Archive for alowe

January Publications with Visiopharm Software

Below is a list of 16 new publications that use Visiopharm software released in January and so far in February. These publications have been added to our website collection of over 450 publications written since 2010.

Image Analysis

1. Draganovic, V., van der Goot, A., Boom, R. & Jonkers, J. Wheat gluten in extruded fish feed: effects on morphology and on physical and functional properties Aquaculture Nutrition, 2013 , pp. n/a-n/a  DOI URL
2. Marshall, S.A., McClain, J.A., Kelso, M.L., Hopkins, D.M., Pauly, J.R. & Nixon, K. Microglial activation is not equivalent to neuroinflammation in alcohol-induced neurodegeneration: The importance of microglia phenotype. Neurobiol Dis, Department of Pharmaceutical Sciences, The University of Kentucky, Lexington, KY 40536-0596, USA., 2013 DOI URL
3. Park, S.-H., Chen, W.-C., Hoffman, C., Marsh, L.M., West, J. & Grunig, G. Modification of hemodynamic and immune responses to exposure with a weak antigen by the expression of a hypomorphic BMPR2 gene. PLoS One, Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York, United States of America., 2013 , Vol. 8 (1) , pp. e55180 DOI URL

Stereology

1. Babiker, H., Ding, M. & Overgaard, S. Demineralized bone matrix and human cancellous bone enhance fixation of porous-coated titanium implants in sheep. J Tissue Eng Regen Med, Department of Orthopaedic Surgery and Traumatology, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark. 2013 DOI URL
2. Barckman, J., Baas, J., Sørensen, M., Bechtold, J.E. & Soballe, K. Periosteal augmentation of allograft bone and its effect on implant fixation – an experimental study on 12 dogs(). Open Orthop J, Orthopaedic Research Laboratory, Aarhus University Hospital, Denmark., 2013 , Vol. 7 , pp. 18-24 DOI URL

3. Cerezuela, R., Fumanal, M., Tapia-Paniagua, S.T., Meseguer, J., Moriñigo, M.Á. & Esteban, M.Á. Changes in intestinal morphology and microbiota caused by dietary administration of inulin and Bacillus subtilis in gilthead sea bream (Sparus aurata L.) specimens. Fish Shellfish Immunol, Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain., 2013 DOI URL
4.Glerup, S., Lume, M., Olsen, D., Nyengaard, J.R., Vaegter, C.B., Gustafsen, C., Christensen, E.I., Kjolby, M., Hay-Schmidt, A., Bender, D., Madsen, P., Saarma, M., Nykjaer, A. & Petersen, C.M. SorLA Controls Neurotrophic Activity by Sorting of GDNF and Its Receptors GFR?1 and RET. Cell Rep, MIND Centre, Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark. 2013 , Vol. 3 (1) , pp. 186-199 DOI URL

5. Hayes, D.M., Deeny, M.A., Shaner, C.A. & Nixon, K. Determining the Threshold for Alcohol-Induced Brain Damage: New Evidence with Gliosis Markers. Alcohol Clin Exp Res, Department of Pharmaceutical Sciences , College of Pharmacy, University of Kentucky, Lexington, Kentucky., 2013 DOI URL

6. Kadkhodaei, B., Alvarsson, A., Schintu, N., Ramsköld, D., Volakakis, N., Joodmardi, E., Yoshitake, T., Kehr, J., Decressac, M., Björklund, A., Sandberg, R., Svenningsson, P. & Perlmann, T. Transcription factor Nurr1 maintains fiber integrity and nuclear-encoded mitochondrial gene expression in dopamine neurons. Proc Natl Acad Sci U S A, Ludwig Institute for Cancer Research Ltd, Stockholm Branch, SE-17177 Stockholm, Sweden., 2013 , Vol. 110 (6) , pp. 2360-2365 DOI URL

7. Linares, E., Seixas, L.V., Dos Prazeres, J.N., Ladd, F.V.L., Ladd, A.A.B.L., Coppi, A.A. & Augusto, O. Tempol Moderately Extends Survival in a hSOD1(G93A) ALS Rat Model by Inhibiting Neuronal Cell Loss, Oxidative Damage and Levels of Non-Native hSOD1(G93A) Forms. PLoS One, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil., 2013 , Vol. 8 (2) , pp. e55868 DOI URL

8. Mateus-Pinheiro, A., Pinto, L., Bessa, J.M., Morais, M., Alves, N.D., Monteiro, S., Patrício, P., Almeida, O.F.X. & Sousa, N. Sustained remission from depressive-like behavior depends on hippocampal neurogenesis. Transl Psychiatry, ICVS/3B’s-PT Government Associate Laboratory, Guimarães, Portugal., 2013 , Vol. 3 , pp. e210 DOI URL

