Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine

MOTIVATION

Despite the increasing evidence of utility of genomic medicine in clinical practice, systematically integrating genomic medicine information and knowledge into clinical systems with a high-level of consistency, scalability and computability remains challenging. A comprehensive terminology is required for relevant concepts and the associated knowledge model for representing relationships. In this study, we leveraged PharmGKB, a comprehensive pharmacogenomics (PGx) knowledgebase, to formulate a terminology for drug response phenotypes that can represent relationships between genetic variants and treatments. We evaluated coverage of the terminology through manual review of a randomly selected subset of 200 sentences extracted from genetic reports that contained concepts for 'Genes and Gene Products' and 'Treatments'.

RESULTS

Results showed that our proposed drug response phenotype terminology could cover 96% of the drug response phenotypes in genetic reports. Among 18 653 sentences that contained both 'Genes and Gene Products' and 'Treatments', 3011 sentences were able to be mapped to a drug response phenotype in our proposed terminology, among which the most discussed drug response phenotypes were response (994), sensitivity (829) and survival (332). In addition, we were able to re-analyze genetic report context incorporating the proposed terminology and enrich our previously proposed PGx knowledge model to reveal relationships between genetic variants and treatments. In conclusion, we proposed a drug response phenotype terminology that enhanced structured knowledge representation of genomic medicine.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Abstract 1177: Introduction of the GA4GH Variation Representation Specification (VRS) and supporting tools for discovery and exchange of clinical genomic and cytogenomic knowledge in cancers

Precision oncology is the practice of interpreting the clinical significance of observed molecular changes in patient neoplasms, potentially impacting medical decision making and care. This process is labor-intensive and (among other challenges) involves accurately translating between variation representation conventions from one resource to the next. For example, differences in representations of Copy Number Variation (CNV) from genomic regions, cytogenomic bands, or gene features create challenges in knowledge matching due to lack of standards covering all of these modalities of observed variation.The Global Alliance for Genomics and Health (GA4GH; ga4gh.org) is an international collaborative of genomic data sharing initiatives (Driver Projects) developing genomic data sharing standards within a human rights framework. GA4GH recently published the Variation Representation Specification (VRS; pronounced “verse”), a standard for the computational representation of biomolecular variation. VRS is a terminology, schema, and associated conventions for creating uniquely identifiable and federatable representations of molecular variation. VRS has formal data classes well-suited to differentiating between variation on a single molecule (e.g. tandem duplications) from variation measured at a systemic level (e.g. genome-wide copy number variation). In addition to molecular sequence variation, VRS also supports variation on cytogenetic coordinate systems and genes, making it well-suited to representing variation associated with cancer biomarkers.We demonstrate the use of VRS to model reported gene-associated CNVs from the AACR Project GENIE cohort, to aid in the computational discovery of evidence from clinico-genomic knowledgebases with genomic or cytogenomic CNV representations. We highlight the use case of knowledge matching to the Atlas of Genetics and Cytogenetics in Oncology and Haematology (“the Atlas”; atlasgeneticsoncology.org), a cytogenetics resource historically driven by user website navigation. Using VRS search tools we developed for the Variant Interpretation for Cancer Consortium (VICC; cancervariants.org) GA4GH Driver Project, we found that 64% of GENIE samples with reported CNVs matched clinically relevant knowledge in the Atlas. This work was enabled by programmatic search tools leveraging standard VRS object structures, demonstrating how VRS enables collection of real-world evidence across more resources without manual interpretation or custom normalization methods. We conclude with a survey of open-source tools supporting this analysis as well as search of other clinico-genomic knowledgebases with VRS, including CIViC (civicdb.org), BRCA Exchange (brcaexchange.org), and the Molecular Oncology Almanac (moalmanac.org).

Citation Format: Matthew Cannon, Kori Kuzma, James Stevenson, Jiachen Liu, Colin O'Sullivan, Bimal P. Chaudhari, Matthew Brush, Robert R. Freimuth, Tristan Nelson, Michael Baudis, Obi L. Griffith, Malachi Griffith, Lawrence Babb, Melissa S. Cline, Xuelu Liu, Brian Walsh, Alex H. Wagner. Introduction of the GA4GH Variation Representation Specification (VRS) and supporting tools for discovery and exchange of clinical genomic and cytogenomic knowledge in cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1177.

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec.

The Data Use Ontology to streamline responsible access to human biomedical datasets

Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset's allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers' discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide.

The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification

Maximizing the personal, public, research, and clinical value of genomic information will require the reliable exchange of genetic variation data. We report here the Variation Representation Specification (VRS, pronounced "verse"), an extensible framework for the computable representation of variation that complements contemporary human-readable and flat file standards for genomic variation representation. VRS provides semantically precise representations of variation and leverages this design to enable federated identification of biomolecular variation with globally consistent and unique computed identifiers. The VRS framework includes a terminology and information model, machine-readable schema, data sharing conventions, and a reference implementation, each of which is intended to be broadly useful and freely available for community use. VRS was developed by a partnership among national information resource providers, public initiatives, and diagnostic testing laboratories under the auspices of the Global Alliance for Genomics and Health (GA4GH).

