bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying biological concepts from a protein-related corpus with a probabilistic topic model
Authors: Zheng Bin , McLean David C , Lu Xinghua 
Published: February 2006

Abstract

Background
Biomedical literature, e.g., MEDLINE, contains a wealth of knowledge regarding functions of proteins. Major recurring biological concepts within such text corpora represent the domains of this body of knowledge. The goal of this research is to identify the major biological topics/concepts from a corpus of protein-related MEDLINE© titles and abstracts by applying a probabilistic topic model.

Results
The latent Dirichlet allocation (LDA) model was applied to the corpus. Based on the Bayesian model selection, 300 major topics were extracted from the corpus. The majority of identified topics/concepts was found to be semantically coherent and most represented biological objects or concepts. The identified topics/concepts were further mapped to the controlled vocabulary of the Gene Ontology (GO) terms based on mutual information.

Conclusion
The major and recurring biological concepts within a collection of MEDLINE documents can be extracted by the LDA model. The identified topics/concepts provide parsimonious and semantically-enriched representation of the texts in a semantic space with reduced dimensionality and can be used to index text.
BAMarray™: Java software for Bayesian analysis of variance for microarray data
Authors: Ishwaran Hemant , Rao J Sunil , Kogalur Udaya B 
Published: February 2006

AbstractBackgroundDNA microarrays open up a new horizon for studying the genetic determinants of disease. The high throughput nature of these arrays creates an enormous wealth of information, but also poses a challenge to data analysis. Inferential problems become even more pronounced as experimental designs used to collect data become more complex. An important example ismultigroup datacollected over different experimental groups, such as data collected from distinct stages of a disease process. We have developed a method specifically addressing these issues termed Bayesian ANOVA for microarrays (BAM). The BAM approach uses a special inferential regularization known as spike-and-slab shrinkage that provides an optimal balance between total false detections and total false non-detections. This translates into more reproducible differential calls. Spike and slab shrinkage is a form of regularization achieved by using information across all genes and groups simultaneously.ResultsBAMarray™ is a graphically oriented Java-based software package that implements the BAM method for detecting differentially expressing genes in multigroup microarray experiments (up to 256 experimental groups can be analyzed). Drop-down menus allow the user to easily select between different models and to choose various run options. BAMarray™ can also be operated in a fully automated mode with preselected run options. Tuning parameters have been preset at theoretically optimal values freeing the user from such specifications. BAMarray™ provides estimates for gene differential effects and automatically estimates data adaptive, optimal cutoff values for classifying genes into biological patterns of differential activity across experimental groups. A graphical suite is a core feature of the product and includes diagnostic plots for assessing model assumptions and interactive plots that enable tracking of prespecified gene lists to study such things as biological pathway perturbations. The user can zoom in and lasso genes of interest that can then be saved for downstream analyses.ConclusionBAMarray™ is user friendly platform independent software that effectively and efficiently implements the BAM methodology. Classifying patterns of differential activity is greatly facilitated by a data adaptive cutoff rule and a graphical suite. BAMarray™ is licensed software freely available to academic institutions. More information can be found athttp://www.bamarray.com.
JLIN: A java based linkage disequilibrium plotter
Authors: Carter Kim W , McCaskie Pamela A , Palmer Lyle J 
Published: February 2006

Abstract

Background
A great deal of effort and expense are being expended internationally in attempts to detect genetic polymorphisms contributing to susceptibility to complex human disease. Techniques such as Linkage Disequilibrium mapping are being increasingly used to examine and compare markers across increasingly large datasets. Visualisation techniques are becoming essential to analyse the ever-growing volume of data and results available with any given analysis.

Results
JLIN (Java LINkage disequilibrium plotter) is a software package designed for customisable, intuitive visualisation of Linkage Disequilibrium (LD) across all common computing platforms. Customisation allows the user to choose particular visualisations, statistical measures and measurement ranges. JLIN also allows the user to export images of the LD visualisation in several common document formats.

