bluuebunny/crossref_metadata_2025_split huggingface dataset:
A time‐dependent discrimination index for survival data
Authors: Antolini Laura , Boracchi Patrizia , Biganzoli Elia 
Published: November 2005

AbstractTo derive models suitable for outcome prediction, a crucial aspect is the availability of appropriate measures of predictive accuracy, which have to be usable for a general class of models. The Harrell'sCdiscrimination index is an extension of the area under the ROC curve to the case of censored survival data, which owns a straightforward interpretability. For a model including covariates with time‐dependent effects and/or time‐dependent covariates, the original definition ofCwould require the prediction of individual failure times, which is not generally addressed in most clinical applications. Here we propose a time‐dependent discrimination indexCtdwhere the whole predicted survival function is utilized as outcome prediction, and the ability to discriminate among subjects having different outcome is summarized over time.Ctdis based on a novel definition of concordance: a subject who developed the event should have a less predicted probability of surviving beyond his/her survival time than any subject who survived longer. The predicted survival function of a subject who developed the event is compared to: (1) that of subjects who developed the event before his/her survival time, and (2) that of subjects who developed the event, or were censored, after his/her survival time. Subjects who were censored are involved in comparisons with subjects who developed the event before their observed times. The index reduces to the previousCin the presence of separation between survival curves on the whole follow‐up. A confidence interval forCtdis derived using the jackknife method on correlated one‐sampleU‐statistics.The proposed index is used to evaluate the discrimination ability of a model, including covariates having time‐dependent effects, concerning time to relapse in breast cancer patients treated with adjuvant tamoxifen. The model was obtained from 596 patients entered prospectively at Istituto Nazionale per lo Studio e la Cura dei Tumori di Milano (INT). The model discrimination ability was validated on an independent testing data set of 175 patients provided by Centro Regionale Indicatori Biochimici di Tumore (CRIBT) in Venice. Copyright © 2005 John Wiley & Sons, Ltd.
Evaluating technologies for classification and prediction in medicine
Authors: Pepe M. S. 
Published: November 2005

AbstractModern technologies promise to provide new ways of diagnosing disease, detecting subclinical disease, predicting prognosis, selecting patient specific treatment, identifying subjects at risk for disease, and so forth. Advances in genomics, proteomics and imaging modalities in particular hold great potential for assisting with classification/prediction in medicine. Before a classifier can be adopted for routine use in health care, its classification accuracy must be determined. Standards for evaluating new clinical classifiers however, lag far behind the well established standards that exist for evaluating new clinical treatments.In this paper, we discuss a phased approach to developing a new classifier (or biomarker). It mirrors the internationally established phase 1–2–3 paradigm for therapeutic drugs. The defined phases lead to a logical sequence of studies for classifier development. We emphasize that evaluating classification accuracy is fundamentally different from simply establishing association with outcome. Therefore, study objectives and designs differ from the familiar methods of clinical trials. We discuss these briefly for each phase.Finally, we argue that classifier development requires some rethinking of traditional data analysis techniques. As an example we show that maximizing the likelihood function to fit a logistic regression model to multiple predictors, can yield a poor classifier. Instead we demonstrate that an approach that maximizes an alternative objective function characterizing classification accuracy performs better. Copyright © 2005 John Wiley & Sons, Ltd.
Bayesian back‐calculation using a multi‐state model with application to HIV
Authors: Sweeting Michael J. , De Angelis Daniela , Aalen Odd O. 
Published: November 2005

AbstractBack‐calculation is a method of obtaining estimates of the number of infections of a disease over time. Data on an endpoint of the disease, together with knowledge of the time from infection to endpoint, allows reconstruction of the incidence of infection. The technique has had much success when applied to the HIV epidemic, using incidence of AIDS diagnoses to inform past HIV infections. In recent years, the period from infection to AIDS has changed considerably due to new regimes of anti‐viral therapies. This has led to attempts to use incidence of first positive HIV test as an alternative basis for back‐calculation. Developing on earlier work, this paper explores the feasibility of a multi‐state formulation of the back‐calculation method that models the disease and diagnosis processes and uses HIV diagnoses as an endpoint. Estimation is carried out in a Bayesian framework, which naturally allows incorporation of external information to inform the diagnosis probabilities. The idea is illustrated on data from the HIV epidemic in homosexuals in England and Wales. Copyright © 2005 John Wiley & Sons, Ltd.
Grid support of a wind farm with active stall wind turbines and AC grid connection
Authors: Hansen Anca D. , Sørensen Poul , Iov Florin , Blaabjerg Frede 
Published: November 2005

