AAWS-Net: Anatomy-aware weakly-supervised learning network for breast mass segmentation

Accurate segmentation of breast masses is an essential step in computer aided diagnosis of breast cancer. The scarcity of annotated training data greatly hinders the model’s generalization ability, especially for the deep learning based methods. However, high-quality image-level annotations are time-consuming and cumbersome in medical image analysis scenarios. In addition, a large amount of weak annotations is under-utilized which comprise common anatomy features. To this end, inspired by teacher-student networks, we propose an Anatomy-Aware Weakly-Supervised learning Network (AAWS-Net) for extracting useful information from mammograms with weak annotations for efficient and accurate breast mass segmentation. Specifically, we adopt a weakly-supervised learning strategy in the Teacher to extract anatomy structure from mammograms with weak annotations by reconstructing the original image. Besides, knowledge distillation is used to suggest morphological differences between benign and malignant masses. Moreover, the prior knowledge learned from the Teacher is introduced to the Student in an end-to-end way, which improves the ability of the student network to locate and segment masses. Experiments on CBIS-DDSM have shown that our method yields promising performance compared with state-of-the-art alternative models for breast mass segmentation in terms of segmentation accuracy and IoU.

Sentiment Analysis of before and after Elections: Twitter Data of U.S. Election 2020

U.S. President Joe Biden took his oath after being victorious in the controversial U.S. elections of 2020. The polls were conducted over postal ballot due to the coronavirus pandemic following delays of the announcement of the election’s results. Donald J. Trump claimed that there was potential rigging against him and refused to accept the results of the polls. The sentiment analysis captures the opinions of the masses over social media for global events. In this work, we analyzed Twitter sentiment to determine public views before, during, and after elections and compared them with actual election results. We also compared opinions from the 2016 election in which Donald J. Trump was victorious with the 2020 election. We created a dataset using tweets’ API, pre-processed the data, extracted the right features using TF-IDF, and applied the Naive Bayes Classifier to obtain public opinions. As a result, we identified outliers, analyzed controversial and swing states, and cross-validated election results against sentiments expressed over social media. The results reveal that the election outcomes coincide with the sentiment expressed on social media in most cases. The pre and post-election sentiment analysis results demonstrate the sentimental drift in outliers. Our sentiment classifier shows an accuracy of 94.58% and a precision of 93.19%.

X-Ray Equipped with Artificial Intelligence: Changing the COVID-19 Diagnostic Paradigm during the Pandemic

PURPOSE

Due to the excessive use of raw materials in diagnostic tools and equipment during the COVID-19 pandemic, there is a dire need for cheaper and more effective methods in the healthcare system. With the development of artificial intelligence (AI) methods in medical sciences as low-cost and safer diagnostic methods, researchers have turned their attention to the use of imaging tools with AI that have fewer complications for patients and reduce the consumption of healthcare resources. Despite its limitations, X-ray is suggested as the first-line diagnostic modality for detecting and screening COVID-19 cases.

METHOD

This systematic review assessed the current state of AI applications and the performance of algorithms in X-ray image analysis. The search strategy yielded 322 results from four databases and google scholar, 60 of which met the inclusion criteria. The performance statistics included the area under the receiver operating characteristics (AUC) curve, accuracy, sensitivity, and specificity.

RESULT

The average sensitivity and specificity of CXR equipped with AI algorithms for COVID-19 diagnosis were >96% (83%-100%) and 92% (80%-100%), respectively. For common X-ray methods in COVID-19 detection, these values were 0.56 (95% CI 0.51-0.60) and 0.60 (95% CI 0.54-0.65), respectively. AI has substantially improved the diagnostic performance of X-rays in COVID-19.

CONCLUSION

X-rays equipped with AI can serve as a tool to screen the cases requiring CT scans. The use of this tool does not waste time or impose extra costs, has minimal complications, and can thus decrease or remove unnecessary CT slices and other healthcare resources.

A Review on Recent Progress in Machine Learning and Deep Learning Methods for Cancer Classification on Gene Expression Data

Data-driven model with predictive ability are important to be used in medical and healthcare. However, the most challenging task in predictive modeling is to construct a prediction model, which can be addressed using machine learning (ML) methods. The methods are used to learn and trained the model using a gene expression dataset without being programmed explicitly. Due to the vast amount of gene expression data, this task becomes complex and time consuming. This paper provides a recent review on recent progress in ML and deep learning (DL) for cancer classification, which has received increasing attention in bioinformatics and computational biology. The development of cancer classification methods based on ML and DL is mostly focused on this review. Although many methods have been applied to the cancer classification problem, recent progress shows that most of the successful techniques are those based on supervised and DL methods. In addition, the sources of the healthcare dataset are also described. The development of many machine learning methods for insight analysis in cancer classification has brought a lot of improvement in healthcare. Currently, it seems that there is highly demanded further development of efficient classification methods to address the expansion of healthcare applications.

Differential evolution and particle swarm optimization against COVID-19

COVID-19 disease, which highly affected global life in 2020, led to a rapid scientific response. Versatile optimization methods found their application in scientific studies related to COVID-19 pandemic. Differential Evolution (DE) and Particle Swarm Optimization (PSO) are two metaheuristics that for over two decades have been widely researched and used in various fields of science. In this paper a survey of DE and PSO applications for problems related with COVID-19 pandemic that were rapidly published in 2020 is presented from two different points of view: 1. practitioners seeking the appropriate method to solve particular problem, 2. experts in metaheuristics that are interested in methodological details, inter comparisons between different methods, and the ways for improvement. The effectiveness and popularity of DE and PSO is analyzed in the context of other metaheuristics used against COVID-19. It is found that in COVID-19 related studies: 1. DE and PSO are most frequently used for calibration of epidemiological models and image-based classification of patients or symptoms, but applications are versatile, even interconnecting the pandemic and humanities; 2. reporting on DE or PSO methodological details is often scarce, and the choices made are not necessarily appropriate for the particular algorithm or problem; 3. mainly the basic variants of DE and PSO that were proposed in the late XX century are applied, and research performed in recent two decades is rather ignored; 4. the number of citations and the availability of codes in various programming languages seems to be the main factors for choosing metaheuristics that are finally used.

Opportunities and challenges of macrogenetic studies

The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.

Blockchain Technology Projects to Provide Telemedical Services: Systematic Review

BACKGROUND

One of the most promising health care development areas is introducing telemedicine services and creating solutions based on blockchain technology. The study of systems combining both these domains indicates the ongoing expansion of digital technologies in this market segment.

OBJECTIVE

This paper aims to review the feasibility of blockchain technology for telemedicine.

METHODS

The authors identified relevant studies via systematic searches of databases including PubMed, Scopus, Web of Science, IEEE Xplore, and Google Scholar. The suitability of each for inclusion in this review was assessed independently. Owing to the lack of publications, available blockchain-based tokens were discovered via conventional web search engines (Google, Yahoo, and Yandex).

RESULTS

Of the 40 discovered projects, only 18 met the selection criteria. The 5 most prevalent features of the available solutions (N=18) were medical data access (14/18, 78%), medical service processing (14/18, 78%), diagnostic support (10/18, 56%), payment transactions (10/18, 56%), and fundraising for telemedical instrument development (5/18, 28%).

