Using multiple reference ontologies: Managing composite annotations

There are a growing number of reference ontologies available across a variety of biomedical domains and current research focuses on their construction, organization and use. An important use case for these ontologies is annotation—where users create metadata that access concepts and terms in reference ontologies. We draw on our experience in physiological modeling to present a compelling use case that demonstrates the potential complexity of such annotations. In the domain of physiological biosimulation, we argue that most annotations require the use of multiple reference ontologies. We suggest that these “composite” annotations should be retained as a repository of knowledge about post-coordination that promotes sharing and interoperation across biosimulation models

Advances in semantic representation for multiscale biosimulation: a case study in merging models

As a case-study of biosimulation model integration, we describe our experiences applying the SemSim methodology to integrate independently-developed, multiscale models of cardiac circulation. In particular, we have integrated the CircAdapt model (written by T. Arts for MATLAB) of an adapting vascular segment with a cardiovascular system model (written by M. Neal for JSim). We report on three results from the model integration experience. First, models should be explicit about simulations that occur on different time scales. Second, data structures and naming conventions used to represent model variables may not translate across simulation languages. Finally, identifying the dependencies among model variables is a non-trivial task. We claim that these challenges will appear whenever researchers attempt to integrate models from others, especially when those models are written in a procedural style (using MATLAB, Fortran, etc.) rather than a declarative format (as supported by languages like SBML, CellML or JSim’s MML)

Idiopathic osteoporosis in men

Over the last decade, the increasingly significant problem of osteoporosis in men has begun to receive much more attention than in the past. In particular, recent observations from large scale population studies in males led to an advance in the understanding of morphologic basis of growth, maintenance and loss of bone in men, as well as new insights about the pathophysiology and treatment of this disorder. While fracture risk consistently increases after age 65 in men (with up to 50 % of cases due to secondary etiologies), osteoporosis and fractures may also occur in young or middle aged males in the absence of an identifiable etiology. For this category (so called idiopathic osteoporosis), there are still major gaps in knowledge, particularly concerning the etiology and the clinical management. This article provides a summary of recent developments in the acquisition and maintenance of bone strength in men, as well as new insights about the pathogenesis, diagnosis, and treatment of idiopathic osteoporosis

Integration of multi-scale biosimulation models via light-weight semantics

Currently, biosimulation researchers use a variety of computational environments and languages to model biological processes. Ideally, researchers should be able to semi- automatically merge models to more effectively build larger, multi-scale models. How- ever, current modeling methods do not capture the underlying semantics of these models sufficiently to support this type of model construction. In this paper, we both propose a general approach to solve this problem, and we provide a specific example that demon- strates the benefits of our methodology. In particular, we describe three biosimulation models: (1) a cardio-vascular fluid dynamics model, (2) a model of heart rate regulation via baroreceptor control, and (3) a sub-cellular-level model of the arteriolar smooth mus- cle. Within a light-weight ontological framework, we leverage reference ontologies to match concepts across models. The light-weight ontology then helps us combine our three models into a merged model that can answer questions beyond the scope of any single model

The TNG Near Infrared Camera Spectrometer

NICS (acronym for Near Infrared Camera Spectrometer) is the near-infrared cooled camera-spectrometer that has been developed by the Arcetri Infrared Group at the Arcetri Astrophysical Observatory, in collaboration with the CAISMI-CNR for the TNG (the Italian National Telescope Galileo at La Palma, Canary Islands, Spain). As NICS is in its scientific commissioning phase, we report its observing capabilities in the near-infrared bands at the TNG, along with the measured performance and the limiting magnitudes. We also describe some technical details of the project, such as cryogenics, mechanics, and the system which executes data acquisition and control, along with the related software.Comment: 7 pages, 5 figures, compiled with A&A macros. A&A in pres

Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies

Abstract—Current methods for annotating biomedical data resources rely on simple mappings between data elements and the contents of a variety of biomedical ontologies and controlled vocabularies. Here we point out that such simple mappings are inadequate for large-scale multiscale, multidomain integrative “virtual human” projects. For such integrative challenges, we describe a “composite annotation” schema that is simple yet sufficiently extensible for mapping the biomedical content of a variety of data sources and biosimulation models to available biomedical ontologies

Solid-phase synthesis of peptides containing reverse-turn mimetic bicyclic lactams

The solid-phase synthesis and characterization of a series of peptides (4-15) containing reverse-turn mimetic bicyclic lactams is reported. The bicyclic lactams (1a, 1b) possess high structural similarity to the two central residues of a Pturn. Amino acid conjugates of these bicyclic lactams were synthesized on solid supports following a g-fluorenylmethoxycarbonyl (FMOC) protection strategy on WangMerrifield resin. Coupling between amino acids was accomplished by means of diisopropylcarbodiimide (DIC)/ hydroxyazabenzotriazole (HOAt). Coupling between amino acids and the mimics was performed with the potent Carpino's reagent O-(7-azabenzotriazol-1-yl)-N,N,N',N'-tetramelhyluronium hexafluorophosphate (HATU). The final compounds were cleaved from the resin and obtained as N-acetylated methyl esters or benzyl amides

Synthesis and Conformational Studies of Peptidomimetics Containing a New Bifunctional Diketopiperazine Scaffold Acting as a \u3b2-Hairpin Inducer

A practical synthesis of a new bifunctional diketopiperazine (DKP) scaffold 1, formally derived from the cyclization of L-aspartic acid and (S)-2,3-diaminopropionic acid, is reported. DKP-1 bears a carboxylic acid and an amino functionalities in a cis relationship, which have been used to grow peptide sequences. Tetra-, penta-, and hexapeptidomimetic sequences were prepared by solution-phase peptide synthesis (Boc strategy). Conformational analysis of these derivatives was carried out by a combination of 1H NMR spectroscopy, IR spectroscopy, CD spectroscopy, and computer modeling, and reveals the formation of beta-hairpin mimics involving 10-membered and 18-membered H-bonded rings and a reverse turn of the growing peptide chain

A Library Approach to the Development of BenzaPhos, Highly Efficient Chiral Supramolecular Ligands for Asymmetric Hydrogenation

A library of chiral supramolecular ligands named BenzaPhos, of straightforward preparation (two steps from commercial or readily available starting materials) and modular structure, was designed and synthesized. The ligands were screened in the search of new rhodium catalysts for the enantioselective hydrogenation of several benchmark and industrially relevant substrates. Once a series of hits were identified, structural modifications were introduced on three of the best ligands and a small second-generation library was created. Members of the latter showed outstanding levels of activity and enantioselectivity in the hydrogenation of challenging olefins such as enamide S4 and beta-dehydroamino ester S5 (> 99% ee: best value ever reported in both cases). A series of control experiments were undertaken in order to clarify the role of hydrogen bonding in determining the catalytic properties of the new ligands. The results of these experiments, together with those of computational studies carried out on four dihydride complexes involved in the catalytic hydrogenation of substrate S4, strongly suggest that a substrate orientation takes place in the catalytic cycle by formation of a hydrogen bond between the ligand amide oxygen and the substrate amide NH

Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology

We introduce and define the Ontology of Physics for Biology (OPB), a reference ontology of physical principles that bridges the gap between bioinformatics modeling of biological structures and the biosimulation modeling of biological processes. Whereas modeling anatomical entities is relatively wellstudied, representing the physics-based semantics of biosimulation and biological processes remains an open research challenge. The OPB bridges this semantic gap--linking the semantics of biosimulation mathematics to structural bio-ontologies. Our design of the OPB is driven both by theory and pragmatics: we have applied systems dynamics theory to build an ontology with pragmatic use for annotating biosimulation models