Quality Control Measures over 30 Years in a Multicenter Clinical Study: Results from the Diabetes Control and Complications Trial / Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) Study

Implementation of multicenter and/or longitudinal studies requires an effective quality assurance program to identify trends, data inconsistencies and process variability of results over time. The Diabetes Control and Complications Trial (DCCT) and the follow-up Epidemiology of Diabetes Interventions and Complications (EDIC) study represent over 30 years of data collection among a cohort of participants across 27 clinical centers. The quality assurance plan is overseen by the Data Coordinating Center and is implemented across the clinical centers and central reading units. Each central unit incorporates specific DCCT/EDIC quality monitoring activities into their routine quality assurance plan. The results are reviewed by a data quality assurance committee whose function is to identify variances in quality that may impact study results from the central units as well as within and across clinical centers, and to recommend implementation of corrective procedures when necessary. Over the 30-year period, changes to the methods, equipment, or clinical procedures have been required to keep procedures current and ensure continued collection of scientifically valid and clinically relevant results. Pilot testing to compare historic processes with contemporary alternatives is performed and comparability is validated prior to incorporation of new procedures into the study. Details of the quality assurance plan across and within the clinical and central reading units are described, and quality outcomes for core measures analyzed by the central reading units (e.g. biochemical samples, fundus photographs, ECGs) are presented.     

National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease.     

Overview of the Consortium of Hospitals Advancing Research on Tobacco (CHART)

ABSTRACT: BACKGROUND: The Consortium of Hospitals Advancing Research on Tobacco (CHART) is a network of six projects and a research coordinating unit funded by the National Heart, Lung, and Blood Institute, the National Cancer Institute, the National Institute on Drug Abuse, and the National Institutes of Health (NIH) Office of Behavioral and Social Science Research. The CHART projects will assess the effectiveness and cost-effectiveness of smoking cessation interventions initiated during hospitalization and continued post-discharge. Methods/design Along with a seventh project funded previously under the NIH Challenge grants, the CHART projects will assess smoking cessation strategies delivered to approximately 10,000 hospitalized smokers across a geographically diverse group of nearly 20 private, public, academic, and community hospitals. The CHART research coordinating unit at Kaiser Permanente Center for Health Research provides organizational and data coordination support, facilitating the development of common measures for combining data from multiple CHART projects. DISCUSSION: The targeted enrollment in CHART, if achieved, will represent the largest, most diverse pooled dataset of hospitalized smokers receiving smoking cessation assistance, and is designed to contribute to the dissemination and implementation of smoking cessation interventions provided by hospital systems.     

The chromosome 4 workshop report

In the concluding session the compilation and availability of available resources on chromosome 4 were discussed. A listing of these resources is available from Jeff Murray at the University of Iowa for anyone with an interest in human chromosome 4. Rick Myers stressed the commitment of the UCSF Genome Center to make resources available to the mapping community as a whole as soon as they have been identified and characterized. There was general agreement that such a philosophy will facilitate the rapid generation and integration of the maps from several groups currently working in this area. The chromosome 4 committee for the Human Gene Mapping workshops was scheduled to meet in August of 1991, and a second chromosome 4-specific meeting is to be held in Leiden on June 13 and 14, 1992 (contact Gert-Jan van Ommen for information). Future venues for the meeting are planned to alternate between countries with groups participating in mapping projects on this chromosome and initially will focus particularly on groups with chromosome wide mapping interests such as EUROGEM and the Human Genome Center.     

Announcement—guidance document for acquiring reliable data in ecological restoration projects

The Laurentian Great Lakes are undergoing intensive ecological restoration in Canada and the United States. In the United States, an interagency committee was formed to facilitate implementation of quality practices for federally funded restoration projects in the Great Lakes basin. The Committee's responsibilities include developing a guidance document that will provide a common approach to the application of quality assurance and quality control (QA/QC) practices for restoration projects. The document will serve as a “how‐to” guide for ensuring data quality during each aspect of ecological restoration projects. In addition, the document will provide suggestions on linking QA/QC data with the routine project data and hints on creating detailed supporting documentation. Finally, the document will advocate integrating all components of the project, including QA/QC applications, into an overarching decision‐support framework. The guidance document is expected to be released by the U.S. EPA Great Lakes National Program Office in 2017.     

Infrastructure for the life sciences: design and implementation of the UniProt website

Background  

The UniProt consortium was formed in 2002 by groups from the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) at Georgetown University, and soon afterwards the website was set up as a central entry point to UniProt resources. Requests to this address were redirected to one of the three organisations' websites. While these sites shared a set of static pages with general information about UniProt, their pages for searching and viewing data were different. To provide users with a consistent view and to cut the cost of maintaining three separate sites, the consortium decided to develop a common website for UniProt. Following several years of intense development and a year of public beta testing, the domain was switched to the newly developed site described in this paper in July 2008.     

