Journal articles

1. Comparing and visualizing titanium implant integration in rat bone using 2D and 3D techniques
   Authors: Anna Arvidsson(1,2), Hamid Sarve, Carina B. Johansson(2)
   (1) Dentsply IH AB, Molndal, Sweden
   (2) The Sahlgrenska Academy, Institute of Odontology, Dept. of Prosthodontics/Dental Materials Science, University of Gothenburg, Göteborg, Sweden
   Journal: Journal of Biomedical Materials Research. Part B - Applied biomaterials, Vol. 103, No. 1, pages 12-20
   Abstract: The aim was to compare the osseointegration of grit-blasted implants with and without a hydrogen fluoride treatment in rat tibia and femur, and to visualize bone formation using state-of-the-art 3D visualization techniques. Grit-blasted implants were inserted in femur and tibia of 10 Sprague-Dawley rats (4 implants/rat). Four weeks after insertion, bone implant samples were retrieved. Selected samples were imaged in 3D using Synchrotron Radiation-based CT (SRCT). The 3D data was quantified and visualized using two novel visualization techniques, thread fly-through and 2D unfolding. All samples were processed to cut and ground sections and 2D histomorphometrical comparisons of bone implant contact (BIC), bone area (BA), and mirror image area (MI) were performed. BA values were statistically significantly higher for test implants than controls (p<0.05), but BIC and MI data did not differ significantly. Thus, the results partly indicate improved bone formation at blasted and hydrogen fluoride treated implants, compared to blasted implants. The 3D analysis was a valuable complement to 2D analysis, facilitating improved visualization. However, further studies are required to evaluate aspects of 3D quantitative techniques, with relation to light microscopy that traditionally is used for osseointegration studies.

2. Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio
   Authors: Carl-Magnus Clausson(1), Linda Arngården(1), Omer Ishaq(2), Axel Klaesson(1), Malte
   Kühnemund(1), Karin Grannas(1), Björn Koos(1), Xiaoyan Qian(3), Petter Ranefall(2), Tomasz Krzywkowski(3), Hjalmar Brismar(4), Mats Nilsson(1,3), Carolina Wählby(2), Ola Söderberg(1)
   (1) Dept. of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Biomedical center, Uppsala, Sweden
   (2) Science for Life Laboratory, Uppsala University, Uppsala, Sweden
   (3) Dept. of Biochemistry and biophysics, Stockholm University, Science for Life Laboratory, Stockholm, Sweden
   (4) Science for Life Laboratory, Royal Institute of Technology, Solna, Sweden
   Journal: Scientific Reports, Vol. 5, Article ID 12317, 10 pages
   Abstract: Rolling circle amplification (RCA) for generation of distinct fluorescent signals in situ relies upon the self-collapsing properties of single-stranded DNA in commonly used RCA-based methods. By introducing a cross-hybridizing DNA oligonucleotide during rolling circle amplification, we demonstrate that the fluorophore-labeled RCA products (RCPs) become smaller. The reduced size of RCPs increases the local concentration of fluorophores and as a result, the signal intensity increases together with the signal-to-noise ratio. Furthermore, we have found that RCPs sometimes tend to disintegrate and may be recorded as several RCPs, a trait that is prevented with our cross-hybridizing DNA oligonucleotide. These effects generated by compaction of RCPs improve accuracy of visual as well as automated in situ analysis for RCA based methods, such as proximity ligation assays (PLA) and padlock probes.

3. Brain - endocast relationship in the Australian lungfish, Neoceratodus forsteri, elucidated from tomographic data (Sarcopterygii: Dipnoi)
   Authors: Alice M. Clement(1,2), Johan Nysjö, Robin Strand, Per E. Ahlberg(1)
   (1) Dept. of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
   (2) Dept. of Sciences, Museum Victoria, Victoria, Australia
   Journal: PLoS ONE, Vol. 10, No. 10, e0141277
   Abstract: Although the brains of the three extant lungfish genera have been previously described, the spatial relationship between the brain and the neurocranium has never before been fully described nor quantified. Through the application of virtual microtomography (mu CT) and 3D rendering software, we describe aspects of the gross anatomy of the brain and labyrinth region in the Australian lungfish, Neoceratodus forsteri and compare this to previous accounts. Unexpected characters in this specimen include short olfactory peduncles connecting the olfactory bulbs to the telencephalon, and an oblong telencephalon. Furthermore, we illustrate the endocast (the mould of the internal space of the neurocranial cavity) of Neoceratodus, also describing and quantifying the brain-endocast relationship in a lungfish for the first time. Overall, the brain of the Australian lungfish closely matches the size and shape of the endocast cavity housing it, filling more than four fifths of the total volume. The forebrain and labyrinth regions of the brain correspond very well to the endocast morphology, while the midbrain and hindbrain do not fit so closely. Our results cast light on the gross neural and endocast anatomy in lungfishes, and are likely to have particular significance for palaeoneurologists studying fossil taxa.

4. Computer assisted pap smear analyser for cervical cancer screening using quantitative microscopy
   Authors: Rajasekharan Usha Deepak(1), Ramakrishnan Rajesh Kumar(1), Neendoorthalackal Balakrishnan Byju(1), Pundluvalu Nataraju Sharathkumar(1), Chandran Pournami(1), Salam Sibi(1), Ewert Bengtsson, Kunjuraman Sujathan(2)
   (1) Health and Software Technology Group, Centre for Development of Advanced Computing, Thiruvananthapuram, Kerala, India
   (2) Division of Cancer Research, Regional Cancer Centre, Medical College Campus, Thiruvananthapuram, Kerala, India
   Journal: Journal of Cytology & Histology, Vol. 6, No. S3, 010
   Abstract: Cervical cancer is the third most common cancer among women. The bulk of the cancer burden is on low and middle income countries where screening is mostly opportunistic rather than systematic. Among the number of screening methods, cytology based screening using Pap smear test is by far the most widely followed and accepted method. In countries where organized screening using Pap test has been introduced, incidence and mortality caused by the disease has significantly subsided. Although the method is effective in controlling the disease, it poses a serious challenge in practical implementation owing to the fact that the method is resource intensive requiring trained professionals skilled enough to identify a handful of abnormal cells among few hundred thousand cells. This motivates the need for automating the screening methodology. Since the 1960-ies numerous projects have developed such automated screening systems leading also to a couple of commercial products. Still these have had limited impact on the screening situation in most of the world. This paper describes a screening system developed by our group in an effort of creating a cost effective screening system that could be widely deployed. The systems digitizes Pap smear slides and carries out cell level and smear level analysis on digitized smear and finally classifies the smear as either normal or suspicious. Clearly normal smears were screened out without any human intervention while suspicious smears were sent for expert cytologist review. A low cost monolayer slide preparation technique has also been identified which produces monolayer slides of quality comparable to that of commercial systems at much lesser cost. The computer aided Pap smear analyzer was validated at the Regional Cancer Centre (RCC), Thiruvananthapuram, India since May 2011. Since then a total of 1107 smears covering all abnormal and normal categories has been evaluated with a specificity of 60