AbstractOne of the main concerns in the grid integration of large wind farms is their ability to behave as active controllable components in the power system. This article presents the design of a new integrated power control system for a wind farm made up exclusively of active stall wind turbines with AC grid connection. The designed control system has the task of enabling such a wind farm to provide the best grid support. It is based on two control levels: a supervisory control level, which controls the power production of the whole farm by sending out reference signals to each individual wind turbine, and a local control level, which ensures that the reference power signals at the wind turbine level are reached. The ability of active stall wind farms with AC grid connection to control the power production to the reference power ordered by the operators is assessed and discussed by means of simulations. Copyright © 2005 John Wiley & Sons, Ltd.
Conservation analysis of large biochemical networks
Authors: Vallabhajosyula Ravishankar Rao , Chickarmane Vijay , Sauro Herbert M. 
Published: November 2005

AbstractMotivation: Large biochemical networks pose a unique challenge from the point of view of evaluating conservation laws. The computational problem in most cases exceeds the capability of available software tools, often resulting in inaccurate computation of the number and form of conserved cycles. Such errors have profound effects on subsequent calculations, particularly in the evaluation of the Jacobian which is a critical quantity in many other calculations. The goal of this paper is to outline a new algorithm that is computationally efficient and robust at extracting the correct conservation laws for very large biochemical networks.Results: We show that our algorithm can perform the conservation analysis of large biochemical networks, and can evaluate the correct conserved cycles when compared with other similar software tools. Biochemical simulators such as Jarnac and COPASI are successful at extracting only a subset of the conservation laws that our algorithm can. This is illustrated with examples for some large networks which show the advantages of our method.Availability: The software is available as part of the latest release of Systems Biology Workbench (SBW version 2.5.0) and can be downloaded from . The software is licensed under the BSD open source license and is freely available at sourceforge.Contact: rrao@kgi.edu
Application of latent semantic analysis to protein remote homology detection
Authors: Dong Qi-wen , Wang Xiao-long , Lin Lei 
Published: November 2005

Abstract
Motivation: Remote homology detection between protein sequences is a central problem in computational biology. The discriminative method such as the support vector machine (SVM) is one of the most effective methods. Many of the SVM-based methods focus on finding useful representations of protein sequence, using either explicit feature vector representations or kernel functions. Such representations may suffer from the peaking phenomenon in many machine-learning methods because the features are usually very large and noise data may be introduced. Based on these observations, this research focuses on feature extraction and efficient representation of protein vectors for SVM protein classification.
Results: In this study, a latent semantic analysis (LSA) model, which is an efficient feature extraction technique from natural language processing, has been introduced in protein remote homology detection. Several basic building blocks of protein sequences have been investigated as the ‘words’ of ‘protein sequence language’, including N-grams, patterns and motifs. Each protein sequence is taken as a ‘document’ that is composed of bags-of-word. The word-document matrix is constructed first. The LSA is performed on the matrix to produce the latent semantic representation vectors of protein sequences, leading to noise-removal and smart description of protein sequences. The latent semantic representation vectors are then evaluated by SVM. The method is tested on the SCOP 1.53 database. The results show that the LSA model significantly improves the performance of remote homology detection in comparison with the basic formalisms. Furthermore, the performance of this method is comparable with that of the complex kernel methods such as SVM-LA and better than that of other sequence-based methods such as PSI-BLAST and SVM-pairwise.
Availability: The source codes are freely available at or upon request from the authors.
Contact: qwdong@insun.hit.edu.cn
Identification of plant microRNA homologs
Authors: Dezulian Tobias , Remmert Michael , Palatnik Javier F. , Weigel Detlef , Huson Daniel H. 
Published: November 2005

Abstract
Summary: MicroRNAs (miRNAs) are a recently discovered class of non-coding RNAs that regulate gene and protein expression in plants and animals. MiRNAs have so far been identified mostly by specific cloning of small RNA molecules, complemented by computational methods. We present a computational identification approach that is able to identify candidate miRNA homologs in any set of sequences, given a query miRNA. The approach is based on a sequence similarity search step followed by a set of structural filters.
Availability: microHARVESTER is offered as a web-service and additionally as source code upon request at
Contact: dezulian@informatik.uni-tuebingen.de
Induced inaccessibility and accessibility in the oat powdery mildew system: insights gained from use of metabolic inhibitors and silicon nutrition
Authors: PRATS ELENA , CARVER TIMOTHY L. W. , LYNGKJÆR MICHAEL F. , ROBERTS PETE C. , ZEYEN RICHARD J. 
Published: November 2005

