bluuebunny/crossref_metadata_2025_split huggingface dataset:
Power‐law species–area relationships and self‐similar species distributions within finite areas
Authors: Šizling Arnošt L. , Storch David 
Published: December 2003

AbstractThe species–area relationship (SAR) is often expressed as a power law, which indicates scale invariance. It has been claimed that the scale invariance – or self‐similarity at the community level – is not compatible with the self‐similarity at the level of spatial distribution of individual species, because the power law would only emerge if distributions for all species had identical fractal dimensions (FD). Here we show that even if species differ in their FD, the resulting SAR is approximately linear on a log–log scale because observed spatial distributions are inevitably spatially restricted – a phenomenon we term the ‘finite‐area effect’. Using distribution atlases, we demonstrate that the apparent power law of SARs for central European birds is attributable to this finite‐area effect affecting species that indeed reveal self‐similar distributions. We discuss implications of this mechanism producing the SAR.
Measurement error and estimates of population extinction risk
Authors: McNamara John M. , Harding Karin C. 
Published: December 2003

AbstractIt is common to estimate the extinction probability for a vulnerable population using methods that are based on the mean and variance of the long‐term population growth rate. The numerical values of these two parameters are estimated from time series of population censuses. However, the proportion of a population that is registered at each census is typically not constant but will vary among years because of stochastic factors such as weather conditions at the time of sampling. Here, we analyse how such sampling errors influence estimates of extinction risk and find sampling errors to produce two opposite effects. Measurement errors lead to an exaggerated overall variance, but also introduce negative autocorrelations in the time series (which means that estimates of annual growth rates tend to alternate in size). If time series data are treated properly these two effects exactly counter balance. We advocate routinely incorporating a measure of among year correlations in estimating population extinction risk.
Combining phylogenetic data with co-regulated genes to identify regulatory motifs
Authors: Wang Ting , Stormo Gary D. 
Published: December 2003

Abstract
Motivation: Discovery of regulatory motifs in unaligned DNA sequences remains a fundamental problem in computational biology. Two categories of algorithms have been developed to identify common motifs from a set of DNA sequences. The first can be called a ‘multiple genes, single species’ approach. It proposes that a degenerate motif is embedded in some or all of the otherwise unrelated input sequences and tries to describe a consensus motif and identify its occurrences. It is often used for co-regulated genes identified through experimental approaches. The second approach can be called ‘single gene, multiple species’. It requires orthologous input sequences and tries to identify unusually well conserved regions by phylogenetic footprinting. Both approaches perform well, but each has some limitations. It is tempting to combine the knowledge of co-regulation among different genes and conservation among orthologous genes to improve our ability to identify motifs.
Results: Based on the Consensus algorithm previously established by our group, we introduce a new algorithm called PhyloCon (Phylogenetic Consensus) that takes into account both conservation among orthologous genes and co-regulation of genes within a species. This algorithm first aligns conserved regions of orthologous sequences into multiple sequence alignments, or profiles, then compares profiles representing non-orthologous sequences. Motifs emerge as common regions in these profiles. Here we present a novel statistic to compare profiles of DNA sequences and a greedy approach to search for common subprofiles. We demonstrate that PhyloCon performs well on both synthetic and biological data.
Availability: Software available upon request from the authors. http://ural.wustl.edu/softwares.html
Scoring clustering solutions by their biological relevance
Authors: Gat-Viks I. , Sharan R. , Shamir R. 
Published: December 2003

