TRANSAUTOPHAGY: European network for multidisciplinary research and translation of autophagy knowledge

A collaborative consortium, named “TRANSAUTOPHAGY,” has been created among European research groups, comprising more than 150 scientists from 21 countries studying diverse branches of basic and translational autophagy. The consortium was approved in the framework of the Horizon 2020 Program in November 2015 as a COST Action of the European Union (COST means: CO-operation in Science and Technology), and will be sponsored for 4 years. TRANSAUTOPHAGY will form an interdisciplinary platform for basic and translational researchers, enterprises and stakeholders of diverse disciplines (including nanotechnology, bioinformatics, physics, chemistry, biology and various medical disciplines). TRANSAUTOPHAGY will establish 5 different thematic working groups, formulated to cooperate in research projects, share ideas, and results through workshops, meetings and short term exchanges of personnel (among other initiatives). TRANSAUTOPHAGY aims to generate breakthrough multidisciplinary knowledge about autophagy regulation, and to boost translation of this knowledge into biomedical and biotechnological applications.     

Teleconference versus Face-to-Face Scientific Peer Review of Grant Application: Effects on Review Outcomes

Teleconferencing as a setting for scientific peer review is an attractive option for funding agencies, given the substantial environmental and cost savings. Despite this, there is a paucity of published data validating teleconference-based peer review compared to the face-to-face process.Our aim was to conduct a retrospective analysis of scientific peer review data to investigate whether review setting has an effect on review process and outcome measures.We analyzed reviewer scoring data from a research program that had recently modified the review setting from face-to-face to a teleconference format with minimal changes to the overall review procedures. This analysis included approximately 1600 applications over a 4-year period: two years of face-to-face panel meetings compared to two years of teleconference meetings. The average overall scientific merit scores, score distribution, standard deviations and reviewer inter-rater reliability statistics were measured, as well as reviewer demographics and length of time discussing applications.The data indicate that few differences are evident between face-to-face and teleconference settings with regard to average overall scientific merit score, scoring distribution, standard deviation, reviewer demographics or inter-rater reliability. However, some difference was found in the discussion time.These findings suggest that most review outcome measures are unaffected by review setting, which would support the trend of using teleconference reviews rather than face-to-face meetings. However, further studies are needed to assess any correlations among discussion time, application funding and the productivity of funded research projects.     

Transgenic Technology meeting 2008 in Toronto, Canada: a meeting report

In a history that goes back to 1999, the Transgenic Technology meetings started out in Sweden and over the years began to attract a growing community of technicians and researchers mainly from Europe. As the meetings started to attract an expanding worldwide audience, the community decided to found the International Society for Transgenic Technologies at the Barcelona meeting in 2005. The 2007 convention was held at Brisbane, Australia, and in 2008, the 8th Transgenic Technology meeting was held for the second time on behalf of ISTT and for the second time outside of Europe in Toronto, Canada. Due to its excellent program with over 400 participants the meeting was able to attract the highest number of delegates of all past TT meetings. With extended times for plenary discussions about technical and organizational aspects, as well as top level scientific presentations, both technicians and scientists enjoyed this as an extremely fruitful meeting from which they could take home solutions for daily routines as well as new insights and ideas for coming projects.     

Developing experimental design and troubleshooting skills in an advanced biochemistry lab

Two skills critically important to all scientists are the ability to design good experiments and to troubleshoot experiments that do not yield the expected results. In spite of their importance, however, these skills are rarely taught as a part of the undergraduate science curriculum. This deficiency was addressed by creating an advanced biochemistry laboratory course that focuses on the development of experimental design and troubleshooting skills. The course provides students with the opportunity to design and evaluate their own experiments through semester-long independent projects that have a common theme (in this case, protein purification, but any theme could be used). Students plan their projects and carry through the experiments by consulting the primary research literature. The instructor provides minimal input in troubleshooting situations, instead allowing the student to think through and implement alternative solutions. A 2-year survey of the course revealed that students were often frustrated but felt the course significantly improved their experimental laboratory skills as well as introducing them to “real-world” laboratory experience. They further indicated that they preferred the approach used in this course to directed “cook-book” laboratory experiences.     

Science, senators, and uncertainty.