TaxonKit: A practical and efficient NCBI taxonomy toolkit

The National Center for Biotechnology Information (NCBI) Taxonomy is widely applied in biomedical and ecological studies. Typical demands include querying taxonomy identifier (TaxIds) by taxonomy names, querying complete taxonomic lineages by TaxIds, listing descendants of given TaxIds, and others. However, existed tools are either limited in functionalities or inefficient in terms of runtime. In this work, we present TaxonKit, a command-line toolkit for comprehensive and efficient manipulation of NCBI Taxonomy data. TaxonKit comprises seven core subcommands providing functions, including TaxIds querying, listing, filtering, lineage retrieving and reformatting, lowest common ancestor computation, and TaxIds change tracking. The practical functions, competitive processing performance, scalability with different scales of datasets and good accessibility can facilitate taxonomy data manipulations. TaxonKit provides free access under the permissive MIT license on GitHub, Brewsci, and Bioconda. The documents are also available at https://bioinf.shenwei.me/taxonkit/.     

Self-complementarity within proteins: bridging the gap between binding and folding

Complementarity, in terms of both shape and electrostatic potential, has been quantitatively estimated at protein-protein interfaces and used extensively to predict the specific geometry of association between interacting proteins. In this work, we attempted to place both binding and folding on a common conceptual platform based on complementarity. To that end, we estimated (for the first time to our knowledge) electrostatic complementarity (Em) for residues buried within proteins. Em measures the correlation of surface electrostatic potential at protein interiors. The results show fairly uniform and significant values for all amino acids. Interestingly, hydrophobic side chains also attain appreciable complementarity primarily due to the trajectory of the main chain. Previous work from our laboratory characterized the surface (or shape) complementarity (Sm) of interior residues, and both of these measures have now been combined to derive two scoring functions to identify the native fold amid a set of decoys. These scoring functions are somewhat similar to functions that discriminate among multiple solutions in a protein-protein docking exercise. The performances of both of these functions on state-of-the-art databases were comparable if not better than most currently available scoring functions. Thus, analogously to interfacial residues of protein chains associated (docked) with specific geometry, amino acids found in the native interior have to satisfy fairly stringent constraints in terms of both Sm and Em. The functions were also found to be useful for correctly identifying the same fold for two sequences with low sequence identity. Finally, inspired by the Ramachandran plot, we developed a plot of Sm versus Em (referred to as the complementarity plot) that identifies residues with suboptimal packing and electrostatics which appear to be correlated to coordinate errors.     

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

The International Molecular Exchange (IMEx) consortium is an international collaboration between major public interaction data providers to share literature-curation efforts and make a nonredundant set of protein interactions available in a single search interface on a common website (http://www.imexconsortium.org/). Common curation rules have been developed, and a central registry is used to manage the selection of articles to enter into the dataset. We discuss the advantages of such a service to the user, our quality-control measures and our data-distribution practices.     

Unbiased measures of transmitted information and channel capacity from multivariate neuronal data

Two measures from information theory, transmitted information and channel capacity, can quantify the ability of neurons to convey stimulus-dependent information. These measures are calculated using probability functions estimated from stimulus-response data. However, these estimates are biased by response quantization, noise, and small sample sizes. Improved estimators are developed in this paper that depend on both an estimate of the sample-size bias and the noise in the data.This work was supported in part by Air Force Office of Scientific Research Grant AFOSR-ISSA-88-0073     

Conducting clinical research in the new NHS: the model of cancer. United Kingdom Coordinating Committee on Cancer Research.

The United Kingdom Coordinating Committee on Cancer Research represents the major organizations funding cancer research in the United Kingdom. The deliberations of a working party convened by the committee to evaluate recently expressed concerns that the changes in the NHS threaten research, especially clinical trials to evaluate new treatments, are reported. A survey of contributors to trials coordinated by the committee showed that half are now experiencing difficulties in continuing to participate in clinical trials. The two major problems identified were lack of time and of staff, especially for NHS staff in non-teaching hospitals. Recent changes in junior doctors'' hours and proposed reductions in the length of time for training will exacerbate this. It is possible to identify the direct and indirect excess costs of conducting research in the NHS, but currently the mechanism does not exist to designate funds specifically for this purpose. Consultation with the regional directors of research and development confirmed that the service increment for teaching and research is not the solution for this. Proposals are made to secure future clinical research in the NHS, including finance, indemnity, the licensing of new drugs, the greater use of nurse counsellors, and the value of cancer registries.     

