Biobanking

Biobanks, more formally known as biological resource centers (BRCs), form an “unsung” yet critical component of the infrastructures for scientific research, industry and conservation, without which much of the current scientific activity involving microbial cultures and cell-lines would be effectively impossible. BRCs are de facto depositories of “biological standards” holding taxonomic and other reference strains on which much of the associated published science and industrial standards are built and upon which some significant international commercial and ethical issues rely. The establishment and maintenance of BRCs is a knowledge- and skill-rich activity that in particular requires careful attention to the implementation of reliable preservation technologies and appropriate quality assurance to ensure that recovered cultures and other biological materials perform in the same way as the originally isolated culture or material. There are many types of BRC, which vary both in the kinds of material they hold and in their functional role. All BRCs are expected to provide materials and information of an appropriate quality for their intended use and work to standards relevant to those applications. There are important industrial, biomedical, and conservation issues that can only be addressed through effective and efficient operation of BRCs in the long term. This requires a high degree of expertise in the maintenance and management of collections of biological materials at ultra-low temperatures, or as freeze-dried material, to secure their long-term integrity and relevance for future research, development, and conservation.     

Quality issues in tissue banking:Quality management systems - A review

The situation in tissue banking changed radically and fundamentally at the beginning of the 1990s. The essential causes are on the one hand, the continually increasing demand for human cells and tissue and other biological material for clinical use and research, and on the other hand, the rapid progress in the medical, technical and natural sciences. Biotechnology in particular, has profited from this. Modern tissue banks could no longer be imagined without its methods.A consequence of these developments and a prerequisite for the fulfilment of the derived requirements is the necessity for national and international cooperation as well as the harmonisation of ethical principles and quality assurance standards and regulations (von Versen (1999) Ann Chir Gynaecol 88: 215-220). The introduction of an all-encompassing Quality Management System (QMS) is a suitable instrument for this purpose.After the presentation of explanations and definitions of quality terminology, this article describes the use of the international standard ISO 9000 as a general QMS, which embraces both the specific methodology as well as the general aspects of Quality Management (research and development, design control, education and training, documentation, traceability, management control, corrective action, etc.) in tissue banking. The individual elements of this system are explained and selected examples are described. The authors look upon this QMS as an indispensable instrument for harmonisation and international cooperation in tissue banking.Finally, the use of such a standard would be a positive sign to the regulatory authorities and the public that tissue banking is making a visible effort to introduce a world-class QMS in its operations.     

Johnson Matthey electronics — a total quality management approach to customer support

Johnson Matthey is committed to Total Quality Management (TQM) aimed at setting standards in customer support. TQM achieves improvements in product quality and standards of service by continually improving production processes, analytical techniques, data processing and distribution channels.The Company has so far invested £1M in TQM training, which involves every employee what ever their role. In addition to TQM, the Company continues to invest heavily in a long term research and strategic acquisition policy, which achieves not only improvements in product quality but also provides new products and solutions to meet customers changing needs.     

Chapter 16: Text Mining for Translational Bioinformatics

Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research—translating basic science results into new interventions—and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.

What to Learn in This Chapter

Text mining is an established field, but its application to translational bioinformatics is quite new and it presents myriad research opportunities. It is made difficult by the fact that natural (human) language, unlike computer language, is characterized at all levels by rampant ambiguity and variability. Important sub-tasks include gene name recognition, or finding mentions of gene names in text; gene normalization, or mapping mentions of genes in text to standard database identifiers; phenotype recognition, or finding mentions of phenotypes in text; and phenotype normalization, or mapping mentions of phenotypes to concepts in ontologies. Text mining for translational bioinformatics can necessitate dealing with two widely varying genres of text—published journal articles, and prose fields in electronic medical records. Research into the latter has been impeded for years by lack of public availability of data sets, but this has very recently changed and the field is poised for rapid advances. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.

This article is part of the “Translational Bioinformatics” collection for PLOS Computational Biology.

