Temporal diffeomorphic Free Form Deformation to quantify changes induced by left and right bundle branch block and pacing

International audienceThis paper presents motion and deformation quantification results obtained from synthetic and in vitro phantom data provided by the second cardiac Motion Analysis Challenge at STACOM-MICCAI. We applied the Temporal Diffeomorphic Free Form Deformation (TDFFD) algorithm to the datasets. This algorithm builds upon a diffeomorphic version of the FFD, to provide a 3D + t continuous and differentiable transform. The similarity metric includes a comparison between consecutive images, and between a reference and each of the following images. Motion and strain accuracy were evaluated on synthetic 3D ultrasound sequences with known ground truth motion. Experiments were also conducted on in vitro acquisitions

Laser capture microdissection of intestinal tissue from sea bass larvae using an optimized RNA integrity assay and validated reference genes

The increasing demand for a sustainable larviculture has promoted research regarding environmental parameters, diseases and nutrition, intersecting at the mucosal surface of the gastrointestinal tract of fish larvae. The combination of laser capture microdissection (LCM) and gene expression experiments allows cell specific expression profiling. This study aimed at optimizing an LCM protocol for intestinal tissue of sea bass larvae. Furthermore, a 3'/5' integrity assay was developed for LCM samples of fish tissue, comprising low RNA concentrations. Furthermore, reliable reference genes for performing qPCR in larval sea bass gene expression studies were identified, as data normalization is critical in gene expression experiments using RT-qPCR. We demonstrate that a careful optimization of the LCM procedure allows recovery of high quality mRNA from defined cell populations in complex intestinal tissues. According to the geNorm and Normfinder algorithms, ef1a, rpl13a, rps18 and faua were the most stable genes to be implemented as reference genes for an appropriate normalization of intestinal tissue from sea bass across a range of experimental settings. The methodology developed here, offers a rapid and valuable approach to characterize cells/tissues in the intestinal tissue of fish larvae and their changes following pathogen exposure, nutritional/environmental changes, probiotic supplementation or a combination thereof

Incompressible image registration using divergence-conforming B-splines

Anatomically plausible image registration often requires volumetric preservation. Previous approaches to incompressible image registration have exploited relaxed constraints, ad hoc optimisation methods or practically intractable computational schemes. Divergence-free velocity fields have been used to achieve incompressibility in the continuous domain, although, after discretisation, no guarantees have been provided. In this paper, we introduce stationary velocity fields (SVFs) parameterised by divergence-conforming B-splines in the context of image registration. We demonstrate that sparse linear constraints on the parameters of such divergence-conforming B-Splines SVFs lead to being exactly divergence-free at any point of the continuous spatial domain. In contrast to previous approaches, our framework can easily take advantage of modern solvers for constrained optimisation, symmetric registration approaches, arbitrary image similarity and additional regularisation terms. We study the numerical incompressibility error for the transformation in the case of an Euler integration, which gives theoretical insights on the improved accuracy error over previous methods. We evaluate the proposed framework using synthetically deformed multimodal brain images, and the STACOM11 myocardial tracking challenge. Accuracy measurements demonstrate that our method compares favourably with state-of-the-art methods whilst achieving volume preservation.Comment: Accepted at MICCAI 201

SPM to the heart: mapping of 4D continuous velocities for motion abnormality quantification

International audienceThis paper proposes to apply parallel transport and statistical atlas techniques to quantify 4D myocardial motion abnormalities. We take advantage of our previous work on cardiac motion , which provided a continuous spatiotemporal representation of velocities, to interpolate and reorient cardiac motion fields to an unbiased reference space. Abnormal motion is quantified using SPM analysis on the velocity fields, which includes a correction based on random field theory to compensate for the spatial smoothness of the velocity fields. This paper first introduces the imaging pipeline for constructing a continuous 4D velocity atlas. This atlas is then applied to quantify abnormal motion patterns in heart failure patients

Fumarate drives EMT in renal cancer

Medical Research Counci

End-to-end Cardiac Ultrasound Simulation for a Better Understanding of Image Quality

International audienceUltrasound imaging is a very versatile and fast medical imag-ing modality, however it can suffer from serious image quality degrada-tion. The origin of such loss of image quality is often difficult to identifyin detail, therefore it makes it difficult to design probes and tools thatare less impacted. The objective of this manuscript is to present an end-to-end simulation pipeline that makes it possible to generate syntheticultrasound images while controlling every step of the pipeline, from thesimulated cardiac function, to the torso anatomy, probe parameters, andreconstruction process. Such a pipeline enables to vary every parameterin order to quantitatively evaluate its impact on the final image quality.We present here first results on classical ultrasound phantoms and a dig-ital heart. The utility of this pipeline is exemplified with the impact ofribs on the resulting cardiac ultrasound image

