A Framework for Managing Core Facilities within the Research Enterprise

Core facilities represent increasingly important operational and strategic components of institutions'' research enterprises, especially in biomolecular science and engineering disciplines. With this realization, many research institutions are placing more attention on effectively managing core facilities within the research enterprise. A framework is presented for organizing the questions, challenges, and opportunities facing core facilities and the academic units and institutions in which they operate. This framework is intended to assist in guiding core facility management discussions in the context of a portfolio of facilities and within the overall institutional research enterprise.     

Metrics for Success: Strategies for Enabling Core Facility Performance and Assessing Outcomes

Core Facilities are key elements in the research portfolio of academic and private research institutions. Administrators overseeing core facilities (core administrators) require assessment tools for evaluating the need and effectiveness of these facilities at their institutions. This article discusses ways to promote best practices in core facilities as well as ways to evaluate their performance across 8 of the following categories: general management, research and technical staff, financial management, customer base and satisfaction, resource management, communications, institutional impact, and strategic planning. For each category, we provide lessons learned that we believe contribute to the effective and efficient overall management of core facilities. If done well, we believe that encouraging best practices and evaluating performance in core facilities will demonstrate and reinforce the importance of core facilities in the research and educational mission of institutions. It will also increase job satisfaction of those working in core facilities and improve the likelihood of sustainability of both facilities and personnel.     

Best Practices for Core Facilities: Handling External Customers

This article addresses the growing interest among U.S. scientific organizations and federal funding agencies in strengthening research partnerships between American universities and the private sector. It outlines how core facilities at universities can contribute to this partnership by offering services and access to high-end instrumentation to both nonprofit organizations and commercial organizations. We describe institutional policies (best practices) and procedures (terms and conditions) that are essential for facilitating and enabling such partnerships. In addition, we provide an overview of the relevant federal regulations that apply to external use of academic core facilities and offer a set of guidelines for handling them. We conclude by encouraging directors and managers of core facilities to work with the relevant organizational offices to promote and nurture such partnerships. If handled appropriately, we believe such partnerships can be a win-win situation for both organizations that will support research and bolster the American economy.     

Enhancing Research Ethics Review Systems in Egypt: The Focus of an International Training Program Informed by an Ecological Developmental Approach to Enhancing Research Ethics Capacity

Recently, training programs in research ethics have been established to enhance individual and institutional capacity in research ethics in the developing world. However, commentators have expressed concern that the efforts of these training programs have placed ‘too great an emphasis on guidelines and research ethics review’, which will have limited effect on ensuring ethical conduct in research. What is needed instead is a culture of ethical conduct supported by national and institutional commitment to ethical practices that are reinforced by upstream enabling conditions (strong civil society, public accountability, and trust in basic transactional processes), which are in turn influenced by developmental conditions (basic freedoms of political freedoms, economic facilities, social opportunities, transparency guarantees, and protective security). Examining this more inclusive understanding of the determinants of ethical conduct enhances at once both an appreciation of the limitations of current efforts of training programs in research ethics and an understanding of what additional training elements are needed to enable trainees to facilitate national and institutional policy changes that enhance research practices. We apply this developmental model to a training program focused in Egypt to describe examples of such additional training activities.     

Coverage and Financial Risk Protection for Institutional Delivery: How Universal Is Provision of Maternal Health Care in India?

Background

India aims to achieve universal access to institutional delivery. We undertook this study to estimate the universality of institutional delivery care for pregnant women in Haryana state in India. To assess the coverage of institutional delivery, we analyze service coverage (coverage of public sector institutional delivery), population coverage (coverage among different districts and wealth quintiles of the population) and financial risk protection (catastrophic health expenditure and impoverishment as a result of out-of-pocket expenditure for delivery).