CONCLUSIONS

These different features (eg, medical data access, medical service processing, epidemiology reporting, diagnostic support, and treatment support) allow us to discuss the possibilities for integration of blockchain technology into telemedicine and health care on different levels. In this area, a wide range of tasks can be identified that could be accomplished based on digital technologies using blockchains.

Usable comprehensive-factor authentication for a secure time attendance system

In information security, it is widely accepted that the more authentication factors are used, the higher the security level. However, more factors cannot guarantee usability in real usage because human and other non-technical factors are involved. This paper proposes the use of all possible authentication factors, called comprehensive-factor authentication, which can maintain the required security level and usability in real-world implementation. A case study of an implementation of a secure time attendance system that applies this approach is presented. The contribution of this paper is therefore to provide a security scheme seamlessly integrating all classical authentication factors plus a location factor into one single system in a real environment with a security and usability focus. Usability factors emerging from the study are related to a seamless process including the least number of actions required, the lowest amount of time taken, health safety during the pandemic, and data privacy compliance.

Deep-learning based detection of COVID-19 using lung ultrasound imagery

BACKGROUND

The COVID-19 pandemic has exposed the vulnerability of healthcare services worldwide, especially in underdeveloped countries. There is a clear need to develop novel computer-assisted diagnosis tools to provide rapid and cost-effective screening in places where massive traditional testing is not feasible. Lung ultrasound is a portable, easy to disinfect, low cost and non-invasive tool that can be used to identify lung diseases. Computer-assisted analysis of lung ultrasound imagery is a relatively recent approach that has shown great potential for diagnosing pulmonary conditions, being a viable alternative for screening and diagnosing COVID-19.

OBJECTIVE

To evaluate and compare the performance of deep-learning techniques for detecting COVID-19 infections from lung ultrasound imagery.

METHODS

We adapted different pre-trained deep learning architectures, including VGG19, InceptionV3, Xception, and ResNet50. We used the publicly available POCUS dataset comprising 3326 lung ultrasound frames of healthy, COVID-19, and pneumonia patients for training and fine-tuning. We conducted two experiments considering three classes (COVID-19, pneumonia, and healthy) and two classes (COVID-19 versus pneumonia and COVID-19 versus non-COVID-19) of predictive models. The obtained results were also compared with the POCOVID-net model. For performance evaluation, we calculated per-class classification metrics (Precision, Recall, and F1-score) and overall metrics (Accuracy, Balanced Accuracy, and Area Under the Receiver Operating Characteristic Curve). Lastly, we performed a statistical analysis of performance results using ANOVA and Friedman tests followed by post-hoc analysis using the Wilcoxon signed-rank test with the Holm's step-down correction.

RESULTS

InceptionV3 network achieved the best average accuracy (89.1%), balanced accuracy (89.3%), and area under the receiver operating curve (97.1%) for COVID-19 detection from bacterial pneumonia and healthy lung ultrasound data. The ANOVA and Friedman tests found statistically significant performance differences between models for accuracy, balanced accuracy and area under the receiver operating curve. Post-hoc analysis showed statistically significant differences between the performance obtained with the InceptionV3-based model and POCOVID-net, VGG19-, and ResNet50-based models. No statistically significant differences were found in the performance obtained with InceptionV3- and Xception-based models.

CONCLUSIONS

Deep learning techniques for computer-assisted analysis of lung ultrasound imagery provide a promising avenue for COVID-19 screening and diagnosis. Particularly, we found that the InceptionV3 network provides the most promising predictive results from all AI-based techniques evaluated in this work. InceptionV3- and Xception-based models can be used to further develop a viable computer-assisted screening tool for COVID-19 based on ultrasound imagery.

Deep Learning Analysis of CT Images Reveals High-Grade Pathological Features to Predict Survival in Lung Adenocarcinoma

We aimed to develop a deep learning (DL) model for predicting high-grade patterns in lung adenocarcinomas (ADC) and to assess the prognostic performance of model in advanced lung cancer patients who underwent neoadjuvant or definitive concurrent chemoradiation therapy (CCRT). We included 275 patients with 290 early lung ADCs from an ongoing prospective clinical trial in the training dataset, which we split into internal-training and internal-validation datasets. We constructed a diagnostic DL model of high-grade patterns of lung ADC considering both morphologic view of the tumor and context view of the area surrounding the tumor (MC3DN; morphologic-view context-view 3D network). Validation was performed on an independent dataset of 417 patients with advanced non-small cell lung cancer who underwent neoadjuvant or definitive CCRT. The area under the curve value of the DL model was 0.8 for the prediction of high-grade histologic patterns such as micropapillary and solid patterns (MPSol). When our model was applied to the validation set, a high probability of MPSol was associated with worse overall survival (probability of MPSol >0.5 vs. <0.5; 5-year OS rate 56.1% vs. 70.7%), indicating that our model could predict the clinical outcomes of advanced lung cancer patients. The subgroup with a high probability of MPSol estimated by the DL model showed a 1.76-fold higher risk of death (HR 1.76, 95% CI 1.16-2.68). Our DL model can be useful in estimating high-grade histologic patterns in lung ADCs and predicting clinical outcomes of patients with advanced lung cancer who underwent neoadjuvant or definitive CCRT.

Analysis of the factors affecting the adoption and compliance of the NHS COVID-19 mobile application: a national cross-sectional survey in England

OBJECTIVES

To conduct an independent study investigating how adults perceive the usability and functionality of the 'National Health Service (NHS) COVID-19' application (app). This study aims to highlight strengths and provide recommendations to improve adoption of future contact tracing developments.

DESIGN

A 60-item, anonymous online questionnaire, disseminated through social media outlets and email lists by a team from Imperial College London.

SETTING

England.

PARTICIPANTS

Convenience sample of 1036 responses, from participants aged 18 years and above, between December 2020 and January 2021.

PRIMARY OUTCOME MEASURES

Evaluate the compliance and public attitude towards the 'NHS COVID-19' app regarding its functionality and features. This included whether participants' expectations were met, and their thoughts on the app privacy and security. Furthermore, to distinguish how usability, perception, and adoption differed with varying demographics and user values.

RESULTS

Fair compliance with the app features was identified, meeting expectations of the 62.1% of participants who stated they downloaded it after weighted analysis. However, participants finding the interface challenging were less likely to read information in the app and had a lesser understanding of its functionality. Furthermore, little understanding regarding the app's functionality and privacy concerns was a possible reason why users did not download it. A readability analysis of the text revealed information within the app was conveyed at a level that may be too complex for up to 43% of the UK population. The study highlighted issues related to the potential of false positives caused by the design choices in the 'Check-In' feature.

CONCLUSION

This study showed that while the 'NHS COVID-19' app was viewed positively, there remained issues regarding participants' perceived knowledge of app functionality, potentially affecting compliance. Therefore, we recommended improvements regarding the delivery and presentation of the app's information, and highlighted the potential need for the ability to check out of venues to reduce the number of false positive contacts.