Abstract 1096: Harmonization standards from the Variant Interpretation for Cancer Consortium

The use of clinical gene sequencing is now commonplace, and genome analysts and molecular pathologists are often tasked with the labor-intensive process of interpreting the clinical significance of large numbers of tumor variants. Numerous independent knowledgebases have been constructed to alleviate this manual burden, however these knowledgebases are non-interoperable. As a result, the analyst is left with a difficult tradeoff: for each knowledgebase used the analyst must understand the nuances particular to that resource and integrate its evidence accordingly when generating the clinical report, but for each knowledgebase omitted there is increased potential for missed findings of clinical significance.The Variant Interpretation for Cancer Consortium (VICC; cancervariants.org) was formed as a driver project of the Global Alliance for Genomics and Health (GA4GH; ga4gh.org) to address this concern. VICC members include representatives from several major somatic interpretation knowledgebases including CIViC, OncoKB, Jax-CKB, the Weill Cornell PMKB, the IRB-Barcelona Cancer Biomarkers Database, and others. Previously, the VICC built and reported on a harmonized meta-knowledgebase of 19,551 biomarker associations of harmonized variants, diseases, drugs, and evidence across the constituent resources.In that study, we analyzed the frequency with which the tumor samples from the AACR Project GENIE cohort would match to harmonized associations. Variant matches increased dramatically from 57% to 86% when broader matching to regions describing categorical variants were allowed. Unlike precise sequence variants with specified alternate alleles, categorical variants describe a collection of potential variants with a common feature, such as “V600” (non-valine alleles at the 600 residue), “Exon 20 mutations” (all non-silent mutations in exon 20), or “Gain-of-function” (hypermorphic alterations that activate or amplify gene activity). However, matching observed sequence variants to categorical variants is challenging, as the latter are typically only described as unstructured text. Here we describe the expressive and computational GA4GH Variation Representation specification (vr-spec.readthedocs.io), which we co-developed as members of the GA4GH Genomic Knowledge Standards work stream. This specification provides a schema for common, precise forms of variation (e.g. SNVs and Indels) and the method for computing identifiers from these objects. We highlight key aspects of the specification and our work to apply it to the characterization of categorical variation, showcasing the variant terminology and classification tools developed by the VICC to support this effort. These standards and tools are free, open-source, and extensible, overcoming barriers to standardized variant knowledge sharing and search.

Citation Format: Alex H. Wagner, Reece K. Hart, Larry Babb, Robert R. Freimuth, Adam Coffman, Yonghao Liang, Beth Pitel, Angshumoy Roy, Matthew Brush, Jennifer Lee, Anna Lu, Thomas Coard, Shruti Rao, Deborah Ritter, Brian Walsh, Susan Mockus, Peter Horak, Ian King, Dmitriy Sonkin, Subha Madhavan, Gordana Raca, Debyani Chakravarty, Malachi Griffith, Obi L. Griffith. Harmonization standards from the Variant Interpretation for Cancer Consortium [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1096.

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven’t been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.

ClinGen advancing genomic data-sharing standards as a GA4GH driver project

The Clinical Genome Resource (ClinGen)'s work to develop a knowledge base to support the understanding of genes and variants for use in precision medicine and research depends on robust, broadly applicable, and adaptable technical standards for sharing data and information. To forward this goal, ClinGen has joined with the Global Alliance for Genomics and Health (GA4GH) to support the development of open, freely-available technical standards and regulatory frameworks for secure and responsible sharing of genomic and health-related data. In its capacity as one of the 15 inaugural GA4GH "Driver Projects," ClinGen is providing input on the key standards needs of the global genomics community, and has committed to participate on GA4GH Work Streams to support the development of: (1) a standard model for computer-readable variant representation; (2) a data model for linking variant data to annotations; (3) a specification to enable sharing of genomic variant knowledge and associated clinical interpretations; and (4) a set of best practices for use of phenotype and disease ontologies. ClinGen's participation as a GA4GH Driver Project will provide a robust environment to test drive emerging genomic knowledge sharing standards and prove their utility among the community, while accelerating the construction of the ClinGen evidence base.

Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay

SMARCC2 (BAF170) is one of the invariable core subunits of the ATP-dependent chromatin remodeling BAF (BRG1-associated factor) complex and plays a crucial role in embryogenesis and corticogenesis. Pathogenic variants in genes encoding other components of the BAF complex have been associated with intellectual disability syndromes. Despite its significant biological role, variants in SMARCC2 have not been directly associated with human disease previously. Using whole-exome sequencing and a web-based gene-matching program, we identified 15 individuals with variable degrees of neurodevelopmental delay and growth retardation harboring one of 13 heterozygous variants in SMARCC2, most of them novel and proven de novo. The clinical presentation overlaps with intellectual disability syndromes associated with other BAF subunits, such as Coffin-Siris and Nicolaides-Baraitser syndromes and includes prominent speech impairment, hypotonia, feeding difficulties, behavioral abnormalities, and dysmorphic features such as hypertrichosis, thick eyebrows, thin upper lip vermilion, and upturned nose. Nine out of the fifteen individuals harbor variants in the highly conserved SMARCC2 DNA-interacting domains (SANT and SWIRM) and present with a more severe phenotype. Two of these individuals present cardiac abnormalities. Transcriptomic analysis of fibroblasts from affected individuals highlights a group of differentially expressed genes with possible roles in regulation of neuronal development and function, namely H19, SCRG1, RELN, and CACNB4. Our findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits.