Methods

We analyzed cross-sectional data collected from a randomly selected sample of 12,191 women who had delivered a child in the last one year from the date of data collection in Haryana state. Five indicators were calculated to evaluate coverage and financial risk protection for institutional delivery—proportion of public sector deliveries, out-of-pocket expenditure, percentage of women who incurred no expenses, prevalence of catastrophic expenditure for institutional delivery and incidence of impoverishment due to out-of-pocket expenditure for delivery. These indicators were calculated for the public and private sectors for 5 wealth quintiles and 21 districts of the state.

Results

The coverage of institutional delivery in Haryana state was 82%, of which 65% took place in public sector facilities. Approximately 63% of the women reported no expenditure on delivery in the public sector. The mean out-of-pocket expenditures for delivery in the public and private sectors in Haryana were INR 771 (USD 14.2) and INR 12,479 (USD 229), respectively, which were catastrophic for 1.6% and 22% of households, respectively.

Conclusion

Our findings suggest that there is considerably high coverage of institutional delivery care in Haryana state, with significant financial risk protection in the public sector. However, coverage and financial risk protection for institutional delivery vary substantially across districts and among different socio-economic groups and must be strengthened. The success of the public sector in providing high coverage and financial risk protection in maternal health provides encouragement for the role that the public sector can play in universalizing health care.     

Organizing core facilities as force multipliers: strategies for research universities

Force multipliers are attributes of an organization that enable the successful completion of multiple essential missions. Core facilities play a critical role in the research enterprise and can be organized as force multipliers. Conceiving of cores in this way influences their organization, funding, and research impact. To function as a force multiplier for the research enterprise, core facilities need to do more than efficiently provide services for investigators and generate revenue to recover their service costs: they must be aligned with the strategic objectives of a research university. When core facilities are organized in this way, they can facilitate recruitment of faculty and trainees; serve to retain talented faculty; drive, acquire, and maintain cutting-edge research platforms; and promote interaction and collaboration across the institution. Most importantly, cores accelerate the discovery and sharing of knowledge that are the foundation of a modern research university. This idea has been systematically implemented through the Emory Integrated Core Facilities (cores.emory.edu), which include 16 distinct core facilities and the Division of Animal Resources. Force multiplier core facilities can significantly contribute to the many essential missions necessary for the success of the research enterprise at research universities.     

U.S. National Institutes of Health Core Consolidation–Investing in Greater Efficiency

The U.S. National Institutes of Health (NIH) invests substantial resources in core research facilities (cores) that support research by providing advanced technologies and scientific and technical expertise as a shared resource. In 2010, the NIH issued an initiative to consolidate multiple core facilities into a single, more efficient core. Twenty-six institutions were awarded supplements to consolidate a number of similar core facilities. Although this approach may not work for all core settings, this effort resulted in consolidated cores that were more efficient and of greater benefit to investigators. The improvements in core operations resulted in both increased services and more core users through installation of advanced instrumentation, access to higher levels of management expertise; integration of information management and data systems; and consolidation of billing; purchasing, scheduling, and tracking services. Cost recovery to support core operations also benefitted from the consolidation effort, in some cases severalfold. In conclusion, this program of core consolidation resulted in improvements in the effective operation of core facilities, benefiting both investigators and their supporting institutions.     

How Did Institut Pasteur’s NGS Core Facility,Biomics, Manage the Coronavirus Disease 2019 Crisis?

In 2020, research entities at the Institut Pasteur (IP) in Paris, as elsewhere around the world, were closed because of the coronavirus disease 2019 (COVID-19) pandemic. However, IP core facilities, laboratories, services, and departments working on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and priority projects were authorized to continue working both on site and remotely. Given the importance of its role in SARS-CoV-2 genome-sequencing initiatives, the IP Biomics core facility was fully functional during the first (i.e., March–June 2020) and second (i.e., November–December 2020) national lockdowns. We describe here how Biomics successfully implemented an emergency management plan to deal with this health crisis. We highlight the internal deployment of the institutional business continuity plan (BCP) through a series of actions. We also address the impact of the COVID-19 crisis on Biomics staff and collaborators. The added value of quality management and the limitations of risk management systems are discussed. Finally, we suggest that the Biomics infrastructure and the BCP described here could be used for benchmarking purposes, for other next-generation sequencing core facilities wishing to implement/improve their processes, and for future major crisis management.     

Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users

Proteomics research infrastructures and core facilities within the Core for Life alliance advocate for community policies for quality control to ensure high standards in proteomics services.

Core facilities and research infrastructures have become an essential part of the scientific ecosystem. In the field of proteomics, national and international networks and research platforms have been established during the past decade that are supposed to set standards for high‐quality services, promote an exchange of professional information, and enable access to cutting‐edge, specialized proteomics technologies. Either centralized or distributed, these national and international proteomics infrastructures and technology platforms are generating massive amounts of data for the research community, and support a broad range of translational, computational and multi‐omics initiatives and basic research projects.By delegating part of their work to these services, researchers expect that the core facility adjusts their analytical protocols appropriately for their project to acquire data conforming best research practice of the scientific community. The implementation of quality assessment measures and commonly accepted quality controls in data generation is therefore crucially important for proteomics research infrastructures and the scientists who rely on them.However, current quality control and quality assessment procedures in proteomics core facilities and research infrastructures are a motley collection of protocols, standards, reference compounds and software tools. Proteomics relies on a customized multi‐step workflow typically consisting of sample preparation, data acquisition and data processing, and the implementation of each step differs among facilities. For example, sample preparation involves enzymatic digestion of the proteins, which can be performed in‐solution, in‐gel, or on‐beads, with often different proteolytic enzymes, chemicals, and conditions among laboratories. Data acquisition protocols are often customized to the particular instrument set up, and the acquired spectra and chromatograms are processed by different software tools provided by equipment vendors, third parties or developed in‐house.

…current quality control and quality assessment procedures in proteomics core facilities and research infrastructures are a motley collection of protocols, standards, reference compounds and software tools.

Moreover, core facilities implement their own guidelines to monitor the performance and quality of the entire workflow, typically utilizing different commercially available standards such as pre‐digested cell lysates, recombinant proteins, protein mixtures, or isotopically labeled peptides. Currently, there is no clear consensus on if, when and how to perform quality control checks. There is even less quality control in walk‐in facilities, where the staff is only responsible for correct usage of the instruments and users select and execute the analytical workflow themselves. It is not surprising therefore that instrument stability and robustness of the applied analytical approach are often unclear, which compromises analytical rigor.     

Simple chemical tools to expand the range of proteomics applications

Proteomics is an expanding technology with potential applications in many research fields. Even though many research groups do not have direct access to its main analytical technique, mass spectrometry, they can interact with proteomics core facilities to incorporate this technology into their projects. Protein identification is the analysis most frequently performed in core facilities and is, probably, the most robust procedure. Here we discuss a few chemical reactions that are easily implemented within the conventional protein identification workflow. Chemical modification of proteins with N-hydroxysuccinimide esters, 4-sulfophenyl isothiocyanate, O-methylisourea or through β-elimination/Michael addition can be easily performed in any laboratory. The reactions are quite specific with almost no side reactions. These chemical tools increase considerably the number of applications and have been applied to characterize protein-protein interactions, to determine the N-terminal residues of proteins, to identify proteins with non-sequenced genomes or to locate phosphorylated and O-glycosylated.     

Managing a mouse mutant resource center...this is not your father's transgenic core

Genetically engineered mice are making an increasingly valuable contribution to biomedical research, and many institutions have begun to assemble dedicated facilities for the development of transgenic animals. The authors describe the structure, function, and management of the transgenic core at NHGRI.     