Members of Congress consider value judgments and the likelihood of successful enactment as well as scientific facts in formulating policy. If scientists would provide a range of scientifically acceptable options at the same time as they recommend the scientifically optimal solutions, politicans could choose the best scientific option that is also politically acceptable. In the context of research funding Congress needs to be presented with more realistic expectations about the time it takes for different levels of research to result in practical applications, so as to provide better continuity in research funding.     

Theme C: Medical information systems and databases – results and future work

This paper presents the activities of the theme C “medical information systems and databases” in the GDR Stic Santé. Six one-day workshops have been organized during the period 2011–2012. They were devoted to 1) sharing anatomical and physiological object models for simulation of clinical medical images, 2) advantages and limitations of datawarehouse for biological data, 3) medical information engineering, 4) systems for sharing medical images for research, 5) knowledge engineering for semantic interoperability in e-health applications, and 6) using context in health. In the future, our activities will continue with a specific interest on information systems for translational medicine and the role of electronic healthcare reports in decision-making. Workshops with other research groups will be organized in particular with the e-health research group.     

我国医疗质量研究30年的历史回顾与基本特征

医药卫生体制改革已走过30年光辉历程。利用CNKI检索系统,采取文献回顾方法,首次全面系统回顾医疗质量研究状况。医疗质量研究可以划分为阶段明显的3个时期,每个历史阶段的基本特征明显。研究发现,卫生质量研究的主题是医疗质量。医疗质量议题由少到多,由冷到热,由边缘到主流,成为卫生政策与医院管理的核心议题。基本结论是,卫生质量与医疗质量的研究目的、动力源泉、研究范围、研究议题、研究方法和理论视角亟待结构调整,以回应国人不断提高的健康需要,深化医药卫生体制改革,加强医学人文关怀,建立卫生保健财政制度,构建和谐医患关系。     

International scientific meetings: relation between structure and function.

Increasing pressure is being placed on the scientific community to evaluate research activities. Scientific meetings consume a small but important fraction of the research budget. Audit of a well established series of scientific meetings showed that they met their immediate objectives in that they were international and multidisciplinary and provided a forum in which all participants actively contributed to discussion. The meetings had a positive outcome for the participants, leading in many cases to the subsequent exchange of research material (60% of participants) and to the establishment of collaborative research projects (31%). The impact of the meetings on the scientific community at large was assessed by citation analysis, which showed that the proceedings were cited early, often, and over a substantial period.     

From cell biology to biotechnology in space

In this article I discuss the main results of our research in space biology from the simple early investigations with human lymphocytes in the early eighties until the projects in tissue engineering of the next decade on the international space station ISS. The discovery that T lymphocyte activation is nearly totally depressed in vitro in 0 g conditions showed that mammalian single cells are sensitive to the gravitational environment. Such finding had important implications in basic research, medicine and biotechnology. Low gravity can be used as a tool to investigate complicated and still obscure biological process from a new perspective not available to earth-bound laboratories. Low gravity may also favor certain bioprocesses involving the growth of tissues and thus lead to commercial and medical applications. However, shortage of crew time and of other resources, lack of sophisticated instrumentation, safety constraints pose serious limits to biological endeavors in space laboratories.     

Biosynthetic pathways for 3-hydroxypropionic acid production

Biobased platform chemicals have attracted growing interest recently. Among them, 3-hydroxypropionic acid receives significant attention due to its applications in the synthesis of novel polymer materials and other derivatives. To establish a biotechnology route instead of the problematic chemical synthesis of 3-hydroxypropionic acid, biosynthetic pathway is required, and the strategies of how to engineer a microbe to produce this product should be considered. In the present review, we summarize and review all known pathways, which could be potentially constructed for 3-hydroxypropionic acid production. Mass and redox balances are discussed in detail. Thermodynamic favorability is evaluated by standard Gibbs free energy. The assembly of pathways and possible solutions are proposed. Several new techniques and future research needs are also covered.     