象白蚁肠道中一个纤维素降解菌群的分离和特性研究

利用滤纸培养基从象白蚁(Nasutitermes sp.)肠道中分离出一个具有纤维素降解能力,能够降解滤纸的混合菌群。在起始pH 6.5,37℃培养条件下培养6d可得到最高的纤维素酶(CMCase和FPase)活性。在优化条件下,混合菌群的滤纸降解率在第15d达到最大值66.3%,显示出较高的滤纸降解效率。酶谱活性染色分析显示,混合菌群在以滤纸为唯一碳源的生长过程中至少表达了8种内切葡聚糖酶和4种木聚糖酶。扫描电镜观察到该混合菌群包含短杆状和球形两种形态的细菌。基于16SrRNA基因的系统发育分析表明,该混合菌群中至少存在两种细菌,分别属于沙雷氏菌属(Serratia)和类芽胞杆菌属(Paenibacillus)。这两种细菌协同降解纤维素的机制值得进一步深入研究。     

Standard guidelines for the chromosome-centric human proteome project

The objective of the international Chromosome-Centric Human Proteome Project (C-HPP) is to map and annotate all proteins encoded by the genes on each human chromosome. The C-HPP consortium was established to organize a collaborative network among the research teams responsible for protein mapping of individual chromosomes and to identify compelling biological and genetic mechanisms influencing colocated genes and their protein products. The C-HPP aims to foster the development of proteome analysis and integration of the findings from related molecular -omics technology platforms through collaborations among universities, industries, and private research groups. The C-HPP consortium leadership has elicited broad input for standard guidelines to manage these international efforts more efficiently by mobilizing existing resources and collaborative networks. The C-HPP guidelines set out the collaborative consensus of the C-HPP teams, introduce topics associated with experimental approaches, data production, quality control, treatment, and transparency of data, governance of the consortium, and collaborative benefits. A companion approach for the Biology and Disease-Driven HPP (B/D-HPP) component of the Human Proteome Project is currently being organized, building upon the Human Proteome Organization's organ-based and biofluid-based initiatives (www.hupo.org/research). The common application of these guidelines in the participating laboratories is expected to facilitate the goal of a comprehensive analysis of the human proteome.     

GO‐FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO‐FAANG) Workshop in Washington, DC on October 7–8, 2015. This consortium is a grass‐roots organization formed to advance the annotation of newly assembled genomes of domesticated and non‐model organisms ( www.faang.org ). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org . In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO‐FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta‐data analysis standards were established.     

The Spanish Translation and Cultural Adaptation of Five Mental Health Outcome Measures

In this paper we report on the process of translating five mental health outcome measures into Spanish and adapting them to Latino culture. The instruments considered are the World Health Organization-Disability Assessment Scale, the Burden Assessment Scale, the Family Burden Scale, Lehman's Quality of Life Interview and the Continuity of Care in Mental Health Services Interview. A systematic process of translation and adaptation of the instruments was followed with the goal of achieving cultural equivalence between the English and Spanish versions of the instruments in five dimensions: semantic, content, technical, construct, and criterion equivalence. In this paper we present data about the semantic, content, and technical equivalence. Various steps were taken to achieve equivalence in these dimensions, including the use of a bilingual committee, a multi-national bilingual committee, back-translation, and focus groups with mental health patients and their relatives.     

Definition and insertion of the GSPC in the political context of Mexico

Mexico as a megadiverse country houses between 6 and 8% of the world's flora. However, the Mexican flora is facing challenges, including the presence of at least 981 threatened plant species and 618 exotic plant species, habitat loss, pollution, overexploitation of natural resources and the adverse effects of climate change, which are compromising its conservation and sustainable use. Mexico has been actively involved in the development and update of the Global Strategy for Plant Conservation (GSPC) adopted by the Convention on Biological Diversity (CBD). As a party to CBD, Mexico has established a Coordinating Committee for the Mexican Strategy for Plant Conservation (MSPC), which has adapted the GSPC to fit national needs and drafted a number of projects, indicators, means of verification and actors to ensure that the MSPC, as a public policy tool, really drives conservation and sustainable use actions among all sectors and lasts beyond the current administration. An agenda is being developed with activities that include the following: approaching Congress, identifying the relevance of the MSPC in the National Development Plan and the Mexican Biodiversity Strategy, making use of current environmental policies and an aggressive awareness programme. The MSPC includes simultaneous programmes of technical and political work.     

Barriers and challenges in clinical ethics consultations: the experiences of nine clinical ethics committees

Clinical ethics committees have recently been established in nearly all Norwegian hospital trusts. One important task for these committees is clinical ethics consultations. This qualitative study explores significant barriers confronting the ethics committees in providing such consultation services. The interviews with the committees indicate that there is a substantial need for clinical ethics support services and, in general, the committee members expressed a great deal of enthusiasm for the committee work. They also reported, however, that tendencies to evade moral disagreement, conflict, and 'outsiders' are common in the hospitals. Sometimes even the committees comply with some of these tendencies. The committees agree that there is a need to improve their routines and procedures, clarify the committees' profile and field of responsibility, to make the committees well-known, to secure adequate operating conditions, and to develop organizational integration and support. Various strategies to meet these challenges on a local, regional or national level are also explored in this paper.