A bagging dynamic deep learning network for diagnosing COVID-19

COVID-19 is a serious ongoing worldwide pandemic. Using X-ray chest radiography images for automatically diagnosing COVID-19 is an effective and convenient means of providing diagnostic assistance to clinicians in practice. This paper proposes a bagging dynamic deep learning network (B-DDLN) for diagnosing COVID-19 by intelligently recognizing its symptoms in X-ray chest radiography images. After a series of preprocessing steps for images, we pre-train convolution blocks as a feature extractor. For the extracted features, a bagging dynamic learning network classifier is trained based on neural dynamic learning algorithm and bagging algorithm. B-DDLN connects the feature extractor and bagging classifier in series. Experimental results verify that the proposed B-DDLN achieves 98.8889% testing accuracy, which shows the best diagnosis performance among the existing state-of-the-art methods on the open image set. It also provides evidence for further detection and treatment.

Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry

Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (Fragaria chiloensis and Fragaria virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication—59–76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that F. × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8 M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis,F. virginiana, and F. × ananassa (π = 0.0059–0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern F. × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.

Chromosomal Characterization of Tripidium arundinaceum Revealed by Oligo-FISH

Sugarcane is of important economic value for producing sugar and bioethanol. Tripidium arundinaceum (old name: Erianthus arundinaceum) is an intergeneric wild species of sugarcane that has desirable resistance traits for improving sugarcane varieties. However, the scarcity of chromosome markers has hindered the cytogenetic study of T. arundinaceum. Here we applied maize chromosome painting probes (MCPs) to identify chromosomes in sorghum and T. arundinaceum using a repeated fluorescence in situ hybridization (FISH) system. Sequential FISH revealed that these MCPs can be used as reliable chromosome markers for T. arundinaceum, even though T. arundinaceum has diverged from maize over 18 MYs (million years). Using these MCPs, we identified T. arundinaceum chromosomes based on their sequence similarity compared to sorghum and labeled them 1 through 10. Then, the karyotype of T. arundinaceum was established by multiple oligo-FISH. Furthermore, FISH results revealed that 5S rDNA and 35S rDNA are localized on chromosomes 5 and 6, respectively, in T. arundinaceum. Altogether, these results represent an essential step for further cytogenetic research of T. arundinaceum in sugarcane breeding.

Musculoskeletal modeling and humanoid control of robots based on human gait data

The emergence of exoskeleton rehabilitation training has brought good news to patients with limb dysfunction. Rehabilitation robots are used to assist patients with limb rehabilitation training and play an essential role in promoting the patient's sports function with limb disease restoring to daily life. In order to improve the rehabilitation treatment, various studies based on human dynamics and motion mechanisms are still being conducted to create more effective rehabilitation training. In this paper, considering the human biological musculoskeletal dynamics model, a humanoid control of robots based on human gait data collected from normal human gait movements with OpenSim is investigated. First, the establishment of the musculoskeletal model in OpenSim, inverse kinematics, and inverse dynamics are introduced. Second, accurate human-like motion analysis on the three-dimensional motion data obtained in these processes is discussed. Finally, a classic PD control method combined with the characteristics of the human motion mechanism is proposed. The method takes the angle values calculated by the inverse kinematics of the musculoskeletal model as a benchmark, then uses MATLAB to verify the simulation of the lower extremity exoskeleton robot. The simulation results show that the flexibility and followability of the method improves the safety and effectiveness of the lower limb rehabilitation exoskeleton robot for rehabilitation training. The value of this paper is also to provide theoretical and data support for the anthropomorphic control of the rehabilitation exoskeleton robot in the future.

DeepFeature: feature selection in nonimage data using convolutional neural network

Artificial intelligence methods offer exciting new capabilities for the discovery of biological mechanisms from raw data because they are able to detect vastly more complex patterns of association that cannot be captured by classical statistical tests. Among these methods, deep neural networks are currently among the most advanced approaches and, in particular, convolutional neural networks (CNNs) have been shown to perform excellently for a variety of difficult tasks. Despite that applications of this type of networks to high-dimensional omics data and, most importantly, meaningful interpretation of the results returned from such models in a biomedical context remains an open problem. Here we present, an approach applying a CNN to nonimage data for feature selection. Our pipeline, DeepFeature, can both successfully transform omics data into a form that is optimal for fitting a CNN model and can also return sets of the most important genes used internally for computing predictions. Within the framework, the Snowfall compression algorithm is introduced to enable more elements in the fixed pixel framework, and region accumulation and element decoder is developed to find elements or genes from the class activation maps. In comparative tests for cancer type prediction task, DeepFeature simultaneously achieved superior predictive performance and better ability to discover key pathways and biological processes meaningful for this context. Capabilities offered by the proposed framework can enable the effective use of powerful deep learning methods to facilitate the discovery of causal mechanisms in high-dimensional biomedical data.

Advances in promoter engineering: novel applications and predefined transcriptional control

Synthetic biology continues to progress by relying on more robust tools for transcriptional control, of which promoters are the most fundamental component. Numerous studies have sought to characterize promoter function, determine principles to guide their engineering, and create promoters with stronger expression or tailored inducible control. In this review, we will summarize promoter architecture and highlight recent advances in the field, focusing on the novel applications of inducible promoter design and engineering towards metabolic engineering and cellular therapeutic development. Additionally, we will highlight how the expansion of new, machine learning techniques for modeling and engineering promoter sequences are enabling more accurate prediction of promoter characteristics. This article is protected by copyright. All rights reserved.

COVLIAS 1.0: Lung Segmentation in COVID-19 Computed Tomography Scans Using Hybrid Deep Learning Artificial Intelligence Models

BACKGROUND

COVID-19 lung segmentation using Computed Tomography (CT) scans is important for the diagnosis of lung severity. The process of automated lung segmentation is challenging due to (a) CT radiation dosage and (b) ground-glass opacities caused by COVID-19. The lung segmentation methodologies proposed in 2020 were semi- or automated but not reliable, accurate, and user-friendly. The proposed study presents a COVID Lung Image Analysis System (COVLIAS 1.0, AtheroPoint™, Roseville, CA, USA) consisting of hybrid deep learning (HDL) models for lung segmentation.

METHODOLOGY

The COVLIAS 1.0 consists of three methods based on solo deep learning (SDL) or hybrid deep learning (HDL). SegNet is proposed in the SDL category while VGG-SegNet and ResNet-SegNet are designed under the HDL paradigm. The three proposed AI approaches were benchmarked against the National Institute of Health (NIH)-based conventional segmentation model using fuzzy-connectedness. A cross-validation protocol with a 40:60 ratio between training and testing was designed, with 10% validation data. The ground truth (GT) was manually traced by a radiologist trained personnel. For performance evaluation, nine different criteria were selected to perform the evaluation of SDL or HDL lung segmentation regions and lungs long axis against GT.

RESULTS

Using the database of 5000 chest CT images (from 72 patients), COVLIAS 1.0 yielded AUC of ~0.96, ~0.97, ~0.98, and ~0.96 (p-value < 0.001), respectively within 5% range of GT area, for SegNet, VGG-SegNet, ResNet-SegNet, and NIH. The mean Figure of Merit using four models (left and right lung) was above 94%. On benchmarking against the National Institute of Health (NIH) segmentation method, the proposed model demonstrated a 58% and 44% improvement in ResNet-SegNet, 52% and 36% improvement in VGG-SegNet for lung area, and lung long axis, respectively. The PE statistics performance was in the following order: ResNet-SegNet > VGG-SegNet > NIH > SegNet. The HDL runs in <1 s on test data per image.

