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Bacteria identification has predominantly been conducted using specific bioreceptors such as antibodies or nucleic acid sequences. This approach may be inappropriate for environmental monitoring when the user does not know the target bacterial species and for screening complex water samples with many unknown bacterial species. In this work, we investigate the supervised machine learning of the bacteria-particle aggregation pattern induced by the peptide sets identified from the biofilm-bacteria interface. Each peptide is covalently conjugated to polystyrene particles and loaded together with bacterial suspensions onto paper microfluidic chips. Each peptide interacts with bacterial species to a different extent, leading to varying sizes of particle aggregation. This aggregation changes the surface tension and viscosity of the liquid flowing through the paper pores, altering the flow velocity at different extents. A smartphone camera captures this flow velocity without being affected by ambient and environmental conditions, towards a low-cost, rapid, and field-ready assay. A collection of such flow velocity data generates a unique fingerprinting profile for each bacterial species. Support vector machine is utilized to classify the species. At optimized conditions, the training model can predict the species at 93.3% accuracy out of five bacteria: Escherichia coli, Staphylococcus aureus, Salmonella Typhimurium, Enterococcus faecium, and Pseudomonas aeruginosa. Flow rates are monitored for less than 6 s and the sample-to-answer assay time is less than 10 min. The demonstrated method can open a new way of analyzing complex biological and environmental samples in a biomimetic manner with machine learning classification.

Medicine has entered the digital era, driven by data from new modalities, especially genomics and imaging, as well as new sources such as wearables and Internet of Things. As we gain a deeper understanding of the disease biology and how diseases affect an individual, we are developing targeted therapies to personalize treatments. There is a need for technologies like Artificial Intelligence (AI) to be able to support predictions for personalized treatments. In order to mainstream AI in healthcare we will need to address issues such as explainability, liability and privacy. Developing explainable algorithms and including AI training in medical education are many of the solutions that can help alleviate these concerns.

Image authentication is one of the methods which can detect the any tampering data. The original grayscale document image is converted into stego image by adding the alpha channel plane. The stego image is in the Portable Network Graphics (PNG) format. This stego image is transmitted over the network. The authentication process is applied on the stego image on the receiver side. In the authentication process the data extracted from this stego image is compared with the data computed from the binary version of the stego image. If the data is matched the image is considered to be authentic. Else the tampered blocks are marked and the image is self-repaired using inverse secret sharing scheme.but in other methods they cannot resist the self substitution attack, the same-position-substitution attack, or the cut- off attack. Furthermore, those attacks can be completed by the popular image editing software Adobe Photoshop. We proposed security enhanced authentication scheme. Our proposed scheme is capable of repairing the content of the given stego-image if attacked by the methods mentioned above.

Research on "PERFORMA" or Paper Test Kits Formalin is as an alternative to improve the quality of food selection. It is aiming to get a paper test kit that can detect formaldehyde contented in foodstuffs practically, fast, easy, and inexpensive. The method used in this study is an experimental method which is part of a quantitative method that aims to manipulate and control variables. The data collection is based on the research and the observation of the color change on the paper test kit is generated from Schiff reagent test, in which the paper test kit will give a purple color response when tested on foodstuffs containing formalin. Based on the analysis of variety of data, it is obtained and expressed as mean ± standard deviation with confidence interval in this study are stated at α 5%. Thus, this research paper expects that formalin test kit can be easily applied and used by the community at large. Keywords: foodstuff, formalin, paper test kits, reagents Schiff

