Publications

Brain tumor segmentation in brain MRI volumes is used in neurosurgical planning and illness staging. It is important to explore the tumor shape and necrosis regions at different points of time to evaluate the disease progression. We propose an algorithm for semi-automatic tumor segmentation and necrosis detection. Our algorithm consists of three parts: conversion of MRI volume to a probability space based on the on-line learned model, tumor probability density estimation, and adaptive segmentation in the probability space. We use manually selected acceptance and rejection classes on a single MRI slice to learn the background and foreground statistical models. Then, we propagate this model to all MRI slices to compute the most probable regions of the tumor. Anisotropic 3D diffusion is used to estimate the probability density. Finally, the estimated density is segmented by the Sobolev active contour (snake) algorithm to select smoothed regions of the maximum tumor probability. The segmentation approach is robust to noise and not very sensitive to the manual initialization in the volumes tested. Also, it is appropriate for low contrast imagery. The irregular necrosis regions are detected by using the outliers of the probability distribution inside the segmented region. The necrosis regions of small width are removed due to a high probability of noisy measurements. The MRI volume segmentation results obtained by our algorithm are very similar to expert manual segmentation.

We used the Iowa Gambling Test (IGT) to examine the relationship of reward learning to both neuropsychological functioning and symptom formation in 65 individuals with schizophrenia. Results indicated that compared to controls, participants with schizophrenia showed significantly reduced reward learning, which in turn correlated with reduced intelligence, memory and executive function, and negative symptoms. The current findings suggested that a disease-related disturbance in reward learning may underlie both cognitive and motivation deficits, as expressed by neuropsychological impairment and negative symptoms in schizophrenia.

Due to advances in the acquisition and analysis of medical imaging, it is currently possible to quantify the tumor phenotype. The emerging field of Radiomics addresses this issue by converting medical images into minable data by extracting a large number of quantitative imaging features. One of the main challenges of Radiomics is tumor segmentation. Where manual delineation is time consuming and prone to inter-observer variability, it has been shown that semi-automated approaches are fast and reduce inter-observer variability. In this study, a semiautomatic region growing volumetric segmentation algorithm, implemented in the free and publicly available 3D-Slicer platform, was investigated in terms of its robustness for quantitative imaging feature extraction. Fifty-six 3D-radiomic features, quantifying phenotypic differences based on tumor intensity, shape and texture, were extracted from the computed tomography images of twenty lung cancer patients. These radiomic features were derived from the 3D-tumor volumes defined by three independent observers twice using 3D-Slicer, and compared to manual slice-by-slice delineations of five independent physicians in terms of intra-class correlation coefficient (ICC) and feature range. Radiomic features extracted from 3D-Slicer segmentations had significantly higher reproducibility (ICC = 0.85±0.15, p = 0.0009) compared to the features extracted from the manual segmentations (ICC = 0.77±0.17). Furthermore, we found that features extracted from 3D-Slicer segmentations were more robust, as the range was significantly smaller across observers (p = 3.819e-07), and overlapping with the feature ranges extracted from manual contouring (boundary lower: p = 0.007, higher: p = 5.863e-06). Our results show that 3D-Slicer segmented tumor volumes provide a better alternative to the manual delineation for feature quantification, as they yield more reproducible imaging descriptors. Therefore, 3D-Slicer can be employed for quantitative image feature extraction and image data mining research in large patient cohorts.

OBJECTIVES: Activation of mineralization process in periradicular tissues following the injuries, is important in repair mechanisms. The objective of this study was to investigate the effects of CEM cement on survival and mineralization of human mesenchymal stem cells (hMSCs) and compare it with MTA. MATERIALS AND METHODS: hMSCs that were planted on test material extracts and culture media were the experimental and control groups, respectively. The cytotoxicity of these materials was investigated using Methyl thiazol tetrazolium assay. After 7 days, alizarin red staining, alkaline phosphatase (ALP) assays, and qRT-PCR were used to assess the mineralization, expression of ALP, and gene expression (collagen type 1 and osteocalcin), respectively. The results were evaluated by ANOVA analysis and multiple comparisons test. P 0.05 was considered as statistically significant. RESULTS: Cell viability was not significantly different. Alizarin red and alkaline phosphatase staining showed mineralization in all three groups. In qRT-PCR, the expression of collagen type 1 is not significantly different among the three groups. Osteocalcin gene expression was significantly higher in the CEM group compared to the control (P 0.05). CONCLUSION: CEM cement has acceptable toxicity and could induce mineralization process and enhance osteocalcin gene expression which is associated with mineralization in hMSCs.

