Genomic landscape of prominent XDR Acinetobacter clonal complexes from Dhaka, Bangladesh.

BACKGROUND: Acinetobacter calcoaceticus-A. baumannii (ACB) complex pathogens are known for their prevalence in nosocomial infections and extensive antimicrobial resistance (AMR) capabilities. While genomic studies worldwide have elucidated the genetic context of antibiotic resistance in major international clones (ICs) of clinical Acinetobacter spp., not much information is available from Bangladesh. In this study, we analysed the AMR profiles of 63 ACB complex strains collected from Dhaka, Bangladesh. Following this, we generated draft genomes of 15 of these strains to understand the prevalence and genomic environments of AMR, virulence and mobilization associated genes in different Acinetobacter clones. RESULTS: Around 84% (n = 53) of the strains were extensively drug resistant (XDR) with two showing pan-drug resistance. Draft genomes generated for 15 strains confirmed 14 to be A. baumannii while one was A. nosocomialis. Most A. baumannii genomes fell under three clonal complexes (CCs): the globally dominant CC1 and CC2, and CC10; one strain had a novel sequence type (ST). AMR phenotype-genotype agreement was observed and the genomes contained various beta-lactamase genes including blaOXA-23 (n = 12), blaOXA-66 (n = 6), and blaNDM-1 (n = 3). All genomes displayed roughly similar virulomes, however some virulence genes such as the Acinetobactin bauA and the type IV pilus gene pilA displayed high genetic variability. CC2 strains carried highest levels of plasmidic gene content and possessed conjugative elements carrying AMR genes, virulence factors and insertion sequences. CONCLUSION: This study presents the first comparative genomic analysis of XDR clinical Acinetobacter spp. from Bangladesh. It highlights the prevalence of different classes of beta-lactamases, mobilome-derived heterogeneity in genetic architecture and virulence gene variability in prominent Acinetobacter clonal complexes in the country. The findings of this study would be valuable in understanding the genomic epidemiology of A. baumannii clones and their association with closely related pathogenic species like A. nosocomialis in Bangladesh.

GCDN-Net: Garbage classifier deep neural network for recyclable urban waste management.

The escalating waste volume due to urbanization and population growth has underscored the need for advanced waste sorting and recycling methods to ensure sustainable waste management. Deep learning models, adept at image recognition tasks, offer potential solutions for waste sorting applications. These models, trained on extensive waste image datasets, possess the ability to discern unique features of diverse waste types. Automating waste sorting hinges on robust deep learning models capable of accurately categorizing a wide range of waste types. In this study, a multi-stage machine learning approach is proposed to classify different waste categories using the "Garbage In, Garbage Out" (GIGO) dataset of 25,000 images. The novel Garbage Classifier Deep Neural Network (GCDN-Net) is introduced as a comprehensive solution, adept in both single-label and multi-label classification tasks. Single-label classification distinguishes between garbage and non-garbage images, while multi-label classification identifies distinct garbage categories within single or multiple images. The performance of GCDN-Net is rigorously evaluated and compared against state-of-the-art waste classification methods. Results demonstrate GCDN-Net's excellence, achieving 95.77% accuracy, 95.78% precision, 95.77% recall, 95.77% F1-score, and 95.54% specificity when classifying waste images, outperforming existing models in single-label classification. In multi-label classification, GCDN-Net attains an overall Mean Average Precision (mAP) of 0.69 and an F1-score of 75.01%. The reliability of network performance is affirmed through saliency map-based visualization generated by Score-CAM (class activation mapping). In conclusion, deep learning-based models exhibit efficacy in categorizing diverse waste types, paving the way for automated waste sorting and recycling systems that can mitigate costs and processing times.

BIO-CXRNET: a robust multimodal stacking machine learning technique for mortality risk prediction of COVID-19 patients using chest X-ray images and clinical data.

Nowadays, quick, and accurate diagnosis of COVID-19 is a pressing need. This study presents a multimodal system to meet this need. The presented system employs a machine learning module that learns the required knowledge from the datasets collected from 930 COVID-19 patients hospitalized in Italy during the first wave of COVID-19 (March-June 2020). The dataset consists of twenty-five biomarkers from electronic health record and Chest X-ray (CXR) images. It is found that the system can diagnose low- or high-risk patients with an accuracy, sensitivity, and F1-score of 89.03%, 90.44%, and 89.03%, respectively. The system exhibits 6% higher accuracy than the systems that employ either CXR images or biomarker data. In addition, the system can calculate the mortality risk of high-risk patients using multivariate logistic regression-based nomogram scoring technique. Interested physicians can use the presented system to predict the early mortality risks of COVID-19 patients using the web-link: Covid-severity-grading-AI. In this case, a physician needs to input the following information: CXR image file, Lactate Dehydrogenase (LDH), Oxygen Saturation (O2%), White Blood Cells Count, C-reactive protein, and Age. This way, this study contributes to the management of COVID-19 patients by predicting early mortality risk. Supplementary Information: The online version contains supplementary material available at 10.1007/s00521-023-08606-w.