Conclusion
JLIN allows the user to visually compare and contrast the results of a range of statistical measures on the input dataset(s). These measures include the commonly used D' and r2 statistics and empirical p-values. JLIN has a number of unique and novel features that improve on existing LD visualisation tools.
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
Authors: Stanke Mario , Schöffmann Oliver , Morgenstern Burkhard , Waack Stephan 
Published: February 2006

Abstract

Background
In order to improve gene prediction, extrinsic evidence on the gene structure can be collected from various sources of information such as genome-genome comparisons and EST and protein alignments. However, such evidence is often incomplete and usually uncertain. The extrinsic evidence is usually not sufficient to recover the complete gene structure of all genes completely and the available evidence is often unreliable. Therefore extrinsic evidence is most valuable when it is balanced with sequence-intrinsic evidence.

Results
We present a fairly general method for integration of external information. Our method is based on the evaluation of hints to potentially protein-coding regions by means of a Generalized Hidden Markov Model (GHMM) that takes both intrinsic and extrinsic information into account. We used this method to extend the ab initio gene prediction program AUGUSTUS to a versatile tool that we call AUGUSTUS+. In this study, we focus on hints derived from matches to an EST or protein database, but our approach can be used to include arbitrary user-defined hints. Our method is only moderately effected by the length of a database match. Further, it exploits the information that can be derived from the absence of such matches. As a special case, AUGUSTUS+ can predict genes under user-defined constraints, e.g. if the positions of certain exons are known. With hints from EST and protein databases, our new approach was able to predict 89% of the exons in human chromosome 22 correctly.

Conclusion
Sensitive probabilistic modeling of extrinsic evidence such as sequence database matches can increase gene prediction accuracy. When a match of a sequence interval to an EST or protein sequence is used it should be treated as compound information rather than as information about individual positions.
Polyphyly of the hawk genera Leucopternis and Buteogallus (Aves, Accipitridae): multiple habitat shifts during the Neotropical buteonine diversification
Authors: do Amaral Fabio S Raposo , Miller Matthew J , Silveira Luís Fábio , Bermingham Eldredge , Wajntal Anita 
Published: February 2006

AbstractBackgroundThe family Accipitridae (hawks, eagles and Old World vultures) represents a large radiation of predatory birds with an almost global distribution, although most species of this family occur in the Neotropics. Despite great morphological and ecological diversity, the evolutionary relationships in the family have been poorly explored at all taxonomic levels. Using sequences from four mitochondrial genes (12S, ATP8, ATP6, and ND6), we reconstructed the phylogeny of the Neotropical forest hawk genusLeucopternisand most of the allied genera of Neotropical buteonines. Our goals were to infer the evolutionary relationships among species ofLeucopternis, estimate their relationships to other buteonine genera, evaluate the phylogenetic significance of the white and black plumage patterns common to mostLeucopternisspecies, and assess general patterns of diversification of the group with respect to species' affiliations with Neotropical regions and habitats.ResultsOur molecular phylogeny for the genusLeucopternisand its allies disagrees sharply with traditional taxonomic arrangements for the group, and we present new hypotheses of relationships for a number of species. The mtDNA phylogenetic trees derived from analysis of the combined data posit a polyphyletic relationship among species ofLeucopternis,ButeogallusandButeo. Three highly supported clades containingLeucopternisspecies were recovered in our phylogenetic reconstructions. The first clade consisted of the sister pairsL. lacernulatusandButeogallus meridionalis, andButeogallus urubitingaandHarpyhaliaetus coronatus, in addition toL. schistaceusandL. plumbeus. The second clade included the sister pairLeucopternis albicollisandL. occidentalisas well asL. polionotus. The third lineage comprised the sister pairL. melanopsandL. kuhli, in addition toL. semiplumbeusandButeo buteo. According to our results, the white and black plumage patterns have evolved at least twice in the group. Furthermore, species found to the east and west of the Andes (cis-Andean andtrans-Andean, respectively) are not reciprocally monophyletic, nor are forest and non-forest species.ConclusionThe polyphyly ofLeucopternis,ButeogallusandButeoestablishes a lack of concordance of current Accipitridae taxonomy with the mtDNA phylogeny for the group, and points to the need for further phylogenetic analysis at all taxonomic levels in the family as also suggested by other recent analyses. Habitat shifts, as well ascis-andtrans-Andean disjunctions, took place more than once during buteonine diversification in the Neotropical region. Overemphasis of the black and white plumage patterns has led to questionable conclusions regarding the relationships ofLeucopternisspecies, and suggests more generally that plumage characters should be used with considerable caution in the taxonomic evaluation of the Accipitridae.
Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data
Authors: Sieh Weiva , Basu Saonli , Fu Audrey Q , Rothstein Joseph H , Scheet Paul A , Stewart William CL , Sung Yun J , Thompson Elizabeth A , Wijsman Ellen M 
Published: February 2006