A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3

Early B cell factor 3 (EBF3) is a member of the highly evolutionarily conserved Collier/Olf/EBF (COE) family of transcription factors. Prior studies on invertebrate and vertebrate animals have shown that EBF3 homologs are essential for survival and that loss-of-function mutations are associated with a range of nervous system developmental defects, including perturbation of neuronal development and migration. Interestingly, aristaless-related homeobox (ARX), a homeobox-containing transcription factor critical for the regulation of nervous system development, transcriptionally represses EBF3 expression. However, human neurodevelopmental disorders related to EBF3 have not been reported. Here, we describe three individuals who are affected by global developmental delay, intellectual disability, and expressive speech disorder and carry de novo variants in EBF3. Associated features seen in these individuals include congenital hypotonia, structural CNS malformations, ataxia, and genitourinary abnormalities. The de novo variants affect a single conserved residue in a zinc finger motif crucial for DNA binding and are deleterious in a fly model. Our findings indicate that mutations in EBF3 cause a genetic neurodevelopmental syndrome and suggest that loss of EBF3 function might mediate a subset of neurologic phenotypes shared by ARX-related disorders, including intellectual disability, abnormal genitalia, and structural CNS malformations.

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype–phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms. Advanced informatics tools can identify phenotypically relevant disease models in research and diagnostic contexts. Large-scale integration of model organism and clinical research data can provide a breadth of knowledge not available from individual sources and can provide contextualization of data back to these sources. The Monarch Initiative (monarchinitiative.org) is a collaborative, open science effort that aims to semantically integrate genotype–phenotype data from many species and sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species.

The Resource Identification Initiative: A Cultural Shift in Publishing

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as “How did other studies use resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the Methods sections of articles and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their articles prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example, a model organism database for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central Web portal (http://scicrunch.org/resources). RRIDs meet three key criteria: they are machine‐readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 articles have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40, with RRIDs appearing in 62 different journals to date. Here we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post‐pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources. J. Comp. Neurol. 524:8–22, 2016. © 2015 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

The Resource Identification Initiative: a cultural shift in publishing

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, that is, reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as "How did other studies use resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example, a model organism database for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( http://scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40 with RRIDs appearing in 62 different journals to date. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources.

Disease insights through cross-species phenotype comparisons

New sequencing technologies have ushered in a new era for diagnosis and discovery of new causative mutations for rare diseases. However, the sheer numbers of candidate variants that require interpretation in an exome or genomic analysis are still a challenging prospect. A powerful approach is the comparison of the patient’s set of phenotypes (phenotypic profile) to known phenotypic profiles caused by mutations in orthologous genes associated with these variants. The most abundant source of relevant data for this task is available through the efforts of the Mouse Genome Informatics group and the International Mouse Phenotyping Consortium. In this review, we highlight the challenges in comparing human clinical phenotypes with mouse phenotypes and some of the solutions that have been developed by members of the Monarch Initiative. These tools allow the identification of mouse models for known disease-gene associations that may otherwise have been overlooked as well as candidate genes may be prioritized for novel associations. The culmination of these efforts is the Exomiser software package that allows clinical researchers to analyse patient exomes in the context of variant frequency and predicted pathogenicity as well the phenotypic similarity of the patient to any given candidate orthologous gene.

Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network

Biomedical ontologies are a critical component in biomedical research and practice. As an ontology evolves, its structure and content change in response to additions, deletions and updates. When editing a biomedical ontology, small local updates may affect large portions of the ontology, leading to unintended and potentially erroneous changes. Such unwanted side effects often go unnoticed since biomedical ontologies are large and complex knowledge structures. Abstraction networks, which provide compact summaries of an ontology's content and structure, have been used to uncover structural irregularities, inconsistencies and errors in ontologies. In this paper, we introduce Diff Abstraction Networks ("Diff AbNs"), compact networks that summarize and visualize global structural changes due to ontology editing operations that result in a new ontology release. A Diff AbN can be used to support curators in identifying unintended and unwanted ontology changes. The derivation of two Diff AbNs, the Diff Area Taxonomy and the Diff Partial-area Taxonomy, is explained and Diff Partial-area Taxonomies are derived and analyzed for the Ontology of Clinical Research, Sleep Domain Ontology, and eagle-i Research Resource Ontology. Diff Taxonomy usage for identifying unintended erroneous consequences of quality assurance and ontology merging are demonstrated.

The Resource Identification Initiative: A cultural shift in publishing

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to allow humans and algorithms to identify the exact resources that are reported or answer basic questions such as "What other studies used resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases). RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( www.scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are generally accurate in performing the task of identifying resources and supportive of the goals of the project. We also show that identifiability of the resources pre- and post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on reproducibility relating to research resources.

The Resource Identification Initiative: A cultural shift in publishing

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to allow humans and algorithms to identify the exact resources that are reported or answer basic questions such as “What other studies used resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases). RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( www.scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are generally accurate in performing the task of identifying resources and supportive of the goals of the project. We also show that identifiability of the resources pre- and post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on reproducibility relating to research resources.

Research resources: curating the new eagle-i discovery system

Development of biocuration processes and guidelines for new data types or projects is a challenging task. Each project finds its way toward defining annotation standards and ensuring data consistency with varying degrees of planning and different tools to support and/or report on consistency. Further, this process may be data type specific even within the context of a single project. This article describes our experiences with eagle-i, a 2-year pilot project to develop a federated network of data repositories in which unpublished, unshared or otherwise ‘invisible’ scientific resources could be inventoried and made accessible to the scientific community. During the course of eagle-i development, the main challenges we experienced related to the difficulty of collecting and curating data while the system and the data model were simultaneously built, and a deficiency and diversity of data management strategies in the laboratories from which the source data was obtained. We discuss our approach to biocuration and the importance of improving information management strategies to the research process, specifically with regard to the inventorying and usage of research resources. Finally, we highlight the commonalities and differences between eagle-i and similar efforts with the hope that our lessons learned will assist other biocuration endeavors.

