Dual-Centre Harmonised Multimodal Positron Emission Tomography/Computed Tomography Image Radiomic Features and Machine Learning Algorithms for Non-small Cell Lung Cancer Histopathological Subtype Phenotype Decoding

AIMS

We aimed to build radiomic models for classifying non-small cell lung cancer (NSCLC) histopathological subtypes through a dual-centre dataset and comprehensively evaluate the effect of ComBat harmonisation on the performance of single- and multimodality radiomic models.

MATERIALS AND METHODS

A public dataset of NSCLC patients from two independent centres was used. Two image fusion methods, namely guided filtering-based fusion and image fusion based on visual saliency map and weighted least square optimisation, were used. Radiomic features were extracted from each scan, including first-order, texture and moment-invariant features. Subsequently, ComBat harmonisation was applied to the extracted features from computed tomography (CT), positron emission tomography (PET) and fused images to correct the centre effect. For feature selection, least absolute shrinkage and selection operator (Lasso) and recursive feature elimination (RFE) were investigated. For machine learning, logistic regression (LR), support vector machine (SVM) and AdaBoost were evaluated for classifying NSCLC subtypes. Training and evaluation of the models were carried out in a robust framework to offset plausible errors and performance was reported using area under the curve, balanced accuracy, sensitivity and specificity before and after harmonisation. N-way ANOVA was used to assess the effect of different factors on the performance of the models.

RESULTS

Support vector machine fed with selected features by recursive feature elimination from a harmonised PET feature set achieved the highest performance (area under the curve = 0.82) in classifying NSCLC histopathological subtypes. Although the performance of the models did not significantly improve for CT images after harmonisation, the performance of PET and guided filtering-based fusion feature signatures significantly improved for almost all models. Although the selection of the image modality and feature selection methods was effective on the performance of the model (ANOVA P-values <0.001), machine learning and harmonisation did not change the performance significantly (ANOVA P-values = 0.839 and 0.292, respectively).

CONCLUSION

This study confirmed the potential of radiomic analysis on PET, CT and hybrid images for histopathological classification of NSCLC subtypes.

Estimating the parameters of a dependent model and applying it to environmental data set

In this paper, a new dependent model is introduced. The model is motivated using the structure of series-parallel systems consisting of two series-parallel systems with a random number of parallel sub-systems that have fixed components connected in series. The dependence properties of the proposed model are studied. Two estimation methods, namely the moment method, and the maximum likelihood method are applied to estimate the parameters of the distributions of the components based on observing the system's lifetime data. A Monte Carlo simulation study is used to evaluate the performance of the estimators. Two real data sets are used to illustrate the proposed method. The results are useful for researchers and practitioners interested in analyzing bivariate data related to extreme events.

Associação do Genótipo e Fenótipo da Paraoxonase-1 com Angiografia Positiva para Doença Arterial Coronariana

Fundamento

Tem sido demonstrado que um aumento dos níveis séricos de PON1 é protetor contra vários distúrbios. Foi relatado que vários polimorfismos de nucleotídeo único (SNPs, single nucleotide polymorphisms ) do gene PON1 estão associados a níveis e atividade de proteínas enzimáticas séricas.

Objetivos

Investigar a associação de SNPs do PON1 e atividade da paraoxonase sérica com a doença arterial coronariana (DAC).

Métodos

Foram estudados 601 pacientes não relacionados submetidos à angiografia coronária, incluindo aqueles com estenose >50% (N=266) e aqueles com estenose <30% (N=335). Os SNPs rs662 e rs840560 do gene da paraoxonase foram determinados utilizando o método ARMS-PCR e o SNP rs705379 foi genotipado utilizando análise de PCR-RFLP. A atividade da paraoxonase sérica foi medida utilizando paraoxon como substrato. O valor de p<0,05 foi considerado significante.

Resultados

A atividade da paraoxonase sérica não foi significativamente diferente entre os grupos de estudo. Após ajuste para idade, sexo, hipertensão, diabetes mellitus e dislipidemia, o genótipo GG e o modelo codominante de rs662 foram positivamente associados a uma angiografia positiva (respectivamente, OR = 2,424, IC 95% [1,123-5,233], p <0,05, OR = 1,663, IC 95% [1,086-2,547]). A atividade da paraoxonase sérica foi significativamente maior no alelo G e variante GG do polimorfismo rs662, alelo A e variante AA de rs854560 e alelo C e variante CC de rs705379. A análise de haplótipos mostrou que o haplótipo ATC foi significativamente mais prevalente no grupo com angiografia negativa. A análise entre os grupos indicou que o alelo A de rs662 foi significativamente associado à menor atividade da paraoxonase no grupo com angiografia positiva (p=0,019).

