Design and Implementation of Intelligent Truck Based on Azure Kinect

In recent years, due to the impact of COVID-19, the market prospect of non-contact handling has improved and the development potential is huge. This paper designs an intelligent truck based on Azure Kinect, which can save manpower and improve efficiency, and greatly reduce the infection risk of medical staff and community workers. The target object is visually recognized by Azure Kinect to obtain the center of mass of the target, and the GPS and Kalman filter are used to achieve accurate positioning. The 4-DOF robot arm is selected to grasp and transport the target object, so as to complete the non-contact handling work. In this paper, different shapes of objects are tested. The experiment shows that the system can accurately complete the positioning function, and the accuracy rate is 95.56%. The target object recognition is combined with the depth information to determine the distance, and the spatial coordinates of the object centroid are obtained in real time. The accuracy rate can reach 94.48%, and the target objects of different shapes can be recognized. When the target object is grasped by the robot arm, it can be grasped accurately according to the depth information, and the grasping rate reaches 92.67%. © 2023, ICST Institute for Computer Sciences, Social Informatics and Telecommunications Engineering.

An efficient computational protocol for template-based design of peptides that inhibit interactions involving SARS-CoV-2 proteins.

The RNA-dependent RNA polymerase (RdRp) complex of SARS-CoV-2 lies at the core of its replication and transcription processes. The interfaces between holo-RdRp subunits are highly conserved, facilitating the design of inhibitors with high affinity for the interaction interface hotspots. We, therefore, take this as a model protein complex for the application of a structural bioinformatics protocol to design peptides that inhibit RdRp complexation by preferential binding at the interface of its core subunit nonstructural protein, nsp12, with accessory factor nsp7. Here, the interaction hotspots of the nsp7-nsp12 subunit of RdRp, determined from a long molecular dynamics trajectory, are used as a template. A large library of peptide sequences constructed from multiple hotspot motifs of nsp12 is screened in-silico to determine sequences with high geometric complementarity and interaction specificity for the binding interface of nsp7 (target) in the complex. Two lead designed peptides are extensively characterized using orthogonal bioanalytical methods to determine their suitability for inhibition of RdRp complexation. Binding affinity of these peptides to accessory factor nsp7, determined using a surface plasmon resonance (SPR) assay, is slightly better than that of nsp12: dissociation constant of 133nM and 167nM, respectively, compared to 473nM for nsp12. A competitive ELISA is used to quantify inhibition of nsp7-nsp12 complexation, with one of the lead peptides giving an IC50 of 25µM . Cell penetrability and cytotoxicity are characterized using a cargo delivery assay and MTT cytotoxicity assay, respectively. Overall, this work presents a proof-of-concept of an approach for rational discovery of peptide inhibitors of SARS-CoV-2 protein-protein interactions.

Privacy-Preserving Fast Three-Factor Authentication and Key Agreement for IoT-Based E-Health Systems

Electronic healthcare (e-health) systems have received renewed interest, particularly in the current COVID-19 pandemic (e.g., lockdowns and changes in hospital policies due to the pandemic). However, ensuring security of both data-at-rest and data-in-transit remains challenging to achieve, particularly since data is collected and sent from less insecure devices (e.g., patients' wearable or home devices). While there have been a number of authentication schemes, such as those based on three-factor authentication, to provide authentication and privacy protection, a number of limitations associated with these schemes remain (e.g., (in)security or computationally expensive). In this study, we present a privacy-preserving three-factor authenticated key agreement scheme that is sufficiently lightweight for resource-constrained e-health systems. The proposed scheme enables both mutual authentication and session key negotiation in addition to privacy protection, with minimal computational cost. The security of the proposed scheme is demonstrated in the Real-or-Random model. Experiments using Raspberry Pi show that the proposed scheme achieves reduced computational cost (of up to 89.9% in comparison to three other related schemes).

Hypothesis of a potential antiviral drug

The approval of mRNA vaccine technique against COVID-19 opens a door to research and the creation of new drugs against different infectious pathologies or even cancer, since for several diseases the therapeutic options are limited, and different viral diseases are treated only symptomatically. For these reasons, this study proposed a hypothesis supported by biological studies, that it provides a theoretical basis for the possible development of a drug that used the mRNA technique and the ribonucleolytic action of a ribonuclease for a possible antiviral therapy, and analyzed a future perspective of this technique in order to provide a bibliographic basis on this hypothesis and motivate researchers to carry out biological studies on this topic.Copyright © 2022, Health Biotechnology and Biopharma. All rights reserved.

