Semi-automatic Liver Tumor Segmentation in Dynamic Contrast-Enhanced CT Scans Using Random Forests and Supervoxels

International audiencePre-operative locoregional treatments (PLT) delay the tumor progression by necrosis for patients with hepato-cellular carcinoma (HCC). Toward an efficient evaluation of PLT response, we address the estimation of liver tumor necrosis (TN) from CT scans. The TN rate could shortly supplant standard criteria (RECIST, mRECIST, EASL or WHO) since it has recently shown higher correlation to survival rates. To overcome the inter-expert variability induced by visual qualitative assessment, we propose a semi-automatic method that requires weak interaction efforts to segment parenchyma, tumoral active and necrotic tissues. By combining SLIC supervoxels and random decision forest, it involves discriminative multi-phase cluster-wise features extracted from registered dynamic contrast-enhanced CT scans. Quantitative assessment on expert groundtruth annotations confirms the benefits of exploiting multi-phase information from semantic regions to accurately segment HCC liver tumors

A PNPLA8 frameshift variant in Australian shepherd dogs with hereditary ataxia

Hereditary ataxias are common among canine breeds with various molecular etiology. We identified a hereditary ataxia in young‐adult Australian Shepherd dogs characterized by uncoordinated movements and spasticity, worsening progressively and leading to inability to walk. Pedigree analysis suggested an autosomal recessive transmission. By whole genome sequencing and variant filtering of an affected dog we identified a PNPLA8:c.1169_1170dupTT variant. This variant, located in PNPLA8 (Patatin Like Phospholipase Domain Containing 8), was predicted to induce a PNPLA8:p.(His391PhefsTer394) frameshift, leading to a premature stop codon in the protein. The truncated protein was predicted to lack the functional patatin catalytic domain of PNPLA8, a calcium‐independent phospholipase. PNPLA8 is known to be essential for maintaining mitochondrial energy production through tailoring mitochondrial membrane lipid metabolism and composition. The Australian Shepherd ataxia shares molecular and clinical features with Weaver syndrome in cattle and the mitochondrial‐related neurodegeneration associated with PNPLA8 loss‐of‐function variants in humans. By genotyping a cohort of 85 control Australian Shepherd dogs sampled in France, we found a 4.7% carrier frequency. The PNPLA8:c.[1169_1170dupTT] allele is easily detectable with a genetic test to avoid at‐risk matings

White Matter Atrophy and Cognitive Dysfunctions in Neuromyelitis Optica

Neuromyelitis optica (NMO) is an inflammatory disease of central nervous system characterized by optic neuritis and longitudinally extensive acute transverse myelitis. NMO patients have cognitive dysfunctions but other clinical symptoms of brain origin are rare. In the present study, we aimed to investigate cognitive functions and brain volume in NMO. The study population consisted of 28 patients with NMO and 28 healthy control subjects matched for age, sex and educational level. We applied a French translation of the Brief Repeatable Battery (BRB-N) to the NMO patients. Using SIENAx for global brain volume (Grey Matter, GM; White Matter, WM; and whole brain) and VBM for focal brain volume (GM and WM), NMO patients and controls were compared. Voxel-level correlations between diminished brain concentration and cognitive performance for each tests were performed. Focal and global brain volume of NMO patients with and without cognitive impairment were also compared. Fifteen NMO patients (54%) had cognitive impairment with memory, executive function, attention and speed of information processing deficits. Global and focal brain atrophy of WM but not Grey Matter (GM) was found in the NMO patients group. The focal WM atrophy included the optic chiasm, pons, cerebellum, the corpus callosum and parts of the frontal, temporal and parietal lobes, including superior longitudinal fascicle. Visual memory, verbal memory, speed of information processing, short-term memory and executive functions were correlated to focal WM volumes. The comparison of patients with, to patients without cognitive impairment showed a clear decrease of global and focal WM, including brainstem, corticospinal tracts, corpus callosum but also superior and inferior longitudinal fascicles. Cognitive impairment in NMO patients is correlated to the decreased of global and focal WM volume of the brain. Further studies are needed to better understand the precise origin of cognitive impairment in NMO patients, particularly in the WM

Functional cerebral changes in multiple sclerosis patients during an autobiographical memory test.

