bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computed tomography angiographic findings in hepatocellular carcinoma less than 2 cm detected during follow‐up in 29 patients
Authors: IWAMOTO SHOZO , SANEFUJI HAYATO , OKUDA KUNIO 
Published: August 2003

AbstractAims:  The early stage of hepatocarcinogenesis is not well understood pathologically and clinically. The present study was designed to define small (early) hepatocellular carcinoma (HCC) angiographically using the angio‐helical computed tomography (CT) system.Methods:  Arterial portography CT and hepatic arteriography CT were carried out in 29 patients in whom small HCC ≤ 20 mm was detected during follow‐up.Results:  There were 17 males and 12 females, aged 47 to 85 years. The offending virus was hepatitis B in four, hepatitis C in 24 and no virus marker in one case. The follow‐up period varied from less than a year to 17 years, averaging 6.4 years. The underlying disease was cirrhosis in 12 and chronic hepatitis in 17 cases. The mass was solitary in 16 and multiple in 13 cases, while the size of the mass ranged from 8‐20 mm. All lesions were low in attenuation on arterial portography CT, and in 23 of 30 lesions hepatic arteriography CT showed high attenuation, suggesting arterial blood supply. In the remaining 7 cases, lesions were perhaps in the transition from portal to arterial.Conclusions:  It was concluded that HCC develops frequently in a liver with chronic hepatitis, often muticentrically, and that early HCC lesions are more often overt HCC already with arterial blood supply, rather than extremely well‐differentiated supplied by the portal vein as generally believed.
γ‐Amino‐butyric acid immunoreactivity in intramucosal colonic tumors
Authors: MAEMURA KENTARO , YAMAUCHI HIROAKI , HAYASAKI HANA , KANBARA KIYOTO , TAMAYAMA TAKUMI , HIRATA ICHIRO , WATANABE MASAHITO 
Published: August 2003

AbstractBackground and Aim:  The level of γ‐amino‐butyric acid (GABA) is reported to be increased in colon cancer. Moreover, data suggests that GABA plays a role in the proliferation or maturation of some types of cells. We examined the expression of GABA in intramucosal colonic tumors to clarify the relation between GABA and the degree of atypia.Methods:  Paraffin sections were prepared from 56 protruded‐type colonic neoplasms, which were classified as intramucosal adenocarcinoma (AC), adenoma with severe atypia (ASA), or adenoma with mild to moderate atypia (AMA). Expression of GABA was investigated immunohistochemically, and GABA immunoreactivity was compared to the staining patterns of carcinoembryonic antigen (CEA) and cancer‐associated antigen (CA19‐9) which were classified into three categories.Results:  Intense GABA immunoreactivity was observed in 73.7%, 54.6%, 13.3%, and 5.4% of AC, ASA, AMA, and normal mucosa specimens, respectively. Kendall's correlation coefficient between GABA immunoreactivity and the degree of atypia was 0.447. Strong, positive CEA staining (pattern 3) was observed in 57.9%, 36.3%, and 13.3% of AC, ASA, and AMA specimens, respectively. Strong, positive CA19‐9 staining was observed: 26.3%, 9.1% and 0%, respectively. In AC and ASA, the proportion of glands with strong GABA immunoreactivity was greater than the proportion of glands that were strongly positive for CA19‐9.Conclusion:  GABA may be useful as a tumor marker in combination with other tumor markers such as CEA and CA19‐9.
Functional localization of cannabinoid receptors and endogenous cannabinoid production in distinct neuron populations of the hippocampus
Authors: Hoffman Alexander F. , Riegel Arthur C. , Lupica Carl R. 
Published: August 2003