COVID-19 Roundtable

The past year was an unprecedentedly challenging period to humanity. The very concept of a pandemic indicates a profound impact across different regions and societal strata, rendering the idea of unscathed human lives almost unimaginable. Still, this image of COVID-19 as a global threat menacing us all must not be allowed to efface the specificity of individual or communal struggles. This caveat is particularly relevant in the context of gender and diversity studies – the pertinence of which has been underscored countlessly over the past months, especially in policy recommendations to the COVID-19 pandemic. From the disproportionately severe measures aggravating isolation and destitution among the elderly to the coalescence of sanitary regulations and the BLM protests or the fire in the Moria refugee camp and the resulting urgency to address the wellbeing of displaced people: issues that relate intimately to notions of marginalization continually surface adjacent to the health crisis proper. Whether explicitly or implicitly, these circumstances call for gender and diversity scholars to commit their expertise to the benefit of those inordinately affected by COVID-19 and the array of responses it has evoked worldwide. At the same time, the conditions affecting these groups and individuals also affect research activities and advocacy work on gender and diversity, inhibiting the active commitment and scholarly involvement the situation demands. In this Spring 2021 General Issue, the Journal of Diversity and Gender Studies (DiGeSt) sought to explore the paradoxes, contradictions and tensions scholars in our field have faced and continue to face during the current COVID-19 crisis. Transcending a formally academic register, the roundtable includes personal, situated accounts that engage tensions between the pandemic and scholarly work in diversity and gender studies

Study of the plant COPII vesicle coat subunits by functional complementation of yeast Saccharomyces cerevisiae mutants

The formation and budding of endoplasmic reticulum ER-derived vesicles depends on the COPII coat protein complex that was first identified in yeast Saccharomyces cerevisiae. The ER-associated Sec12 and the Sar1 GTPase initiate the COPII coat formation by recruiting the Sec23-Sec24 heterodimer following the subsequent recruitment of the Sec13-Sec31 heterotetramer. In yeast, there is usually one gene encoding each COPII protein and these proteins are essential for yeast viability, whereas the plant genome encodes multiple isoforms of all COPII subunits. Here, we used a systematic yeast complementation assay to assess the functionality of Arabidopsis thaliana COPII proteins. In this study, the different plant COPII subunits were expressed in their corresponding temperature-sensitive yeast mutant strain to complement their thermosensitivity and secretion phenotypes. Secretion was assessed using two different yeast cargos: the soluble alpha-factor pheromone and the membranous v-SNARE (vesicle-soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein receptor) Snc1 involved in the fusion of the secretory vesicles with the plasma membrane. This complementation study allowed the identification of functional A. thaliana COPII proteins for the Sec12, Sar1, Sec24 and Sec13 subunits that could represent an active COPII complex in plant cells. Moreover, we found that AtSec12 and AtSec23 were co-immunoprecipitated with AtSar1 in total cell extract of 15 day-old seedlings of A. thaliana. This demonstrates that AtSar1, AtSec12 and AtSec23 can form a protein complex that might represent an active COPII complex in plant cells

Pits and fissures: etch resistance in prismless enamel walls

The document attached has been archived with permission from the Australian Dental Association. An external link to the publisher’s copy is included.Background: In a previous study to examine the nature of etching on the walls of fissures, there was a consistent result of resistance to deep etching on parts of the walls and a zone of lesser etching on part of the walls as evidenced by the uptake of stain. The staining had been used to examine the nature of the etch pattern. The aims of this study were to define the nature of this etch resistant area. Methods: A sample of 55 teeth, both molars and premolars, were divided into three groups. In the first group the wetting of fissures by the etchant was examined; the second group tested for the effects of pellicle-cuticle-debris or air entrapment on the etching process. The final group looked at alternative mechanical treatments of the fissure prior to etching. Results: The specimens split along the fissures showed clearly that the etch resistant zone was not due to lack of contact with the etchant or the presence of a pellicle-cuticle-debris covering, but to the presence of a prismless enamel structure. This study showed that this zone inhibited tag development on the fissure walls. Conclusions: The mechanical removal of this prismless layer of enamel within the fissure system should result in an improved bonding of a fissure sealant through better tag development, in turn leading to a reduction in the failure rate of a sealant used to prevent caries.MF Burrow, JF Burrow and OF Makinso