3D functional models of monkey brain through elastic registration of histological sections

In this paper we describe a method for the reconstruction and visualization of functional models of monkey brains. Models are built through the registration of high resolution images obtained from the scanning of histological sections with reference photos taken during the brain slicing. From the histological sections it is also possible to acquire specifically activated neuron coordinates introducing functional information in the model. Due to the specific nature of the images (texture information is useless and the sections could be deformed when they were cut and placed on glass) we solved the registration problem by extracting corresponding cerebral cortex borders (extracted with a snake algorithm), and computing from their deformation an image transform modeled as an affine deformation plus a non-linear field evaluated as an elastically constrained deformation minimizing contour distances. Registered images and contours are used then to build 3D models of specific brains by a software tool allowing the interactive visualization of cortical volumes together with the spatially referenced neurons classified and differently colored according to their functionalities

Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways

<p>Abstract</p> <p>Background</p> <p>There is little information about the DNA sequence variation within and between closely related plant species. The combination of re-sequencing technologies, large-scale DNA pools and availability of reference gene sequences allowed the extensive characterisation of single nucleotide polymorphisms (SNPs) in genes of four biosynthetic pathways leading to the formation of ecologically relevant secondary metabolites in <it>Eucalyptus</it>. With this approach the occurrence and patterns of SNP variation for a set of genes can be compared across different species from the same genus.</p> <p>Results</p> <p>In a single GS-FLX run, we sequenced over 103 Mbp and assembled them to approximately 50 kbp of reference sequences. An average sequencing depth of 315 reads per nucleotide site was achieved for all four eucalypt species, <it>Eucalyptus globulus</it>, <it>E. nitens</it>, <it>E. camaldulensis </it>and <it>E. loxophleba</it>. We sequenced 23 genes from 1,764 individuals and discovered 8,631 SNPs across the species, with about 1.5 times as many SNPs per kbp in the introns compared to exons. The exons of the two closely related species (<it>E. globulus </it>and <it>E. nitens</it>) had similar numbers of SNPs at synonymous and non-synonymous sites. These species also had similar levels of SNP diversity, whereas <it>E. camaldulensis </it>and <it>E. loxophleba </it>had much higher SNP diversity. Neither the pathway nor the position in the pathway influenced gene diversity. The four species share between 20 and 43% of the SNPs in these genes.</p> <p>Conclusion</p> <p>By using conservative statistical detection methods, we were confident about the validity of each SNP. With numerous individuals sampled over the geographical range of each species, we discovered one SNP in every 33 bp for <it>E. nitens </it>and one in every 31 bp in <it>E. globulus</it>. In contrast, the more distantly related species contained more SNPs: one in every 16 bp for <it>E. camaldulensis </it>and one in 17 bp for <it>E. loxophleba</it>, which is, to the best of our knowledge, the highest frequency of SNPs described in woody plant species.</p

A new approach to the assessment of lumen visibility of coronary artery stent at various heart rates using 64-slice MDCT

Coronary artery stent lumen visibility was assessed as a function of cardiac movement and temporal resolution with an automated objective method using an anthropomorphic moving heart phantom. Nine different coronary stents filled with contrast fluid and surrounded by fat were scanned using 64-slice multi-detector computed tomography (MDCT) at 50–100 beats/min with the moving heart phantom. Image quality was assessed by measuring in-stent CT attenuation and by a dedicated tool in the longitudinal and axial plane. Images were scored by CT attenuation and lumen visibility and compared with theoretical scoring to analyse the effect of multi-segment reconstruction (MSR). An average increase in CT attenuation of 144 ± 59 HU and average diminished lumen visibility of 29 ± 12% was observed at higher heart rates in both planes. A negative correlation between image quality and heart rate was non-significant for the majority of measurements (P > 0.06). No improvement of image quality was observed in using MSR. In conclusion, in-stent CT attenuation increases and lumen visibility decreases at increasing heart rate. Results obtained with the automated tool show similar behaviour compared with attenuation measurements. Cardiac movement during data acquisition causes approximately twice as much blurring compared with the influence of temporal resolution on image quality

Automated diffeomorphic registration of anatomical structures with rigid parts: application to dynamic cervical MRI.

International audienceWe propose an iterative two-step method to compute a diffeomorphic non-rigid transformation between images of anatomical structures with rigid parts, without any user intervention or prior knowledge on the image intensities. First we compute spatially sparse, locally optimal rigid transformations between the two images using a new block matching strategy and an efficient numerical optimiser (BOBYQA). Then we derive a dense, regularised velocity field based on these local transformations using matrix logarithms and M-smoothing. These two steps are iterated until convergence and the final diffeomorphic transformation is defined as the exponential of the accumulated velocity field. We show our algorithm to outperform the state-of-the-art log-domain diffeomorphic demons method on dynamic cervical MRI data

Be Stars: Rapidly Rotating Pulsators

I will show that Be stars are, without exception, a class of rapidly rotating stars, which are in the majority of cases pulsating stars as well, while none of them does possess a large scale (i.e. with significant dipolar contribution) magnetic field.Comment: Review talk given at "XX Stellar Pulsation Conference Series: Impact of new instrumentation and new insights in stellar pulsations", Granada, 5-9 September 2011, in press in AIP Conf. Se

