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"Biomedical Research standards."
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Survey of laboratory-acquired infections around the world in biosafety level 3 and 4 laboratories
Laboratory-acquired infections due to a variety of bacteria, viruses, parasites, and fungi have been described over the last century, and laboratory workers are at risk of exposure to these infectious agents. However, reporting laboratory-associated infections has been largely voluntary, and there is no way to determine the real number of people involved or to know the precise risks for workers. In this study, an international survey based on volunteering was conducted in biosafety level 3 and 4 laboratories to determine the number of laboratory-acquired infections and the possible underlying causes of these contaminations. The analysis of the survey reveals that laboratory-acquired infections have been infrequent and even rare in recent years, and human errors represent a very high percentage of the cases. Today, most risks from biological hazards can be reduced through the use of appropriate procedures and techniques, containment devices and facilities, and the training of personnel.
Journal Article
Increasing disparities between resource inputs and outcomes, as measured by certain health deliverables, in biomedical research
Society makes substantial investments in biomedical research, searching for ways to better human health. The product of this research is principally information published in scientific journals. Continued investment in science relies on society’s confidence in the accuracy, honesty, and utility of research results. A recent focus on productivity has dominated the competitive evaluation of scientists, creating incentives to maximize publication numbers, citation counts, and publications in high-impact journals. Some studies have also suggested a decreasing quality in the published literature. The efficiency of society’s investments in biomedical research, in terms of improved health outcomes, has not been studied. We show that biomedical research outcomes over the last five decades, as estimated by both life expectancy and New Molecular Entities approved by the Food and Drug Administration, have remained relatively constant despite rising resource inputs and scientific knowledge. Research investments by the National Institutes of Health over this time correlate with publication and author numbers but not with the numerical development of novel therapeutics. We consider several possibilities for the growing input-outcome disparity including the prior elimination of easier research questions, increasing specialization, overreliance on reductionism, a disproportionate emphasis on scientific outputs, and other negative pressures on the scientific enterprise. Monitoring the efficiency of research investments in producing positive societal outcomes may be a useful mechanism for weighing the efficacy of reforms to the scientific enterprise. Understanding the causes of the increasing input-outcome disparity in biomedical research may improve society’s confidence in science and provide support for growing future research investments.
Journal Article
Clinical research and the law
The legal implications of conducting clinical research and trials are becoming more complex. Everyone involved in clinical research increasingly needs to be aware of not only the ethical issues at stake but also how the law affects medical practice and research. Much of clinical research and trial law and litigation is comparatively recent and researchers need to ensure current compliance on a wide range of issues. Including: standards and duty of care informed consent conflicts of interest research contracts establishing clinical trials the disclosure and withholding of clinical trial results Clinical Research and the Law comprehensively discusses these topics and provides the answers to the legal questions and potential pitfalls encountered in medical research. It is an up-to-date, practical guide for clinical investigators and their institutional administrators, particularly risk managers and research administrators, as well as healthcare administrators and members of institutional review boards. This book is also a key resource for medical students, postgraduate research students, practicing attorneys and counselors for teaching hospitals and institutions undertaking clinical research and contract research organizations.
eBook
Improving the trustworthiness, usefulness, and ethics of biomedical research through an innovative and comprehensive institutional initiative
The reproducibility crisis triggered worldwide initiatives to improve rigor, reproducibility, and transparency in biomedical research. There are many examples of scientists, journals, and funding agencies adopting responsible research practices. The QUEST (Quality-Ethics-Open Science-Translation) Center offers a unique opportunity to examine the role of institutions. The Berlin Institute of Health founded QUEST to increase the likelihood that research conducted at this large academic medical center would be trustworthy, useful for scientists and society, and ethical. QUEST researchers perform \"science of science\" studies to understand problems with standard practices and develop targeted solutions. The staff work with institutional leadership and local scientists to incentivize and support responsible practices in research, funding, and hiring. Some activities described in this paper focus on the institution, whereas others may benefit the national and international scientific community. Our experience, approaches, and recommendations will be informative for faculty leadership, administrators, and researchers interested in improving scientific practice.
Journal Article
IOF position on scientists and societies operating in conflict zones
This position paper of the International Osteoporosis Foundation reports the findings of an IOF Commission to consider to recommend rules of partnership with scientists belonging to a country which is currently responsible for an armed conflict, anywhere in the world. The findings and recommendations have been adopted unanimously by the Board of IOF.
Journal Article
Strategies to improve clinical research in surgery through international collaboration
More than 235 million patients undergo surgery every year worldwide, but less than 1% are enrolled in surgical clinical trials—few of which are international collaborations. Several levels of action are needed to improve this situation. International research collaborations in surgery between developed and developing countries could encourage capacity building and quality improvement, and mutually enhance care for patients with surgical disorders. Low-income and middle-income countries increasingly report much the same range of surgical diseases as do high-income countries (eg, cancer, cardiovascular disease, and the surgical sequelae of metabolic syndrome); collaboration is therefore of mutual interest. Large multinational trials that cross cultures and levels of socioeconomic development might have faster results and wider applicability than do single-country trials. Surgeons educated in research methods, and aided by research networks and trial centres, are needed to foster these international collaborations. Barriers to collaboration could be overcome by adoption of global strategies for regulation, health insurance, ethical approval, and indemnity coverage for doctors.
Journal Article
Why rankings of biomedical image analysis competitions should be interpreted with care
International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges has not yet been performed. In this paper, we present a comprehensive analysis of biomedical image analysis challenges conducted up to now. We demonstrate the importance of challenges and show that the lack of quality control has critical consequences. First, reproducibility and interpretation of the results is often hampered as only a fraction of relevant information is typically provided. Second, the rank of an algorithm is generally not robust to a number of variables such as the test data used for validation, the ranking scheme applied and the observers that make the reference annotations. To overcome these problems, we recommend best practice guidelines and define open research questions to be addressed in the future.
Biomedical image analysis challenges have increased in the last ten years, but common practices have not been established yet. Here the authors analyze 150 recent challenges and demonstrate that outcome varies based on the metrics used and that limited information reporting hampers reproducibility.
Journal Article
Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers
The rapid growth of high-throughput technologies has transformed biomedical research. With the increasing amount and complexity of data, scalability and reproducibility have become essential not just for experiments, but also for computational analysis. However, transforming data into information involves running a large number of tools, optimizing parameters, and integrating dynamically changing reference data. Workflow managers were developed in response to such challenges. They simplify pipeline development, optimize resource usage, handle software installation and versions, and run on different compute platforms, enabling workflow portability and sharing. In this Perspective, we highlight key features of workflow managers, compare commonly used approaches for bioinformatics workflows, and provide a guide for computational and noncomputational users. We outline community-curated pipeline initiatives that enable novice and experienced users to perform complex, best-practice analyses without having to manually assemble workflows. In sum, we illustrate how workflow managers contribute to making computational analysis in biomedical research shareable, scalable, and reproducible.This Perspective highlights workflow managers, which are useful for developing and managing complex bioinformatics pipelines.
Journal Article