Reconstruction of 3D Surface Maps from Anterior Segment Optical Coherence Tomography Images Using Graph Theory and Genetic Algorithms

Automatic segmentation of anterior segment optical coherence tomography images provides an important tool to aid management of ocular diseases. Previous studies have mainly focused on 2D segmentation of these images. A novel technique capable of producing 3D maps of the anterior segment is presented here. This method uses graph theory and dynamic programming with shape constraint to segment the anterior and posterior surfaces in individual 2D images. Genetic algorithms are then used to align 2D images to produce a full 3D representation of the anterior segment. In order to validate the results of the 2D segmentation comparison is made to manual segmentation over a set of 39 images. For the 3D reconstruction a data set of 17 eyes is used. These have each been imaged twice so a repeatability measurement can be made. Good agreement was found with manual segmentation for the 2D segmentation method achieving a Dice similarity coefficient of 0.96, which is comparable to the inter-observer agreement. Good repeatability of results was demonstrated with the 3D registration method. A mean difference of 1.77 pixels was found between the anterior surfaces found from repeated scans of the same eye

Extraction, Refining and Characterization of the Fixed Oil of Basil (Ocimumbasilicum L.) Seeds

Basil is considered one of the important medicinal and aromatic plants in Sudan and worldwide. It is very rich sources of phytochemicals which have vital properties affecting human health in reduce risks and diseases. The present study aimed to evaluate the physicochemical characteristics of basil seeds and the oil extracted from them. This included four accessions of basil grown in National Oil Seed Processing Research Institute (NOPRI) farm- University of Gezira- Sudan: (two local accessions of NOPRI and Umteraibat, and two accessions (Egyptian and Maldivian) obtained from Institute for Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany. Themethods used the American Oil Chemists Society (AOCS) official methods. The percentage of moisture content (4-5), oil content (19-28%), crude protein (15-20%), crude fiber (30-36%)and ash (5-8%)for basil seeds. The physical properties of crude oil were specific gravity at room temperature (0.92-0.93) and refractive index (1.4809-1.4823) at 20°C. The Lovibond readings for crude oil color were in the range (0.6-2.5) for the red color and (18-70) for the yellow color, while for the refined oil the red color was (0.2-0.5) and yellow was (2.5-6.2). Chemical properties were: free fatty acids for crude oil (0.2-0.76%) and (0.04-0.06%) for refined oil; peroxide and saponification values and the unsaponifiable matter were (5.7-24.9) ml.eqv.\kg, (195-198) mg KOH/g and (1.6-2.2%) respectively. The fatty acid composition was analyzed using GC-MS, and the percentage of the unsaturated fatty acids oleic, linoleic and linolenic were (0.78-2.13), (22.91-40.39%)and (22.83-39.32%)respectively; the most abundant saturated fatty acids were palmitic and stearic at (14.7-16.67%) and (9.18-11.57%) respectively

Use of quercetin in animal feed : effects on the P-gp expression and pharmacokinetics of orally administrated enrofloxacin in chicken

Modulation of P-glycoprotein (P-gp, encoded by Mdr1) by xenobiotics plays central role in pharmacokinetics of various drugs. Quercetin has a potential to modulate P-gp in rodents, however, its effects on P-gp modulation in chicken are still unclear. Herein, study reports role of quercetin in modulation of P-gp expression and subsequent effects on the pharmacokinetics of enrofloxacin in broilers. Results show that P-gp expression was increased in a dose-dependent manner following exposure to quercetin in Caco-2 cells and tissues of chicken. Absorption rate constant and apparent permeability coefficient of rhodamine 123 were decreased, reflecting efflux function of P-gp in chicken intestine increased by quercetin. Quercetin altered pharmacokinetic of enrofloxacin by decreasing area under curve, peak concentration, and time to reach peak concentration and by increasing clearance rate. Molecular docking shows quercetin can form favorable interactions with binding pocket of chicken xenobiotic receptor (CXR). Results provide convincing evidence that quercetin induced P-gp expression in tissues by possible interaction with CXR, and consequently reducing bioavailability of orally administered enrofloxacin through restricting its intestinal absorption and liver/kidney clearance in broilers. The results can be further extended to guide reasonable use of quercetin to avoid drug-feed interaction occurred with co-administered enrofloxacin or other similar antimicrobials.Peer reviewedFinal Published versio

Update to the College of American Pathologists Reporting on Thyroid Carcinomas

Background The reporting of thyroid carcinomas follows the recommendations of the College of American Pathologists (CAP) protocols and includes papillary carcinoma, follicular carcinoma, anaplastic carcinoma and medullary carcinoma. Despite past and recent efforts, there are a number of controversial issues in the classification and diagnosis of thyroid carcinomas (TC) that, potentially impact on therapy and prognosis of patients with TC. Discussion The most updated version of the CAP thyroid cancer protocol incorporates recent changes in histologic classification as well as changes in the staging of thyroid cancers as per the updated American Joint Commission on Cancer staging manual. Among the more contentious issues in the pathology of thyroid carcinoma include the defining criteria for tumor invasiveness. While there are defined criteria for invasion, there is not universal agreement in what constitutes capsular invasion, angioinvasion and extrathyroidal invasion. Irrespective of the discrepant views on invasion, pathologists should report on the presence and extent (focal, widely) of capsular invasion, angioinvasion and extrathyroidal extension. These findings assist clinicians in their assessment of the recurrence risk and potential for metastatic disease. It is beyond the scope of this paper to detail the entire CAP protocol for thyroid carcinomas; rather, this paper addresses some of the more problematic issues confronting pathologists in their assessment and reporting of thyroid carcinomas. Conclusion The new CAP protocol for reporting of thyroid carcinomas is a step toward improving the clinical value of the histopathologic reporting of TC. Large meticulous clinico-pathologic and molecular studies with long term follow up are still needed in order to increase the impact of microscopic examination on the prognosis and management of TC