9. Park, Y.M., Lee, W.T., Bokara, K.K., Seo, S.K., Park, S.H., Kim, J.H., Yenari, M.A., Park, K.A. & Lee, J.E. The Multifaceted Effects of Agmatine on Functional Recovery after Spinal Cord Injury through Modulations of BMP-2/4/7 Expressions in Neurons and Glial Cells. PLoS One, Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea ; BK 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea., 2013 , Vol. 8 (1) , pp. e53911 DOI URL

10. Podolin, P.L., Foley, J.P., Carpenter, D.C., Bolognese, B.J., Logan, G.A., Long, 3rd, E., Harrison, O.J. & Walsh, P.T. T cell depletion protects against alveolar destruction due to chronic cigarette smoke exposure in mice. Am J Physiol Lung Cell Mol Physiol, 1GlaxoSmithKline., 2013 DOI URL

11. Shynlova, O., Nedd-Roderique, T., Li, Y., Dorogin, A., Nguyen, T. & Lye, S.J.  Infiltration of myeloid cells into decidua is a critical early event in the labour cascade and post-partum uterine remodelling. J Cell Mol Med, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada, M5G 1X5., 2013 DOI URL

12. Vonder Haar, C., Friend, D.M., Mudd, D.B. & Smith, J.S. Successive bilateral frontal controlled cortical impact injuries show behavioral savings. Behav Brain Res, Restorative Neuroscience Laboratory, Center for Integrated Research in Cognitive and Neural Sciences, Department of Psychology, Southern Illinois University, Carbondale, IL, USA., 2013 , Vol. 240 , pp. 153-159  DOI URL

13. Wittwer, T., Madershahian, N., Rahmanian, P., Choi, Y.-H., Neef, K., Frank, K., Müller-Ehmsen, J., Ochs, M., Mühlfeld, C. & Wahlers, T. Surfactant application in experimental lung transplantation. J Heart Lung Transplant, Department of Cardiothoracic Surgery, Heart Center., 2013 DOI URL

Webinar on Progression Markers in Non-Muscle Invasive Bladder Cancer

appicon-10012On February 28, 2013 at 9 AM EST / 3 PM CET Visiopharm will host a webinar titled “Progression Markers in Non-Muscle Invasive Bladder Cancer” presented by Dr. Niels Fristrup from Aarhus University Hospital, Denmark.   This webinar coordinates with Visiopharm’s Cancer Research APPs for Bladder Cancer.  Our current six Bladder Cancer APPs include:

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Abstract

Transcripts from the four genes encoding cyclin D1, MCM7, TRIM29, and UBE2C have previously been included in gene expression signatures for outcome prediction in stage Ta/T1 urothelial carcinomas. Here, we investigated the prognostic value of the protein expressions in patients with stage Ta/T1 urothelial carcinomas. We used four different tissue microarrays with a total of 859 Ta/T1 urothelial carcinomas from Danish, Swedish, Spanish, and Taiwanese patient cohorts with long-term follow-up. Protein expression was measured by immunohistochemistry, and antibody specificity was validated by Western blotting.We found the expression of cyclin D1, MCM7, TRIM29, and UBE2C to be significantly associated with progression to muscle-invasive bladder cancer (log-rank test; p<0.001) in the Danish training cohort (n=283). Multivariate Cox regression analysis identified cyclin D1 (p=0.003), TRIM29 (p=0.001), and UBE2C (p<0.001) as independent prognostic markers. The prognostic value of the four proteins was validated in a joint validation cohort from Sweden, Spain, and Taiwan (n=576). We applied computer-assisted image analysis of the prognostic markers and produced results comparable to those obtained by manual scoring. Finally, a four-protein maximum-likelihood classifier was trained on the Danish training cohort; and applied to the validation cohort. The four protein markers may help optimize treatment of patients with Ta/T1 bladder cancer. Additional prospective studies are needed for further validation of their clinical relevance.

php27Gd9LAMAbout our Speaker

Niels Fristrup was educated as medical doctor from the University of Aarhus in 2010. His research started in 2008, primarily concerning prognostic protein markers in non-muscle invasive bladder cancer, now also focusing on predictive markers of Bacillus Calmette Guérin (BCG) treatment response. In his research Niels works to correlate advanced molecular analyses of cancer tissues from patients suffering from bladder cancer with extensive long-term follow-up of large patient cohorts. The goal is to create new, precise ways of identifying the aggressiveness of the cancers as early as possible, or the responsiveness towards BCG immunotherapy. This resarch could potentially lead to a more precise prognostication, again leading towards personalized medicine; the right treatment for each patient. Niels publication list encompasses 10 peer-reviewed articles in renowned journals as The American Journal of Pathology, Oncogene, and Cancer Research.

