bluuebunny/crossref_metadata_2025_split huggingface dataset:
BicAT: a biclustering analysis toolbox
Authors: Barkow Simon , Bleuler Stefan , Prelić Amela , Zimmermann Philip , Zitzler Eckart 
Published: March 2006

Abstract
Summary: Besides classical clustering methods such as hierarchical clustering, in recent years biclustering has become a popular approach to analyze biological data sets, e.g. gene expression data. The Biclustering Analysis Toolbox (BicAT) is a software platform for clustering-based data analysis that integrates various biclustering and clustering techniques in terms of a common graphical user interface. Furthermore, BicAT provides different facilities for data preparation, inspection and postprocessing such as discretization, filtering of biclusters according to specific criteria or gene pair analysis for constructing gene interconnection graphs. The possibility to use different biclustering algorithms inside a single graphical tool allows the user to compare clustering results and choose the algorithm that best fits a specific biological scenario. The toolbox is described in the context of gene expression analysis, but is also applicable to other types of data, e.g. data from proteomics or synthetic lethal experiments.
Availability: The BicAT toolbox is freely available at and runs on all operating systems. The Java source code of the program and a developer's guide is provided on the website as well. Therefore, users may modify the program and add further algorithms or extensions.
Contact: barkow@tik.ee.ethz.ch
XQTav: an XQuery processor for Taverna environment
Authors: Sroka Jacek , Kaczor Grzegorz , Tyszkiewicz Jerzy , Kierzek Andrzej M. 
Published: March 2006

Abstract
Taverna workbench is an environment for construction, visualization and execution of bioinformatic workflows that integrate specialized tools available through the internet. It is gaining popularity fast, because of supporting the most important bioinformatic services and its simple, yet robust graphical notation. Here we present XQTav—an extension of Taverna that provides full integration with XQuery (the query language for XML) engine. XQTav allows execution of XQuery scripts in Taverna workflow diagrams. All existing Taverna processors can be accessed in the XQuery scripts. This provides an alternative way of specifying subworkflows in Taverna and is useful when one deals with query-like algorithms (e.g. filters and inner joins). Moreover, XQtav may be used to automatically generate an XQuery script that is equivalent to Taverna's workflow. This constitutes another way of creating and enacting bioinformatic workflows: overall structure of a diagram is drawn in Taverna environment, XQuery code is generated and possibly adjusted by hand. It can be executed by XQuery engines or incorporated into other software environments.
Availability: XQtav is an open source software. It may be downloaded from . The page also contains various tutorials and examples, including the one described in this report.
Contact: sroka@mimuw.edu.pl, a.kierzek@surrey.ac.uk
Phylogeny-independent detection of functional residues
Authors: Pazos Florencio , Rausell Antonio , Valencia Alfonso 
Published: March 2006

Abstract
Motivation: Current projects for the massive characterization of proteomes are generating protein sequences and structures with unknown function. The difficulty of experimentally determining functionally important sites calls for the development of computational methods. The first techniques, based on the search for fully conserved positions in multiple sequence alignments (MSAs), were followed by methods for locating family-dependent conserved positions. These rely on the functional classification implicit in the alignment for locating these positions related with functional specificity. The next obvious step, still scarcely explored, is to detect these positions using a functional classification different from the one implicit in the sequence relationships between the proteins. Here, we present two new methods for locating functional positions which can incorporate an arbitrary external functional classification which may or may not coincide with the one implicit in the MSA. The Xdet method is able to use a functional classification with an associated hierarchy or similarity between functions to locate positions related to that classification. The MCdet method uses multivariate statistical analysis to locate positions responsible for each one of the functions within a multifunctional family.
Results: We applied the methods to different cases, illustrating scenarios where there is a disagreement between the functional and the phylogenetic relationships, and demonstrated their usefulness for the phylogeny-independent prediction of functional positions.
Availability: All computer programs and datasets used in this work are available from the authors for academic use.
Contact: pazos@cnb.uam.es
Supplementary information: Supplementary data are available at
UniSave: the UniProtKB Sequence/Annotation Version database
Authors: Leinonen Rasko , Nardone Francesco , Zhu Weimin , Apweiler Rolf 
Published: March 2006