Modeling of SARS-CoV-2 Virus Proteins: Implications on Its Proteome.

COronaVIrus Disease 19 (COVID-19) is a severe acute respiratory syndrome (SARS) caused by a group of beta coronaviruses, SARS-CoV-2. The SARS-CoV-2 virus is similar to previous SARS- and MERS-causing strains and has infected nearly six hundred and fifty million people all over the globe, while the death toll has crossed the six million mark (as of December, 2022). In this chapter, we look at how computational modeling approaches of the viral proteins could help us understand the various processes in the viral life cycle inside the host, an understanding of which might provide key insights in mitigating this and future threats. This understanding helps us identify key targets for the purpose of drug discovery and vaccine development.

Ion-Imprinted Polymer Structurally Preorganized Using a Phenanthroline-Divinylbenzoate Complex with the Cu(II) Ion as Template and Some Adsorption Results.

The novel [Cuphen(VBA)2H2O] complex (phen: phenanthroline, VBA: vinylbenzoate) was prepared and used as a functional monomer to preorganize a new ion-imprinted polymer (IIP). By leaching the Cu(II) from the molecular imprinted polymer (MIP), [Cuphen(VBA)2H2O-co-EGDMA]n (EGDMA: ethylene glycol dimethacrylate), the IIP was obtained. A non-ion-imprinted polymer (NIIP) was also prepared. The crystal structure of the complex and some physicochemical, spectrophotometric techniques were also used for the MIP, IIP, and NIIP characterization. The results showed that the materials are nonsoluble in water and polar solvents, which are the main features of polymers. The surface area of the IIP is higher than the NIIP demonstrated by the blue methylene method. The SEM images show monoliths and particles smoothly packed together on spherical and prismatic-spherical surfaces in the morphology of MIP and IIP, respectively. Moreover, the MIP and IIP could be considered as mesoporous and microporous materials, shown by the size of the pores determined by the BET and BJH methods. Furthermore, the adsorption performance of the IIP was studied using copper(II) as a contaminant heavy metal. The maximum adsorption capacity of IIP was 287.45 mg/g at 1600 mg/L Cu2+ ions with 0.1 g of IIP at room temperature. The Freundlich model was found to best describe the equilibrium isotherm of the adsorption process. The competitive results indicate that the stability of the Cu-IIP complex is higher than the Ni-IIP complex with a selectivity coefficient of 1.61.

MLFW: A Database for Face Recognition on Masked Faces

As more and more people begin to wear masks due to current COVID-19 pandemic, existing face recognition systems may encounter severe performance degradation when recognizing masked faces. To figure out the impact of masks on face recognition model, we build a simple but effective tool to generate masked faces from unmasked faces automatically, and construct a new database called Masked LFW (MLFW) based on Cross-Age LFW (CALFW) database. The mask on the masked face generated by our method has good visual consistency with the original face. Moreover, we collect various mask templates, covering most of the common styles appeared in the daily life, to achieve diverse generation effects. Considering realistic scenarios, we design three kinds of combinations of face pairs. The recognition accuracy of SOTA models declines 5%–16% on MLFW database compared with the accuracy on the original images. MLFW database can be viewed and downloaded at http://whdeng.cn/mlfw. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Deletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes.

The analysis of deletions may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that SARS-CoV-2 has shown since its emergence. To understand the factors governing genomic stability, it is important to define the molecular mechanisms of deletions in the viral genome. In this work, we performed a statistical analysis of deletions. Specifically, we analyzed correlations between deletions in the SARS-CoV-2 genome and repetitive elements and documented a significant association of deletions with runs of identical (poly-) nucleotides and direct repeats. Our analyses of deletions in the accessory genes of SARS-CoV-2 suggested that there may be a hypervariability in ORF7A and ORF8 that is not associated with repetitive elements. Such recurrent search in a "sequence space" of accessory genes (that might be driven by natural selection) did not yet cause increased viability of the SARS-CoV-2 variants. However, deletions in the accessory genes may ultimately produce new variants that are more successful compared to the viral strains with the conventional architecture of the SARS-CoV-2 accessory genes.