Deep Learning Assisted Automated Assessment of Thalassaemia from Haemoglobin Electrophoresis Images.

Haemoglobin (Hb) electrophoresis is a method of blood testing used to detect thalassaemia. However, the interpretation of the result of the electrophoresis test itself is a complex task. Expert haematologists, specifically in developing countries, are relatively few in number and are usually overburdened. To assist them with their workload, in this paper we present a novel method for the automated assessment of thalassaemia using Hb electrophoresis images. Moreover, in this study we compile a large Hb electrophoresis image dataset, consisting of 103 strips containing 524 electrophoresis images with a clear consensus on the quality of electrophoresis obtained from 824 subjects. The proposed methodology is split into two parts: (1) single-patient electrophoresis image segmentation by means of the lane extraction technique, and (2) binary classification (normal or abnormal) of the electrophoresis images using state-of-the-art deep convolutional neural networks (CNNs) and using the concept of transfer learning. Image processing techniques including filtering and morphological operations are applied for object detection and lane extraction to automatically separate the lanes and classify them using CNN models. Seven different CNN models (ResNet18, ResNet50, ResNet101, InceptionV3, DenseNet201, SqueezeNet and MobileNetV2) were investigated in this study. InceptionV3 outperformed the other CNNs in detecting thalassaemia using Hb electrophoresis images. The accuracy, precision, recall, f1-score, and specificity in the detection of thalassaemia obtained with the InceptionV3 model were 95.8%, 95.84%, 95.8%, 95.8% and 95.8%, respectively. MobileNetV2 demonstrated an accuracy, precision, recall, f1-score, and specificity of 95.72%, 95.73%, 95.72%, 95.7% and 95.72% respectively. Its performance was comparable with the best performing model, InceptionV3. Since it is a very shallow network, MobileNetV2 also provides the least latency in processing a single-patient image and it can be suitably used for mobile applications. The proposed approach, which has shown very high classification accuracy, will assist in the rapid and robust detection of thalassaemia using Hb electrophoresis images.

Microwave brain imaging system to detect brain tumor using metamaterial loaded stacked antenna array.

In this paper, proposes a microwave brain imaging system to detect brain tumors using a metamaterial (MTM) loaded three-dimensional (3D) stacked wideband antenna array. The antenna is comprised of metamaterial-loaded with three substrate layers, including two air gaps. One 1 × 4 MTM array element is used in the top layer and middle layer, and one 3 × 2 MTM array element is used in the bottom layer. The MTM array elements in layers are utilized to enhance the performance concerning antenna's efficiency, bandwidth, realized gain, radiation directionality in free space and near the head model. The antenna is fabricated on cost-effective Rogers RT5880 and RO4350B substrate, and the optimized dimension of the antenna is 50 × 40 × 8.66 mm3. The measured results show that the antenna has a fractional bandwidth of 79.20% (1.37-3.16 GHz), 93% radiation efficiency, 98% high fidelity factor, 6.67 dBi gain, and adequate field penetration in the head tissue with a maximum of 0.0018 W/kg specific absorption rate. In addition, a 3D realistic tissue-mimicking head phantom is fabricated and measured to verify the performance of the antenna. Later, a nine-antenna array-based microwave brain imaging (MBI) system is implemented and investigated by using phantom model. After that, the scattering parameters are collected, analyzed, and then processed by the Iteratively Corrected delay-multiply-and-sum algorithm to detect and reconstruct the brain tumor images. The imaging results demonstrated that the implemented MBI system can successfully detect the target benign and malignant tumors with their locations inside the brain.

QCovSML: A reliable COVID-19 detection system using CBC biomarkers by a stacking machine learning model.