     

城市生态观测:质量控制对象、体系和规范编制

城市生态系统长期观测是开展城市生态安全评价和制定人居环境健康管理政策的基础。为了确保城市生态观测数据的准确性和科学性,通过辨识城市生态观测质量控制的概念,基于"人机料法环"理论构建了城市生态观测质量控制体系,结合城市生态观测质量控制相关规范的编制与实施现状,探讨了城市生态观测质量控制规范的编制技术。结果表明：（1）城市生态观测质量控制是面向城市生态观测内容（要素、空间格局、功能、服务）,为保证生态观测全过程质量要求、提高生态观测结果的准确性而实施的质量控制活动和措施。（2）城市生态观测质量控制体系可从对象和过程这两个维度进行界定：对象维度方面,包括"人"-人员、"机"-仪器设备、"料"-数据、"法"-文件和"环"-观测过程5个方面;过程维度方面,涵盖城市生态观测全过程,包括城市生态观测前期准备工作、观测过程中以及观测后的数据录入、审核与评价等环节的质量控制措施。（3）我国已发布的生态观测相关技术标准中,发布的时间越晚,质量控制内容越完整,目前生态观测相关标准共102则,仅38则明确提出了质量控制具体要求。（4）《城市生态观测质量控制规范》编制需包含质量体系和质量控制措施两项技术内容,主要包括前引、正文和附录三个章节,对生态观测全过程质量保证和质量控制技术进行规定。     

The impact of the International Atomic Energy Agency (IAEA) program on radiation and tissue banking in Brazil

Until 2000, efforts into organising tissue banks in Brazil had not progressed far beyond small “in house” tissue storage repositories, usually annexed to Orthopaedic Surgery Services. Despite the professional entrepreneurship of those working as part time tissue bankers in such operations, best practices in tissue banking were not always followed due to the lack of regulatory standards, specialised training, adequate facilities and dedicated personnel. The Skin Bank of the Plastic Surgery Department of the Hospital das Clinicas of Sao Paulo, the single skin bank in Brazil, was not an exception. Since 1956, restricted and unpredictable amounts of skin allografts were stored under refrigeration for short periods under very limited quality controls. As in most “tissue banks” at that time in Brazil, medical and nursing staff worked on a volunteer and informal basis undergoing no specific training. IAEA supported the implementation of the tissue banking program in Brazil through the regional project RLA/7/009 “Quality system for the production of irradiated sterilised grafts” (1998–2000) and through two interregional projects INT/6/049 “Interregional Centre of Excellence in Tissue Banking”, during the period 2002–2004 and INT/6/052 “Improving the Quality of Production and Uses of Radiation Sterilised Tissue Grafts”, during the period 2002–2004. In 2001–2002, the first two years of operation of the HC-Tissue Bank, 53 skin transplants were carried out instead of the previous 4–5 a year. During this period, 75 individuals donated skin tissue, generating approximately 90,000 cm² of skin graft. The IAEA program were of great benefit to Brazilian tissue banking which has evolved from scattered make shift small operations to a well-established, high quality tissue banking scenario.     

El duro peregrinaje de las revistas biomédicas españolas hacia la excelencia: ¿quién nos ayuda? Calidad,impacto y méritos de la investigación

Biomedical journals must adhere to strict standards of editorial quality. In a globalized academic scenario, biomedical journals must compete firstly to publish the most relevant original research and secondly to obtain the broadest possible visibility and the widest dissemination of their scientific contents. The cornerstone of the scientific process is still the peer-review system but additional quality criteria should be met. Recently access to medical information has been revolutionized by electronic editions.Bibliometric databases such as MEDLINE, the ISI Web of Science and Scopus offer comprehensive online information on medical literature. Classically, the prestige of biomedical journals has been measured by their impact factor but, recently, other indicators such as SCImago SJR or the Eigenfactor are emerging as alternative indices of a journal's quality. Assessing the scholarly impact of research and the merits of individual scientists remains a major challenge. Allocation of authorship credit also remains controversial.Furthermore, in our Kafkaesque world, we prefer to count rather than read the articles we judge. Quantitative publication metrics (research output) and citations analyses (scientific influence) are key determinants of the scientific success of individual investigators. However, academia is embracing new objective indicators (such as the “h” index) to evaluate scholarly merit. The present review discusses some editorial issues affecting biomedical journals, currently available bibliometric databases, bibliometric indices of journal quality and, finally, indicators of research performance and scientific success.     

