| 1. |
- Carninci, P, et al.
(författare)
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The transcriptional landscape of the mammalian genome
- 2005
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 309:5740, s. 1559-1563
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Tidskriftsartikel (refereegranskat)abstract
- This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5′ and 3′ boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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| 2. |
- Mulder, J., et al.
(författare)
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Bayesian model selection of informative hypotheses for repeated measurements
- 2009
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Ingår i: Journal of mathematical psychology (Print). - : Elsevier. - 0022-2496 .- 1096-0880. ; 53:6, s. 530-546
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Tidskriftsartikel (refereegranskat)abstract
- When analyzing repeated measurements data, researchers often have expectations about the relations between the measurement means. The expectations can often be formalized using equality and inequality constraints between (i) the measurement means over time, (ii) the measurement means between groups, (iii) the means adjusted for time-invariant covariates, and (iv) the means adjusted for time-varying covariates. The result is a set of informative hypotheses. In this paper, the Bayes factor is used to determine which hypothesis receives most support from the data. A pivotal element in the Bayesian framework is the specification of the prior. To avoid subjective prior specification, training data in combination with restrictions on the measurement means are used to obtain so-called constrained posterior priors. A simulation study and an empirical example from developmental psychology show that this prior results in Bayes factors with desirable properties.
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| 3. |
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| 4. |
- Brose, Ulrich, et al.
(författare)
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Spatial aspects of food webs
- 2005
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Ingår i: Dynamic Food Webs. - London, UK : Elsevier. - 9780120884582 - 0120884585 ; , s. 463-469
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Konferensbidrag (refereegranskat)abstract
- Aspects of spatial scale have until recently been largely ignored in empirical and theoretical food web studies (e.g., Cohen & Briand 1984, Martinez 1992, but see Bengtsson et al. 2002, Bengtsson & Berg, this book). Most ecologists tend to conceptualize and represent food webs as static representations of communities, depicting a community assemblage as sampled at a particular point in time, or highly aggregated trophic group composites over broader scales of time and space (Polis et al. 1996). Moreover, most researchers depict potential food webs, which contain all species sampled and all potential trophic links based on literature reviews, several sampling events, or laboratory feeding trials. In reality, however, not all these potential feeding links are realized as not all species co-occur, and not all samples in space or time can contain all species (Schoenly & Cohen 1991), hence, yielding a variance of food web architecture in space (Brose et al. 2004). In recent years, food web ecologists have recognized that food webs are open systems – that are influence by processes in adjacent systems – and spatially heterogeneous (Polis et al. 1996). This influence of adjacent systems can be bottom-up, due to allochthonous inputs of resources (Polis & Strong 1996, Huxel & McCann 1998, Mulder & De Zwart 2003), or top-down due to the regular or irregular presence of top predators (e.g., Post et al. 2000, Scheu 2001). However, without a clear understanding of the size of a system and a definition of its boundaries it is not possible to judge if flows are internal or driven by adjacent systems. Similarly, the importance of allochthony is only assessable when the balance of inputs and outputs are known relative to the scale and throughputs within the system itself. At the largest scale of the food web – the home range of a predator such as wolf, lion, shark or eagle of roughly 50 km2 to 300 km2 –the balance of inputs and outputs caused by wind and movement of water may be small compared to the total trophic flows within the home range of the large predator (Cousins 1990). Acknowledging these issues of space, Polis et al (1996) argued that progress toward the next phase of food web studies would require addressing spatial and temporal processes. Here, we present a conceptual framework with some nuclei about the role of space in food web ecology. Although we primarily address spatial aspects, this framework is linked to a more general concept of spatio-temporal scales of ecological research.
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| 5. |
- de Boer, NKH, et al.
