Deep transfer learning-based fully automated detection and classification of Alzheimer's disease on brain MRI

OBJECTIVES

To employ different automated convolutional neural network (CNN)-based transfer learning (TL) methods for both binary and multiclass classification of Alzheimer's disease (AD) using brain MRI.

METHODS

Herein, we applied three popular pre-trained CNN models (ResNet101, Xception, and InceptionV3) using a fine-tuned approach of TL on 3D T1-weighted brain MRI from a subset of ADNI dataset (n = 305 subjects). To evaluate power of TL, the aforementioned networks were also trained from scratch for performance comparison. Initially, Unet network segmentedthe MRI scans into characteristic components of gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF). The proposed networks were trained and tested over the pre-processed and augmented segmented and whole images for both binary (NC/AD + progressive mild cognitive impairment (pMCI)+stable MCI (sMCI)) and 4-class (AD/pMCI/sMCI/NC) classification. Also, two independent test sets from the OASIS (n = 30) and AIBL (n = 60) datasets were used to externally assess the performance of the proposed algorithms.

RESULTS

The proposed TL-based CNN models achieved better performance compared to the training CNN models from scratch. On the ADNI test set, InceptionV3-TL achieved the highest accuracy of 93.75% and AUC of 92.0% for binary classification, as well as the highest accuracy of 93.75% and AUC of 96.0% for multiclass classification of AD on the whole images. On the OASIS test set, InceptionV3-TL outperformed two other models by achieving 93.33% accuracy with 93.0% AUC in binary classification of AD on the whole images. On the AIBL test set, InceptionV3-TL also outperformed two other models in both binary and multiclass classification tasks on the whole MR images and achieved accuracy/AUC of 93.33%/95.0% and 90.0%/93.0%, respectively. The GM segment as input provided the highest performance in both binary and multiclass classification of AD, as compared to the WM and CSF segments.

CONCLUSION

This study demonstrates the potential of applying deep TL approach for automated detection and classification of AD using brain MRI with high accuracy and robustness across internal and external test data, suggesting that these models can possibly be used as a supportive tool to assist clinicians in creating objective opinion and correct diagnosis.

ADVANCES IN KNOWLEDGE

We used CNN-based TL approaches and the augmentation techniques to overcome the insufficient data problem. Our study provides evidence that deep TL algorithms can be used for both binary and multiclass classification of AD with high accuracy.

A historical literature review on the role of posterior axillary boost field in the axillary lymph node coverage and development of lymphedema following regional nodal irradiation in breast cancer

To elucidate whether (1) a posterior axillary boost (PAB) field is an optimal method to target axillary lymph nodes (LNs); and (2) the addition of a PAB increases the incidence of lymphedema, a systematic review was undertaken. A literature search was performed in the PubMed database. A total of 16 studies were evaluated. There were no randomized studies. Seven articles have investigated dosimetric aspects of a PAB. The remaining 9 articles have determined the effect of a PAB field on the risk of lymphedema. Only 2 of 9 articles have prospectively reported the impact of a PAB on the risk of lymphedema development. There are conflicting reports on the necessity of a PAB. The PAB field provides a good coverage of level I/II axillary LNs because these nodes are usually at a greater depth. The main concern regarding a PAB is that it produces a hot spot in the anterior region of the axilla. Planning studies optimized a traditional PAB field. Prospective studies and the vast majority of retrospective studies have reported the use of a PAB field does not result in increasing the risk of lymphedema development over supraclavicular-only field. The controversies in the incidence of lymphedema suggest that field design may be more important than field arrangement. A key factor regarding the use of a PAB is the depth of axillary LNs. The PAB field should not be used unless there is an absolute indication for its application. Clinicians should weigh lymphedema risk in individual patients against the limited benefit of a PAB, in particular after axillary dissection. The testing of the inclusion of upper arm lymphatics in the regional LN irradiation target volume, and universal methodology measuring lymphedema are all areas for possible future studies.