Abstract
We performed multipoint linkage analysis of the electrophysiological trait ECB21 on chromosome 4 in the full pedigrees provided by the Collaborative Study on the Genetics of Alcoholism (COGA). Three Markov chain Monte Carlo (MCMC)-based approaches were applied to the provided and re-estimated genetic maps and to five different marker panels consisting of microsatellite (STRP) and/or SNP markers at various densities. We found evidence of linkage near the GABRB1 STRP using all methods, maps, and marker panels. Difficulties encountered with SNP panels included convergence problems and demanding computations.
Using mixture models to characterize disease-related traits
Authors: Duan Tao , Finch Stephen J , Ye Kenny Q , Chase Gary A , Mendell Nancy R 
Published: February 2006

AbstractWe consider 12 event-related potentials and one electroencephalogram measure as disease-related traits to compare alcohol-dependent individuals (cases) to unaffected individuals (controls). We use two approaches: 1) two-way analysis of variance (with sex and alcohol dependency as the factors), and 2) likelihood ratio tests comparing sex adjusted values of cases to controls assuming that within each group the trait has a 2 (or 3) component normal mixture distribution. In the second approach, we test the null hypothesis that the parameters of the mixtures are equal for the cases and controls. Based on the two-way analysis of variance, we find 1) males have significantly (p< 0.05) lower mean response values than females for 7 of these traits. 2) Alcohol-dependent cases have significantly lower mean response than controls for 3 traits. The mixture analysis of sex-adjusted values of 1 of these traits, the event-related potential obtained at the parietal midline channel (ttth4), found the appearance of a 3-component normal mixture in cases and controls. The mixtures differed in that the cases had significantly lower mean values than controls and significantly different mixing proportions in 2 of the 3 components. Implications of this study are: 1) Sex needs to be taken into account when studying risk factors for alcohol dependency to prevent finding a spurious association between alcohol dependency and the risk factor. 2) Mixture analysis indicates that for the event-related potential "ttth4", the difference observed reflects strong evidence of heterogeneity of response in both the cases and controls.
Many genes in fish have species-specific asymmetric rates of molecular evolution
Authors: Steinke Dirk , Salzburger Walter , Braasch Ingo , Meyer Axel 
Published: February 2006

Abstract

Background
Gene and genome duplication events increase the amount of genetic material that might then contribute to an increase in the genomic and phenotypic complexity of organisms during evolution. Thus, it has been argued that there is a relationship between gene copy number and morphological complexity and/or species diversity. This hypothesis implies that duplicated genes have subdivided or evolved novel functions compared to their pre-duplication proto-orthologs. Such a functional divergence might be caused by an increase in evolutionary rates in one ortholog, by changes in expression, regulatory evolution, insertion of repetitive elements, or due to positive Darwinian selection in one copy. We studied a set of 2466 genes that were present in Danio rerio, Takifugu rubripes, Tetraodon nigroviridis and Oryzias latipes to test (i) for forces of positive Darwinian selection; (ii) how frequently duplicated genes are retained, and (iii) whether novel gene functions might have evolved.