Our aim was to investigate the functional underpinnings of autobiographical memory (AM) impairment in multiple sclerosis (MS) patients. To that end, 18 patients and 18 controls underwent the autobiographical interview (AI). Subsequently, the 36 participants underwent a functional magnetic resonance imaging (fMRI) session designed to assess the construction and elaboration of AMs. A categorical control task was also presented. Patients were trained in the fMRI procedure to optimise the procedural aspects accompanying the task itself. Although the patients obtained significantly poorer AI scores (p < .001), their performance on the easier AM fMRI task was efficiently carried out, allowing relevant comparisons with healthy controls. Relatively to healthy controls, the patients showed increased and bilateral cerebral activations (p < .005) during the construction and elaboration phases. The prefrontal, temporal and posterior cerebral region activations were located within the core network sustaining AM, with the bilateral prefrontal region being centrally involved. The parametric neural responses to the difficulty of access and amount of details of memories were also significantly different for the two groups, with the right hippocampal region showing a particularly increased recruitment (p < .005). The findings suggested the presence of functional cerebral changes during AM performance and supported the presence of AM retrieval deficit in MS patients.journal articleresearch support, non-u.s. gov't20152014 09 22importe

Review. Divergent selection for residual feed intake in the growing pig

To view supplementary material for this article, please visit https:/doi.org/10.1017/S175173111600286XThis review summarizes the results from the INRA (Institut National de la Recherche Agronomique) divergent selection experiment on residual feed intake (RFI) in growing Large White pigs during nine generations of selection. It discusses the remaining challenges and perspectives for the improvement of feed efficiency in growing pigs. The impacts on growing pigs raised under standard conditions and in alternative situations such as heat stress, inflammatory challenges or lactation have been studied. After nine generations of selection, the divergent selection for RFI led to highly significant ( P<0.001) line differences for RFI (−165 g/day in the low RFI (LRFI) line compared with high RFI line) and daily feed intake (−270 g/day). Low responses wereobserved on growth rate (−12.8 g/day, P <0.05) and body composition (+0.9mm backfat thickness, P = 0.57; −2.64% lean meat content, P<0.001) with a marked response on feed conversion ratio (−0.32 kg feed/kg gain, P<0.001). Reduced ultimate pH and increased lightness of the meat ( P<0.001) were observed in LRFI pigs with minor impact on the sensory quality of the meat. These changes in meat quality were associated with changes of the muscular energy metabolism. Reduced maintenance energy requirements (−10% after five generations of selection) and activity (−21% of time standing after six generations of selection) of LRFI pigs greatly contributed to the gain in energy efficiency. However, the impact of selection for RFI on the protein metabolism of the pig remains unclear. Digestibility of energy and nutrients was not affected by selection, neither for pigs fed conventional diets nor for pigs fed high-fibre diets. A significant improvement of digestive efficiency could likely be achieved by selecting pigs on fibre diets. No convincing genetic or blood biomarker has been identified for explaining the differences in RFI, suggesting that pigs have various ways to achieve an efficient use of feed. No deleterious impact of the selection on the sow reproduction performance was observed. The resource allocation theory states that low RFI may reduce the ability to cope with stressors,via the reduction of a buffer compartment dedicated to responses to stress. None of the experiments focussed on the response of pigs to stress or challenges could confirm this theory. Understanding the relationships between RFI and responses to stress and energy demanding processes, as such immunity and lactation, remains a major challenge for a better understanding of the underlying biological mechanisms of the trait and to reconcile the experimental results with the resource allocation theory

Front Aging Neurosci

We studied the influence of emotions on autobiographical memory (AbM) in patients with Alzheimer's disease (AD), characteristically triggering atrophy in the hippocampus and the amygdala, two crucial structures sustaining memory and emotional processing. Our first aim was to analyze the influence of emotion on AbM in AD patients, on both the proportion and the specificity of emotional memories. Additionally, we sought to determine the relationship of emotional AbM to amygdalar-hippocampal volumes. Eighteen prodromal to mild AD patients and 18 age-matched healthy controls were included. We obtained 30 autobiographical memories per participant using the modified Crovitz test (MCT). Analyses were performed on global scores, rates and specificity scores of the emotional vs. neutral categories of memories. Amygdalar-hippocampal volumes were extracted from 3D T1-weighted MRI scans and tested for correlations with behavioral data. Overall, AD patients displayed a deficit in emotional AbMs as they elicited less emotional memories than the controls, however, the specificity of those memories was preserved. The deficit likely implied retrieval or storage as it was extended in time and without reminiscence bump effect. Global scores and rates of emotional memories, but not the specificity scores, were correlated to right amygdalar and hippocampal volumes, indicating that atrophy in these structures has a central role in the deficit observed. Conversely, emotional memories were more specific than neutral memories in both groups, reflecting an enhancement effect of emotion that could be supported by other brain regions that are spared during the early stages of the disease

Neural correlates of visual hallucinations in dementia with Lewy bodies.