(författare)
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6-thioguanine treatment in inflammatory bowel disease : A critical appraisal by a European 6-TG working party
- 2006
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Ingår i: Digestion. - : S. Karger AG. - 0012-2823 .- 1421-9867. ; 73:1, s. 25-31
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Tidskriftsartikel (refereegranskat)abstract
- Recently, the suggestion to use 6-thioguanine (6-TG) as an alternative thiopurine in patients with inflammatory bowel disease (IBD) has been discarded due to reports about possible (hepato) toxicity. During meetings arranged in Vienna and Prague in 2004, European experts applying 6-TG further on in IBD patients presented data on safety and efficacy of 6-TG. After thorough evaluation of its risk-benefit ratio, the group consented that 6-TG may still be considered as a rescue drug in stringently defined indications in IBD, albeit restricted to a clinical research setting. As a potential indication for administering 6-TG, we delineated the requirement for maintenance therapy as well as intolerance and/or resistance to aminosalicylates, azathioprine, 6-mercaptopurine, methotrexate and infliximab. Furthermore, indications are preferred in which surgery is thought to be inappropriate. The standard 6-TG dosage should not exceed 25 mg daily. Routine laboratory controls are mandatory in short intervals. Liver biopsies should be performed after 6-12 months, three years and then three-yearly accompanied by gastroduodenoscopy, to monitor for potential hepatotoxicity, including nodular regenerative hyperplasia (NRH) and veno-occlusive disease (VOD). Treatment with 6-TG must be discontinued in case of overt or histologically proven hepatotoxicity. Copyright (c) 2006 S. Karger AG, Basel.
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| 6. |
- Engelfriet, P, et al.
(författare)
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Adherence to guidelines in the clinical care for adults with congenital heart disease: The Euro Heart Survey on adult congenital heart disease
- 2006
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Ingår i: European Heart Journal. - : Oxford University Press (OUP). - 1522-9645 .- 0195-668X. ; 27:6, s. 737-745
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Tidskriftsartikel (refereegranskat)abstract
- Aims To investigate the role of guidelines in structuring the clinical care for adult patients with congenital heart disease (CHD), and to assess adherence to the guidelines in Europe. Methods and results A selected number of current guidelines were chosen pertaining to operative procedures, investigations, and the use of medication ('interventions'). The source for this analysis was the database of the Euro Heart Survey on adult CHD, which contains retrospectively collected data on 4110 patients followed-up for a median of 5.1 years. For each guideline investigated, patients were selected from the database for whom the particular guideline was relevant. The selected cases were classified according to two criteria: was there an indication for the particular intervention and did the intervention take place? In this manner, cases of 'undue treatment' and 'insufficient treatment' were identified. Adherence to guidelines was found to be good in the case of operative procedures and prophylactic drug treatment. However, regarding diagnostic procedures there had been adherence to guidelines in only slightly more than half of the cases. Conclusion Guidelines have an important role in the actual clinical care of adults with CHD. However, large outcome studies are needed to develop more precise guidelines.
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| 7. |
- Engelfriet, P, et al.
(författare)
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The spectrum of adult congenital heart disease in Europe: morbidity and mortality in a 5 year follow-up period - The Euro Heart Survey on adult congenital heart disease
- 2005
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Ingår i: European Heart Journal. - : Oxford University Press (OUP). - 1522-9645 .- 0195-668X. ; 26:21, s. 2325-2333
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Tidskriftsartikel (refereegranskat)abstract
- Aims To describe clinical and demographic characteristics at baseline of a European cohort of adults with congenital heart disease (CHD) and to assess mortality and morbidity in a 5 year follow-up period. Methods and results Data collected as part of the Euro Heart Survey on adult CHD was analysed. This entailed information transcribed from the files of 4110 patients diagnosed with one of eight congenital heart conditions ('defects'), who consecutively visited the outpatient clinics of one of the participating centres in 1998. The patients were included retrospectively and followed until the end of 2003 for a median follow-up of 5.1 years. Notwithstanding their overall relatively good functional class and low mortality over the follow-up period, a considerable proportion of the patients had a history of endocarditis, arrhythmias, or vascular events. There were major differences between the eight defects, both in morbidity and regarding specific characteristics. Outcomes were worst in cyanotic defects and in the Fontan circulation, but a considerable proportion of the other patients also suffer from cardiac symptoms. In particular, arrhythmias are common. Conclusion The spectrum of adult CHD in Europe emerging from this survey is one of a predominantly young population with substantial morbidity but relatively low mortality in a 5 year period.