CONCLUSIONS

The COVLIAS 1.0 system can be applied in real-time for radiology-based clinical settings.

Modeling a deep transfer learning framework for the classification of COVID-19 radiology dataset

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Coronavirus-2 or SARS-CoV-2), which came into existence in 2019, is a viral pandemic that caused coronavirus disease 2019 (COVID-19) illnesses and death. Research showed that relentless efforts had been made to improve key performance indicators for detection, isolation, and early treatment. This paper used Deep Transfer Learning Model (DTL) for the classification of a real-life COVID-19 dataset of chest X-ray images in both binary (COVID-19 or Normal) and three-class (COVID-19, Viral-Pneumonia or Normal) classification scenarios. Four experiments were performed where fine-tuned VGG-16 and VGG-19 Convolutional Neural Networks (CNNs) with DTL were trained on both binary and three-class datasets that contain X-ray images. The system was trained with an X-ray image dataset for the detection of COVID-19. The fine-tuned VGG-16 and VGG-19 DTL were modelled by employing a batch size of 10 in 40 epochs, Adam optimizer for weight updates, and categorical cross-entropy loss function. The results showed that the fine-tuned VGG-16 and VGG-19 models produced an accuracy of 99.23% and 98.00%, respectively, in the binary task. In contrast, in the multiclass (three-class) task, the fine-tuned VGG-16 and VGG-19 DTL models produced an accuracy of 93.85% and 92.92%, respectively. Moreover, the fine-tuned VGG-16 and VGG-19 models have MCC of 0.98 and 0.96 respectively in the binary classification, and 0.91 and 0.89 for multiclass classification. These results showed strong positive correlations between the models' predictions and the true labels. In the two classification tasks (binary and three-class), it was observed that the fine-tuned VGG-16 DTL model had stronger positive correlations in the MCC metric than the fine-tuned VGG-19 DTL model. The VGG-16 DTL model has a Kappa value of 0.98 as against 0.96 for the VGG-19 DTL model in the binary classification task, while in the three-class classification problem, the VGG-16 DTL model has a Kappa value of 0.91 as against 0.89 for the VGG-19 DTL model. This result is in agreement with the trend observed in the MCC metric. Hence, it was discovered that the VGG-16 based DTL model classified COVID-19 better than the VGG-19 based DTL model. Using the best performing fine-tuned VGG-16 DTL model, tests were carried out on 470 unlabeled image dataset, which was not used in the model training and validation processes. The test accuracy obtained for the model was 98%. The proposed models provided accurate diagnostics for both the binary and multiclass classifications, outperforming other existing models in the literature in terms of accuracy, as shown in this work.

Bioacoustic classification of avian calls from raw sound waveforms with an open-source deep learning architecture

The use of autonomous recordings of animal sounds to detect species is a popular conservation tool, constantly improving in fidelity as audio hardware and software evolves. Current classification algorithms utilise sound features extracted from the recording rather than the sound itself, with varying degrees of success. Neural networks that learn directly from the raw sound waveforms have been implemented in human speech recognition but the requirements of detailed labelled data have limited their use in bioacoustics. Here we test SincNet, an efficient neural network architecture that learns from the raw waveform using sinc-based filters. Results using an off-the-shelf implementation of SincNet on a publicly available bird sound dataset (NIPS4Bplus) show that the neural network rapidly converged reaching accuracies of over 65% with limited data. Their performance is comparable with traditional methods after hyperparameter tuning but they are more efficient. Learning directly from the raw waveform allows the algorithm to select automatically those elements of the sound that are best suited for the task, bypassing the onerous task of selecting feature extraction techniques and reducing possible biases. We use publicly released code and datasets to encourage others to replicate our results and to apply SincNet to their own datasets; and we review possible enhancements in the hope that algorithms that learn from the raw waveform will become useful bioacoustic tools.

A Deep-Learning Based Posture Detection System for Preventing Telework-Related Musculoskeletal Disorders

The change from face-to-face work to teleworking caused by the pandemic has induced multiple workers to spend more time than usual in front of a computer; in addition, the sudden installation of workstations in homes means that not all of them meet the necessary characteristics for the worker to be able to position himself/herself comfortably with the correct posture in front of their computer. Furthermore, from the point of view of the medical personnel in charge of occupational risk prevention, an automated tool able to quantify the degree of incorrectness of a postural habit in a worker is needed. For this purpose, in this work, a system based on the postural detection of the worker is designed, implemented and tested, using a specialized hardware system that processes video in real time through convolutional neural networks. This system is capable of detecting the posture of the neck, shoulders and arms, providing recommendations to the worker in order to prevent possible health problems, due to poor posture. The results of the proposed system show that this video processing can be carried out in real time (up to 25 processed frames/sec) with a low power consumption (less than 10 watts) using specialized hardware, obtaining an accuracy of over 80% in terms of the pattern detected.

A stacking ensemble deep learning approach to cancer type classification based on TCGA data

Cancer tumor classification based on morphological characteristics alone has been shown to have serious limitations. Breast, lung, colorectal, thyroid, and ovarian are the most commonly diagnosed cancers among women. Precise classification of cancers into their types is considered a vital problem for cancer diagnosis and therapy. In this paper, we proposed a stacking ensemble deep learning model based on one-dimensional convolutional neural network (1D-CNN) to perform a multi-class classification on the five common cancers among women based on RNASeq data. The RNASeq gene expression data was downloaded from Pan-Cancer Atlas using GDCquery function of the TCGAbiolinks package in the R software. We used least absolute shrinkage and selection operator (LASSO) as feature selection method. We compared the results of the new proposed model with and without LASSO with the results of the single 1D-CNN and machine learning methods which include support vector machines with radial basis function, linear, and polynomial kernels; artificial neural networks; k-nearest neighbors; bagging trees. The results show that the proposed model with and without LASSO has a better performance compared to other classifiers. Also, the results show that the machine learning methods (SVM-R, SVM-L, SVM-P, ANN, KNN, and bagging trees) with under-sampling have better performance than with over-sampling techniques. This is supported by the statistical significance test of accuracy where the p-values for differences between the SVM-R and SVM-P, SVM-R and ANN, SVM-R and KNN are found to be p = 0.003, p =  < 0.001, and p =  < 0.001, respectively. Also, SVM-L had a significant difference compared to ANN p = 0.009. Moreover, SVM-P and ANN, SVM-P and KNN are found to be significantly different with p-values p =  < 0.001 and p =  < 0.001, respectively. In addition, ANN and bagging trees, ANN and KNN were found to be significantly different with p-values p =  < 0.001 and p = 0.004, respectively. Thus, the proposed model can help in the early detection and diagnosis of cancer in women, and hence aid in designing early treatment strategies to improve survival.

The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution

Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. This large amount of reshuffling within chromosomes with few inter-chromosomal events contrasts with patterns seen in mammals in which the chromosomes tend to exchange larger blocks of material more readily. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta in a phylogenetic framework. For the first time, we find that synteny decays at an exponential rate relative to phylogenetic distance. Additionally, there are significant differences in decay rates between insect orders, this pattern was not driven by Lepidoptera alone which has a substantially different rate.

