrophy. We propose that coupling the rate of protein degradation to that of protein synthesis is a fundamental mechanism by which neurotrophic factors maintain homeostatic control of neuronal size and perhaps growth.
An Evaluation Cost Model of Consideration Sets
Authors: Hauser John R. , Wernerfelt Birger 
Published: July 2002

Abstract
If utility (net of price) varies by consumption occasion, the consideration set of a rational consumer will represent trade-offs between decision costs and the incremental benefits of choosing from a larger set of brands. If evaluating a brand decreases biases and uncertainty in perceived utility, the decision to evaluate a brand for inclusion in a consideration set is different from the decision to consider an evaluated brand. The decision to consume is, in turn, different from the decision to consider. This article provides analytical expressions for these decision criteria and presents four aggregate implications of the model: (1 ) distributions of consideration set sizes, (2) order-of-entry penalties, (3) dynamic advertising response, and (4) competitive promotion intensity.
Wood dust exposure in the Danish furniture industry using conventional and passive monitors
Authors: Schlünssen Vivi , Vinzents Peter S. , Mikkelsen Anders B. , Schaumburg Inger 
Published: July 2002

Abstract
A study of wood dust exposure at furniture factories in one county in Denmark was performed as a cross sectional study. Dust exposure was measured with personal passive dust monitors and calibrated against active sampling on filters. Measurements of 1685 workers were included in the exposure assessment. The passive dust monitor conversion models for equivalent concentrations of inhalable dust and total dust based on data from the present study were not significantly different from the original models. Therefore models based on all available data were used. The parameters of the distribution of equivalent concentration of inhalable dust were 0.94 mg/m3 (geometric mean) and 2.10 (geometric standard deviation). Compared with a national cross sectional study from 1988 the exposure level (geometric mean) was reduced by a factor 2.0. Inhalable dust exposure was about 50% higher than exposure measured by the Danish ‘total’ dust method.
Xlandscape: the graphical display of word frequencies in sequences.
Authors: Levy S , Compagnoni L , Myers E W , Stormo G D 
Published: July 2002

Abstract
MOTIVATION: To provide a graphical interface for the generation, display and manipulation of a sequence landscape that will run on all X-windows-based Unix workstations. RESULTS: The sequence landscape approach enables the representation of the frequency of occurrence of all query sequence sub-words within a database. The landscape approach can detect tandem and other repeating word motifs, specific sub-words that are over-represented words in a particular database using Markov probability and the preference for sub-words belonging to either one of two databases. All these features aid in the classification of a query sequence. Given the open-text format for sequences and databases, the Xlandscape tool can be applied to a wide range of problems.
A new criterion to classify globular proteins based on their secondary structure contents.
Authors: Zhang C T , Zhang R 
Published: July 2002

Abstract
MOTIVATION: With the enlargement of protein structure databases, it is hoped that a method to classify proteins automatically will be developed. Although the classification criterion proposed by Nakashima et al. ( J. Biochem., 1986, 99, 153-162) was widely used in the literature, it leads to some inconsistencies with the classification databases currently available in the class assignment of protein structures. To improve their work, a new classification criterion is proposed relying on statistical analysis of the secondary structure contents of more than 200 proteins with well-known structural classes. The Fisher linear discriminant algorithm is used to derive the new classification criterion. RESULTS: Three cross-validation tests are performed to evaluate the new criterion. In the jackknife test, of the 210 proteins used to derive the criterion, 206 are correctly classified with an accuracy of 98.10%. Of the 16 proteins of purely intermediate structure (i.e. structures lying near borderlines between two classes) in the first test set, 15 are correctly classified with an accuracy of 93.75%. For the second test set which consists of 200 proteins selected randomly from SCOP, a testing accuracy of 94.00% is obtained. For comparison, the criterion of Nakashima et al. is also used to classify the 210, 16 and 200 proteins, respectively. Consequently, accuracies of 94.76%, 62.50% and 91.50% are obtained, respectively. On average, the accuracy of the new classification criterion is 4% higher than that of Nakashima et al. AVAILABILITY: The program is available on request from the first author. CONTACT: ctzhang@tju.edu.cn
VHMPT: a graphical viewer and editor for helical membrane protein topologies.
Authors: Lin W J , Hwang M J 
Published: July 2002

