Biomedical Engineering and Computational Biology最新文献

{"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":"7 Suppl 1","pages":"17-27"},"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":"7 Suppl 2","pages":"15-26"},"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":"7 ","pages":"19-24"},"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":"7 Suppl 2","pages":"1-14"},"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":"7 1","pages":"1-18"},"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":"7 1","pages":"27 - 33"},"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}

{"title":"A Review of Imaging Methods for Prostate Cancer Detection","authors":"Saradwata Sarkar, Sudipta Das","doi":"10.4137/BECB.S34255","DOIUrl":"https://doi.org/10.4137/BECB.S34255","url":null,"abstract":"Imaging is playing an increasingly important role in the detection of prostate cancer (PCa). This review summarizes the key imaging modalities–multiparametric ultrasound (US), multiparametric magnetic resonance imaging (MRI), MRI-US fusion imaging, and positron emission tomography (PET) imaging–-used in the diagnosis and localization of PCa. Emphasis is laid on the biological and functional characteristics of tumors that rationalize the use of a specific imaging technique. Changes to anatomical architecture of tissue can be detected by anatomical grayscale US and T2-weighted MRI. Tumors are known to progress through angiogenesis–-a fact exploited by Doppler and contrast-enhanced US and dynamic contrast-enhanced MRI. The increased cellular density of tumors is targeted by elastography and diffusion-weighted MRI. PET imaging employs several different radionuclides to target the metabolic and cellular activities during tumor growth. Results from studies using these various imaging techniques are discussed and compared.","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"7 1","pages":"1 - 15"},"PeriodicalIF":2.8,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S34255","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70685741","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}

{"title":"Design strategies of biodegradable scaffolds for tissue regeneration.","authors":"Khalil N Bitar,&nbsp;Elie Zakhem","doi":"10.4137/BECB.S10961","DOIUrl":"https://doi.org/10.4137/BECB.S10961","url":null,"abstract":"<p><p>There are numerous available biodegradable materials that can be used as scaffolds in regenerative medicine. Currently, there is a huge emphasis on the designing phase of the scaffolds. Materials can be designed to have different properties in order to match the specific application. Modifying scaffolds enhances their bioactivity and improves the regeneration capacity. Modifications of the scaffolds can be later characterized using several tissue engineering tools. In addition to the material, cell source is an important component of the regeneration process. Modified materials must be able to support survival and growth of different cell types. Together, cells and modified biomaterials contribute to the remodeling of the engineered tissue, which affects its performance. This review focuses on the recent advancements in the designs of the scaffolds including the physical and chemical modifications. The last part of this review also discusses designing processes that involve viability of cells. </p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"6 ","pages":"13-20"},"PeriodicalIF":2.8,"publicationDate":"2014-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S10961","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32724651","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":"Quality and safety of minimally invasive surgery: past, present, and future.","authors":"Bernadette McCrory,&nbsp;Chad A LaGrange,&nbsp;Ms Hallbeck","doi":"10.4137/BECB.S10967","DOIUrl":"https://doi.org/10.4137/BECB.S10967","url":null,"abstract":"<p><p>Adverse events because of medical errors are a leading cause of death in the United States (US) exceeding the mortality rates of motor vehicle accidents, breast cancer, and AIDS. Improvements can and should be made to reduce the rates of preventable surgical errors because they account for nearly half of all adverse events within hospitals. Although minimally invasive surgery (MIS) has proven patient benefits such as reduced postoperative pain and hospital stay, its operative environment imposes substantial physical and cognitive strain on the surgeon increasing the risk of error. To mitigate errors and protect patients, a multidisciplinary approach is needed to improve MIS. Clinical human factors, and biomedical engineering principles and methodologies can be used to develop and assess laparoscopic surgery instrumentation, practices, and procedures. First, the foundational understanding and the imperative to transform health care into a high-quality and safe system is discussed. Next, a generalized perspective is presented on the impact of the design and redesign of surgical technologies and processes on human performance. Finally, the future of this field and the research needed to further improve the quality and safety of MIS is discussed. </p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"6 ","pages":"1-11"},"PeriodicalIF":2.8,"publicationDate":"2014-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S10967","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32725349","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":"Study of Stress Induced Failure of the Blood-gas Barrier and the Epithelial-epithelial Cells Connections of the Lung of the Domestic Fowl, Gallus gallus Variant Domesticus after Vascular Perfusion.","authors":"John N Maina,&nbsp;Sikiru A Jimoh","doi":"10.4137/BECB.S12988","DOIUrl":"https://doi.org/10.4137/BECB.S12988","url":null,"abstract":"<p><p>Complete blood-gas barrier breaks (BGBBs) and epithelial-epithelial cells connections breaks (E-ECCBs) were enumerated in the lungs of free range chickens, Gallus gallus variant domesticus after vascular perfusion at different pressures. The E-ECCBs surpassed the BGBBs by a factor of ~2. This showed that the former parts of the gas exchange tissue were structurally weaker or more vulnerable to failure than the latter. The differences in the numbers of BGBBs and E-ECCBs in the different regions of the lung supplied with blood by the 4 main branches of the pulmonary artery (PA) corresponded with the diameters of the blood vessels, the angles at which they bifurcated from the PA, and the positions along the PA where they branched off. Most of the BGBBs and the E-ECCBs occurred in the regions supplied by the accessory- and the caudomedial branches: the former is the narrowest branch and the first blood vessel to separate from the PA while the latter is the most direct extension of the PA and is the widest. The E-ECCBs appeared to separate and fail from tensing of the blood capillary walls, as the perfusion- and intramural pressures increased. Compared to the mammalian lungs on which data are available, i.e., those of the rabbit, the dog, and the horse, the blood-gas barrier of the lung of free range chickens appears to be substantially stronger for its thinness. </p>","PeriodicalId":42484,"journal":{"name":"Biomedical Engineering and Computational Biology","volume":"5 ","pages":"77-88"},"PeriodicalIF":2.8,"publicationDate":"2013-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/BECB.S12988","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32725348","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}