Biomedical Engineering and Computational Biology最新文献

{"title":"A Scoping Review of Digital Twins in the Context of the Covid-19 Pandemic.","authors":"Asiya Khan, Madison Milne-Ives, Edward Meinert, Gloria E Iyawa, Ray B Jones, Alex N Josephraj","doi":"10.1177/11795972221102115","DOIUrl":"10.1177/11795972221102115","url":null,"abstract":"<p><strong>Background: </strong>Digital Twins (DTs), virtual copies of physical entities, are a promising tool to help manage and predict outbreaks of Covid-19. By providing a detailed model of each patient, DTs can be used to determine what method of care will be most effective for that individual. The improvement in patient experience and care delivery will help to reduce demand on healthcare services and to improve hospital management.</p><p><strong>Objectives: </strong>The aim of this study is to address 2 research questions: (1) How effective are DTs in predicting and managing infectious diseases such as Covid-19? and (2) What are the prospects and challenges associated with the use of DTs in healthcare?</p><p><strong>Methods: </strong>The review was structured according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) framework. Titles and abstracts of references in PubMed, IEEE Xplore, Scopus, ScienceDirect and Google Scholar were searched using selected keywords (relating to digital twins, healthcare and Covid-19). The papers were screened in accordance with the inclusion and exclusion criteria so that all papers published in English relating to the use of digital twins in healthcare were included. A narrative synthesis was used to analyse the included papers.</p><p><strong>Results: </strong>Eighteen papers met the inclusion criteria and were included in the review. None of the included papers examined the use of DTs in the context of Covid-19, or infectious disease outbreaks in general. Academic research about the applications, opportunities and challenges of DT technology in healthcare in general was found to be in early stages.</p><p><strong>Conclusions: </strong>The review identifies a need for further research into the use of DTs in healthcare, particularly in the context of infectious disease outbreaks. Based on frameworks identified during the review, this paper presents a preliminary conceptual framework for the use of DTs for hospital management during the Covid-19 outbreak to address this research gap.</p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"13 1","pages":"11795972221102115"},"PeriodicalIF":2.3,"publicationDate":"2022-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9136438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46722620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OligoPrime: An Information System for Oligonucleotide Management.","authors":"Šimen Ravnik,&nbsp;Ines Žabkar,&nbsp;Uršula Prosenc Zmrzljak,&nbsp;Ivana Jovčevska,&nbsp;Neja Šamec,&nbsp;Miha Moškon,&nbsp;Alja Videtič Paska","doi":"10.1177/11795972211041983","DOIUrl":"https://doi.org/10.1177/11795972211041983","url":null,"abstract":"<p><p>With the increasing number of molecular biology techniques, large numbers of oligonucleotides are frequently involved in individual research projects. Thus, a dedicated electronic oligonucleotide management system is expected to provide several benefits such as increased oligonucleotide traceability, facilitated sharing of oligonucleotides between laboratories, and simplified (bulk) ordering of oligonucleotides. Herein, we describe OligoPrime, an information system for oligonucleotide management, which presents a computational support for all steps in an oligonucleotide lifecycle, namely, from its ordering and storage to its application, and disposal. OligoPrime is easy to use since it is accessible <i>via</i> a web browser and does not require any installation from the end user's perspective. It allows filtering and search of oligonucleotides by various parameters, which include the exact location of an oligonucleotide, its sequence, and availability. The oligonucleotide database behind the system is shared among the researchers working in the same laboratory or research group. Users might have different roles which define the access permissions and range from students to researchers and primary investigators. Furthermore, OligoPrime is easy to manage and install and is based on open-source software solutions. Its code is freely available at https://github.com/OligoPrime. Moreover, an implementation of OligoPrime, which can be used for testing is available at http://oligoprime.xyz/. To our knowledge, OligoPrime is the only software solution dedicated specifically to oligonucleotide management. We strongly believe that it has a large potential to enhance the transparency of use and to simplify the management of oligonucleotides in academic laboratories and research groups.</p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"12 ","pages":"11795972211041983"},"PeriodicalIF":2.8,"publicationDate":"2021-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8442484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39430710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tissue Phantoms for Biomedical Applications in Raman Spectroscopy: A Review.","authors":"Martha Z Vardaki,&nbsp;Nikolaos Kourkoumelis","doi":"10.1177/1179597220948100","DOIUrl":"https://doi.org/10.1177/1179597220948100","url":null,"abstract":"<p><p>Raman spectroscopy is a group of analytical techniques, currently applied in several research fields, including clinical diagnostics. Tissue-mimicking optical phantoms have been established as an essential intermediate stage for medical applications with their employment from spectroscopic techniques to be constantly growing. This review outlines the types of tissue phantoms currently employed in different biomedical applications of Raman spectroscopy, focusing on their composition and optical properties. It is therefore an attempt to present an informed range of options for potential use to the researchers.</p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"11 ","pages":"1179597220948100"},"PeriodicalIF":2.8,"publicationDate":"2020-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1179597220948100","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38342665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Granular Cell Tumor Imaging Using Optical Coherence Tomography.","authors":"David Tes, Ahmed Aber, Mohsin Zafar, Luke Horton, Audrey Fotouhi, Qiuyun Xu, Ali Moiin, Andrew D Thompson, Tatiana Cristina Moraes Pinto Blumetti, Steven Daveluy, Wei Chen, Mohammadreza Nasiriavanaki","doi":"10.1177/1179597218790250","DOIUrl":"10.1177/1179597218790250","url":null,"abstract":"<p><strong>Background: </strong>Granular cell tumor (GCT) is a relatively uncommon tumor that may affect the skin. The tumor can develop anywhere on the body, although it is predominately seen in oral cavities and in the head and neck regions. Here, we present the results of optical coherence tomography (OCT) imaging of a large GCT located on the abdomen of a patient. We also present an analytical method to differentiate between healthy tissue and GCT tissues.</p><p><strong>Materials and methods: </strong>A multibeam, Fourier domain, swept source OCT was used for imaging. The OCT had a central wavelength of 1305 ± 15 nm and lateral and axial resolutions of 7.5 and 10 µm, respectively. Qualitative and quantitative analyses of the tumor and healthy skin are reported.</p><p><strong>Results: </strong>Abrupt changes in architectures of the dermal and epidermal layers in the GCT lesion were observed. These architectural changes were not observed in healthy skin.</p><p><strong>Discussion: </strong>To quantitatively differentiate healthy skin from tumor regions, an optical attenuation coefficient analysis based on single-scattering formulation was performed. The methodology introduced here could have the capability to delineate boundaries of a tumor prior to surgical excision.</p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"9 ","pages":"1179597218790250"},"PeriodicalIF":2.8,"publicationDate":"2018-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5b/e2/10.1177_1179597218790250.PMC6088518.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36405562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and Optimization of a Fluorescent Imaging System to Detect Amyloid-β Proteins: Phantom Study.","authors":"David Tes,&nbsp;Karl Kratkiewicz,&nbsp;Ahmed Aber,&nbsp;Luke Horton,&nbsp;Mohsin Zafar,&nbsp;Nour Arafat,&nbsp;Afreen Fatima,&nbsp;Mohammad Rn Avanaki","doi":"10.1177/1179597218781081","DOIUrl":"https://doi.org/10.1177/1179597218781081","url":null,"abstract":"<p><p>Alzheimer disease is the most common form of dementia, affecting more than 5 million people in the United States. During the progression of Alzheimer disease, a particular protein begins to accumulate in the brain and also in extensions of the brain, ie, the retina. This protein, amyloid-β (Aβ), exhibits fluorescent properties. The purpose of this research article is to explore the implications of designing a fluorescent imaging system able to detect Aβ proteins in the retina. We designed and implemented a fluorescent imaging system with a range of applications that can be reconfigured on a fluorophore to fluorophore basis and tested its feasibility and capabilities using Cy5 and CRANAD-2 imaging probes. The results indicate a promising potential for the imaging system to be used to study the Aβ biomarker. A performance evaluation involving ex vivo and in vivo experiments is planned for future study.