New APPs Available for Osteoarthritis

Identify Chondrocytes in Cartilage

 

slide-10054-4Background

Traditionally, the evaluation of the severity of cartilage damage is done by subjective semi-quantitative grading of the different histopathological features using defined scoring systems. However, even with ‘blinding’ of the observers and sample randomization, this methodology is prone to bias, suffers from low sensitivity to change and requires considerable experience in histopathology. On the other hand, quantitative digital histomorphometry of cartilage destruction can offer an objective, less time consuming and more sensitive assessment of OA histopathology.

This APP can be used for quantifying profile density of chondrocytes in cartilage explants from bovine joints and is of relevance for different OA models, concerning pro anabolic or anti catabolic factors. To answer this specific question a Ehrlich Triacid staining was choosen, because it allows the best differentiation between cartilage, bone and nuclei. The APP has been verified in treatment studies.  Learn more…

Methods

This APP can be used on whole slide images with several sections on each slide. The first step is the tissue detection on the slides. Followed by marking the tissue pieces and allocate them to ROI 1 to 4. In a second step the cartilage area and the number of nuclei profiles can be obtained for calculation of the profile density.

Quantitative Output Variables

The output variables obtained from this APP include:

  • Area of Cartilage = Sum of the cartilage area
  • Count of profiles in Cartilage = Number of nuclei profiles in the region of interest.  

This APP was developed for, and validated by, Dr. Sven Lindemann, Simone Hartl, Merck KGaA, Osteoarthritis, General Research and Early Development.

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Measure Fibrillation Index, Bone Density, and Cartilage Area 

 

slide-10061-3Background

Traditionally, the evaluation of the severity of joint damage is done by subjective semi-quantitative grading of the different histopathological features using defined scoring systems [See REFERENCES: 2]. However, even with “blinding’ of the observers and sample randomization, this methodology is prone to bias, suffers from low sensitivity to change and requires considerable experience in histopathology. On the other hand, quantitative digital histomorphometry of cartilage destruction and subchondral bone sclerosis can offer an objective, less time consuming and more sensitive assessment of OA histopathology [See REFERENCES: 3].

This APP can be used for quantifying a number of parameters relating to joint damage: Cartilage volume/area, surface fibrillation and proteoglycan loss (intensity measure). The APP has been verified in treatment studies. Learn more…

Methods

This APP can be used on virtual slides, where an Analysis Box with a predefined size is placed manually at a tibia or femur cartilage region, including potential lesion area and excluding osteophytes.  The APP will delineate the residual cartilage, the proteoglycan-stained cartilage, bone, and joint space within the Analysis Box.  Learn more…

Quantitative Output Variables

The output variables obtained from this APP include:

  • Cartilage Area – Proteoglycan = Area of Safranin-O stained cartilage within the Analysis Box
  • Cartilage Area = Total area of cartilage within the Analysis Box
  • Cartilage Area Fraction – Proteoglycan = Fraction of cartilage stained with Safranin-O
  • Fibrillation Index = Euclidean distance between ends of cartilage surface towards femur divided with distance between ends of cartilage along cartilage surface
  • Bone Density = Part of bone area consisting of solid bone

 This APP was developed in corporation with and verified by, Dr. Sven Lindemann and Donata Harazin, Merck KGaA, Germany, Osteoarthritis Research & Early Clinical Development.

 

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Visiopharm Launches Workshop Series in Sweden

Join us for an engaging workshop on Cancer Research where you can learn about the latest advantages in quantitative digital pathology including Tissue Microarray core construction and management, whole slide imaging, and high throughput image analysis. Attendees can sign up for a two week complimentary trial of Visiopharm’s Tissuemorph software and choose up to three application protocol packages (APPs). APPs are available for HER2, ER, PR, Ki-67, CISH, FISH and more.

Our Sweden workshop series includes:

Lund, Sweden

Monday, February 18, 2013
Location: Belfrage Lecture Hall
Biomedical Center (BMC), floor D15
Klinikgatan 32

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Eventbrite - Digital Pathology Cancer Research Workshop

Göteborg, Sweden

Wednesday, February 20, 2013
Location: Konferenscentrum Wallenberg
Medicinaregatan 20 A
Room: Radiovågen

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Eventbrite - Digital Pathology Cancer Research Workshop

Stockholm, Sweden

Friday, February 22, 2013
Location: Haga Forum
Annerovagen 4
Room: Hörsalen
169 70 Solna

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Eventbrite - Digital Pathology Cancer Research Workshop

This will be the first of many workshops in 2013 throughout Europe and the United States.  To learn more about our workshops, trainings sessions, and scientific meetings, please visit our events page.

 

Recent Webinar on Quantification of IHC Intensity Available For Download

Our webinar earlier this week, “Can Chromogenic Immunohistochemistry Quantify Intensity?” presented by Diana Fahrer of Biogen Idec, was a great success! If you missed it, it is available on our YouTube channel or for download on our website.  To request a copy of the presentation, please email us.

Thank you to all who participated!

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