Theme A: Modeling and simulation in biomedical research. Results and future works

This paper presents the activity of the theme A “Modeling and simulation in biomedical research” within the GdR STIC Santé. This group has organized four scientific meetings and has managed one action, together with the theme B “Biomedical Signal and Image Processing”, during the period 2011–2012. The meetings have focused on modeling of the cardiorespiratory control, on the modeling and physiopathology of cardiovascular system and on Complex Systems in Biology and Medicine (co-organized with the GDR “Dynamique et Contrôle des Systèmes Complexes” – DYCOEC). The fourth one represents the official start of the “VPH-France” network that has been labeled by the Réseau National de Systèmes Complexes (RNSC). The SIGnal-processing and Modeling methods to Undertake Neonatal care during Development (SIGMUND) action has concerned seven hospitals and five CIC-IT (Clinical Technological Innovation Center) and has brought to the development of a regional project (Care-Premi) including three of the seven hospitals. The future works will focus: on strengthening the interactions with other topics of this GDR and with other GDRs, on application of modeling to solve real clinical heath problems, on the better acceptation of modeling by the industrial community.     

WHO ARE THE BENEFICIARIES?

Is it defensible that society spends money on medical or research projects intended to help people solve their fertility problems? Suppose that we want to answer this question from the point of view of a utilitarian cost-benefit analysis. The answer to the question then depends, of course, on how expensive these projects turn out to be, relative to the costs of other possible projects. But it depends also on how we assess the benefits of these projects. To whom do they accrue? Who are the beneficiaries of these projects?     

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.     

Professional societies and industry support: what is the quid pro quo?

Professional medical societies have become increasingly dependent on pharmaceutical, device, and biotechnology companies for ongoing support of their programs, but the internal influence of this financial largesse on medical societies' practices is well hidden. Many examples exist in which societies' educational products, including clinical practice guidelines and professional publications, have been tainted by involvement by industry-paid individuals. These examples show that professional judgments of organizations can be affected in ways that are not in the best interests of our patients. Society leaders should develop policies that leave critical decisions, especially those that affect patient care, in the hands of members without financial ties to industry. Society leaders should not accept funds designated for specific industry-recommended projects unless such programs are already part of their planned agenda. These leaders, who typically serve for only a year or two, should delve into arrangements that salaried society executives make with industry, and insure that no promises are made that compromise an organization's professional goals. Professional societies should also find ways of reducing the vast, embarrassing industry involvement at their national meetings, especially the vulgar circus-like displays and the drug company-sponsored symposia. We must reduce commercialism and restore professionalism to our medical meetings.     

Medical research; the program of the U.S. Public Health Service

Federal Government expenditures for medical research have increased apace in the last ten years. The increase in federal research funds has stimulated support from private sources; contributions from other than federal sources have doubled. More than half of medical research funds are being used by universities, hospitals, and other nonprofit institutions, and less than one-fourth by laboratories of the Federal Government.Grants-in-aid of research, fellowships and extended training are made on the advice of Advisory Councils made up of leaders in the various research fields. The previous record of research by staffs and faculties of institutions is taken into account. Special attention is given to unknown investigators and small projects. Noninterference with a scientist in the conduct of research is a basic principle of all grants. He may change the direction of his research to pursue promising leads without asking permission. Continuity of grants so that promising projects need not be abandoned at the end of a grant period is given special consideration.     

MEDICAL RESEARCH—The Program of the U. S. Public Health Service

Federal Government expenditures for medical research have increased apace in the last ten years. The increase in federal research funds has stimulated support from private sources; contributions from other than federal sources have doubled.More than half of medical research funds are being used by universities, hospitals, and other nonprofit institutions, and less than one-fourth by laboratories of the Federal Government.Grants-in-aid of research, fellowships and extended training are made on the advice of Advisory Councils made up of leaders in the various research fields. The previous record of research by staffs and faculties of institutions is taken into account. Special attention is given to unknown investigators and small projects.Noninterference with a scientist in the conduct of research is a basic principle of all grants. He may change the direction of his research to pursue promising leads without asking permission.Continuity of grants so that promising projects need not be abandoned at the end of a grant period is given special consideration.     

Mangrove Restoration: Do We Know Enough?