Abstract
Motivation: A central step in the analysis of gene expression data is the identification of groups of genes that exhibit similar expression patterns. Clustering gene expression data into homogeneous groups was shown to be instrumental in functional annotation, tissue classification, regulatory motif identification, and other applications. Although there is a rich literature on clustering algorithms for gene expression analysis, very few works addressed the systematic comparison and evaluation of clustering results. Typically, different clustering algorithms yield different clustering solutions on the same data, and there is no agreed upon guideline for choosing among them.
Results: We developed a novel statistically based method for assessing a clustering solution according to prior biological knowledge. Our method can be used to compare different clustering solutions or to optimize the parameters of a clustering algorithm. The method is based on projecting vectors of biological attributes of the clustered elements onto the real line, such that the ratio of between-groups and within-group variance estimators is maximized. The projected data are then scored using a non-parametric analysis of variance test, and the score's confidence is evaluated. We validate our approach using simulated data and show that our scoring method outperforms several extant methods, including the separation to homogeneity ratio and the silhouette measure. We apply our method to evaluate results of several clustering methods on yeast cell-cycle gene expression data.
Availability: The software is available from the authors upon request.
Classification of protein quaternary structure with support vector machine
Authors: Zhang Shao-Wu , Pan Quan , Zhang Hong-Cai , Zhang Yun-Long , Wang Hai-Yu 
Published: December 2003

Abstract
Motivation: Since the gap between sharply increasing known sequences and slow accumulation of known structures is becoming large, an automatic classification process based on the primary sequences and known three-dimensional structure becomes indispensable. The classification of protein quaternary structure based on the primary sequences can provide some useful information for the biologists. So a fully automatic and reliable classification system is needed. This work tries to look for the effective methods of extracting attribute and the algorithm for classifying the quaternary structure from the primary sequences.
Results: Both of the support vector machine (SVM) and the covariant discriminant algorithms have been first introduced to predict quaternary structure properties from the protein primary sequences. The amino acid composition and the auto-correlation functions based on the amino acid index profile of the primary sequence have been taken into account in the algorithms. We have analyzed 472 amino acid indices and selected the four amino acid indices as the examples, which have the best performance. Thus the five attribute parameter data sets (COMP, FASG, NISK, WOLS and KYTJ) were established from the protein primary sequences. The COMP attribute data set is composed of amino acid composition, and the FASG, NISK, WOLS and KYTJ attribute data sets are composed of the amino acid composition and the auto-correlation functions of the corresponding amino acid residue index. The overall accuracies of SVM are 78.5, 87.5, 83.2, 81.7 and 81.9%, respectively, for COMP, FASG, NISK, WOLS and KYTJ data sets in jackknife test, which are 19.6, 7.8, 15.5, 13.1 and 15.8%, respectively, higher than that of the covariant discriminant algorithm in the same test. The results show that SVM may be applied to discriminate between the primary sequences of homodimers and non-homodimers and the two protein sequence descriptors can reflect the quaternary structure information. Compared with previous Robert Garian's investigation, the performance of SVM is almost equal to that of the Decision tree models, and the methods of extracting feature vector from the primary sequences are superior to Robert's binning function method.
Availability: Programs are available on request from the authors.
A random variance model for detection of differential gene expression in small microarray experiments
Authors: Wright George W. , Simon Richard M. 
Published: December 2003

Abstract
Motivation: Microarray techniques provide a valuable way of characterizing the molecular nature of disease. Unfortunately expense and limited specimen availability often lead to studies with small sample sizes. This makes accurate estimation of variability difficult, since variance estimates made on a gene by gene basis will have few degrees of freedom, and the assumption that all genes share equal variance is unlikely to be true.
Results: We propose a model by which the within gene variances are drawn from an inverse gamma distribution, whose parameters are estimated across all genes. This results in a test statistic that is a minor variation of those used in standard linear models. We demonstrate that the model assumptions are valid on experimental data, and that the model has more power than standard tests to pick up large changes in expression, while not increasing the rate of false positives.
Availability: This method is incorporated into BRB-ArrayTools version 3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html).
Supplementary material: ftp://linus.nci.nih.gov/pub/techreport/RVM_supplement.pdf
KISS for STRAP: user extensions for a protein alignment editor
Authors: Gille Christoph , Lorenzen Stephan , Michalsky Elke , Frömmel Cornelius 
Published: December 2003