Automated detection of pneumonia cases using deep transfer learning with paediatric chest X-ray images

OBJECTIVE

Pneumonia is a lung infection and causes the inflammation of the small air sacs (Alveoli) in one or both lungs. Proper and faster diagnosis of pneumonia at an early stage is imperative for optimal patient care. Currently, chest X-ray is considered as the best imaging modality for diagnosing pneumonia. However, the interpretation of chest X-ray images is challenging. To this end, we aimed to use an automated convolutional neural network-based transfer-learning approach to detect pneumonia in paediatric chest radiographs.

METHODS

Herein, an automated convolutional neural network-based transfer-learning approach using four different pre-trained models (i.e. VGG19, DenseNet121, Xception, and ResNet50) was applied to detect pneumonia in children (1-5 years) chest X-ray images. The performance of different proposed models for testing data set was evaluated using five performances metrics, including accuracy, sensitivity/recall, Precision, area under curve, and F1 score.

RESULTS

All proposed models provide accuracy greater than 83.0% for binary classification. The pre-trained DenseNet121 model provides the highest classification performance of automated pneumonia classification with 86.8% accuracy, followed by Xception model with an accuracy of 86.0%. The sensitivity of the proposed models was greater than 91.0%. The Xception and DenseNet121 models achieve the highest classification performance with F1-score greater than 89.0%. The plotted area under curve of receiver operating characteristics of VGG19, Xception, ResNet50, and DenseNet121 models are 0.78, 0.81, 0.81, and 0.86, respectively.

CONCLUSION

Our data showed that the proposed models achieve a high accuracy for binary classification. Transfer learning was used to accelerate training of the proposed models and resolve the problem associated with insufficient data. We hope that these proposed models can help radiologists for a quick diagnosis of pneumonia at radiology departments. Moreover, our proposed models may be useful to detect other chest-related diseases such as novel Coronavirus 2019.

ADVANCES IN KNOWLEDGE

Herein, we used transfer learning as a machine learning approach to accelerate training of the proposed models and resolve the problem associated with insufficient data. Our proposed models achieved accuracy greater than 83.0% for binary classification.

Effectiveness of rectal displacement devices during prostate external-beam radiation therapy: A review

Dose-escalated prostate radiotherapy (RT) can improve treatment outcomes, but rectal toxicity is the main limiting factor for introducing dose-escalated RT. Pushing rectal wall away from the prostate reduces the volume of the rectum in high-dose region, which can decrease both short- and long-term rectal toxicities after RT. This review focuses on the literature using different rectal displacement devices such as endorectal balloons, tissue spacers, rectal retractor, and ProSpare during prostate External beam radiotherapy, with regard to dosimetric effects, clinical benefits, prostate motion, and postoperative RT setting.

Rectal wall sparing effect of a rectal retractor in prostate intensity-modulated radiotherapy

Purpose

The objective of the study was to evaluate the effectiveness of a rectal retractor (RR) designed to protect rectal tissue in intensity-modulated radiotherapy (IMRT) by pushing rectal wall (RW) away from the prostate.

Materials and Methods

Twelve patients with localized prostate cancer were enrolled into this study. Patients underwent two computed tomography (CT) scans without and with RR. A prescription of 80 Gy in 40 fractions was planned on CT scans with and without RR. This study evaluates the ability of the RR in RW dose reduction, in particular reduction of the RW V_70Gy≥ 25% in comparison with the plan without RR dose-volume histograms were generated with and without RR. The patient's tolerance was assessed by patient-reported outcomes.

Results

The planning target volume coverage was equal for both without and with RR (P = 0.155). The mean dose to the RW was statistically significantly lower for the plan with RR than that for the plan without RR, a mean reduction of 5.8 Gy (P = 0.003). Significant relative reductions in rectal dose-volume parameters whether in absolute volume (cc) or as a percentage of contoured RW were detected. A relative reduction more than 25% in RW V_70Gy(%) in 100% of patients was achieved. The rectal retraction resulted in a significant increase in the prostate to the rectum space at the prostate midgland level, an absolute increase of 2.7 mm. The retraction of the rectum induced a mean (±standard deviation) pain score of 2.7 (±1.3) according to the visual analog score.