Mangrove restoration projects have been attempted, with mixed results, throughout the world. In this paper, I first examine goals of existing mangrove restoration projects and determine whether these goals are clear and adequate, and whether or not they account for the full range of biological diversity and ecological processes of mangrove ecosystems. Many restored mangrove forests resemble forest plantations rather than truly integrated ecosystems, but mangrove plantations can be a first step toward mangrove rehabilitation. Mangrove restoration projects that involve associated aquaculture or mariculture operations tend to be more likely to approximate the biological diversity and ecological processes of undisturbed mangrove ecosystems than are projects that focus only on the trees. These integrated restoration projects also provide a higher economic return than do silvicultural projects alone. Second, I briefly assess whether existing ecological data are sufficient to undergird successful restoration of mangal and define criteria for determining whether or not a mangrove ecosystem has been restored successfully. These criteria include characteristics of vegetation (forest) structure, levels of primary production, composition of associated animal communities, and hydrology. Finally, I suggest ways to improve mangrove restoration projects and identify key research needs required to support these efforts. Ecological theories derived from other wetland and upland systems rarely have been applied to either “basic” or “applied” mangrove forest studies, to the detriment of restoration projects, whereas lessons from restoration of the relatively species‐poor mangrove ecosystems could be beneficially applied to restoration projects in other contexts. An international database of mangrove restoration projects would reduce the likelihood that unsuccessful restoration projects would be repeated elsewhere. Clear criteria for evaluating success, greater accessibility of information by managers in the developing world, intensified international cooperation, and application of relevant ecological theories will improve the success rate of mangrove restoration projects.     

An international basic science and clinical research summer program for medical students

An important part of training the next generation of physicians is ensuring that they are exposed to the integral role that research plays in improving medical treatment. However, medical students often do not have sufficient time to be trained to carry out any projects in biomedical and clinical research. Many medical students also fail to understand and grasp translational research as an important concept today. In addition, since medical training is often an international affair whereby a medical student/resident/fellow will likely train in many different countries during his/her early training years, it is important to provide a learning environment whereby a young medical student experiences the unique challenges and value of an international educational experience. This article describes a program that bridges the gap between the basic and clinical research concepts in a unique international educational experience. After completing two semester curricula at Alfaisal University in Riyadh, Kingdom of Saudi Arabia, six medical students undertook a summer program at St. Boniface Hospital Research Centre, in Winnipeg, MB, Canada. The program lasted for 2 mo and addressed advanced training in basic science research topics in medicine such as cell isolation, functional assessment, and molecular techniques of analysis and manipulation as well as sessions on the conduct of clinical research trials, ethics, and intellectual property management. Programs such as these are essential to provide a base from which medical students can decide if research is an attractive career choice for them during their clinical practice in subsequent years. An innovative international summer research course for medical students is necessary to cater to the needs of the medical students in the 21st century.     

Perspectives in marine science: A European point of view

Marine research has always been a field in science which was particularly open to, and at times dependent on, international cooperation, and this has become even more obvious during the last decade when issues of global change became central to any discussion. The global nature of scientific and other problems, required the development of new concepts and led to the establishment of new structures in research, coordination and funding on an international level. In Europe the 12 member European Community often served as a nucleus for larger networks and initiatives (e.g. COST, EUREKA), and in 1989 the EC itself launched a specific programme on marine research and technology (MAST). The various initiatives are not meant to replace, national efforts but to complement them — where added value arises from international cooperation, e.g. in global programmes like IGBP, WCRP and their various core projects. The focus of support for these programmes through international funding agencies and networks is not primarily on additional research money but more on structural support and coordination. In contrast, the MAST targeted projects on the North Atlantic margin and the Mediterranean also receive substantial basic support, and are designed to fill gaps left by other international research projects. Both EC and other projects profit from the coordinating measures offered by the EC Commission. A more efficient use of facilities (research vessels, special equipment) can be achieved by having central information services. Well-integrated international projects also require additional efforts in standardization of instrumentation, methods and units, with respect to sampling, sample processing and data treatment. Furthermore, the scope of the task to tackle questions of global change demands the development of new technologies like ROVs, biosensors, automatized sample and data acquisition and treatment, etc. Full exploitation of the results in scientific, political and economical terms is only facilitated through special concertation. Mathematical modelling of ecosystems is still in its infancy and needs further cooperative development in order to provide tools for forecasting and management. Finally, training and exchange of personnel on a European, and possibly wider, level needs to be intensified in order to meet the requirements of modern science.     

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

Background

Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups.

Results

We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects.

Conclusions

The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities.