一种基于本体集成的生物医学数据库中语义映射维护方法研究

生物医学数据库到生物医学本体的语义映射是基于本体集成生物医学数据库系统的一个重要环节.而生物医学本体随着学科的发展不断演化,造成了集成系统不稳定.针对这个问题,本文在本体演化条件下,分析并发现了语义映射的变化规律,设计了对应的维护流程和维护方法,并通过计算维护收益率证明了该方法对映射的维护是有效性的,从而增强了集成系统在本体演化条件下的稳定性.     

一种基于本体集成的生物医学数据库中语义映射维护方法研究

生物医学数据库到生物医学本体的语义映射是基于本体集成生物医学数据库系统的一个重要环节。而生物医学本体随着学科的发展不断演化,造成了集成系统不稳定。针对这个问题,本文在本体演化条件下,分析并发现了语义映射的变化规律,设计了对应的维护流程和维护方法,并通过计算维护收益率证明了该方法对映射的维护是有效性的,从而增强了集成系统在本体演化条件下的稳定性。     

Complex biomedical systems: from basic science to translation

The Department of Biomedical Engineering (BME) of the University of Southern California (BME@USC) has a longstanding tradition of advancing biomedicine through the development and application of novel engineering ideas. More than 80 primary and affiliated faculty members conduct cutting-edge research in a wide variety of areas, such as neuroengineering, biosystems and biosignal analysis, medical devices (including biomicroelectromechanical systems (bioMEMS) and bionanotechnology), biomechanics, bioimaging, and imaging informatics. Currently, the department hosts six internationally recognized research centers: the Biomimetic MicroElectronic Systems Engineering Research Center (funded by the National Science Foundation), the Biomedical Simulations Resource [funded by the National Institutes of Health (NIH)], the Medical Ultrasonic Transducer Center (funded by NIH), the Center for Neural Engineering, the Center for Vision Science and Technology (funded by an NIH Bioengineering Research Partnership Grant), and the Center for Genomic and Phenomic Studies in Autism (funded by NIH). BME@USC ranks in the top tier of all U.S. BME departments in terms of research funding per faculty.     

UCSD's Institute of Engineering in Medicine: fostering collaboration through research and education

The University of California, San Diego (UCSD) was established in 1961 as a new research university that emphasizes innovation, excellence, and interdisciplinary research and education. It has a School of Medicine (SOM) and the Jacobs School of Engineering (JSOE) in close proximity, and both schools have national rankings among the top 15. In 1991, with the support of the Whitaker Foundation, the Whitaker Institute of Biomedical Engineering was formed to foster collaborations in research and education. In 2008, the university extended the collaboration further by establishing the Institute of Engineering in Medicine (IEM), with the mission of accelerating the discoveries of novel science and technology to enhance health care through teamwork between engineering and medicine, and facilitating the translation of innovative technologies for delivery to the public through clinical application and commercialization.     

CONTEMPORARY MEDICAL ETHICS: AN OVERVIEW FROM IRAN

The growing potential of biomedical technologies has increasingly been associated with discussions surrounding the ethical aspects of the new technologies in different societies. Advances in genetics, stem cell research and organ transplantation are some of the medical issues that have raised important ethical and social issues. Special attention has been paid towards moral ethics in Islam and medical and religious professions in Iran have voiced the requirement for an emphasis on ethics. In the last decade, great strides have been made in biomedical ethics, especially in the field of education, research and legislation. In this article, contemporary medical ethics in Iran, and the related moral philosophy, have been reviewed in brief and we have discussed some of the activities in the field of medical ethics that have been carried out in our country within recent years. These activities have included the establishment of the National and Regional Committees for Medical Research Ethics and the production of national codes of ethics in biomedical research in the 1990s and the introduction of a comprehensive strategic plan for medical ethics at the national level in 2002. This paper will discuss these issues, along with the production, in 2005, of the Specific National Ethical Guidelines for Biomedical Research.     

