Alterations in the volume and shape of the basal ganglia and thalamus in schizophrenia with auditory hallucinations

Different lines of evidence indicate that the structure and physiology of the basal ganglia and the thalamus is disturbed in schizophrenia. However, it is unknown whether the volume and shape of these subcortical structures are affected in schizophrenia with auditory hallucinations (AH), a core positive symptom of the disorder. We took structural MRI from 63 patients with schizophrenia, including 36 patients with AH and 27 patients who had never experienced AH (NAH), and 51 matched healthy controls. We extracted volumes for the left and right thalamus, globus pallidus, putamen, caudate and nucleus accumbens. Shape analysis was also carried out. When comparing to controls, the volume of the right globus pallidus, thalamus, and putamen, was only affected in AH patients. The volume of the left putamen was also increased in individuals with AH, whereas the left globus pallidus was affected in both groups of patients. The shapes of right and left putamen and thalamus were also affected in both groups. The shape of the left globus pallidus was only altered in patients lacking AH, both in comparison to controls and to cases with AH. Lastly, the general PANSS subscale was correlated with the volume of the right thalamus, and the right and left putamen, in patients with AH. We have found volume and shape alterations of many basal ganglia and thalamus in patients with and without AH, suggesting in some cases a possible relationship between this positive symptom and these morphometric alterations.

Accuracy of formula-based volume and image segmentation-based volume in calculation of preoperative cystic jaw lesions' volume

OBJECTIVE

The aim of this study was to assess the accuracy of formula-based volume measurements and the 3D volume analysis with different software packages in the calculation of preoperative cystic jaw lesions' volume. The secondary aim was to assess the reliability and the accuracy of 3 imaging software programs for measuring the cystic jaw lesions' volume in CBCT images.

MATERIALS AND METHODS

This study consisted of two parts: an in vitro part using 2 dry human mandibles that were used to create simulated osteolytic lesions to assess the accuracy of the volumetric analysis and formula-based volume. As a gold standard, the volume of each bone defect was determined by taking an impression using rapid soft silicone (Vinylight) and then quantifying the volume of the replica. Afterward, each tooth socket was scanned using a high-resolution CBCT. A retrospective part using archived CBCT radiographs that were taken from the database of the outpatient clinic of the oral and maxillofacial radiology department, Faculty of Dentistry, Minia University to assess the reliability of the 3 software packages. The volumetric data set was exported for volume quantification using the 3 software packages (MIMICS-OnDemand and InVesalius software). Also, the three greatest orthogonal diameters of the lesions were calculated, and the volume was assessed using the ellipsoid formula. Dunn's test was used for pair-wise comparisons when Friedman's test was significant. The inter-examiner agreement was assessed using Cronbach's alpha reliability coefficient and intra-class correlation coefficient.

RESULTS

Regarding the results of the retrospective part, there was a statistically significant difference between volumetric measurements by equation and different software (P value < 0.001, Effect size = 0.513). The inter-observer reliability of the measurements of the cystic lesions using the different software packages was very good. The highest inter-examiner agreement for volume measurement was found with InVesalius (Cronbach's alpha = 0.992). On the other hand, there was a statistically significant difference between dry mandible volumetric measurements and Gold Standard. All software showed statistically significantly lower dry mandible volumetric measurements than the gold standard.

CONCLUSION

Computer-aided assessment of cystic lesion volume using InVesalius, OnDemand, and MIMICS is a readily available, easy to use, non-invasive option. It confers an advantage over formula-based volume as it gives the exact morphology of the lesion so that potential problems can be detected before surgery. Volume analysis with InVesalius software was accurate in determining the volume of simulated periapical defects in a human cadaver mandible as compared to true volume. InVesalius software proved that open-source software can be robust yet user-friendly with the advantage of minimal cost to use.

Enzyme Cascade Reactions on DNA Origami Scaffold

The protocols for constructing, characterizing, and analyzing enzyme cascade reaction systems on the DNA scaffold are described. Two-step and three-step enzyme cascade reactions were adapted from the xylose metabolic pathway as the example of natural metabolic pathway and were assembled on the DNA scaffold by using the DNA binding adaptors.

