bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple statistical method for discriminating outer membrane proteins with better accuracy
Authors: Gromiha M. Michael , Suwa Makiko 
Published: November 2004

AbstractMotivation: Discriminating outer membrane proteins from other folding types of globular and membrane proteins is an important task both for identifying outer membrane proteins from genomic sequences and for the successful prediction of their secondary and tertiary structures.Results: We have systematically analyzed the amino acid composition of globular proteins from different structural classes and outer membrane proteins. We found that the residues, Glu, His, Ile, Cys, Gln, Asn and Ser, show a significant difference between globular and outer membrane proteins. Based on this information, we have devised a statistical method for discriminating outer membrane proteins from other globular and membrane proteins. Our approach correctly picked up the outer membrane proteins with an accuracy of 89% for the training set of 337 proteins. On the other hand, our method has correctly excluded the globular proteins at an accuracy of 79% in a non-redundant dataset of 674 proteins. Furthermore, the present method is able to correctly exclude α-helical membrane proteins up to an accuracy of 80%. These accuracy levels are comparable to other methods in the literature, and this is a simple method, which could be used for dissecting outer membrane proteins from genomic sequences. The influence of protein size, structural class and specific residues for discrimination is discussed.Availability: A program for the discrimination method is available upon request from the corresponding author. The datasets used in this work are available at http://www.cbrc.jp/~gromiha/omp/dataset.htmlContact: michael-gromiha@aist.go.jp
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins
Authors: Yuan Xin , Bystroff Christopher 
Published: November 2004

AbstractMotivation: Proteins of the same class often share a secondary structure packing arrangement but differ in how the secondary structure units are ordered in the sequence. We find that proteins that share a common core also share local sequence–structure similarities, and these can be exploited to align structures with different topologies. In this study, segments from a library of local sequence–structure alignments were assembled hierarchically, enforcing the compactness and conserved inter-residue contacts but not sequential ordering. Previous structure-based alignment methods often ignore sequence similarity, local structural equivalence and compactness.Results: The new program, SCALI (Structural Core ALIgnment), can efficiently find conserved packing arrangements, even if they are non-sequentially ordered in space. SCALI alignments conserve remote sequence similarity and contain fewer alignment errors. Clustering of our pairwise non-sequential alignments shows that recurrent packing arrangements exist in topologically different structures. For example, the three-layer sandwich domain architecture may be divided into four structural subclasses based on internal packing arrangements. These subclasses represent an intermediate level of structure classification, more general than topology, but more specific than architecture as defined in CATH. A strategy is presented for developing a set of predictive hidden Markov models based on multiple SCALI alignments.Availability: An online topology-independent SCALI structure comparison server is available at http://www.bioinfo.rpi.edu/~bystrc/scali.htmlContact: bystrc@rpi.edu
Husserl's Theory of the Phenomenological Reduction: Between Life-world and Cartesianism
Authors: Luft Sebastian 
Published: November 2004

This essay attempts a renewed, critical exposition of Husserl's theory of the phenomenological reduction, incorporating manuscript material that has been published since the defining essays of the first generation of Husserl research. The discussion focuses on points that
remain
especially crucial, i.e., the concept of the natural attitude, the ways into the reduction (and their systematics), and finally the question of the "meaning of the reduction." Indeed, in the reading attempted here, this final question leads to two, not necessarily related, focal points: a Cartesian and a Life-world tendency. It is my claim that in following these two paths, Husserl was consistent in pursuing two evident leads in his philosophical enterprise; however, he was at the same time unable to systematically unify these two strands. Thus, I am offering an interpretation which might be called a modified "departure from Cartesianism" reading that Landgrebe proposed in his famous essay from the 1950s, in which he was clearly influenced by Heidegger (a reading that is still valid in many contemporary expositions of Husserl's thought). This discussion should make apparent that Husserl's theory of the phenomenological reduction deserves a renewed look both in light of material that has since appeared in the
Husserliana
and in light of a new incorporation of the most important results of recent tendencies in Husserl research.
Establishing Trust via Technology: Long Distance Practices and Pitfalls
Authors: Naquin Charles , Paulson Gaylen 
Published: November 2004

AbstractGlobal negotiators often depend upon communication technologies to convey information and strike deals. Unfortunately, negotiations conducted via more "lean" media (e.g., e-mail, telephone) have been associated with low levels of trust and difficulties in reaching agreements. We explore two approaches to building trust while communicating via the internet. Derived from the literature on interpersonal trust, negotiators were asked to adopt one of two strategies. The first was to build personal rapport. The second was to discuss ground rules and procedures for the negotiation. Negotiators who spent time building rapport reported greater levels of trust, and were more confident and satisfied with their outcomes. These perceptions were evident even though outcomes were comparable across conditions. The most negatively perceived negotiations were those that included rules discussions without the benefit of rapport. Implications of these findings for theory and practice are discussed.
d-matrix – database exploration, visualization and analysis
Authors: Seelow Dominik , Galli Raffaello , Mebus Siegrun , Sperling Hans-Peter , Lehrach Hans , Sperling Silke 
Published: November 2004

Abstract
Background
Motivated by a biomedical database set up by our group, we aimed to develop a generic database front-end with embedded knowledge discovery and analysis features. A major focus was the human-oriented representation of the data and the enabling of a closed circle of data query, exploration, visualization and analysis.

