Information retrieval and knowledge discovery utilising a biomedical Semantic Web

Although various ontologies and knowledge sources have been developed in recent years to facilitate biomedical research, it is difficult to assimilate information from multiple knowledge sources. To enable researchers to easily gain understanding of a biomedical concept, a biomedical Semantic Web that seamlessly integrates knowledge from biomedical ontologies, publications and patents would be very helpful. In this paper, current research efforts in representing biomedical knowledge in Semantic Web languages are surveyed. Techniques are presented for information retrieval and knowledge discovery from the Semantic Web that extend traditional keyword search and database querying techniques. Finally, some of the challenges that have to be addressed to make the vision of a biomedical Semantic Web a reality are discussed.     

High-tech biomedical research: lessons from Iran's experience

Iran has recently made a significant progress in the field of biomedical science and launched an appreciable number of new high-tech biomedical research projects. Review of Iran's experience in advancing its biomedical research and the pitfalls the country encountered during the years of its progress could be of interest to other countries with similar technological conditions. As needs assessment and human resources have pivotal roles in any research infrastructure, here, we have delineated these factors and explored ways by which optimum advantage could be gained from them.     

The emergence of biomedical anthropology and its implications for the future

Primarily during the past 15 years a distinct new area within physical anthropology has emerged, biomedical anthropology. Physical anthropologists have become heavily involved in studying problems of relevance to the health and illness patterns of living humans. There has been a proportionate increase in biomedically focused papers published in the American Journal of Physical Anthropology, in biomedically focused papers presented at annual meetings of the American Association of Physical Anthropologists, and in physical anthropology doctoral dissertations oriented toward modern biomedical phenomena. Proportionately more physical anthropologists are now employed in medical schools and there has been recent growth in the proportion of physical anthropologists in anthropology departments who claim some aspect of biomedical anthropology as a research interest. Increasingly, physical anthropologists are focusing their research on cardiovascular disease, the leading cause of death in America. These distinct trends are partially a result of the nature of physical anthropology and its unique biocultural perspective. However the growth of applied anthropology, the present academic marketplace, and the availability of research funds are probably also contributing factors. The emergency of biomedical anthropology holds promise for the future of physical anthropology and for its current employment crisis. Careers with academic and nonacademic organizations engaged in biomedical research appear to be a viable alternative to careers in departments of anthropology, for biomedical anthropologists. This will entail some reorientation of graduate training for physical anthropologists. More emphasis will have to be placed on substantive biomedical subjects, research methods, and data management and analysis.     

Harold Varmus [interview by Karen Birmingham

He may have stepped away from the hottest seat in biomedical research, but Nobel Laureate Harold Varmus shows no signs of withdrawing from the frontline of the biomedical research community, and he still displays the inimitable combination of political astuteness and scientific expertise that made his reign as director of the United States National Institutes of Health so successful. Varmus spoke to Nature Medicine for the first in a series of profiles that the journal will run on scientists that make a difference to biomedical research.     

Future of biobanking in microbiology for medical research.

Biobanks are actively contributing to advances in biomedical research by offering opportunities to link laboratory research with clinical applications and by accelerating developments in personalized medicine. Microbiologists have a long tradition of storing microorganisms as part of projects focused on microbial genetics or phenotypic investigations. However, the impressive recent advances of biomedical translational research demand the integration of biobanks with high-level technological infrastructures in genomics, proteomics, bioinformatics, patient information systems and disease registries, where data originating from microorganisms are linked with human clinical information with the ultimate aim of improving healthcare by increasing the quality of biomedical research.     

宁乡猪实验动物化研究及在生物医学研究中的应用

宁乡猪为脂肪型猪种,具有遗传性稳定、食用价值高、生长快、适应性强及繁育力强等特征,已逐渐被应用于生物医学研究领域。本文对宁乡猪在封闭群培育、近交系培育、生物学特性及在生物医学研究领域中的应用等研究进展进行了综述。实验宁乡猪已封闭繁殖14年,可能是研究动脉粥样硬化、糖尿病有利模型。     

光镊和拉曼光镊在生物医学研究中的应用

光镊是由美国科学家Arthur Ashkin于1986年发明的,是一种利用高度汇聚的激光束产生的三维梯度势阱来俘获、操纵微小粒子的技术。因其可俘获、操纵单个细胞,并在细胞和亚细胞层次上为生物医学研究提供方便,近年来,已越来越多地被应用于生物医学研究中。本文在介绍光镊的原理和特点的基础上,阐述了光镊(尤其是拉曼光镊)技术在生物医学领域中的研究进展、现状和展望。     

转基因家兔模型制作方法

作为生物医学研究重要的实验动物模型,转基因家兔已经被广泛应用在人类心脑血管疾病、艾滋病以及癌症等生物医学研究领域,特别是利用转基因家兔模型在人类动脉粥样硬化实验研究中已经取得了令人注目的成绩。本文结合我们自己制作转基因家兔的经验、研究成果以及文献资料,详细介绍了利用原核显微注射法、直接将外源基因注入受精卵雄原核中的转基因家兔制作技术,回顾了利用转基因家兔模型在生物医学研究中取得的重要进展。     

Preparing chimpanzees for laboratory research

The chimpanzee is the only representative of the Great Apes that is extensively involved in biomedical research in primate laboratories. These apes are used as animal models in a variety of studies, including research on infectious disease, parasitic disease, pharmacokinetic studies, neuroscience, cognition, and behavior. Chimpanzees used in biomedical research in the United States reside largely in six specialized research and holding facilities, and most of the research with them is conducted at these sites. Given the relatively small population of chimpanzees and its importance to biomedical research, it is imperative that we carefully manage the care, production, and use of these animals in biomedical research studies. Selection criteria and preparation techniques are reviewed in this article in an effort to begin a discussion on best practices for choosing and handling chimpanzees participating in biomedical research. The use of routine health assessment information is described for subject selection, as are behavioral issues to be considered. Due to the relatively small number of chimpanzees available, issues related to experimental design and multiple uses of chimpanzees are discussed. Practices related to the transportation and acclimation of chimpanzees are described. Finally, behavioral conditioning procedures are discussed, including habituation, desensitization, and positive reinforcement training that have been applied to reduce animal distress and improve the quality of the science being conducted with chimpanzee subjects.     

Word sense disambiguation in the biomedical domain: an overview.

There is a trend towards automatic analysis of large amounts of literature in the biomedical domain. However, this can be effective only if the ambiguity in natural language is resolved. In this paper, the current state of research in word sense disambiguation (WSD) is reviewed. Several methods for WSD have already been proposed, but many systems have been tested only on evaluation sets of limited size. There are currently only very few applications of WSD in the biomedical domain. The current direction of research points towards statistically based algorithms that use existing curated data and can be applied to large sets of biomedical literature. There is a need for manually tagged evaluation sets to test WSD algorithms in the biomedical domain. WSD algorithms should preferably be able to take into account both known and unknown senses of a word. Without WSD, automatic metaanalysis of large corpora of text will be error prone.     

Protecting human subjects in research--occasional views along a road less traveled

Public trust in biomedical research is eroding rapidly because too many investigators participating in human subjects research have failed to take personal responsibility for their actions. In this essay, taken partly from an address to the 66th Annual Research Colloquium of the Massachusetts General Hospital, January 2001, and a presentation to the research community of the Washington University School of Medicine in September, 2000, in St. Louis, Missouri; Greg Koski shares his views about protecting human subjects in biomedical research.     

Perspectives on an Education in Computational Biology and Medicine

The mainstream application of massively parallel, high-throughput assays in biomedical research has created a demand for scientists educated in Computational Biology and Bioinformatics (CBB). In response, formalized graduate programs have rapidly evolved over the past decade. Concurrently, there is increasing need for clinicians trained to oversee the responsible translation of CBB research into clinical tools. Physician-scientists with dedicated CBB training can facilitate such translation, positioning themselves at the intersection between computational biomedical research and medicine. This perspective explores key elements of the educational path to such a position, specifically addressing: 1) evolving perceptions of the role of the computational biologist and the impact on training and career opportunities; 2) challenges in and strategies for obtaining the core skill set required of a biomedical researcher in a computational world; and 3) how the combination of CBB with medical training provides a logical foundation for a career in academic medicine and/or biomedical research.     