SUMMARYFungal‐induced inaccessibility in oat to Blumeria graminis requires active cell processes. These are reiterative de novo cell processes involved in inherent penetration resistance. Therefore, induced inaccessibility may well involve cellular memory of the initial attack. Phenylpropanoid biosynthesis inhibitors (AOPP and OH‐PAS) and phosphate scavengers (DDG and d‐mannose) strongly suppressed induced inaccessibility, but silicon nutrition had no effect. Induced accessibility was modulated by the presence of fungal haustoria inside cells. Haustoria actively suppress or reprogram infected plant cells toward a constant state of penetration susceptibility. Neither inhibitor treatments nor silicon nutrition affected fungal‐induced accessibility.
National audit of continence care for older people: results of a pilot study*
Authors: Wagg Adrian , Mian Sarah , Lowe Derek , Potter Jonathan , Michael Pearson MD FRCP  
Published: November 2005

AbstractIntroduction and aim  Bladder and bowel problems are common in the elderly and are associated with a considerable morbidity and impact on quality of life. Inequalities in service provision and access to services have been recognized but there has been no systematic approach to measuring the quality of continence care for older people. This study aimed to develop quality standards, to assess the reliability and utility of the resulting audit package and to report on the standards of care provided in primary care, secondary care and care home setting.Method  Fifteen sites in secondary care, primary care and in long‐term care settings were randomly selected to pilot the audit package. Data collectors completed audit questionnaires relating to the structure [organization] of care, the outcomes of care, and the process of care for 20 subjects with urinary incontinence and 10 subjects with faecal or double incontinence.  Results  The audit tool was reliable (median kappa score of 0.7). Access to integrated continence services, as defined by Good Practice in Continence Services was inadequate. Eighty‐five per cent of hospitals had no written policy for continence care. There were deficiencies in obtaining information, in carrying out basic and specialist examinations and investigations and in determining the cause of incontinence. There was a high prevalence of catheter use in secondary care settings.Conclusion  The pilot has indicated significant inadequacies in continence care and demonstrates that in many sites the National Service Framework milestone for integrated continence services has not been met. A national audit of continence care is required to determine the extent of inadequate continence care.
Measuring the perceived impact of facilitation on implementing recommendations from external assessment: lessons from the Dutch visitatie programme for medical specialists
Authors: Lombarts M. J. M. H. (Kiki) , Klazinga N. S. (Niek) , Redekop K (Ken) 
Published: November 2005

AbstractObjective  To evaluate the impact of facilitation by management consultants on implementing recommendations from external quality assessment (visitatie).Design  Data collection through a postal survey amongst 205 medical specialists, representing 50 hospital‐based specialist groups in  the  Netherlands. Setting  Under the auspices of the specialty societies of surgeons, paediatricians and gynaecologists, 25 groups were offered ∼20 h of management consulting to support the implementation of recommendations for quality improvement and were compared to 25 specialist groups not receiving the support.Intervention  The Quality Consultation (QC) took a site‐specific multifaceted implementation approach.Main measures  Self‐reported degree of implementation of recommendations, specialists’ judgement of implementation result and process; experienced obstructing factors in implementing recommendations.Results  The response rate was 54% (n = 110). The supported specialist groups were more successful in partially or fully implementing the recommendations from external peer assessment: 66.1% vs. 53.8%. The implementation result and process were also rated significantly higher for the supported groups. The supported groups reported significantly less (P < 0.005) obstructing factors; in particular for the barriers ‘expectation of implementation advantages’, ‘acceptance of the recommendations’ and ‘assessed self‐efficacy’. The experienced obstructing factors are strongly related with the degree of implementation (spearman rho 0.57–32.5%).Conclusions  This study suggests QC is a powerful implementation strategy. It also shows the limitations of merely quantitatively analysing multifaceted strategies: it does not offer any insight into the ‘black box’ of the QC. It is recommended that these limitations are met by also exploring multifaceted strategies qualitatively.
Speciation in reverse: morphological and genetic evidence of the collapse of a three‐spined stickleback (Gasterosteus aculeatus) species pair
Authors: TAYLOR E. B. , BOUGHMAN J. W. , GROENENBOOM M. , SNIATYNSKI M. , SCHLUTER D. , GOW J. L. 
Published: November 2005

AbstractHistorically, six small lakes in southwestern British Columbia each contained a sympatric species pair of three‐spined sticklebacks (Gasterosteus aculeatus). These pairs consisted of a ‘benthic’ and ‘limnetic’ species that had arisen postglacially and, in four of the lakes, independently. Sympatric sticklebacks are considered biological species because they are morphologically, ecologically and genetically distinct and because they are strongly reproductively isolated from one another. The restricted range of the species pairs places them at risk of extinction, and one of the pairs has gone extinct after the introduction of an exotic catfish. In another lake, Enos Lake, southeastern Vancouver Island, an earlier report suggested that its species pair is at risk from elevated levels of hybridization. We conducted a detailed morphological analysis, as well as genetic analysis of variation at five microsatellite loci for samples spanning a time frame of 1977 to 2002 to test the hypothesis that the pair in Enos Lake is collapsing into a hybrid swarm. Our morphological analysis showed a clear breakdown between benthics and limnetics. Bayesian model‐based clustering indicated that two morphological clusters were evident in 1977 and 1988, which were replaced by 1997 by a single highly variable cluster. The most recent 2000 and 2002 samples confirm the breakdown. Microsatellite analysis corroborated the morphological results. Bayesian analyses of population structure in a sample collected in 1994 indicated two genetically distinct populations in Enos Lake, but only a single genetic population was evident in 1997, 2000, and 2002. In addition, genetic analyses of samples collected in 1997, 2000, and 2002 showed strong signals of ‘hybrids’; they were genetically intermediate to parental genotypes. Our results support the idea that the Enos Lake species pair is collapsing into a hybrid swarm. Although the precise mechanism(s) responsible for elevated hybridization in the lake is unknown, the demise of the Enos Lake species pair follows the appearance of an exotic crayfish,Pascifasticus lenisculus, in the early 1990s.
Screening for rapidly evolving genes in the ectomycorrhizal fungusPaxillus involutususing cDNA microarrays
Authors: LE QUÉRÉ ANTOINE , ASTRUP ERIKSEN KASPER , RAJASHEKAR BALAJI , SCHÜTZENDÜBEL ANDRES , CANBÄCK BJÖRN , JOHANSSON TOMAS , TUNLID ANDERS 
Published: November 2005

AbstractWe have examined the variations in gene content and sequence divergence that could be associated with symbiotic adaptations in the ectomycorrhizal fungusPaxillus involutusand the closely related speciesPaxillus filamentosus. Strains with various abilities to form mycorrhizae were analysed by comparative genomic hybridizations using a cDNA microarray containing 1076 putative unique genes ofP. involutus.To screen for genes diverging at an enhanced and presumably non‐neutral rate, we implemented a simple rate test using information from both the variations in hybridizations signal and data on sequence divergence of the arrayed genes relative to the genome ofCoprinus cinereus.C. cinereusis a free‐living saprophyte and is the closest evolutionary relative toP. involutusthat has been fully sequenced. Approximately 17% of the genes investigated were detected as rapidly diverging withinPaxillus. Furthermore, 6% of the genes varied in copy numbers between the analysed strains. Genome rearrangements associated with this variation including duplications and deletions may also play a role in adaptive evolution. The cohort of divergent and duplicated genes showed an over‐representation of either orphans, genes whose products are located at membranes, or genes encoding for components of stress/defence reactions. Some of the identified genomic changes may be associated with the variation in host specificity of ectomycorrhizal fungi. The proposed procedure could be generally applicable to screen for rapidly evolving genes in closely related strains or species where at least one has been sequenced or characterized by expressed sequence tag analysis.
Microsatellite analysis reveals strong but differential impact of a social parasite on its two host species
Authors: FISCHER‐BLASS BIRGIT , HEINZE JÜRGEN , FOITZIK SUSANNE 
Published: November 2005

AbstractThe speed and the dynamics of the co‐evolutionary process strongly depend on the relative strengths of reciprocal selection pressures exerted by the interacting species. Here, we investigate the influence of an obligate social parasite, the slave‐making ant Harpagoxenus sublaevis, on populations of the two main host species Leptothorax acervorum and Leptothorax muscorum from a German ant community. A combination of genetic and demographic data allowed us to analyse the consequences of raiding pressure on the hosts’ life history and possible host preferences of the parasite. We can demonstrate that slave raids during which the social parasite pillages brood from neighbouring host colonies are both frequent and extremely destructive for both host species. Microsatellite analysis showed that, on average, a single slave‐maker colony conducts more than three raids per year and that host colonies mostly perish in the aftermath of these parasite attacks. Only in few cases, surviving nests of previously raided host colonies were found in the surroundings of slave‐maker colonies. As a consequence of the high prevalence of parasites and their recurrent and devastating slave raids on host colonies, the life expectancy of host colonies was severely reduced. Combining our results on host‐specific parasitic colony founding and raiding frequencies with the post‐raid survival rate, we can demonstrate an overall higher mortality rate for the smaller host species L. muscorum. This might be caused by a preference of H. sublaevis for this secondary host species as demographic data on host species usage indicate.