Conclusion

The application of a RR showed a remarkable rectal sparing effect during prostate IMRT. This may lead to reduced acute and late rectal toxicities in prostate IMRT.

Evaluation of different drying processes by energy consumption in an insulated and not insulated laboratory convection dryer

Drying is a process to increase the shelf-life of fruits by decreasing their water content. It is one of the energy consuming processes in food engineering. In many studies, the drying time duration and quality of dried fruits were investigated. In this study, the energy consumption in different drying conditions was investigated for the apple in a laboratory convection dryer. The drying conditions were the application of the temperatures of 40, 50, and 60°C and the speeds of 0.5 and 1 ms-1 for the drying air using the insulated and non-insulated drying chambers. Independent from drying duration, the highest energy consumption was recorded as 11.2 kWh for the non-insulated dryer under the drying air condition of 40°C and 0.5 ms-1 . While the lowest energy consumption was only 5.8 kWh for the insulated dryer with the drying air condition of 40 and 50°C and the same 0.5 ms-1 . The drying duration for these conditions was 537, 313, and 233 mins. To achieve the shortest drying time (153 mins), the condition of 60°C and 1 ms-1 in the insulated dryer was used which caused the energy consumption of 7.2 kWh.

Analysis of trace elements in human hair through X-ray fluorescence spectroscopy for screening of prostate cancer

Background: Use of hair samples to analyze the trace element concentrations is one of the interesting fields among many researchers. X-ray fluorescence (XRF) is considered as one of the most common methods in studying the concentration of elements in tissues and also crystalline materials, using low energy X-ray. In the present study, we aimed to evaluate the concentration of the trace elements in the scalp hair sample through XRF spectroscopy using signal processing techniques as a screening tool for prostate cancer. Methods: Hair samples of 22 men (including 11 healthy and 11 patients) were analyzed. All the sample donors were Iranian men. EDXRF method was used for the measurements. Signals were analyzed, and signal features such as mean, root-mean-square (RMS), variance, and standard deviation, skewness, and energy were investigated. The Man-Whitney U test was used to compare the trace element concentrations. The analysis of variance (ANOVA) test was used to identify which extracted feature could help to identify healthy and patient people. P values ≤ 0.05 were considered statistically significant. Statistical analysis was performed using SPSS 16.0 software. Results: The mean±SD age was 67.8±8.7 years in the patient group and 61.4±6.9 years in the healthy group. There were statistically significant differences in the aluminum (Al, P<0.001), silicon (Si, P=0.006), and phosphorus (P, P=0.028) levels between healthy and patient groups. Skewness and variance were found to be relevant in identifying people with cancer, as signal features. Conclusion: The use of EDXRF is a feasible method to study the concentration of elements in the hair sample, and this technique may be effective in prostate cancer screening. Further study with a large sample size will be required to elucidate the efficacy of the present method in prostate cancer screening.

Assessment of background radiation levels in the southeast of Iran

Background: Measuring background radiation (BR) is highly important from different perspectives, especially from that of human health. This study was conducted to measure BR in the southeast of Iran.

Methods: BR was measured in Hormozgan and Sistan-Bluchestan provinces using portable Environmental Radiation Meter Type 6- 80 detector. The average value was used to calculate the absorbed dose rate and indoor annual effective dose (AED) from BR. In addition, excess lifetime cancer risk (ELCR) was evaluated.

Results: The results showed that the maximum and minimum absorbed dose rates were 71.9 and 34.2 nGy.h-1 in Abomoosa and Minab in Hormozgan province and 90.0 and 47.8 nGy.h-1 in Zahedan and Chabahar in Sistan-Bluchestan province, respectively. Data indicated that these areas had a lower BR level compared with the worldwide level. The ELCR from indoor AED was larger compared with the worldwide average of 0.29 × 10-3.

Conclusion: This study provided a reference for designing and developing specific regional surveys associated with the measurement of natural BR in the southeast of Iran.