This paper describes the concept of eigenspine, a concept applicable for determining the correlation between pair-wise combinations of measures useful for describing the three-dimensional spinal deformities associated with adolescent idiopathic scoliosis. The proposed data analysis scheme is based upon the use of principal component analysis (PCA) and canonical correlation analysis (CCA). PCA is employed to reduce the dimensionality of the data space, thereby providing a regularization of the measurements, and CCA is employed to determine the linear dependence between pair-wise combinations of different measures. The usefulness of the eigenspine concept is demonstrated by analyzing the position and the rotation of all lumbar and thoracic vertebrae as obtained from 46 patients suffering from adolescent idiopathic scoliosis. The analysis showed that the strongest linear relationship is found between the lateral displacement and the coronal rotation of the vertebrae, and that a somewhat weaker but still strong correlation is found between the coronal rotation and the axial rotation of the vertebrae. These results are well in-line with the general understanding of idiopathic scoliosis. Noteworthy though is that the correlation between the anterior-posterior displacement and the sagittal rotation was not as strong as expected and that the obtained results further indicate the need for including the axial vertebral rotation as a measure when characterizing different types of idiopathic scoliosis. Apart from analyzing pair-wise correlations between different measures, the method is believed to be suitable for finding a maximally descriptive low-dimensional combination of measures describing spinal deformities in idiopathic scoliosis.

We investigated the association between the Val158Met polymorphism of the catechol-O-methyltransferase (COMT) gene, the Val66Met polymorphism of the brain-derived neurotrophic factor (BDNF) gene, and white matter changes in patients with major depressive disorder (MDD) and healthy subjects using diffusion tensor imaging (DTI). We studied 30 patients with MDD (17 males and 13 females, with mean age ± standard deviation [SD] =44±12 years) and 30 sex- and age-matched healthy controls (17 males and 13 females, aged 44±13 years). Using DTI analysis with a tract-based spatial statistics (TBSS) approach, we investigated the differences in fractional anisotropy, radial diffusivity, and axial diffusivity distribution among the three groups (patients with the COMT gene Val158Met, those with the BDNF gene Val66Met, and the healthy subjects). In a voxel-wise-based group comparison, we found significant decreases in fractional anisotropy and axial diffusivity within the temporal lobe white matter in the Met-carriers with MDD compared with the controls (P

The ability of lyotropic liquid crystals to form intricate structures on a range of length scales can be utilized for the synthesis of structurally complex inorganic materials, as well as in devices for controlled drug delivery. Here we employ magnetic resonance imaging (MRI) for non-invasive characterization of nano-, micro-, and millimeter scale structures in liquid crystals. The structure is mirrored in the translational and rotational motion of the water, which we assess by measuring spatially resolved self-diffusion tensors and 2H spectra. Our approach differs from previous works in that the MRI parameters are mapped with spatial resolution in all three dimensions, thus allowing for detailed studies of liquid crystals with complex millimeter-scale morphologies that are stable on the measurement time-scale of 10 hours. The 2H data conveys information on the nanometer-scale structure of the liquid crystalline phase, while the combination of diffusion and 2H data permits an estimate of the orientational distribution of micrometer-scale anisotropic domains. We study lamellar phases consisting of the nonionic surfactant C10E3 in 2H2O, and follow their structural equilibration after a temperature jump and the cessation of shear. Our experimental approach may be useful for detailed characterization of liquid crystalline materials with structures on multiple length scales, as well as for studying the mechanisms of phase transitions.

