Investigation of the Effect of Peptide p5 Targeting CDK5-p25 Hyperactivity on Munc18-1 (P67) Regulating Neuronal Exocytosis Using Molecular Simulations.

Munc18-1 is an SM (sec1/munc-like) family protein involved in vesicle fusion and neuronal exocytosis. Munc18-1 is known to regulate the exocytosis process by binding with closed- and open-state conformations of Syntaxin1, a protein belonging to the SNARE family established to be central to the exocytosis process. Our previous work studied peptide p5 as a promising drug candidate for CDK5-p25 complex, an Alzheimer's disease (AD) pathological target. Experimental in vivo and in vitro studies suggest that Munc18-1 promotes p5 to selectively inhibit the CDK5-p25 complex without affecting the endogenous CDK5 activity, a characteristic of remarkable therapeutic implications. In this paper, we identify several binding modes of p5 with Munc18-1 that could potentially affect the Munc18-1 binding with SNARE proteins and lead to off-target effects on neuronal communication using molecular dynamics simulations. Recent studies indicate that disruption of Munc18-1 function not only disrupts neurotransmitter release but also results in neurodegeneration, exhibiting clinical resemblance to other neurodegenerative conditions such as AD, causing diagnostic and treatment challenges. We characterize such interactions between p5 and Munc18-1, define the corresponding pharmacophores, and provide guidance for the in vitro validation of our findings to improve therapeutic efficacy and safety of p5.

Modeling, validation and verification of three-dimensional cell-scaffold contacts from terabyte-sized images.

BACKGROUND: Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and three types of scaffolds (i.e., spun coat, large microfiber, and medium microfiber). Our analysis of the acquired terabyte-sized collection is motivated by the need to understand the nature of the shape dimensionality (1D vs 2D vs 3D) of cell-scaffold interactions relevant to tissue engineers that grow cells on biomaterial scaffolds. RESULTS: We designed five statistical and three geometrical contact models, and then down-selected them to one from each category using a validation approach based on physically orthogonal measurements to CLSM. The two selected models were applied to 414 z-stacks with three scaffold types and all contact results were visually verified. A planar geometrical model for the spun coat scaffold type was validated from atomic force microscopy images by computing surface roughness of 52.35 nm ±31.76 nm which was 2 to 8 times smaller than the CLSM resolution. A cylindrical model for fiber scaffolds was validated from multi-view 2D scanning electron microscopy (SEM) images. The fiber scaffold segmentation error was assessed by comparing fiber diameters from SEM and CLSM to be between 0.46% to 3.8% of the SEM reference values. For contact verification, we constructed a web-based visual verification system with 414 pairs of images with cells and their segmentation results, and with 4968 movies with animated cell, scaffold, and contact overlays. Based on visual verification by three experts, we report the accuracy of cell segmentation to be 96.4% with 94.3% precision, and the accuracy of cell-scaffold contact for a statistical model to be 62.6% with 76.7% precision and for a geometrical model to be 93.5% with 87.6% precision. CONCLUSIONS: The novelty of our approach lies in (1) representing cell-scaffold contact sites with statistical intensity and geometrical shape models, (2) designing a methodology for validating 3D geometrical contact models and (3) devising a mechanism for visual verification of hundreds of 3D measurements. The raw and processed data are publicly available from https://isg.nist.gov/deepzoomweb/data/ together with the web -based verification system.

Computational Study of the Allosteric Effects of p5 on CDK5-p25 Hyperactivity as Alternative Inhibitory Mechanisms in Neurodegeneration.

The cyclin-dependent kinase (CDK5) forms a stable complex with its activator p25, leading to the hyperphosphorylation of tau proteins and to the formation of plaques and tangles that are considered to be one of the typical causes of Alzheimer's disease (AD). Hence, the pathological CDK5-p25 complex is a promising therapeutic target for AD. Small peptides, obtained from the truncation of CDK5 physiological activator p35, have shown promise in inhibiting the pathological complex effectively while also crossing the blood-brain barrier. One such small 24-residue peptide, p5, has shown selective inhibition toward the pathological complex in vivo. Our previous research focused on the characterization of a computationally predicted CDK5-p5 binding mode and of its pharmacophore, which was consistent with competitive inhibition. In continuation of our previous work, herein, we investigate four additional binding modes to explore other possible mechanisms of interaction between CDK5 and p5. The quantitative description of the pharmacophore is consistent with both competitive and allosteric p5-induced inhibition mechanisms of CDK5-p25 pathology. The gained insights can direct further in vivo/in vitro tests and help design small peptides, linear or cyclic, or peptidomimetic compounds as adjuvants of orthosteric inhibitors or as part of a cocktail of drugs with enhanced effectiveness and lower side effects.