In regard to Cuccia et al.: impact of hydrogel peri-rectal spacer insertion on prostate gland intra-fraction motion during 1.5 T MR-guided stereotactic body radiotherapy

We read the article entitled “Impact of hydrogel peri-rectal spacer insertion on prostate gland intra-fraction motion during 1.5 T MR-guided stereotactic body radiotherapy” with great interest. In that study, the author reported that there is a statistically significant difference in the rotational antero-posterior shifts between the spacer and the non-spacer groups. Also, there was no statistically significant difference between the groups in terms of translational shifts. However, there are some points about the study. In this letter, we aimed to clarify these points.

Molecular imaging in tracking cancer stem cells: A review

Cancer stem cells (CSCs) have critical roles in tumor development, progression, and recurrence. They are responsible for current cancer treatment failure and remain questionable for the design and development of new therapeutic strategies. With this issue, medical imaging provides several clues for finding biological mechanisms and strategies to treat CSCs. This review aims to summarize current molecular imaging approaches for detecting CSCs. In addition, some promising issues for CSCs finding and explaining biological mechanisms have been addressed. Among the molecular imaging approaches, modalities including Magnetic resonance imaging (MRI) and positron emission tomography (PET) have the greatest roles and several new approaches such as optical imaging are in progress.

Regulation of CSF and Brain Tissue Sodium Levels by the Blood-CSF and Blood-Brain Barriers During Migraine

Cerebrospinal fluid (CSF) and brain tissue sodium levels increase during migraine. However, little is known regarding the underlying mechanisms of sodium homeostasis disturbance in the brain during the onset and propagation of migraine. Exploring the cause of sodium dysregulation in the brain is important, since correction of the altered sodium homeostasis could potentially treat migraine. Under the hypothesis that disturbances in sodium transport mechanisms at the blood-CSF barrier (BCSFB) and/or the blood-brain barrier (BBB) are the underlying cause of the elevated CSF and brain tissue sodium levels during migraines, we developed a mechanistic, differential equation model of a rat's brain to compare the significance of the BCSFB and the BBB in controlling CSF and brain tissue sodium levels. The model includes the ventricular system, subarachnoid space, brain tissue and blood. Sodium transport from blood to CSF across the BCSFB, and from blood to brain tissue across the BBB were modeled by influx permeability coefficients P_BCSFB and P_BBB, respectively, while sodium movement from CSF into blood across the BCSFB, and from brain tissue to blood across the BBB were modeled by efflux permeability coefficients PBCSFB′ and PBBB′, respectively. We then performed a global sensitivity analysis to investigate the sensitivity of the ventricular CSF, subarachnoid CSF and brain tissue sodium concentrations to pathophysiological variations in P_BCSFB, P_BBB, PBCSFB′ and PBBB′. Our results show that the ventricular CSF sodium concentration is highly influenced by perturbations of P_BCSFB, and to a much lesser extent by perturbations of PBCSFB′. Brain tissue and subarachnoid CSF sodium concentrations are more sensitive to pathophysiological variations of P_BBB and PBBB′ than variations of P_BCSFB and PBCSFB′ within 30 min of the onset of the perturbations. However, P_BCSFB is the most sensitive model parameter, followed by P_BBB and PBBB′, in controlling brain tissue and subarachnoid CSF sodium levels within 3 h of the perturbation onset.

Application of rectal retractor for postprostatectomy salvage radiotherapy of prostate cancer: A case report and literature review

Using a rectal retractor (RR) during salvage radiotherapy after radical prostatectomy is a promising approach for reducing dose to the rectum. The patient well tolerated the daily RR insertion. This area of research encourages researchers for a comprehensive evaluation of the role of the RR in postprostatectomy radiotherapy.

Optimization of prostate brachytherapy techniques with polyethylene glycol-based hydrogel spacers: A systematic review

PURPOSE

The objective of this overview was to critically evaluate the effect of polyethylene glycol (PEG)-based hydrogel spacers during prostate brachytherapy with regard to dosimetric and clinical benefits, as well as procedure-related toxicity.

METHODS AND MATERIALS

A systematic search in the PubMed database was performed.

