bluuebunny/crossref_metadata_2025_split huggingface dataset:
PAQ: Partition Analysis of Quasispecies
Authors: Baccam Prasith , Thompson Robert J. , Fedrigo Olivier , Carpenter Susan , Cornette James L. 
Published: July 2002

Abstract
Motivation: The complexities of genetic data may not be accurately described by any single analytical tool. Phylogenetic analysis is often used to study the genetic relationship among different sequences. Evolutionary models and assumptions are invoked to reconstruct trees that describe the phylogenetic relationship among sequences. Genetic databases are rapidly accumulating large amounts of sequences. Newly acquired sequences, which have not yet been characterized, may require preliminary genetic exploration in order to build models describing the evolutionary relationship among sequences. There are clustering techniques that rely less on models of evolution, and thus may provide nice exploratory tools for identifying genetic similarities. Some of the more commonly used clustering methods perform better when data can be grouped into mutually exclusive groups. Genetic data from viral quasispecies, which consist of closely related variants that differ by small changes, however, may best be partitioned by overlapping groups.
Results: We have developed an intuitive exploratory program, Partition Analysis of Quasispecies (PAQ), which utilizes a non-hierarchical technique to partition sequences that are genetically similar. PAQ was used to analyze a data set of human immunodeficiency virus type 1 (HIV-1) envelope sequences isolated from different regions of the brain and another data set consisting of the equine infectious anemia virus (EIAV) regulatory gene rev. Analysis of the HIV-1 data set by PAQ was consistent with phylogenetic analysis of the same data, and the EIAV rev variants were partitioned into two overlapping groups. PAQ provides an additional tool which can be used to glean information from genetic data and can be used in conjunction with other tools to study genetic similarities and genetic evolution of viral quasispecies.
Availability: http://www.vetmed.iastate.edu/units/carplab/PAQ/main.html
Contact: pbaccam@lanl.gov
6 To whom correspondence should be addressed at Los Alamos National Laboratory, MS K-710, Theoretical Biology and Biophysics, Los Alamos, NM 87545, USA.
Estimation of P-values for global alignments of protein
sequences
Authors: Webber Caleb , Barton Geoffrey J. 
Published: July 2002

Abstract
Motivation: The global alignment of protein sequence pairs is often used in the classification and analysis of full-length sequences. The calculation of a Z-score for the comparison gives a length and composition corrected measure of the similarity between the sequences. However, the Z-score alone, does not indicate the likely biological significance of the similarity. In this paper, all pairs of domains from 250 sequences belonging to different SCOP folds were aligned and Z-scores calculated. The distribution of Z-scores was fitted with a peak distribution from which the probability of obtaining a given Z-score from the global alignment of two protein sequences of unrelated fold was calculated. A similar analysis was applied to subsequence pairs found by the Smith–Waterman algorithm. These analyses allow the probability that two protein sequences share the same fold to be estimated by global sequence alignment.
Results: The relationship between Z-score and probability varied little over the matrix/gap penalty combinations examined. However, an average shift of +4.7was observed for Z-scores derived from global alignment of locally-aligned subsequences compared to global alignment of the full-length sequences. This shift was shown to be the result of pre-selection by local alignment, rather than any structural similarity in the subsequences. The search ability of both methods was benchmarked against the SCOP superfamily classification and showed that global alignment Z-scores generated from the entire sequence are as effective as SSEARCH at low error rates and more effective at higher error rates. However, global alignment Z-scores generated from the best locally-aligned subsequence were significantly less effective than SSEARCH. The method of estimating statistical significance described here was shown to give similar values to SSEARCH and BLAST, providing confidence in the significance estimation.
Availability: Software to apply the statistics to global alignments is available from http://barton.ebi.ac.uk.
Contact: geoff@ebi.ac.uk
* To whom correspondence should be addressed. Present address: School of Life Sciences, University of Dundee, Dow St., Dundee, DD1 5EH.
A hierarchical unsupervised growing neural network for
clustering gene expression patterns
Authors: Herrero Javier , Valencia Alfonso , Dopazo Joaquı́n 
Published: July 2002