We are very pleased and honoured to present this special issue of Bioinspiration & Biomimetics that gathers a set of nine peer-reviewed articles whose results were in large part presented at the International Workshop on Bio-Inspired Robots which was held in Nantes, France, from 6?8 April 2011. The participants in this event have enthusiastic memories of the workshop, which was organized within the framework of EU-funded Future Emerging Technologies (ICT/FET) projects named Angels and Lampetra and hosted by the Ecole des Mines de Nantes and the IRCCyN Lab, Nantes, France. Following the workshop in Nantes, the general topic of this special issue is therefore on bio-inspired robots. The core theme of the special issue reflects a growing interest in developing bio-inspired autonomous robots that can interact with an unknown environment. This innovative scientific approach is first based on biological observations of animals from the point of view of locomotion, perception and their sensory-motor integration. Aquatic, aerial or terrestrial locomotion modes are of paramount importance for their high capabilities in terms of maneuverability/agility and energy efficiency. In the present special issue, [1] presents a swimming fully autonomous robot inspired by the species Lampetra fluviatilis which shows high maneuverability and efficiency, replicating the one of its natural counterpart. Such high performance swimming derives from the recovery of the energy that underwater moving vehicles usually leave in their wake. The Lampetra robot is actuated by an innovative technological solution that exploits the compliancy of a passive backbone to enhance swimming energetic efficiency. With [2] and [3], we shift from swimming to flying, by taking inspiration from insects. Insects, like hummingbirds, are capable of extremely rapid and precise aerial maneuvers. A rapidly growing community of researchers is gathering around the understanding of flapping-wing flight, and its mechanical imitation. At the boundaries of fluid mechanics, structural mechanics and robotics, these new kinds of aerial robots are envisaged to fly in inhabited areas. In this context, a challenging problem concerns the role and exploitation of the wing flexibility for maneuverability, control and actuation efficiency. The focus of [2] is on the effects of the structural flexibility of wings in the flapping flight of a butterfly. In [3], the authors show how flapping aerodynamics can lead to a most-advanced complete autonomous system: the Delfly robot from Delft University. At large, the use of flexible flapping wings is an example of a new emerging topic named `soft robotics' since it aims at solving robotics problems by exploiting the characteristics of soft organs. One of the challenging tasks of soft robotics is to design new actuators capable of reproducing the performance of living animals in terms of integration, rheology, efficiency and control. This perspective is at the foundation of a new generation of robots in our current life, i.e. capable of interacting with humans in a safe manner. The aim of [4]?[6] is to design such a new generation of soft actuators. Mainly taking inspiration from the hydrostats, they report on current works performed in the framework of the EU funded project Octopus, which aims at designing and building an underwater robot inspired by this animal. Beyond their specific scopes, these three articles are emblematic of the bio-inspired methodology, by going from Nature to robotics via mathematical modeling. Sensing is also of interest because inspiration from nature offers new sensory modalities and working principles. The extraordinary performance of supposedly simple animals is a source of wonder and new ideas for researchers. For example, with only a few hundred neurons, a fly is capable of aerial acrobatics beyond what the most sophisticated flying machine can achieve. By exploiting this idea, which consists of extracting simple concepts from neuroethology studies, [7] opens new perspectives in vision, based on the human ability to quickly select intrinsically salient targets in a visual scene: an ability which is fundamental for swift decision-making processes in unpredictable and unknown circumstances. Sensory?motor integration of animals, even the simplest ones, also presents many interesting sources of knowledge for control engineering. The nervous system integrates the information necessary to link perception to action. The active collaboration between roboticists and neurobiologists has already lead to transposition of the functional role of the lamprey's spinal cord into command algorithms for swimming robots (see again [1]). Two other cases of such fruitful collaborations are illustrated in [8] and [9]. These last two papers give a complementary point of view to the bio-inspired approach when applied to higher levels of autonomy. In particular one of the crucial problems of the collaboration between roboticists and neurobiologists is that brains and computers do not use the same principle to encode information. In this regard, [8] presents an interface which encodes sensory data from a humanoid robot into spikes and decodes spikes into motor commands that are sent to the robot. Finally, this issue ends with a biologically inspired navigation system for the mobile rat-like robot named Psikharpax, allowing self-localization and autonomous navigation in an initially unknown environment [9]. This last article represents the highest level (from body to cognition) of bio-inspiration and also completes the picture initiated with the Lampetra robot depicted in the first article. Finally, we are confident that this issue can represent a nice set of new ideas and research references and we really hope that readers enjoy the result of this effort. References [1] Stefanini C, Orofino S, Manfredi L, Mintchev S, Marrazza S, Assaf T, Capantini L, Sinibaldi E, Grillner S, Wall?n P and Dario P 2012 A novel autonomous, bioinspired swimming robot developed by neuroscientists and bioengineers Bioinspir. Biomim. 7 025001 [2] Senda K, Obara T, Kitamura M and Yokoyama N 2012 Effects of structural flexibility of wings in flapping flight of butterfly Bioinspir. Biomim. 7 025002 [3] de Croon G C H E, Groen M A, De Wagter C, Remes B, Ruijsink R and van Oudheusden B W 2012 Design, aerodynamics and autonomy of the DelFly Bioinspir. Biomim. 7 025003 [4] Margheri L, Laschi C and Mazzolai B 2012 Soft robotic arm inspired by the octopus: I. From biological functions to artificial requirements Bioinspir. Biomim. 7 025004 [5] Mazzolai B, Margheri L, Cianchetti M, Dario P and Laschi C 2012 Soft robotic arm inspired by the octopus. II. From artificial requirements to innovative technological solutions Bioinspir. Biomim. 7 025005 [6] Renda F, Cianchetti M, Giorelli M, Arienti A and Laschi C 2012 A 3D Steady-state model of a tendon-driven continuum soft manipulator inspired by the octopus arm Bioinspir. Biomim. 7 025006 [7] Schiavone G, Izzo F, Simoes L F and de Croon G C H E 2012 Autonomous spacecraft landing through human pre-attentive vision Bioinspir. Biomim. 7 025007 [8] Gamez D, Fidjeland A K and Lazdins E 2012 iSpike: A spiking neural interface for the iCub robot Bioinspir. Biomim. 7 025008 [9] Caluwaerts K, Staffa M, N'Guyen S, Grand C, Dolle L, Favre-Felix A, Girard B and Khamassi M 2012 A biologically inspired meta-control navigation system for the Psikharpax rat robot Bioinspir. Biomim. 7 025009

[ J. R. Soc. Interface 9 , 1093–1099 (2012; Published online 9 November 2011) ([doi:10.1098/rsif.2011.0608][2])][2] In our recently published article, we stated in the Abstract that ‘Tangential speeds and accelerations of the trunk and tail were roughly similar in aerial and non-aerial shakes

Objectives: To conduct a systematic survey of published techniques for automated diagnosis and prognosis of COVID-19 diseases using medical imaging, assessing the validity of reported performance and investigating the proposed clinical use-case. To conduct a scoping review into the authors publishing such work. Methods: The Scopus database was queried and studies were screened for article type, and minimum source normalized impact per paper and citations, before manual relevance assessment and a bias assessment derived from a subset of the Checklist for Artificial Intelligence in Medical Imaging (CLAIM). The number of failures of the full CLAIM was adopted as a surrogate for risk-of-bias. Methodological and performance measurements were collected from each technique. Each study was assessed by one author. Comparisons were evaluated for significance with a two-sided independent t-test. Findings: Of 1002 studies identified, 390 remained after screening and 81 after relevance and bias exclusion. The ratio of exclusion for bias was 71%, indicative of a high level of bias in the field. The mean number of CLAIM failures per study was 8.3 ± 3.9 [1,17] (mean ± standard deviation [min,max]). 58% of methods performed diagnosis versus 31% prognosis. Of the diagnostic methods, 38% differentiated COVID-19 from healthy controls. For diagnostic techniques, area under the receiver operating curve (AUC) = 0.924 ± 0.074 [0.810,0.991] and accuracy = 91.7% ± 6.4 [79.0,99.0]. For prognostic techniques, AUC = 0.836 ± 0.126 [0.605,0.980] and accuracy = 78.4% ± 9.4 [62.5,98.0]. CLAIM failures did not correlate with performance, providing confidence that the highest results were not driven by biased papers. Deep learning techniques reported higher AUC (p