RESULTS

A total of 12 studies, involving 615 patients with PEG hydrogel injection, were included. Overall, patients well tolerated the implantation of PEG hydrogel spacers with an excellent safety profile. However, although there were some procedure-related complications, rates of these complications were very rare. Toxicities related to the spacer were limited to Grade 1 rectal discomfort and pain (9/615 patients), Grade 2 rectal ulceration (1 in 615 patients), perineal abscess (1 in 615 patients), and bacterial prostatitis (2/615 patients) according to Common Terminology Criteria for Adverse Events v4.0 grading scheme. The application of PEG hydrogel spacers significantly reduced radiation doses to the rectum during prostate brachytherapy in the different setting. Although there was no prospective randomized clinical trial, retrospective studies showed that reducing rectal doses by the implantation of PEG hydrogel may result in an improvement in rectal toxicity.

CONCLUSIONS

The insertion of hydrogel spacers is safe, resulting in a significant decrease in rectal doses. This may lead to a reduction in rectal or gastrointestinal toxicity. Prospective randomized clinical trials are warranted to confirm the clinical impact of rectal dosimetric improvements.

Reject analysis in digital radiography: A local study on radiographers and students' attitude in Iran

Reject analysis is as a quality indicator and critical tool for dose and image quality optimization in radiology departments. By reducing image rejection rate (RR), radiation dose to patients can be reduced effectively, yielding increased total cost-effectiveness. The aims of this study were to assess the rate of image rejection at 2 direct digital radiography (DR) departments to find the sources of rejection and to observe how radiology students and radiographers deal with image rejection.

Two radiology departments were surveyed during a 3-month period for all imaging procedures. Type of examination, numbers, and reasons for digital image rejection were obtained by systems and questionnaire. A predefined questionnaire, including 13 causes for rejection, was filled by radiographers and students.

Out of the 14 022 acquired images, 1116 were rejected, yielding an overall RR of 8%. Highest RRs were found for examination of cervical spine and lumbosacral. Positioning errors and improper patient preparation were the main reasons for digital image rejection.

The image RR was small, but there is a need for optimizing radiographic practice, and enhancing radiographer’s knowledge may enhance the performance.

Fiducial markers in prostate cancer image-guided radiotherapy

Background: Image-guided radiotherapy (IGRT) is recommended to reduce the risk of geometrical miss when modern radiotherapy technologies with high grades of conformity are used. The purpose of this study was to evaluate the efficacy of fiducial markers (FMs) for electronic portal imaging in prostate cancer radiotherapy in term of evaluating the complications associated with FMs implantation, quantifying inter-fraction prostate motion, and determination of optimal planning target volume (PTV) margins.

Methods: In this single institution, prospective, consecutive study, 27 patients underwent implantation of three-gold seed FMs into the prostate gland before prostate radiotherapy. Prior to computed tomography planning, all patients were asked to report any complication associated with FMs implantation that have experienced to date. Daily pre-treatment electronic portal images were captured, and prostate position errors were corrected if they were greater than 2 mm along three translational directions. Optimal PTV expansions were computed using van Herk formula [PTV-margin= 2.5Σ + 0.7σ].

Results: FMs implantation was successful with an acceptable toxicity profile in all patients. Without IGRT, margins of 5.4 mm, 5.8 mm and 5.5 mm, in vertical, longitudinal and lateral directions, respectively, are needed for a 95% confidence level of complete clinical target volume (CTV) coverage in each treatment session. The PTV margins of 3.0 mm, 3.3 mm and 4.0 mm in corresponding directions were calculated when FMs based electronic portal imaging was applied.

Conclusion: FMs based electronic portal imaging is an effective tool for prostate cancer IGRT.

Analysis of the role of thrombomodulin in all-trans retinoic acid treatment of coagulation disorders in cancer patients

BACKGROUND

Clinical studies have shown that all-trans retinoic acid (RA), which is often used in treatment of cancer patients, improves hemostatic parameters and bleeding complications such as disseminated intravascular coagulation (DIC). However, the mechanisms underlying this improvement have yet to be elucidated. In vitro studies have reported that RA upregulates thrombomodulin (TM) expression on the endothelial cell surface. The objective of this study was to investigate how and to what extent the TM concentration changes after RA treatment in cancer patients, and how this variation influences the blood coagulation cascade.

