bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of a system for chemical sterilization of packages
Authors: Abreu L. F. , Faria J. A. F. 
Published: March 2004

AbstractA system was evaluated for the chemical sterilization of packages, based on its sporicidal efficiency using inoculated Bacillus subtilis inside polyethylene terephthalate (PET) bottles. Different combinations of contact time, temperature and peracetic acid concentrations were tested, delineated according to a factorial planning of 23. The results, expressed as decimal reduction counts, proved that peracetic acid showed good sporicidal efficiency at 1.2% concentration in the temperature range 30–50°C. With this performance, the tested system can be used to sterilize plastic bottles and other similar packages, achieving a count reduction of spores by up to 10−7. Copyright © 2004 John Wiley & Sons, Ltd.
Alu insertion polymorphisms in the Balkans and the origins of the Aromuns
Authors: Comas D. , Schmid H. , Braeuer S. , Flaiz C. , Busquets A. , Calafell F. , Bertranpetit J. , Scheil H.‐G. , Huckenbeck W. , Efremovska L. , Schmidt H. 
Published: March 2004

SummaryWe have analysed 11 human‐specific Alu insertion polymorphisms in the Balkans to elucidate the origins of the Aromuns, a linguistic isolate inhabiting scattered areas in the Balkan Peninsula. Four Aromun samples (two from the Republic of Macedonia, one from Albania, and one from Romania) and five neighbouring populations (Macedonians, Albanians, Romanians, Greeks, and Turks) were analysed by means of genetic distances, principal components and analyses of the molecular variance (AMOVA). Three hypotheses were tested: Aromuns are Romanophonic Greeks; the result of a Romanian southward migration; or local descendants of the Thracians. The analyses show that the Aromuns do not constitute a homogeneous group separated from the rest of the Balkan populations. Grouping by language or geography does not explain the genetic differences observed in the region, suggesting a lack of genetic structure in the area. Aromuns do not seem to be particularly related to Greeks, Romanians, or to other Romance speakers. The Aromuns might have their origin to the south of the Danube river, with extensive gene flow with the neighbouring populations. The present results suggest a common ancestry of all Balkan populations, including Aromuns, with a lack of correlation between genetic differentiation and language or ethnicity, stressing that no major migration barriers have existed in the making of the complex Balkan human puzzle.
Admixture in the Hispanics of the San Luis Valley, Colorado, and its implications for complex trait gene mapping
Authors: Bonilla C. , Parra E. J. , Pfaff C. L. , Dios S. , Marshall J. A. , Hamman R. F. , Ferrell R. E. , Hoggart C. L. , McKeigue P. M. , Shriver M. D. 
Published: March 2004

SummaryHispanic populations are a valuable resource that can and should facilitate the identification of complex trait genes by means of admixture mapping (AM). In this paper we focus on a particular Hispanic population living in the San Luis Valley (SLV) in Southern Colorado.We used a set of 22 Ancestry Informative Markers (AIMs) to describe the admixture process and dynamics in this population. AIMs are defined as genetic markers that exhibit allele frequency differences between parental populations ≥30%, and are more informative for studying admixed populations than random markers. The ancestral proportions of the SLV Hispanic population are estimated as 62.7 ± 2.1% European, 34.1 ± 1.9% Native American and 3.2 ± 1.5% West African. We also estimated the ancestral proportions of individuals using these AIMs. Population structure was demonstrated by the excess association of unlinked markers, the correlation between estimates of admixture based on unlinked marker sets, and by a highly significant correlation between individual Native American ancestry and skin pigmentation (R2= 0.082, p < 0.001). We discuss the implications of these findings in disease gene mapping efforts.
A Multiwavelength Study of CC Eridani
Authors: Slee O. B. , Budding E. , Carter B. D. , Mengel M. W. , Waite I. , Donati J.-F. 
Published: March 2004