Auto informing COVID-19 detection result from x-ray/CT images based on deep learning

It is no secret to all that the corona pandemic has caused a decline in all aspects of the world. Therefore, offering an accurate automatic diagnostic system is very important. This paper proposed an accurate COVID-19 system by testing various deep learning models for x-ray/computed tomography (CT) medical images. A deep preprocessing procedure was done with two filters and segmentation to increase classification results. According to the results obtained, 99.94% of accuracy, 98.70% of sensitivity, and 100% of specificity scores were obtained by the Xception model in the x-ray dataset and the InceptionV3 model for CT scan images. The compared results have demonstrated that the proposed model is proven to be more successful than the deep learning algorithms in previous studies. Moreover, it has the ability to automatically notify the examination results to the patients, the health authority, and the community after taking any x-ray or CT images.

Efficient deep neural networks for classification of COVID-19 based on CT images: Virtualization via software defined radio

The novel 2019 coronavirus disease (COVID-19) has infected over 141 million people worldwide since April 20, 2021. More than 200 countries around the world have been affected by the coronavirus pandemic. Screening for COVID-19, we use fast and inexpensive images from computed tomography (CT) scans. In this paper, ResNet-50, VGG-16, convolutional neural network (CNN), convolutional auto-encoder neural network (CAENN), and machine learning (ML) methods are proposed for classifying Chest CT Images of COVID-19. The dataset consists of 1252 CT scans that are positive and 1230 CT scans that are negative for COVID-19 virus. The proposed models have priority over the other models that there is no need of pre-trained networks and data augmentation for them. The classification accuracies of ResNet-50, VGG-16, CNN, and CAENN were obtained 92.24%, 94.07%, 93.84%, and 93.04% respectively. Among ML classifiers, the nearest neighbor (NN) had the highest performance with an accuracy of 94%.

Lot-Size Models with Uncertain Demand Considering Its Skewness/Kurtosis and Stochastic Programming Applied to Hospital Pharmacy with Sensor-Related COVID-19 Data

Governments have been challenged to provide timely medical care to face the COVID-19 pandemic. Under this pandemic, the demand for pharmaceutical products has changed significantly. Some of these products are in high demand, while, for others, their demand falls sharply. These changes in the random demand patterns are connected with changes in the skewness (asymmetry) and kurtosis of their data distribution. Such changes are critical to determining optimal lots and inventory costs. The lot-size model helps to make decisions based on probabilistic demand when calculating the optimal costs of supply using two-stage stochastic programming. The objective of this study is to evaluate how the skewness and kurtosis of the distribution of demand data, collected through sensors, affect the modeling of inventories of hospital pharmacy products helpful to treat COVID-19. The use of stochastic programming allows us to obtain results under demand uncertainty that are closer to reality. We carry out a simulation study to evaluate the performance of our methodology under different demand scenarios with diverse degrees of skewness and kurtosis. A case study in the field of hospital pharmacy with sensor-related COVID-19 data is also provided. An algorithm that permits us to use sensors when submitting requests for supplying pharmaceutical products in the hospital treatment of COVID-19 is designed. We show that the coefficients of skewness and kurtosis impact the total costs of inventory that involve order, purchase, holding, and shortage. We conclude that the asymmetry and kurtosis of the demand statistical distribution do not seem to affect the first-stage lot-size decisions. However, demand patterns with high positive skewness are related to significant increases in expected inventories on hand and shortage, increasing the costs of second-stage decisions. Thus, demand distributions that are highly asymmetrical to the right and leptokurtic favor high total costs in probabilistic lot-size systems.

Boolean logic algebra driven similarity measure for text based applications

In Information Retrieval (IR), Data Mining (DM), and Machine Learning (ML), similarity measures have been widely used for text clustering and classification. The similarity measure is the cornerstone upon which the performance of most DM and ML algorithms is completely dependent. Thus, till now, the endeavor in literature for an effective and efficient similarity measure is still immature. Some recently-proposed similarity measures were effective, but have a complex design and suffer from inefficiencies. This work, therefore, develops an effective and efficient similarity measure of a simplistic design for text-based applications. The measure developed in this work is driven by Boolean logic algebra basics (BLAB-SM), which aims at effectively reaching the desired accuracy at the fastest run time as compared to the recently developed state-of-the-art measures. Using the term frequency-inverse document frequency (TF-IDF) schema, the K-nearest neighbor (KNN), and the K-means clustering algorithm, a comprehensive evaluation is presented. The evaluation has been experimentally performed for BLAB-SM against seven similarity measures on two most-popular datasets, Reuters-21 and Web-KB. The experimental results illustrate that BLAB-SM is not only more efficient but also significantly more effective than state-of-the-art similarity measures on both classification and clustering tasks.

COVID-Nets: deep CNN architectures for detecting COVID-19 using chest CT scans

In this paper we propose two novel deep convolutional network architectures, CovidResNet and CovidDenseNet, to diagnose COVID-19 based on CT images. The models enable transfer learning between different architectures, which might significantly boost the diagnostic performance. Whereas novel architectures usually suffer from the lack of pretrained weights, our proposed models can be partly initialized with larger baseline models like ResNet50 and DenseNet121, which is attractive because of the abundance of public repositories. The architectures are utilized in a first experimental study on the SARS-CoV-2 CT-scan dataset, which contains 4173 CT images for 210 subjects structured in a subject-wise manner into three different classes. The models differentiate between COVID-19, non-COVID-19 viral pneumonia, and healthy samples. We also investigate their performance under three binary classification scenarios where we distinguish COVID-19 from healthy, COVID-19 from non-COVID-19 viral pneumonia, and non-COVID-19 from healthy, respectively. Our proposed models achieve up to 93.87% accuracy, 99.13% precision, 92.49% sensitivity, 97.73% specificity, 95.70% F1-score, and 96.80% AUC score for binary classification, and up to 83.89% accuracy, 80.36% precision, 82.04% sensitivity, 92.07% specificity, 81.05% F1-score, and 94.20% AUC score for the three-class classification tasks. We also validated our models on the COVID19-CT dataset to differentiate COVID-19 and other non-COVID-19 viral infections, and our CovidDenseNet model achieved the best performance with 81.77% accuracy, 79.05% precision, 84.69% sensitivity, 79.05% specificity, 81.77% F1-score, and 87.50% AUC score. The experimental results reveal the effectiveness of the proposed networks in automated COVID-19 detection where they outperform standard models on the considered datasets while being more efficient.

Constructing a cohesive pattern for collective navigation based on a swarm of robotics

Swarm robotics carries out complex tasks beyond the power of simple individual robots. Limited capabilities of sensing and communication by simple mobile robots have been essential inspirations for aggregation tasks. Aggregation is crucial behavior when performing complex tasks in swarm robotics systems. Many difficulties are facing the aggregation algorithm. These difficulties are as such: this algorithm has to work under the restrictions of no information about positions, no central control, and only local information interaction among robots. This paper proposed a new aggregation algorithm. This algorithm combined with the wave algorithm to achieve collective navigation and the recruitment strategy. In this work, the aggregation algorithm consists of two main phases: the searching phase, and the surrounding phase. The execution time of the proposed algorithm was analyzed. The experimental results showed that the aggregation time in the proposed algorithm was significantly reduced by 41% compared to other algorithms in the literature. Moreover, we analyzed our results using a one-way analysis of variance. Also, our results showed that the increasing swarm size significantly improved the performance of the group.