Since the outbreak of the COVID-19 pandemic, computer vision researchers have been working on automatic identification of this disease using radiological images. The results achieved by automatic classification methods far exceed those of human specialists, with sensitivity as high as 100% being reported. However, prestigious radiology societies have stated that the use of this type of imaging alone is not recommended as a diagnostic method. According to some experts the patterns presented in these images are unspecific and subtle, overlapping with other viral pneumonias. This report seeks to evaluate the analysis the robustness and generalizability of different approaches using artificial intelligence, deep learning and computer vision to identify COVID-19 using chest X-rays images. We also seek to alert researchers and reviewers to the issue of "shortcut learning". Recommendations are presented to identify whether COVID-19 automatic classification models are being affected by shortcut learning. Firstly, papers using explainable artificial intelligence methods are reviewed. The results of applying external validation sets are evaluated to determine the generalizability of these methods. Finally, studies that apply traditional computer vision methods to perform the same task are considered. It is evident that using the whole chest X-Ray image or the bounding box of the lungs, the image regions that contribute most to the classification appear outside of the lung region, something that is not likely possible. In addition, although the investigations that evaluated their models on data sets external to the training set, the effectiveness of these models decreased significantly, it may provide a more realistic representation as how the model will perform in the clinic. The results indicate that, so far, the existing models often involve shortcut learning, which makes their use less appropriate in the clinical setting.

COVID-19 is an infectious disease, which has adversely affected public health and the economy across the world. On account of the highly infectious nature of the disease, rapid automated diagnosis of COVID-19 is urgently needed. A few recent findings suggest that chest X-rays and CT scans can be used by machine learning for the diagnosis of COVID-19. Herein, we employed semi-supervised learning (SSL) approaches to detect COVID-19 cases accurately by analyzing digital chest X-rays and CT scans. On a relatively small COVID-19 radiography dataset, which contains only 219 COVID-19 positive images, 1341 normal and 1345 viral pneumonia images, our algorithm, COVIDCon, which takes advantage of data augmentation, consistency regularization, and multicontrastive learning, attains 97.07% average class prediction accuracy, with 1000 labeled images, which is 7.65% better than the next best SSL method, virtual adversarial training. COVIDCon performs even better on a larger COVID-19 CT Scan dataset that contains 82,767 images. It achieved an excellent accuracy of 99.13%, at 20,000 labels, which is 6.45% better than the next best pseudo-labeling approach. COVIDCon outperforms other state-of-the-art algorithms at every label that we have investigated. These results demonstrate COVIDCon as the benchmark SSL algorithm for potential diagnosis of COVID-19 from chest X-rays and CT-Scans. Furthermore, COVIDCon performs exceptionally well in identifying COVID-19 positive cases from a completely unseen repository with a confirmed COVID-19 case history. COVIDCon, may provide a fast, accurate, and reliable method for screening COVID-19 patients.

Tuberculosis (TB) remains one of the major health problems in modern times with a high mortality rate. While efforts are being made to make early diagnosis accessible and more reliable in high burden TB countries, digital chest radiography has become a popular source for this purpose. However, the screening process requires expert radiologists which may be a potential barrier in developing countries. A fully automatic computer-aided diagnosis system can reduce the need of trained personnel for early diagnosis of TB using chest X-ray images. In this paper, we have proposed a novel TB detection technique that combines hand-crafted features with deep features (convolutional neural network-based) through Ensemble Learning. Handcrafted features were extracted via Gabor Filter and deep features were extracted via pre-trained deep learning models. Two publicly available datasets namely (i) Montgomery and (ii) Shenzhen were used to evaluate the proposed system. The proposed methodology was validated with a k-fold cross-validation scheme. The area under receiver operating characteristics curves of 0.99 and 0.97 were achieved for Shenzhen and Montgomery datasets respectively which shows the superiority of the proposed scheme.

According to the World Health Organization (WHO), novel coronavirus (COVID-19) is an infectious disease and has a significant social and economic impact. The main challenge in fighting against this disease is its scale. Due to the outbreak, medical facilities are under pressure due to case numbers. A quick diagnosis system is required to address these challenges. To this end, a stochastic deep learning model is proposed. The main idea is to constrain the deep-representations over a Gaussian prior to reinforce the discriminability in feature space. The model can work on chest X-ray or CT-scan images. It provides a fast diagnosis of COVID-19 and can scale seamlessly. The work presents a comprehensive evaluation of previously proposed approaches for X-ray based disease diagnosis. The approach works by learning a latent space over X-ray image distribution from the ensemble of state-of-the-art convolutional-nets, and then linearly regressing the predictions from an ensemble of classifiers which take the latent vector as input. We experimented with publicly available datasets having three classes: COVID-19, normal and pneumonia yielding an overall accuracy and AUC of 0.91 and 0.97, respectively. Moreover, for robust evaluation, experiments were performed on a large chest X-ray dataset to classify among Atelectasis, Effusion, Infiltration, Nodule, and Pneumonia classes. The results demonstrate that the proposed model has better understanding of the X-ray images which make the network more generic to be later used with other domains of medical image analysis.