Results
We introduce a non-task-specific database front-end with a new visualization strategy and built-in analysis features, so called d-matrix. d-matrix is web-based and compatible with a broad range of database management systems. The graphical outcome consists of boxes whose colors show the quality of the underlying information and, as the name suggests, they are arranged in matrices. The granularity of the data display allows consequent drill-down. Furthermore, d-matrix offers context-sensitive categorization, hierarchical sorting and statistical analysis.

Conclusions
d-matrix enables data mining, with a high level of interactivity between humans and computer as a primary factor. We believe that the presented strategy can be very effective in general and especially useful for the integration of distinct data types such as phenotypical and molecular data.
Incremental genetic K-means algorithm and its application in gene expression data analysis
Authors: Lu Yi , Lu Shiyong , Fotouhi Farshad , Deng Youping , Brown Susan J 
Published: November 2004

Abstract
Background
In recent years, clustering algorithms have been effectively applied in molecular biology for gene expression data analysis. With the help of clustering algorithms such as K-means, hierarchical clustering, SOM, etc, genes are partitioned into groups based on the similarity between their expression profiles. In this way, functionally related genes are identified. As the amount of laboratory data in molecular biology grows exponentially each year due to advanced technologies such as Microarray, new efficient and effective methods for clustering must be developed to process this growing amount of biological data.

Results
In this paper, we propose a new clustering algorithm, Incremental Genetic K-means Algorithm (IGKA). IGKA is an extension to our previously proposed clustering algorithm, the Fast Genetic K-means Algorithm (FGKA). IGKA outperforms FGKA when the mutation probability is small. The main idea of IGKA is to calculate the objective value Total Within-Cluster Variation (TWCV) and to cluster centroids incrementally whenever the mutation probability is small. IGKA inherits the salient feature of FGKA of always converging to the global optimum. C program is freely available at http://database.cs.wayne.edu/proj/FGKA/index.htm.

Conclusions
Our experiments indicate that, while the IGKA algorithm has a convergence pattern similar to FGKA, it has a better time performance when the mutation probability decreases to some point. Finally, we used IGKA to cluster a yeast dataset and found that it increased the enrichment of genes of similar function within the cluster.
The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)
Authors: Le Novère Nicolas , Donizelli Marco 
Published: November 2004

Abstract
Background
DopaNet http://www.dopanet.org is a Systems Biology initiative that aims to investigate precisely and quantitatively all the aspects of neurotransmission in a specific neuronal system, the mesotelencephalic dopamine system. The project should lead to large-scale models of molecular and cellular processes involved in neuronal signaling. A prerequisite is the proper storage of knowledge coming from the literature.

Methods
DopaNet Molecular Pages are highly structured descriptions of quantitative parameters related to a specific molecular complex involved in neuronal signal processing. A Molecular Page is built by maintainers who are experts in the field, and responsible for the quality of the page content. Each piece of data is identified by a specific ontology code, annotated (method of acquisition, species, etc.) and linked to the relevant bibliography. The Molecular Pages are stored as XML files, and processed through the DopaNet Web Service, which provides functionalities to edit the Molecular Pages, to cross-link the Pages and generate the public display, and to search them.

Conclusions
DopaNet Molecular Pages are one of the core resources of the DopaNet project but should be of widespread utility in the field of Systems Neurobiology.
An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution
Authors: Glusman Gustavo , Kaur Amardeep , Hood Leroy , Rowen Lee 
Published: November 2004

Abstract
Background
The runt domain transcription factors are key regulators of developmental processes in bilaterians, involved both in cell proliferation and differentiation, and their disruption usually leads to disease. Three runt domain genes have been described in each vertebrate genome (the RUNX gene family), but only one in other chordates. Therefore, the common ancestor of vertebrates has been thought to have had a single runt domain gene.