Transforming Health Care through Digital Revolutions.

The Internet, which has spanned several networks in a broad range of domains, is having a significant impact on every aspect of our lives. The next generation of networks will utilize a wide variety of resources with significant sensing capabilities. Such networks will extend beyond physically linked computers to include multimodal-information from biological, cognitive, semantic, and social networks. This paradigm shift will involve symbiotic networks of smart medical devices, and smart phones or mobile personal computing and communication devices. These devices-and the network-will be constantly sensing, monitoring, and interpreting the environment; this is sometimes referred to as the Internet of Things (IoT). We are also witnessing considerable interest in the "Omics" paradigm, which can be viewed as the study of a domain in a massive scale, at different levels of abstraction, in an integrative manner. The IoT revolution, combined with the Omics revolution (genomics and socio-omics or social networks) and artificial intelligence resurgence, will have significant implications for the way health care is delivered in the United States. After discussing a vision for health care in the future, we introduce the P9 health care concept, followed by a discussion of a framework for smart health care. Then, we present a case study and research directions, followed by examples of ongoing work at the National Institute of Standards and Technology (NIST).

Artificial Intelligence and Digital Tools: Future of Diabetes Care.

Diabetes mellitus has become a global threat, especially in the emerging economies. In the United States, there are about 24 million people with diabetes mellitus. Diabetes represents a trove of physiologic and sociologic data that are only superficially understood by the health care system. Artificial intelligence can address many problems posed by the prevalence of diabetes mellitus and the impact of diabetes on individual and societal health. We provide a brief overview of artificial intelligence and discuss case studies that illustrate how artificial intelligence can enhance diabetes care.

Imaging as a Biomarker: Standards for Change Measurements in Therapy workshop summary.

Biomarkers are biological indicators of disease or therapeutic effects that can be measured by in vivo biomedical/molecular imaging, as well as other in vitro or laboratory methods. Recent work has shown that biomedical imaging can provide an early indication of drug response by use of x-ray, computed tomography (CT), positron-emission tomography/CT (PET/CT), or magnetic resonance imaging (MRI). There are three primary sources of uncertainty in using imaging as a biomarker: 1) the biological variability, 2) the variability associated with the clinicians interpreting the images, and 3) the physical measurement variability associated with image data collection and analysis across the same or different imaging platforms. Although biological variability is a large source of error, the physical uncertainty often significantly reduces the robustness of the imaging methods and the clinical decision tools required for quantitative measurement of therapy response over time. Physical and biological measurement uncertainties may be addressed prior to designing a clinical trial and thus help in reducing the case size and cost of a clinical trial associated with a drug submission to the U.S. Food and Drug Administration (FDA). The National Institute of Standards and Technology (NIST) has been approached over the last few years by several industry and medical stakeholders to address the physical sources of measurement uncertainty. NIST's initial research discovered that the characterization of measurement uncertainty poses many complex metrology and standardization problems on a scale that appears to need significant collaboration across the different medical imaging stakeholders. Many of the issues are similar to other scientific domains that NIST has addressed as part of its mission to provide metrology standards to enhance the competitiveness of U.S. industries. To better assess the measurement and standards needs for using imaging as a biomarker, NIST engaged leading representatives from many of the different imaging societies, the imaging, pharmaceutical and e-health and other health care stakeholders, as well as other key federal agencies (the National Institutes of Health Institutes and Centers [NIH ICs], and FDA) to organize and conduct a United States Measurement System (USMS) workshop: http://usms.nist.gov/workshops. The workshop entitled Imaging as a Biomarker: Standards for Change Measurements in Therapy, was thus held on September 14-15, 2006, at NIST in Gaithersburg, Maryland. (Workshop agenda, presentations. and final workshop report will be available at http://usms.nist.gov/workshops/bioimaging.htm.)

Generating Domain Terminologies using Root- and Rule-Based Terms.

Motivated by the need for flexible, intuitive, reusable, and normalized terminology for guiding search and building ontologies, we present a general approach for generating sets of such terminologies from natural language documents. The terms that this approach generates are root- and rule-based terms, generated by a series of rules designed to be flexible, to evolve, and, perhaps most important, to protect against ambiguity and standardize semantically similar but syntactically distinct phrases to a normal form. This approach combines several linguistic and computational methods that can be automated with the help of training sets to quickly and consistently extract normalized terms. We discuss how this can be extended as natural language technologies improve and how the strategy applies to common use-cases such as search, document entry and archiving, and identifying, tracking, and predicting scientific and technological trends.

MitoMorphy: an alignment and annotation tool for human mitochondrial DNA polymorphisms.