Results
25% (610) of all investigated genes show significantly smaller or higher genetic distances in the genomes of particular fish species compared to their human ortholog than their orthologs in other fish according to relative rate tests. We identified 49 new paralogous pairs of duplicated genes in fish, in which one of the paralogs is under positive Darwinian selection and shows a significantly higher rate of molecular evolution in one of the four fish species, whereas the other copy apparently did not undergo adaptive changes since it retained the original rate of evolution. Among the genes under positive Darwinian selection, we found a surprisingly high number of ATP binding proteins and transcription factors.

Conclusion
The significant rate difference suggests that the function of these rate-changed genes might be essential for the respective fish species. We demonstrate that the measurement of positive selection is a powerful tool to identify divergence rates of duplicated genes and that this method has the capacity to identify potentially interesting candidates for adaptive gene evolution.
Acceleration of epithelial cell syndecan-1 shedding by anthrax hemolytic virulence factors
Authors: Popova Taissia G , Millis Bryan , Bradburne Chris , Nazarenko Svetlana , Bailey Charles , Chandhoke Vikas , Popov Serguei G 
Published: February 2006

AbstractBackgroundIt has been recently reported that major pathogensStaphylococcus aureusandPseudomonas aeruginosaaccelerate a normal process of cell surface syndecan-1 (Synd1) ectodomain shedding as a mechanism of host damage due to the production of shedding-inducing virulence factors. We tested if acceleration of Synd1 shedding takes placein vitroupon treatment of epithelial cells withB. anthracishemolysins, as well asin vivoduring anthrax infection in mice.ResultsThe isolated anthrax hemolytic proteins AnlB (sphingomyelinase) and AnlO (cholesterol-binding pore-forming factor), as well as ClnA (B. cereushomolog ofB. anthracisphosphatidyl choline-preferring phospholipase C) cause accelerated shedding of Synd1 and E-cadherin from epithelial cells and compromise epithelial barrier integrity within a few hours. In comparison with hemolysins in a similar range of concentrations, anthrax lethal toxin (LT) also accelerates shedding albeit at slower rate. Individual components of LT, lethal factor and protective antigen are inactive with regard to shedding. Inhibition experiments favor a hypothesis that activities of tested bacterial shedding inducers converge on the stimulation of cytoplasmic tyrosine kinases of the Syk family, ultimately leading to activation of cellular sheddase. Both LT and AnlO modulate ERK1/2 and p38 MAPK signaling pathways, while JNK pathway seems to be irrelevant to accelerated shedding. Accelerated shedding of Synd1 also takes place in DBA/2 mice challenged withBacillus anthracis(Sterne) spores. Elevated levels of shed ectodomain are readily detectable in circulation after 24 h.ConclusionThe concerted acceleration of shedding by several virulence factors could represent a new pathogenic mechanism contributing to disruption of epithelial or endothelial integrity, hemorrhage, edema and abnormal cell signaling during anthrax infection.
An extremely rich repertoire of bursting patterns during the development of cortical cultures
Authors: Wagenaar Daniel A , Pine Jerome , Potter Steve M 
Published: February 2006

Abstract

Background
We have collected a comprehensive set of multi-unit data on dissociated cortical cultures. Previous studies of the development of the electrical activity of dissociated cultures of cortical neurons each focused on limited aspects of its dynamics, and were often based on small numbers of observed cultures. We followed 58 cultures of different densities – 3000 to 50,000 neurons on areas of 30 to 75 mm2 – growing on multi-electrode arrays (MEAs) during the first five weeks of their development.

Results
Plating density had a profound effect on development. While the aggregate spike detection rate scaled linearly with density, as expected from the number of cells in proximity to electrodes, dense cultures started to exhibit bursting behavior earlier in development than sparser cultures. Analysis of responses to electrical stimulation suggests that axonal outgrowth likewise occurred faster in dense cultures. After two weeks, the network activity was dominated by population bursts in most cultures. In contrast to previous reports, development continued with changing burst patterns throughout the observation period. Burst patterns were extremely varied, with inter-burst intervals between 1 and 300 s, different amounts of temporal clustering of bursts, and different firing rate profiles during bursts. During certain stages of development bursts were organized into tight clusters with highly conserved internal structure.

