Sun, 20 Jul 2008 21:39:42 BST CiteULike: jyuh Thomsen http://www.citeulike.org/user/jyuh/author/Thomsen CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/jyuh/article/1205200 <i>Genome Biology, Vol. 8 (02 April 2007), R45.</i> Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 ESTs Jan Gorodkin Susanna Cirera Jakob Hedegaard Michael Gilchrist Frank Panitz Claus Jorgensen Karsten Scheibye-Knudsen Troels Arvin Steen Lumholdt Milena Sawera Trine Green Bente Nielsen Jakob Havgaard Carina Rosenkilde Jun Wang Heng Li Ruiqiang Li Bin Liu Songnian Hu Wei Dong Wei Li Jun Yu Jiang Wang Hans-Henrik Staerfeltd Rasmus Wernersson Lone Madsen Bo Thomsen Henrik Hornshoj Zhan Bujie Xuegang Wang Xuefei Wang Lars Bolund Soren Brunak Huanming Yang Christian Bendixen Merete Fredholm doi:10.1186/gb-2007-8-4-r45 Genome Biology, Vol. 8 (02 April 2007), R45. 2007-04-03T22:50:40-00:00 2007 Genome Biology 1465-6906 8 R45 microarray pig http://www.citeulike.org/user/jyuh/article/2896224 <i>Family practice, Vol. 23, No. 4. (August 2006), pp. 407-413.</i><br /><br />BACKGROUND: Evaluation of health care contacts from first events alone often misses large amounts of potentially important data and may produce different results than evaluation of all data including recurrent events. OBJECTIVE: We aim to bring the different methodological approaches for analysing longitudinal health care data to the attention of researchers in primary care. METHODS: We used hospital admission data from the Ebeltoft Health Promotion Project, a randomized trial in primary care examining the effect of preventive health checks. Comparisons included three randomized groups: an intervention group receiving health checks, a group where intervention consisted of a health check followed by a health discussion with the GP and one control group. RESULTS: Both intervention groups had approximately 20% fewer hospital admissions than the control group over a 6 year period. If dependence among recurrent events is excluded, such a reduction amounts to a highly significant effect. Use of the standard Poisson distribution for analysing recurrent events and exclusion of their dependent structure causes data interpretation to be incorrect, because the model does not account for the extra variability between persons; the resulting 95% CIs would therefore be too small. CONCLUSION: Analysis of health care contacts should embrace both first and recurrent events and it should use a model appropriate to these data. An individual rate model that includes a parameter of an unspecified individual event distribution frailty may be a natural choice when analysing longitudinal data of contacts to the health care system in broad terms. Methods for analysing recurrent events in health care data. Examples from admissions in Ebeltoft Health Promotion Project. JL Thomsen ET Parner Family practice, Vol. 23, No. 4. (August 2006), pp. 407-413. 2008-06-15T14:05:32-00:00 2006 Family practice 0263-2136 23 4 407 413 cox recutrrent http://www.citeulike.org/user/jyuh/article/2855746 <i>Scandinavian journal of public health, Vol. 35, No. 4. (2007), pp. 365-372.</i><br /><br />AIMS: The intention was to investigate whether preventive health checks and health discussions are cost effective. METHODS: In a randomized trial the authors compared two intervention groups (A and B) and one control group. In 1991 2,000 30- to 49-year-old persons were invited and those who accepted were randomized. Both intervention groups were offered a broad (multiphasic) screening including cardiovascular risk and a personal letter including screening results and advice on healthy living. Individuals in group A could contact their family physician for a normal consultation whereas group B were given fixed appointments for health consultations. The follow-up period was six years. Analysis was carried out on the "intention to treat" principle. Outcome parameters were life years gained, and direct and total health costs (including productivity costs), discounted by 3% annually. Costs were based on register data. Univariate sensitivity analysis was carried out. RESULTS: Both intervention groups have significantly better life expectancy than the control group (no intervention). Group B and (A) significantly gain 0.14 (0.08) life years more than the control group. There were no differences in average direct (3,255 euro (3,703 euro) versus 4,186 euro) and total costs (10,409 euro (9,399 euro) versus 10,667 euro). The effect in group B is, however, better than in group A with no significant differences in costs. The results are insensitive to a range of assumptions regarding costs, effects, and discount rates. CONCLUSIONS: Preventive health screening and consultation in primary care in 30- to 49-year-olds produce significantly better life expectancy without extra direct and total costs over a six-year follow-up period. Preventive health screenings and health consultations in primary care increase life expectancy without increasing costs. SR Rasmussen JL Thomsen J Kilsmark A Hvenegaard M Engberg T Lauritzen J Søgaard doi:10.1080/14034940701219642 Scandinavian journal of public health, Vol. 35, No. 4. (2007), pp. 365-372. 2008-06-02T03:25:38-00:00 2007 Scandinavian journal of public health 1403-4948 35 4 365 372 cost-effective prevention http://www.citeulike.org/user/jyuh/article/2784528 <i>Journal of immunological methods, Vol. 301, No. 1-2. (June 2005), pp. 102-113.