A Template Matching Based Cough Detection Algorithm Using IMU Data From Earbuds

Coughing is a common symptom across different clinical conditions and has gained further relevance in the past years due to the COVID-19 pandemic. An automated cough detection for continuous health monitoring could be developed using Earbud, a wearable sensor platform with audio and inertial measurement unit (IMU) sensors. Though several previous works have investigated audio-based automated cough detection, audio-based methods can be highly power-consuming for wearable sensor applications and raise privacy concerns. In this work, we develop IMU-based cough detection using a template matching-based algorithm. IMU provides a low-power privacy-preserving solution to complement audio-based algorithms. Similarly, template matching has low computational and memory needs, suitable for on-device implementations. The proposed method uses feature transformation of IMU signal and unsupervised representative template selection to improve upon our previous work. We obtained an AUC (AUC-ROC) of 0.85 and 0.83 for cough detection in a lab-based dataset with 45 participants and a controlled free-living dataset with 15 participants, respectively. These represent an AUC improvement of 0.08 and 0.10 compared to the previous work. Additionally, we conducted an uncontrolled free-living study with 7 participants where continuous measurements over a week were obtained from each participant. Our cough detection method achieved an AUC of 0.85 in the study, indicating that the proposed IMU-based cough detection translates well to the varied challenging scenarios present in free-living conditions. © 2022 IEEE.

Unique Molecular Identifiers and Multiplexing Amplicons Maximize the Utility of Deep Sequencing To Critically Assess Population Diversity in RNA Viruses.

Next generation sequencing (NGS)/deep sequencing has become an important tool in the study of viruses. The use of unique molecular identifiers (UMI) can overcome the limitations of PCR errors and PCR-mediated recombination and reveal the true sampling depth of a viral population being sequenced in an NGS experiment. This approach of enhanced sequence data represents an ideal tool to study both high and low abundance drug resistance mutations and more generally to explore the genetic structure of viral populations. Central to the use of the UMI/Primer ID approach is the creation of a template consensus sequence (TCS) for each genome sequenced. Here we describe a series of experiments to validate several aspects of the Multiplexed Primer ID (MPID) sequencing approach using the MiSeq platform. We have evaluated how multiplexing of cDNA synthesis and amplicons affects the sampling depth of the viral population for each individual cDNA and amplicon to understand the relationship between broader genome coverage versus maximal sequencing depth. We have validated reproducibility of the MPID assay in the detection of minority mutations in viral genomes. We have also examined the determinants that allow sequencing reads of PCR recombinants to contaminate the final TCS data set and show how such contamination can be limited. Finally, we provide several examples where we have applied MPID to analyze features of minority variants and describe limits on their detection in viral populations of HIV-1 and SARS-CoV-2 to demonstrate the generalizable utility of this approach with any RNA virus.

A Mixed-Methods Evaluation of a Virtual Rehabilitation Program for Self-Management in Post-COVID-19 Syndrome (Long COVID).

Long COVID (LC) symptoms can be long standing, diverse and debilitating; comprehensive multidisciplinary rehabilitation programs are required to address this. A 10-week LC Virtual Rehabilitation Program (VRP) was developed to provide early education and self-management techniques to address the main symptoms of LC and was delivered to a group of persons with Long COVID (PwLC) online, facilitated by members of the multi-disciplinary rehabilitation team. This paper describes an evaluation of this VRP. Questionnaires completed by Healthcare Professionals (HCP) delivering the VRP were thematically analyzed to gain a priori themes and design semi-structured telephone interview questions for PwLC. Template analysis (TA) was used to analyze interview data. Routinely collected patient demographics and service data were also examined. Seventeen HCP survey responses were obtained and 38 PwLC telephone questionnaires were completed. The HCP interviews generated three a priori themes (1. Attendance and Availability, 2. Content, 3. Use of Digital Technology). TA was applied and three further themes emerged from the combined HCP and PwLC responses (4. Group Dynamics, 5. Individual Factors, 6. Internal Change). Key outcomes demonstrated that: the VRP was highly valued; digital delivery enabled self-management; barriers to attendance included work/life balance, use of technology, health inequalities; and LC was poorly understood by employers. Recommendations are provided for the design of VRPs for LC.

On the Origins of Omicron's Unique Spike Gene Insertion.

