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Discovering Related Clinical Concepts Using Large Amounts of Clinical Notes 利用大量临床笔记发现相关临床概念
IF 2.8 Pub Date : 2016-01-01 DOI: 10.4137/BECB.S36155
Kavita A. Ganesan, S. Lloyd, V. Sarkar
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.
查找高度相关的临床概念的能力对于许多应用程序至关重要,例如假设生成、医学文献搜索的查询扩展、搜索结果过滤、ICD-10代码过滤和许多其他应用程序。虽然人工构建的医学术语(如SNOMED CT)可以显示某些相关概念,但这些术语是不够的,因为它们依赖于几个主题专家的专业知识,使得术语管理过程容易受到地理和语言偏见的影响。此外,这些术语也没有提供可量化的证据来证明这些概念之间的相关性。在这项工作中,我们探索了一种无监督的图形方法,通过利用大量临床笔记中的体积来挖掘相关概念。我们的评估表明,我们能够使用数据驱动的方法来发现各种搜索词的高度相关概念,包括药物、症状和疾病。
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引用次数: 6
A Review of Imaging Methods for Prostate Cancer Detection 前列腺癌影像学检测方法综述
IF 2.8 Pub Date : 2016-01-01 DOI: 10.4137/BECB.S34255
Saradwata Sarkar, Sudipta Das
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.
影像学在前列腺癌(PCa)的检测中发挥着越来越重要的作用。本文综述了多参数超声(US)、多参数磁共振成像(MRI)、MRI-US融合成像和正电子发射断层扫描(PET)成像等主要成像方式在前列腺癌诊断和定位中的应用。重点放在肿瘤的生物学和功能特征上,使特定成像技术的使用合理化。组织解剖结构的变化可以通过解剖灰度US和t2加权MRI检测到。肿瘤是通过血管生成进展的,这一事实可以通过多普勒、超声增强和动态磁共振增强来证实。通过弹性成像和弥散加权MRI检查肿瘤细胞密度的增加。PET成像采用几种不同的放射性核素来靶向肿瘤生长过程中的代谢和细胞活动。这些不同的成像技术的研究结果进行了讨论和比较。
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引用次数: 86
Design strategies of biodegradable scaffolds for tissue regeneration. 生物可降解组织再生支架的设计策略。
IF 2.8 Pub Date : 2014-05-08 eCollection Date: 2014-01-01 DOI: 10.4137/BECB.S10961
Khalil N Bitar, Elie Zakhem

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.

有许多可用的可生物降解材料可以用作再生医学的支架。目前,人们非常重视支架的设计阶段。材料可以设计成具有不同的性能,以匹配特定的应用。改性支架增强了其生物活性,提高了再生能力。支架的修饰可以稍后使用几种组织工程工具进行表征。除了材料外,细胞来源也是再生过程的重要组成部分。修饰材料必须能够支持不同类型细胞的生存和生长。细胞和改良的生物材料共同促进工程组织的重塑,从而影响其性能。本文综述了近年来支架设计的最新进展,包括物理修饰和化学修饰。本综述的最后一部分还讨论了涉及细胞活力的设计过程。
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引用次数: 47
Quality and safety of minimally invasive surgery: past, present, and future. 微创手术的质量和安全性:过去、现在和未来。
IF 2.8 Pub Date : 2014-04-21 eCollection Date: 2014-01-01 DOI: 10.4137/BECB.S10967
Bernadette McCrory, Chad A LaGrange, Ms Hallbeck

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.

在美国,由医疗差错引起的不良事件是导致死亡的主要原因,超过了机动车事故、乳腺癌和艾滋病的死亡率。可以而且应该做出改进,以降低可预防的手术差错的发生率,因为它们占医院内所有不良事件的近一半。尽管微创手术(MIS)已被证明对患者有益,如减少术后疼痛和住院时间,但其手术环境对外科医生施加了巨大的身体和认知压力,增加了出错的风险。为了减少错误和保护患者,需要多学科的方法来改善MIS。临床人为因素和生物医学工程原理和方法可用于开发和评估腹腔镜手术器械、实践和程序。首先,讨论了将医疗保健转变为高质量和安全系统的基本认识和必要性。接下来,从广义的角度介绍了手术技术和过程的设计和重新设计对人类表现的影响。最后,对该领域的发展前景和进一步提高管理信息系统的质量和安全性所需要进行的研究进行了展望。
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引用次数: 29
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. 血管灌注后应激诱导的家鸡肺血气屏障破坏及上皮-上皮细胞连接的研究。
IF 2.8 Pub Date : 2013-11-20 eCollection Date: 2013-01-01 DOI: 10.4137/BECB.S12988
John N Maina, Sikiru A Jimoh

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.

