The development and deployment of Common Data Elements for tissue banks for translational research in cancer – An emerging standard based approach for the Mesothelioma Virtual Tissue Bank

<p>Abstract</p> <p>Background</p> <p>Recent advances in genomics, proteomics, and the increasing demands for biomarker validation studies have catalyzed changes in the landscape of cancer research, fueling the development of tissue banks for translational research. A result of this transformation is the need for sufficient quantities of clinically annotated and well-characterized biospecimens to support the growing needs of the cancer research community. Clinical annotation allows samples to be better matched to the research question at hand and ensures that experimental results are better understood and can be verified. To facilitate and standardize such annotation in bio-repositories, we have combined three accepted and complementary sets of data standards: the College of American Pathologists (CAP) Cancer Checklists, the protocols recommended by the Association of Directors of Anatomic and Surgical Pathology (ADASP) for pathology data, and the North American Association of Central Cancer Registry (NAACCR) elements for epidemiology, therapy and follow-up data. Combining these approaches creates a set of International Standards Organization (ISO) – compliant Common Data Elements (CDEs) for the mesothelioma tissue banking initiative supported by the National Institute for Occupational Safety and Health (NIOSH) of the Center for Disease Control and Prevention (CDC).</p> <p>Methods</p> <p>The purpose of the project is to develop a core set of data elements for annotating mesothelioma specimens, following standards established by the CAP checklist, ADASP cancer protocols, and the NAACCR elements. We have associated these elements with modeling architecture to enhance both syntactic and semantic interoperability. The system has a Java-based multi-tiered architecture based on Unified Modeling Language (UML).</p> <p>Results</p> <p>Common Data Elements were developed using controlled vocabulary, ontology and semantic modeling methodology. The CDEs for each case are of different types: demographic, epidemiologic data, clinical history, pathology data including block level annotation, and follow-up data including treatment, recurrence and vital status. The end result of such an effort would eventually provide an increased sample set to the researchers, and makes the system interoperable between institutions.</p> <p>Conclusion</p> <p>The CAP, ADASP and the NAACCR elements represent widely established data elements that are utilized in many cancer centers. Herein, we have shown these representations can be combined and formalized to create a core set of annotations for banked mesothelioma specimens. Because these data elements are collected as part of the normal workflow of a medical center, data sets developed on the basis of these elements can be easily implemented and maintained.</p

National Mesothelioma Virtual Bank: A standard based biospecimen and clinical data resource to enhance translational research

Background: Advances in translational research have led to the need for well characterized biospecimens for research. The National Mesothelioma Virtual Bank is an initiative which collects annotated datasets relevant to human mesothelioma to develop an enterprising biospecimen resource to fulfill researchers' need. Methods: The National Mesothelioma Virtual Bank architecture is based on three major components: (a) common data elements (based on College of American Pathologists protocol and National North American Association of Central Cancer Registries standards), (b) clinical and epidemiologic data annotation, and (c) data query tools. These tools work interoperably to standardize the entire process of annotation. The National Mesothelioma Virtual Bank tool is based upon the caTISSUE Clinical Annotation Engine, developed by the University of Pittsburgh in cooperation with the Cancer Biomedical Informatics Grid™ (caBIG™, see http://cabig.nci.nih.gov). This application provides a web-based system for annotating, importing and searching mesothelioma cases. The underlying information model is constructed utilizing Unified Modeling Language class diagrams, hierarchical relationships and Enterprise Architect software. Result: The database provides researchers real-time access to richly annotated specimens and integral information related to mesothelioma. The data disclosed is tightly regulated depending upon users' authorization and depending on the participating institute that is amenable to the local Institutional Review Board and regulation committee reviews. Conclusion: The National Mesothelioma Virtual Bank currently has over 600 annotated cases available for researchers that include paraffin embedded tissues, tissue microarrays, serum and genomic DNA. The National Mesothelioma Virtual Bank is a virtual biospecimen registry with robust translational biomedical informatics support to facilitate basic science, clinical, and translational research. Furthermore, it protects patient privacy by disclosing only de-identified datasets to assure that biospecimens can be made accessible to researchers. © 2008 Amin et al; licensee BioMed Central Ltd

