Biomedical Engineering and Computational Biology最新文献

{"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":null,"pages":null},"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":null,"pages":null},"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":"IMAGE AND VIDEO ACQUISITION AND PROCESSING FOR CLINICAL APPLICATIONS.","authors":"Elie Zakhem,&nbsp;Sean V Murphy,&nbsp;Matthew L Davis,&nbsp;Shreya Raghavan,&nbsp;Mai T Lam","doi":"10.4137/BECB.S40272","DOIUrl":"https://doi.org/10.4137/BECB.S40272","url":null,"abstract":"","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2016-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S40272","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34611685","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":null,"pages":null},"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}

{"title":"Lung-On-A-Chip Technologies for Disease Modeling and Drug Development.","authors":"Dipasri Konar,&nbsp;Mahesh Devarasetty,&nbsp;Didem V Yildiz,&nbsp;Anthony Atala,&nbsp;Sean V Murphy","doi":"10.4137/BECB.S34252","DOIUrl":"https://doi.org/10.4137/BECB.S34252","url":null,"abstract":"<p><p>Animal and two-dimensional cell culture models have had a profound impact on not only lung research but also medical research at large, despite inherent flaws and differences when compared with in vivo and clinical observations. Three-dimensional (3D) tissue models are a natural progression and extension of existing techniques that seek to plug the gaps and mitigate the drawbacks of two-dimensional and animal technologies. In this review, we describe the transition of historic models to contemporary 3D cell and organoid models, the varieties of current 3D cell and tissue culture modalities, the common methods for imaging these models, and finally, the applications of these models and imaging techniques to lung research. </p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2016-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S34252","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34440156","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":"Prediction of Peaks of Seasonal Influenza in Military Health-Care Data.","authors":"Anna L Buczak,&nbsp;Benjamin Baugher,&nbsp;Erhan Guven,&nbsp;Linda Moniz,&nbsp;Steven M Babin,&nbsp;Jean-Paul Chretien","doi":"10.4137/BECB.S36277","DOIUrl":"https://doi.org/10.4137/BECB.S36277","url":null,"abstract":"<p><p>Influenza is a highly contagious disease that causes seasonal epidemics with significant morbidity and mortality. The ability to predict influenza peak several weeks in advance would allow for timely preventive public health planning and interventions to be used to mitigate these outbreaks. Because influenza may also impact the operational readiness of active duty personnel, the US military places a high priority on surveillance and preparedness for seasonal outbreaks. A method for creating models for predicting peak influenza visits per total health-care visits (ie, activity) weeks in advance has been developed using advanced data mining techniques on disparate epidemiological and environmental data. The model results are presented and compared with those of other popular data mining classifiers. By rigorously testing the model on data not used in its development, it is shown that this technique can predict the week of highest influenza activity for a specific region with overall better accuracy than other methods examined in this article. </p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S36277","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34440155","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":"A Unified Frequency Domain Model to Study the Effect of Demyelination on Axonal Conduction.","authors":"Saurabh Chaubey,&nbsp;Shikha J Goodwin","doi":"10.4137/BECB.S38554","DOIUrl":"https://doi.org/10.4137/BECB.S38554","url":null,"abstract":"Multiple sclerosis is a disease caused by demyelination of nerve fibers. In order to determine the loss of signal with the percentage of demyelination, we need to develop models that can simulate this effect. Existing time-based models does not provide a method to determine the influences of demyelination based on simulation results. Our goal is to develop a system identification approach to generate a transfer function in the frequency domain. The idea is to create a unified modeling approach for neural action potential propagation along the length of an axon containing number of Nodes of Ranvier (N). A system identification approach has been used to identify a transfer function of the classical Hodgkin-Huxley equations for membrane voltage potential. Using this approach, we model cable properties and signal propagation along the length of the axon with N node myelination. MATLAB/ Simulink platform is used to analyze an N node-myelinated neuronal axon. The ability to transfer function in the frequency domain will help reduce effort and will give a much more realistic feel when compared to the classical time-based approach. Once a transfer function is identified, the conduction as a cascade of each linear time invariant system-based transfer function can be modeled. Using this approach, future studies can model the loss of myelin in various parts of nervous system.","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2016-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S38554","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34481953","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":"Network-Based Enriched Gene Subnetwork Identification: A Game-Theoretic Approach.","authors":"Abolfazl Razi,&nbsp;Fatemeh Afghah,&nbsp;Salendra Singh,&nbsp;Vinay Varadan","doi":"10.4137/BECB.S38244","DOIUrl":"https://doi.org/10.4137/BECB.S38244","url":null,"abstract":"<p><p>Identifying subsets of genes that jointly mediate cancer etiology, progression, or therapy response remains a challenging problem due to the complexity and heterogeneity in cancer biology, a problem further exacerbated