Quantifying the quality of coral bleaching predictions

Techniques that utilize sea surface temperature (SST) observations to predict coral reef bleaching are in common use and form the foundation for predicted global coral reef ecosystem demise within this century. Yet, quality assessments of these methods are typically qualitative or anecdotal. Quality is the correspondence of forecasts with observations and has standard quantitative measures. Here a forecast verification method, commonly used in meteorology, is presented and used to measure the quality of the degree heating weeks (DHW) technique as an exploration of insights that can be gleaned from this methodology. DHW values were calculated from NOAA Optimum Interpolation SST version 2 data and compared to a database of bleaching observations from 1990–2007. Quality is expressed with an objective measure, the Peirce Skill Score (PSS). The quality at varying DHW thresholds above which bleaching was projected to occur is calculated. By selecting the thresholds that maximize quality, the predictive technique is objectively optimized. This results in optimal threshold maps, showing reefs more prone and more resistant to bleaching. Optimization increases the quality of DHW as a predictor of bleaching from PSS = 0.55 to PSS = 0.83, in global average, but the optimal PSS and corresponding DHW values vary significantly from location to location. The coral reef research and management community are urged to adopt the simple, but rigorous tools of forecast verification routinely used in other disciplines so that bleaching forecasts can be quantitatively compared and their quality improved.     

Emergence of norms for biomedical research. At the origin of the Huriet law (1975-1988)

The French law for the Protection of persons involved in biomedical research, known as "Loi Huriet", defines the frame in which biomedical experimentations on human subjects can take place. Insisting on the emergent character of the norms (laws, scientific standards...) for clinical research in France, this paper presents the general context in which such a law was promulgated. It gives an historical focus on its principal dispositions and underlines the conceptual issues raised by the public acknowledgment of the existence of scientific investigations on humans. This paper contributes to the debate on the meaning of the main notions of the French normative system applying to biomedical researches (protection of the person, individual direct benefice...)     

Towards best practices in research: Role of academic core facilities

Academic Core Facilities are optimally situated to improve the quality of preclinical research by implementing quality control measures and offering these to their users. Subject Categories: Methods & Resources, Science Policy & Publishing

During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, ²⁰¹⁶; Bespalov & Steckler, ²⁰¹⁸; Heddleston et al, ²⁰²¹). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, ²⁰²¹). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference.It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting‐edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, ²⁰²⁰). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.     

From Rhetoric to Reality: Using Specific Environmental Concerns to Identify Critical Sustainability Issues

Natural resource managers, environmental interest groups, and public agencies are interested in appropriate, identifiable, and measurable indicators of sustainability. At the same time, public agencies, including natural resource management agencies, are attempting to identify research and management priorities that address major environmental concerns at local and broad scales. The Identify the Specifics approach, described here, uses local (ecodistrict or smaller) ecological/biological “experts' ” knowledge to identify and prioritize the local natural resources of concern (commonly species), associated management practices and ecosystems to form a concern matrix. Local ecological/biological concerns form the environmental base of a broader-scale (ecoregion/ecozone) concern matrix. This matrix identifies similarities and differences among local matrices and appropriate components for promotion to broader scales. Scale-specific matrices identify appropriate local, regional, and broader-scale indicators to monitor and assess, and provide public agencies with direction for documenting effects of management and identifying where research is needed. This approach can provide industries, public agencies, environmental interest groups, and governments with ecosystem-based, prioritized information for balancing social, economic, and ecological concerns on public and private lands. Received 22 July 1997; accepted 7 January 1998.     

An innovative LC/MS approach applied to the determination of zeralenone in maize: Alternate Isotope-coded Derivatization Assay (AIDA)

Zearalenone is a mycotoxin mainly produced by severalFusarium species, which are known to colonize grains in temperate climates. The purpose of the study is to provide a reliable isotope dilution method for the quantification of this mycotoxin. A derivative of the analyte to be used as standard is obtained by reaction with acetic anhydride, which is available in two pure isotopic forms, a protonated (“light”) and a hexadeuterated (“heavy”). The derivatized standards are added to the matrix split intwo parts. Then, the derivatization procedure is repeated on both matrices derivatizing the part containing the “heavy” labelled standard with the “light” acetic anhydride and the part containing the “light” labelled standard with the “heavy” acetic anhydride. Both extracted mixtures are analyzed by LC/MS, monitoring the “light” and the “heavy” labelled analytes and using the former as standard for the latter in one case and viceversa in the other case. The method allowed to obtain very good results, without the need of IAC purification. Presented at the 27^th Mykotoxin-Workshop, Dortmund, Germany, June 13–15, 2005. Financial support: The Italian Ministry of Health     