An international survey of Training Needs and Career Paths of Core Facility Staff

Core facilities (CFs) provide a centralised access to costly equipment, scientific expertise, experimental design, day-to-day technical support and training of users. CFs have a tremendous impact on research outputs, skills and educational agendas, increasing the competencies of staff, researchers and students. However, the rapid development of new technologies and methodologies for the life sciences requires fast adaptation and development of existing core facilities and their technical and scientific staff. Given the scarcity of well-defined CF career paths, CF staff positions are typically filled by people having followed either academic or technical tracks. Each academic institution follows different policies and often fails to adequately recognize the merits of CF personnel and to support their training efficiently. Thus, the Core Technologies for Life Science association (CTLS), through the Training working group, has conducted an anonymous online survey to assess the training needs of CF personnel, as well as to identify common characteristics and challenges in this relatively new and dynamic career type. 275 individuals, including core managers and directors, technicians, technologists and administrators, participated in the survey. The survey was divided into 2 sections; the first, applied to all respondents, and the second, specifically targeted core management issues. Training needs in technological areas, financial and soft skills, management and administrative issues were surveyed as well. The lack of clarity and consistency regarding established career paths for CF professionals was evident from the second part of the survey, highlighting geographical or cultural differences. Gender balance was achieved and the distribution was always taken into account. The results of this survey highlight a need to develop better training resources for CF staff, to improve their recognition within academic institutions, and to establish a recognized career pathway.     

Life-long well being: applying animal welfare science to nonhuman primates in sanctuaries

Nonhuman primates have become common in sanctuaries, and a few such facilities even specialize in their care. Sanctuaries can improve the well being of many unwanted primates, especially in terms of housing and socialization. However, diverse facilities call themselves sanctuaries, and they have varying conditions, care programs, and restrictions. In addition, a general lack of regulation of sanctuaries for nonhuman animals creates problems in enforcing even minimal standards. The application of animal welfare science in the sanctuary setting can help foster high standards and empirically based decision making. Sanctuaries offer excellent environments for studying primates without the limitations inherent in breeding, exhibition, and medical research facilities. However, some sanctuaries avoid scientific study. Many sanctuaries have little opportunity to study animal welfare in a systematic manner due to financial considerations or a lack of specific expertise among staff and volunteers. Most published sanctuary research involves reintroduction procedures at sanctuaries in source countries. Nevertheless, one chimpanzee sanctuary's successes in performing long-term studies and using simple evaluation methods, such as check sheets, have demonstrated the benefits of applying animal welfare science to sanctuary-housed nonhuman primates.     

Life-Long Well Being: Applying Animal Welfare Science to Nonhuman Primates in Sanctuaries

Nonhuman primates have become common in sanctuaries, and a few such facilities even specialize in their care. Sanctuaries can improve the well being of many unwanted primates, especially in terms of housing and socialization. However, diverse facilities call themselves sanctuaries, and they have varying conditions, care programs, and restrictions. In addition, a general lack of regulation of sanctuaries for nonhuman animals creates problems in enforcing even minimal standards. The application of animal welfare science in the sanctuary setting can help foster high standards and empirically based decision making. Sanctuaries offer excellent environments for studying primates without the limitations inherent in breeding, exhibition, and medical research facilities. However, some sanctuaries avoid scientific study. Many sanctuaries have little opportunity to study animal welfare in a systematic manner due to financial considerations or a lack of specific expertise among staff and volunteers. Most published sanctuary research involves reintroduction procedures at sanctuaries in source countries. Nevertheless, one chimpanzee sanctuary's successes in performing long-term studies and using simple evaluation methods, such as check sheets, have demonstrated the benefits of applying animal welfare science to sanctuary-housed nonhuman primates.     