AbstractRadio and optical observations from December 2001 and January 2002 of the active RS CVn-like binary CC Eri are presented. The star was monitored at 4.80 and 8.64 GHz over 3 × 12 h allocations with the Australia Telescope Compact Array on 28 to 30 December 2001. The Anglo-Australian Telescope was used for simultaneous optical spectropolarimetry during a 0.5 h period on 30 December. Data from four nights of broadband photometry gathered around the same period are also included in this present multiwavelength study.The low levels of radio emission were circularly polarised at ∼20% with slightly positive spectral indices of ∼0.26. Two flare-like increases were observed on successive nights with steep positive spectral indices and no detectable polarisation. Cross-correlation analysis of the 4.80 and 8.64 GHz intensities over the stronger flare showed that the higher frequency emission preceded that at the lower frequency by ∼5 min, a result consistent with the propagation of a hydromagnetic disturbance outwards through the corona. On the same night, a significant cross-correlation in the ‘quiescent’ emission indicates the presence of micro-flaring, although its low intensity does not permit the evaluation of a time delay. The emission parameters on the three nights are compatible with a gyrosyncrotron mechanism, in which the radio source becomes optically thick during strong flaring. We develop a simple model, which is based on assuming that the number of radiating electrons is a given function of the magnetic field in the source region, and derive feasible values for the field, source radius, and number of emitting electrons, which are not strongly dependent on the field modelling function or the aspect ratio of the source. Spectropolarimetry demonstrates the presence of a strong surface magnetic field. Optical photometry, covering a sufficient amount of the orbit, indicates a maculation region of significant size (∼14° radius).The results help develop a three-dimensional picture of a large stellar magnetically active region and encourage more detailed follow-up multiwavelength studies of this and similar stars.
PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes
Authors: Lavigne R. , Sun W.D. , Volckaert G. 
Published: March 2004

Abstract
Motivation: In silico genome analysis of bacteriophage genomes focuses mainly on gene discovery and functional assignment. The search for regulatory elements contained within these genome sequences is often based on prior knowledge of other genomic elements or on learning algorithms of experimentally determined data, potentially leading to a biased prediction output.
The PHage In silico Regulatory Elements (PHIRE) program is a standalone program in Visual Basic. It performs an algorithmic string-based search on bacteriophage genome sequences to uncover and extract subsequence alignments hinting at regulatory elements contained within these genomes, in a deterministic manner without any prior experimental or predictive knowledge.
Results: The PHIRE program was tested on known phage genomes with experimentally verified regulatory elements. PHIRE was able to extract phage regulatory sequences correctly for bacteriophages T7, T3, ϕYeO3-12 and λ, based solely on the genome sequence. For 11 bacteriophages, new predictions of conserved phage-specific putative regulatory elements were made, further corroborating this approach.
Availability: http://www.agr.kuleuven.ac.be/logt/PHIRE.htm. Freely available for academic use. Commercial users should contact the corresponding author.
Disulfide connectivity prediction using recursive neural networks and evolutionary information
Authors: Vullo Alessandro , Frasconi Paolo 
Published: March 2004

Abstract
Motivation: We focus on the prediction of disulfide bridges in proteins starting from their amino acid sequence and from the knowledge of the disulfide bonding state of each cysteine. The location of disulfide bridges is a structural feature that conveys important information about the protein main chain conformation and can therefore help towards the solution of the folding problem. Existing approaches based on weighted graph matching algorithms do not take advantage of evolutionary information. Recursive neural networks (RNN), on the other hand, can handle in a natural way complex data structures such as graphs whose vertices are labeled by real vectors, allowing us to incorporate multiple alignment profiles in the graphical representation of disulfide connectivity patterns.
Results: The core of the method is the use of machine learning tools to rank alternative disulfide connectivity patterns. We develop an ad-hoc RNN architecture for scoring labeled undirected graphs that represent connectivity patterns. In order to compare our algorithm with previous methods, we report experimental results on the SWISS-PROT 39 dataset. We find that using multiple alignment profiles allows us to obtain significant prediction accuracy improvements, clearly demonstrating the important role played by evolutionary information.
Availability: The Web interface of the predictor is available at http://neural.dsi.unifi.it/cysteines
Variance-stabilizing transformations for two-color microarrays
Authors: Durbin Blythe P. , Rocke David M. 
Published: March 2004

