bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conceptualizing and Measuring Historical Trauma Among American Indian People
Authors: Whitbeck Les B. , Adams Gary W. , Hoyt Dan R. , Chen Xiaojin 
Published: May 2004

AbstractThis article reports on the development of two measures relating to historical trauma among American Indian people: The Historical Loss Scale and The Historical Loss Associated Symptoms Scale. Measurement characteristics including frequencies, internal reliability, and confirmatory factor analyses were calculated based on 143 American Indian adult parents of children aged 10 through 12 years who are part of an ongoing longitudinal study of American Indian families in the upper Midwest. Results indicate both scales have high internal reliability. Frequencies indicate that the current generation of American Indian adults have frequent thoughts pertaining to historical losses and that they associate these losses with negative feelings. Two factors of the Historical Loss Associated Symptoms Scale indicate one anxiety/depression component and one anger/avoidance component. The results are discussed in terms of future research and theory pertaining to historical trauma among American Indian people.
You Can't Get There from Here: Identifying Process Routes to Replication
Authors: Primavera Judy 
Published: May 2004

AbstractAll too often the reports of our community research and action are presented in an ahistorical and decontextualized fashion focused more on the content of what was done than on the process of how the work was done and why. The story of the university–community partnership and the family literacy intervention that was developed illustrates the importance of several key process variables in project development and implementation. More specifically, the role of the social–ecological context, prehistory, personality, self‐correction, and unexpected serendipitous events are discussed. If, as community psychologists, we are serious about conducting our work in the most efficient and effective manner possible, if we truly wish to make our work available for replication, and if we seek to develop standards of “best practice” that are meaningful, our communication regarding process must shift from the anecdotal to a position of central importance.
On Community Leadership: Stories About Collaboration in Action Research
Authors: Kelly James G. , Azelton L. Sean , Lardon Cecile , Mock Lynne O. , Tandon S. Darius , Thomas Mamie 
Published: May 2004

AbstractThis article provides an account of a 10‐year collaborative documentation of community leadership in an African American community on the South side of Chicago. The stories are oriented to several critical incidents in the life course of the collaboration. They are told from the perspectives of one university professor, four graduate students, and one community leader. Together they provide an account of how this research was shaped by the interactions of the research team with members of the community, how research questions emerged, methodologies were developed, ways of gathering data were tried and tested, and interpretations of data unfolded. Special attention is given to the ways in which the process and products of this research contributed to the community's own process of leadership development. The stories also discuss the various roles participants in this collaboration played both in the academic arena and in the community, and how they experienced gender, race, nationality, and social status.
Beyond the Frontstage: Trust, Access, and the Relational Context in Research with Refugee Communities
Authors: Miller Kenneth E. 
Published: May 2004

AbstractThis paper examines the role of trust and the concept of access as they affect the relational context in which community research, and research with refugee communities in particular, is conducted. Sociologist Irving Goffman's metaphor of frontstage and backstage behavior is used to illustrate the complexity and importance of developing of relations of trust, and thereby gaining “backstage” access, in communities that are generally closed to outsiders. It is argued that gaining authentic (“backstage”) access to refugee communities, as well as other communities that have developed a self‐protective insularity, is essential if we are to gather data that accurately reflect the actual beliefs, feelings, and experiences of community members. The paper then examines the puzzling lack of discussion regarding issues of trust, access, and the relational context in the literature on refugee mental health. Explanations for this apparent inattention are sought in the influence of the prevailing scientific paradigm that guides most research with refugees, and that shapes the values of the field's “gatekeepers,” the editors and reviewers of scholarly journals. Throughout the paper, key points are illustrated with examples drawn from the author's research with refugees from Guatemala, Bosnia, and Afghanistan.
Gene co-expression network topology provides a framework for molecular characterization of cellular state
Authors: Carter Scott L. , Brechbühler Christian M. , Griffin Michael , Bond Andrew T. 
Published: May 2004