AbstractThe possible localization of cannabinoid (CB) receptors to glutamatergic and GABAergic synaptic terminals impinging upon GABAergic interneurons in the CA1 region of the rat hippocampus was examined using the electrophysiological measurement of neurotransmitter release in brain slices. Whereas activation of cannabinoid receptors via the application of the cannabinoid agonist WIN55,212‐2 significantly and dose‐dependently reduced evoked IPSCs recorded from interneurons possessing somata located in the stratum radiatum (S.R.) and stratum oriens (S.O.) lamellae, evoked glutamatergic EPSCs were unaffected in both neuronal populations. However, in agreement with previous reports, WIN55,212‐2 significantly reduced EPSCs recorded from CA1 pyramidal neurons. Additional experiments confirmed that the effects of WIN55,212‐2 on IPSCs were presynaptic and that they could be blocked by the CB1 receptor antagonist SR141716A. The involvement of endogenous cannabinoids in the presynaptic inhibition of GABA release was also examined in the interneurons and pyramidal cells using a depolarization‐induced suppression of inhibition (DSI) paradigm. DSI was observed in CA1 pyramidal neurons under control conditions, and its incidence was greatly increased by the cholinergic agonist carbachol. However, DSI was not observed in the S.R. or S.O. interneuron populations, in either the presence or absence of carbachol. Whereas DSI was not present in these interneurons, the inhibitory inputs to these cells were modulated by the synthetic cannabinoid WIN55,212‐2. These data support the hypothesis that cannabinoid receptors are located on inhibitory, but not excitatory, axon terminals impinging upon hippocampal interneurons, and that CA1 pyramidal neurons, and not interneurons, are capable of generating endogenous cannabinoids during prolonged states of depolarization.
Language perception activates the hand motor cortex: implications for motor theories of speech perception
Authors: Flöel Agnes , Ellger Tanja , Breitenstein Caterina , Knecht Stefan 
Published: August 2003

AbstractThe precise mechanisms of how speech may have developed are still unknown to a large extent. Gestures have proven a powerful concept for explaining how planning and analysing of motor acts could have evolved into verbal communication. According to this concept, development of an action‐perception network allowed for coding and decoding of communicative gestures. These were manual or manual/articulatory in the beginning and then became increasingly elaborate in the articulatory mode. The theory predicts that listening to the ‘gestures’ that compose spoken language should activate an extended articulatory and manual action‐perception network. To examine this hypothesis, we assessed the effects of language on cortical excitability of the hand muscle representation by transcranial magnetic stimulation. We found the hand motor system to be activated by linguistic tasks, most notably pure linguistic perception, but not by auditory or visuospatial processing. The amount of motor system activation was comparable in both hemispheres. Our data support the theory that language may have evolved within a general and bilateral action‐perception network.
Changes of effective connectivity between the lateral and medial parts of the prefrontal cortex during a visual task
Authors: Chaminade Thierry , Fonlupt Pierre 
Published: August 2003

AbstractStructural equation modelling was used to study the change of connectivity during a visual task with continuous variation of the attention load. The model was based on areas defined by the haemodynamic responses described elsewhere [Mazoyer, P., Wicker, B. & Fonlupt, P. (2002) A neural network elicited by parametric manipulation of the attention load. Neuroreport, 13, 2331–2334], including occipitotemporal, parietal, temporal and prefrontal (lateral and medial areas) cortices. We have studied stationary‐ (which does not depend on the attentional load) and attention‐related coupling between areas. This allowed the segregation of two subsystems. The first could reflect a system performing the integration step of the visual signal and the second a system participating in response selection. The major finding is the mutual negative influence between the lateral and medial parts of the prefrontal cortex. This negative influence between these two brain regions increased with the attention load. This is interpreted as a modification of the balance between integration and decision processes that are needed for the task to be efficiently completed.
Class prediction and discovery using gene microarray and
proteomics mass spectroscopy data: curses, caveats, cautions
Authors: Somorjai R.L. , Dolenko B. , Baumgartner R. 
Published: August 2003