Conclusões

A presença do alelo G do polimorfismo de nucleotídeo único rs662 está independentemente associada ao aumento do risco de DAC.

Monitoring the quality of frozen-thawed venous segments using bioimpedance spectroscopy

OBJECTIVE

Storage at temperatures as low as -80 °C and below (cryopreservation) is considered a method for long-term preservation of cells and tissues, and especially blood vessel segments, which are to be used for clinical operations such as transplantation. However, the freezing and thawing processes themselves can induce injuries to the cells and tissue by damaging the structure and consequently functionality of the cryopreserved tissue. In addition, the level of damage is dependent on the rate of cooling and warming used during the freezing-thawing process. Current methods for monitoring the viability and integrity of cells and tissues after going through the freezing-thawing cycle are usually invasive and destructive to the cells and tissues. Therefore, employing monitoring methods which are not destructive to the cryopreserved tissues, such as bioimpedance measurement techniques, is necessary. In this study we aimed to design a bioimpedance measurement setup to detect changes in venous segments after freezing-thawing cycles in a noninvasive manner.

APPROACH

A bioimpedance spectroscopy measurement technique with a two-electrode setup was employed to monitor ovine jugular vein segments after each cycle during a process of seven freezing-thawing cycles.

MAIN RESULTS

The results demonstrated changes in the impedance spectra of the measured venous segments after each freezing-thawing cycle.

SIGNIFICANCE

This indicates that bioimpedance spectroscopy has the potential to be developed into a novel method for non-invasive and non-destructive monitoring of the viability of complex tissue after cryopreservation.

Finite Element Simulation of the Impedance Response of a Vascular Segment as a Function of Changes in Electrode Configuration

Monitoring a biological tissue as a three dimensional (3D) model is of high importance. Both the measurement technique and the measuring electrode play substantial roles in providing accurate 3D measurements. Bioimpedance spectroscopy has proven to be a noninvasive method providing the possibility of monitoring a 3D construct in a real time manner. On the other hand, advances in electrode fabrication has made it possible to use flexible electrodes with different configurations, which makes 3D measurements possible. However, designing an experimental measurement set-up for monitoring a 3D construct can be costly and time consuming and would require many tissue models. Finite element modeling methods provide a simple alternative for studying the performance of the electrode and the measurement set-up before starting with the experimental measurements. Therefore, in this study we employed the COMSOL Multiphysics finite element modeling method for simulating the effects of changing the electrode configuration on the impedance spectroscopy measurements of a venous segment. For this purpose, the simulations were performed for models with different electrode configurations. The simulation results provided us with the possibility of finding the optimal electrode configuration including the geometry, number and dimensions of the electrodes, which can be later employed in the experimental measurement set-up.

Quantum transport through the edge states of zigzag phosphorene nanoribbons in presence of a single point defect: analytic Green's function method

Zigzag phosphorene nanoribbons have quasi-flat band edge modes entirely detached from bulk states. We analytically study the electronic transport through such edge states in the presence of a localized defect for semi-infinite and finite ribbon widths. Using the tight-binding model, we derive analytical expressions for the Green's function and transmission amplitude of both pristine and defective nanoribbons. We find that the transmission of ribbons with both semi-infinite and finite width is sensitive to the location of a single impurity defect with respect to the edge. By the presence of an impurity on the outermost edge site of the ribbon, the transmission through the edge channel, similar to a one-dimensional chain, strongly suppresses for the entire energy spectrum of the quasi-flat band. In contrast, the transmission of low-energy [Formula: see text] states, is robust as the impurity is moved one position far away from the edge on the same sub-lattice. The analytical calculations are also complemented by exact numerical transport computations using the Landauer approach.

Paraoxonase-1 Q192R polymorphism and its association with hs-CRP and fasting blood glucose levels and risk of coronary artery disease

AIMS

Paraoxonase-1 (PON1) has been shown to protect low-density lipoprotein cholesterol (LDL-C) and high-density lipoprotein cholesterol (HDL-C) against oxidative-modification and thereby might protect against coronary-artery-disease (CAD). Here we explored the relationship of a genetic variant (a substitution (R) Arg with (Q) Gln at position 192) of PON1 in 250 patients with/without CAD.

MATERIALS AND METHODS

Genotyping of PON1 Q192R was carried out using Real-Time-PCR TaqMan-based-probe. Demographic-characteristics and biochemical-analyses, including fasting blood sugar (FBS), HDL, LDL, triglycerides (TG) and C-reactive protein (CRP) were evaluated. Univariate/multivariate analyses were performed to determine the association of the genetic polymorphism and CAD as well as with clinical-characteristics of population.