Abstract
Summary: The Structural Alignment Program STRAP is a comfortable comprehensive editor and analyzing tool for protein alignments. A wide range of functions related to protein sequences and protein structures are accessible with an intuitive graphical interface. Recent features include mapping of mutations and polymorphisms onto structures and production of high quality figures for publication. Here we address the general problem of multi-purpose program packages to keep up with the rapid development of bioinformatical methods and the demand for specific program functions. STRAP was remade implementing a novel design which aims at Keeping Interfaces in STRAP Simple (KISS). KISS renders STRAP extendable to bio-scientists as well as to bio-informaticians. Scientists with basic computer skills are capable of implementing statistical methods or embedding existing bioinformatical tools in STRAP themselves. For bio-informaticians STRAP may serve as an environment for rapid prototyping and testing of complex algorithms such as automatic alignment algorithms or phylogenetic methods. Further, STRAP can be applied as an interactive web applet to present data related to a particular protein family and as a teaching tool.
Requirements: JAVA-1.4 or higher.
Availability: http://www.charite.de/bioinf/strap/
SNOW: Standard NOmenclature Wizard to help searching for (bio) chemical standardized names
Authors: Aguilar Daniel , Oliva Baldomero , Aviles Francesc X. , Querol Enrique 
Published: December 2003

Abstract
Summary: When developing bioinformatical tools dealing with enzymatic activity, metabolism or enzymatic networks, the problem of the lack of a clear nomenclature for biochemical compounds often arises. This problem leads us to develop a small web-based tool (SNOW, Standard NOmenclature Wizard) which may help to find recommended and trivial names or the correct closest spelling for a query compound name, if it exists.
Availability: Web-based interface available at http://ibb.uab.es/snow/
Supplementary information: http://ibb.uab.es/snow/snow_moreinfo.html
Machaon CVE: cluster validation for gene expression data
Authors: Bolshakova Nadia , Azuaje Francisco 
Published: December 2003

Abstract
Summary: This paper presents a cluster validation tool for gene expression data. Machaon CVE (Clustering and Validation Environment) system aims to partition samples or genes into groups characterized by similar expression patterns, and to evaluate the quality of the clusters obtained.
Availability: The program is freely available for non-profit use on request at http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html
Supplementary information: http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html
DnaSP, DNA polymorphism analyses by the coalescent and other methods
Authors: Rozas Julio , Sánchez-DelBarrio Juan C. , Messeguer Xavier , Rozas Ricardo 
Published: December 2003

Abstract
Summary: DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (∼5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results.
Availability: The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
A CART-based approach to discover emerging patterns in microarray data
Authors: Boulesteix Anne-Laure , Tutz Gerhard , Strimmer Korbinian 
Published: December 2003

Abstract
Motivation: Cancer diagnosis using gene expression profiles requires supervised learning and gene selection methods. Of the many suggested approaches, the method of emerging patterns (EPs) has the particular advantage of explicitly modeling interactions among genes, which improves classification accuracy. However, finding useful (i.e. short and statistically significant) EP is typically very hard.
Methods: Here we introduce a CART-based approach to discover EPs in microarray data. The method is based on growing decision trees from which the EPs are extracted. This approach combines pattern search with a statistical procedure based on Fisher's exact test to assess the significance of each EP. Subsequently, sample classification based on the inferred EPs is performed using maximum-likelihood linear discriminant analysis.
Results: Using simulated data as well as gene expression data from colon and leukemia cancer experiments we assessed the performance of our pattern search algorithm and classification procedure. In the simulations, our method recovers a large proportion of known EPs while for real data it is comparable in classification accuracy with three top-performing alternative classification algorithms. In addition, it assigns statistical significance to the inferred EPs and allows to rank the patterns while simultaneously avoiding overfit of the data. The new approach therefore provides a versatile and computationally fast tool for elucidating local gene interactions as well as for classification.
Availability: A computer program written in the statistical language R implementing the new approach is freely available from the web page http://www.stat.uni-muenchen.de/~socher/
The Development of Middle English Expletive Negative Sentences
Authors: Ingham Richard 
Published: December 2003