Experimental analysis of the prey catching behavior ofHydromantes italicus Dunn (Amphibia,Plethodontidae)

Summary 1. The Italian bolitoglossine salamanderHydromantes italicus shows a periodic cave life. In spring and in the fall it leaves the caves after which it lives under stones, in leaves and crevices. Inside the limestone caves,H. i. can be found both in the zone of dim light near the entrance and in total darkness. 2. Corresponding to these two environments there are two guidance systems of the prey catching behavior: one visual and one olfactory. 3. The visually guided prey catching behavior is determined by the stimulus parameters: velocity, size, contrast, and ambient illumination. Continuously moving objects are effective within a velocity range of 0.05 to 6 cm/s with an optimum at 1.25 cm/s (Fig. 2). Stimuli moving stepwise elicit fixation of the prey and complete approach more frequently than continuously moving stimuli. The prey size which elicits prey catching ranges from 0.5 to 10 mm² with an optimum size between 2.5–5.0 mm² (Fig. 3). The prey catching behavior is hardly impaired by a decrease in ambient illumination down to 0.03 cd/m². Beyond 0.03 cd/m², the prey catching activity decreases sharply, but there are still responses at an illumination level of 0.003 cd/m² (Fig. 4). 4.H.i. also responds to stationary non-smelling visual stimuli following stimulation by smell or movement.H.i. is able to detect prey by smell only both in total darkness and in the light (Fig. 5 A). In the light, the prey catching behavior with regard to smelling objects is inhibited by the absence of visual contrast (Fig. 5B).I would like to thank Prof. Dr. R. Altevogt, University of Münster (Germany) for his generous help and constant encouragement. Furthermore, I want to express my gratitude to Prof. Dr. D.B. Wake, University of California, Berkeley (USA), Prof. Dr. P. Mancino, University of Pisa (Italy), and Prof. Dr. J.-P. Ewert, University (GH) of Kassel (Germany) for stimulating discussions and helpful comments.     

Issues on research integrity: a perspective

This paper discusses several key issues that are relevant to the integrity and success of the biomedical research enterprise. Attention to these issues will improve research outcomes and reduce negative consequences in research. Subjects addressed include normative practices in research; the importance of quality data; mentoring of young scientists; how to proceed when a member of the scientific community discovers misconduct or other breaches of integrity; and the level of harm to public confidence in research due to misconduct and lack of transparency in research findings.     

Seasonal courses of key parameters of nitrogen,carbon and water balance in European beech (<Emphasis Type="Italic">Fagus sylvatica</Emphasis> L.) grown on four different study sites along a European North–South climate gradient during the 2003 drought

During the growing season of the exceptionally dry and warm year 2003, we assessed seasonal changes in nitrogen, carbon and water balance related parameters of mature naturally grown European beech (Fagus sylvatica L.) along a North–South transect in Europe that included a beech forest stand in central Germany, two in southern Germany and one in southern France. Indicators for N balance assessed at all four sites were foliar N contents and total soluble non-protein nitrogen compounds (TSNN) in xylem sap, leaves and phloem exudates; C and water balance related parameters determined were foliar C contents, δ¹³C and δ¹⁸O signatures. Tissue sampling was performed in May, July and September. The N related parameters displayed seasonal courses with highest concentrations during N remobilization in May. Decreased total foliar N contents as well as higher C/N ratios in the stands in central Germany and southern France compared to the other study sites point to an impaired N nutrition status due to lower soil N contents and precipitation perception. TSNN concentrations in leaves and phloem exudates of all study sites were in ranges previously reported, but xylem sap content of amino compounds in July was lower at all study sites when compared to literature data (c. 1 μmol N mL⁻¹). In September, TSNN concentrations increased again at the two study sites in southern Germany after a rain event, whereas they remained constant at sites in central Germany and southern France which hardly perceived precipitation during that time. Thus, TSNN concentrations in the xylem sap might be indicative for water balance related N supply in the beech trees. TSNN profiles at all study sites, however, did not indicate drought stress. Foliar δ¹³C, but not foliar C and δ¹⁸O followed a seasonal trend at all study sites with highest values in May. Differences in foliar δ¹³C and δ¹⁸O did not reflect climatic differences between the sites, and are attributed to differences in altitude, photosynthesis and δ¹⁸O signatures of the water sources. Except of low TSNN concentrations in the xylem sap, no physiological indications of drought stress were detected in the trees analysed. We suppose that the other parameters assessed might not have been sensitive to the drought events because of efficient regulation mechanisms that provide a suitable physiological setting even under conditions of prolonged water limitation. The uniform performance of the trees from southern France and central Germany under comparably dry climate conditions denotes that the metabolic plasticity of mature beech from the different sites studied might be similar.     