Abstract
MOTIVATION: Lacking structures resolved at atomic resolution, the great majority of membrane proteins have typically been depicted in a schematic two-dimensional (2D) topology consisting of putative transmembrane domains predicted from hydropathy plots. As more and more sequences of membrane proteins become available from genome projects, there is a need to automate the process of generating the schematic topology while allowing important information, such as the individual amino acid and the extent to which it is conserved in evolution, to be conveniently inspected. We addressed this need by developing a program called VHMPT. RESULTS: VHMPT (a graphical V iewer and editor for H elical line M embrane P rotein T opologies) can automatically generate a schematic 2D topology for a protein with transmembrane helices. Through an interactive graphical interface, VHMPT allows users to modify the layout of the generated topology, label specific amino acid or amino acid groups, and annotate with arrows and texts. Given a multiple sequence alignment file, VHMPT can also color code a normalized conservation score for each amino acid on the generated topology, allowing ready visual recognition of highly conserved (or variable) topological regions. VHMPT is written in Tcl/Tk and can run on platforms that have installed the Tcl/Tk interpreter. AVAILABILITY: The source code and a user manual for VHMPT are available for download at http://www. ibms.sinica.edu.tw/mjhwang/vhmpt. CONTACT: mjhwang@mail.ibms.sinica.edu.tw
Mapmerge: merge genomic maps.
Authors: Nadkarni P 
Published: July 2002

Abstract
MOTIVATION: When two or more genomic maps of a chromosomal region are available, it is useful to be able to synthesize them to create a merged map. RESULTS: We show that map merging is an exploratory process because there are multiple ways to combine data based upon what the user wishes to focus on, and upon which particular data subset emphasis is desired. We describe Mapmerge, a program for merging two genomic maps, discuss its limitations, and illustrate an example of its use. AVAILABILITY: Freely available (ANSI C source code, a Make file, test data files, documentation) on request from the author. CONTACT: Prakash.Nadkarni@yale.edu
CloneIt: finding cloning strategies, in-frame deletions and frameshifts.
Authors: Lindenbaum P 
Published: July 2002

Abstract
MOTIVATION: The CloneIt program searches for sub-cloning strategies, in-frame deletions and frameshifts within a plasmid sequence. AVAILABILITY: The program, written in ANSI-C language, is available at http://locus.jouy.inra.fr/soft/cloneit/clonei t.html CONTACT: lindenb@biotec.jouy.inra.fr
EUCLID: automatic classification of proteins in functional classes by their database annotations.
Authors: Tamames J , Ouzounis C , Casari G , Sander C , Valencia A 
Published: July 2002

Abstract
SUMMARY: A tool is described for the automatic classification of sequences in functional classes using their database annotations. The Euclid system is based on a simple learning procedure from examples provided by human experts. AVAILABILITY: Euclid is freely available for academics at http://www.gredos.cnb.uam.es/EUCLID, with the corresponding dictionaries for the generation of three, eight and 14 functional classes. Contact: E-mail: valencia@cnb.uam.es SUPPLEMENTARY INFORMATION: The results of the EUCLID classification of different genomes are available at http://www.sander.ebi.ac. uk/genequiz/. A detailed description of the different applications mentioned in the text is available at http://www.gredos.cnb.uam. es/EUCLID/Full_Paper
New phylogenetic venues opened by a novel implementation of the DNAml algorithm.
Authors: Trelles O , Ceron C , Wang H C , Dopazo J , Carazo J M 
Published: July 2002