Database URL:www.eagle-i.net

Phosphorylation of PDZ1 Domain Attenuates NHERF-1 Binding to Cellular Targets

NHERF-1 (Na(+)-H(+) exchanger regulatory factor 1, also known as EBP50 ezrin-binding protein of 50 kDa) is a phosphoprotein that assembles multiprotein complexes via two PDZ domains and a C-terminal ezrin-binding domain. Current work utilized metabolic labeling in cultured cells expressing wild type GFP-NHERF-1 to define the physiological importance of NHERF-1 phosphorylation. Treatment of cells with phosphatase inhibitors calyculin A and okadaic acid enhanced NHERF-1 phosphorylation and inhibited its dimerization. Eliminating C-terminal serines abolished the modulation of NHERF-1 dimerization by phosphatase inhibitors and identified the phosphorylation of the PDZ1 domain that attenuated its binding to physiological targets, including beta(2)-adrenergic receptor, platelet-derived growth factor receptor, cystic fibrosis transmembrane conductance regulator, and sodium-phosphate cotransporter type IIa. The major covalent modification of PDZ1 was mapped to serine 77. Confocal microscopy of cultured cells suggested key roles for PDZ1 and ERM-binding domain in localizing NHERF-1 at the cell surface. The substitution S77A eliminated PDZ1 phosphorylation and increased NHERF-1 localization at the cell periphery. In contrast, S77D reduced NHERF-1 colocalization with cortical actin cytoskeleton. These data suggested that serine 77 phosphorylation played key role in modulating NHERF-1 association with plasma membrane targets and identified a novel mechanism by which PDZ1 phosphorylation may transduce hormonal signals to regulate the function of membrane proteins in epithelial tissues.

Hematopoietic stem cell transplantation for systemic sclerosis with rapid improvement in skin scores: is neoangiogenesis occurring?

Systemic sclerosis (SSc) is presumed to be an immune-mediated vasculopathy of unknown etiology. SSc is unresponsive to most immune-modulating therapies except for intravenous cyclophosphamide, which is reported to demonstrate some benefit. We, therefore, dose-escalated cyclophosphamide to 200 mg/kg and added rabbit ATG 7.5 mg/kg along with infusion of unselected hematopoietic stem cells to minimize the cytopenic interval. Engraftment occurred rapidly (day 8) with minimal unexpected toxicity, no infections, and unexpectedly rapid improvement in the modified Rodnan Skin Score.

Screening of acyl hydrazide proteinase inhibitors for antiparasitic activity against Trypanosoma brucei

The major cysteine proteinase (brucipain) of Trypanosoma brucei is a target for chemotherapy of African Sleeping Sickness. We have screened a non-peptidyl acyl hydrazide proteinase inhibitor library of 500 compounds for inhibition of brucipain. Those 21 compounds with IC(50) values of <40 microM were tested for efficacy against bloodstream forms of T. brucei in cell culture. Eight acyl hydrazides showed 50% or more inhibition of trypanosome replication at <1 microM. The trypanocidal acitivity of the most effective compounds was comparable with those of the commercial antitrypanosomal drugs suramin and diminazene aceturate. However, these acyl hydrazides exhibited varying cytotoxicity towards human HL-60 cells and therefore, only less favourable selectivity indices compared with the commercially available drugs. Nevertheless, the data support the potential of acyl hydrazides as antitrypanosomal chemotherapeutic agents for treatment of sleeping sickness.

Engraftment syndrome: a common cause for rash and fever following autologous hematopoietic stem cell transplantation for multiple sclerosis

Autologous hematopoietic stem cell transplantation (HSCT) is currently being evaluated as a therapy for patients with progressive multiple sclerosis (MS) at risk of debilitating neurological impairment. While preliminary results from a few studies have been reported, little is known about toxicities or outcome of HSCT for MS. We report a relatively frequent triad of non-infectious fever, rash and fatigue or lassitude that may also be associated with pruritus, pulmonary symptoms, and eosinophilia and frequently occurs around engraftment. This syndrome occurred in 26% of our series of patients (5/19) undergoing HSCT for multiple sclerosis. The engraftment syndrome is usually self-limited but may require intervention with systemic corticosteroids.

Identifying dementia in the primary care practice

BACKGROUND

The purpose of this study was to evaluate the utility (i.e., positive and negative predictive value) of the 7 Minute Screen in identifying patients with probable Alzheimer's disease (AD) in a primary care practice. A second objective was to estimate the number of undiagnosed AD patients in a typical primary care practice.

METHODS

One hundred thirty-seven successive admissions (96%) of patients over the age of 60 to a primary care practice over a 53-day period who completed informed consent documents were administered the 7 Minute Screen. All patients who screened positive (n = 13) and a random sample of those who screened negative (n = 26) returned for full diagnostic evaluation. Positive predictive value (PPV) and negative predictive value (NPV) of the 7 Minute Screen were determined using the criterion standard of clinical diagnosis established by examination, history, and laboratory studies. Test-retest reliability and time for administration were also determined.