The COVID-19 pandemic has generated the need to evolve health services to reduce the risk of contagion and promote a collaborative environment even remotely. Advances in Industry 4.0, including the internet of things, mobile networks, cloud computing, and artificial intelligence make Health 4.0 possible to connect patients with healthcare professionals. Hence, the focus of this work is analyzing the potentiality, and challenges of state-of-the-art Health 4.0 applications to face the COVID-19 pandemic including augmented environments, diagnosis of the virus, forecasts, medical robotics, and remote clinical services. It is concluded that Health 4.0 can be applied in the prevention of contagion, improve diagnosis, promote virtual learning environments, and offer remote services. However, there are still ethical, technical, security, and legal challenges to be addressed. Additionally, more imaging datasets for COVID-19 detection need to be made available to the scientific community. Working in the areas of opportunity will help to address the new normal. Likewise, Health 4.0 can be applied not only in the COVID-19 pandemic, but also in future global viruses and natural disasters.

Assessing the current Artificial intelligence (AI) situation is a crucial step towards its implementation into radiology practice. The study aimed to assess radiographer willingness to accept AI in radiology work practice and the impact of AI in work performance. An exploratory cross-sectional online survey conducted for radiographers working within the Middle East and India was conducted from May–August 2020. A previously validated survey used to obtain radiographer's demographics, knowledge, perceptions, organization readiness, and challenges of integrating AI into radiology. The survey was accessible for radiographers and distributed through the societies page. The survey was completed by 549 radiographers distributed as (77.6%, n = 426) from the Middle East while (22.4%, n = 123) from India. A majority (86%, n = 773) agreed that AI currently plays an important role in radiology and (88.0%, n = 483) expected that AI would play a role in radiology practice and image production. The challenges for AI implementation in practice were developing AI skills (42.8%, n = 235) and AI knowledge development (37.0%, n = 203). Participants showed high interest to integrate AI in under and postgraduate curriculum. There is excitement about what AI could offer, but education input is a requirement. Fears are expressed about job security and how radiology may work across all ages and educational backgrounds. Radiographers become aware of AI role and challenges, which can be improved by education and training.

For advanced tongue cancer, the choice between surgery and organ-sparing treatment is often dependent on the expected loss of tongue functionality after treatment. Biomechanical models might assist in this choice by simulating the post-treatment function loss. However, this function loss varies between patients and should, therefore, be predicted for each patient individually. In the present study, the goal was to better predict the postoperative range of motion (ROM) of the tongue by personalizing biomechanical models using diffusion-weighted MRI and constrained spherical deconvolution reconstructions of tongue muscle architecture. Diffusion-weighted MRI scans of ten healthy volunteers were obtained to reconstruct their tongue musculature, which were subsequently registered to a previously described population average or atlas. Using the displacement fields obtained from the registration, the segmented muscle fiber tracks from the atlas were morphed back to create personalized muscle fiber tracks. Finite element models were created from the fiber tracks of the atlas and those of the individual tongues. Via inverse simulation of a protruding, downward, left and right movement, the ROM of the tongue was predicted. This prediction was compared to the ROM measured with a 3D camera. It was demonstrated that biomechanical models with personalized muscles bundles are better in approaching the measured ROM than a generic model. However, to achieve this result a correction factor was needed to compensate for the small magnitude of motion of the model. Future versions of these models may have the potential to improve the estimation of function loss after treatment for advanced tongue cancer.

Modern bioprocess development employs statistically optimized design of experiments (DOE) and regression modeling to find optimal bioprocess set points. Using modeling software, such as JMP Pro, it is possible to leverage artificial neural networks (ANNs) to improve model accuracy beyond the capabilities of regression models. Herein, we bridge the gap between a DOE skill set and a machine learning skill set by demonstrating a novel use of DOE to systematically create and evaluate ANN architecture using JMP Pro software. Additionally, we run a mammalian cell culture process at historical, one factor at a time, standard least squares regression, and ANN-derived set points. This case study demonstrates the significant differences between one factor at a time bioprocess development, DOE bioprocess development and the relative power of linear regression versus an ANN-DOE hybrid modeling approach. Supplementary Information The online version contains supplementary material available at 10.1007/s00449-021-02529-3.

General practice in the United Kingdom has been using electronic health records for over two decades, but coding clinical information remains poor. Lack of interest and training are considerable barriers preventing code use levels improvement. Tailored training could be the way forward, to break barriers in the uptake of coding; to do so it is paramount to understand coding use of the particular clinicians, to recognise their needs. It should be possible to easily assess text quantity and quality in medical consultations. A tool to measure these parameters, which could be used to tailor training needs and assess change, is demonstrated. The tool is presented and a preliminary study using a randomised sample of five recent consultations from thirteen different clinicians is used as an example. The tool, based on using a word processor and a spread-sheet, allowed quantitative analysis among clinicians while word clouds permitted a qualitative comparison between coded and free text. The average amount of free text per consultation was 68.2 words, (ranging from 25.4 and 130.2 among clinicians); an average of 6% of the text was coded (ranging from 0 to 13%). Patterns among clinicians could be identified. Using Word cloud, a different text use was demonstrated depending on its purpose. Some free text could be turned into code but nomenclature probably prevented some of the codings, like the expression of time. This proof of concept demonstrated that it is possible to calculate what percentage of consultations are coded and what codes are used. This allowed understanding clinicians’ preferences; training needs and gaps in nomenclature.

The application of non-destructive process analytical technologies in the area of food science got a lot of attention the past years. In this work we used hyperspectral imaging to detect mould on milk agar and cheese. Principal component analysis is applied to hyperspectral data to localise and visualise mycelia on the samples’ surface. It is also shown that the PCA loadings obtained from a set of training samples can be applied to hyperspectral data from new test samples to detect the presence of mould on these. For both the agar and cheeselets, the first three principal components contained more than 99 % of the total variance. The spatial projection of the second principal component highlights the presence of mould on cheeselets. The proposed analysis methods can be adopted in industry to detect mould on cheeselets at an early stage and with further testing this application may also be extended to other food products., Graphical abstract Image 1, Highlights • Hyperspectral imaging can be used for non-destructive analysis of contamination in food products. • Principal component analysis (PCA) was applied to milk agar and cheeselet samples to localise and visualise mould growing on the samples. • The results from PCA applied to hyperspectral data shows that the technique can be used to identify and localise growth of mould on food samples.