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| 8. |
- Krege, Susanne, et al.
(författare)
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European consensus conference on diagnosis and treatment of germ cell cancer: A report of the second meeting of the European Germ Cell Cancer Consensus Group (EGCCCG): Part I
- 2008
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Ingår i: European Urology. - : Elsevier BV. - 1873-7560 .- 0302-2838. ; 53:3, s. 478-496
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Forskningsöversikt (refereegranskat)abstract
- Objectives: The first consensus report presented by the European Germ Cell Cancer Consensus Group (EGCCCG) in the year 2004 has found widespread approval by many colleagues throughout the world. In November 2006, the group met a second time under the auspices of the Department of Urology of the Amsterdam Medical Center, Amsterdam, The Netherlands. Methods: Medical oncologists, urological surgeons, radiation oncologists as well as pathologists from several European countries reviewed and discussed the data that had emerged since the 2002 conference, and incorporated the new data into updated and revised guidelines. As for the first meeting, the methodology of evidence-based medicine (EBM) was applied. The results of the discussion were compiled by the writing committee. All participants have agreed to this final update. Results: The first part of the consensus paper describes the clinical presentation of the primary tumor, its treatment, the importance and treatment of testicular intraepithelial neoplasia (TIN), histological classification, staging and prognostic factors, and treatment of stage I seminoma and non-seminoma. Conclusions: Whereas the vast majority of the recommendations made in 2004 remain valid 3 yr later, refinements in the treatment of early- and advanced-stage testicular cancer have emerged from clinical trials. Despite technical improvements, expert clinical skills will continue to be one of the major determinants for the prognosis of patients with germ cell cancer. In addition, the particular needs of testicular cancer survivors have been acknowledged. (C) 2007 European Association of Urology. Published by Elsevier B.V. All rights reserved.
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| 9. |
- Krege, Susanne, et al.
(författare)
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European consensus conference on diagnosis and treatment of germ cell cancer: A report of the second meeting of the European Germ Cell Cancer Consensus Group (EGCCCG): Part II
- 2008
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Ingår i: European Urology. - : Elsevier BV. - 1873-7560 .- 0302-2838. ; 53:3, s. 497-513
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Forskningsöversikt (refereegranskat)abstract
- Objectives: The first consensus report that had been presented by the European Germ Cell Cancer Consensus Group (EGCCCG) in 2004 has found widespread approval by many colleagues throughout the world. In November 2006, the group met a second time under the auspices of the Department of Urology of the Amsterdam Medical Center, The Netherlands. Methods: Medical oncologists, urologic surgeons, radiation oncologists as well as pathologists from several European countries reviewed and discussed the data that had emerged since the 2002 conference and incorporated the new data into updated and revised guidelines. As for the first meeting the methodology of evidence-based medicine (EBM) was applied. The results of the discussion were compiled by the writing committee. All participants have agreed to this final update. Results: The second part of the consensus paper includes the treatment of metastasised disease, residual tumour resection, salvage therapy, follow-up, and late toxicities. Conclusions: Whereas the vast majority of the recommendations made in 2004 remain valid 3 yr later, refinements in the treatment of early-stage as well as of advanced-stage testicular cancer have emerged from clinical trials. Despite technical improvements, expert clinical skills will continue to be one of the major determinants for the prognosis of patients with germ cell cancer. in addition, the particular needs of testicular cancer survivors have been acknowledged. (C) 2007 European Association of Urology. Published by Elsevier B.V. All rights reserved.
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