Abstract
Motivation: Authors of several recent papers have independently introduced a family of transformations (the generalized-log family), which stabilizes the variance of microarray data up to the first order. However, for data from two-color arrays, tests for differential expression may require that the variance of the difference of transformed observations be constant, rather than that of the transformed observations themselves.
Results: We introduce a transformation within the generalized-log family which stabilizes, to the first order, the variance of the difference of transformed observations. We also introduce transformations from the ‘started-log’ and log-linear-hybrid families which provide good approximate variance stabilization of differences. Examples using control–control data show that any of these transformations may provide sufficient variance stabilization for practical applications, and all perform well compared to log ratios.
404 not found: the stability and persistence of URLs published in MEDLINE
Authors: Wren Jonathan D. 
Published: March 2004

Abstract
Motivation: The advent of the World Wide Web has enabled unprecedented supplementation of traditional journal publications, allowing access to resources, such as video, sound, software, databases, datasets too large to publish, and even supplementary information and discussion. However, unlike traditional publications, continued availability of these online resources is not guaranteed. An automated survey was conducted to quantify the growth in Uniform Resource Locators (URLs) published to date in MEDLINE abstracts, their current availability and distribution by journal.
Results: Of 1630 unique URLs identified, formatting and/or spelling errors were detected within 201 (12%) of them as published. After corrections were made, a survey revealed that ∼63% of these URLs were consistently available, and another 19% were available intermittently. The rate of failure was far worse for anonymous login to FTP sites, with only 12 of 33 sites (36%) responding. This survey also shows that journals vary disproportionately in the number of web citations published, suggesting policy implementation among a few could have a profound impact overall. Out of the 306 journals with a URL published in an abstract, Bioinformatics published the most (12% of total).
Availability: URL database and program available by request.
Comparison of various algorithms for recognizing short coding sequences of human genes
Authors: Gao Feng , Zhang Chun-Ting 
Published: March 2004

Abstract
Motivation: Since the early 1980s of the twentieth century, there has been great progress in the development of computational gene-finding algorithms. Some problems, however, have not yet been solved currently. Recognizing short genes in prokaryotes and short exons in eukaryotes is one of such problems. The paper is devoted to assessing various algorithms, including those currently available and the new ones proposed here, in order to find the best algorithm to solve the issue.
Results: The databases consisting of phase-specific coding and non-coding sequences of human genes with length of 192, 162, 129, 108, 87, 63 and 42 bp, respectively, have been established. Based on the databases and a standard benchmark, 19 algorithms were evaluated, which include the methods of Markov models with orders of 1 through 5, codon usage, hexamer usage, codon preference, amino acid usage, codon prototype, Fourier transform and 8 Z curve methods with various numbers of parameters. Consequently, the Z curve methods with 69 and 189 parameters are the best ones among them, based on the databases constructed here. In addition to the highest recognition accuracy confirmed by 10-fold cross-validation tests, the Z curve methods are much simpler computationally than the second best one, the fifth-order Markov chain model, in which 12 288 parameters are used. We hope that the Z curve methods presented in this paper would be beneficial to the further development of gene-finding algorithms.
Availability: The programs of various Z curve methods are available on request.
A statistical framework for combining and interpreting proteomic datasets
Authors: Gilchrist Michael A. , Salter Laura A. , Wagner Andreas 
Published: March 2004