RESULTS

Of the 137 patients evaluated, 13 screened positive and 124 screened negative. Eleven of the 13 patients who screened positive were willing to return to the primary care practice for follow-up evaluation. A random sample of 26 patients who screened negative all agreed to return for follow-up evaluation. Of the 11 patients who screened positive and who returned for evaluation, 10 were subsequently diagnosed with probable AD. The remaining patient was diagnosed with mixed dementia. The caregivers of the two patients who refused to return were contacted and both indicated that the patients were having significant cognitive problems as verified by an activities of daily living scale. Of the 26 patients who screened negative, 25 were judged to be cognitively normal and the 26th was judged to have mild cognitive impairment.

DISCUSSION

In successive admissions of patients over the age of 60 in a primary care practice, the 7 Minute Screen showed a PPV of 91% and an NPV of 96% in identifying patients who were subsequently identified with AD or other dementing disorder. These data suggest that this may be a useful instrument in identifying patients who should undergo diagnostic evaluation for AD and other dementing disorders. Additionally, extrapolation from the data in this practice suggests that there may be between 75 and 100 AD patients in the typical primary care practice, many of whom may not be diagnosed.

The mini-cog: a cognitive 'vital signs' measure for dementia screening in multi-lingual elderly

OBJECTIVES

The Mini-Cog, a composite of three-item recall and clock drawing, was developed as a brief test for discriminating demented from non-demented persons in a community sample of culturally, linguistically, and educationally heterogeneous older adults.

SUBJECTS

All 129 who met criteria for probable dementia based on informant interviews and 120 with no history of cognitive decline were included; 124 were non-English speakers.

METHODS

Sensitivity, specificity, and diagnostic value of the Mini-Cog were compared with those of the Mini-Mental State Exam (MMSE) and Cognitive Abilities Screening Instrument (CASI).

RESULTS

The Mini-Cog had the highest sensitivity (99%) and correctly classified the greatest percentage (96%) of subjects. Moreover, its diagnostic value was not influenced by education or language, while that of the CASI was adversely influenced by low education, and both education and language compromised the diagnostic value of the MMSE. Administration time for the Mini-Cog was 3 minutes vs 7 minutes for the MMSE.

CONCLUSIONS

The Mini-Cog required minimal language interpretation and training to administer, and no test forms of scoring modifications were needed to compensate for the extensive linguistic and educational heterogeneity of the sample. Validation in clinical and population-based samples is warranted, as its brevity and ease of administration suggest that the Mini-Cog might be readily incorporated into general practice and senior care settings as a routine 'cognitive vital signs' measure.

Autologous hematopoietic stem cell transplantation in refractory rheumatoid arthritis: sustained response in two of four patients

OBJECTIVE

To investigate the safety and efficacy of immune ablation with subsequent autologous hematopoietic stem cell transplantation (HSCT) in severe rheumatoid arthritis (RA).

METHODS

Four patients with refractory RA and poor prognostic indicators were treated. Stem cells were collected and lymphocytes were depleted by 2.3-4.0 logs. The conditioning regimen included cyclophosphamide (200 mg/kg), antithymocyte globulin (90 mg/kg), and, for 1 patient, total body irradiation (TBI) with 400 cGy. Improvement was evaluated according to the American College of Rheumatology (ACR) preliminary definition of improvement in RA (ACR 20), and also according to the ACR 50 and ACR 70 criteria.

RESULTS

HSCT was well tolerated. Three patients fulfilled the ACR 70 criteria at 1 month and 3 months post-HSCT. One patient did not fulfill the ACR 20 criteria because of persistent joint tenderness, despite improvement of the joint swelling. At 6 months post-HSCT, 1 patient fulfilled the ACR 70 criteria and 1 fulfilled the ACR 50 criteria, and these 2 patients fulfilled the ACR 70 criteria at 9 months post-HSCT. The other 2 patients (including the patient who received TBI) did not meet the ACR 20 criteria at 6 months and 9 months post-HSCT. The only patient with followup of >9 months fulfilled the ACR 70 criteria at 20 months post-HSCT.

CONCLUSION

In this series, autologous HSCT was safe and effective in inducing major clinical response and maintained significant benefit for 2 patients at 9 months and 20 months posttreatment, respectively. Sustained response did not occur for 2 of 4 patients. A regimen dose-response effect may exist, but the addition of TBI did not prevent disease relapse for 1 of the patients. More aggressive T cell depletion of the autograft, use of a myeloablative regimen, or use of an allograft may be necessary to decrease relapse rates.

The Clock Drawing Test: utility for dementia detection in multiethnic elders

BACKGROUND

Disproportionate increases in dementia morbidity in ethnic minorities challenge established screening methodologies because of language and culture barriers, varying access to health services, and a relative paucity of cross-cultural data validating their use. Simple screening techniques adapted to a range of health and social service settings would accelerate dementia detection and social and health services planning for demented minority elders.

METHODS

The effectiveness of the Clock Drawing Test (CDT) for dementia detection was compared with that of the Mini-Mental State Examination (MMSE) and the Cognitive Abilities Screening Instrument (CASI) in community-dwelling elders of diverse linguistic, ethnic, and educational backgrounds. Subjects (N = 295) were tested at home in their native languages (English, n = 141; another language, n = 154). An informant-based clinical dementia history and functional severity index derived from the Consortium to Establish a Registry for Alzheimer's Disease (CERAD) protocols were used to classify subjects as probably demented (n = 170), and probably not demented (n = 125).