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles)

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the United States National Cancer Institute convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: 1) an evolving list of comprehensive quality metrics and 2) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.     

The Ethics of Research on Less Expensive,Less Effective Interventions: A Case for Analysis

The Kennedy Krieger lead paint study is a landmark case in human experimentation and a classic case in research ethics. In this paper I use the lead paint study to assist in the analysis of the ethics of research on less expensive, less effective interventions. I critically evaluate an argument by Buchanan and Miller who defend both the Kennedy Krieger lead paint study and public health research on less expensive, less effective interventions. I conclude that Buchanan and Miller’s argument is flawed but that does not mean that research designed to find less effective interventions cannot be justified in some situations. Based on my analysis, I suggest questions to ask when considering such research and I offer some principles to guide us. In the process, light is shed on the various debates and issues raised by the lead paint study; e.g. standards of care, researchers’ responsibilities to research subjects, the distinction between treatment and research and the question of what it is that legitimizes public health research. Merle Spriggs is supported by a grant from the Alfred Felton Bequest which is managed by ANZ Trustees.     

Large Loss of Dissolved Organic Nitrogen from Nitrogen-Saturated Forests in Subtropical China

Dissolved organic nitrogen (DON) has recently been recognized as an important component of terrestrial N cycling, especially under N-limited conditions; however, the effect of increased atmospheric N deposition on DON production and loss from forest soils remains controversial. Here we report DON and dissolved organic carbon (DOC) losses from forest soils receiving very high long-term ambient atmospheric N deposition with or without additional experimental N inputs, to investigate DON biogeochemistry under N-saturated conditions. We studied an old-growth forest, a young pine forest, and a young mixed pine/broadleaf forest in subtropical southern China. All three forests have previously been shown to have high nitrate (NO₃⁻) leaching losses, with the highest loss found in the old-growth forest. We hypothesized that DON leaching loss would be forest specific and that the strongest response to experimental N input would be in the N-saturated old-growth forest. Our results showed that under ambient deposition (35–50 kg N ha⁻¹ y⁻¹ as throughfall input), DON leaching below the major rooting zone in all three forests was high (6.5–16.9 kg N ha⁻¹ y⁻¹). DON leaching increased 35–162% following 2.5 years of experimental input of 50–150 kg N ha⁻¹ y⁻¹. The fertilizer-driven increase of DON leaching comprised 4–17% of the added N. A concurrent increase in DOC loss was observed only in the pine forest, even though DOC:DON ratios declined in all three forests. Our data showed that DON accounted for 23–38% of total dissolved N in leaching, highlighting that DON could be a significant pathway of N loss from forests moving toward N saturation. The most pronounced N treatment effect on DON fluxes was not found in the old-growth forest that had the highest DON loss under ambient conditions. DON leaching was highly correlated with NO₃⁻ leaching in all three forests. We hypothesize that abiotic incorporation of excess NO₃⁻ (through chemically reactive NO₂⁻) into soil organic matter and the consequent production of N-enriched dissolved organic matter is a major mechanism for the consistent and large DON loss in the N-saturated subtropical forests of southern China. Dr. YT Fang performed research, analyzed data, and wrote the paper; Prof. WX Zhu participated in the initial experimental design, analyzed data, and took part in writing the paper; Prof. P Gundersen conceived the study and took part in writing; Prof. JM Mo and Prof. GY Zhou conceived study; Prof. M Yoh analyzed part of the data and contributed to the development of DON model.