Tracing CVE Vulnerability Information to CAPEC Attack Patterns Using Natural Language Processing Techniques

For effective vulnerability management, vulnerability and attack information must be collected quickly and efficiently. A security knowledge repository can collect such information. The Common Vulnerabilities and Exposures (CVE) provides known vulnerabilities of products, while the Common Attack Pattern Enumeration and Classification (CAPEC) stores attack patterns, which are descriptions of common attributes and approaches employed by adversaries to exploit known weaknesses. Due to the fact that the information in these two repositories are not linked, identifying related CAPEC attack information from CVE vulnerability information is challenging. Currently, the related CAPEC-ID can be traced from the CVE-ID using Common Weakness Enumeration (CWE) in some but not all cases. Here, we propose a method to automatically trace the related CAPEC-IDs from CVE-ID using three similarity measures: TF–IDF, Universal Sentence Encoder (USE), and Sentence-BERT (SBERT). We prepared and used 58 CVE-IDs as test input data. Then, we tested whether we could trace CAPEC-IDs related to each of the 58 CVE-IDs. Additionally, we experimentally confirm that TF–IDF is the best similarity measure, as it traced 48 of the 58 CVE-IDs to the related CAPEC-ID.

Benchmarking Transfer Entropy Methods for the Study of Linear and Nonlinear Cardio-Respiratory Interactions

Transfer entropy (TE) has been used to identify and quantify interactions between physiological systems. Different methods exist to estimate TE, but there is no consensus about which one performs best in specific applications. In this study, five methods (linear, k-nearest neighbors, fixed-binning with ranking, kernel density estimation and adaptive partitioning) were compared. The comparison was made on three simulation models (linear, nonlinear and linear + nonlinear dynamics). From the simulations, it was found that the best method to quantify the different interactions was adaptive partitioning. This method was then applied on data from a polysomnography study, specifically on the ECG and the respiratory signals (nasal airflow and respiratory effort around the thorax). The hypothesis that the linear and nonlinear components of cardio-respiratory interactions during light and deep sleep change with the sleep stage, was tested. Significant differences, after performing surrogate analysis, indicate an increased TE during deep sleep. However, these differences were found to be dependent on the type of respiratory signal and sampling frequency. These results highlight the importance of selecting the appropriate signals, estimation method and surrogate analysis for the study of linear and nonlinear cardio-respiratory interactions.

Diagnosis of vertebral column pathologies using concatenated resampling with machine learning algorithms

Medical diagnosis through the classification of biomedical attributes is one of the exponentially growing fields in bioinformatics. Although a large number of approaches have been presented in the past, wide use and superior performance of the machine learning (ML) methods in medical diagnosis necessitates significant consideration for automatic diagnostic methods. This study proposes a novel approach called concatenated resampling (CR) to increase the efficacy of traditional ML algorithms. The performance is analyzed leveraging four ML approaches like tree-based ensemble approaches, and linear machine learning approach for automatic diagnosis of inter-vertebral pathologies with increased. Besides, undersampling, over-sampling, and proposed CR techniques have been applied to unbalanced training dataset to analyze the impact of these techniques on the accuracy of each of the classification model. Extensive experiments have been conducted to make comparisons among different classification models using several metrics including accuracy, precision, recall, and F ₁ score. Comparative analysis has been performed on the experimental results to identify the best performing classifier along with the application of the re-sampling technique. The results show that the extra tree classifier achieves an accuracy of 0.99 in association with the proposed CR technique.

Introductory programming course: review and future implications

The introductory programming course (IPC) holds a special significance in computing disciplines as this course serves as a prerequisite for studying the higher level courses. Students generally face difficulties during their initial stages of learning how to program. Continuous efforts are being made to examine this course for identifying potential improvements. This article presents the review of the state-of-the-art research exploring various components of IPC by examining sixty-six articles published between 2014 and 2020 in well-reputed research venues. The results reveal that several useful methods have been proposed to support teaching and learning in IPC. Moreover, the research in IPC presented useful ways to conduct assessments, and also demonstrated different techniques to examine improvements in the IPC contents. In addition, a variety of tools are evaluated to support the related course processes. Apart from the aforementioned facets, this research explores other interesting dimensions of IPC, such as collaborative learning, cognitive assessments, and performance predictions. In addition to reviewing the recent advancements in IPC, this study proposes a new taxonomy of IPC research dimensions. Furthermore, based on the successful practices that are listed in the literature, some useful guidelines and advices for instructors have also been reported in this article. Lastly, this review presents some pertinent open research issues to highlight the future dimensions for IPC researchers.

DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning

DNA-binding proteins (DBPs) perform an influential role in diverse biological activities like DNA replication, slicing, repair, and transcription. Some DBPs are indispensable for understanding many types of human cancers (i.e. lung, breast, and liver cancer) and chronic diseases (i.e. AIDS/HIV, asthma), while other kinds are involved in antibiotics, steroids, and anti-inflammatory drugs designing. These crucial processes are closely related to DBPs types. DBPs are categorized into single-stranded DNA-binding proteins (ssDBPs) and double-stranded DNA-binding proteins (dsDBPs). Few computational predictors have been reported for discriminating ssDBPs and dsDBPs. However, due to the limitations of the existing methods, an intelligent computational system is still highly desirable. In this work, features from protein sequences are discovered by extending the notion of dipeptide composition (DPC), evolutionary difference formula (EDF), and K-separated bigram (KSB) into the position-specific scoring matrix (PSSM). The highly intrinsic information was encoded by a compression approach named discrete cosine transform (DCT) and the model was trained with support vector machine (SVM). The prediction performance was further boosted by the genetic algorithm (GA) ensemble strategy. The novel predictor (DBP-GAPred) acquired 1.89%, 0.28%, and 6.63% higher accuracies on jackknife, 10-fold, and independent dataset tests, respectively than the best predictor. These outcomes confirm the superiority of our method over the existing predictors.

The effect of psychological nursing on the short- and long-term negative emotions and quality of life of cervical cancer patients undergoing postoperative chemotherapy

OBJECTIVE

The purpose of this study was to analyze the effect of psychological nursing intervention on the short- and long-term negative emotions and changes in the quality of life in patients with cervical cancer who underwent postoperative chemotherapy.

METHODS

141 patients with cervical cancer who received postoperative chemotherapy in our hospital were recruited as the study cohort. They were divided into the study group (80 cases) and the control group (61 cases) according to the different nursing methods each underwent. The patients in the control group underwent routine nursing, and the study group also underwent psychological nursing. The changes in the quality of life and the negative emotions of the patients in the two groups before and after the intervention were compared, and the correlation between the quality of life and the negative emotions were explored.

RESULTS

The patients' Quality of Life Questionnaire (EROTC-QLQ-C30) and Self-rating Anxiety Scale (SAS) scores in the two groups before the intervention were not significantly different (P > 0.05). A re-evaluation at the end of the 90 day-intervention showed that the EROTC-QLQ-C30 scores in the study group were significantly higher than they were in the control group (P < 0.05). A dynamic evaluation showed that the proportion of patients with mild anxiety in the study group was higher than it was in the control group at 30, 60, and 90 days of intervention (P < 0.05). A Spearman correlation analysis showed that the SAS scale and EROTC-QLQ-C30 scores were negatively correlated (r=-0.4438, P < 0.05).