Abstract
Motivation: We describe a new approach to the analysis of gene expression data coming from DNA array experiments, using an unsupervised neural network. DNA array technologies allow monitoring thousands of genes rapidly and efficiently. One of the interests of these studies is the search for correlated gene expression patterns, and this is usually achieved by clustering them. The Self-Organising Tree Algorithm, (SOTA) (Dopazo,J. and Carazo,J.M. (1997) J. Mol. Evol. , 44, 226–233), is a neural network that grows adopting the topology of a binary tree. The result of the algorithm is a hierarchical cluster obtained with the accuracy and robustness of a neural network.
Results: SOTA clustering confers several advantages over classical hierarchical clustering methods. SOTA is a divisive method: the clustering process is performed from top to bottom, i.e. the highest hierarchical levels are resolved before going to the details of the lowest levels. The growing can be stopped at the desired hierarchical level. Moreover, a criterion to stop the growing of the tree, based on the approximate distribution of probability obtained by randomisation of the original data set, is provided. By means of this criterion, a statistical support for the definition of clusters is proposed. In addition, obtaining average gene expression patterns is a built-in feature of the algorithm. Different neurons defining the different hierarchical levels represent the averages of the gene expression patterns contained in the clusters.
Since SOTA runtimes are approximately linear with the number of items to be classified, it is especially suitable for dealing with huge amounts of data. The method proposed is very general and applies to any data providing that they can be coded as a series of numbers and that a computable measure of similarity between data items can be used.
Availability: A server running the program can be found at: http://bioinfo.cnio.es/sotarray
Contact: jdopazo@cnio.es
* To whom correspondence should be addressed.
Automated extraction of information on protein–protein
interactions from the biological literature
Authors: Ono Toshihide , Hishigaki Haretsugu , Tanigami Akira , Takagi Toshihisa 
Published: July 2002

Abstract
Motivation: To understand biological process, we must clarify how proteins interact with each other. However, since information about protein–protein interactions still exists primarily in the scientific literature, it is not accessible in a computer-readable format. Efficient processing of large amounts of interactions therefore needs an intelligent information extraction method. Our aim is to develop an efficient method for extracting information on protein–protein interaction from scientific literature.
Results: We present a method for extracting information on protein–protein interactions from the scientific literature. This method, which employs only a protein name dictionary, surface clues on word patterns and simple part-of-speech rules, achieved high recall and precision rates for yeast (recall \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(=\) \end{document}86.8% and precision \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(=\) \end{document}94.3%) and Escherichia coli (recall \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(=\) \end{document}82.5% and precision \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(=\) \end{document}93.5%). The result of extraction suggests that our method should be applicable to any species for which a protein name dictionary is constructed.
Availability: The program is available on request from the authors.
Contact: ono@otsuka.gr.jp
* To whom correspondence should be addressed.
Automated image analysis for array hybridization experiments
Authors: Steinfath Matthias , Wruck Wasco , Seidel Henrik , Lehrach Hans , Radelof Uwe , O’Brien John 
Published: July 2002

Abstract
Motivation: Image analysis is a major part of data evaluation for array hybridization experiments in molecular biology. The program presented here is designed to analyze automatically images from hybridization experiments with various arrangements: different kinds of probes (oligonucleotides or complex probes), different supports (nylon filters or glass slides), different labeling of probes (radioactively or fluorescently). The program is currently applied to oligonucleotide fingerprinting projects and complex hybridizations. The only precondition for the use of the program is that the targets are arrayed in a grid, which can be approximately transformed to an orthogonal equidistant grid by a projective mapping.
Results: We demonstrate that our program can cope with the following problems: global distortion of the grid, missing of grid nodes, local deviation of the spot from its specified grid position. This is checked by different quality measures. The image analysis of oligonucleotide fingerprint experiments on an entire genetic library is used, in clustering procedures, to group related clones together. The results show that the program yields automatically generated high quality input data for follow up analysis such as clustering procedures.
Availability: The executable files will be available upon request for academics.
Contact: steinfat@molgen.mpg.de
* To whom correspondence should be addressed.
Predicting reliable regions in protein sequence alignments
Authors: Cline Melissa , Hughey Richard , Karplus Kevin 
Published: July 2002