Early risk assessments and interventions for metabolic syndrome (MetS) are limited because of a lack of effective biomarkers. In the present study, several candidate genes were selected as a blood-based transcriptomic signature for MetS. We collected so far the largest MetS-associated peripheral blood high-throughput transcriptomics data and put forward a novel feature selection strategy by combining weighted gene co-expression network analysis, protein-protein interaction network analysis, LASSO regression and random forest approaches. Two gene modules and 51 hub genes as well as a 9-hub-gene signature associated with metabolic syndrome were identified. Then, based on this 9-hub-gene signature, we performed logistic analysis and subsequently established a web nomogram calculator for metabolic syndrome risk (https://xjtulgz.shinyapps.io/DynNomapp/). This 9-hub-gene signature showed excellent classification and calibration performance (AUC = 0.968 in training set, AUC = 0.883 in internal validation set, AUC = 0.861 in external validation set) as well as ideal potential clinical benefit.

Coronavirus disease 2019 (COVID-19) is a major threat throughout the world. The latest advancements in the field of computational techniques based on Artificial Intelligence (AI), Machine Learning (ML) and Big Data can help in detecting, monitoring and forecasting the severity of the COVID-19 pandemic. We aim to review the detection of the COVID-19 pandemic empowered by AI, major implications, challenges and the future of smart health care at a glance. The AI plays a pioneering role in rapid and improved detection of the disease. It helps in modeling the disease activity and predicting the severity for better decision making and preparedness by healthcare authorities and policymakers. It is a promising technology for automatic and fully transparent monitoring system to track and treat the patients remotely without spreading the virus to others. The future application areas of AI-based healthcare are also identified. The role of AI in tackling the COVID-19 pandemic is reviewed in this paper. AI proves beneficial in early detection with improved results. It also provides solution for contact tracing, prediction, drug development thus reducing the workload of medical industry.

As expenditure on drug development increases exponentially, the overall drug discovery process requires a sustainable revolution. Since artificial intelligence (AI) is leading the fourth industrial revolution, AI can be considered as a viable solution for unstable drug research and development. Generally, AI is applied to fields with sufficient data such as computer vision and natural language processing, but there are many efforts to revolutionize the existing drug discovery process by applying AI. This review provides a comprehensive, organized summary of the recent research trends in AI-guided drug discovery process including target identification, hit identification, ADMET prediction, lead optimization, and drug repositioning. The main data sources in each field are also summarized in this review. In addition, an in-depth analysis of the remaining challenges and limitations will be provided, and proposals for promising future directions in each of the aforementioned areas.

An exponential rise in patient data provides an excellent opportunity to improve the existing health care infrastructure. In the present work, a method to enable cardiovascular digital twin is proposed using inverse analysis. Conventionally, accurate analytical solutions for inverse analysis in linear problems have been proposed and used. However, these methods fail or are not efficient for nonlinear systems, such as blood flow in the cardiovascular system (systemic circulation) that involves high degree of nonlinearity. To address this, a methodology for inverse analysis using recurrent neural network for the cardiovascular system is proposed in this work, using a virtual patient database. Blood pressure waveforms in various vessels of the body are inversely calculated with the help of long short-term memory (LSTM) cells by inputting pressure waveforms from three non-invasively accessible blood vessels (carotid, femoral and brachial arteries). The inverse analysis system built this way is applied to the detection of abdominal aortic aneurysm (AAA) and its severity using neural networks.

Finite element head (FE) models are important numerical tools to study head injuries and develop protection systems. The generation of anatomically accurate and subject-specific head models with conforming hexahedral meshes remains a significant challenge. The focus of this study is to present two developmental works: first, an anatomically detailed FE head model with conforming hexahedral meshes that has smooth interfaces between the brain and the cerebrospinal fluid, embedded with white matter (WM) fiber tracts; second, a morphing approach for subject-specific head model generation via a new hierarchical image registration pipeline integrating Demons and Dramms deformable registration algorithms. The performance of the head model is evaluated by comparing model predictions with experimental data of brain–skull relative motion, brain strain, and intracranial pressure. To demonstrate the applicability of the head model and the pipeline, six subject-specific head models of largely varying intracranial volume and shape are generated, incorporated with subject-specific WM fiber tracts. DICE similarity coefficients for cranial, brain mask, local brain regions, and lateral ventricles are calculated to evaluate personalization accuracy, demonstrating the efficiency of the pipeline in generating detailed subject-specific head models achieving satisfactory element quality without further mesh repairing. The six head models are then subjected to the same concussive loading to study the sensitivity of brain strain to inter-subject variability of the brain and WM fiber morphology. The simulation results show significant differences in maximum principal strain and axonal strain in local brain regions (one-way ANOVA test, p

In recent years, the incidence of lung cancer has been increasing. Lung cancer detection is based on computed tomography (CT) imaging of the lung area to determine whether there are pulmonary nodules. And then judge what’s good and what’s bad. However, due to the traditional way of manual reading and lack of experience and other problems. This leads to visual fatigue and misdiagnosis and missed diagnosis. In order to detect pulmonary nodules early and accurately, a new assistant diagnosis method for pulmonary nodules is proposed. Firstly, the image is preprocessed and denoised by median filter, the lung parenchyma is segmented by random walk algorithm and the region of interest is extracted, and then, according to the continuity of the CT slices, the texture feature extraction method of pulmonary nodules based on volume local direction ternary pattern is used to extract the features. Finally, the pulmonary nodules are identified and classified by the assistant diagnosis model of pulmonary nodules based on Stacking algorithm. In order to illustrate the validity of the diagnosis model, the experiments are carried out by cross-validation of ten folds. Experiments using data from LIDC database show that the accuracy, sensitivity and specificity of the proposed method are 82.2%, 85.7%, and 78.8%, respectively. Texture Recognition method based on volume vocal direction ternary pattern is feasible for the identification of pulmonary nodules and provides a reference value for doctor-assisted diagnosis., GRAPHICAL ABSTRACT