Common controls driven conceptual leadership framework

The forthcoming social welfare and healthcare reform in Finland with its organizational, financing and steering changes challenges the leadership. All service systems levels of the social welfare and healthcare have to achieve performance objectives whilst at the same time also meeting conformance requirements. However, there are hundreds authority documents (e.g., best practices, guidelines, regulations and standards) the common controls of which are adapted partly manually and partly by leveraging automation in organizations. Leaders review and develop their practices around performance and conformity (i.e., conformance or compliance) within frameworks that are mainly the sets of principles. However, the common controls affect into the main tasks of the governance (i.e., direct, evaluate and monitor). Therefore, we construct a conceptual leadership framework to highlight the meaning of the common controls and the meaning of criteria for performance and conformity. The constructed framework contains the terms (e.g., a control objective, decision criteria, event, insight, and transaction) that are mainly defined in the glossaries of the authority documents. The terms are used to find out terms and definitions for the leadership framework to figure out cognitive meanings for the concepts of the common controls driven leadership

Personality and technology: Big five personality traits as descriptors of universal acceptance and usage of technology UTAUT.

Presently, information professionals are progressively dependent on information and communication technologies to complete their everyday tasks. As, result dependence on PC frameworks, programming and data innovation-related technologies are increasing for better working and providing quality services. Therefore, to understand, analyze and evaluate the acceptance and use of this technology several models of technology acceptance and use have been formulated in information science literature. Using eight such models, Venkatesh, Morris, Davis and Davis proposed a unified model called the Unified Theory of Acceptance and Use of Technology or (UTAUT) model. The UTAUT model has been studied and analyzed in various spheres including education, banking, health, tourism, e-government services and its recent application in the personality studies. The application of UTAUT model to the core constructs of big five personality traits have been utilized to predict the adoption and usage of technology according to different personality types such as neurotic, open to experience, extravert, conscientious and agreeabl

Applying Logic Modeling to the Higher Education Accreditation Process

In recent years, regional accreditation and the regional accreditation associations for higher education have experienced continuing criticism and become the objects of increased scrutiny. Higher education institutions look to the accreditation process as one of the principal means of justifying their actions and activities relative to their performance and results. Since the complaints and criticism directed toward higher education have not diminished but continued, and even increased, the regional accreditation associations find themselves to be the focus of similar complaints and criticisms. In the United States, we have no national system of accreditation. We rely on the actions and activities of one of the six regional accreditation associations. Each of these associations has its own separate and, in some cases, unique accreditation processes. Each publishes its own standards, its own handbooks, its own policies and practices, its own newsletters, and its own rules and regulations for accreditation. This situation can lead to inconsistencies, and could be a source of much confusion and misunderstanding when discussing the implications of an institution being accredited within a particular region. Logic models are diagrams or visual schematics that convey relationships between program processes and outcomes. This study uses logic modeling and logic model theory as the framework for an examination of the components of accreditation within two regional accreditation associations. A systematic and detailed methodology was developed in order to construct a logic model from existing handbooks and documents. As a result, two regional logic models were constructed, as well as a combined model based upon common elements. Implications of this study include the possible construction of a national accreditation logic model if the methodology is applied in the additional regional associations. This conceptual approach could lead to more consistency in the design, communication, and application of accreditation processes. Better understanding of, and less confusion concerning, the myriad of activities and processes required in a successful regional accreditation could lead to better, more effective, and more meaningful accreditation activities and results. This, in turn, could generate true growth and improvement in the actions, activities, and results achieved by our higher education institutions

BMC Cancer

BackgroundRecent advances in genomics, proteomics, and the increasing demands for biomarker validation studies have catalyzed changes in the landscape of cancer research, fueling the development of tissue banks for translational research. A result of this transformation is the need for sufficient quantities of clinically annotated and well-characterized biospecimens to support the growing needs of the cancer research community. Clinical annotation allows samples to be better matched to the research question at hand and ensures that experimental results are better understood and can be verified. To facilitate and standardize such annotation in bio-repositories, we have combined three accepted and complementary sets of data standards: the College of American Pathologists (CAP) Cancer Checklists, the protocols recommended by the Association of Directors of Anatomic and Surgical Pathology (ADASP) for pathology data, and the North American Association of Central Cancer Registry (NAACCR) elements for epidemiology, therapy and follow-up data. Combining these approaches creates a set of International Standards Organization (ISO) \ue2\u20ac\u201c compliant Common Data Elements (CDEs) for the mesothelioma tissue banking initiative supported by the National Institute for Occupational Safety and Health (NIOSH) of the Center for Disease Control and Prevention (CDC).MethodsThe purpose of the project is to develop a core set of data elements for annotating mesothelioma specimens, following standards established by the CAP checklist, ADASP cancer protocols, and the NAACCR elements. We have associated these elements with modeling architecture to enhance both syntactic and semantic interoperability. The system has a Java-based multi-tiered architecture based on Unified Modeling Language (UML).ResultsCommon Data Elements were developed using controlled vocabulary, ontology and semantic modeling methodology. The CDEs for each case are of different types: demographic, epidemiologic data, clinical history, pathology data including block level annotation, and follow-up data including treatment, recurrence and vital status. The end result of such an effort would eventually provide an increased sample set to the researchers, and makes the system interoperable between institutions.ConclusionThe CAP, ADASP and the NAACCR elements represent widely established data elements that are utilized in many cancer centers. Herein, we have shown these representations can be combined and formalized to create a core set of annotations for banked mesothelioma specimens. Because these data elements are collected as part of the normal workflow of a medical center, data sets developed on the basis of these elements can be easily implemented and maintained.1U19OH009077-01/OH/NIOSH CDC HHS/United StatesUL1 TR000005/TR/NCATS NIH HHS/United State