Results
Analysis of the genome draft of the fugu pufferfish (Takifugu rubripes) reveals the existence of a fourth runt domain gene, FrRUNT, in addition to the orthologs of human RUNX1, RUNX2 and RUNX3. The tiny FrRUNT packs six exons and two putative promoters in just 3 kb of genomic sequence. The first exon is located within an intron of FrSUPT3H, the ortholog of human SUPT3H, and the first exon of FrSUPT3H resides within the first intron of FrRUNT. The two gene structures are therefore "interlocked". In the human genome, SUPT3H is instead interlocked with RUNX2. FrRUNT has no detectable ortholog in the genomes of mammals, birds or amphibians. We consider alternative explanations for an apparent contradiction between the phylogenetic data and the comparison of the genomic neighborhoods of human and fugu runt domain genes. We hypothesize that an ancient RUNT locus was lost in the tetrapod lineage, together with FrFSTL6, a member of a novel family of follistatin-like genes.

Conclusions
Our results suggest that the runt domain family may have started expanding in chordates much earlier than previously thought, and exemplify the importance of detailed analysis of whole-genome draft sequence to provide new insights into gene evolution.
The use of Open Reading frame ESTs (ORESTES) for analysis of the honey bee transcriptome
Authors: Nunes Francis MF , Valente Valeria , Sousa Josane F , Cunha Marco AV , Pinheiro Daniel G , Maia Rafaela M , Araujo Daniela D , Costa Maria CR , Martins Waleska K , Carvalho Alex F , Monesi Nadia , Nascimento Adriana M , Peixoto Pablo MV , Silva Maria FR , Ramos Ricardo GP , Reis Luis FL , Dias-Neto Emmanuel , Souza Sandro J , Simpson Andrew JG , Zago Marco A , Soares Ademilson EE , Bitondi Marcia MG , Espreafico Enilza M , Espindola Foued S , Paco-Larson Maria L , Simoes Zila LP , Hartfelder Klaus , Silva Wilson A 
Published: November 2004

Abstract
Background
The ongoing efforts to sequence the honey bee genome require additional initiatives to define its transcriptome. Towards this end, we employed the Open Reading frame ESTs (ORESTES) strategy to generate profiles for the life cycle of Apis mellifera workers.

Results
Of the 5,021 ORESTES, 35.2% matched with previously deposited Apis ESTs. The analysis of the remaining sequences defined a set of putative orthologs whose majority had their best-match hits with Anopheles and Drosophila genes. CAP3 assembly of the Apis ORESTES with the already existing 15,500 Apis ESTs generated 3,408 contigs. BLASTX comparison of these contigs with protein sets of organisms representing distinct phylogenetic clades revealed a total of 1,629 contigs that Apis mellifera shares with different taxa. Most (41%) represent genes that are in common to all taxa, another 21% are shared between metazoans (Bilateria), and 16% are shared only within the Insecta clade. A set of 23 putative genes presented a best match with human genes, many of which encode factors related to cell signaling/signal transduction. 1,779 contigs (52%) did not match any known sequence. Applying a correction factor deduced from a parallel analysis performed with Drosophila melanogaster ORESTES, we estimate that approximately half of these no-match ESTs contigs (22%) should represent Apis-specific genes.

Conclusions
The versatile and cost-efficient ORESTES approach produced minilibraries for honey bee life cycle stages. Such information on central gene regions contributes to genome annotation and also lends itself to cross-transcriptome comparisons to reveal evolutionary trends in insect genomes.
Thymus-derived glucocorticoids are insufficient for normal thymus homeostasis in the adult mouse
Authors: Pruett Stephen B , Padgett Eric L 
Published: November 2004

Abstract
Background
It is unclear if thymus-derived glucocorticoids reach sufficient local concentrations to support normal thymus homeostasis, or if adrenal-derived glucocorticoids from the circulation are required. Modern approaches to this issue (transgenic mice that under or over express glucocorticoid receptor in the thymus) have yielded irreconcilably contradictory results, suggesting fundamental problems with one or more the transgenic mouse strains used. In the present study, a more direct approach was used, in which mice were adrenalectomized with or without restoration of circulating corticosterone using timed release pellets. Reversal of the increased number of thymocytes caused by adrenalectomy following restoration of physiological corticosterone concentrations would indicate that corticosterone is the major adrenal product involved in thymic homeostasis.

Results
A clear relationship was observed between systemic corticosterone concentration, thymus cell number, and percentage of apoptotic thymocytes. Physiological concentrations of corticosterone in adrenalectomized mice restored thymus cell number to normal values and revealed differential sensitivity of thymocyte subpopulations to physiological and stress-inducible corticosterone concentrations.

Conclusion
This indicates that thymus-derived glucocorticoids are not sufficient to maintain normal levels of death by neglect in the thymus, but that apoptosis and possibly other mechanisms induced by physiological, non stress-induced levels of adrenal-derived corticosterone are responsible for keeping the total number of thymocytes within the normal range.
A common genetic factor underlies hypertension and other cardiovascular disorders
Authors: Williams Frances MK , Cherkas Lynn F , Spector Tim D , MacGregor Alex J 
Published: November 2004

Abstract
Background
Certain conditions characterised by blood vessel occlusion or vascular spasm have been found to cluster together in epidemiological studies. However the biological causes for these associations remain controversial. This study used a classical twin design to examine whether these conditions are linked through shared environmental exposures or by a common underlying genetic propensity to vasospasm.