Abstract
Motivation: Gene expression data have become an instrumental resource in describing the molecular state associated with various cellular phenotypes and responses to environmental perturbations. The utility of expression profiling has been demonstrated in partitioning clinical states, predicting the class of unknown samples and in assigning putative functional roles to previously uncharacterized genes based on profile similarity. However, gene expression profiling has had only limited success in identifying therapeutic targets. This is partly due to the fact that current methods based on fold-change focus only on single genes in isolation, and thus cannot convey causal information. In this paper, we present a technique for analysis of expression data in a graph-theoretic framework that relies on associations between genes. We describe the global organization of these networks and biological correlates of their structure. We go on to present a novel technique for the molecular characterization of disparate cellular states that adds a new dimension to the fold-based methods and conclude with an example application to a human medulloblastoma dataset.
Results: We have shown that expression networks generated from large model-organism expression datasets are scale-free and that the average clustering coefficient of these networks is several orders of magnitude higher than would be expected for similarly sized scale-free networks, suggesting an inherent hierarchical modularity similar to that previously identified in other biological networks. Furthermore, we have shown that these properties are robust with respect to the parameters of network construction. We have demonstrated an enrichment of genes having lethal knockout phenotypes in the high-degree (i.e. hub) nodes in networks generated from aggregate condition datasets; using process-focused Saccharomyces cerivisiae datasets we have demonstrated additional high-degree enrichments of condition-specific genes encoding proteins known to be involved in or important for the processes interrogated by the microarrays. These results demonstrate the utility of network analysis applied to expression data in identifying genes that are regulated in a state-specific manner. We concluded by showing that a sample application to a human clinical dataset prominently identified a known therapeutic target.
Availability: Software implementing the methods for network generation presented in this paper is available for academic use by request from the authors in the form of compiled linux binary executables.
Analyzing time series gene expression data
Authors: Bar-Joseph Ziv 
Published: May 2004

Abstract
Motivation: Time series expression experiments are an increasingly popular method for studying a wide range of biological systems. However, when analyzing these experiments researchers face many new computational challenges. Algorithms that are specifically designed for time series experiments are required so that we can take advantage of their unique features (such as the ability to infer causality from the temporal response pattern) and address the unique problems they raise (e.g. handling the different non-uniform sampling rates).
Results: We present a comprehensive review of the current research in time series expression data analysis. We divide the computational challenges into four analysis levels: experimental design, data analysis, pattern recognition and networks. For each of these levels, we discuss computational and biological problems at that level and point out some of the methods that have been proposed to deal with these issues. Many open problems in all these levels are discussed. This review is intended to serve as both, a point of reference for experimental biologists looking for practical solutions for analyzing their data, and a starting point for computer scientists interested in working on the computational problems related to time series expression analysis.
Incremental generation of summarized clustering hierarchy for protein family analysis
Authors: Chen Chien-Yu , Oyang Yen-Jen , Juan Hsueh-Fen 
Published: May 2004

Abstract
Motivation: Protein sequence clustering has been widely exploited to facilitate in-depth analysis of protein functions and families. For some applications of protein sequence clustering, it is highly desirable that a hierarchical structure, also referred to as dendrogram, which shows how proteins are clustered at various levels, is generated. However, as the sizes of contemporary protein databases continue to grow at rapid rates, it is of great interest to develop some summarization mechanisms so that the users can browse the dendrogram and/or search for the desired information more effectively.
Results: In this paper, the design of a novel incremental clustering algorithm aimed at generating summarized dendrograms for analysis of protein databases is described. The proposed incremental clustering algorithm employs a statistics-based model to summarize the distributions of the similarity scores among the proteins in the database and to control formation of clusters. Experimental results reveal that, due to the summarization mechanism incorporated, the proposed incremental clustering algorithm offers the users highly concise dendrograms for analysis of protein clusters with biological significance. Another distinction of the proposed algorithm is its incremental nature. As the sizes of the contemporary protein databases continue to grow at fast rates, due to the concern of efficiency, it is desirable that cluster analysis of a protein database can be carried out incrementally, when the protein database is updated. Experimental results with the Swiss-Prot protein database reveal that the time complexity for carrying out incremental clustering with k new proteins added into the database containing n proteins is O(n2βlogn), where β ≅ 0.865, provided that k ≪ n.
Availability: The Linux executable is available on the following supplementary page.
Supplementary information: http://mars.csie.ntu.edu.tw/~cychen/protein_clustering/psc.htm
Distribution of information in biomedical abstracts and full-text publications
Authors: Schuemie M. J. , Weeber M. , Schijvenaars B. J. A. , van Mulligen E. M. , van der Eijk C. C. , Jelier R. , Mons B. , Kors J. A. 
Published: May 2004

Abstract
Motivation: Full-text documents potentially hold more information than their abstracts, but require more resources for processing. We investigated the added value of full text over abstracts in terms of information content and occurrences of gene symbol—gene name combinations that can resolve gene-symbol ambiguity.
Results: We analyzed a set of 3902 biomedical full-text articles. Different keyword measures indicate that information density is highest in abstracts, but that the information coverage in full texts is much greater than in abstracts. Analysis of five different standard sections of articles shows that the highest information coverage is located in the results section. Still, 30–40% of the information mentioned in each section is unique to that section. Only 30% of the gene symbols in the abstract are accompanied by their corresponding names, and a further 8% of the gene names are found in the full text. In the full text, only 18% of the gene symbols are accompanied by their gene names.
GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms
Authors: Smid Marcel , Dorssers Lambert C. J. 
Published: May 2004