The outermost layer of the skin, the stratum corneum (SC), is a lipid-protein membrane that experiences considerable osmotic stress from a dry and cold climate. The natural moisturizing factor (NMF) comprises small and polar substances, which like osmolytes can protect living systems from osmotic stress. NMF is commonly claimed to increase the water content in the SC and thereby protect the skin from dryness. In this work we challenge this proposed mechanism, and explore the influence of NMF on the lipid and protein components in the SC. We employ natural-abundance (13)C solid-state NMR methods to investigate how the SC molecular components are influenced by urea, glycerol, pyrrolidone carboxylic acid (PCA), and urocanic acid (UCA), all of which are naturally present in the SC as NMF compounds. Experiments are performed with intact SC, isolated corneocytes and model lipids. The combination of NMR experiments provides molecularly resolved qualitative information on the dynamics of different SC lipid and protein components. We obtain completely novel molecular information on the interaction of these NMF compounds with the SC lipids and proteins. We show that urea and glycerol, which are also common ingredients in skin care products, increase the molecular mobility of both SC lipids and proteins at moderate relative humidity where the SC components are considerably more rigid in the absence of these compounds. This effect cannot be attributed to increased SC water content. PCA has no detectable effect on SC molecular mobility under the conditions investigated. It is finally shown that the more apolar compound, UCA, specifically influences the mobility of the SC lipid regions. The present results show that the NMF components act to retain the fluidity of the SC molecular components under dehydrating conditions in such a way that the SC properties remain largely unchanged as compared to more hydrated SC. These findings provide a new molecular insight into how small polar molecules in NMF and skin care products act to protect the human skin from drying.

The goal of this study was to assess integrity of the cingulum bundle in patients diagnosed with first episode schizophrenia, chronic schizophrenia, and matched controls as well as to determine the relationship between diffusion measures of cingulum bundle integrity and severity of patients’ delusions of reference. Participants, who comprised 18 first episode patients, 20 chronic patients, and two groups of matched controls (20 subjects in each), underwent 3 T MRI diffusion tensor imaging. Patients diagnosed with schizophrenia (chronic+first episode) showed decreased fractional anisotropy in the right cingulum bundle compared with controls. First episode patients exhibited higher trace bilaterally, compared with matched controls, and on the left compared with chronic patients. Axial diffusivity was increased in first episode patients, bilaterally, compared with matched controls and chronic patients. Radial diffusivity was also higher, bilaterally, in first episode patients compared with matched controls, and on the right compared with chronic patients. Trace diffusity and radial diffusivity in first episode patients were significantly correlated with increased severity of delusions of reference. Given that the abnormalities were present only in first episode patients and were not observed in chronic cases, it appears that they normalize over time. These abnormalities in first episode patients involved diffusivity measures in all directions (trace, radial and axial), suggesting a likely acute, partially reversible process in which there is an increase in brain water content, i.e., swelling, edema, or inflammation, that may reflect an early neuroinflammatory response in first episode patients.

BACKGROUND: Early unilateral brain lesions can lead to different types of corticospinal (re-)organization of motor networks. In one group of patients, the contralesional hemisphere exerts motor control not only over the contralateral non-paretic hand but also over the (ipsilateral) paretic hand, as the primary motor cortex is (re-)organized in the contralesional hemisphere. Another group of patients with early unilateral lesions shows "normal" contralateral motor projections starting in the lesioned hemisphere. AIM: We investigated how these different patterns of cortical (re-)organization affect interhemispheric transcallosal connectivity in patients with congenital hemiparesis. METHOD: Eight patients with ipsilateral motor projections (group IPSI) versus 7 patients with contralateral motor projections (group CONTRA) underwent magnetic resonance diffusion tensor imaging (DTI). The corpus callosum (CC) was subdivided in 5 areas (I-V) in the mid-sagittal slice and volumetric information. The following diffusion parameters were calculated: fractional anisotropy (FA), trace, radial diffusivity (RD), and axial diffusivity (AD). RESULTS: DTI revealed significantly lower FA, increased trace and RD for group IPSI compared to group CONTRA in area III of the corpus callosum, where transcallosal motor fibers cross the CC. In the directly neighboring area IV, where transcallosal somatosensory fibers cross the CC, no differences were found for these DTI parameters between IPSI and CONTRA. Volume of callosal subsections showed significant differences for area II (connecting premotor cortices) and III, where group IPSI had lower volume. INTERPRETATION: The results of this study demonstrate that the callosal microstructure in patients with congenital hemiparesis reflects the type of cortical (re-)organization. Early lesions disrupting corticospinal motor projections to the paretic hand consecutively affect the development or maintenance of transcallosal motor fibers.