Methods
We investigated the association between hypertension, migraine, Raynaud's phenomenon and coronary artery disease in twins from a national register. Phenotype status was determined using a questionnaire and the genetic and environmental association between phenotypes was estimated through variance components analysis.

Results
Responses were obtained from 2,204 individuals comprising 525 monozygotic and 577 dizygotic pairs. There was a significant genetic contribution to all four traits with heritabilities ranging from 0.34 to 0.64. Multivariate model-fitting demonstrated that a single common genetic factor underlies the four conditions.

Conclusions
We have confirmed an association between hypertension, migraine, Raynaud's phenomenon and coronary artery disease, and shown that a single genetic factor underlies them. The demonstration of a shared genetic factor explains the association between them and adds weight to the theory of an inherited predisposition to vasospasm.
Elevated serum procollagen type III peptide in splanchnic and peripheral circulation of patients with inflammatory bowel disease submitted to surgery
Authors: De Simone Matilde , Cioffi Ugo , Contessini-Avesani Ettore , Oreggia Barbara , Paliotti Roberta , Pierini Alberto , Bolla Gianni , Oggiano Elide , Ferrero Stefano , Magrini Fabio , Ciulla Michele M 
Published: November 2004

Abstract
Background
In the hypothesis that the increased collagen metabolism in the intestinal wall of patients affected by inflammatory bowel disease (IBD) is reflected in the systemic circulation, we aimed the study to evaluate serum level of procollagen III peptide (PIIIP) in peripheral and splanchnic circulation by a commercial radioimmunoassay of patients with different histories of disease.

Methods
Twenty-seven patients, 17 with Crohn and 10 with ulcerative colitis submitted to surgery were studied. Blood samples were obtained before surgery from a peripheral vein and during surgery from the mesenteric vein draining the affected intestinal segment. Fifteen healthy age and sex matched subjects were studied to determine normal range for peripheral PIIIP.

Results
In IBD patients peripheral PIIIP level was significantly higher if compared with controls (5.0 ± 1.9 vs 2.7 ± 0.7 μg/l; p = 0.0001); splanchnic PIIIP level was 5.5 ± 2.6 μg/l showing a positive gradient between splanchnic and peripheral concentrations of PIIIP. No significant differences between groups nor correlations with patients' age and duration of disease were found.

Conclusions
We provide evidence that the increased local collagen metabolism in active IBD is reflected also in the systemic circulation irrespective of the history of the disease, suggesting that PIIIP should be considered more appropiately as a marker of the activity phases of IBD.
Lipoprotein lipase in hemodialysis patients: indications that low molecular weight heparin depletes functional stores, despite low plasma levels of the enzyme
Authors: Näsström Birgit , Stegmayr Bernd , Olivecrona Gunilla , Olivecrona Thomas 
Published: November 2004

Abstract
Background
Lipoprotein lipase (LPL) has a central role in the catabolism of triglyceride-rich lipoproteins. The enzyme is anchored to the vascular endothelium through interaction with heparan sulphate proteoglycans and is displaced from this interaction by heparin. When heparin is infused, there is a peak of LPL activity accompanied by a reduction in triglycerides (TG) during the first hour, followed by a decrease in LPL activity to a stable plateau during the remaining session while TG increase towards and beyond baseline. This suggests that tissue stores of LPL become depleted. It has been argued that low molecular weight (LMW) heparins cause less disturbance of the LPL system than conventional heparin does.

Methods
We have followed LPL activity and TG during a dialysis-session with a LMW heparin (dalteparin) using the same patients and regime as in a previous study with conventional heparin, i.e. a primed infusion.

Results
The shape of the curve for LPL activity resembled that during the earlier dialyses with conventional heparin, but the values were lower during dialysis with dalteparin. The area under the curve for LPL activity during the peak period (0–180 minutes) was only 27% and for the plateau period (180–240 minutes) it was only 36% of that observed with conventional heparin (p < 0.01). These remarkably low plasma LPL activities prompted us to re-analyze LPL activity and to measure LPL mass in frozen samples from our earlier studies. There was excellent correlation between the new and old values which rules out the possibility of assay variations as a confounding factor. TG increased from 2.14 mmol/L before, to 2.59 mmol/L after the dialysis (p < 0.01). From 30 minutes on, the TG values were significantly higher after dalteparin compared to conventional heparin (p < 0.05).

Conclusion
These results indicate that LMW heparins disturb the LPL system as much or more than conventional heparin does.