by the relatively small number of cancer samples profiled as compared with the sheer number of potential molecular factors involved. Pure data-driven methods that merely rely on multiomics data have been successful in discovering potentially functional genes but suffer from high false-positive rates and tend to report subsets of genes whose biological interrelationships are unclear. Recently, integrative data-driven models have been developed to integrate multiomics data with signaling pathway networks in order to identify pathways associated with clinical or biological phenotypes. However, these approaches suffer from an important drawback of being restricted to previously discovered pathway structures and miss novel genomic interactions as well as potential crosstalk among the pathways. In this article, we propose a novel coalition-based game-theoretic approach to overcome the challenge of identifying biologically relevant gene subnetworks associated with disease phenotypes. The algorithm starts from a set of seed genes and traverses a protein-protein interaction network to identify modulated subnetworks. The optimal set of modulated subnetworks is identified using Shapley value that accounts for both individual and collective utility of the subnetwork of genes. The algorithm is applied to two illustrative applications, including the identification of subnetworks associated with (i) disease progression risk in response to platinum-based therapy in ovarian cancer and (ii) immune infiltration in triple-negative breast cancer. The results demonstrate an improved predictive power of the proposed method when compared with state-of-the-art feature selection methods, with the added advantage of identifying novel potentially functional gene subnetworks that may provide insights into the mechanisms underlying cancer progression. </p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2016-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S38244","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34464402","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":"Artificial Neural Networks as Decision Support Tools in Cytopathology: Past, Present, and Future.","authors":"Abraham Pouliakis, Efrossyni Karakitsou, Niki Margari, Panagiotis Bountris, Maria Haritou, John Panayiotides, Dimitrios Koutsouris, Petros Karakitsos","doi":"10.4137/BECB.S31601","DOIUrl":"10.4137/BECB.S31601","url":null,"abstract":"<p><strong>Objective: </strong>This study aims to analyze the role of artificial neural networks (ANNs) in cytopathology. More specifically, it aims to highlight the importance of employing ANNs in existing and future applications and in identifying unexplored or poorly explored research topics.</p><p><strong>Study design: </strong>A systematic search was conducted in scientific databases for articles related to cytopathology and ANNs with respect to anatomical places of the human body where cytopathology is performed. For each anatomic system/organ, the major outcomes described in the scientific literature are presented and the most important aspects are highlighted.</p><p><strong>Results: </strong>The vast majority of ANN applications are related to cervical cytopathology, specifically for the ANN-based, semiautomated commercial diagnostic system PAPNET. For cervical cytopathology, there is a plethora of studies relevant to the diagnostic accuracy; in addition, there are also efforts evaluating cost-effectiveness and applications on primary, secondary, or hybrid screening. For the rest of the anatomical sites, such as the gastrointestinal system, thyroid gland, urinary tract, and breast, there are significantly less efforts relevant to the application of ANNs. Additionally, there are still anatomical systems for which ANNs have never been applied on their cytological material.</p><p><strong>Conclusions: </strong>Cytopathology is an ideal discipline to apply ANNs. In general, diagnosis is performed by experts via the light microscope. However, this approach introduces subjectivity, because this is not a universal and objective measurement process. This has resulted in the existence of a gray zone between normal and pathological cases. From the analysis of related articles, it is obvious that there is a need to perform more thorough analyses, using extensive number of cases and particularly for the nonexplored organs. Efforts to apply such systems within the laboratory test environment are required for their future uptake.</p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2016-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70685672","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":"Discovering Related Clinical Concepts Using Large Amounts of Clinical Notes","authors":"Kavita A. Ganesan, S. Lloyd, V. Sarkar","doi":"10.4137/BECB.S36155","DOIUrl":"https://doi.org/10.4137/BECB.S36155","url":null,"abstract":"The ability to find highly related clinical concepts is essential for many applications such as for hypothesis generation, query expansion for medical literature search, search results filtering, ICD-10 code filtering and many other applications. While manually constructed medical terminologies such as SNOMED CT can surface certain related concepts, these terminologies are inadequate as they depend on expertise of several subject matter experts making the terminology curation process open to geographic and language bias. In addition, these terminologies also provide no quantifiable evidence on how related the concepts are. In this work, we explore an unsupervised graphical approach to mine related concepts by leveraging the volume within large amounts of clinical notes. Our evaluation shows that we are able to use a data driven approach to discovering highly related concepts for various search terms including medications, symptoms and diseases.","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S36155","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70685835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}