Abstract
SUMMARY: This note describes the parallelization of a key biological application, such as the construction of phylogenetic trees, using the DNAml program. A careful run-time analysis allowed us to propose an efficient parallelization that scaled very well to large problem sizes. AVAILABILITY: By anonymous ftp at ftp.ac.uma. es (/pub/ots/pDNAml) or from our web site http://www.cnb.uam. es/www/software/software_index.htmlCONTACT: ots@ac.uma.es
Issues in developing integrated genomic databases and application to the human X chromosome.
Authors: Leser U , Lehrach H , Roest Crollius H 
Published: July 2002

Abstract
MOTIVATION: In the past decade, a vast amount of mapping data has been generated on the human X chromosome, without a mechanism which would provide a global view of exactly what has been achieved. Large datasets are available electronically, but in heterogeneous formats and with incompatible access modes. In addition, relationships between objects in different datasets are often not specified. RESULTS: We discuss the problem of integrating these data into one database and define a number of requirements that are vital for any integration approach. We have developed IXDB, the Integrated X chromosome database, which fulfils those requirements and aims at providing a global view on genomic data at a chromosomal level. IXDB represents a conceptual framework based on identifying, storing and analysing relationships between biological objects, and includes a series of tools to automate the integration of such information. It currently focuses on physical mapping data, as a starting point towards a map of the human X chromosome that should provide a uniform and global research resource for ongoing and future sequencing and functional studies. AVAILABILITY: IXDB is available at http://ixdb.mpimg-berlin-dahlem.mpg.de. The iace2ixdb software and a description of the Iace data format are available from the authors. CONTACT: hrc@genoscope.cns.fr
Recognition of splice junctions on DNA sequences by BRAIN learning algorithm.
Authors: Rampone S 
Published: July 2002

Abstract
MOTIVATION: The problem addressed in this paper is the prediction of splice site locations in human DNA. The aims of the proposed approach are explicit splicing rule description, high recognition quality, and robust and stable 'one shot' data processing. RESULTS: These results are achieved by means of a new learning algorithm [BRAIN (Batch Relevance-based Artificial INtelligence)], described in the paper, inferring Boolean formulae from examples, and by considering the splicing rules as disjunctive normal form (DNF) formulae. The formula terms are computed in an iterative way, by identifying from the training set a relevance coefficient for each attribute. The classification is then refined by a neural network and combined with a discriminant analysis procedure. This splice site recognition method shows low error rates (0.0002 and 0.0003) and high correlation coefficient measures (0.83 and 0.81) for donor and acceptor sites, respectively; better than other methods. AVAILABILITY: The BRAIN package (Borland Turbo Pascal for Windows) is available on the EMBL file server. (ftp://ftp.ebi.ac.uk/pub/software/dos under nnbrain$.exe). CONTACT: rampo@vaxsa.csied.unisa.it
Prediction of RNA secondary structure based on helical regions distribution.
Authors: WuJu L , JiaJin W 
Published: July 2002