Risk and sustainability assessment (RSA) framework for ‘water scarcity – water reuse’ situations: Conceptualisation, operationalisation, and testing

The number of regions undergoing water scarcity, where the quantity of available water is not enough to meet human demand, is expected to increase in the future. Water reuse measures have been widely implemented to face these situations as a means of increasing the supply of water resources. Thus, ‘water scarcity – water reuse’ (WS-WR) situations will likely become more common. In these cases, water resources management to secure enough water supply is key. Risk and sustainability concepts have been consolidated as guiding discourses that also support the management of water resources. In particular, in the case of WS-WR situations, they can guide decision-makers towards reducing the risk of water scarcity and striving for the implementation of sustainable water reuse measures. In particular, the use of risk and sustainability assessments helps to deal with various social, economic, and environmental requirements and constraints. However, there is still the call for a more comprehensive and integrated assessments. This dissertation aims at providing new ideas for the integration of risk and sustainability in the case of WS-WR situations. Three objectives guide this research: (A) to develop a conceptual assessment framework to support decision-making concerning sustainable water reuse in regions facing risk of water scarcity; (B) to advance the conceptual framework interrelating existing risk and sustainability assessment methodologies and indicators in the context of decision support; and (C) to test the conceptual and methodological framework using a case study in Latin America. Each objective is associated with a research question: (RQ1) How is decision-making regarding water reuse understood and supported towards reducing the risk of water scarcity sustainably – and how can it be represented in a conceptual assessment framework?; (RQ2) How can a conceptual framework for assessing water reuse as sustainable water scarcity risk reduction measures be operationalised through a methodological framework?; and (RQ3) What are the findings from testing the framework in a case study – and what can be incorporated into the framework? Each objective and its respective research question was addressed as a separate step of the research approach, comprising the development of an integrated Risk and Sustainability Assessment (RSA) Framework for WS-WR situations, its operationalisation and testing. The research approach followed a deductive to inductive rationale relying on qualitative and quantitative methods. The outputs of this research are three scientific publications that build this cumulative dissertation (two published and one submitted for revision). The development of the conceptual framework followed three steps: (i) defining the concepts of ‘water scarcity’, ‘water reuse’, ‘risk’ and ‘risk assessment’, ‘sustainability’ and ‘sustainability assessment’, and ‘decision-making’; (ii) integrating these concepts by interpreting water scarcity from a risk perspective and water reuse from a sustainability perspective, and relating assessments with decision-making; and (iii) structuring the RSA Framework, following a risk assessment and framing it by the social, economic, and environmental dimensions of sustainability. Results allowed defining decision-making in WS-WR situations as a four-step cyclic process that can be supported by an integrated RSA that comprises an analysis (descriptive and objective) and evaluation (subjective). The methodological aspects for the operationalisation of the RSA conceptual framework focused mainly on developing an analytical concept to support an adequate derivation of the information required in an integrated RSA for WS-WR situations. The resulting concept is based on (i) understanding the WS-WR situation as a Coupled Human and Natural System (CHANS) and identifying the main biophysical elements (endpoints); (ii) translating the CHANS endpoints into an information system via a Multi-Layer (ML) approach using generic descriptors and specific indicators; and (iii) identifying and characterising interlinkages between the indicators via a Lane-Based (LB) approach. Additional methodological aspects related to the evaluation include the use of indicator-based multi-criteria decision-making methods that include the weighting and aggregation of these indicators, as well as the selection of threshold values as evaluation criteria. The testing of the integrated RSA Framework was carried out in Cerrillos de Tamaya, Chile. It involved an ex-post RSA of a water reuse measure