Groupwise Multimodal Image Registration using Joint Total Variation

In medical imaging it is common practice to acquire a wide range of modalities (MRI, CT, PET, etc.), to highlight different structures or pathologies. As patient movement between scans or scanning session is unavoidable, registration is often an essential step before any subsequent image analysis. In this paper, we introduce a cost function based on joint total variation for such multimodal image registration. This cost function has the advantage of enabling principled, groupwise alignment of multiple images, whilst being insensitive to strong intensity non-uniformities. We evaluate our algorithm on rigidly aligning both simulated and real 3D brain scans. This validation shows robustness to strong intensity non-uniformities and low registration errors for CT/PET to MRI alignment. Our implementation is publicly available at https://github.com/brudfors/coregistration-njtv

Rising utilization of coronary CT angiography across Europe over the last decade: insights from a large prospective European registry

Abstract Background/Introduction The recently updated 2019 ESC guidelines for the diagnosis and management of chronic coronary syndromes endorse the use of coronary computed tomography angiography (CCTA) for exclusion of obstructive coronary artery disease in patients with a low clinical likelihood (Class I, LOE B). Higher demand for CCTA requires broad availability, inevitably involving smaller healthcare providers, such as non-academic hospitals and private practices. Nevertheless, most published data on CCTA image quality and safety rely on exams performed in high-volume academic centers, and little is known about CCTA in non-academic settings. Purpose To investigate the utilization of CCTA across Europe over the last decade, focusing on differences between academic and non-academic centers. Methods We included patients with stable chest pain and suspected coronary artery disease (CAD) who received CCTA and were included in the European Society of Cardiovascular Radiology MR/CT registry 01/2010–01/2020. We compared CT equipment, image quality, radiation dose, the incidence of periprocedural adverse events, patient characteristics, and CCTA findings between academic (high volume university hospitals) and non-academic centers (non-academic hospitals and private practices). Results Overall, 64,317 patients (41.2% women; age 60±13 years) from 212 sites across 19 European countries were included. Academic centers submitted most cases in 2010—2014 (51.6%), whereas non-academic centers accounted for 71.3% of records in 2015–2020. While non-academic centers used less advanced technology, radiation dose remained low (4.54 [interquartile range (IQR) 2.28–6.76] mSv) with a 30% decline of high-dose scans (&gt;7 mSv) over time. Diagnostic image quality was reported in 97.7% of cases, and the rate of acute scan-related events was low (0.4%) (Figure 1). From 2010–2014 to 2015–2020, CCTA nearly doubled in patients with low to intermediate pretest-probability, women &gt;50, and 40–60 years old men (Figure 2). CAD presence and extent decreased slightly over time (prevalence: 2010–2014: 41.5% vs. 2015–2020: 40.6%), (multi-vessel disease in those with CAD: 2010–2014: 61.9% vs. 2015–2020: 55.9%; all p&lt;0.01). Conclusion CCTA expands rapidly to non-academic centers across Europe, increasing availability while maintaining relatively low radiation dose, high diagnostic image quality, and safety. Broad availability of high-quality CCTA is essential for a successfully implementation of the recently updated guidelines for the diagnosis and management of chronic coronary syndromes. Funding Acknowledgement Type of funding sources: None. Changes in CCTA utilizationChanges in patient characteristic

Detection of a Hot Subdwarf Companion to the Be Star FY Canis Majoris

The rapid rotation of Be stars may be caused in some cases by past mass and angular momentum accretion in an interacting binary in which the mass donor is currently viewed as a small, hot subdwarf stripped of its outer envelope. Here we report on the spectroscopic detection of such a subdwarf in the Be binary system FY Canis Majoris from the analysis of data acquired by the IUE spacecraft and KPNO Coude Feed Telescope over the course of 16 and 21 years, respectively. We present a double-lined spectroscopic orbit for the binary based upon radial velocities from the IUE spectra and use the orbital solutions with a Doppler tomography algorithm to reconstruct the components' UV spectra. The subdwarf is hot (T_eff = 45+/-5 kK) and has a mass of about 1.3 M_sun and a radius of about 0.6 R_sun. It contributes about 4% as much flux as the Be star does in the FUV. We also present observations of the H-alpha and He I 6678 emission features that are formed in the circumstellar disk of the Be star. Orbital flux and velocity variations in the He I 6678 profile indicate that much of the emission forms along the disk rim facing the hot subdwarf where the disk is probably heated by the incident radiation from the subdwarf. A study of the FUV infall shell lines discovered in the 1980s confirms their episodic presence but reveals that they tend to be found around both quadrature phases, unlike the pattern in Algol binaries. Phase-dependent variations in the UV N V doublet suggest the presence of a N-enhanced wind from the subdwarf and a possible shock-interaction region between the stars where the subdwarf's wind collides with the disk of the Be star.Comment: 46 pages, 15 figures, ApJ in pres