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

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

Технология синтеза и очистки гликолида

Данная работа посвящена технологии получения и очистки гликолида, как мономера для биоразлагаемых полимеров. Основные потери продукта происходят на стадии получения и очистки мономера. Потери составляют порядка 50-60 %. Целью данной работы является выбор оптимального пути и очистки гликолида. В данной работе проведён и представлен всесторонний литературный обзор по методам получения гликолевой кислоты, гликолида, очистки и полимеризации гликолида. Сравнивались различные катализаторы на стадиях поликонденсации, деполимеризации и полимеризации гликолида. В работе описаны характеристики сырья, описаны способы получения, очистки и полимеризации гликолида. Изложены методики анализа гликолида.This paper is devoted to the technology of production and purification of glycolide as a monomer for biodegradable polymers. The main product losses occur at the stage of monomer production and purification. Losses are about 50-60%. The purpose of this work is to choose the optimal path and purification of glycolide. In this paper, we conducted and presented a comprehensive literature review on methods for producing glycolic acid, glycolide, and purification and polymerization of glycolide. Different catalysts were compared at the stages of glycolide polycondensation, depolymerization, and polymerization. The work describes the characteristics of the raw materials, describes the methods of production, purification, and polymerization of glycolide

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

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

Designing for emergence and innovation: Redesigning design

We reveal the surprising and counterintuitive truth that the design process, in and of itself, is not always on the forefront of innovation. Design is a necessary but not a sufficient condition for the success of new products and services. We intuitively sense a connection between innovative design and emergence. The nature of design, emergence and innovation to understand their interrelationships and interdependencies is examined. We propose that design must harness the process of emergence; for it is only through the bottom-up and massively iterative unfolding of emergence that new and improved products and services are successfully refined, introduced and diffused into the marketplace. The relationships among design, emergence and innovation are developed. What designers can learn from nature about emergence and evolution that will impact the design process is explored. We examine the roles that design and emergence play in innovation. How innovative organizations can incorporate emergence into their design process is explored. We demarcate the boundary between invention and innovation. We also articulate the similarities and differences of design and emergence. We then develop the following three hypotheses: Hypothesis 1: “An innovative design is an emergent design.” Hypothesis 2: “A homeostatic relationship between design and emergence is a required condition for innovation.”Hypothesis 3: “Since design is a cultural activity and culture is an emergent phenomenon, it follows that design leading to innovation is also an emergent phenomenon” We provide a number of examples of how design and emergence have worked together and led to innovation. Examples include the tool making of early man; the evolutionary chain of the six languages speech, writing, math, science, computing and the Internet; the Gutenberg printing press and techniques of collaborative filtering associated with the Internet. We close by describing the relationship between human and naturally “designed” systems and the notion a key element of a design is its purpose as is the case with a living organism

The Mantle Transition Zone Beneath West Antarctica: Seismic Evidence for Hydration and Thermal Upwellings

Although prior work suggests that a mantle plume is associated with Cenozoic rifting and volcanism in West Antarctica, the existence of a plume remains conjectural. Here we use P wave receiver functions (PRFs) from the Antarctic POLENET array to estimate mantle transition zone thickness, which is sensitive to temperature perturbations, throughout previously unstudied parts of West Antarctica. We obtain over 8000 high-quality PRFs using an iterative, time domain deconvolution method filtered with a Gaussian width of 0.5 and 1.0, corresponding to frequencies less than ∼0.24 and ∼0.48 Hz, respectively. Single-station and common conversion point stacks, migrated to depth using the AK135 velocity model, indicate that mantle transition zone thickness throughout most of West Antarctica does not differ significantly from the global average, except in two locations; one small region exhibits a vertically thinned (210 ± 15 km) transition zone beneath the Ruppert Coast of Marie Byrd Land and another laterally broader region shows slight, vertical thinning (225 ± 25 km) beneath the Bentley Subglacial Trench. We also observe the 520 discontinuity and a prominent negative peak above the mantle transition zone throughout much of West Antarctica. These results suggest that the mantle transition zone may be hotter than average in two places, possibly due to upwelling from the lower mantle, but not broadly across West Antarctica. Furthermore, we propose that the transition zone may be hydrated due to \u3e100 million years of subduction beneath the region during the early Mesozoic