Abstract
Summary: The UniProtKB Sequence/Annotation Version database (UniSave) is a comprehensive archive of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions. All changed Swiss-Prot and TrEMBL entries are loaded into the UniSave as part of the public bi-weekly UniProtKB releases. Unlike the UniProtKB, which contains only the latest Swiss-Prot and TrEMBL entry versions, the UniSave provides access to previous versions of these entries.
Availability:
Contact: rolf.apweiler@ebi.ac.uk
Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients
Authors: Broët Philippe , Kuznetsov Vladimir A. , Bergh Jonas , Liu Edison T. , Miller Lance D. 
Published: March 2006

AbstractMotivation: In recent years, microarray technology has revealed many tumor-expressed genes prognostic of clinical outcomes in early-stage breast cancer patients. However, in the presence of cured patients, evaluating gene effect on time to relapse is quite complex since it may affect either the probability of never experiencing a relapse (cure effect) or the time to relapse among the uncured patients (disease progression effect) or both. In this context, we propose a simple and an efficient method for identifying gene expression changes that characterize early and late recurrence for uncured patients.Results: Simulation results show the good performance of the proposed statistic for detecting a disease progression effect. In a study of early-stage breast cancer, our results show that the proposed statistic provides a more powerful basis for gene selection than the classical Cox model-based statistic. From a biological perspective, many of the genes identified here as associated with the speed of disease recurrence have known roles in tumorigenesis.Contact: broet@vjf.inserm.fr; kuznetsov@gis.a-star.edu.sg
AtMBD9: a protein with a methyl‐CpG‐binding domain regulates flowering time and shoot branching in Arabidopsis
Authors: Peng Mingsheng , Cui Yuhai , Bi Yong‐Mei , Rothstein Steven J. 
Published: March 2006

SummaryThe functional characterization of mammalian proteins containing a methyl‐CpG‐binding domain (MBD) has revealed that MBD proteins can decipher the epigenetic information encoded by DNA methylation, and integrate DNA methylation, modification of chromatin structure and repression of gene expression. The Arabidopsis genome has 13 putative genes encoding MBD proteins, and no specific biological function has been defined for any AtMBD genes. In this study, we identified three T‐DNA insertion mutant alleles at the AtMBD9 locus, and found that all of them exhibited obvious developmental abnormalities. First, the atmbd9 mutants flowered significantly earlier than wild‐type plants. The expression of FLOWERING LOCUS C (FLC), a major repressor of Arabidopsis flowering, was markedly attenuated by the AtMBD9 mutations. This FLC transcription reduction was associated with a significant decrease in the acetylation level in histone H3 and H4 of FLC chromatin in the atmbd9 mutants. Secondly, the atmbd9 mutants produced more shoot branches by increasing the outgrowth of axillary buds when compared with wild‐type plants. The two known major factors controlling the outgrowth of axillary buds in Arabidopsis, auxin and the more axillary growth (MAX) pathway, were found not to be involved in producing this enhanced shoot branching phenotype in atmbd9 mutants, indicating that AtMBD9 may regulate a novel pathway to control shoot branching. This pathway is not related to FLC expression as over‐expression of FLC in atmbd9‐2 restored its flowering time to one similar to that of the wild type, but did not alter the shoot branching phenotype.
A mutation in the uvi4 gene promotes progression of endo‐reduplication and confers increased tolerance towards ultraviolet B light
Authors: Hase Yoshihiro , Trung Khuat Huu , Matsunaga Tsukasa , Tanaka Atsushi 
Published: March 2006