The reverse transcription-polymerase chain reaction (RT-PCR) test is considered the current gold standard for the detection of coronavirus disease (COVID-19), although it suffers from some shortcomings, namely comparatively longer turnaround time, higher false-negative rates around 20-25%, and higher cost equipment. Therefore, finding an efficient, robust, accurate, and widely available, and accessible alternative to RT-PCR for COVID-19 diagnosis is a matter of utmost importance. This study proposes a complete blood count (CBC) biomarkers-based COVID-19 detection system using a stacking machine learning (SML) model, which could be a fast and less expensive alternative. This study used seven different publicly available datasets, where the largest one consisting of fifteen CBC biomarkers collected from 1624 patients (52% COVID-19 positive) admitted at San Raphael Hospital, Italy from February to May 2020 was used to train and validate the proposed model. White blood cell count, monocytes (%), lymphocyte (%), and age parameters collected from the patients during hospital admission were found to be important biomarkers for COVID-19 disease prediction using five different feature selection techniques. Our stacking model produced the best performance with weighted precision, sensitivity, specificity, overall accuracy, and F1-score of 91.44%, 91.44%, 91.44%, 91.45%, and 91.45%, respectively. The stacking machine learning model improved the performance in comparison to other state-of-the-art machine learning classifiers. Finally, a nomogram-based scoring system (QCovSML) was constructed using this stacking approach to predict the COVID-19 patients. The cut-off value of the QCovSML system for classifying COVID-19 and Non-COVID patients was 4.8. Six datasets from three different countries were used to externally validate the proposed model to evaluate its generalizability and robustness. The nomogram demonstrated good calibration and discrimination with the area under the curve (AUC) of 0.961 for the internal cohort and average AUC of 0.967 for all external validation cohort, respectively. The external validation shows an average weighted precision, sensitivity, F1-score, specificity, and overall accuracy of 92.02%, 95.59%, 93.73%, 90.54%, and 93.34%, respectively.

Exploring the effect of image enhancement techniques on COVID-19 detection using chest X-ray images.

Computer-aided diagnosis for the reliable and fast detection of coronavirus disease (COVID-19) has become a necessity to prevent the spread of the virus during the pandemic to ease the burden on the healthcare system. Chest X-ray (CXR) imaging has several advantages over other imaging and detection techniques. Numerous works have been reported on COVID-19 detection from a smaller set of original X-ray images. However, the effect of image enhancement and lung segmentation of a large dataset in COVID-19 detection was not reported in the literature. We have compiled a large X-ray dataset (COVQU) consisting of 18,479 CXR images with 8851 normal, 6012 non-COVID lung infections, and 3616 COVID-19 CXR images and their corresponding ground truth lung masks. To the best of our knowledge, this is the largest public COVID positive database and the lung masks. Five different image enhancement techniques: histogram equalization (HE), contrast limited adaptive histogram equalization (CLAHE), image complement, gamma correction, and balance contrast enhancement technique (BCET) were used to investigate the effect of image enhancement techniques on COVID-19 detection. A novel U-Net model was proposed and compared with the standard U-Net model for lung segmentation. Six different pre-trained Convolutional Neural Networks (CNNs) (ResNet18, ResNet50, ResNet101, InceptionV3, DenseNet201, and ChexNet) and a shallow CNN model were investigated on the plain and segmented lung CXR images. The novel U-Net model showed an accuracy, Intersection over Union (IoU), and Dice coefficient of 98.63%, 94.3%, and 96.94%, respectively for lung segmentation. The gamma correction-based enhancement technique outperforms other techniques in detecting COVID-19 from the plain and the segmented lung CXR images. Classification performance from plain CXR images is slightly better than the segmented lung CXR images; however, the reliability of network performance is significantly improved for the segmented lung images, which was observed using the visualization technique. The accuracy, precision, sensitivity, F1-score, and specificity were 95.11%, 94.55%, 94.56%, 94.53%, and 95.59% respectively for the segmented lung images. The proposed approach with very reliable and comparable performance will boost the fast and robust COVID-19 detection using chest X-ray images.

Development and Validation of an Early Scoring System for Prediction of Disease Severity in COVID-19 Using Complete Blood Count Parameters.

The coronavirus disease 2019 (COVID-19) after outbreaking in Wuhan increasingly spread throughout the world. Fast, reliable, and easily accessible clinical assessment of the severity of the disease can help in allocating and prioritizing resources to reduce mortality. The objective of the study was to develop and validate an early scoring tool to stratify the risk of death using readily available complete blood count (CBC) biomarkers. A retrospective study was conducted on twenty-three CBC blood biomarkers for predicting disease mortality for 375 COVID-19 patients admitted to Tongji Hospital, China from January 10 to February 18, 2020. Machine learning based key biomarkers among the CBC parameters as the mortality predictors were identified. A multivariate logistic regression-based nomogram and a scoring system was developed to categorize the patients in three risk groups (low, moderate, and high) for predicting the mortality risk among COVID-19 patients. Lymphocyte count, neutrophils count, age, white blood cell count, monocytes (%), platelet count, red blood cell distribution width parameters collected at hospital admission were selected as important biomarkers for death prediction using random forest feature selection technique. A CBC score was devised for calculating the death probability of the patients and was used to categorize the patients into three sub-risk groups: low (<=5%), moderate (>5% and <=50%), and high (>50%), respectively. The area under the curve (AUC) of the model for the development and internal validation cohort were 0.961 and 0.88, respectively. The proposed model was further validated with an external cohort of 103 patients of Dhaka Medical College, Bangladesh, which exhibits in an AUC of 0.963. The proposed CBC parameter-based prognostic model and the associated web-application, can help the medical doctors to improve the management by early prediction of mortality risk of the COVID-19 patients in the low-resource countries.