观察了不同压力下放养鸡、变型家鸡肺血管灌注后的完全血气屏障破裂(BGBBs)和上皮-上皮细胞连接破裂(E-ECCBs)。e - eccb比BGBBs高出约2倍。这表明气体交换组织的前一部分在结构上比后者更弱或更容易失败。肺动脉4支供血区域BGBBs和e - eccb数量的差异与血管直径、血管从肺动脉分叉的角度以及血管沿肺动脉分叉的位置有关。BGBBs和e - eccb大多发生在副支和尾支供应的区域:前者是最窄的分支,是最早与PA分离的血管,后者是PA最直接的延伸,也是最宽的。随着灌注压力和壁内压力的增加,E-ECCBs似乎从毛细血管壁的张力中分离并失效。与有数据可查的哺乳动物的肺相比,如兔子、狗和马的肺,放养鸡肺的血气屏障似乎因其薄而明显更强。
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引用次数: 7
Cardiac electrophysiological dynamics from the cellular level to the organ level. 心脏电生理动力学从细胞水平到器官水平。
IF 2.8 Pub Date : 2013-08-26 eCollection Date: 2013-01-01 DOI: 10.4137/BECB.S10960
Daisuke Sato, Colleen E Clancy

Cardiac alternans describes contraction of the ventricles in a strong-weak-strong-weak sequence at a constant pacing frequency. Clinically, alternans manifests as alternation of the T-wave on the ECG and predisposes individuals to arrhythmia and sudden cardiac death. In this review, we focus on the fundamental dynamical mechanisms of alternans and show how alternans at the cellular level underlies alternans in the tissue and on the ECG. A clear picture of dynamical mechanisms underlying alternans is important to allow development of effective anti-arrhythmic strategies.

心脏交替描述心室在恒定起搏频率下以强-弱-强-弱顺序收缩。在临床上,交替表现为心电图上t波的交替,使个体易发生心律失常和心源性猝死。在这篇综述中,我们关注交替的基本动力学机制,并展示细胞水平上的交替如何影响组织和心电图上的交替。一个清晰的动态机制图是重要的,以允许开发有效的抗心律失常的策略。
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引用次数: 17
Automated Identification of Fiducial Points on 3D Torso Images. 三维躯干图像上基准点的自动识别。
IF 2.8 Pub Date : 2013-07-02 eCollection Date: 2013-01-01 DOI: 10.4137/BECB.S11800
Manas M Kawale, Gregory P Reece, Melissa A Crosby, Elisabeth K Beahm, Michelle C Fingeret, Mia K Markey, Fatima A Merchant

Breast reconstruction is an important part of the breast cancer treatment process for many women. Recently, 2D and 3D images have been used by plastic surgeons for evaluating surgical outcomes. Distances between different fiducial points are frequently used as quantitative measures for characterizing breast morphology. Fiducial points can be directly marked on subjects for direct anthropometry, or can be manually marked on images. This paper introduces novel algorithms to automate the identification of fiducial points in 3D images. Automating the process will make measurements of breast morphology more reliable, reducing the inter- and intra-observer bias. Algorithms to identify three fiducial points, the nipples, sternal notch, and umbilicus, are described. The algorithms used for localization of these fiducial points are formulated using a combination of surface curvature and 2D color information. Comparison of the 3D co-ordinates of automatically detected fiducial points and those identified manually, and geodesic distances between the fiducial points are used to validate algorithm performance. The algorithms reliably identified the location of all three of the fiducial points. We dedicate this article to our late colleague and friend, Dr. Elisabeth K. Beahm. Elisabeth was both a talented plastic surgeon and physician-scientist; we deeply miss her insight and her fellowship.

乳房重建是许多女性乳腺癌治疗过程的重要组成部分。最近,整形外科医生已经使用2D和3D图像来评估手术结果。不同基准点之间的距离经常被用作表征乳房形态的定量措施。基准点可以直接标记在受试者上进行直接人体测量,也可以手动标记在图像上。本文介绍了一种新的算法来自动识别三维图像中的基准点。该过程的自动化将使乳房形态的测量更加可靠,减少观察者之间和内部的偏差。算法,以确定三个基点,乳头,胸骨切迹,和脐部,被描述。用于定位这些基点的算法是使用曲面曲率和二维颜色信息的组合来制定的。通过比较自动检测的基准点与人工识别的基准点的三维坐标,以及基准点之间的测地线距离来验证算法的性能。该算法可靠地识别了所有三个基点的位置。我们把这篇文章献给我们已故的同事和朋友,伊丽莎白·k·比姆博士。伊丽莎白是一位才华横溢的整形外科医生和内科科学家;我们深深地怀念她的洞察力和她的友谊。
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引用次数: 8
Neurotrauma and Repair Research: Traumatic Brain Injury (TBI) and its Treatments. 神经创伤与修复研究:创伤性脑损伤及其治疗。
IF 2.8 Pub Date : 2013-06-23 eCollection Date: 2013-01-01 DOI: 10.4137/BECB.S10968
Hanna Algattas, Jason H Huang