Conclusion
Dissociated cultures of cortical cells exhibited a much richer repertoire of activity patterns than previously reported. Except for the very sparsest cultures, all cultures exhibited globally synchronized bursts, but bursting patterns changed over the course of development, and varied considerably between preparations. This emphasizes the importance of using multiple preparations – not just multiple cultures from one preparation – in any study involving neuronal cultures.
These results are based on 963 half-hour-long recordings. To encourage further investigation of the rich range of behaviors exhibited by cortical cells in vitro, we are making the data available to other researchers, together with Matlab code to facilitate access.
The initial Mayo Clinic experience using high-frequency oscillatory ventilation for adult patients: a retrospective study
Authors: Finkielman Javier D , Gajic Ognjen , Farmer J Christopher , Afessa Bekele , Hubmayr Rolf D 
Published: February 2006

AbstractBackgroundHigh-frequency oscillatory ventilation (HFOV) was introduced in our institution in June 2003. Since then, there has been no protocol to guide the use of HFOV, and all decisions regarding ventilation strategies and settings of HFOV were made by the treating intensivist. The aim of this study is to report our first year of experience using HFOV.MethodsIn this retrospective study, we reviewed all 14 adult patients, who were consecutively ventilated with HFOV in the intensive care units of a tertiary medical center, from June 2003 to July 2004.ResultsThe mean age of the patients was 56 years, 10 were males, and all were whites. The first day median APACHE II score and its predicted hospital mortality were 35 and 83%, respectively, and the median SOFA score was 11.5. Eleven patients had ARDS, two unilateral pneumonia with septic shock, and one pulmonary edema. Patients received conventional ventilation for a median of 1.8 days before HFOV. HFOV was used 16 times for a median of 3.2 days. Improvements in oxygenation parameters were observed after 24 hours of HFOV (mean PaO2/FIO2increased from 82 to 107,P< 0.05; and the mean oxygenation index decreased from 42 to 29;P< 0.05). In two patients HFOV was discontinued, in one because of equipment failure and in another because of severe hypotension that was unresponsive to fluids. No change in mean arterial pressure, or vasopressor requirements was noted after the initiation of HFOV. Eight patients died (57 %, 95% CI: 33–79); life support was withdrawn in six and two suffered cardiac arrest.ConclusionDuring our first year of experience, HFOV was used as a rescue therapy in very sick patients with refractory hypoxemia, and improvement in oxygenation was observed after 24 hours of this technique. HFOV is a reasonable alternative when a protective lung strategy could not be achieved on conventional ventilation.
Cross-sectional relationship between physical fitness components and functional performance in older persons living in long-term care facilities
Authors: Singh Amika S , Chin A Paw Marijke JM , Bosscher Ruud J , van Mechelen Willem 
Published: February 2006

AbstractBackgroundThe age-related deterioration of physiological capacities such as muscle strength and balance is associated with increased dependence. Understanding the contribution of physical fitness components to functional performance facilitates the development of adequate exercise interventions aiming at preservation of function and independence of older people. The aim of the study was to investigate the relationship between physical fitness components and functional performance in older people living in long-term care facilities.MethodsDesigncross-sectional studySubjects226 persons living in long-term care facilities (mean age: 81.6 ± 5.6).Outcome measuresPhysical fitness and functional performance were measured by performance-based tests.ResultsKnee and elbow extension strength were significantly higher in men (difference = 44.5 and 50.0 N, respectively), whereas women were more flexible (difference sit & reach test = 7.2 cm). Functional performance was not significantly different between the genders. In men, motor coordination (eye-hand coordination) and measures of strength were the main contributors to functional performance, whereas in women flexibility (sit and reach test) and motor coordination (tandem stance and eye-hand coordination) played a major role.ConclusionThe results of this study show that besides muscle strength, fitness components such as coordination and flexibility are associated with functional performance of older people living in long-term care facilities.This suggests that men and women living in long-term care facilities, differ considerably concerning the fitness factors contributing to functional performance. Women and men may, therefore, need exercise programs emphasizing different fitness aspects in order to improve functional performance.