Modeling Diffusion Directions of Corpus Callosum

Diffusion Tensor Imaging (DTI) has been used to study the characteristics of Multiple Sclerosis (MS) in the brain. The von Mises- Fisher distribution (vmf) is a probability distribution for modeling directional data on the unit hypersphere. In this paper we modeled the diffusion directions of the Corpus Callosum (CC) as a mixture of vmf distributions for both MS subjects and healthy controls. Higher diffusion concentration around the mean directions and smaller sum of angles between the mean directions are observed on the normal-appearing CC of the MS subjects as compared to the healthy controls

Fast preparation route to high-performances textured Sr-doped Ca 3 Co 4 O 9 thermoelectric materials through precursor powder modification

This work presents a short and very efficientmethod to produce high performance textured Ca3Co4O9thermoelectric materials through initial powders modifica-tion. Microstructure has shown good grain orientation, andlow porosity while slightly lower grain sizes were obtained insamples prepared from attrition milled powders. All samplesshow the high density of around 96% of the theoretical value.These similar characteristics are reflected in, approximately,the same electrical resistivity and Seebeck coefficient valuesfor both types of samples. However, in spite of similar powerfactor (PF) at low temperatures, it is slightly higher at hightemperature for the attrition milled samples. On the otherhand, the processing time reduction (from 38 to 2 h) whenusing attrition milled precursors, leads to lower mechanicalproperties in these samples. All these data clearly point out tothe similar characteristics of both kinds of samples, with adrastic processing time decrease when using attrition milledprecursors, which is of the main economic importance whenconsidering their industrial production

Ischemia-Reperfusion Injury and Pregnancy Initiate Time-Dependent and Robust Signs of Up-Regulation of Cardiac Progenitor Cells

To explore how cardiac regeneration and cell turnover adapts to disease, different forms of stress were studied for their effects on the cardiac progenitor cell markers c-Kit and Isl1, the early cardiomyocyte marker Nkx2.5, and mast cells. Adult female rats were examined during pregnancy, after myocardial infarction and ischemia-reperfusion injury with/out insulin like growth factor-1(IGF-1) and hepatocyte growth factor (HGF). Different cardiac sub-domains were analyzed at one and two weeks post-intervention, both at the mRNA and protein levels. While pregnancy and myocardial infarction up-regulated Nkx2.5 and c-Kit (adjusted for mast cell activation), ischemia-reperfusion injury induced the strongest up-regulation which occurred globally throughout the entire heart and not just around the site of injury. This response seems to be partly mediated by increased endogenous production of IGF-1 and HGF. Contrary to c-Kit, Isl1 was not up-regulated by pregnancy or myocardial infarction while ischemia-reperfusion injury induced not a global but a focal up-regulation in the outflow tract and also in the peri-ischemic region, correlating with the up-regulation of endogenous IGF-1. The addition of IGF-1 and HGF did boost the endogenous expression of IGF and HGF correlating to focal up-regulation of Isl1. c-Kit expression was not further influenced by the exogenous growth factors. This indicates that there is a spatial mismatch between on one hand c-Kit and Nkx2.5 expression and on the other hand Isl1 expression. In conclusion, ischemia-reperfusion injury was the strongest stimulus with both global and focal cardiomyocyte progenitor cell marker up-regulations, correlating to the endogenous up-regulation of the growth factors IGF-1 and HGF. Also pregnancy induced a general up-regulation of c-Kit and early Nkx2.5+ cardiomyocytes throughout the heart. Utilization of these pathways could provide new strategies for the treatment of cardiac disease

Systematical Detection of Significant Genes in Microarray Data by Incorporating Gene Interaction Relationship in Biological Systems

Many methods, including parametric, nonparametric, and Bayesian methods, have been used for detecting differentially expressed genes based on the assumption that biological systems are linear, which ignores the nonlinear characteristics of most biological systems. More importantly, those methods do not simultaneously consider means, variances, and high moments, resulting in relatively high false positive rate. To overcome the limitations, the SWang test is proposed to determine differentially expressed genes according to the equality of distributions between case and control. Our method not only latently incorporates functional relationships among genes to consider nonlinear biological system but also considers the mean, variance, skewness, and kurtosis of expression profiles simultaneously. To illustrate biological significance of high moments, we construct a nonlinear gene interaction model, demonstrating that skewness and kurtosis could contain useful information of function association among genes in microarrays. Simulations and real microarray results show that false positive rate of SWang is lower than currently popular methods (T-test, F-test, SAM, and Fold-change) with much higher statistical power. Additionally, SWang can uniquely detect significant genes in real microarray data with imperceptible differential expression but higher variety in kurtosis and skewness. Those identified genes were confirmed with previous published literature or RT-PCR experiments performed in our lab