SummaryWe have isolated and characterized a new ultraviolet B (UV‐B)‐resistant mutant, uvi4 (UV‐B‐insensitive 4), of Arabidopsis. The fresh weight (FW) of uvi4 plants grown under supplemental UV‐B light was more than twice that of the wild‐type. No significant difference was found in their ability to repair the UV‐B‐induced cyclobutane pyrimidine dimers, or in the amount of UV‐B absorptive compounds, both of which are well‐known factors that contribute to UV sensitivity. Positional cloning revealed that the UVI4 gene encodes a novel basic protein of unknown function. We found that the hypocotyl cells in uvi4 undergo one extra round of endo‐reduplication. The uvi4 mutation also promoted the progression of endo‐reduplication during leaf development. The UVI4 gene is expressed mainly in actively dividing cells. In the leaves of PUVI4::GUS plants, the GUS signal disappeared in basipetal fashion as the leaf developed. The total leaf blade area was not different between uvi4 and the wild‐type through leaf development, while the average cell area in the adaxial epidermis was considerably larger in uvi4, suggesting that the uvi4 leaves have fewer but larger epidermal cells. These results suggest that UVI4 is necessary for the maintenance of the mitotic state, and the loss of UVI4 function stimulated endo‐reduplication. Tetraploid Arabidopsis was hyper‐resistant to UV‐B compared to diploid Arabidopsis, suggesting that the enhanced polyploidization is responsible for the increased UV‐B tolerance of the uvi4 mutant.
Colorectal cancer – a prospective evaluation of symptom duration and GP referral patterns in an inner city teaching hospital
Authors: Khattak I. , Eardley N. J. , Rooney P. S. 
Published: March 2006

AbstractObjective  A high percentage of colorectal cancer patients (CRC) present as an emergency. Our aim was to evaluate delays in referral based on patient and general practitioner (GP) factors to see if there was any difference between elective and emergency patients.Method  Symptom questionnaires were prospectively collected from 101 consecutive patients presenting to a single colorectal unit (58 male, 43 female; median age 72 years) and entered into a database. Questionnaires assessed time from symptom onset until first GP visit, time for GP to refer, and type of admission. Symptoms and Dukes stage were noted.Results  Fifty‐eight (57%) patients presented electively and 43 (43%) as an emergency. Eighty‐eight patients (87%) saw their GP of which 34 (39%) later presented as emergency; 13 (13%) did not see their GP. The median time before patients first sought medical advice was 30 days (0–1095 days). Median delay until treatment was 90 days (range 0–1460 days). Emergency patients waited a median of 11.5 days before visiting the GP, and elective a median of 49.5 days (P = 0.04) (Mann–Whitney U). Nine of 13 patients who did not see their GP presented as an emergency (median wait 44 days). The median time taken for a GP to refer to a hospital specialist was 28 days in elective patients and 14 days in the emergency group. (P = ns) Thirty (38%) patients took longer than six weeks to be referred (33% as an emergency). Thirty‐six patients had Dukes A or B and took a median of 30 days to first presentation. Sixty‐five had Dukes C or D and took a median of 32 days to first presentation. (P = ns)Conclusion  Emergency patients have symptoms for less time before seeking medical advice compared to elective patients. The duration of these symptoms is unrelated to the histological stage at diagnosis. Although the majority of GPs referred CRC patients within six weeks, there was no association between time taken to refer and mode of presentation. The factors that relate to disease stage occur before symptoms are acted on.
Nurse led flexible sigmoidoscopy in primary care – the first thousand patients
Authors: Maruthachalam K. , Stoker E. , Nicholson G. , Horgan A. F. 
Published: March 2006

AbstractObjectives  Secondary care Trusts have traditionally been providers of flexible sigmoidoscopy services in the United Kingdom. The aim of this study was to establish a Nurse‐led flexible sigmoidoscopy clinic that would provide a patient orientated service in a primary care setting.Patients and methods  A protocol driven flexible sigmoidoscopy clinic was established in a primary care setting. The first thousand patients who underwent flexible sigmoidoscopy at the community clinic were prospectively studied.Results  A nurse endoscopist performed 1002 procedures on 1000 patients. Median time from referral to flexible sigmoidoscopy was 35 days (Range 1–180 days). Two hundred and twenty‐two (22%) patients were diagnosed with significant colonic pathology including 25 (2.5%) patients with colorectal cancer. Median time from referral to histological diagnosis of colorectal cancer was 26 days (range 7–87 days). No complications were encountered. Patients who required further follow‐up were referred to a Consultant led (29%) or Nurse led clinic (5%) in secondary care. Patient satisfaction as assessed by postal questionnaire indicated that 447 (99%) patients were satisfied with the service.Conclusions  A community endoscopy clinic can provide a safe and effective flexible sigmoidoscopy service with high levels of patient satisfaction. Nurse Endoscopists can extend their role in primary care with adequate training and support from secondary care hospitals.
Work factors as predictors of persistent fatigue: a prospective study of nurses’ aides
Authors: Eriksen W 
Published: March 2006