RESULTS

Our findings showed that RR-genotype was more frequent in CAD-patients, compared to the wild-type genotype. Moreover, CAD patients with RR-genotype had an odd ratio of 5.0 (95% CI: 1.3-18.6; p = 0.017), versus wild-type genotype, in multivariate-analysis. Of note we also observed that CAD-patients with QQ-genotype had a significantly lower Hs-CRP level, compared to the RR-genotype.

CONCLUSION

we demonstrate that PON1-Q192R-polymorphism was associated with CRP and FBS levels; R-allele of PON1-Q192R may be an independent risk factor for CAD. Further studies are warranted to determine the value of this marker as a surrogate marker in CAD patients.

Littoral Cell Angioma of the Spleen: An Additional Report of Four Cases with Emphasis on the Association with Visceral Organ Cancers

Aims and background

Littoral cell angioma (LCA) is an uncommon vascular tumor of the spleen recently described and interpreted as the tumoral counterpart of the normally present littoral cells lining the splenic sinus channels of red pulp. The diagnosis of LCA is suggested by a quite characteristic morphology and confirmed by the demonstration of a hybrid endothelial/histiocytic phenotype.

Methods

Four original and previously unreported cases of LCA are presented. All four splenic vascular tumors were investigated by light microscopy and immunohistochemistry for endothelial and histiocytic markers.

Results

All four cases were associated with visceral epithelial malignancies (colorectal adenocarcinoma in two cases, renal and pancreatic adenocarcinoma in one case each). One case was also associated with an intracranial tentorial meningioma.

Conclusions

We consider our findings as a novelty and signal the possible existence of a clinical syndrome. Five of a total of 21 previously reported cases in the literature were also described as being associated with other cancers (non-Hodgkin's lymphoma in two cases, two not further specified tumors of the liver and brain, an epithelial ovarian cancer, and a non-small cell lung cancer in one case each). Close follow-up and careful investigation in search of a second visceral neoplasm are strongly recommended in cases of LCA, but further clinical observations and more in-depth genetic and molecular studies are needed before any valid conclusions can be drawn.

Applications of Bioimpedance Measurement Techniques in Tissue Engineering

Rapid development in the field of tissue engineering necessitates implementation of monitoring methods for evaluation of the viability and characteristics of the cell cultures in a real-time, non-invasive and non-destructive manner. Current monitoring techniques are mainly histological and require labeling and involve destructive tests to characterize cell cultures. Bioimpedance measurement technique which benefits from measurement of electrical properties of the biological tissues, offers a non-invasive, label-free and real-time solution for monitoring tissue engineered constructs. This review outlines the fundamentals of bioimpedance, as well as electrical properties of the biological tissues, different types of cell culture constructs and possible electrode configuration set ups for performing bioimpedance measurements on these cell cultures. In addition, various bioimpedance measurement techniques and their applications in the field of tissue engineering are discussed.

Antimicrobial efficacy of different concentration of sodium hypochlorite on the biofilm of Enterococcus faecalis at different stages of development

Background

Persistent infection of the root canal due to the presence of resistance bacterial species, such as Enterococcus faecalis, has always been one of the most important reasons for endodontic treatment failure. This study investigated the antimicrobial efficacy of 1%, 2.5 % and 5% sodium hypochlorite in eliminating E. faecalis biofilms at different stages of development.

Material and Methods

In this study 4-, 6- and 10-week-old E. faecalis biofilms were subjected to one of the following approaches: phosphate-buffered saline solution (PBS) or 1%, 2.5% and 5% NaOCl. Dentin chip suspensions were used for colony forming unit (CFU) counting to estimate remaining E. faecalis counts. Statistical comparison of the means was carried out with Kruskal-Wallis test, and pair-wise comparisons were made by Mann-Whitney U test, at a significance level of P<0.05.

Results

The results showed that 2.5% and 5% NaOCl completely eliminated E. faecalis biofilms in three stages of biofilm development, whereas 1% NaOCl resulted in 85.73%, 81.88% and 78.62% decreases in bacterial counts in 4-, 6- and 10-week-old biofilms, respectively, which was significantly more than those with PBS (p<0.05).

Conclusions

The bacteria in mature and old biofilms were more resistant to 1% NaOCl than were the bacteria in young biofilms. Overall survival rate and residual bacteria increased with biofilm aging.

Key words:Antibacterial, biofilm, E. faecalis, sodium hypochlorite.