Abstract
Motivation: To identify accurately protein function on a proteome-wide scale requires integrating data within and between high-throughput experiments. High-throughput proteomic datasets often have high rates of errors and thus yield incomplete and contradictory information. In this study, we develop a simple statistical framework using Bayes’ law to interpret such data and combine information from different high-throughput experiments. In order to illustrate our approach we apply it to two protein complex purification datasets.
Results: Our approach shows how to use high-throughput data to calculate accurately the probability that two proteins are part of the same complex. Importantly, our approach does not need a reference set of verified protein interactions to determine false positive and false negative error rates of protein association. We also demonstrate how to combine information from two separate protein purification datasets into a combined dataset that has greater coverage and accuracy than either dataset alone. In addition, we also provide a technique for estimating the total number of proteins which can be detected using a particular experimental technique.
Availability: A suite of simple programs to accomplish some of the above tasks is available at www.unm.edu/~compbio/software/DatasetAssess
Java-based application framework for visualization of gene regulatory region annotations
Authors: Sun Hao , Davuluri Ramana V. 
Published: March 2004

Abstract
Motivation: The genome sequences of several organisms are either complete, or being sequenced. Each genome needs to be integrated with various types of annotations, e.g. locations of genes, promoters and other functional elements such as transcriptional regulatory elements. A robust application framework will be useful for developing web-based applications to visualize various genome annotations.
Results: We developed genome data visualization toolkit (GDVTK) as an application framework that consists of a set of data structures and core classes, using Java™ technology. GDVTK is a sound framework for developing web-based applications to present the gene regulatory region annotations in visual form. The current version of GDVTK consists of eight packages and 38 Java classes that are portable, reusable and extensible for plugging in new data sources and models. We implemented GDVTK for visualization of promoter annotations in Mammalian Promoter Database (MPromDb), a web-based gene-regulatory information server.
Availability: GDVTK is available under GNU general public license. Source code and software documentation can be found at the URL http://bioinformatics.med.ohio-state.edu/GDVTK.
ESPD: a pattern detection model underlying gene expression profiles
Authors: Tang Chun , Zhang Aidong , Ramanathan Murali 
Published: March 2004

Abstract
Motivation: DNA arrays permit rapid, large-scale screening for patterns of gene expression and simultaneously yield the expression levels of thousands of genes for samples. The number of samples is usually limited, and such datasets are very sparse in high-dimensional gene space. Furthermore, most of the genes collected may not necessarily be of interest and uncertainty about which genes are relevant makes it difficult to construct an informative gene space. Unsupervised empirical sample pattern discovery and informative genes identification of such sparse high-dimensional datasets present interesting but challenging problems.
Results: A new model called empirical sample pattern detection (ESPD) is proposed to delineate pattern quality with informative genes. By integrating statistical metrics, data mining and machine learning techniques, this model dynamically measures and manipulates the relationship between samples and genes while conducting an iterative detection of informative space and the empirical pattern. The performance of the proposed method with various array datasets is illustrated.
Availability: Software code is available by request from the first author. All programs were written in MATLAB.
Algorithms for variable length Markov chain modeling
Authors: Bejerano Gill 
Published: March 2004

Abstract
Summary: We present a general purpose implementation of variable length Markov models. Contrary to fixed order Markov models, these models are not restricted to a predefined uniform depth. Rather, by examining the training data, a model is constructed that fits higher order Markov dependencies where such contexts exist, while using lower order Markov dependencies elsewhere. As both theoretical and experimental results show, these models are capable of capturing rich signals from a modest amount of training data, without the use of hidden states.
Availability: The source code is freely available at http://www.soe.ucsc.edu/~jill/src/
CAAT-Box, contigs-Assembly and Annotation Tool-Box for genome sequencing projects
Authors: Frangeul L. , Glaser P. , Rusniok C. , Buchrieser C. , Duchaud E. , Dehoux P. , Kunst F. 
Published: March 2004