Objectives:To identify work factors that predict persistent fatigue in nurses’ aides.Methods:The sample comprised 5547 Norwegian nurses’ aides, not on leave when they completed a mailed questionnaire in 1999. Of these, 4645 (83.7%) completed a second questionnaire 15 months later. The outcome measure was the occurrence of persistent fatigue, defined as having felt “usually fatigued” or “always fatigued” in daytime during the previous 14 days.Results:In respondents without persistent fatigue at baseline, medium and high work demands, heavy smoking, being single, and having long term health problems were associated with increased risk of persistent fatigue at follow up. Medium and high rewards for well done work, medium levels of leadership fairness, and regular physical exercise were associated with reduced risk of persistent fatigue at follow up. In respondents with persistent fatigue at baseline, medium and high levels of positive challenges at work, high support from immediate superior, medium feedback about quality of one’s work, and changes of work or work tasks that resulted in less heavy work or lower work pace were associated with increased odds of recovery (no persistent fatigue at follow up). Working in a nursing home and being intensely bothered by long term health problems were associated with reduced odds of recovery.Conclusions:High demands and lack of rewards at work may cause persistent fatigue in nurses’ aides. Reduction of demands, adequate feedback, and mental stimulation in the form of support and positive challenges may facilitate recovery in those who have persistent fatigue. Leaders in the health services may be in a position to regulate factors that influence the level of fatigue in nurses’ aides.
Does enhanced information exchange between social insurance physicians and occupational physicians improve patient work resumption? A controlled intervention study
Authors: Mortelmans A K , Donceel P , Lahaye D , Bulterys S 
Published: March 2006

Background:Patient work resumption after sickness absence varies even among patients with similar pathologies and characteristics. Explanations remain uncertain. One newly investigated field is “information asymmetry”, a situation in which critical information is not appropriately exchanged between stakeholders in disability management. It is hypothesised that information asymmetry between social insurance physicians and occupational physicians prolongs sickness absence.Objectives:To assess the influence of enhanced information exchange between these physicians on patient outcome.Methods:Non-randomised controlled intervention study. The setting was the work inability assessment consultation of social insurance physicians in Belgium. Inclusion criteria were: employee, age 18–50, and subacute (more than one month) sickness absence. The intervention was a structured information exchange (through the use of a communication form) between the patient’s social insurance physician and occupational physician. The intervention started when the patient’s sickness absence reached the subacute stage, and ended when the sickness absence benefit was ceased or the duration exceeded one year. The primary outcome measure was the sickness absence benefit status of the patient assessed one year after benefit onset.Results:Of the 1883 patients asked to enrol in the study, 1564 (84%) participated; 505 (32%) of 1564 patients were assigned to the intervention group and 1059 (68%) to the control group; 1553 (99%) of 1564 patients completed the study. In the intervention group, 86% received no sickness absence benefit at the end of the study, versus 84% in the control group (95% CI 0.91–1.15). No significant differences in other outcome parameters were obtained.Conclusions:Information exchange between physicians may not be enough to influence work resumption among patients on sickness absence. Further research on stakeholders’ information asymmetry and its effect on the outcome of patients are necessary. The complexity of information asymmetry in disability management cannot be underestimated.
Occupational sunlight exposure, polymorphism of glutathione S-transferase M1, and senile cataract risk: Table 1
Authors: Saadat M , Farvardin-Jahromi M 
Published: March 2006