State-of-the-art biomolecular core facilities: a comprehensive survey

A survey of 124 protein and/or nucleic acid chemistry facilities has provided a basis for estimating the resources needed to establish a facility, the financial support needed to keep it operating, and the technical capabilities it might reasonably be expected to achieve. Based on these data, an average core facility occupied 870 ft2, was staffed by three full-time personnel, and was equipped with 4-5 major instrument systems. Because user fees generated an average of about $101,000/year in income compared with an average operating budget of about $197,000/year, even a facility that charged user fees would, on average, still require an annual subsidy of about $96,000. Although most government and industrial core facilities did not assess user fees, at least 83 of the 124 respondents did have a preestablished schedule of service charges that enabled a compilation to be made of the average cost of providing a number of typical facility analyses and syntheses. The greater than 100-fold range in charges assessed in core facilities for seemingly identical services was shown to result from the equally large range in the degree of subsidization of these laboratories. Although an average facility might be expected to offer four or five of the following six major services--amino acid sequencing, amino acid analysis, HPLC peptide isolation, peptide synthesis, fragmentation of proteins and DNA synthesis--less than 10% of the responding laboratories provided mass spectrometry, capillary zone electrophoresis, or RNA synthesis. With the exception of peptide synthesis, which had an average turn-around time of about 24 days, all other major services had turn-around times that averaged in the range of 4-9 days. Additional data are summarized regarding average sample throughput in core laboratories and the amount of protein that is needed for hydrolysis/amino acid analysis and sequencing.     

eCOMPAGT – efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology

Background  

High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-related personal information, which needs to be handled with care by following data privacy protection guidelines. In addition, genotyping core facilities handling cooperative projects require a straightforward solution to monitor the status and financial resources of the different projects.     

Challenges for proteomics core facilities

Many analytical techniques have been executed by core facilities established within academic, pharmaceutical and other industrial institutions. The centralization of such facilities ensures a level of expertise and hardware which often cannot be supported by individual laboratories. The establishment of a core facility thus makes the technology available for multiple researchers in the same institution. Often, the services within the core facility are also opened out to researchers from other institutions, frequently with a fee being levied for the service provided. In the 1990s, with the onset of the age of genomics, there was an abundance of DNA analysis facilities, many of which have since disappeared from institutions and are now available through commercial sources. Ten years on, as proteomics was beginning to be utilized by many researchers, this technology found itself an ideal candidate for being placed within a core facility. We discuss what in our view are the daily challenges of proteomics core facilities. We also examine the potential unmet needs of the proteomics core facility that may also be applicable to proteomics laboratories which do not function as core facilities.     

Should society allow research ethics boards to be run as for-profit enterprises?

BACKGROUND TO THE DEBATE: An important mechanism for protecting human research participants is the prior approval of a clinical study by a research ethics board, known in the United States as an institutional review board (IRB). Traditionally, IRBs have been run by volunteer committees of scientists and clinicians working in the academic medical centers where the studies they review are being carried out. However, for-profit organizations are increasingly being hired to conduct ethics reviews. Proponents of for-profit IRBs argue that these IRBs are just as capable as academic IRBs at providing high-quality ethics reviews. Critics argue that for-profit IRBs have a conflict of interest because they generate their income from clients who have a direct financial interest in obtaining approval.     

构建茶树资源核心种质的设想

本文介绍核心种质的概念、原理和研究内容,指出在当前人力物力不足的情况下,构建茶树遗传资源的核心种质库,是解决基础研究的长期性与生产实际的迫切需要之间矛盾的一种有效途径;并提出构建茶树核心种质库的三步程序和工作设想。     

The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses

Resource (core) facilities have played an ever-increasing role in furnishing the scientific community with specialized instrumentation and expertise for proteomics experiments in a cost-effective manner. The Proteomics Research Group (PRG) of the Association of Biomolecular Resource Facilities (ABRF) has sponsored a number of research studies designed to enable participants to try new techniques and assess their capabilities relative to other laboratories analyzing the same samples. Presented here are results from three PRG studies representing different samples that are typically analyzed in a core facility, ranging from simple protein identification to targeted analyses, and include intentional challenges to reflect realistic studies. The PRG2008 study compares different strategies for the qualitative characterization of proteins, particularly the utility of complementary methods for characterizing truncated protein forms. The use of different approaches for determining quantitative differences for several target proteins in human plasma was the focus of the PRG2009 study. The PRG2010 study explored different methods for determining specific constituents while identifying unforeseen problems that could account for unanticipated results associated with the different samples, and included (15) N-labeled proteins as an additional challenge. These studies provide a valuable educational resource to research laboratories and core facilities, as well as a mechanism for establishing good laboratory practices.