Irbm最新文献

{"title":"CRISPR-OTE: Prediction of CRISPR On-Target Efficiency Based on Multi-Dimensional Feature Fusion","authors":"J. Xie ,&nbsp;M. Liu ,&nbsp;L. Zhou","doi":"10.1016/j.irbm.2022.07.003","DOIUrl":"https://doi.org/10.1016/j.irbm.2022.07.003","url":null,"abstract":"<div><h3>Objective</h3><p>Clustered Regularly Interspaced Short Palindromic Repeats<span> (CRISPR) is a powerful genome editing<span> technology. Guide RNA (gRNA) plays an essential guiding role in the CRISPR system by complementary base pairing with target DNA. Since the CRISPR targeting mechanism problem has not yet been fully resolved, it remains a challenge to predict gRNA on-target efficiency. Current gRNA design tools often lack efficient information extraction and cannot learn the target efficiency patterns thoroughly.</span></span></p></div><div><h3>Material and methods</h3><p>In this study, CRISPR-OTE is proposed to consider both multi-dimensional sequence information and important complementary prior knowledge based on a simple but effective framework. CRISPR-OTE consists of the local-contextual information branch and the prior knowledge branch. The local-contextual information branch extracts multi-dimensional sequence features from the DNA primary sequence by a parallel framework of Convolutional Neural Networks<span> (CNN) and bidirectional Long Short-Term Memory networks (biLSTM). The prior knowledge branch selects the optimal subset of physicochemical features to provide the neural network with complementary knowledge, such as complex secondary structures. A simple feature fusion strategy is also adopted to fully utilize multi-modal data from the two branches.</span></p></div><div><h3>Results</h3><p>The experimental results show that the optimal subset of physicochemical features (RNA secondary structure and melting temperature of 34nt target) can effectively improve the prediction performance. Additionally, combining multi-dimensional sequence features and multi-modal features can extract information more comprehensively. Through transfer learning, CRISPR-OTE trained on the CRISPR-Cpf1 system can also be successfully applied to the CRISPR-Cas9 system.</p></div><div><h3>Conclusion</h3><p>The performance of CRISPR-OTE is superior to other methods in different CRISPR systems and species. Therefore, CRISPR-OTE is a simple on-target efficiency prediction framework with better accuracy and generalization performance.</p></div>","PeriodicalId":14605,"journal":{"name":"Irbm","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49704846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acknowledging our reviewers","authors":"","doi":"10.1016/S1959-0318(23)00010-6","DOIUrl":"https://doi.org/10.1016/S1959-0318(23)00010-6","url":null,"abstract":"","PeriodicalId":14605,"journal":{"name":"Irbm","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49704732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design of a Robotized Magnetic Platform for Targeted Drug Delivery in the Cochlea","authors":"M. Abbes ,&nbsp;K. Belharet ,&nbsp;M. Souissi ,&nbsp;H. Mekki ,&nbsp;G. Poisson","doi":"10.1016/j.irbm.2022.06.003","DOIUrl":"https://doi.org/10.1016/j.irbm.2022.06.003","url":null,"abstract":"<div><p><span>Inner ear disorders' treatment remains challenging due to anatomical barriers<span>. Robotic assistance seems to be a promising approach to enhance inner ear treatments<span> and, more particularly, lead to effective targeted drug delivery into the human cochlea. In this paper we present a combination of a micro-macro system that was designed and realized in order to efficiently control the navigation of </span></span></span>magnetic nanoparticles in an open-loop scheme throughout the cochlea, considering that the magnetic particles cannot be located in real time.</p><p><span>In order to respect the anatomical constraints, we established the characteristics that the new platform must present then proceeded to the design of the latter. The developed system is composed of a magnetic actuator that aims to guide nanoparticles into the cochlea. Mounted on a </span>robotic manipulator<span>, it ensures its positioning around the patient's head. The magnetic device integrates four parallelepiped-rectangle permanent magnets. Their arrangement in space, position and orientation, allows the creation of an area of convergence of magnetic forces where nanoparticles can be pushed/pulled to. To ensure the reachability<span><span> of the desired orientations and positions, a 3 DOF robot based on a Remote Centre of Motion (RCM) mechanism was developed. It features three concurrent rotational joints that generate a spherical workspace around the head. The control of the latter is based on </span>kinematic models.</span></span></p><p><span><span>A prototype of this platform was realized to validate the actuation process. Both magnetic actuator and robotic manipulator were realized using an </span>additive manufacturing<span> approach. We also designed a virtual human head with a life-size cochlea inside. A laser was mounted on the end effector to track the positioning of the actuator. This permitted to experimentally prove the capacity of the </span></span>robotic system to reach the desired positions and orientations in accordance with the medical needs.