For the existing medical image edge detection algorithm image reconstruction accuracy is not high, the fitness of optimization coefficient is low, resulting in the detection results of low information recall, poor smoothness and low detection accuracy, we proposes an edge detection algorithm of cancer image based on deep learning. Firstly, the three-dimensional surface structure reconstruction model of cancer image was constructed. Secondly, the edge contour feature extraction method was used to extract the fine-grained features of cancer cells in the cancer image. Finally, the multi-dimensional pixel feature distributed recombination model of cancer image was constructed, and the fine-grained feature segmentation method was adopted to realize regional fusion and information recombination, and the ultra-fine particle feature was extracted. The adaptive optimization of edge detection was realized by combining with deep learning algorithm. The adaptive optimization in the process of edge detection was realized by combining with the deep learning algorithm. The experimental results show that the three-dimensional reconstruction accuracy of the proposed algorithm is about 95%, the fitness of the optimization coefficient is high, the algorithm has a strong edge information detection ability, and the output result smoothness and the accuracy of edge feature detection are high, which can effectively realize the detection of cancer image edge., GRAPHICAL ABSTRACT

Knee Osteoarthritis (ΚΟΑ) is a degenerative joint disease of the knee that results from the progressive loss of cartilage. Due to KOA’s multifactorial nature and the poor understanding of its pathophysiology, there is a need for reliable tools that will reduce diagnostic errors made by clinicians. The existence of public databases has facilitated the advent of advanced analytics in KOA research however the heterogeneity of the available data along with the observed high feature dimensionality make this diagnosis task difficult. The objective of the present study is to provide a robust Feature Selection (FS) methodology that could: (i) handle the multidimensional nature of the available datasets and (ii) alleviate the defectiveness of existing feature selection techniques towards the identification of important risk factors which contribute to KOA diagnosis. For this aim, we used multidisciplinary data obtained from the Osteoarthritis Initiative database for individuals without or with KOA. The proposed fuzzy ensemble feature selection methodology aggregates the results of several FS algorithms (filter, wrapper and embedded ones) based on fuzzy logic. The effectiveness of the proposed methodology was evaluated using an extensive experimental setup that involved multiple competing FS algorithms and several well-known ML models. A 73.55 % classification accuracy was achieved by the best performing model (Random Forest classifier) on a group of twenty-one selected risk factors. Explainability analysis was finally performed to quantify the impact of the selected features on the model’s output thus enhancing our understanding of the rationale behind the decision-making mechanism of the best model.

The highly contagious nature of Coronavirus disease 2019 (Covid-19) resulted in a global pandemic. Due to the relatively slow and taxing nature of conventional testing for Covid-19, a faster method needs to be in place. The current researches have suggested that visible irregularities found in the chest X-ray of Covid-19 positive patients are indicative of the presence of the disease. Hence, Deep Learning and Image Classification techniques can be employed to learn from these irregularities, and classify accordingly with high accuracy. This research presents an approach to create a classifier model named StackNet-DenVIS which is designed to act as a screening process before conducting the existing swab tests. Using a novel approach, which incorporates Transfer Learning and Stacked Generalization, the model aims to lower the False Negative rate of classification compensating for the 30% False Negative rate of the swab tests. A dataset gathered from multiple reliable sources consisting of 9953 Chest X-rays (868 Covid and 9085 Non-Covid) was used. Also, this research demonstrates handling data imbalance using various techniques involving Generative Adversarial Networks and sampling techniques. The accuracy, sensitivity, and specificity obtained on our proposed model were 95.07%, 99.40% and 94.61% respectively. To the best of our knowledge, the combination of accuracy and false negative rate obtained by this paper outperforms the current implementations. We must also highlight that our proposed architecture also considers other types of viral pneumonia. Given the unprecedented sensitivity of our model we are optimistic it contributes to a better Covid-19 detection.

With the development of modern chemical synthesis technology, toxic and harmful compounds increase sharply. In order to improve the removal efficiency of refractory organic matter in waste water, the method of adding powdered activated carbon (PAC) to the system for adsorption was adopted. Through the analysis of organic matter removal rule before and after waste water treatment, it can be found that PAC is easy to adsorb hydrophobic organic matter, while activated sludge is easy to remove hydrophilic and weakly hydrophobic neutral organic matter. Powdered activated carbon-activated sludge SBR system (PAC-AS) system is obviously superior to AS and PAC system in removing organic matter of hydrophilic and hydrophobic components, that is, biodegradation and PAC adsorption are additive. Compared with the control system, the Chemical Oxygen Demand (COD) removal rate of refractory substances increased by 8.36%, and PAC had a good adsorption effect on small molecular weight organic compounds, but with the increase of molecular weight of organic compounds, the adsorption effect of PAC gradually weakened, and it had no adsorption effect on macromolecular organic compounds. Based on the research of fuzzy control theory, an Agent control system for ozone oxidation process of industrial waste water based on Mobile Agent Server (MAS) theory was established, which was realized by fuzzy control method. The simulation results showed strong stability and verified the feasibility and adaptability of the distributed intelligent waste water treatment system based on MAS theory in the actual control process.