The late Middle English expletive negative (EN) construction, as in:
(1) per wull no man gewe so myche for themPaston 209, 12 (1471)
has been analysed in Ingham (1998, 2000) as involving movement of a negated subject NP from Spec VP to Spec NegP, thus appearing to the right of the finite verb. The prefinite position was occupied by expletive there. In the present study two questions are addressed: (a) whether the construction in (1) was an idiosyncratic feature of the Paston correspondents, and (b) whether it existed in earlier stages of Middle English. Three 15th century religious works (Middle English Sermons, Book of Margery Kempe, and Dives et Pauper I) were searched for this construction, as were eight early 13th century South‐Eastern and West Midland religious prose texts. The EN construction was common in all three 15th century texts, in both matrix and embedded clauses. In the 13th century prose texts, however, the EN construction was non‐existent. Postfinite subjects were found, but almost exclusively in matrix clauses, as in:
(2) Ne mei nan uvel hearmen ðeHM 68 (a. 1225)
Expletive there was always lacking in such cases. We analyse (2) in terms of movement of the finite verb to C, with the negated subject in Spec IP. An alternative analysis in which pro stood in Spec IP, and the negated subject moved to, but not through, Spec NegP, is considered but rejected. If movement only as far as Spec NegP had been possible, postfinite subjects would have been productive in embedded clauses, counter to the evidence obtained from these samples. Theoretical support for this analysis is obtained from the shift postulated by va: Kemenade (1997) from C to I as the dominant head in Middle English clause structure around the 14th century. An NP was assigned case in the minimal domain of C until the 14th century, thus forcing negated subjects to move higher than Spec NegP. When I became the dominant head in the 14th century a subject NP was assigned Case within its minimal domin, which could be NegP, as long as Spec IP in finite clauses was filled with an expletive. The emergence of the EN construction between the early 13th century and early 15th century is examined using 13th and 14th century verse, in which evidence is found for the decline of Infal to Comp movement in negated clauses, as well as some evidence for the EN construction.
If you’re no good at computer games, don’t operate endoscopically!
Authors: Miskry Tariq , Magos Tiarnan , Magos Adam 
Published: December 2003

ABSTRACTObjective  To evaluate whether innate surgical endoscopic skill could be predicted by ability to play computer video games.Design  Prospective study.Subjects  46 consecutive delegates attending an endoscopy workshop completed timed trials of laparoscopic and hysteroscopic skills stations and a commercial video game. These results were compared to identify any correlation.Results  There was a highly statistically significant correlation between skills tests and game time.Conclusion  This finding could be utilized to identify aptitude prior to or during surgical training.
Laparoscopic management of an ovarian ectopic pregnancy after intracytoplasmic sperm injection
Authors: Atabekoglu Cem S. , Bulent Berker , Ilkkan Dunder 
Published: December 2003

ABSTRACTObjective  To report a case of laparoscopic management of a patient with a ruptured primary ovarian pregnancy following ovulation induction, intracytoplasmic sperm injection and embryo transfer.Methods  The clinical records of the patient were reviewed.Results  Laparoscopy was performed in a patient with suspicion of a ruptured ectopic pregnancy. Pathological examination confirmed the presence of ovarian tissue around the chorionic villi. The patient made an uneventful postoperative recovery and was discharged on postoperative day 3. Follow up showed a gradual decrease of human chorionic gonadotrophin concentrations until a negative result (<5 mIU mL−1) was obtained.Conclusion  The laparoscopic approach is feasible and should be attempted both for the diagnosis and treatment of ovarian ectopic pregnancy, especially in those patients desirous of having children with the aid of assisted reproductive techniques.
Evaluation of intrauterine disorders by hysteroscopy and transvaginal sonography
Authors: Feng Limin , Li Dingheng 
Published: December 2003