RESULTS

All tests were significantly affected by education (p < .001) but not by primary language (p > .05). Sensitivities and specificities for probable dementia were 82% and 92%, respectively, for the CDT; 92% and 92% for the MMSE; and 93% and 97% for the CASI for subjects completing each test. However, in poorly educated non-English speakers, the CDT detected demented subjects with higher sensitivity than the two longer instruments (sensitivity and specificity 85% and 94% for the CDT, 46% and 100% for the MMSE, and 75% and 95% for the CASI). Moreover less information was lost due to noncompletion of the CDT than the MMSE or CASI (severe dementia or refusal: CDT 8%, MMSE 12%, and CASI 16%).

CONCLUSIONS

Overall, the CDT may be as effective as the MMSE or CASI as a first-level dementia screen for clinical use in multiethnic, multilingual samples of older adults. Its brevity (1-5 minutes), minimal language requirements, high acceptability, and lack of dependence on specialized testing materials are well adapted for screening of non-English-speaking elderly persons in settings where bilingual interpreters are not readily available and screening time is at a premium.

Autologous hematopoietic stem cell transplantation in refractory rheumatoid arthritis: sustained response in two of four patients

OBJECTIVE

To investigate the safety and efficacy of immune ablation with subsequent autologous hematopoietic stem cell transplantation (HSCT) in severe rheumatoid arthritis (RA).

METHODS

Four patients with refractory RA and poor prognostic indicators were treated. Stem cells were collected and lymphocytes were depleted by 2.3-4.0 logs. The conditioning regimen included cyclophosphamide (200 mg/kg), antithymocyte globulin (90 mg/kg), and, for 1 patient, total body irradiation (TBI) with 400 cGy. Improvement was evaluated according to the American College of Rheumatology (ACR) preliminary definition of improvement in RA (ACR 20), and also according to the ACR 50 and ACR 70 criteria.

RESULTS

HSCT was well tolerated. Three patients fulfilled the ACR 70 criteria at 1 month and 3 months post-HSCT. One patient did not fulfill the ACR 20 criteria because of persistent joint tenderness, despite improvement of the joint swelling. At 6 months post-HSCT, 1 patient fulfilled the ACR 70 criteria and 1 fulfilled the ACR 50 criteria, and these 2 patients fulfilled the ACR 70 criteria at 9 months post-HSCT. The other 2 patients (including the patient who received TBI) did not meet the ACR 20 criteria at 6 months and 9 months post-HSCT. The only patient with followup of >9 months fulfilled the ACR 70 criteria at 20 months post-HSCT.

CONCLUSION

In this series, autologous HSCT was safe and effective in inducing major clinical response and maintained significant benefit for 2 patients at 9 months and 20 months posttreatment, respectively. Sustained response did not occur for 2 of 4 patients. A regimen dose-response effect may exist, but the addition of TBI did not prevent disease relapse for 1 of the patients. More aggressive T cell depletion of the autograft, use of a myeloablative regimen, or use of an allograft may be necessary to decrease relapse rates.

Changes in expression of adenyl cyclase activity in human endometrium during hormone replacement therapy and ovarian stimulation

We have investigated membrane fractions prepared from human endometrium for activity of the signalling adenyl cyclase (AC). We characterized the AC guanine nucleotide-binding proteins (G proteins) and examined the changes in AC activity during evaluation cycles of oestrogen and progesterone replacement therapy as well during ovarian stimulation cycles. AC activity was determined by the conversion of substrate ATP into cyclic AMP under basal conditions and in the presence of guanine nucleotide or forskolin. G proteins were determined by Western Blot using specific polyclonal antibodies against Gsalpha, Gi1,2alpha and Gi3alpha. Our results indicate that endometrial AC was highly responsive to activation by both guanine nucleotide and forskolin and its rate of cyclic AMP production was highly pronounced. Mean activity reached 920 pmol/l/min/mg membrane protein in the presence of forskolin, a value approximately 5-fold higher than those detected in corpus luteum. Hormonal induction of AC activities increased Gsalpha protein, which couples with and stimulates the catalytic component of AC. We conclude that human endometrium is rich in AC and that enzyme activity is induced by oestrogen and progesterone treatment. These data strongly support the concept that the transmembrane signalling AC system and its messenger cyclic AMP are major regulators of endometrial function in the human.

Calpain-calpastatin: a novel, complete calcium-dependent protease system in human spermatozoa

Calpain, a calcium (Ca2+)-activated cysteine protease presents in several somatic mammalian cells, has been demonstrated to mediate specific Ca2+-dependent reactions including cell fusion. Because spermatozoa cells have an absolute Ca2+ requirement for penetration of oocytes, we have postulated that calpain would also be found in mammalian spermatozoa. Here we show that whole sperm homogenate and cell fractions prepared from ejaculated human spermatozoa contain calpain activity. Specific calpain inhibitors impaired this proteolytic activity. Unlike the enzyme described in somatic cells, sperm calpain was mostly particulate in nature and its activity was maximal at pH 9.0. Presence of sperm calpain was confirmed by immunoblot analysis using specific anti-calpain I and anti-calpain II antibodies. A 67 kDa calpain II protein and a 75 kDa calpain I protein were detected. Also spermatozoa contain the endogenous calpain inhibitor, calpastatin. We detected 158.8 +/- 24.5 (mean +/- SD) fmol calpastatin/mg sperm protein. Immunoblot analysis using specific antibodies showed a 68 kDa calpastatin protein located in the cytosolic fraction. This is the first demonstration that a complete calpain-calpastatin system exists in mammalian spermatozoa. Because calpain is a unique effector system for calcium-dependent processes, our data reveals a novel mechanism by which calcium exerts its regulatory functions in spermatozoa.