</i><br /><br />This paper describes simple procedures to process digital images in quantitative immunofluorescence microscopy. Monoclonal antibodies directed against the sarcoplasmic myosin heavy chain isoforms and against laminin, located on the basement membranes, were applied to sections of human skeletal muscle. The localisation and staining intensity of a fluorescent secondary antibody were recorded using an indirect histochemical method. The digitised images were pre-processed and the luminosities of appropriate structures were determined using existing tools in the widely used image processing software Photoshop from Adobe. Procedures to obtain a quantitative measure for the specific fluorescence signal (the background corrected fluorescence in the object) were developed. In addition, antibody binding to individual cells could be quantified whether these cells are well separated or not. The relation between the specific fluorescence signal and the dilution factor of the primary antibody could be measured to determine a suitable concentration of the antibody for incubation of the sections. The potential fading of the fluorescence signal with time and prolonged exposure to light from the microscope was explored and analysed. With the tools described in the present report it is thus possible also to optimize the topical immunohistochemical protocol in order to quantify the fluorescence signal. Quantitative immunohistochemistry of fluorescence labelled probes using low-cost software. S Kirkeby CE Thomsen doi:10.1016/j.jim.2005.04.006 Journal of immunological methods, Vol. 301, No. 1-2. (June 2005), pp. 102-113. 2008-05-11T15:03:11-00:00 2005 Journal of immunological methods 0022-1759 301 1-2 102 113 no-tag http://www.citeulike.org/user/jyuh/article/1654327 <i>Bioinformatics, Vol. 23, No. 13. (1 July 2007)</i><br /><br />MOTIVATION: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data in public repositories makes it feasible to evaluate SNP predictions on the DNA chromatogram level. MAVIANT, a platform-independent Multipurpose Alignment VIewing and Annotation Tool, provides DNA chromatogram and alignment views and facilitates evaluation of predictions. In addition, it supports direct manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non-synonymous SNPs were analyzed for their potential effect on the protein structure/function using the PolyPhen and SIFT prediction programs. Predicted SNPs and annotations are stored in a web-based database. Using MAVIANT SNPs can visually be verified based on the DNA sequencing traces. A subset of candidate SNPs was selected for experimental validation by resequencing and genotyping. This study provides a web-based DNA chromatogram and contig browser that facilitates the evaluation and selection of candidate SNPs, which can be applied as genetic markers for genome wide genetic studies. AVAILABILITY: The stand-alone version of MAVIANT program for local use is freely available under GPL license terms at http://snp.agrsci.dk/maviant. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. F Panitz H Stengaard H Hornshøj J Gorodkin J Hedegaard S Cirera B Thomsen LB Madsen A Høj RK Vingborg B Zahn X Wang X Wang R Wernersson CB Jørgensen K Scheibye-Knudsen T Arvin S Lumholdt M Sawera T Green BJ Nielsen JH Havgaard S Brunak M Fredholm C Bendixen Bioinformatics, Vol. 23, No. 13. (1 July 2007) 2007-09-14T04:08:37-00:00 2007 Bioinformatics 1460-2059 23 13 no-tag http://www.citeulike.org/user/jyuh/article/1579383 <i>N Engl J Med, Vol. 355, No. 19. (9 November 2006)</i> Videos in clinical medicine. Paracentesis. TW Thomsen RW Shaffer B White GS Setnik doi:10.1056/NEJMvcm062234 N Engl J Med, Vol. 355, No. 19. (9 November 2006) 2007-08-21T09:17:02-00:00 2006 N Engl J Med 1533-4406 355 19 no-tag http://www.citeulike.org/user/jyuh/article/1579384 <i>N Engl J Med, Vol. 355, No. 17. (26 October 2006)</i> Videos in clinical medicine. Basic laceration repair. TW Thomsen DA Barclay GS Setnik doi:10.1056/NEJMvcm064238 N Engl J Med, Vol. 355, No. 17. (26 October 2006) 2007-08-21T09:17:04-00:00 2006 N Engl J Med 1533-4406 355 17 no-tag http://www.citeulike.org/user/jyuh/article/1579385 <i>N Engl J Med, Vol. 355, No. 15. (12 October 2006)</i> Videos in clinical medicine. Thoracentesis. TW Thomsen J DeLaPena GS Setnik doi:10.1056/NEJMvcm053812 N Engl J Med, Vol. 355, No. 15. (12 October 2006) 2007-08-21T09:17:07-00:00 2006 N Engl J Med 1533-4406 355 15 no-tag http://www.citeulike.org/user/jyuh/article/1579387 <i>N Engl J Med, Vol. 354, No. 21. (25 May 2006)</i> Videos in clinical medicine. Male urethral catheterization. TW Thomsen GS Setnik doi:10.1056/NEJMvcm054648 N Engl J Med, Vol. 354, No. 21. (25 May 2006) 2007-08-21T09:17:13-00:00 2006 N Engl J Med 1533-4406 354 21 no-tag http://www.citeulike.org/user/jyuh/article/1579389 <i>N Engl J Med, Vol. 354, No. 19. (11 May 2006)</i> Videos in clinical medicine. Arthrocentesis of the knee. TW Thomsen S Shen RW Shaffer GS Setnik doi:10.1056/NEJMvcm051914 N Engl J Med, Vol. 354, No. 19. (11 May 2006) 2007-08-21T09:17:15-00:00 2006 N Engl J Med 1533-4406 354 19 no-tag http://www.citeulike.org/user/jyuh/article/1579390 <i>N Engl J Med, Vol. 354, No. 17. (27 April 2006)</i> Videos in clinical medicine. Nasogastric intubation. TW Thomsen RW Shaffer GS Setnik doi:10.1056/NEJMvcm050183 N Engl J Med, Vol. 354, No. 17. (27 April 2006) 2007-08-21T09:17:17-00:00 2006 N Engl J Med 1533-4406 354 17 no-tag http://www.citeulike.org/user/jyuh/article/1579379 <i>N Engl J Med, Vol. 356, No. 17. (26 April 2007)</i> Videos in clinical medicine. Orotracheal intubation. C Kabrhel TW Thomsen GS Setnik RM Walls doi:10.1056/NEJMvcm063574 N Engl J Med, Vol. 356, No. 17. (26 April 2007) 2007-08-21T09:16:23-00:00 2007 N Engl J Med 1533-4406 356 17 no-tag