Abstract
MOTIVATION: RNAs play an important role in many biological processes and knowing their structure is important in understanding their function. Due to difficulties in the experimental determination of RNA secondary structure, the methods of theoretical prediction for known sequences are often used. Although many different algorithms for such predictions have been developed, this problem has not yet been solved. It is thus necessary to develop new methods for predicting RNA secondary structure. The most-used at present is Zuker's algorithm which can be used to determine the minimum free energy secondary structure. However many RNA secondary structures verified by experiments are not consistent with the minimum free energy secondary structures. In order to solve this problem, a method used to search a group of secondary structures whose free energy is close to the global minimum free energy was developed by Zuker in 1989. When considering a group of secondary structures, if there is no experimental data, we cannot tell which one is better than the others. This case also occurs in combinatorial and heuristic methods. These two kinds of methods have several weaknesses. Here we show how the central limit theorem can be used to solve these problems. RESULTS: An algorithm for predicting RNA secondary structure based on helical regions distribution is presented, which can be used to find the most probable secondary structure for a given RNA sequence. It consists of three steps. First, list all possible helical regions. Second, according to central limit theorem, estimate the occurrence probability of every helical region based on the Monte Carlo simulation. Third, add the helical region with the biggest probability to the current structure and eliminate the helical regions incompatible with the current structure. The above processes can be repeated until no more helical regions can be added. Take the current structure as the final RNA secondary structure. In order to demonstrate the confidence of the program, a test on three RNA sequences: tRNAPhe, Pre-tRNATyr, and Tetrahymena ribosomal RNA intervening sequence, is performed. AVAILABILITY: The program is written in Turbo Pascal 7.0. The source code is available upon request. CONTACT: Wujj@nic.bmi.ac.cn or Liwj@mail.bmi.ac.cn
GeneTree: comparing gene and species phylogenies using reconciled trees.
Authors: Page R D 
Published: July 2002

Abstract
SUMMARY: GeneTree is a program for comparing gene and species trees using reconciled trees. The program can compute the cost of embedding a gene tree within a species tree, visually display the location and number of gene duplications and losses, and search for optimal species trees. AVAILABILITY: The program is free and is available at ((http://taxonomy.zoology.gla.ac. uk/rod/genetree/genetree.html)).
SPEM: a parser for EMBL style flat file database entries.
Authors: Pocock M R , Hubbard T , Birney E 
Published: July 2002

Abstract
SUMMARY: We present a set of Perl modules for the flexible and robust parsing and editing of EMBL/SWISS-PROT databases. AVAILABILITY: The Web page at http://www.sanger.ac. uk/Software/PerlModule/ provides information about downloading the SPEM and PrEMBL modules, and provides links to documentation and example code.
An Internet linkage and mutation database for the complex phenotype asthma.
Authors: Wjst M , Immervoll T 
Published: July 2002

Abstract
SUMMARY: The paper presents details of database construction, website installation and server architecture of the asthma and allergy gene database. AVAILABILITY: Database and server templates are available on request from the first author. SUPPLEMENTARY INFORMATION: The URL of the asthma and allergy gene database is http://cooke.gsf.de
ORBIT: an integrated environment for user-customized bioinformatics tools.
Authors: Bellgard M I , Hiew H L , Hunter A , Wiebrands M 
Published: July 2002

Abstract
MOTIVATION: There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. RESULTS: We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.
A simple algorithm for detecting circular permutations in
proteins
Authors: Uliel S. , Fliess A. , Amir A. , Unger R. 
Published: July 2002

Abstract
Motivation: Circular permutation of a protein is a genetic operation in which part of the C-terminal of the protein is moved to its N-terminal. Recently, it has been shown that proteins that undergo engineered circular permutations generally maintain their three dimensional structure and biological function. This observation raises the possibility that circular permutation has occured in Nature during evolution. In this scenario a protein underwent circular permutation into another protein, thereafter both proteins further diverged by standard genetic operations. To study this possibility one needs an efficient algorithm that for a given pair of proteins can detect the underlying event of circular permutations. A possible formal description of the question is: given two sequences, find a circular permutation of one of them under which the edit distance between the proteins is minimal. A naive algorithm might take time proportional to N3 or even N4, which is prohibitively slow for a large-scale survey. A sophisticated algorithm that runs in asymptotic time of N2 was recently suggested, but it is not practical for a large-scale survey.
Results: A simple and efficient algorithm that runs in time N2 is presented. The algorithm is based on duplicating one of the two sequences, and then performing a modified version of the standard dynamic programming algorithm. While the algorithm is not guaranteed to find the optimal results, we present data that indicate that in practice the algorithm performs very well.
Availability: A Fortran program that calculates the optimal edit distance under circular permutation is available upon request from the authors.
Contact: ron@biocom1.ls.biu.ac.il