A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

Partial logics with two kinds of negation as a foundation for knowledge-based reasoning

We show how to use model classes of partial logic to define semantics of general knowledge-based reasoning. Its essential benefit is that partial logics allow us to distinguish two sorts of negative information: the absence of information and the explicit rejection or falsification of information. Another general advantage of partial logic, which we discuss in the first part, is that its meta-theory is very close to the meta-theory of classical logic. In the second part notions of minimal, paraminimal and stable models are presented in terms of partial logic and we show how the resulting definitions can be used to define the semantics of knowledge bases such as relational and deductive databases, and extended logic programs

Static capacitive pressure sensing using a single graphene drum

To realize nanomechanical graphene-based pressure and gas sensors, it is beneficial to have a method to electrically readout the static displacement of a suspended graphene membrane. Capacitive readout, typical in micro-electro-mechanical systems (MEMS), gets increasingly challenging as one starts shrinking the dimensions of these devices, since the expected responsivity of such devices is below 0.1 aF/Pa. To overcome the challenges of detecting small capacitance changes, we design an electrical readout device fabricated on top of an insulating quartz substrate, maximizing the contribution of the suspended membrane to the total capacitance of the device. The capacitance of the drum is further increased by reducing the gap size to 110 nm. Using external pressure load, we demonstrate successful detection of capacitance changes of a single graphene drum down to 50 aF, and pressure differences down to 25 mbar

Reverse taxonomy for elucidating diversity of insect-associated nematodes: a case study with termites

BACKGROUND: The molecular operational taxonomic unit(MOTU)has recently been applied to microbial and microscopic animal biodiversity surveys. However, in many cases, some of the MOTUs cannot be definitively tied to any of the taxonomic groups in current databases. To surmount these limitations, the concept of "reverse taxonomy" has been proposed, i.e. to primarily list the MOTUs with morphological information, and then identify and/or describe them at genus/species level using subsamples or by re-isolating the target organisms. Nevertheless, the application of "reverse taxonomy" has not been sufficiently evaluated. Therefore, the practical applicability of "reverse taxonomy" is tested using termite-associated nematodes as a model system for phoretic/parasitic organisms which have high habitat specificity and a potential handle (their termite host species) for re-isolation attempts. METHODOLOGY: Forty-eight species (from 298 colonies) of termites collected from the American tropics and subtropics were examined for their nematode associates using the reverse taxonomy method and culturing attempts (morphological identification and further sequencing efforts). The survey yielded 51 sequence types (= MOTUs) belonging to 19 tentatively identified genera. Within these, four were identified based on molecular data with preliminary morphological observation, and an additional seven were identified or characterized from successful culturing, leaving eight genera unidentified. CONCLUSIONS: That 1/3 of the genera were not successfully identified suggests deficiencies in the depth of available sequences in the database and biological characters, i.e. usually isolated as phoretic/parasitic stages which are not available for morphological identification, and too many undiscovered lineages of nematodes. Although there still is the issue of culturability of nematodes, culturing attempts could help to make reverse taxonomy methods more effective. However, expansion of the database, i.e., production of more DNA barcodes tied to biological information by finding and characterizing additional new and known lineages, is necessary for analyzing functional diversity.Natsumi Kanzaki, Robin M. Giblin-Davis, Rudolf H. Scheffrahn, Hisatomo Taki, Alejandro Esquivel, Kerrie A. Davies and E. Allen Herr

Micro-cantilever testing of diamond - silicon carbide interfaces in silicon carbide bonded diamond materials produced by reactive silicon infiltration

SiC-bonded diamond materials produced by pressureless reactive infiltration of diamond preforms with silicon show high hardness and wear resistance. These properties are due to the relatively high diamond volume content of approximately 50 vol% and the mechanically strong interface between diamond and SiC. To determine the bending strength of individual interfaces between diamond and SiC, micro-cantilevers were prepared by focused ion beam milling at 13 grain boundaries and in-situ bending tests were carried out in a scanning electron microscope. The determined strength of cantilevers showing interface fracture was 10.4 ± 4.0 GPa. Fracture surfaces were analyzed to verify the fracture behavior and initiation. In addition to fracture at the interface diamond/SiC, fracture occurred inside the SiC grains and at the SiC/silicon interface at comparable strength values. The results prove the high diamond/SiC-interface bonding strength

Ontology patterns for the representation of quality changes of cells in time

Background: Cell tracking experiments, based on time-lapse microscopy, have become an important tool in biomedical research. The goal is the reconstruction of cell migration patterns, shape and state changes, and, comprehensive genealogical information from these data. This information can be used to develop process models of cellular dynamics. However, so far there has been no structured, standardized way of annotating and storing the tracking results, which is critical for comparative analysis and data integration. The key requirement to be satisfied by an ontology is the representation of a cell’s change over time. Unfortunately, popular ontology languages, such as Web Ontology Language (OWL), have limitations for the representation of temporal information. The current paper addresses the fundamental problem of modeling changes of qualities over time in biomedical ontologies specified in OWL. Results: The presented analysis is a result of the lessons learned during the development of an ontology, intended for the annotation of cell tracking experiments. We present, discuss and evaluate various representation patterns for specifying cell changes in time. In particular, we discuss two patterns of temporally changing information: n-ary relation reification and 4d fluents.These representation schemes are formalized within the ontology language OWL and are aimed at the support for annotation of cell tracking experiments. We analyze the performance of each pattern with respect to standard criteria used in software engineering and data modeling, i.e. simplicity, scalability, extensibility and adequacy. We further discuss benefits, drawbacks, and the underlying design choices of each approach. Conclusions: We demonstrate that patterns perform differently depending on the temporal distribution of modeled information. The optimal model can be constructed by combining two competitive approaches. Thus, we demonstrate that both reification and 4d fluents patterns can work hand in hand in a single ontology. Additionally, we have found that 4d fluents can be reconstructed by two patterns well known in the computer science community, i.e. state modeling and actor-role pattern

SUGOI: Automated Ontology Interchangeability

A foundational ontology can solve interoperability issues among the domain ontologies aligned to it. However, several foundational ontologies have been developed, hence such interoperability issues exist among domain ontologies. The novel SUGOI tool, {\em Software Used to Gain Ontology Interchangeability}, allows a user to interchange automatically a domain ontology among the DOLCE, BFO and GFO foundational ontologies. The success of swapping varies due to differences in coverage, and amount of mappings both between the foundational ontologies and the alignment mappings between the domain and the foundational ontology. In this demo we present the tool, and attendees can bring their preferred ontology for interchange by SUGOI, and will be assisted with the analysis of the results in terms of `good' and `bad' entity linking to assess how feasible it is to change it over to the other foundational ontology

Results of Catheter Ablation of Ventricular Tachycardia Using Direct Current Shocks

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74779/1/j.1540-8159.1989.tb02654.x.pd