Linking engineering and medicine: fostering collaboration skills in interdisciplinary teams

Biomedical engineering embodies the spirit of combining disciplines. The engineer's pragmatic approach to--and appetite for--solving problems is matched by a bounty of technical challenges generated in medical domains. From nanoscale diagnostics to the redesign of systems of health-care delivery, engineers have been connecting advances in basic and applied science with applications that have helped to improve medical care and outcomes. Increasingly, however, integrating these areas of knowledge and application is less individualistic and more of a team sport. Success increasingly relies on a direct focus on practicing and developing collaboration skills in interdisciplinary teams. Such an approach does not fit easily into individual-focused, discipline-based programs. Biomedical engineering has done its fair share of silo busting, but new approaches are needed to inspire interdisciplinary teams to form around challenges in particular areas. Health care offers a wide variety of complex challenges across an array of delivery settings that can call for new interdisciplinary approaches. This was recognized by the deans of the University of Southern California's (USC's) Medical and Engineering Schools when they began the planning process, leading to the creation of the Health, Technology, and Engineering (HTE@USC or HTE for short) program. “Health care and technology are changing rapidly, and future physicians and engineers need intellectual tools to stay ahead of this change,” says Carmen A. Puliafito, dean of the Keck School of Medicine. His goal is to train national leaders in the quest for devices and processes to improve health care.     

Engineering excellence in breakthrough biomedical technologies: bioengineering at the University of California, Riverside

The Department of Bioengineering at the University of California, Riverside (UCR), was established in 2006 and is the youngest department in the Bourns College of Engineering. It is an interdisciplinary research engine that builds strength from highly recognized experts in biochemistry, biophysics, biology, and engineering, focusing on common critical themes. The range of faculty research interests is notable for its diversity, from the basic cell biology through cell function to the physiology of the whole organism, each directed at breakthroughs in biomedical devices for measurement and therapy. The department forges future leaders in bioengineering, mirroring the field in being energetic, interdisciplinary, and fast moving at the frontiers of biomedical discoveries. Our educational programs combine a solid foundation in bio logical sciences and engineering, diverse communication skills, and training in the most advanced quantitative bioengineering research. Bioengineering at UCR also includes the Bioengineering Interdepartmental Graduate (BIG) program. With its slogan Start-Grow-Be-BIG, it is already recognized for its many accomplishments, including being third in the nation in 2011 for bioengineering students receiving National Science Foundation graduate research fellowships as well as being one of the most ethnically inclusive programs in the nation.     

Science education and popularization of science in the biomedical area: its role for the future of science and of society

This paper presents the main subjects discussed in the round-table: "Educational Base for Biomedical Research", during the International Symposium on Biomedical Research in the 21st century; two main aspects will be focused: (1) the importance of popularizing science in order to stimulate comprehension of the scientific process and progress, their critical thinking, citizenship and social commitment, mainly in the biomedical area, considering the new advances of knowledge and the resulting technology; (2) the importance to stimulate genuine scientific vocation among young people, by giving them opportunity to early experience scientific environment, through the hands of well prepared master in a humanistic atmosphere.     

生命伦理学基本原则讨论

介绍当代西方主流生命伦理学具有代表性的4种基本原则并对其进行理论分析和评价,进一步深入探讨在全球化的多元文化背景下当代中国生命伦理学发展的理论定位和实践应用中的问题和误区,发展具有中国特色的生命伦理学,为构建未来中国生命伦理学原则和实践提供理论借鉴。     

Time to Tenure in Spanish Universities: An Event History Analysis

Understanding how institutional incentives and mechanisms for assigning recognition shape access to a permanent job is important. This study, based on data from questionnaire survey responses and publications of 1,257 university science, biomedical and engineering faculty in Spain, attempts to understand the timing of getting a permanent position and the relevant factors that account for this transition, in the context of dilemmas between mobility and permanence faced by organizations. Using event history analysis, the paper looks at the time to promotion and the effects of some relevant covariates associated to academic performance, social embeddedness and mobility. We find that research productivity contributes to career acceleration, but that other variables are also significantly associated to a faster transition. Factors associated to the social elements of academic life also play a role in reducing the time from PhD graduation to tenure. However, mobility significantly increases the duration of the non-tenure stage. In contrast with previous findings, the role of sex is minor. The variations in the length of time to promotion across different scientific domains is confirmed, with faster career advancement for those in the Engineering and Technological Sciences compared with academics in the Biological and Biomedical Sciences. Results show clear effects of seniority, and rewards to loyalty, in addition to some measurements of performance and quality of the university granting the PhD, as key elements speeding up career advancement. Findings suggest the existence of a system based on granting early permanent jobs to those that combine social embeddedness and team integration with some good credentials regarding past and potential future performance, rather than high levels of mobility.     