</p><p>This promising robotic approach, makes it possible to overcome anatomical barriers and steer magnetic nanoparticles to a targeted location in the inner ear and, more precisely, inside the cochlea.</p></div>","PeriodicalId":14605,"journal":{"name":"Irbm","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49704730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Deep Learning Approach for Predicting Subject-Specific Human Skull Shape from Head Toward a Decision Support System for Home-Based Facial Rehabilitation","authors":"H.-Q. Nguyen ,&nbsp;T.-N. Nguyen ,&nbsp;V.-D. Tran ,&nbsp;T.-T. Dao","doi":"10.1016/j.irbm.2022.05.005","DOIUrl":"https://doi.org/10.1016/j.irbm.2022.05.005","url":null,"abstract":"<div><h3>Objective</h3><p>Prediction of human skull shape from head is a complex and challenging engineering task for the development of a computer-aided vision system. Skull-to-face generation has been commonly performed in forensic facial reconstruction<span>. Classical statistical approaches were usually used. However, the head-to-skull relationship is still misunderstood. Recently, novel deep learning (DL) models have showed their efficiency and robustness for a large range of applications. The present study aimed to develop a novel approach based on deep learning models to reconstruct the human skull shape from head.</span></p></div><div><h3>Material and methods</h3><p>A head-to-skull generation workflow was developed and evaluated. A database of computed tomography (CT) images of 209 subjects was established for training and testing purposes. Three-dimension (3-D) head and skull geometries were reconstructed and then their respective descriptors (head/skull volumes, sampling feature points and point-to-center distances, head-skull thickness, Gaussian curvatures) were extracted. Two deep learning models (regression neural network and long-short term memory (LSTM)) were implemented and evaluated with different learning configurations. A 10-fold cross-validation was performed. Finally, the best and worst predicted cases were analyzed and discussed.</p></div><div><h3>Results</h3><p>The mean errors from 10-fold cross-validation showed a better accuracy level for the regression neural network model according to the long short-term memory model. The mean error between the DL-predicted skull shapes and CT-based skull shapes ranges from 1.67 mm to 3.99 mm by using the regression deep learning model and the best learning configuration. The volume deviation between predicted skull shapes and CT-based skull shapes is smaller than 5%.</p></div><div><h3>Conclusions</h3><p>The present study suggested that regression deep learning model allows human skull to be predicted from a given head with a good level of accuracy. This opens new avenues for the rapid generation of human skull shape from visual sensors (e.g. Microsoft Kinect) toward a computer-aided vision system for facial mimic rehabilitation. As perspectives, muscle network will be incorporated into the present workflow. Then, facial mimic movements will be tracked and animated to evaluate and optimize the rehabilitation movements and exercises.</p></div>","PeriodicalId":14605,"journal":{"name":"Irbm","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49704770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Automatic Detection of Severely and Mildly Infected COVID-19 Patients with Supervised Machine Learning Models","authors":"M.T. Huyut","doi":"10.1016/j.irbm.2022.05.006","DOIUrl":"10.1016/j.irbm.2022.05.006","url":null,"abstract":"<div><h3>Objectives</h3><p>When the prognosis of COVID-19 disease can be detected early, the intense-pressure and loss of workforce in health-services can be partially reduced. The primary-purpose of this article is to determine the feature-dataset consisting of the routine-blood-values (RBV) and demographic-data that affect the prognosis of COVID-19. Second, by applying the feature-dataset to the supervised machine-learning (ML) models, it is to identify severely and mildly infected COVID-19 patients at the time of admission.</p></div><div><h3>Material and methods</h3><p>The sample of this study consists of severely (n = 192) and mildly (n = 4010) infected-patients hospitalized with the diagnosis of COVID-19 between March-September, 2021. The RBV-data measured at the time of admission and age-gender characteristics of these patients were analyzed retrospectively. For the selection of the features, the minimum-redundancy-maximum-relevance (MRMR) method, principal-components-analysis and forward-multiple-logistics-regression analyzes were used. The features set were statistically compared between mild and severe infected-patients. Then, the performances of various supervised-ML-models were compared in identifying severely and mildly infected-patients using the feature set.</p></div><div><h3>Results</h3><p>In this study, 28 RBV-parameters and age-variable were found as the feature-dataset. The effect of features on the prognosis of the disease has been clinically proven. The ML-models with the highest overall-accuracy in identifying patient-groups were found respectively, as follows: local-weighted-learning (LWL)-97.86%, K-star (K*)-96.31%, Naive-Bayes (NB)-95.36% and k-nearest-neighbor (KNN)-94.05%. Also, the most successful models with the highest area-under-the-receiver-operating-characteristic-curve (AUC) values in identifying patient groups were found respectively, as follows: LWL-0.95%, K*-0.91%, NB-0.85% and KNN-0.75%.