NTRODUCTION: The aim of this study was to investigate the association between visual hallucinations in dementia with Lewy bodies (DLB) and brain perfusion using single-photon emission computed tomography. METHODS: We retrospectively included 66 patients with DLB, 36 of whom were having visual hallucinations (DLB-hallu) and 30 of whom were not (DLB-c). We assessed visual hallucination severity on a 3-point scale of increasing severity: illusions, simple visual hallucinations and complex visual hallucinations. We performed voxel-level comparisons between the two groups and assessed correlations between perfusion and visual hallucinations severity. RESULTS: We found a significant decrease in perfusion in the left anterior cingulate cortex, the left orbitofrontal cortex and the left cuneus in the DLB-hallu group compared with the DLB-c group. We also found a significant correlation between decreased bilateral anterior cingulate cortex, left orbitofrontal cortex, right parahippocampal gyrus, right inferior temporal cortex and left cuneus perfusion with the severity of hallucinations. CONCLUSIONS: Visual hallucinations seem to be associated with the impairment of anterior and posterior regions (secondary visual areas, orbitofrontal cortex and anterior cingulate cortex) involved in a top-down and bottom-up mechanism, respectively. Furthermore, involvement of the bilateral anterior cingulate cortex and right parahippocampal gyrus seems to lead to more complex hallucinations.journal article20152015 02 17importe

3D non rigid brain image registration with topology preservation constraint

Cette thèse aborde la problématique du recalage non rigide d'images cérébrales tridimensionnelles inter-patients. Le modèle de déformation considéré repose sur une représentation paramétrique multiéchelle dans une base de fonctions B-splines, dont les paramètres sont estimés par minimisation d'une fonctionnelle d'énergie basée sur la différence des intensités (cas monomodal). La contribution principale de ce travail est de garantir à la transformation estimée de préserver l'intégrité des structures déformées dans le cas 3D. Cette propriété, dite de conservation de la topologie, requiert d'imposer la positivité du jacobien de la transformation sur le domaine continu sous-jacent de l'image. Le problème d'optimisation sous contraintes correspondant est résolu grâce à des techniques issues de l'analyse par intervalles.Ce travail aborde par ailleurs différents aspects du recalage, à savoir le choix du critère de similarité et sa symétrisation, la régularisation du champ de déformation et la normalisation des intensités entre deux images. Une méthode originale de normalisation des intensités est proposée, basée sur l'estimation d'un mélange de lois gaussiennes à partir de l'histogramme conjoint. Cette méthode, dans un premier temps conçue pour lever des difficultés rencontrées dans le cadre du recalage d'images monomodales, a permis d'étendre la méthode au cas d'images IRM de pondérations différentes.Enfin, la mise en place d'un cadre de validation a permis d'évaluer l'influence des différents paramètres de la méthode et d'effectuer des comparaisons avec d'autres méthodes de recalage (recalage affine et l'algorithme des démons).This dissertation deals with non-rigid registration of 3D inter-patient cerebral images. The deformation model considered is based on a hierarchical parametric representation using B-spline basis functions, the parameters being estimated by minimizing a cost function relying on the intensity difference between images (monomodal case). The main contribution of this work is to warrant the estimated transformation to preserve the integrity of warped structures in the 3D case. This property, called topology preservation, is ensured by imposing the positivity of the jacobian of the transformation on the underlying continuous domain of the image. This constrained optimization problem is solved by resorting to interval analysis techniques.Furthermore, other aspects of the registration problem are considered, namely the choice of the similarity criterion and its symmetrization, the regularization of the deformation field and the intensity normalization between images. An original intensity normalization procedure, based on the estimation of a Gaussian mixture model of the joint histogram, is presented. This method, initially proposed to overcome some problems encountered with monomodal image registration, has been extended to the registration of multimodal MRI images. Finally, a validation framework is devised in order to evaluate the influence of the different parameters of the method and to carry out comparisons with other registration methods (affine registration and the demons algorithm)