Abstract
Motivation: Protein sequence alignments have a myriad of applications in bioinformatics, including secondary and tertiary structure prediction, homology modeling, and phylogeny. Unfortunately, all alignment methods make mistakes, and mistakes in alignments often yield mistakes in their application. Thus, a method to identify and remove suspect alignment positions could benefit many areas in protein sequence analysis.
Results: We tested four predictors of alignment position reliability, including near-optimal alignment information, column score, and secondary structural information. We validated each predictor against a large library of alignments, removing positions predicted as unreliable. Near-optimal alignment information was the best predictor, removing 70% of the substantially-misaligned positions and 58% of the over-aligned positions, while retaining 86% of those aligned accurately.
Availability: The shift score alignment comparison algorithm is available online at http://www.soe.ucsc.edu/research/compbio/HMM-apps/compare-align.html and from the authors on request.
Contact: cline@soe.ucsc.edu
The EBI SRS server—recent developments
Authors: Zdobnov Evgeni M. , Lopez Rodrigo , Apweiler Rolf , Etzold Thure 
Published: July 2002

Abstract
Motivation: The current data explosion is intractable without advanced data management systems. The numerous data sets become really useful when they are interconnected under a uniform interface—representing the domain knowledge. The SRS has become an integration system for both data retrieval and applications for data analysis. It provides capabilities to search multiple databases by shared attributes and to query across databases fast and efficiently.
Results: Here we present recent developments at the EBI SRS server (http://srs.ebi.ac.uk). The EBI SRS server contains today more than 130 biological databases and integrates more than 10 applications. It is a central resource for molecular biology data as well as a reference server for the latest developments in data integration. One of the latest additions to the EBI SRS server is the InterPro database—Integrated Resource of Protein Domains and Functional Sites. Distributed in XML format it became a turning point in low level XML–SRS integration. We present InterProScan as an example of data analysis applications, describe some advanced features of SRS6, and introduce the SRSQuickSearch JavaScript interfaces to SRS.
Availability: SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration.
Contact: Rodrigo.Lopez@EBI.ac.uk; Evgueni.Zdobnov@EBI.ac.uk
Novel mutations of PKD1 gene in Chinese patients with autosomal dominant polycystic kidney disease
Authors: Ding Lan , Zhang Sizhong , Qiu Weimin , Xiao Cuiying , Wu Shaoqing , Zhang Ge , Cheng Lu , Zhang Sixiao 
Published: July 2002

Abstract
Background. Autosomal dominant polycystic kidney disease (ADPKD) is a common disease in China. The major gene responsible for ADPKD, PKD1, has been fully characterized and shown to encode an integral membrane protein, polycystin 1, which is thought to be involved in cell–cell and cell–matrix interaction. Until now, 82 mutations of PKD1 gene have been reported in European, American, and Asian populations. However, there has been no report on mutations of the PKD1 gene in a Chinese population.
Methods. Eighty Chinese patients in 60 families with ADPKD were screened for mutations in the 3′ region of the PKD1 gene using polymerase chain reaction–single-strand conformation polymorphism (PCR–SSCP) and DNA-sequencing techniques.
Results. Three mutations were found. The first mutation is a 12593delA frameshift mutation in exon 45, and the polycystin change is 4129WfsX4197, 107 amino acids shorter than the normal polycystin (4302aa). The second mutation is a 12470InsA frameshift mutation in exon 45, producing 4088DfsX4156, and the predicted protein is 148 amino acids shorter than the normal. The third one is a 11151C→T transition in exon 37 converting Pro3648 to Leu. In addition, nine DNA variants, including IVS44delG, were identified.
Conclusions. Three mutations in Chinese ADPKD patients are described and all of them are de novo mutations. Data obtained from mutation analysis also suggests that the mutation rate of the 3′ single-copy region of PKD1 in Chinese ADPKD patients is very low, and there are no mutation hot spots in the PKD1 gene. Mutations found in Chinese ADPKD patients, including nucleotide substitution and minor frameshift, are similar to the findings reported by other researchers. Many mutations of the PKD1 gene probably exist in the duplicated region, promoter region, and the introns of PKD1.
A cofactor‐dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus is actually a broad specificity phosphatase
Authors: Rigden Daniel J. , Bagyan Irina , Lamani Ejvis , Setlow Peter , Jedrzejas Mark J. 
Published: July 2002