</p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"9 ","pages":"1179597218781081"},"PeriodicalIF":2.8,"publicationDate":"2018-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1179597218781081","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36285800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and Retrospective Clinical Assessment of a Patient-Specific Closed-Form Integro-Differential Equation Model of Plasma Dilution.","authors":"Glen Atlas,&nbsp;John K-J Li,&nbsp;Shawn Amin,&nbsp;Robert G Hahn","doi":"10.1177/1179597217730305","DOIUrl":"https://doi.org/10.1177/1179597217730305","url":null,"abstract":"<p><p>A closed-form integro-differential equation (IDE) model of plasma dilution (PD) has been derived which represents both the intravenous (IV) infusion of crystalloid and the postinfusion period. Specifically, PD is mathematically represented using a combination of constant ratio, differential, and integral components. Furthermore, this model has successfully been applied to preexisting data, from a prior human study, in which crystalloid was infused for a period of 30 minutes at the beginning of thyroid surgery. Using Euler's formula and a Laplace transform solution to the IDE, patients could be divided into two distinct groups based on their response to PD during the infusion period. Explicitly, Group 1 patients had an infusion-based PD response which was modeled using an exponentially decaying hyperbolic sine function, whereas Group 2 patients had an infusion-based PD response which was modeled using an exponentially decaying trigonometric sine function. Both Group 1 and Group 2 patients had postinfusion PD responses which were modeled using the same combination of hyperbolic sine and hyperbolic cosine functions. Statistically significant differences, between Groups 1 and 2, were noted with respect to the area under their PD curves during both the infusion and postinfusion periods. Specifically, Group 2 patients exhibited a response to PD which was most likely consistent with a preoperative hypovolemia. Overall, this IDE model of PD appears to be highly \"adaptable\" and successfully fits clinically-obtained human data on a patient-specific basis, during both the infusion and postinfusion periods. In addition, patient-specific IDE modeling of PD may be a useful adjunct in perioperative fluid management and in assessing clinical volume kinetics, of crystalloid solutions, in real time.</p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"8 ","pages":"1179597217730305"},"PeriodicalIF":2.8,"publicationDate":"2017-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1179597217730305","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35594652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diffusion in Tube Dialyzer.","authors":"Yohannes Nigatie","doi":"10.1177/1179597217732006","DOIUrl":"https://doi.org/10.1177/1179597217732006","url":null,"abstract":"<p><p>Nowadays, kidney failure is a problem of many peoples in the world. We know that the main function of kidney is maintaining the chemical quality of blood particularly removing urea through urine. But when they malfunction, the pathologic state known as uremia results in a condition in which the urea is retained in the body. Failure of the kidney results in building up of harmful wastes and excess fluids in the body. Kidney diseases (failures) can be due to infections, high blood pressure (hypertension), diabetes, and/or extensive use of medication. The best form of treatment is the implantation of a healthy kidney from a donor. However, this is often not possible due to the limited availability of human organs. Chronic kidney failure requires the treatment using a tube dialyzer called dialysis. Blood is taken out of the body and passes through a special membrane that removes waste and extra fluids. The clean blood is then returned to the body. The process is controlled by a dialysis machine (tube dialyzer) which is equipped with a blood pump and monitoring systems to ensure safety. So this article investigates the real application of mathematics (diffusion) in medical science, and it also contains the mathematical formulation and interpretation of tube dialyzer in relation to diffusion.