Stem cell component therapy: supplementation of unmanipulated marrow with CD34 enriched peripheral blood stem cells

Eleven patients with hematologic malignancies and two with aplastic anemia were treated using unmanipulated marrow and immunoselected CD34+ blood cells. Donors began G-CSF (10 microg/kg) injections 1 day after undergoing bone marrow harvest. Blood stem cells were collected on day 5 of G-CSF. Peripheral blood lymphocytes were depleted via CD34-positive selection. If, after marrow and blood harvest, less than 2.0 x 10(6) CD34 cells/kg were mobilized, leukapheresis was repeated on day 6. Median time to an absolute neutrophil count greater than 500 microl was day 10; transfusion-independent platelet count greater than 20,000/microl was day 13; average hospital discharge was day 14; and average inpatient hospital charges were 101,870 US dollars. Acute GVHD grade II occurred in five of 13 patients. No patient developed grade III or IV acute GVHD. At a median follow-up of 10 months, no patient has developed extensive chronic GVHD. Allografts of unmanipulated bone marrow supplemented with G-CSF-mobilized and CD34 immunoselected blood cells may prevent an increased risk of GVHD while preserving the rapid engraftment kinetics of peripheral blood. Supplementation of marrow with CD34 enriched blood cells appears to result in rapid engraftment, early hospital discharge, lower inpatient charges, decreased regimen-related toxicity, and no apparent increase in GVHD.

Treatment of autoimmune disease by intense immunosuppressive conditioning and autologous hematopoietic stem cell transplantation

Multiple sclerosis, systemic lupus erythematosus, and rheumatoid arthritis are immune-mediated diseases that are responsive to suppression or modulation of the immune system. For patients with severe disease, immunosuppression may be intensified to the point of myelosuppression or hematopoietic ablation. Hematopoiesis and immunity may then be rapidly reconstituted by reinfusion of CD34(+) progenitor cells. In 10 patients with these autoimmune diseases, autologous hematopoietic stem cells were collected from bone marrow or mobilized from peripheral blood with either granulocyte colony-stimulating factor (G-CSF) or cyclophosphamide and G-CSF. Stem cells were enriched ex vivo using CD34(+) selection and reinfused after either myelosuppressive conditioning with cyclophosphamide (200 mg/kg), methylprednisolone (4 g) and antithymocyte globulin (ATG; 90 mg/kg) or myeloablative conditioning with total body irradiation (1,200 cGy), methylprednisolone (4 g), and cyclophosphamide (120 mg/kg). Six patients with multiple sclerosis, 2 with systemic lupus erythematosus, and 2 with rheumatoid arthritis have undergone hematopoietic stem cell transplantation. Mean time to engraftment of an absolute neutrophil count greater than 500/microL (0.5 x 10(9)/L) and a nontransfused platelet count greater than 20,000/microL (20 x 10(9)/L) occurred on day 10 and 14, respectively. Regimen-related nonhematopoietic toxicity was minimal. All patients improved and/or had stabilization of disease with a follow-up of 5 to 17 months (median, 11 months). We conclude that intense immunosuppressive conditioning and autologous T-cell-depleted hematopoietic transplantation was safely used to treat these 10 patients with severe autoimmune disease. Although durability of response is as yet unknown, all patients have demonstrated stabilization or improvement.

T cell-depleted autologous hematopoietic stem cell transplantation for multiple sclerosis: report on the first three patients

Multiple sclerosis (MS) is a disease of the central nervous system characterized by immune-mediated destruction of myelin. In patients with progressive deterioration, we have intensified immunosuppression to the point of myeloablation. Subsequently, a new hematopoietic and immune system is generated by infusion of CD34-positive hematopoietic stem cells (HSC). Three patients with clinical MS and a decline of their Kurtzke extended disability status scale (EDSS) by 1.5 points over the 12 months preceding enrollment and a Kurtzke EDSS of 8.0 at the time of enrollment were treated with hematopoietic stem cell (HSC) transplantation using a myeloablative conditioning regimen of cyclophosphamide (120 mg/kg), methylprednisolone (4 g) and total body irradiation (1200 cGy). Reconstitution of hematopoiesis was achieved with CD34-enriched stem cells. The average time of follow-up is 8 months (range 6-10 months). Despite withdrawal of all immunosuppressive medications, functional improvements have occurred in all three patients. We conclude that T cell-depleted hematopoietic stem cell transplantation can be performed safely in patients with severe and debilitating multiple sclerosis. Stem cell transplantation has resulted in modest neurologic improvements for the first time since onset of progressive disease although no significant changes in EDSS or NRS scales are evident at this time.

A 7 minute neurocognitive screening battery highly sensitive to Alzheimer's disease

OBJECTIVE

To determine the validity and reliability of a rapidly administered neurocognitive screening battery consisting of 4 brief tests (Enhanced Cued Recall, Temporal Orientation, Verbal Fluency, and Clock Drawing) to distinguish between patients with probable Alzheimer's disease (AD) and healthy control subjects.