Abstract
Motivation: Retrieval of information on biological processes from large-scale expression data is still a time-consuming task. An automated analysis utilizing all expression information would greatly increase our understanding of the samples under study.
Results: We describe here a novel method to obtain a functional analysis of complex gene expression data. Instead of applying a predefined expression threshold, Gene Ontology (GO) terms are weighted using the actual measured levels of expression of all associated genes. Based on this concept, the application GO-Mapper was developed to quantitatively link gene expression levels to GO-terms for multiple experiments in an automated way. The applicability of GO-Mapper was developed and validated on in house and public human microarray data and mouse SAGE data. We demonstrate that the GO-Mapper allows for interrelating relevant biological functions with the experiments under study.
Availability: The GO-Mapper application is free of charge available from our website.
Supplementary information: http://www.erasmusmc.nl/gatcplatform
THEA: ontology-driven analysis of microarray data
Authors: Pasquier C. , Girardot F. , Jevardat de Fombelle K. , Christen R. 
Published: May 2004

Abstract
Motivation: Microarray technology makes it possible to measure thousands of variables and to compare their values under hundreds of conditions. Once microarray data are quantified, normalized and classified, the analysis phase is essentially a manual and subjective task based on visual inspection of classes in the light of the vast amount of information available. Currently, data interpretation clearly constitutes the bottleneck of such analyses and there is an obvious need for tools able to fill the gap between data processed with mathematical methods and existing biological knowledge.
Results: THEA (Tools for High-throughput Experiments Analysis) is an integrated information processing system allowing convenient handling of data. It allows to automatically annotate data issued from classification systems with selected biological information coming from a knowledge base and to either manually search and browse through these annotations or automatically generate meaningful generalizations according to statistical criteria (data mining).
Availability: The software is available on the website http://thea.unice.fr/
Supplementary information: Supplementary tables as well as files containing the biological data used in this publication can be downloaded from our website http://bioinfo.unice.fr/publications/thea_article/
Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins
Authors: Kinjo Akira R. , Nishikawa Ken 
Published: May 2004

Abstract
Summary: The pattern of amino acid substitutions and sequence conservation over many structure-based alignments of protein sequences was analyzed as a function of percentage sequence identity. The statistics of the amino acid substitutions were converted into the form of log-odds amino acid substitution matrices to which eigenvalue decomposition was applied. It was found that the most important component of the substitution matrices exhibited a sharp transition at the sequence identity of 30–35%, which coincides with the twilight zone. Above the transition point, the most dominant component is related to the mutability of amino acids and it acts to disfavor any substitutions, whereas below the transition point, the most dominant component is related to the hydrophobicity of amino acids and substitutions between residues of similar hydrophobic character are positively favored. Implications for protein evolution and sequence analysis are discussed.
Supplementary information: http://maccl01.genes.nig.ac.jp/~akinjo/aasm/
A collaborative database of inbred mouse strain characteristics
Authors: Grubb Stephen C. , Churchill Gary A. , Bogue Molly A. 
Published: May 2004

Abstract
Summary: A database and website (MPD: Mouse Phenome Database) have been developed to serve as a consolidated home for mouse strain characterization data being generated by the scientific community. Physiological, anatomical and behavioral data are being collected and integrated into a common framework for tabulation by strain and sex. Genotypic data are being collected as well. The current focus is on a set of 40 inbred strains. The MPD as of February 2004 contains approximately 500 phenotypic parameters relevant to human health, voluntarily contributed by several dozen investigators and laboratories.
Availability: http://www.jax.org/phenome
Supplementary information: Guidelines for investigators who may be interested in contributing data are available at http://aretha.jax.org/phenome/dataguide.html
Lucy2: an interactive DNA sequence quality trimming and vector removal tool
Authors: Li Song , Chou Hui-Hsien 
Published: May 2004

Abstract
Summary: Lucy2 is a raw DNA sequence trimming and visualization tool based on the popular command-line Lucy1. Users can change parameters, trim multiple sequences and visualize the results within an integrated, easy-to-use graphical user interface. Lucy2 is designed specifically for non-programmers to use, and is currently available on Windows, Linux and MacOS X. Source code is also available for porting to the other platforms.
Availability: Lucy2 is distributed under the GNU General Public License and can be downloaded from www.complex.iastate.edu
WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA
Authors: Bi Chengpeng , Benham Craig J. 
Published: May 2004