RESULTS

In this study, we introduced an ordinary differential equation (ODE) model of gene expression for the RA-induced upregulation of TM concentration. Coupling the gene expression model with a two-compartment pharmacokinetic model of RA, we obtained the time-dependent changes in TM and thrombomodulin-mRNA (TMR) concentrations following oral administration of RA. Our results indicated that the TM concentration reached its peak level almost 14 h after taking a single oral dose (110 [Formula: see text]) of RA. Continuous treatment with RA resulted in oscillatory expression of TM on the endothelial cell surface. We then coupled the gene expression model with a mechanistic model of the coagulation cascade, and showed that the elevated levels of TM over the course of RA therapy with a single daily oral dose (110 [Formula: see text]) of RA, reduced the peak thrombin levels and endogenous thrombin potential (ETP) up to 50 and 49%, respectively. We showed that progressive reductions in plasma levels of RA, observed in continuous RA therapy with a once-daily oral dose (110 [Formula: see text]) of RA, did not affect TM-mediated reduction of thrombin generation significantly. This finding prompts the hypothesis that continuous RA treatment has more consistent therapeutic effects on coagulation disorders than on cancer.

CONCLUSIONS

Our results indicate that the oscillatory upregulation of TM expression on the endothelial cells over the course of RA therapy could potentially contribute to the treatment of coagulation abnormalities in cancer patients. Further studies on the impacts of RA therapy on the procoagulant activity of cancer cells are needed to better elucidate the mechanisms by which RA therapy improves hemostatic abnormalities in cancer.

Identification of influential proteins in the classical retinoic acid signaling pathway

Background

In the classical pathway of retinoic acid (RA) mediated gene transcription, RA binds to a nuclear hormone receptor dimer composed of retinoic acid receptor (RAR) and retinoid X receptor (RXR), to induce the expression of its downstream target genes. In addition to nuclear receptors, there are other intracellular RA binding proteins such as cellular retinoic acid binding proteins (CRABP1 and CRABP2) and cytochrome P450 (CYP) enzymes, whose contributions to the RA signaling pathway have not been fully understood. The objective of this study was to compare the significance of various RA binding receptors, i.e. CRABP1, CRABP2, CYP and RAR in the RA signaling pathway. In this regard, we developed a mathematical model of the RA pathway, which is one of the few models, if not the only one, that includes all main intracellular RA binding receptors. We then performed a global sensitivity analysis (GSA) to investigate the contribution of the RA receptors to RA-induced mRNA production, when the cells were treated with a wide range of RA levels, from physiological to pharmacological concentrations.

Results

Our results show that CRABP2 and RAR are the most and the least important proteins, respectively, in controlling the model performance at physiological concentrations of RA (1–10 nM). However, at higher concentrations of RA, CYP and RAR are the most sensitive parameters of the system. Furthermore, we found that depending on the concentrations of all RA binding proteins, the rate of metabolism of RA can either change or remain constant following RA therapy. The cellular levels of CRABP1 are more important than that of CRABP2 in controlling RA metabolite formation at pharmacological conditions (RA = 0.1–1 μM). Finally, our results indicate a significant negative correlation between total mRNA production and total RA metabolite formation at pharmacological levels of RA.

Conclusions

Our simulations indicate that the significance of the RA binding proteins in the RA pathway of gene expression strongly depends on intracellular concentration of RA. This study not only can explain why various cell types respond to RA therapy differently, but also can potentially help develop pharmacological methods to increase the efficacy of the drug.

Electronic supplementary material

The online version of this article (10.1186/s12976-018-0088-7) contains supplementary material, which is available to authorized users.

New physical approaches to treat cancer stem cells: a review

Cancer stem cells (CSCs) have been identified as the main center of tumor therapeutic resistance. They are highly resistant against current cancer therapy approaches particularly radiation therapy (RT). Recently, a wide spectrum of physical methods has been proposed to treat CSCs, including high energetic particles, hyperthermia (HT), nanoparticles (NPs) and combination of these approaches. In this review article, the importance and benefits of the physical CSCs therapy methods such as nanomaterial-based heat treatments and particle therapy will be highlighted.