The emergence of a heavily mutated SARS-CoV-2 variant (Omicron; Pango lineage B.1.1.529 and BA sublineages) and its rapid spread to over 75 countries raised a global public health alarm. Characterizing the mutational profile of Omicron is necessary to interpret its clinical phenotypes which are shared with or distinctive from those of other SARS-CoV-2 variants. We compared the mutations of the initially circulating Omicron variant (now known as BA.1) with prior variants of concern (Alpha, Beta, Gamma, and Delta), variants of interest (Lambda, Mu, Eta, Iota, and Kappa), and ~1500 SARS-CoV-2 lineages constituting ~5.8 million SARS-CoV-2 genomes. Omicron's Spike protein harbors 26 amino acid mutations (23 substitutions, 2 deletions, and 1 insertion) that are distinct compared to other variants of concern. While the substitution and deletion mutations appeared in previous SARS-CoV-2 lineages, the insertion mutation (ins214EPE) was not previously observed in any other SARS-CoV-2 lineage. Here, we consider and discuss various mechanisms through which the nucleotide sequence encoding for ins214EPE could have been acquired, including local duplication, polymerase slippage, and template switching. Although we are not able to definitively determine the mechanism, we highlight the plausibility of template switching. Analysis of the homology of the inserted nucleotide sequence and flanking regions suggests that this template-switching event could have involved the genomes of SARS-CoV-2 variants (e.g., the B.1.1 strain), other human coronaviruses that infect the same host cells as SARS-CoV-2 (e.g., HCoV-OC43 or HCoV-229E), or a human transcript expressed in a host cell that was infected by the Omicron precursor.

Exploring the anti-SARS-CoV-2 main protease potential of FDA approved marine drugs using integrated machine learning templates as predictive tools.

Since the inception of COVID-19 pandemic in December 2019, socio-economic crisis begins to rise globally and SARS-CoV-2 was responsible for this outbreak. With this outbreak, currently, world is in need of effective and safe eradication of COVID-19. Hence, in this study anti-SAR-Co-2 potential of FDA approved marine drugs (Biological macromolecules) data set is explored computationally using machine learning algorithm of Flare by Cresset Group, Field template, 3D-QSAR and activity Atlas model was generated against FDA approved M-pro SARS-CoV-2 repurposed drugs including Nafamostat, Hydroxyprogesterone caporate, and Camostat mesylate. Data sets were categorized into active and inactive molecules on the basis of their structural and biological resemblance with repurposed COVID-19 drugs. Then these active compounds were docked against the five different M-pro proteins co-crystal structures. Highest LF VS score of Holichondrin B against all main protease co-crystal structures ranked it as lead drug. Finally, this new technique of drug repurposing remained efficient to explore the anti-SARS-CoV-2 potential of FDA approved marine drugs.

Intelligent Drug Delivery Vehicle System Based on STM32

In the context of the new coronavirus epidemic, medical systems throughout the world has suffered tremendous pressure, the most intuitive problem is a shortage of human resources. In this regard, the 'intelligent drug delivery vehicle' puts forward a feasible scheme, which can replace manual work in a specific hospital area to complete the delivery of drugs. The system is based on STM32F103ZET6 core processor, controlling the OpenMV visual module to identify the hospital corridor information, and then through the pressure detection module, gray detection tracking module and angle sensing module information, the core processor controls the motor drive module to make the vehicle move. The system modifies the algorithm under the traditional NCC template matching algorithm, and uses the zoom image to reduce the pixels which improve the camera frame rate and recognition accuracy. At the same time, the Bluetooth communication module is installed to enable different vehicles to execute the drug delivery operations at the same time, therefore reducing manual work saving. © 2022 IEEE.

Towards Efficient and Accurate SARS-CoV-2 Genome Sequence Typing Based on Supervised Learning Approaches.

Despite the active development of SARS-CoV-2 surveillance methods (e.g., Nextstrain, GISAID, Pangolin), the global emergence of various SARS-CoV-2 viral lineages that potentially cause antiviral and vaccine failure has driven the need for accurate and efficient SARS-CoV-2 genome sequence classifiers. This study presents an optimized method that accurately identifies the viral lineages of SARS-CoV-2 genome sequences using existing schemes. For Nextstrain and GISAID clades, a template matching-based method is proposed to quantify the differences between viral clades and to play an important role in classification evaluation. Furthermore, to improve the typing accuracy of SARS-CoV-2 genome sequences, an ensemble model that integrates a combination of machine learning-based methods (such as Random Forest and Catboost) with optimized weights is proposed for Nextstrain, Pangolin, and GISAID clades. Cross-validation is applied to optimize the parameters of the machine learning-based method and the weight settings of the ensemble model. To improve the efficiency of the model, in addition to the one-hot encoding method, we have proposed a nucleotide site mutation-based data structure that requires less computational resources and performs better in SARS-CoV-2 genome sequence typing. Based on an accumulated database of >1 million SARS-CoV-2 genome sequences, performance evaluations show that the proposed system has a typing accuracy of 99.879%, 97.732%, and 96.291% for Nextstrain, Pangolin, and GISAID clades, respectively. A single prediction only takes an average of <20 ms on a portable laptop. Overall, this study provides an efficient and accurate SARS-CoV-2 genome sequence typing system that benefits current and future surveillance of SARS-CoV-2 variants.