Abstract
Motivation: Two practical realities constrain the analysis of microarray data, mass spectra from proteomics, and biomedical infrared or magnetic resonance spectra. One is the ‘curse of dimensionality’: the number of features characterizing these data is in the thousands or tens of thousands. The other is the‘ curse of dataset sparsity’: the number of samples is limited. The consequences of these two curses are far-reaching when such data are used to classify the presence or absence of disease.
Results: Using very simple classifiers, we show for several publicly available microarray and proteomics datasets how these curses influence classification outcomes. In particular, even if the sample per feature ratio is increased to the recommended 5–10 by feature extraction/reduction methods, dataset sparsity can render any classification result statistically suspect. In addition, several ‘optimal’ feature sets are typically identifiable for sparse datasets, all producing perfect classification results, both for the training and independent validation sets. This non-uniqueness leads to interpretational difficulties and casts doubt on the biological relevance of any of these ‘optimal’ feature sets. We suggest an approach to assess the relative quality of apparently equally good classifiers.
Contact: Ray.Somorjai@nrc-cnrc.gc.ca
* To whom correspondence should be addressed.
Probabilistic scoring measures for profile–profile
comparison yield more accurate short seed alignments
Authors: Mittelman David , Sadreyev Ruslan , Grishin Nick 
Published: August 2003

Abstract
Motivation: The development of powerful automatic methods for the comparison of protein sequences has become increasingly important. Profile-to-profile comparisons allow for the use of broader information about protein families, resulting in more sensitive and accurate comparisons of distantly related sequences. A key part in the comparison of two profiles is the method for the calculation of scores for the position matches. A number of methods based on various theoretical considerations have been proposed. We implemented several previously reported scoring functions as well as our own functions, and compared them on the basis of their ability to produce accurate short ungapped alignments of a given length.
Results: Our results suggest that the family of the probabilistic methods (log-odds based methods and prof_sim) may be the more appropriate choice for the generation of initial ‘seeds’ as the first step to produce local profile–profile alignments. The most effective scoring systems were the closely related modifications of functions previously implemented in the COMPASS and Picasso methods.
Contact: sadreyev@chop.swmed.edu
* To whom correspondence should be addressed.
Development of a four-body statistical pseudo-potential
to discriminate native from non-native protein conformations
Authors: Krishnamoorthy Bala , Tropsha Alexander 
Published: August 2003

Abstract
Motivation: Most scoring functions used in protein fold recognition employ two-body (pseudo) potential energies. The use of higher-order terms may improve the performance of current algorithms.
Methods: Proteins are represented by the side chain centroids of amino acids. Delaunay tessellation of this representation defines all sets of nearest neighbor quadruplets of amino acids. Four-body contact scoring function (log likelihoods of residue quadruplet compositions) is derived by the analysis of a diverse set of proteins with known structures. A test protein is characterized by the total score calculated as the sum of the individual log likelihoods of composing amino acid quadruplets.
Results: The scoring function distinguishes native from partially unfolded or deliberately misfolded structures. It also discriminates between pre- and post-transition state and native structures in the folding simulations trajectory of Chymotrypsin Inhibitor 2 (CI2).
Availability: All codes are written in C/C++. Programs are available from the authors on request..
Contact: alex_tropsha@unc.edu
* To whom correspondence should be addressed.
Molecular evaluation using in silico protein
interaction profiles
Authors: Hayashi Yoshiharu , Sakaguchi Katsuyoshi , Kobayashi Mime , Kobayashi Masaki , Kikuchi Yo , Ichiishi Eiichiro 
Published: August 2003

Abstract
Motivation: To find a correlation between the activities and structures of molecules is one of the most important subjects for molecular evaluation study. Traditional quantitative structure-activity relationship (QSAR) methodologies represent those attempts using physicochemical descriptors. Creating a new molecular description factor based on the results of a computational docking study will add new dimensions to molecular evaluation.
Results: We propose a new molecular description factor analysis system called the Comparative Molecular Interaction Profile Analysis (CoMIPA) system in which the AutoDock program is used for docking evaluation of small molecule compound–protein complexes. Interaction energies are calculated, and the data sets obtained are called interaction profiles (IPFs). Using the IPF as a scoring indicator, the system could be a powerful tool to cluster the interacting properties between small molecules and bio macromolecules such as ligand–receptor bindings. Further development of the system will enable us to predict the adverse effects of a drug candidate.
Contact: yhayashi@enkaku.co.jp
* To whom correspondence should be addressed.
† Presend address: New Industry Creation Hatchery Center, Tohoku University, 10 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan.
ClustalW-MPI: ClustalW analysis using distributed and parallel computing
Authors: Li Kuo-Bin 
Published: August 2003