AbstractThe distribution of phosphoglycerate mutase (PGM) activity in bacteria is complex, with some organisms possessing both a cofactor‐dependent and a cofactor‐independent PGM and others having only one of these enzymes. Although Bacillus species contain only a cofactor‐independent PGM, genes homologous to those encoding cofactor‐dependent PGMs have been detected in this group of bacteria, but in at least one case the encoded protein lacks significant PGM activity. Here we apply sequence analysis, molecular modeling, and enzymatic assays to the cofactor‐dependent PGM homologs from B. stearothermophilus and B. subtilis, and show that these enzymes are phosphatases with broad substrate specificity. Homologs from other gram‐positive bacteria are also likely to possess phosphatase activity. These studies clearly show that the exploration of genomic sequences through three‐dimensional modeling is capable of producing useful predictions regarding function. However, significant methodological improvements will be needed before such analysis can be carried out automatically.
Modeling of the structural features of integral‐membrane proteins reverse‐environment prediction of integral membrane protein structure (REPIMPS)
Authors: Dastmalchi Siavoush , Morris Michael B. , Church W. Bret 
Published: July 2002

AbstractThe Profiles‐3D application, an inverse‐folding methodology appropriate for water‐soluble proteins, has been modified to allow the determination of structural properties of integral‐membrane proteins (IMPs) and for testing the validity of solved and model structures of IMPs. The modification, known as reverse‐environment prediction of integral membrane protein structure (REPIMPS), takes into account the fact that exposed areas of side chains for many residues in IMPs are in contact with lipid and not the aqueous phase. This (1) allows lipid‐exposed residues to be classified into the correct physicochemical environment class, (2) significantly improves compatibility scores for IMPs whose structures have been solved, and (3) reduces the possibility of rejecting a three‐dimensional structure for an IMP because the presence of lipid was not included. Validation tests of REPIMPS showed that it (1) can locate the transmembrane domain of IMPs with single transmembrane helices more frequently than a range of other methodologies, (2) can rotationally orient transmembrane helices with respect to the lipid environment and surrounding helices in IMPs with multiple transmembrane helices, and (3) has the potential to accurately locate transmembrane domains in IMPs with multiple transmembrane helices. We conclude that correcting for the presence of the lipid environment surrounding the transmembrane segments of IMPs is an essential step for reasonable modeling and verification of the three‐dimensional structures of these proteins.
The Settlement of the Blue Cross Blue Shield Antitrust Litigation
Authors: Brennan Troyen 
Published: December 2022