Background With advances in science and technology, biotechnology is becoming more accessible to people of all demographics. These advances inevitably hold the promise to improve personal and population well-being and welfare substantially. It is paradoxical that while greater access to biotechnology on a population level has many advantages, it may also increase the likelihood and frequency of biodisasters due to accidental or malicious use. Similar to “Disease X” (describing unknown naturally emerging pathogenic diseases with a pandemic potential), we term this unknown risk from biotechnologies “Biodisaster X.” To date, no studies have examined the potential role of information technologies in preventing and mitigating Biodisaster X. Objective This study aimed to explore (1) what Biodisaster X might entail and (2) solutions that use artificial intelligence (AI) and emerging 6G technologies to help monitor and manage Biodisaster X threats. Methods A review of the literature on applying AI and 6G technologies for monitoring and managing biodisasters was conducted on PubMed, using articles published from database inception through to November 16, 2020. Results Our findings show that Biodisaster X has the potential to upend lives and livelihoods and destroy economies, essentially posing a looming risk for civilizations worldwide. To shed light on Biodisaster X threats, we detailed effective AI and 6G-enabled strategies, ranging from natural language processing to deep learning–based image analysis to address issues ranging from early Biodisaster X detection (eg, identification of suspicious behaviors), remote design and development of pharmaceuticals (eg, treatment development), and public health interventions (eg, reactive shelter-at-home mandate enforcement), as well as disaster recovery (eg, sentiment analysis of social media posts to shed light on the public’s feelings and readiness for recovery building). Conclusions Biodisaster X is a looming but avoidable catastrophe. Considering the potential human and economic consequences Biodisaster X could cause, actions that can effectively monitor and manage Biodisaster X threats must be taken promptly and proactively. Rather than solely depending on overstretched professional attention of health experts and government officials, it is perhaps more cost-effective and practical to deploy technology-based solutions to prevent and control Biodisaster X threats. This study discusses what Biodisaster X could entail and emphasizes the importance of monitoring and managing Biodisaster X threats by AI techniques and 6G technologies. Future studies could explore how the convergence of AI and 6G systems may further advance the preparedness for high-impact, less likely events beyond Biodisaster X.

This study presents an application of machine learning (ML) methods for detecting the presence of stenoses and aneurysms in the human arterial system. Four major forms of arterial disease -- carotid artery stenosis (CAS), subclavian artery stenosis (SAC), peripheral arterial disease (PAD), and abdominal aortic aneurysms (AAA) -- are considered. The ML methods are trained and tested on a physiologically realistic virtual patient database (VPD) containing 28,868 healthy subjects, which is adapted from the authors previous work and augmented to include the four disease forms. Six ML methods -- Naive Bayes, Logistic Regression, Support Vector Machine, Multi-layer Perceptron, Random Forests, and Gradient Boosting -- are compared with respect to classification accuracies and it is found that the tree-based methods of Random Forest and Gradient Boosting outperform other approaches. The performance of ML methods is quantified through the F1 score and computation of sensitivities and specificities. When using all the six measurements, it is found that maximum F1 scores larger than 0.9 are achieved for CAS and PAD, larger than 0.85 for SAS, and larger than 0.98 for both low- and high-severity AAAs. Corresponding sensitivities and specificities are larger than 90% for CAS and PAD, larger than 85% for SAS, and larger than 98% for both low- and high-severity AAAs. When reducing the number of measurements, it is found that the performance is degraded by less than 5% when three measurements are used, and less than 10% when only two measurements are used for classification. For AAA, it is shown that F1 scores larger than 0.85 and corresponding sensitivities and specificities larger than 85% are achievable when using only a single measurement. The results are encouraging to pursue AAA monitoring and screening through wearable devices which can reliably measure pressure or flow-rates, Changelog: Added a bullet point in the discussion (end of section 3.3)

The structure of the human musculo-skeletal systems shows complex passive dynamic properties, critical for adaptive grasping and motions. Through wrist and arm actuation, these passive dynamic properties can be exploited to achieve nuanced and diverse environment interactions. We have developed a passive anthropomorphic robot hand that shows complex passive dynamics. We require arm/wrist control with the ability to exploit these. Due to the soft hand structures and high degrees of freedom during passive-object interactions, bespoke generation of wrist trajectories is challenging. We propose a new approach, which takes existing wrist trajectories and adapts them to changes in the environment, through analysis and classification of the interactions. By analysing the interactions between the passive hand and object, the required wrist motions to achieve them can be mapped back to control of the hand. This allows the creation of trajectories which are parameterized by object size or task. This approach shows up to 86% improvement in grasping success rate with a passive hand for object size changes up to +/-50%., EPSRC Doctoral Training Programme Studentship and Arm Ltd (RG99055).

Root cause analysis (RCA) is one of the most prominent tools used to comprehensively evaluate a biopharmaceutical production process. Despite of its widespread use in industry, the Food and Drug Administration has observed a lot of unsuitable approaches for RCAs within the last years. The reasons for those unsuitable approaches are the use of incorrect variables during the analysis and the lack in process understanding, which impede correct model interpretation. Two major approaches to perform RCAs are currently dominating the chemical and pharmaceutical industry: raw data analysis and feature-based approach. Both techniques are shown to be able to identify the significant variables causing the variance of the response. Although they are different in data unfolding, the same tools as principal component analysis and partial least square regression are used in both concepts. Within this article we demonstrate the strength and weaknesses of both approaches. We proved that a fusion of both results in a comprehensive and effective workflow, which not only increases better process understanding. We demonstrate this workflow along with an example. Hence, the presented workflow allows to save analysis time and to reduce the effort of data mining by easy detection of the most important variables within the given dataset. Subsequently, the final obtained process knowledge can be translated into new hypotheses, which can be tested experimentally and thereby lead to effectively improving process robustness.