ABSTRACTObjective  To compare the diagnostic accuracy of transvaginal sonography and hysteroscopy for intrauterine disorders.Design  300 patients were investigated by transvaginal sonography for abnormal vaginal bleeding. Of these, 112 had subsequent hysteroscopic examination and then had concomitant surgery.Results  The accuracy of findings at hysteroscopy and transvaginal ultrasonography were compared with the histopathological and surgical results as the gold standard diagnosis. The sensitivity, specificity, positive predictive value and negative predictive value of transvaginal ultrasonography were 77.4%, 50%, 49% and 78.1%, respectively, for transvaginal ultrasonography, and those of hysteroscopy were 92.3%, 97.4%, 97.3% and 92.6% respectively.Conclusion  Hysteroscopy is quick, well tolerated, and more accurate in detecting intrauterine pathology than transvaginal ultrasonography. The uterine cavity can be observed directly under hysteroscopy and this examination can provide a high diagnostic accuracy. Biopsy and treatment can be done at the time of the hysteroscopic examination. Thus it is preferable to transvaginal ultrasound examination.
A randomized prospective trial of rigid and flexible hysteroscopy in an outpatient setting
Authors: Baxter Andrew J. , Beck Barbara , Phillips Kevin 
Published: December 2003

ABSTRACTObjective  To compare flexible and rigid hysteroscopy in an outpatient hysteroscopy clinic.Design  A randomized, single‐blinded prospective study.Setting  A one‐stop, outpatient hysteroscopy clinic in a district general hospital.Subjects  96 women referred to the clinic with abnormal uterine bleeding.Main outcome measures  Patient pain scores, local anaesthetic usage, need for cervical dilation, quality of view, correlation of clinical and histological findings, duration of procedure, operator's assessment of the ease of the procedure.Results  Data from 83 women were analysed; three declined to enter the study, one failed to complete the pain scores and nine also had an operative hysteroscopy. Immediate median pain scores were statistically lower in the flexible hysteroscopy group, 1.2 vs. 3.6 (P = 0.001). The difference persisted 30 min after the procedure (0.4 vs. 1.1, P = 0.031). Pain experienced with endometrial biopsy was similar in the two groups (2.5 vs. 3.0, P = 0.16). There were no statistical differences between the two study arms with regard to procedure duration, quality of view, need for cervical dilation, anaesthetic usage or operator assessment of the ease of the procedure. There was agreement in clinical and histological diagnoses in all cases. The operators’ assessment of patients’ pain level correlated highly with patient pain scores. There were no statistically significant differences in any end‐point between the two operators.Conclusion  Flexible hysteroscopy is associated with lower levels of patient discomfort than rigid hysteroscopy. Other study variables were comparable for the two types of hysteroscopy.
Development of a GIS‐based Methodology for Quantifying Predation Risk in a Spatial Context
Authors: Kliskey Andrew D , Byrom Andrea E 
Published: December 2003

AbstractWe used GIS‐based techniques and inductive‐spatial modelling to analyse spatial interactions between predator and prey populations, a unique example of an extension to an existing ecological approach. The approach identifies spatial predictors of predation and is demonstrated for braided riverbed habitat in the Mackenzie Basin, New Zealand. This habitat is highly modified and is the focus of intensive management because of the presence of introduced mammalian predators and their native prey (primarily nests of ground‐nesting native birds that are extremely vulnerable to predators). Native prey are currently in decline due to predation; GIS techniques therefore have the potential to augment conventional ecological techniques and management practices. Predation risk to nests of ground‐nesting birds was interpolated across an area using inverse distance weighting. A linear regression model for spatio‐temporal predictors of nest predation was deter‐mined using a predation risk surface and three separate surfaces representing predator abundance, prey abundance, and habitat structure. These measures can enhance the non‐spatial results from conventional ecological inquiry and help solve pest management problems affecting the natural environment.