Evaluation of biomedical text-mining systems: lessons learned from information retrieval

Biomedical text-mining systems have great promise for improving the efficiency and productivity of biomedical researchers. However, such systems are still not in routine use. One impediment to their development is the lack of systematic and rigorous evaluation, comparable to the approaches developed for information retrieval systems. The developers of text-mining systems need to improve both test collections for system-oriented evaluation and undertake user-oriented evaluations to determine the most effective use of their systems for their intended audience.     

Computational structural modelling of coronary stent deployment: a review

The finite element (FE) method is a powerful investigative tool in the field of biomedical engineering, particularly in the analysis of medical devices such as coronary stents whose performance is extremely difficult to evaluate in vivo. In recent years, a number of FE studies have been carried out to simulate the deployment of coronary stents, and the results of these studies have been utilised to assess and optimise the performance of these devices. The aim of this paper is to provide a thorough review of the state-of-the-art research in this area, discussing the aims, methods and conclusions drawn from a number of significant studies. It is intended that this paper will provide a valuable reference for future research in this area.     

A new paradigm for graduate research and training in the biomedical sciences and engineering

98Emphasis on the individual investigator has fostered discovery for centuries, yet it is now recognized that the complexity of problems in the biomedical sciences and engineering requires collaborative efforts from individuals having diverse training and expertise. Various approaches can facilitate interdisciplinary interactions, but we submit that there is a critical need for a new educational paradigm for the way that we train biomedical engineers, life scientists, and mathematicians. We cannot continue to train graduate students in isolation within single disciplines, nor can we ask any one individual to learn all the essentials of biology, engineering, and mathematics. We must transform how students are trained and incorporate how real-world research and development are done-in diverse, interdisciplinary teams. Our fundamental vision is to create an innovative paradigm for graduate research and training that yields a new generation of biomedical engineers, life scientists, and mathematicians that is more diverse and that embraces and actively pursues a truly interdisciplinary, team-based approach to research based on a known benefit and mutual respect. In this paper, we describe our attempt to accomplish this via focused training in biomechanics, biomedical optics, mathematics, mechanobiology, and physiology. The overall approach is applicable, however, to most areas of biomedical research.     

Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge

Cell cultures used in biomedical experiments come in the form of both sample biopsy primary cells, and maintainable immortalised cell lineages. The rise of bioinformatics and high-throughput technologies has led us to the requirement of ontology representation of cell types and cell lines. The Cell Ontology (CL) and Cell Line Ontology (CLO) have long been established as reference ontologies in the OBO framework. We have compiled a series of the challenges and the proposals of solutions in this CELLS (Cells in ExperimentaL Life Sciences) thematic series that cover the grounds of standing issues and the directions, which were discussed in the First International Workshop on CELLS at the the International Conference on Biomedical Ontology (ICBO). This workshop focused on the extension of the current CL and CLO to cover a wider set of biological questions and challenges needing semantic infrastructure for information modeling. We discussed data-driven use cases that leverage linkage of CL, CLO and other bio-ontologies. This is an established approach in data-driven ontologies such as the Experimental Factor Ontology (EFO), and the Ontology for Biomedical Investigation (OBI). The First International Workshop on CELLS at the International Conference on Biomedical Ontology has brought together experimental biologists and biomedical ontologists to discuss solutions to organizing and representing the rapidly evolving knowledge gained from experimental cells. The workshop has successfully identified the areas of challenge, and the gap in connecting the two domains of knowledge. The outcome of this workshop yielded practical implementation plans to filled in this gap.This CELLS workshop also provided a venue for panel discussions of innovative solutions as well as challenges in the development and applications of biomedical ontologies to represent and analyze experimental cell data.     