Abstract
Summary: WebSIDD is a Web-based service designed to predict locations and extents of stress-induced duplex destabilization (SIDD) that occur in a double-stranded DNA molecule of specified base sequence, on which a specified level of superhelical stress is imposed. The algorithm calculates the approximate equilibrium statistical mechanical distribution of a population of identical molecules among its accessible states. The user inputs the DNA sequence, and the program outputs the calculated transition probability and destabilization energy of each base pair in the sequence. As options, the user can specify the temperature and the level of superhelicity. The values of all structural and energy parameters used in the calculation have been experimentally measured. WebSIDD should prove useful for finding SIDD-susceptible sites in genomic sequences, and correlating their occurrence with locations involved in regulatory and pathological processes. This strategy already has illuminated the roles of SIDD in diverse biological regulatory processes, including transcriptional initiation and termination, and the eukaryotic nuclear scaffold attachments that partition chromosomes into domains.
Availability: http://orange.genomecenter.ucdavis.edu/benham/sidd/index.html
Triacylglycerol accumulation in human obesity and type 2 diabetes is associated with increased rates of skeletal muscle fatty acid transport and increased sarcolemmal FAT/CD36
Authors: Bonen Arend , Parolin Michelle L. , Steinberg Gregory R. , Calles‐Escandon Jorge , Tandon Narendra N. , Glatz Jan F. C. , Luiken Joost J. F. P. , Heigenhauser George. J. F. , Dyck David J. 
Published: May 2004

ABSTRACTWe examined whether, in human obesity and type 2 diabetes, long chain fatty acid (LCFA) transport into skeletal muscle is upregulated and contributes to an excess intramuscular triacylglycerol accumulation. In giant sarcolemmal vesicles prepared from human skeletal muscle, LCFA transport rates were upregulated ~4‐fold and were associated with an increased intramuscular triacylglycerol content in obese individuals and in type 2 diabetics. In these individuals, the increased sarcolemmal LCFA transport rate was not associated with an altered expression of FAT/CD36 or FABPpm. Instead, the increase in the LCFA transport rate was associated with an increase in sarcolemmal FAT/CD36 but not sarcolemmal FABPpm. Rates of fatty acid esterification were increased threefold in isolated human muscle strips obtained from obese subjects, while concomitantly rates of fatty acid oxidation were not altered. Thus, the increased rate of fatty acid transport may contribute to the increased rates of triacylglycerol accumulation in human skeletal muscle. The altered FAT/CD36 trafficking in muscle from obese subjects and type 2 diabetics juxtaposes the known alterations in GLUT4 trafficking, i.e., GLUT4 is known to be retained in its intracellular depots while FAT/CD36 is retained at the sarcolemma. This redistribution of FAT/CD36 to the sarcolemma may contribute to the etiology of insulin resistance in human muscle, and hence, FAT/CD36 provides another potential therapeutic target for the prevention and/or treatment of insulin resistance.
Structurally different RGTAs modulate collagen‐type expression by cultured aortic smooth muscle cells via different pathways involving fibroblast growth factor‐2 or transforming growth factor‐β1
Authors: Alexakis Catherine , Mestries Patricia , Garcia Stéphanie , Petit Emmanuel , Barbier Véronique , Papy‐Garcia Dulce , Sagot Marie‐Astride , Barritault Denis , Caruelle Jean Pierre , Kern Patrick 
Published: May 2004

ABSTRACTWe have engineered polymers called ReGeneraTing Agents (RGTAs), which mimic the protecting and potentiating properties of heparan sulfates toward heparin‐binding growth factors (HBGF). RGTAs have been shown to optimize cell growth and regulate collagen production in vitro. Here, we studied relationships between RGTA structure and collagen‐type expression in aortic smooth muscle cells by using two RGTAs, the carboxylmethylsulfate dextran RG‐1503 and the carboxylmethylsulfate dextran with added benzylamide RG‐1192. RG‐1192 specifically induced a fivefold decrease in collagen III synthesis. This effect was abolished by FGF‐2 neutralizing antibody. RG‐1192 and FGF‐2 acted synergistically to decrease collagen III. RG‐ 1192 was more effective than heparin in this process. RG‐1192 increased the pericellular localization of FGF‐2 and protected FGF‐2 from proteolysis. Surface plasmon resonance analysis indicated a Kd of 15.7 nM for the RG‐1192/FGF‐2 interaction (10.6 nM for the heparin/FGF‐2 interaction). The structurally different RG‐1503 (without benzylamide) did not interact with FGF‐2 and worked synergistically with TGF‐β1 to specifically induce a twofold increase in collagen V. RGTAs with different structures exert different modulating effects on the collagen phenotype. Selection of appropriate RGTAs, which had been shown to enhance in vivo tissue repair, may provide a mean of correcting collagen abnormalities in vascular disorders and more generally in fibrotic diseases.