</p></div><div><h3>Conclusion</h3><p>The findings in this article have significant a motivation for the healthcare professionals to detect at admission severely and mildly infected COVID-19 patients.</p></div>","PeriodicalId":14605,"journal":{"name":"Irbm","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9158375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10647081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Non-Invasive Honey-Cell CSRR Glucose Sensor: Design Considerations and Modelling","authors":"K. Abdesselam ,&nbsp;C. Hannachi ,&nbsp;R. Shahbaz ,&nbsp;F. Deshours ,&nbsp;G. Alquie ,&nbsp;H. Kokabi ,&nbsp;A. Omer ,&nbsp;J.-M. Davaine","doi":"10.1016/j.irbm.2022.04.002","DOIUrl":"https://doi.org/10.1016/j.irbm.2022.04.002","url":null,"abstract":"<div><h3>Objective</h3><p>Over the years, microwave techniques have demonstrated their ability to characterise biological tissues. This study aimed to employ this approach to investigate the changes in the finger's glucose levels and to develop a sensitive sensor that people with diabetes can use.</p></div><div><h3>Materials and methods</h3><p>A simplified four-layer tissue model of the human fingertip was developed to validate the sensor's ability to detect variations in glucose levels. 3D electromagnetic simulations of the sensor with human fingertips inserted in the sensing region while varying the pressure were performed and compared to obtained experimental results using a VNA (vector network analyser).</p></div><div><h3>Results</h3><p>When varying the finger layers thicknesses independently, it was observed that the change in the skin layer thickness influences the frequency the most. It was also noticed that the higher the finger pressure, the more the resonance shifted towards low frequencies with a decreasing magnitude.</p></div><div><h3>Conclusion</h3><p>The achieved results show the impact of the finger's pressure on the sensor. Further investigations are in progress to obtain a good reproducibility of experimental results using a best-fitted pressure protocol on diabetic subjects.</p></div>","PeriodicalId":14605,"journal":{"name":"Irbm","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49704785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Variations in Hemiparetic Gait Patterns on Improvements in Walking Speed","authors":"T. Scone ,&nbsp;M. Saadat ,&nbsp;H. Barton ,&nbsp;A. Rastegarpanah","doi":"10.1016/j.irbm.2022.08.001","DOIUrl":"https://doi.org/10.1016/j.irbm.2022.08.001","url":null,"abstract":"<div><h3>Introduction</h3><p>Current research suggests that self-selected walking speed is an important indicator of hemiparetic gait rehabilitation outcome and can be targeted for improvement. Analysis of the relationship between walking speed and the kinematic profiles of the hemiparetic gait cycle can be expanded by comparing variations in their time dependant waveforms.</p></div><div><h3>Methods</h3><p>This paper is a pilot study to explore utilising the Linear Fit Method to compare the gait of a group of stroke survivors against a healthy baseline with respect to walking speed. This produced a set of parameters with clear physiological meaning that describe the variation of the hemiparetic gait pattern from the healthy pattern. A linear regression analysis was then performed comparing the resulting parameters against gait speed.</p></div><div><h3>Results</h3><p>Significant linear relationships (<span><math><mi>p</mi><mo>&lt;</mo><mn>0.05</mn></math></span>) were found between the Linear Fit parameters describing the hemiparetic gait pattern variations and walking speed in both paretic and non-paretic limbs. Most notably peak paretic knee flexion reduced by 20° and peak paretic hip abductions reducing to a nearly normal pattern while peak paretic hip flexions increased by 10°. The non-paretic hip flexion peak extensions remained 10° below the healthy comparison hip abduction offset was reduced but remained at nearly 2.5° to 5° from the healthy comparison.</p></div><div><h3>Conclusions</h3><p>As stroke survivors achieved higher walking speeds some aspects of their gait became more similar to the healthy comparison though others had no relation, or their differences became more pronounced. Combined, these relations show how paretic and non-paretic joint kinematics can be used to start identifying and quantifying effective compensatory hemiparetic gait patterns.</p></div>","PeriodicalId":14605,"journal":{"name":"Irbm","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49704808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design of Adjustable Frame-Type Prosthetic Socket for Lower Limb","authors":"M.H. Wang ,&nbsp;Q.J. Nong ,&nbsp;Y. Qian ,&nbsp;Y.H. Huang ,&nbsp;Y.H. Wang ,&nbsp;H.L. Yu","doi":"10.1016/j.irbm.2022.07.002","DOIUrl":"https://doi.org/10.1016/j.irbm.2022.07.002","url":null,"abstract":"<div><h3>Objectives</h3><p>Prosthetic socket is the contact interface between the stump and the prosthesis, and also the interface component that transmits forces from the stump to the prosthesis distal. The current prosthetic socket fit is a major factor affecting rehabilitation, especially with the stump volume fluctuations. The main goal of this article is to design an adjustable frame-type prosthetic socket with constant force to adapt to the stump volume fluctuations.