Traumatic brain injury (TBI) affects a growing portion of the population and continues to take national spotlight with advances in imaging technology and understanding of long-term effects. However, there is large variance in TBI treatment protocols due to injury variability and lack of both mechanistic understanding and strong treatment recommendations. Recent practice suggests three disparate treatment approaches, all which aim at promoting neuroprotection after TBI, show promise: immediate hypothermia, hyperbaric oxygen, and progesterone supplementation. The research is controversial at times, yet there are abundant opportunities to develop the technology behind hypothermia and hyperbaric oxygen treatments which would surely aid in aligning the current data. Additionally, while progesterone has already been packaged in nanoparticle form it may benefit from continued formulation and administration research. The treatments and the avenues for improvement are reviewed in the present paper.

创伤性脑损伤(TBI)影响了越来越多的人口,随着成像技术的进步和对长期影响的理解,它继续成为全国关注的焦点。然而,由于损伤的可变性以及缺乏对机制的理解和强有力的治疗建议,TBI的治疗方案存在很大差异。最近的实践表明,三种不同的治疗方法都旨在促进创伤性脑损伤后的神经保护,它们都有希望:立即降低体温、高压氧和补充黄体酮。这项研究有时是有争议的,但有很多机会来开发低温和高压氧治疗背后的技术,这肯定有助于调整当前的数据。此外,虽然黄体酮已经被包装成纳米颗粒形式,但它可能受益于持续的配方和给药研究。本文对其处理方法和改进途径进行了综述。
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引用次数: 5
Sequencing and computational approaches to identification and characterization of microbial organisms. 测序和计算方法鉴定和表征微生物有机体。
IF 2.8 Pub Date : 2013-05-20 eCollection Date: 2013-01-01 DOI: 10.4137/BECB.S10886
Brijesh Singh Yadav, Venkateswarlu Ronda, Dinesh P Vashista, Bhaskar Sharma

The recent advances in sequencing technologies and computational approaches are propelling scientists ever closer towards complete understanding of human-microbial interactions. The powerful sequencing platforms are rapidly producing huge amounts of nucleotide sequence data which are compiled into huge databases. This sequence data can be retrieved, assembled, and analyzed for identification of microbial pathogens and diagnosis of diseases. In this article, we present a commentary on how the metagenomics incorporated with microarray and new sequencing techniques are helping microbial detection and characterization.

测序技术和计算方法的最新进展正在推动科学家们更接近于完全理解人类与微生物的相互作用。强大的测序平台正在迅速产生大量的核苷酸序列数据,这些数据被汇编成庞大的数据库。这些序列数据可以被检索、组装和分析,以鉴定微生物病原体和诊断疾病。在这篇文章中,我们介绍了宏基因组学与微阵列和新的测序技术如何帮助微生物检测和表征。
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引用次数: 7
An Empirical Muscle Intracellular Action Potential Model with Multiple Erlang Probability Density Functions based on a Modified Newton Method. 基于改进牛顿法的多Erlang概率密度肌肉细胞内动作电位经验模型。
IF 2.8 Pub Date : 2013-04-14 eCollection Date: 2013-01-01 DOI: 10.4137/BECB.S11646
Gyutae Kim, Mohammed M Ferdjallah, Frederic D McKenzie

The convolution of the transmembrane current of an excitable cell and a weighting function generates a single fiber action potential (SFAP) model by using the volume conductor theory. Here, we propose an empirical muscle IAP model with multiple Erlang probability density functions (PDFs) based on a modified Newton method. In addition, we generate SFAPs based on our IAP model and referent sources, and use the peak-to-peak ratios (PPRs) of SFAPs for model verification. Through this verification, we find that the relation between an IAP profile and the PPR of its SFAP is consistent with some previous studies, and our IAP model shows close profiles to the referent sources. Moreover, we simulate and discuss some possible ionic activities by using the Erlang PDFs in our IAP model, which might present the underlying activities of ions or their channels during an IAP.

利用体积导体理论,将可兴奋细胞的跨膜电流与加权函数进行卷积,得到单纤维动作电位模型。在这里,我们提出了一个基于改进牛顿方法的具有多个Erlang概率密度函数(pdf)的经验肌肉IAP模型。此外,我们基于我们的IAP模型和参考源生成SFAPs,并使用SFAPs的峰峰比(ppr)进行模型验证。通过验证,我们发现一个IAP profile与其SFAP的PPR之间的关系与之前的一些研究是一致的,我们的IAP模型与参考来源表现出接近的profile。此外,我们通过在IAP模型中使用Erlang pdf来模拟和讨论一些可能的离子活动,这些活动可能会呈现IAP期间离子或其通道的潜在活动。
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引用次数: 2
期刊
Biomedical Engineering and Computational Biology
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