SUBJECTS

Sixty successive referrals to the Memory Disorders Clinic at Southwestern Vermont Medical Center, Bennington, who were diagnosed as having probable AD and 60 community-dwelling volunteers of comparable age, sex distribution, and education.

DESIGN

Interrater and test-retest reliability, intergroup comparisons between patients with AD and control subjects on the 4 individual tests, and determination of probability of dementia for patients with AD and control subjects using the entire battery of tests.

SETTING

Outpatient care.

MAIN OUTCOME MEASURE

Comparison of the probability of dementia on the 7 Minute Screen with the criterion standard of clinical diagnosis established by examination and laboratory studies.

SECONDARY OUTCOME MEASURES

Test-retest and interrater reliability (correlation coefficients), time for administration.

RESULTS

Mean time of administration was 7 minutes 42 seconds. Mean scores for patients with AD and control subjects on all 4 individual tests were significantly different (for each, P<.001). When the 4 tests were combined in a logistic regression, the battery had a sensitivity of 100% and a specificity of 100%. A series of 1000 repeated random samples of 30 patients with AD and 30 control subjects taken from the overall sample of 60 patients with AD and 60 control subjects had a mean sensitivity of 92% and a mean specificity of 96%. The battery was equally sensitive to patients with mild AD as demonstrated by correctly classifying all 13 patients with AD using Mini-Mental State Examination scores of 24 or higher. Neither age nor education was a statistically significant factor when added as a covariate. Test-retest reliabilities for individual tests ranged from 0.83 to 0.93. Test-retest reliability for the entire battery was 0.91. Interrater reliability for the entire battery was 0.92.

CONCLUSIONS

The 7 Minute Screen appears highly sensitive to AD and may be useful in helping to make initial distinctions between patients experiencing cognitive changes related to the normal aging process and those experiencing cognitive deficits related to dementing disorders such as AD. It has reasonable interrater and test-retest reliability, can be administered in a brief period, and requires no clinical judgment and minimal training.

Status of hCG/LH receptor and G proteins in human endometrium during artificial cycles of hormone replacement therapy

OBJECTIVES

We examined the existence of hCG/LH receptors and associated GTP-binding (G) proteins in membrane fractions of nonpregnant human endometrium and investigated whether their expression is affected, in vivo, by estrogen and progesterone replacement therapy.

METHODS

A pool of normal endometrial biopsy specimens (n = 5) was initially used to characterize receptors and G proteins. Subsequently, biopsy specimens (n = 22) were obtained from 11 patients undergoing evaluation cycles of hormone replacement therapy (HRT). From each patient, two specimens were collected on successive cycle days: on day 0 (last day of estrogen) and on either day 3, 6, or 9 of progesterone supplementation. Both hCG/LH receptor and G proteins were determined in membrane (10,000 x g) fractions by immunoblot analysis using specific polyclonal antibodies against synthetic fragments of hCG/LH receptor and against G proteins. Membrane fractions from rat brain and rat corpus luteum were used as controls. Proteins were loaded on the gel under reducing conditions.

RESULTS

The receptor antibody immunoreacted with a protein of approximately 68 kd in endometrial membranes. A similar protein was detected in rat corpus luteum. The G-protein antibodies detected Gs alpha, Gi3 alpha, Gi1 alpha/Gi2 alpha, and common beta subunits in endometrial membranes with a molecular weight of 48-42 kd, 41 kd, 40 kd, and 37 kd, respectively. Analysis of membranes obtained during HRT indicated that levels of hCG/LH receptors remained fairly constant throughout the cycle days (days 0, 3, 6, and 9). Similar results were observed for Gi1 alpha/Gi2 alpha and Gi3 alpha. In great contrast, Gs alpha was low at day 0 but increased with the administration of progesterone (days 3, 6, and 9).

CONCLUSIONS

Human endometrium contains both membrane-bound hCG/LH receptors and associated G proteins. During HRT, progesterone supplementation to estrogen therapy enhances the expression of Gs alpha protein subunit, but not hCG/LH receptors.

Interaction of antistasin-related peptides with factor Xa: identification of a core inhibitory sequence

Antistasin, isolated from the Mexican leech, is a 119 amino acid protein which is a selective and potent inhibitor of coagulation Factor Xa. Previous studies indicated that an arginine residue located at position 34 of the inhibitor was cleaved by Factor Xa during the inhibition reaction. To evaluate this residue as the reactive site of antistasin, and to define shorter fragments of antistasin displaying Factor Xa-inhibitory activity, a series of peptides were synthesized corresponding to amino acids 27-49 of the inhibitor. The most potent peptide synthesized was a disulfide-bridged, 19 amino acid peptide, ATS29-47, which inhibited Factor Xa with a Ki = 35 nM, and increased plasma clotting times by over 4-fold at a concentration of 33 uM. Reduction or sulfation of the cysteine residues in ATS29-47 reduced Factor Xa inhibitory activity by over 95%. Peptides as short as seven residues corresponding to position 33-39 of antistasin displayed Factor Xa inhibitory activity. The peptides did not inhibit thrombin or trypsin at concentrations 1000-fold higher than used in Factor Xa assays. The shortest peptide displaying anticoagulant activity in human plasma was the disulfide-bridged peptide, D-Arg-Cys-Arg-Val-His-Cys-Pro, which increased clotting times by 50% at micromolar concentrations. These results demonstrate that antistasin-related peptide sequences can serve as model structures for the development of novel, low molecular weight anticoagulants.