Ethics and biomedical research

Ethics in biomedical research took off from the 1947 Nuremberg Code to its own right in the wake of the Declaration of Helsinki in 1964. Since then, (inter)national regulations and guidelines providing a framework for clinical studies and protection for study participants have been drafted and implemented, while ethics committees and drug evaluation agencies have sprung up throughout the world. These two developments were crucial in bringing about the protection of rights and safety of the participants and harmonization of the conduct of biomedical research. Ethics committees and drug evaluation agencies deliver ethical and scientific assessments on the quality and safety of the projects submitted to them and issue respectively approvals and authorizations to carry out clinical trials, while ensuring that they comply with regulatory requirements, ethical principles, and scientific guidelines. The advent of biomedical ethics, together with the responsible commitment of clinical investigators and of the pharmaceutical industry, has guaranteed respect for the patient, for whom and with whom research is conducted. Just as importantly, it has also ensured that patients reap the benefit of what is the primary objective of biomedical research: greater life expectancy, well-being, and quality of life.     

普鲁士蓝纳米粒子在生物医学诊断和治疗中的应用及进展

随着生物医学诊断和治疗的持续深入研究,出现了多种医学诊断和治疗新方法,为人类的健康提供了更大的保证,其中纳米生物技术在生物医学诊断和治疗中的应用日益增多,基于纳米技术,开发传统材料的生物医学新应用成为了人们的研究热点。普鲁士蓝是一种历史悠久的蓝色染料,其制备过程简单、绿色、成本低,化学结构稳定,具有优良的物理、化学、光学以及磁性等性能,已经在许多领域得到了广泛的应用。近年来,普鲁士蓝开始在生物医学诊断和治疗领域中崭露头角,它已经成功的被开发为新型的核磁共振造影剂和光声成像造影剂,并且在药物输送系统和光热治疗等领域也开始占有一席之地,开发基于纳米技术的普鲁士蓝的生物医学应用已经成为极具吸引力的研究方向。本文对普鲁士蓝在生物医学诊断和治疗中的应用及进展进行综述。     

氢气生物医学研究进展

氢气以其安全、有效、渗透性强、代谢产物只有水等特点,逐渐进入医学研究者和临床工作者的视野,并在近年来快速发展。大量研究证明,氢气对于包括肿瘤、炎症损伤、代谢疾病、神经性疾病等百余种疾病具有潜在的治疗作用。2020年新型冠状病毒肺炎（新冠肺炎）疫情全球大流行期间,氢气在新冠肺炎辅助治疗中也崭露头角。对氢气在生物医学的动物学、细胞学和临床研究领域的研究进展进行了总结,并主要综述了氢气在代谢性疾病、神经退行性疾病、急救和创伤医学以及肿瘤领域的研究进展,以期为氢气在生物医学领域的应用研究提供参考。     

A decade and genome of change

Innovations in genomic technologies have generated huge advances in biomedical research over the last decade.     

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.     

The distribution of biomedical research resources and international justice

According to some estimates, less than 10% of the world's biomedical research funds are dedicated to addressing problems that are responsible for 90% of the world's burden of disease. This paper explains why this disparity exists and what should be done about it. It argues that the disparity exists because: 1) multinational pharmaceutical and biotechnology companies do not regard research and development investments on the health problems of developing nations to be economically lucrative; and 2) governmental agencies that sponsor biomedical research face little political pressure to allocate funds for the problems of developing nations. This paper argues that developed nations have an obligation to address disparities related to biomedical research funding. To facilitate this effort, developed countries should establish a trust fund dedicated to research on the health problems of developing nations similar to the Global AIDS Fund.     

Advances in biomedical applications of pectin gels

Pectin, due to its simple and cytocompatible gelling mechanism, has been recently exploited for different biomedical applications including drug delivery, gene delivery, wound healing and tissue engineering. Recent studies involving pectin for the biomedical field are reviewed, with the aim to capture the state of art on current research about pectin gels for biomedical applications, moving outside the traditional fields of application such as the food industry or pharmaceutics. Pectin structure, sources and extraction procedures have been discussed focussing on the properties of the polysaccharide that can be tuned to optimize the gels for a desired application and possess a fundamental role in application of pectin in the biomedical field.