CONCLUSION

The implementation of psychological intervention can help alleviate the short- and long-term negative emotions of cervical cancer patients who underwent postoperative chemotherapy, and it is feasible and conducive to the patients' quality of life. We recommend carrying out the clinical promotion and application of this psychological intervention.

Improving patient rehabilitation performance in exercise games using collaborative filtering approach

BACKGROUND

Virtual reality is utilised in exergames to help patients with disabilities improve on the movement of their limbs. Exergame settings, such as the game difficulty, play important roles in the rehabilitation outcome. Similarly, suboptimal exergames' settings may adversely affect the accuracy of the results obtained. As such, the improvement in patients' movement performances falls below the desired expectations. In this paper, a recommender system is incorporated to suggest the most preferred movement setting for each patient, based on the movement history of the patient.

METHOD

The proposed recommender system (ResComS) suggests the most suitable setting necessary to optimally improve patients' rehabilitation performances. In the course of developing the recommender system, three methods are proposed and compared: ReComS (K-nearest neighbours and collaborative filtering algorithms), ReComS+ (k-means, K-nearest neighbours, and collaborative filtering algorithms) and ReComS++ (bacterial foraging optimisation, k-means, K-nearest neighbours, and collaborative filtering algorithms). The experimental datasets are collected using the Medical Interactive Recovery Assistant (MIRA) software platform.

RESULT

Experimental results, validated by the patients' exergame performances, reveal that the ReComS++ approach predicts the best exergame settings for patients with 85.76% accuracy.

A tool for assessing alignment of biomedical data repositories with open, FAIR, citation and trustworthy principles

Increasing attention is being paid to the operation of biomedical data repositories in light of efforts to improve how scientific data is handled and made available for the long term. Multiple groups have produced recommendations for functions that biomedical repositories should support, with many using requirements of the FAIR data principles as guidelines. However, FAIR is but one set of principles that has arisen out of the open science community. They are joined by principles governing open science, data citation and trustworthiness, all of which are important aspects for biomedical data repositories to support. Together, these define a framework for data repositories that we call OFCT: Open, FAIR, Citable and Trustworthy. Here we developed an instrument using the open source PolicyModels toolkit that attempts to operationalize key aspects of OFCT principles and piloted the instrument by evaluating eight biomedical community repositories listed by the NIDDK Information Network (dkNET.org). Repositories included both specialist repositories that focused on a particular data type or domain, in this case diabetes and metabolomics, and generalist repositories that accept all data types and domains. The goal of this work was both to obtain a sense of how much the design of current biomedical data repositories align with these principles and to augment the dkNET listing with additional information that may be important to investigators trying to choose a repository, e.g., does the repository fully support data citation? The evaluation was performed from March to November 2020 through inspection of documentation and interaction with the sites by the authors. Overall, although there was little explicit acknowledgement of any of the OFCT principles in our sample, the majority of repositories provided at least some support for their tenets.

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes.

An “Animated Spatial Time Machine” in Co-Creation: Reconstructing History Using Gamification Integrated into 3D City Modelling, 4D Web and Transmedia Storytelling

More and more digital 3D city models might evolve into spatiotemporal instruments with time as the 4th dimension. For digitizing the current situation, 3D scanning and photography are suitable tools. The spatial future could be integrated using 3D drawings by public space designers and architects. The digital spatial reconstruction of lost historical environments is more complex, expensive and rarely done. Three-dimensional co-creative digital drawing with citizens’ collaboration could be a solution. In 2016, the City of Ghent (Belgium) launched the “3D city game Ghent” project with time as one of the topics, focusing on the reconstruction of disappeared environments. Ghent inhabitants modelled in open-source 3D software and added animated 3D gamification and Transmedia Storytelling, resulting in a 4D web environment and VR/AR/XR applications. This study analyses this low-cost interdisciplinary 3D co-creative process and offers a framework to enable other cities and municipalities to realise a parallel virtual universe (an animated digital twin bringing the past to life). The result of this co-creation is the start of an “Animated Spatial Time Machine” (AniSTMa), a term that was, to the best of our knowledge, never used before. This research ultimately introduces a conceptual 4D space–time diagram with a relation between the current physical situation and a growing number of 3D animated models over time.

Genome-Wide Comparative Analysis of Flowering-Time Genes; Insights on the Gene Family Expansion and Evolutionary Perspective

In polyploids, whole genome duplication (WGD) played a significant role in genome expansion, evolution and diversification. Many gene families are expanded following polyploidization, with the duplicated genes functionally diversified by neofunctionalization or subfunctionalization. These mechanisms may support adaptation and have likely contributed plant survival during evolution. Flowering time is an important trait in plants, which affects critical features, such as crop yields. The flowering-time gene family is one of the largest expanded gene families in plants, with its members playing various roles in plant development. Here, we performed genome-wide identification and comparative analysis of flowering-time genes in three palnt families i.e., Malvaceae, Brassicaceae, and Solanaceae, which indicate these genes were expanded following the event/s of polyploidization. Duplicated genes have been retained during evolution, although genome reorganization occurred in their flanking regions. Further investigation of sequence conservation and similarity network analyses provide evidence for functional diversification of duplicated genes during evolution. These functionally diversified genes play important roles in plant development and provide advantages to plants for adaptation and survival in response to environmental changes encountered during evolution. Collectively, we show that flowering-time genes were expanded following polyploidization and retained as large gene family by providing advantages from functional diversification during evolution.

Dilated Semantic Segmentation for Breast Ultrasonic Lesion Detection Using Parallel Feature Fusion

Breast cancer is becoming more dangerous by the day. The death rate in developing countries is rapidly increasing. As a result, early detection of breast cancer is critical, leading to a lower death rate. Several researchers have worked on breast cancer segmentation and classification using various imaging modalities. The ultrasonic imaging modality is one of the most cost-effective imaging techniques, with a higher sensitivity for diagnosis. The proposed study segments ultrasonic breast lesion images using a Dilated Semantic Segmentation Network (Di-CNN) combined with a morphological erosion operation. For feature extraction, we used the deep neural network DenseNet201 with transfer learning. We propose a 24-layer CNN that uses transfer learning-based feature extraction to further validate and ensure the enriched features with target intensity. To classify the nodules, the feature vectors obtained from DenseNet201 and the 24-layer CNN were fused using parallel fusion. The proposed methods were evaluated using a 10-fold cross-validation on various vector combinations. The accuracy of CNN-activated feature vectors and DenseNet201-activated feature vectors combined with the Support Vector Machine (SVM) classifier was 90.11 percent and 98.45 percent, respectively. With 98.9 percent accuracy, the fused version of the feature vector with SVM outperformed other algorithms. When compared to recent algorithms, the proposed algorithm achieves a better breast cancer diagnosis rate.