Abstract
Summary: ClustalW is a tool for aligning multiple protein or nucleotide sequences. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is a distributed and parallel implementation of ClustalW. All three steps have been parallelized to reduce the execution time. The software uses a message-passing library called MPI (Message Passing Interface) and runs on distributed workstation clusters as well as on traditional parallel computers.
Availability:The source codes are written in ISO C and are available at http://www.bii.a-star.edu.sg/software/clustalw-mpi/. An open source implementations of MPI http://www-unix.mcs.anl.gov/mpi/.
Contact: kuobin@bii.a-star.edu.sg
Evaluation of ontology development tools for bioinformatics
Authors: Lambrix Patrick , Habbouche Manal , Pérez Marta 
Published: August 2003

Abstract
Ontologies are being used nowadays in many areas, including bioinformatics. To assist users in developing and maintaining ontologies a number of tools have been developed. In this paper we compare four such tools, Protégé-2000, Chimaera, DAG-Edit and OilEd. As test ontologies we have used ontologies from the Gene Ontology Consortium. No system is preferred in all situations, but each system has its own strengths and weaknesses.
Contact: patla@ida.liu.se
* To whom correspondence should be addressed.
Digital extractor: analysis of digital differential display output
Authors: Madden Stephen F. , O’Donovan Barry , Furney Simon J. , Brady Hugh R. , Silvestre Guenole , Doran Peter P. 
Published: August 2003

Abstract
Summary: Digital Extractor is a program for the high-throughput processing of data sets derived from digital differential display-based comparisons of EST libraries. These comparisons can be utilized to identify discrete subsets of genes whose expression is restricted to distinct tissue types. The program facilitates these investigations by permitting parallel annotation of genes identified as being differentially expressed.
Availability: The executable program, suitable for use on all UNIX-based platforms is freely available to non-profit users.
Contact: pdoran.genome@mater.ie
* To whom correspondence should be addressed.
Comprehensive aligned sequence construction
for automated design of effective probes (CASCADE-P) using 16S rDNA
Authors: DeSantis T. Z. , Dubosarskiy I. , Murray S. R. , Andersen G. L. 
Published: August 2003

Abstract
Motivation: Prokaryotic organisms have been identified utilizing the sequence variation of the 16S rRNA gene. Variations steer the design of DNA probes for the detection of taxonomic groups or specific organisms. The long-term goal of our project is to create probe arrays capable of identifying 16S rDNA sequences in unknown samples. This necessitated the authentication, categorization and alignment of the &gt;75 000 publicly available‘ 16S’ sequences. Preferably, the entire process should be computationally administrated so the aligned collection could periodically absorb 16S rDNA sequences from the public records. A complete multiple sequence alignment would provide a foundation for computational probe selection and facilitates microbial taxonomy and phylogeny.
Results: Here we report the alignment and similarity clustering of 62 662 16S rDNA sequences and an approach for designing effective probes for each cluster. A novel alignment compression algorithm, NAST (Nearest Alignment Space Termination), was designed to produce the uniform multiple sequence alignment referred to as the prokMSA. From the prokMSA, 9020 Operational Taxonomic Units (OTUs) were found based on transitive sequence similarities. An automated approach to probe design was straightforward using the prokMSA clustered into OTUs. As a test case, multiple probes were computationally picked for each of the 27 OTUs that were identified within the Staphylococcus Group. The probes were incorporated into a customized microarray and were able to correctly categorize Staphylococcus aureus and Bacillus anthracis into their correct OTUs. Although a successful probe picking strategy is outlined, the main focus of creating the prokMSA was to provide a comprehensive, categorized, updateable 16S rDNA collection useful as a foundation for any probe selection algorithm.
Availability: http://greengenes.llnl.gov/16S/
Contact: GLAndersen@lbl.gov
Supplementary Information: Complete prokMSA in aligned fasta format: http://greengenes.llnl.gov/16S_cgi/download/update_28Dec02/prokMSA_aligned.fasta.Z Sequences within each Operational Taxonomic Unit: http://greengenes.llnl.gov/16S_cgi/download/update_15Mar02/SeqDescByOTU.txt DNA probe sequences: http://greengenes.llnl.gov/16S_cgi/download/update_15Mar02/15Mar02_StaphGrpPrbs.xls
* To whom correspondence should be addressed.
Rapid classification of a protein fold family using a
statistical analysis of dipolar couplings
Authors: Valafar Homayoun , Prestegard James H. 
Published: August 2003