Continental flood basalts derived from the hydrous mantle transition zone

It has previously been postulated that the Earth's hydrous mantle transition zone may play a key role in intraplate magmatism, but no confirmatory evidence has been reported. Here we demonstrate that hydrothermally altered subducted oceanic crust was involved in generating the late Cenozoic Chifeng continental flood basalts of East Asia. This study combines oxygen isotopes with conventional geochemistry to provide evidence for an origin in the hydrous mantle transition zone. These observations lead us to propose an alternative thermochemical model, whereby slab-triggered wet upwelling produces large volumes of melt that may rise from the hydrous mantle transition zone. This model explains the lack of pre-magmatic lithospheric extension or a hotspot track and also the arc-like signatures observed in some large-scale intracontinental magmas. Deep-Earth water cycling, linked to cold subduction, slab stagnation, wet mantle upwelling and assembly/breakup of supercontinents, can potentially account for the chemical diversity of many continental flood basalts

Preference Transitivity and Symbolic Representation in Capuchin Monkeys (Cebus apella)

BACKGROUND: Can non-human animals comprehend and employ symbols? The most convincing empirical evidence comes from language-trained apes, but little is known about this ability in monkeys. Tokens can be regarded as symbols since they are inherently non-valuable objects that acquire an arbitrarily assigned value upon exchange with an experimenter. Recent evidence suggested that capuchin monkeys, which diverged from the human lineage 35 million years ago, can estimate, represent and combine token quantities. A fundamental and open question is whether monkeys can reason about symbols in ways similar to how they reason about real objects. METHODOLOGY/PRINCIPAL FINDINGS: Here we examined this broad question in the context of economic choice behavior. Specifically, we assessed whether, in a symbolic context, capuchins' preferences satisfy transitivity--a fundamental trait of rational decision-making. Given three options A, B and C, transitivity holds true if A > or = B, B > or = C and A > or = C (where > or = indicates preference). In this study, we trained monkeys to exchange three types of tokens for three different foods. We then compared choices monkeys made between different types of tokens with choices monkeys made between the foods. Qualitatively, capuchins' preferences revealed by the way of tokens were similar to those measured with the actual foods. In particular, when choosing between tokens, monkeys displayed strict economic preferences and their choices satisfied transitivity. Quantitatively, however, values measured by the way of tokens differed systematically from those measured with the actual foods. In particular, for any pair of foods, the relative value of the preferred food increased when monkeys chose between the corresponding tokens. CONCLUSIONS/SIGNIFICANCE: These results indicate that indeed capuchins are capable of treating tokens as symbols. However, as they do so, capuchins experience the cognitive burdens imposed by symbolic representation

Stochastic Inversion of P-to-S Converted Waves for Mantle Composition and Thermal Structure: Methodology and Application

We present a new methodology for inverting P‐to‐S receiver function (RF) waveforms directly for mantle temperature and composition. This is achieved by interfacing the geophysical inversion with self‐consistent mineral phase equilibria calculations from which rock mineralogy and its elastic properties are predicted as a function of pressure, temperature, and bulk composition. This approach anchors temperatures, composition, seismic properties, and discontinuities that are in mineral physics data, while permitting the simultaneous use of geophysical inverse methods to optimize models of seismic properties to match RF waveforms. Resultant estimates of transition zone (TZ) topography and volumetric seismic velocities are independent of tomographic models usually required for correcting for upper mantle structure. We considered two end‐member compositional models: the equilibrated equilibrium assemblage (EA) and the disequilibrated mechanical mixture (MM) models. Thermal variations were found to influence arrival times of computed RF waveforms, whereas compositional variations affected amplitudes of waves converted at the TZ discontinuities. The robustness of the inversion strategy was tested by performing a set of synthetic inversions in which crustal structure was assumed both fixed and variable. These tests indicate that unaccounted‐for crustal structure strongly affects the retrieval of mantle properties, calling for a two‐step strategy presented herein to simultaneously recover both crustal and mantle parameters. As a proof of concept, the methodology is applied to data from two stations located in the Siberian and East European continental platforms.This work was supported by a grant from the Swiss National Science Foundation (SNF project 200021_159907). B. T. was funded by a Délégation CNRS and Congé pour Recherches et Conversion Thématique from the Université de Lyon to visit the Research School of Earth Sciences (RSES), The Australian National University (ANU). B. T. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement 79382