Modeling COVID-19 Cases Statistically and Evaluating Their Effect on the Economy of Countries

COVID-19 infections have plagued the world and led to deaths with a heavy pneumonia manifestation. The main objective of this investigation is to evaluate the performance of certain economies during the crisis derived from the COVID-19 pandemic. The gross domestic product (GDP) and global health security index (GHSI) of the countries belonging–or not–to the Organization for Economic Cooperation and Development (OECD) are considered. In this paper, statistical models are formulated to study this performance. The models’ specifications include, as the response variable, the GDP variation/growth percentage in 2020, and as the covariates: the COVID-19 disease rate from its start in March 2020 until 31 December 2020; the GHSI of 2019; the countries’ risk by default spreads from July 2019 to May 2020; belongingness or not to the OECD; and the GDP per capita in 2020. We test the heteroscedasticity phenomenon present in the modeling. The variable “COVID-19 cases per million inhabitants” is statistically significant, showing its impact on each country’s economy through the GDP variation. Therefore, we report that COVID-19 cases affect domestic economies, but that OECD membership and other risk factors are also relevant.

Performance of gender detection tools: a comparative study of name-to-gender inference services

Objective:

To evaluate the performance of gender detection tools that allow the uploading of files (e.g., Excel or CSV files) containing first names, are usable by researchers without advanced computer skills, and are at least partially free of charge.

Methods:

The study was conducted using four physician datasets (total number of physicians: 6,131; 50.3% female) from Switzerland, a multilingual country. Four gender detection tools met the inclusion criteria: three partially free (Gender API, NamSor, and genderize.io) and one completely free (Wiki-Gendersort). For each tool, we recorded the number of correct classifications (i.e., correct gender assigned to a name), misclassifications (i.e., wrong gender assigned to a name), and nonclassifications (i.e., no gender assigned). We computed three metrics: the proportion of misclassifications excluding nonclassifications (errorCodedWithoutNA), the proportion of nonclassifications (naCoded), and the proportion of misclassifications and nonclassifications (errorCoded).

Results:

The proportion of misclassifications was low for all four gender detection tools (errorCodedWithoutNA between 1.5 and 2.2%). By contrast, the proportion of unrecognized names (naCoded) varied: 0% for NamSor, 0.3% for Gender API, 4.5% for Wiki-Gendersort, and 16.4% for genderize.io. Using errorCoded, which penalizes both types of error equally, we obtained the following results: Gender API 1.8%, NamSor 2.0%, Wiki-Gendersort 6.6%, and genderize.io 17.7%.

Conclusions:

Gender API and NamSor were the most accurate tools. Genderize.io led to a high number of nonclassifications. Wiki-Gendersort may be a good compromise for researchers wishing to use a completely free tool. Other studies would be useful to evaluate the performance of these tools in other populations (e.g., Asian).

IoT-Enabled Smart Cities: Evolution and Outlook

For the last decade the Smart City concept has been under development, fostered by the growing urbanization of the world’s population and the need to handle the challenges that such a scenario raises. During this time many Smart City projects have been executed–some as proof-of-concept, but a growing number resulting in permanent, production-level deployments, improving the operation of the city and the quality of life of its citizens. Thus, Smart Cities are still a highly relevant paradigm which needs further development before it reaches its full potential and provides robust and resilient solutions. In this paper, the focus is set on the Internet of Things (IoT) as an enabling technology for the Smart City. In this sense, the paper reviews the current landscape of IoT-enabled Smart Cities, surveying relevant experiences and city initiatives that have embedded IoT within their city services and how they have generated an impact. The paper discusses the key technologies that have been developed and how they are contributing to the realization of the Smart City. Moreover, it presents some challenges that remain open ahead of us and which are the initiatives and technologies that are under development to tackle them.

Chest X-ray pneumothorax segmentation using U-Net with EfficientNet and ResNet architectures

Medical imaging refers to visualization techniques to provide valuable information about the internal structures of the human body for clinical applications, diagnosis, treatment, and scientific research. Segmentation is one of the primary methods for analyzing and processing medical images, which helps doctors diagnose accurately by providing detailed information on the body's required part. However, segmenting medical images faces several challenges, such as requiring trained medical experts and being time-consuming and error-prone. Thus, it appears necessary for an automatic medical image segmentation system. Deep learning algorithms have recently shown outstanding performance for segmentation tasks, especially semantic segmentation networks that provide pixel-level image understanding. By introducing the first fully convolutional network (FCN) for semantic image segmentation, several segmentation networks have been proposed on its basis. One of the state-of-the-art convolutional networks in the medical image field is U-Net. This paper presents a novel end-to-end semantic segmentation model, named Ens4B-UNet, for medical images that ensembles four U-Net architectures with pre-trained backbone networks. Ens4B-UNet utilizes U-Net's success with several significant improvements by adapting powerful and robust convolutional neural networks (CNNs) as backbones for U-Nets encoders and using the nearest-neighbor up-sampling in the decoders. Ens4B-UNet is designed based on the weighted average ensemble of four encoder-decoder segmentation models. The backbone networks of all ensembled models are pre-trained on the ImageNet dataset to exploit the benefit of transfer learning. For improving our models, we apply several techniques for training and predicting, including stochastic weight averaging (SWA), data augmentation, test-time augmentation (TTA), and different types of optimal thresholds. We evaluate and test our models on the 2019 Pneumothorax Challenge dataset, which contains 12,047 training images with 12,954 masks and 3,205 test images. Our proposed segmentation network achieves a 0.8608 mean Dice similarity coefficient (DSC) on the test set, which is among the top one-percent systems in the Kaggle competition.

Convolutional neural network-based ensemble methods to recognize Bangla handwritten character

In this era of advancements in deep learning, an autonomous system that recognizes handwritten characters and texts can be eventually integrated with the software to provide better user experience. Like other languages, Bangla handwritten text extraction also has various applications such as post-office automation, signboard recognition, and many more. A large-scale and efficient isolated Bangla handwritten character classifier can be the first building block to create such a system. This study aims to classify the handwritten Bangla characters. The proposed methods of this study are divided into three phases. In the first phase, seven convolutional neural networks i.e., CNN-based architectures are created. After that, the best performing CNN model is identified, and it is used as a feature extractor. Classifiers are then obtained by using shallow machine learning algorithms. In the last phase, five ensemble methods have been used to achieve better performance in the classification task. To systematically assess the outcomes of this study, a comparative analysis of the performances has also been carried out. Among all the methods, the stacked generalization ensemble method has achieved better performance than the other implemented methods. It has obtained accuracy, precision, and recall of 98.68%, 98.69%, and 98.68%, respectively on the Ekush dataset. Moreover, the use of CNN architectures and ensemble methods in large-scale Bangla handwritten character recognition has also been justified by obtaining consistent results on the BanglaLekha-Isolated dataset. Such efficient systems can move the handwritten recognition to the next level so that the handwriting can easily be automated.

The SPARC DRC: Building a Resource for the Autonomic Nervous System Community

The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps, and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. A data portal has been developed that allows discovery of data and models both via semantic search and via an interface that includes Google Map-like 2D flatmaps for displaying connectivity, and 3D anatomical organ scaffolds that provide a common coordinate framework for cross-species comparisons. We discuss examples that illustrate the data pipeline, which includes data upload, curation, segmentation (for image data), registration against the flatmaps and scaffolds, and finally display via the web portal, including the link to freely available online computational facilities that will enable neuromodulation hypotheses to be investigated by the autonomic neuroscience community and device manufacturers.