Abstract
Motivation: One of the primary aims of the structural genomics initiative is the determination of representative structures from each protein fold family. Given this objective, it is important to rapidly identify proteins that belong to a family that is already well populated (so they can be eliminated from further studies), or more importantly identify proteins that represent new families of fold.
Results: A method for rapid classification to a fold family by the statistical analyses of unassigned the 15N–1H residual dipolar couplings is presented. The required NMR data can be quickly acquired and analyzed. Using this method, structure determination efforts can be focused on more unique and interesting structures, and the overall efficiency in the construction of an information-rich library can be increased.
Contact: jpresteg@ccrc.uga.edu
* To whom correspondence should be addressed.
UniFrag and GenomePrimer:
selection of primers for genome-wide production of unique amplicons
Authors: van Hijum Sacha A. F. T. , de Jong Anne , Buist Girbe , Kok Jan , Kuipers Oscar P. 
Published: August 2003

Abstract
Summary: the complementary programs UniFrag and GenomePrimer were developed to provide a reliable high-throughput method to select the most unique regions within genomic DNA sequence(s) and design primers therein, involving minimal user intervention and maximum flexibility.
Availability: Freely available for educational and research purposes by non-profit institutions at http://molgen.biol.rug.nl/molgen/research/molgensoftware.php
Contact: jonga@biol.rug.nl
Supplementary information: http://molgen.biol.rug.nl/publication/primer_data/
* To whom correspondence should be addressed.
PISCES: a protein sequence culling server
Authors: Wang Guoli , Dunbrack Roland L. 
Published: August 2003

Abstract
Summary: PISCES is a public server for culling sets of protein sequences from the Protein Data Bank (PDB) by sequence identity and structural quality criteria. PISCES can provide lists culled from the entire PDB or from lists of PDB entries or chains provided by the user. The sequence identities are obtained from PSI-BLAST alignments with position-specific substitution matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists than servers that use BLAST, which is unable to identify many relationships below 40% sequence identity and often overestimates sequence identity by aligning only well-conserved fragments. PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output.
Availability: The server is located at http://www.fccc.edu/research/labs/dunbrack/pisces
Contact: rl_dunbrack@fccc.edu
* To whom correspondence should be addressed.
Three Distinct Rice Cellulose Synthase Catalytic Subunit Genes Required for Cellulose Synthesis in the Secondary Wall
Authors: Tanaka Katsuyuki , Murata Kazumasa , Yamazaki Muneo , Onosato Katsura , Miyao Akio , Hirochika Hirohiko 
Published: September 2003

Abstract
Several brittle culm mutations of rice (Oryza sativa) causing fragility of plant tissues have been identified genetically but not characterized at a molecular level. We show here that the genes responsible for three distinct brittle mutations of rice, induced by the insertion of the endogenous retrotransposon Tos17, correspond to CesA (cellulose synthase catalytic subunit) genes, OsCesA4, OsCesA7 and OsCesA9. Three CesA genes were expressed in seedlings, culms, premature panicles, and roots but not in mature leaves, and the expression profiles were almost identical among the three genes. Cellulose contents were dramatically decreased (8.9%-25.5% of the wild-type level) in the culms of null mutants of the three genes, indicating that these genes are not functionally redundant. Consistent with these results, cell walls in the cortical fiber cells were shown to be thinner in all the mutants than in wild-type plants. Based on these observations, the structure of a cellulose-synthesizing complex involved in the synthesis of the secondary cell wall is discussed.