Synthesis of N, N-dimethyl N-ethyl Chitosan as a Carrier for Oral Delivery of Peptide Drugs

N, N-dimethyl N-ethyl chitosan (DMEC), a quanternized derivative of chitosan was synthesized based on a modified two-step method via a 22 factorial design to optimize the preparative conditions. The degree of deacetylation of the starting chitosan was determined by FTIR and NMR methods and was 95%. In the first step of the synthesis, mono-ethyl chitosan was prepared by introducing an ethyl group onto the amine group of chitosan via a Schiff base and in the next step methyl iodide was added to produce DMEC which was water soluble in a pH range of 4-8. The DMEC polymers with different degrees of quaternization were obtained and fully characterized using FTIR and 1H-NMR spectroscopic methods. Based on 1H-NMR calculations, the degree of quaternization was 52% by optimizing the two-step process.

Optimized Synthesis and Characterization of N-Triethyl Chitosan

Chitosan exhibits poor solubility at pH values above 6 which prevents its enhancing effects at drugs absorption of sites. In the present work, N-triethylated chitosan (TEC) was prepared based on a modified one-step process via a 22 factorial design to optimize the preparative conditions. TEC polymer with different degree of quaternization for pharmacological and pharmaceutical experiments was achieved. Ethyl iodide and sodium hydroxide concentrations were chosen as independent variables. The degree of deacetylation of the starting chitosan was predetermined by pH-metric titration, infrared, and NMR methods. TEC chloride was fully characterized using FTIR and 1H-NMR spectroscopies. Based on NMR calculations, a high degree of quaternization was achieved through the optimized one-step process. These highly N-triethylated chitosan chlorides were soluble in water at room temperature.

Enhanced Cellular Cytotoxicity and Antibacterial Activity of 18-β-Glycyrrhetinic Acid by Albumin-conjugated PLGA Nanoparticles

The aim of the present work was to encapsulate 18-β-Glycyrrhetinic acid (GLA) in albumin conjugated poly(lactide-co-glycolide) (PLGA) nanoparticles by a modified nanoprecipitation method. Nanoparticles (NPs) were prepared by different drug to polymer ratios, human serum albumin (HSA) content, dithiothreitol (as producer of free thiol groups) content, and acetone (as non-solvent in nanoprecipitation). NPs with a size ranging from 126 to 174 nm were achieved. The highest entrapment efficiency (89.4±4.2%) was achieved when the ratio of drug to polymer was 1:4. The zeta potential of NPs was fairly negative (-8 to -12). Fourier transform infrared spectroscopy and differential scanning calorimetry proved the conjugation of HSA to PLGA NPs. In vitro release profile of NPs showed 2 phases: an initial burst for 4 h (34-49%) followed by a slow release pattern up to the end. The antibacterial effects of NPs against Staphylococcus aureus, Staphylococcus epidermidis and Pseudomonas aeruginosa were studied by microdilution method. The GLA-loaded NPs showed more antibacterial effect than pure GLA (2-4 times). The anticancer MTT test revealed that GLA-loaded NPs were approximately 9 times more effective than pure GLA in Hep G2 cells.

A Three-rooted Mandibular Second Premolar: A Case Report

Presence of extra roots and canals should be considered before initiation of root canal treatment for the success of endodontic treatment. A mandibular second premolar with three separate roots is very rare and its prevalence has been reported to be around 0.1%. This case report explains non-surgical endodontic treatment of a mandibular second premolar with three separate roots and three separate mesiobuccal, midbuccal, and lingual canal orifices. Close attention to anatomic variations, thorough radiographic examinations, thorough evaluation of the pulp chamber floor, and use of magnifying and optical devices have been recommended for the success of endodontic treatment of mandibular second premolars with complicated root canal system anatomy.

Reform in medical and health sciences educational system: a Delphi study of faculty members' views at Shiraz University of Medical Sciences

Despite the strengths in the Iranian medical and health sciences educational system, areas in need of improvement have been noted. The purpose of this study was to understand the views of faculty members at Shiraz University of Medical Sciences about current and future needs for medical and health sciences education, with the goal of improving the quality of the educational system. The data were collected using a Delphi consensus method. Analysis of the findings identified the following key themes among the factors likely to contribute to medical and health sciences education and training: adding and/or increasing student numbers in higher degrees in preference to associate degrees; providing more interactive, student-centred teaching methods; improving the educational content with more practical and research-based courses tailored to society's needs; and an emphasis on outcome-based student evaluation techniques. These changes aim to respond to health trends in society and enhance the close relationship between medical education and the needs of the Iranian society.