</p></div><div><h3>Materials and methods</h3><p>In this paper, an adjustable frame-type prosthetic socket with constant force is designed. The constant force device is designed based on the superelasticity of the shape memory alloy<span> for maintaining constant stump-socket interface stress and automatically adapting to certain volume fluctuations. The constant force extrusion performance of this prosthetic socket was verified and optimized by finite element analysis.</span></p></div><div><h3>Results</h3><p>The results suggest that the constant force unit may maintain constant interface stress. According to the optimization results, the shape memory alloy dimensional parameters could be selected according to different requirements.</p></div><div><h3>Conclusion</h3><p>The adjustable frame-type prosthetic socket allows the user to adjust the socket volume through the cable system and has a large heat dissipation area. The constant force unit maintains constant interface stress and automatically adapts to stump volume fluctuations.</p></div>","PeriodicalId":14605,"journal":{"name":"Irbm","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49704844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biomechanical Evaluation of an Exoskeleton for Rehabilitation of Individuals with Parkinson's Disease","authors":"S. Costa ,&nbsp;I.A. Marques ,&nbsp;A. Bevilaqua ,&nbsp;A. Rabelo ,&nbsp;L. Luiz ,&nbsp;A. Cabral ,&nbsp;N. Faustino ,&nbsp;M. Okereke ,&nbsp;M. Fraga Vieira ,&nbsp;A. de Oliveira Andrade","doi":"10.1016/j.irbm.2022.11.002","DOIUrl":"https://doi.org/10.1016/j.irbm.2022.11.002","url":null,"abstract":"<div><p>Objective: Prior to implementing any robotic device or new rehabilitation technique into clinical practice, it is essential to examine metrics that reflect the instrument's utility and range of action. For this purpose, this study assesses, based on biomechanical data, the ergonomics and action range of a wrist exoskeleton that may be implemented into clinical practice for the rehabilitation of this joint in patients with Parkinson' disease (PD). Materials and Methods: Eleven individuals with rigidity caused by PD participated in the study. Two distinct tasks were proposed: maximum voluntary contraction and sequential wrist flexion and extension; while electromyography and kinematic data were collected in two stages, with and without the exoskeleton. For statistical analysis, Bootstrap resampling, Kolmogorov-Smirnov, and paired Wilcoxon Mann tests were used. Results and Conclusion: Using the exoskeleton resulted in a 22% increase in muscle activation of the carpal extensors and a 9% decrease in wrist extension. According to the biomechanical parameters evaluated, the exoskeleton guaranteed the amplitude considered functional for the wrist joint, indicating good mechanical adequacy for use in clinical practice.</p></div>","PeriodicalId":14605,"journal":{"name":"Irbm","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49729783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combining Cultural Probes and Interviews with Caregivers to Co-Design a Social Mobile Robotic Solution","authors":"M. Olivier ,&nbsp;S. Rey ,&nbsp;D. Voilmy ,&nbsp;J.-G. Ganascia ,&nbsp;K. Lan Hing Ting","doi":"10.1016/j.irbm.2022.06.004","DOIUrl":"https://doi.org/10.1016/j.irbm.2022.06.004","url":null,"abstract":"<div><h3>Objectives</h3><p>The objective of our research is to study the social organization within institutions welcoming dependent older adults and the potential impact of introducing a social robot.</p></div><div><h3>Materials and methods</h3><p>In a co-design approach with professionals, the observation of behaviors, regulated by social rules and norms, will allow, in a way coherent with our empirical approach, to question the conditions necessary for the design of an acceptable human–robot interaction. The ethnographic observations, which were cancelled due to the Covid crisis, led us to use the “cultural probes” method combined with interviews, to understand the daily work of health professionals better.</p></div><div><h3>Results</h3><p><span>The analysis of the collected data allows us to identify 5 recurrent themes – Time and personnel, the health situation,</span><span>¹</span> Communication/Attention, Guiding, Activities – for which we have listed, in this article, the issues encountered, the questions raised and ideas of potential solutions with the use of a social robot.</p></div><div><h3>Conclusion</h3><p>The Cultural Probes approach may seem time-consuming and requires a significant investment, but it has allowed us to maintain regular contact during the pandemic. In addition, the qualitative data collected proved to be a good discussion tool.</p></div>","PeriodicalId":14605,"journal":{"name":"Irbm","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49766844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}