</p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"8 ","pages":"1179597217732006"},"PeriodicalIF":2.8,"publicationDate":"2017-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1179597217732006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35483329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optical Coherence Tomography Technology and Quality Improvement Methods for Optical Coherence Tomography Images of Skin: A Short Review.","authors":"Saba Adabi, Zahra Turani, Emad Fatemizadeh, Anne Clayton, Mohammadreza Nasiriavanaki","doi":"10.1177/1179597217713475","DOIUrl":"10.1177/1179597217713475","url":null,"abstract":"<p><p>Optical coherence tomography (OCT) delivers 3-dimensional images of tissue microstructures. Although OCT imaging offers a promising high-resolution method, OCT images experience some artifacts that lead to misapprehension of tissue structures. Speckle, intensity decay, and blurring are 3 major artifacts in OCT images. Speckle is due to the low coherent light source used in the configuration of OCT. Intensity decay is a deterioration of light with respect to depth, and blurring is the consequence of deficiencies of optical components. In this short review, we summarize some of the image enhancement algorithms for OCT images which address the abovementioned artifacts.</p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"8 ","pages":"1179597217713475"},"PeriodicalIF":2.8,"publicationDate":"2017-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f5/d4/10.1177_1179597217713475.PMC5470862.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35108809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FSI Simulations of Pulse Wave Propagation in Human Abdominal Aortic Aneurysm: The Effects of Sac Geometry and Stiffness.","authors":"Han Li,&nbsp;Kexin Lin,&nbsp;Danial Shahmirzadi","doi":"10.4137/BECB.S40094","DOIUrl":"https://doi.org/10.4137/BECB.S40094","url":null,"abstract":"<p><p>This study aims to quantify the effects of geometry and stiffness of aneurysms on the pulse wave velocity (PWV) and propagation in fluid-solid interaction (FSI) simulations of arterial pulsatile flow. Spatiotemporal maps of both the wall displacement and fluid velocity were generated in order to obtain the pulse wave propagation through fluid and solid media, and to examine the interactions between the two waves. The results indicate that the presence of abdominal aortic aneurysm (AAA) sac and variations in the sac modulus affect the propagation of the pulse waves both qualitatively (eg, patterns of change of forward and reflective waves) and quantitatively (eg, decreasing of PWV within the sac and its increase beyond the sac as the sac stiffness increases). The sac region is particularly identified on the spatiotemporal maps with a region of disruption in the wave propagation with multiple short-traveling forward/reflected waves, which is caused by the change in boundary conditions within the saccular region. The change in sac stiffness, however, is more pronounced on the wall displacement spatiotemporal maps compared to those of fluid velocity. We conclude that the existence of the sac can be identified based on the solid and fluid pulse waves, while the sac properties can also be estimated. This study demonstrates the initial findings in numerical simulations of FSI dynamics during arterial pulsations that can be used as reference for experimental and in vivo studies. Future studies are needed to demonstrate the feasibility of the method in identifying very mild sacs, which cannot be detected from medical imaging, where the material property degradation exists under early disease initiation. </p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"7 ","pages":"25-36"},"PeriodicalIF":2.8,"publicationDate":"2016-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S40094","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34721844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fluorescent Cell Imaging in Regenerative Medicine.","authors":"Etai Sapoznik,&nbsp;Guoguang Niu,&nbsp;Yu Zhou,&nbsp;Sean V Murphy,&nbsp;Shay Soker","doi":"10.4137/BECB.S39045","DOIUrl":"https://doi.org/10.4137/BECB.S39045","url":null,"abstract":"<p><p>Fluorescent protein imaging, a promising tool in biological research, incorporates numerous applications that can be of specific use in the field of regenerative medicine. To enhance tissue regeneration efforts, scientists have been developing new ways to monitor tissue development and maturation in vitro and in vivo. To that end, new imaging tools and novel fluorescent proteins have been developed for the purpose of performing deep-tissue high-resolution imaging. These new methods, such as intra-vital microscopy and Förster resonance energy transfer, are providing new insights into cellular behavior, including cell migration, morphology, and phenotypic changes in a dynamic environment. Such applications, combined with multimodal imaging, significantly expand the utility of fluorescent protein imaging in research and clinical applications of regenerative medicine. </p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"7 Suppl 1","pages":"29-33"},"PeriodicalIF":2.8,"publicationDate":"2016-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S39045","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34466399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}