A Uniquely Stable Trimeric Model of SARS-CoV-2 Spike Transmembrane Domain.

Understanding fusion mechanisms employed by SARS-CoV-2 spike protein entails realistic transmembrane domain (TMD) models, while no reliable approaches towards predicting the 3D structure of transmembrane (TM) trimers exist. Here, we propose a comprehensive computational framework to model the spike TMD only based on its primary structure. We performed amino acid sequence pattern matching and compared the molecular hydrophobicity potential (MHP) distribution on the helix surface against TM homotrimers with known 3D structures and selected an appropriate template for homology modeling. We then iteratively built a model of spike TMD, adjusting "dynamic MHP portraits" and residue variability motifs. The stability of this model, with and without palmitoyl modifications downstream of the TMD, and several alternative configurations (including a recent NMR structure), was tested in all-atom molecular dynamics simulations in a POPC bilayer mimicking the viral envelope. Our model demonstrated unique stability under the conditions applied and conforms to known basic principles of TM helix packing. The original computational framework looks promising and could potentially be employed in the construction of 3D models of TM trimers for a wide range of membrane proteins.

Alternative role of motif B in template dependent polymerase inhibition

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) relies on the central molecular machine RNA-dependent RNA polymerase (RdRp) for the viral replication and transcription. Remdesivir at the template strand has been shown to effectively inhibit the RNA synthesis in SARS-CoV-2 RdRp by deactivating not only the complementary UTP incorporation but also the next nucleotide addition. However, the underlying molecular mechanism of the second inhibitory point remains unclear. In this work, we have performed molecular dynamics simulations and demonstrated that such inhibition has not directly acted on the nucleotide addition at the active site. Instead, the translocation of Remdesivir from +1 to-1 site is hindered thermodynamically as the post-Translocation state is less stable than the pre-Translocation state due to the motif B residue G683. Moreover, another conserved residue S682 on motif B further hinders the dynamic translocation of Remdesivir due to the steric clash with the 1′-cyano substitution. Overall, our study has unveiled an alternative role of motif B in mediating the translocation when Remdesivir is present in the template strand and complemented our understanding about the inhibitory mechanisms exerted by Remdesivir on the RNA synthesis in SARS-CoV-2 RdRp. © 2022 Chinese Physical Society.

Hand hygiene monitoring and compliance system using convolution neural networks.

Hand hygiene monitoring and compliance systems play a significant role in curbing the spread of healthcare associated infections and the COVID-19 virus. In this paper, a model has been developed using convolution neural networks (CNN) and computer vision to detect an individual's germ level, monitor their hand wash technique and create a database containing all records. The proposed model ensures all individuals entering a public place prevent the spread of healthcare associated infections (HCAI). In our model, the individual's identity is verified using two-factor authentication, followed by checking the hand germ level. Furthermore, if required the model will request sanitizing/ hand wash for completion of the process. During this time, the hand movements are checked to ensure each hand wash step is completed according to World Health Organization (WHO) guidelines. Upon completion of the process, a database with details of the individual's germ level is created. The advantage of our model is that it can be implemented in every public place and it is easily integrable. The performance of each segment of the model has been tested on real-time images an validated. The accuracy of the model is 100% for personal identification, 96.87% for hand detection, 93.33% for germ detection and 85.5% for the compliance system respectively.

COUGHTRIGGER: EARBUDS IMU BASED COUGH DETECTION ACTIVATOR USING AN ENERGY-EFFICIENT SENSITIVITY-PRIORITIZED TIME SERIES CLASSIFIER

Persistent coughs are a major symptom of respiratory-related diseases. Increasing research attention has been paid to detecting coughs using wearables, especially during the COVID-19 pandemic. Microphone is most widely used sensor to detect coughs. However, the intense power consumption needed to process audio hinders continuous audio-based cough detection on battery-limited commercial wearables, such as earbuds. We present CoughTrigger, which utilizes a lower-power sensor, inertial measurement unit (IMU), in earbuds as a cough detection activator to trigger a higher-power sensor for audio processing and classification. It runs all-the-time as a standby service with minimal battery consumption and triggers the audio-based cough detection when a candidate cough is detected from IMU. Besides, the use of IMU brings the benefit of improved specificity of cough detection. Experiments are conducted on 45 subjects and CoughTrigger achieved 0.77 AUC score. We also validated its effectiveness on free-living data and through on-device implementation. © 2022 IEEE