MitoMorphy uses a number of publicly available human mitochondrial DNA (mtDNA) sequences from different ethnic groups to compare and annotate the associated polymorphic data. It provides an integrated display of mtDNA sequence comparison, sequence variation, and annotation for 695 different mtDNA sequences from many different ethnic groups around the world.

Data standards for proteomics: mitochondrial two-dimensional polyacrylamide gel electrophoresis data as a model system.

Proteomics has emerged as a major discipline that led to a re-examination of the need for consensus and a nationally sanctioned set of proteomics technology standards. Such standards for databases and data reporting may be applied to two-dimensional polyacrylamide gel electrophoresis (2D PAGE) technology as a pilot project for assessing global and national needs in proteomics, and the role of the National Institute of Standards and Technology (NIST) and other similar standards and measurement organizations. The experience of harmonizing the heterogeneous data included in the Protein Data Bank (PDB) provides a paradigm for technology in an area where significant heterogeneity in technical detail and data storage has evolved. Here we propose an approach toward standardizing mitochondrial 2D PAGE data in support of a globally relevant proteomics consensus.

Workflow and electronic health records in small medical practices.

This paper analyzes the workflow and implementation of electronic health record (EHR) systems across different functions in small physician offices. We characterize the differences in the offices based on the levels of computerization in terms of workflow, sources of time delay, and barriers to using EHR systems to support the entire workflow. The study was based on a combination of questionnaires, interviews, in situ observations, and data collection efforts. This study was not intended to be a full-scale time-and-motion study with precise measurements but was intended to provide an overview of the potential sources of delays while performing office tasks. The study follows an interpretive model of case studies rather than a large-sample statistical survey of practices. To identify time-consuming tasks, workflow maps were created based on the aggregated data from the offices. The results from the study show that specialty physicians are more favorable toward adopting EHR systems than primary care physicians are. The barriers to adoption of EHR systems by primary care physicians can be attributed to the complex workflows that exist in primary care physician offices, leading to nonstandardized workflow structures and practices. Also, primary care physicians would benefit more from EHR systems if the systems could interact with external entities.

Evaluation of the interaction of cyclin-dependent kinase 5 with activator p25 and with p25-derived inhibitor CIP.

A high-affinity inhibitor protein called CIP, produced by small truncations of p35, was experimentally identified. P35 is a physiological activator of the cyclin-dependent kinase cdk5. P25 is derived from proteolytic truncation of p35 within "stressed" neurons, and it is associated with the hyperphosphorylation of specific neuronal proteins, typically occurring in neurodegenerative diseases such as Alzheimer's. Here, we report a study of the binding mechanisms of the cdk5-p25 and cdk5-CIP complexes. This provides a better understanding of the source of the inhibitory activity of the protein CIP. We use a geometry-based technique to test the hypothesis that p25's truncation increases the flexibility of CIP and thus prevents cdk5 from reaching its active conformation. Our study is based on a geometry-based alignment algorithm, which aligns two given protein conformations with respect to their interfaces. Our results support the flexibility hypothesis and will be used as a basis for targeted molecular dynamics simulations.

A model of deformable rings for interpretation of wireless capsule endoscopic videos.

Wireless Capsule Endoscopy (WCE) provides a means to obtain a detailed video of the small intestine. A single session with WCE may produce nearly 8h of video. Its interpretation is tedious task, which requires considerable expertise and is very stressful. The Model of Deformable Rings (MDR) was developed to preprocess WCE video and aid clinicians with its interpretation. The MDR uses a simplified model of a capsule's motion to flexibly match (register) consecutive video frames. Essentially, it computes motion-descriptive characteristics and produces a two-dimensional representation of the gastrointestinal (GI) tract's internal surface - a map. The motion-descriptive characteristics are used to indicate video fragments which exhibit segmentary contractions, peristalsis, refraction phases and areas of capsule retention. Within maps, certain characteristics that indicate areas of bleeding, ulceration and obscuring froth could be recognized. Therefore, the maps allow quick identification of such abnormal areas. The experimental results demonstrate that the number of discovered pathologies and gastrointestinal landmarks increases with the MDR technique.

Ongoing development of two-dimensional polyacrylamide gel electrophoresis data standards.

We present an approach toward standardizing two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) data in support of developing a globally relevant proteomics consensus in order to provide more efficient database querying and data comparisons through the establishment of the necessary definitions and interdisciplinary reference fields for both the 2-D PAGE community, particularly in the proteomics area, and the clinical and experimental biological research communities, in general. This article covers the need for unifying the 2-D PAGE data through a common data repository, and its usefulness in data standards and data interoperability.