Interactive Analysis for Large Volume Data from Fluorescence Microscopy at Cellular Precision

The main objective for understanding fluorescence microscopy data is to investigate and evaluate the fluorescent signal intensity distributions as well as their spatial relationships across multiple channels. The quantitative analysis of 3D fluorescence microscopy data needs interactive tools for researchers to select and focus on relevant biological structures. We developed an interactive tool based on volume visualization techniques and GPU computing for streamlining rapid data analysis. Our main contribution is the implementation of common data quantification functions on streamed volumes, providing interactive analyses on large data without lengthy preprocessing. Data segmentation and quantification are coupled with brushing and executed at an interactive speed. A large volume is partitioned into data bricks, and only user-selected structures are analyzed to constrain the computational load. We designed a framework to assemble a sequence of GPU programs to handle brick borders and stitch analysis results. Our tool was developed in collaboration with domain experts and has been used to identify cell types. We demonstrate a workflow to analyze cells in vestibular epithelia of transgenic mice.

Atomic Force Microscopy Reveals that the Drosophila Telomere-Capping Protein Verrocchio Is a Single-Stranded DNA-Binding Protein

Atomic force microscopy (AFM) is a scanning probe technique that allows visualization of biological samples with a nanometric resolution. Determination of the physical properties of biological molecules at a single-molecule level is achieved through topographic analysis of the sample adsorbed on a flat and smooth surface. AFM has been widely used for the structural analysis of nucleic acid-protein interactions, providing insights on binding specificity and stoichiometry of proteins forming complexes with DNA substrates. Analysis of single-stranded DNA-binding proteins by AFM requires specific single-stranded/double-stranded hybrid DNA molecules as substrates for protein binding. In this chapter we describe the protocol for AFM characterization of binding properties of Drosophila telomeric protein Ver using DNA constructs that mimic the structure of chromosome ends. We provide details on the methodology used, including the procedures for the generation of DNA substrates, the preparation of samples for AFM visualization, and the data analysis of AFM images. The presented procedure can be adapted for the structural studies of any single-stranded DNA-binding protein.

New Method of Quantitative Analysis of Hard Exudate Using Optical Coherence Tomography: Application in Diabetic Macular Edema

PURPOSE

In the present study, the volume of hard exudates (HEs) was quantitatively measured using optical coherence tomography (OCT) and the agreement and correlation with area of HEs in fundus photography were analyzed.

METHODS

The medical records of patients with diabetic macular edema who underwent focal laser treatment and were followed up more than 3 months were retrospectively evaluated. An automated customized program designed for measuring HE volume was used. The HEs in each OCT B-scan binary image were measured using 512 × 128 pixels, 6 mm × 6 mm OCT cube scans. The volume was measured by summing the segmented HEs in each 128 B-scan image. The area was measured in 6 mm x 6 mm fundus photography. The volume and area were measured before and 3 months after the treatment. The agreement of increase and decrease in HEs, and the correlation of volume and area of HEs were analyzed.

RESULTS

A total of 35 patients (39 eyes) were included in the study. The volume was significantly reduced from 0.07978 to 0.02565 mm³ at 3 months (p < 0.001). The area was also significantly reduced from 15.35 to 8.60 mm² at 3 months (p < 0.001). The volume was decreased in 34 eyes and increased in 5 eyes. The area was decreased in 37 eyes and increased in 2 eyes. A significant correlation between volume and area was found (p < 0.001) as well as agreement between increase and decrease in volume and area.

CONCLUSIONS

In the 3-dimensional quantitative volumetric analysis, the volume and area of HEs were correlated and the direction of increase and decrease was concordant. Considering the distribution of HEs in multiple layers of the retina, volumetric analysis could be considered a substitute for the analysis of HE area.

Analysis of DNA-Protein Complexes by Atomic Force Microscopy Imaging: The Case of TRF2-Telomeric DNA Wrapping

Atomic force microscopy (AFM) is a non-optical microscopy that enables the acquisition at the nanoscale level of a 3D topographical image of the sample. For 30 years, AFM has been a valuable tool in life sciences to study biological samples in the field of tissue, cellular and molecular imaging, of mechanical properties and of force spectroscopy. Since the early beginnings of the technique, AFM has been extensively exploited as an imaging tool for structural studies of nucleic acids and nucleoprotein complexes. The morphometric analysis performed on the images can unveil specific structural and functional aspects of the sample, such as the multimerization state of proteins bound to DNA, or DNA conformational changes led by the DNA-binding proteins. Herein, a method for analyzing a complex formed by a telomeric DNA sequence wrapped around the TRF2 binding protein is presented. The described procedure could be applied to the study of any type of DNA-protein complex.