Repurposing biomedical muscle tissue engineering for cellular agriculture: challenges and opportunities

Cellular agriculture is an emerging field rooted in engineering meat-mimicking cell-laden structures using tissue engineering practices that have been developed for biomedical applications, including regenerative medicine. Research and industrial efforts are focused on reducing the cost and improving the throughput of cultivated meat (CM) production using these conventional practices. Due to key differences in the goals of muscle tissue engineering for biomedical versus food applications, conventional strategies may not be economically and technologically viable or socially acceptable. In this review, these two fields are critically compared, and the limitations of biomedical tissue engineering practices in achieving the important requirements of food production are discussed. Additionally, the possible solutions and the most promising biomanufacturing strategies for cellular agriculture are highlighted.     

生物医学工程的研究范围

“生物医学工程”这个词汇蕴含了三个专业领域的相互影响：生物学（最广义的范围讲是基于物理学和化学的一门基础科学）、医学（治疗疾病的科学）和工程学（设计及建造对人类有用的物品的科学）。在20世纪50年代中期,我被任命组建一个实验室,这个实验室需要结合这三大学科,并致力于听觉研究。在过去的50年中,我们的实验室（由麻省理工大学、哈佛大学、麻省总医院及麻省眼耳医院共同管理）树立了一个优秀的范例,证明虽然有一些实际的困难,科学家、临床医师和工程师们仍然可以很好地合作。我们的经验之一是,往往一些最成功的发现是基于对基本科学知识的发展,而不是来源于对特定临床需要的靶向性研究。然而,“研究与发展”常常需要有技术创新教育背景,并能与数个领域的专家充分交流的特殊工作人员。因此,在目前这个环境与社会问题需要传统意义上非生物医学工程领域的技术专家的时代,生物医学工程师的培养问题及资源应如何在发达国家与发展中国家之间分配的问题的探讨,都具有十分重要的现实意义。     

系统生物科学与工程的高科技产业化

系统生物科学最早开创于贝塔郎菲的理论生物学和一般系统论。系统生物科学或生物系统科学研究分子、细胞、器官和群体各层次的生物系统,尤其是心智和遗传的信息系统。系统生物工程(曾邦哲1994年)采用实验分析和系统逻辑的双重方法论,探索改造和仿造生物系统的工程技术,包括:1)生化工程、生态工程,2)生物反应器、遗传工程,3)高分子传感器、仿生工程,4)生物遗传计算、智能工程等领域,将促进系统医学、转基因生物反应器、生物计算机、智能机器人和中医药现代化的发展。现代城市生态、工业网络的系统藕合、循环、再生的无污染、无烟化工业生态工程将带来自然、工业、人文之间的和谐。     

Using contextual and lexical features to restructure and validate the classification of biomedical concepts

Background  

Biomedical ontologies are critical for integration of data from diverse sources and for use by knowledge-based biomedical applications, especially natural language processing as well as associated mining and reasoning systems. The effectiveness of these systems is heavily dependent on the quality of the ontological terms and their classifications. To assist in developing and maintaining the ontologies objectively, we propose automatic approaches to classify and/or validate their semantic categories. In previous work, we developed an approach using contextual syntactic features obtained from a large domain corpus to reclassify and validate concepts of the Unified Medical Language System (UMLS), a comprehensive resource of biomedical terminology. In this paper, we introduce another classification approach based on words of the concept strings and compare it to the contextual syntactic approach.     

The use of ruminant models in biomedical perinatal research

Animal models are of critical importance in biomedical research. Although rodents and lagomorphs are the most commonly used species, larger species are required, especially when surgical approaches or new medical devices have to be evaluated. In particular, in the field of perinatal medicine, they are critical for the evaluation of new pharmacologic treatments and the development of new invasive procedures in fetuses. In some areas, such as developmental genetics, reproductive biotechnologies and metabolic programming, the contribution of ruminants is essential. The current report focuses on some of the most outstanding examples of great biomedical advances carried out with ruminant models in the field of perinatal research. Experiments recently carried in our research unit using ruminants are also briefly described.