ImportanceThe recent settlement of the class action antitrust lawsuit against the Blue Cross Blue Shield (BCBS) Association and 34 plans will bring substantial change to insurance markets in the US; however, not enough is known about the implications for insurance markets and health policy.ObjectiveTo detail the nature of the antitrust claims against the BCBS plans and their Association, and the required changes in their business practices that are a critical part of the settlement.Evidence ReviewThis analysis relies on the court documents that will set the new parameters under which BCBS plans must operate.FindingsFor many of the past 70 years, BCBS plans have enjoyed substantial market power in the state in which each operates. Other BCBS plans were not allowed to compete against other “Blues” plans, and any corporation resident in a plan’s territory was allowed to deal solely with the local plan if the corporation sought BCBS insurance for its employees. The settlement recognizes that these restrictions reduced competition; therefore, they are not allowed under federal antitrust laws going forward. The BCBS Association also will have less control over mergers and acquisitions by individual BCBS plans. Finally, the BCBS plans and the Association must pay $2.67 billion in damages to clients.Conclusions and RelevanceThese findings suggest that BCBS plans will face competition from their fellow plans for business, and they will be allowed to diversify the services they provide. These changes will be likely to threaten the smaller BCBS plans and could bring consolidation to the health insurance industry. These changes should also promote sharper efforts toward health care cost management, with broad implications for other parts of the health insurance industry, and for hospitals and other health care services.
Bayesian Analysis of
MAP
2
and Related Processes
Authors: Wiper Michael P. 
Published: December 2022

Abstract
Methods for inference for the Markov arrival process (MAP) are examined, concentrating particularly on Bayesian inference for the . Given that the is overparameterized in its original form, a canonical form of the is applied. This allows inference to be carried out via Gibbs sampling, treating the process as a hidden Markov model, and simulating the unobserved states using a forward–backward algorithm.
Dodona
Authors: Dieterle Martina 
Published: December 2022

Abstract

As is clear from Homer, the shrine of Zeus at Dodona in Epirus was uniquely significant in the Hellenic world with an importance equal to that of Delphi and Delos. Among things particular to this sanctuary were that Zeus was associated with his wife Dione; there was a holy oak with prophetic doves; priests slept on the ground. Excavation shows that Dodona already existed in the Bronze Age, but whether it was initially a tree sanctuary, an oracle, a settlement or a mixture of the three is still unclear. A surge in building activities including the impressive theater, took place during the third century
bce
; the Naia games also began during this period. The site continued in existence until the sixth century
ce
when it was apparently abandoned.
Aratos of Soloi (Aratus of Soli)
Authors: Lewis Anne‐Marie 
Published: December 2022

Abstract

Aratos (ca. 310–240
bce
), a Greek poet and scholar, is the author of the
Phaenomena
, a didactic poem that was the most widely read work of Greek literature in antiquity after Homer's
Iliad
and
Odyssey
.
Quantitative assessment of helical tomotherapy plans complexity
Authors: Cavinato Samuele , Fusella Marco , Paiusco Marta , Scaggion Alessandro 
Published: December 2022

AbstractPurposeAn unnecessary amount of complexity in radiotherapy plans affects the efficiency of the treatments, increasing the uncertainty of dose deposition and its susceptibility to anatomical changes or setup errors. To date, tools for quantitatively assessing the complexity of tomotherapy plans are still limited. In this study, new metrics were developed to characterize different aspects of helical tomotherapy (HT) plans, and their actual effectiveness was investigated.MethodsThe complexity of 464 HT plans delivered on a Radixact platform was evaluated. A new set of metrics was devised to assess beam geometry, leaf opening time (LOT) variability, and modulation over space and time. Sixty‐five complexity metrics were extracted from the dataset using the newly in‐house developed software library TCoMX: 29 metrics already proposed in the literature and 36 newly developed metrics. Their reciprocal relation is discussed. Their effectiveness was evaluated through correlation analyses with patient‐specific quality assurance (PSQA) results.ResultsAn inverse linear relation was found between the average number of closed leaves and the average number of MLC openings and closures as well as between the choice of the modulation factor and the discontinuity of the field, suggesting some intrinsic link between the LOT distribution and the geometrical complexity of the MLC openings. The newly proposed metrics were at least as correlated as the existing ones to the PSQA results. Metrics describing the geometrical complexity of the MLC openings showed the strongest connection to the PSQA results. Significant correlations were found between at least one of the new metrics and the γ index passing rate for six out of seven groups of plans considered.ConclusionThe new metrics proposed were shown to be effective to characterize more comprehensively the complexity of HT plans. A software library for their automatic extraction is described and made available.