implemented in 2018 to face the local water scarcity situation. The testing included (i) describing the case study location and adapting the RSA Framework to fit the local context; (ii) translating the case study’s CHANS via the ML approach and identifying and characterising interlinkages via the LB approach; and (iii) evaluating the degree of risk of water scarcity and sustainability of water reuse via the distance-based method TOPSIS. The results of the testing provided feedback for the RSA Framework. These mainly referred to the influence of the conceptualisation behind the indicators and their use, and the methodological challenges for integrating risk and sustainability evaluation. Further recommendations to the RSA framework are: the inclusion of interlinkage directionality; the use of existing system dynamics modelling approaches (e.g., CLD, SFD); the development of an established database of indicators; the automation of the interlinkages analysis (LB approach); and advance the use of scenarios for sustainability evaluation for better coupling with risk evaluation methods. Overall this research provides evidence of (a) the conceptual integration of risk and sustainability discourses under one decision support framework for the case of WS-WR situations; (b) the use of a system thinking approach for interpreting the WS-WR situation; (c) the relevance of indicators as a means of representing the situation; (d) the interlinkage of social, economic, environmental information; (e) the benefits of the use of conceptual maps; (f) gaps in the process of measuring the effect of water reuse on water scarcity levels via indicators; (g) the gap between a simulation-based risk assessment and a snapshot-focused sustainability assessment that hinders an operational integration; (h) the possibility of the RSA framework to bridge a system thinking view with a traditional assessment-based decision-making view.:Acknowledgements Abstract Contents List of Figures List of Tables Acronyms and Abbreviations Symbols Chapter 1 - Introduction 1.1 Background and problem statement 1.1.1 Water resources for water security 1.1.2 Risk and sustainability discourses for water-related decision-making 1.1.3 Problem statement and research focus 1.2 Objectives and research questions 1.3 Research approach and structure of the document 1.3.1 Research approach 1.3.2 Structure of the document 1.4 Chapter references Chapter 2 - Conceptual Framework 2.1 Introduction 2.2 Developing the conceptual framework 2.2.1 Definition and interpretation of the subject at stake 2.2.2 Identification and definition of key concepts 2.2.3 Construction of the conceptual framework 2.3 Results and discussion 2.3.1 Defining and interpreting the ‘water scarcity – water reuse’ situation 2.3.2 Identifying and defining key concepts 2.3.3 Construction of the integrated RSA Framework 2.4 Conclusions and outlook 2.5 Acknowledgements 2.6 Chapter references Chapter 3 - Methodological Aspects 3.1 Introduction 3.2 RSA Framework for a WS-WR situation 3.3 Systems thinking in a WS-WR situation 3.3.1 Identifying elements of a WS-WR situation and its interpretation as a system 3.3.2 Translation of the CHANS into an information system 3.4 Characterisation and interlinkage of indicators 3.4.1 Type and number of indicators 3.4.2 Type and number of interlinkages 3.4.3 Indicator connectivity 3.4.4 Structuring via a lane-based approach 3.5 RSA analytical concept and exemplification 3.5.1 RSA analytical concept 3.5.2 Exemplification of the analyitical concept 3.6 Discussion 3.6.1 Translating the CHANS into an information system 3.6.2 Supporting decision-making via the analytical concept 3.7 Conclusions 3.8 Acknowledgements 3.9 Chapter references Chapter 4 - Framework Testing 4.1 Introduction 4.2 Approach 4.2.1 RSA Framework 4.2.2 Case study site 4.3 Results 4.3.1 Analysis 4.3.2 Evaluation 4.3.3 General results for the case 4.4 Discussion 4.4.1 Analysis 4.4.2 Evaluation 4.4.3 Overall discussion on the testing of the RSA Framework 4.5 Conclusions 4.6 Acknowledgements 4.7 Chapter References Chapter 5 - Synthesis 5.1 Conceptual aspects 5.2 Methodological aspects 5.3 Testing aspects 5.4 Placing the RSA Framework in a broader context 5.5 Chapter References Chapter 6 - Conclusions and Outlook Annexes Annex A - Literature review: Found records Annex B - Example list of endpoints, descriptors, indicators, and attributes Annex C - Technique for Order Preference by Similarly to Ideal Solution (TOPSIS) Annex D - Translation into the Information System (from endpoints to attributes) Annex E - Interlinkages Identification Matrix Annex F - List of Most Interlinked Indicators (MII) Annex G - List of indicators, scores, and threshold