Motivation High-throughput gene expression can be used to address a wide range of fundamental biological problems, but datasets of an appropriate size are often unavailable. Moreover, existing transcriptomics simulators have been criticized because they fail to emulate key properties of gene expression data. In this article, we develop a method based on a conditional generative adversarial network to generate realistic transcriptomics data for Escherichia coli and humans. We assess the performance of our approach across several tissues and cancer-types. Results We show that our model preserves several gene expression properties significantly better than widely used simulators, such as SynTReN or GeneNetWeaver. The synthetic data preserve tissue- and cancer-specific properties of transcriptomics data. Moreover, it exhibits real gene clusters and ontologies both at local and global scales, suggesting that the model learns to approximate the gene expression manifold in a biologically meaningful way. Availability and implementation Code is available at: https://github.com/rvinas/adversarial-gene-expression. Supplementary information Supplementary data are available at Bioinformatics online.

Spectral and VOCs data are important to determine the genuineness of the EVOO. The aim of this work is to apply an open-source device for VIS–NIR spectrophotometric measurements and a VOCs analyzer to identify some types of sophistication. 96 samples were analyzed. Samples included pure EVOO compound olive oil pure seed oils and olive oil samples adulterated with 7 different seed oils at different ratios. An artificial intelligence model was applied to identify adulterations from the spectral and VOCs data. The models built on both spectral and VOCs data showed perfect classification of pure EVOO samples with respect to sophisticated ones in both model and test sets. The most important spectral values and VOCs were extracted. Artificial intelligence applicative models aimed not only to identify sophisticated samples but also to understand the most informative spectra and VOCs to prototype specific devices for anti-fraud control.

Motivation Protein fold recognition is a key step for template-based modeling approaches to protein structure prediction. Although closely related folds can be easily identified by sequence homology search in sequence databases, fold recognition is notoriously more difficult when it involves the identification of distantly related homologs. Recent progress in residue–residue contact and distance prediction opens up the possibility of improving fold recognition by using structural information contained in predicted distance and contact maps. Results Here we propose to use the congruence coefficient as a metric of similarity between maps. We prove that this metric has several interesting mathematical properties which allow one to compute in polynomial time its exact mean and variance over all possible (exponentially many) alignments between two symmetric matrices, and assess the statistical significance of similarity between aligned maps. We perform fold recognition tests by recovering predicted target contact/distance maps from the two most recent Critical Assessment of Structure Prediction editions and over 27 000 non-homologous structural templates from the ECOD database. On this large benchmark, we compare fold recognition performances of different alignment tools with their own similarity scores against those obtained using the congruence coefficient. We show that the congruence coefficient overall improves fold recognition over other methods, proving its effectiveness as a general similarity metric for protein map comparison. Availability and implementation The congruence coefficient software CCpro is available as part of the SCRATCH suite at: http://scratch.proteomics.ics.uci.edu/. Supplementary information Supplementary data are available at Bioinformatics online.

The novel Coronavirus disease (COVID-19), which first appeared at the end of December 2019, continues to spread rapidly in most countries of the world. Respiratory infections occur primarily in the majority of patients treated with COVID-19. In light of the growing number of COVID-19 cases, the need for diagnostic tools to identify COVID-19 infection at early stages is of vital importance. For decades, chest X-ray (CXR) technologies have proven their ability to accurately detect respiratory diseases. More recently, with the availability of COVID-19 CXR scans, deep learning algorithms have played a critical role in the healthcare arena by allowing radiologists to recognize COVID-19 patients from their CXR images. However, the majority of screening methods for COVID-19 reported in recent studies are based on 2D convolutional neural networks (CNNs). Although 3D CNNs are capable of capturing contextual information compared to their 2D counterparts, their use is limited due to their increased computational cost (i.e. requires much extra memory and much more computing power). In this study, a transfer learning-based hybrid 2D/3D CNN architecture for COVID-19 screening using CXRs has been developed. The proposed architecture consists of the incorporation of a pre-trained deep model (VGG16) and a shallow 3D CNN, combined with a depth-wise separable convolution layer and a spatial pyramid pooling module (SPP). Specifically, the depth-wise separable convolution helps to preserve the useful features while reducing the computational burden of the model. The SPP module is designed to extract multi-level representations from intermediate ones. Experimental results show that the proposed framework can achieve reasonable performances when evaluated on a collected dataset (3 classes to be predicted: COVID-19, Pneumonia, and Normal). Notably, it achieved a sensitivity of 98.33%, a specificity of 98.68% and an overall accuracy of 96.91.

Since the outbreak of the pandemic Coronavirus Disease 2019, the world is in search of novel non-invasive methods for safer and early detection of lung diseases. The pulmonary pathological symptoms reflected through the lung sound opens a possibility of detection through auscultation and of employing spectral, fractal, nonlinear time series and principal component analyses. Thirty-five signals of vesicular and expiratory wheezing breath sound, subjected to spectral analyses shows a clear distinction in terms of time duration, intensity, and the number of frequency components. An investigation of the dynamics of air molecules during respiration using phase portrait, Lyapunov exponent, sample entropy, fractal dimension, and Hurst exponent helps in understanding the degree of complexity arising due to the presence of mucus secretions and constrictions in the respiratory airways. The feature extraction of the power spectral density data and the application of principal component analysis helps in distinguishing vesicular and expiratory wheezing and thereby, giving a ray of hope in accomplishing an early detection of pulmonary diseases through sound signal analysis.

The high frequency data in intensive care unit is flashed on a screen for a few seconds and never used again. However, this data can be used by machine learning and data mining techniques to predict patient outcomes. Learning finite-state transducers (FSTs) have been widely used in problems where sequences need to be manipulated and insertions, deletions and substitutions need to be modeled. In this paper, we learned the edit distance costs of a symbolic univariate time series representation through a stochastic finite-state transducer to predict patient outcomes in intensive care units. The Nearest-Neighbor method with these learned costs was used to classify the patient status within an hour after 10 h of data. Several experiments were developed to estimate the parameters that better fit the model regarding the prediction metrics. Our best results are compared with published works, where most of the metrics (i.e., Accuracy, Precision and F-measure) were improved.