Abstract
Motivation: Contigs-Assembly and Annotation Tool-Box (CAAT-Box) is a software package developed for the computational part of a genome project where the sequence is obtained by a shotgun strategy. CAAT-Box contains new tools to predict links between contigs by using similarity searches with other whole genome sequences. Most importantly, it allows annotation of a genome to commence during the finishing phase using a gene-oriented strategy. For this purpose, CAAT-Box creates an Individual Protein file (IPF) for each ORF of an assembly. The nucleotide sequence reported in an IPF corresponds to the sequence of the ORF with 500 additional bases before the ORF and 200 bases after. For annotation, additional information like Blast results can be added or linked to the IPFs as well as automatic and/or manual annotations. When a new assembly is performed, CAAT-Box creates new IPFs according to the old IPF panel. CAAT-Box recognizes the modified IPFs which are the only ones used for a new automatic analysis after each assembly. Using this strategy, the user works with a group of IPFs independently of the closure phase progression. The IPFs are accessible by a web server and can therefore be modified and commented by different groups.
Result: CAAT-Box was used to obtain and to annotate several complete genomes like Listeria monocytogenes or Strepcoccus agalactiae.
Availability: The program may be obtained from the authors and is freely available to non-profit organisations.
In silico analysis of complete bacterial genomes: PCR, AFLP–PCR and endonuclease restriction
Authors: Bikandi Joseba , Millán Rosario San , Rementeria Aitor , Garaizar Javier 
Published: March 2004

Abstract
Summary: We have developed a website, www.in-silico.com, which runs a software program that performs three basic tasks in completely sequenced bacterial genomes by in silico analysis: PCR amplification, amplified fragment length polymorphism (AFLP–PCR) and endonuclease restriction. For PCR, after selection of the genome and introduction of primers, fragment size, DNA sequence and corresponding open reading frame (ORF) identity of the resulting PCR product is computed. Plasmids of sequenced species may be included in the analysis. Theoretical AFLP–PCR analyzes similar parameters, and includes a suggestion tool providing a list of commercial restriction enzyme pairs yielding up to 50 amplicons in the selected genome. Endonuclease restriction analysis of complete genomes and plasmids calculates the number of restriction sites for endonucleases in a given genome. If the number of fragments is 50 or fewer, pulsed field gel electrophoresis image and restriction maps are illustrated. Other tools that have been included in this site are ORF search by name and DNA to protein translation as well as restriction digestion of user-defined DNA sequences.
Availability: This is a new molecular biology resource freely available over the Internet at http://www.in-silico.com
Gene selection for oligonucleotide array: an approach using PM probe level data
Authors: Chen Dung-Tsa , Lin Sue-Hwa , Soong Seng-jaw 
Published: March 2004

Abstract
Motivation: Analysis of oligonucleotide array data, especially to select genes of interest, is a highly challenging task because of the large volume of information and various experimental factors. Moreover, interaction effect (i.e. expression changes depend on probe effects) complicates the analysis because current methods often use an additive model to analyze data. We propose an approach to address these issues with the aim of producing a more reliable selection of differentially expressed genes. The approach uses the rank for normalization, employs the percentile-range to measure expression variation, and applies various filters to monitor expression changes.
Results: We compare our approach with MAS and Dchip models. A data set from an angiogenesis study is used for illustration. Results show that our approach performs better than other methods either in identification of the positive control gene or in PCR confirmatory tests. In addition, the invariant set of genes in our approach provides an efficient way for normalization.
Optimizing substitution matrices by separating score distributions
Authors: Hourai Yuichiro , Akutsu Tatsuya , Akiyama Yutaka 
Published: March 2004

Abstract
Motivation:Homology search is one of the most fundamental tools in Bioinformatics. Typical alignment algorithms use substitution matrices and gap costs. Thus, the improvement of substitution matrices increases accuracy of homology searches. Generally, substitution matrices are derived from aligned sequences whose relationships are known, and gap costs are determined by trial and error. To discriminate relationships more clearly, we are encouraged to optimize the substitution matrices from statistical viewpoints using both positive and negative examples utilizing Bayesian decision theory.
Results: Using Cluster of Orthologous Group (COG) database, we optimized substitution matrices. The classification accuracy of the obtained matrix is better than that of conventional substitution matrices to COG database. It also achieves good performance in classifying with other databases.
Availability: The optimized substitution matrices and the programs are available from the http://olab.is.s.u-tokyo.ac.jp/~hourai/optssd/index.html