Background:The pathogenesis of cataract is influenced by a number of factors including oxidative stress. Glutathione S-transferase (GST) catalyses the nucleophilic addition of the thiol of GST to electrophilic acceptors. It is important for detoxification of xenobiotics in order to protect tissues from oxidative damage.Objectives:To examine whether the interaction of polymorphism of GSTM1 gene and occupational sunlight exposure modulate the risk of cataract.Methods:Blood samples from 95 subjects with cataract and 95 age and sex matched healthy persons were collected. The genotypes of GSTM1 were determined using PCR.Results:The null genotype of GSTM1 was associated with an increase in cataract risk in the indoor workplace, but this association was not significant in the outdoor subjects.Conclusion:The active genotype of GSTM1 has lost its protective role in persons who work outdoors. It is suggested that activity of the GSTμ enzyme may be inhibited in the human lens after occupational exposure to UV light.
A probabilistic assessment of the impact of interventions on oncology nurses’ exposure to antineoplastic agents
Authors: Meijster T , Fransman W , van Hemmen J , Kromhout H , Heederik D , Tielemans E 
Published: March 2006

Objective:The main goal was to investigate the potential of a probabilistic approach for exposure assessment and use this information to evaluate the impact of a complex of policy actions/interventions on dermal exposure to antineoplastic agents among oncology nurses. The central theme of this study was to make optimal use of existing data, supplemented only with limited additional information from a questionnaire survey.Methods:A task based exposure model was used to estimate dermal exposure of the hands among oncology nurses in non-academic hospitals in the Netherlands. Monte Carlo simulation was used to integrate information from available (exposure) studies and generate exposure distributions for the total population of oncology nurses in both pre- and post-intervention situation. Graphs and descriptive statistics of the simulated exposure distributions were used to evaluate trends in population exposure.Results:The inventory showed that important intervention occurred in the preparation and administering of antineoplastic agents and in the handling of urine. Hardly any changes were identified in de nursing tasks. The use of gloves seemed to have decreased for a number of tasks. The results of the analysis show that the interventions did not affect the median exposure. However frequencies of occurrence of individuals with very high and very low total dermal exposures decreased substantially in the post-intervention situation. Analysis of the effect of pregnancy showed that pregnancy is very unlikely to influence exposure or any of the key input variables.Conclusions:The present study shows that the probabilistic approach adds valuable information to deterministic exposure assessment, especially when extrapolating data on a subpopulation to populations of individuals at large. The results show that the identified changes in the past decade in Dutch non-academic hospitals resulted in changes in the exposure distribution of antineoplastic agents among oncology nurses.
Occupational exposure to power frequency magnetic fields and risk of non-Hodgkin lymphoma
Authors: Karipidis K , Benke G , Sim M , Fritschi L , Yost M , Armstrong B , Hughes A M , Grulich A , Vajdic C M , Kaldor J , Kricker A 
Published: March 2006

Objectives:To investigate the risk of non-Hodgkin lymphoma (NHL) using a job-exposure matrix (JEM) to assess exposure to occupational magnetic fields at the power frequencies of 50/60 Hz.Methods:The study population consisted of 694 cases of NHL, first diagnosed between 1 January 2000 and 31 August 2001, and 694 controls from two regions in Australia, matched by age, sex and region of residence. A detailed occupational history was given by each subject. Exposure to power frequency magnetic fields was estimated using a population-based JEM which was specifically developed in the United States to assess occupational magnetic field exposure. The cumulative exposure distribution was divided into quartiles and adjusted odds ratios were calculated using the lowest quartile as the referent group.Results:For the total work history, the odds ratio (OR) for workers in the upper quartile of exposure was 1.48 (95% CI 1.02 to 2.16) compared to the referent (p value for trend was 0.006). When the exposure was lagged by 5 years the OR was 1.59 (95% CI 1.07 to 2.36) (p value for trend was 0.003). Adjusting for other occupational exposures did not significantly alter the results.Conclusions:These findings provide weak support for the hypothesis that occupational exposure to 50/60 Hz magnetic fields increases the risk of NHL.