Phenex: Ontological Annotation of Phenotypic Diversity

Phenex is a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic variation using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Despite the centrality of the phenotype to so much of biology, traditions for communicating information about phenotypes are idiosyncratic to different disciplines. Phenotypes seem to elude standardized descriptions due to the variety of traits that compose them and the difficulty of capturing the complex forms and subtle differences among organisms that we can readily observe. Consequently, phenotypes are refractory to attempts at data integration that would allow computational analyses across studies and study systems. Phenex addresses this problem by allowing scientists to employ standard ontologies and syntax to link computable phenotype annotations to evolutionary character matrices, as well as to link taxa and specimens to ontological identifiers. Ontologies have become a foundational technology for establishing shared semantics, and, more generally, for capturing and computing with biological knowledge

Modeling the flow of non-Newtonian fluids in packed beds at the pore scale

Flow and transport in porous media are important in many science and engineering applications such as composite materials, subsurface water contamination, packed-bed reactors, and enhanced oil recovery. The general approach to modeling such processes is at the continuum scale. Semi-empirical expressions, such as Darcy\u27s law, are substituted for velocity in the continuity equation, which is then coupled with a momentum, mass, and energy balance. While a continuum approach is acceptable in some cases, additional modeling is required for certain non-linear flows, such as multi-phase flows, inertial flows, non-Newtonian flows, and reactive flows. Pore-scale modeling is a first-principles approach to modeling flow and transport in porous media. In this work, network models that are physically representative of specific unconsolidated media are created. The networks can be used to model a wide range of flows, but the focus here is on polymers and suspensions that exhibit non-Newtonian behavior. The network models are used to model steady flow as well as displacement by less viscous fluids. The transient displacement is used to investigate important viscous fingering patterns. While simple boundary conditions are typically imposed in network modeling (e.g. a pressure gradient in one dimension), a more general approach has been developed where boundary conditions are also imposed by direct coupling to an adjacent continuum region. Important qualitative and quantitative results are obtained from the network model for non-Newtonian fluids. Preferential flow pathways form in the network due to the inherent heterogeneity and interconnectivity in porous media. Quantitative results of Darcy velocity versus applied pressure gradient show different behavior than semi-empirical models (analogous to Darcy\u27s law) for non-Newtonian fluids. The transient displacement patterns for non-Newtonian fluids are also different than for Newtonian fluids. If the fluid exhibits a yield stress, a steady state is reached in which some of the original non-Newtonian fluid is left trapped in the network. The displacement patterns are affected by the boundary conditions, which can be determined from direct coupling to a continuum region

Adaptive Feedforward Control of Wastewater Neutralization.

The purpose of this dissertation is to show the development and testing of an adaptive feedforward control of a wastewater neutralization process. The adaptive controller is compared to a nonlinear proportional-integral-derivative (NPID) controller developed by Shinskey (1970). The process and controllers were simulated digitally. The adaptive controller utilizes two pH probes, a feedforward probe and a feedback probe (this measurement is used in the adaptive gain calculation). The feedback measurement provides the adaptive controller with a form of reset action. Probe noise and lag, valve hysteresis and lag, and dead time were included in the simulation. The process simulated for control combines a strong (hydrochloric) and weak (carbonic) acid neutralized by a strong base (sodium hydroxide). The adaptive controller was shown to give superior responses both for step changes in the strong acid and the buffer (weak acid) concentration. The tuning constant limits for the adaptive controller are correlated versus the buffer concentration of the incoming solution for a base case. The sensitivity of the adaptive control to changes in certain parameters (probe noise and lag, valve hysteresis and lag, and dead time) are illustrated. Also shown is the effect of a step change in flow rate to the system. Noise in the feedforward pH probe and the dead time between the reagent addition and the feedback probe had the largest effect on the adaptive controller performance. Efforts to solve the many problems involved in the control of the pH of effluent streams have failed to yield acceptable control algorithm for this very difficult process. This research provides a significant step toward the solution of these problems. An additional bonus of the adaptive controller is the use of only two tuning parameters (many controllers in use today require five or more tuning parameters)

Microfluidic systems for the analysis of the viscoelastic fluid flow phenomena in porous media

In this study, two microfluidic devices are proposed as simplified 1-D microfluidic analogues of a porous medium. The objectives are twofold: firstly to assess the usefulness of the microchannels to mimic the porous medium in a controlled and simplified manner, and secondly to obtain a better insight about the flow characteristics of viscoelastic fluids flowing through a packed bed. For these purposes, flow visualizations and pressure drop measurements are conducted with Newtonian and viscoelastic fluids. The 1-D microfluidic analogues of porous medium consisted of microchannels with a sequence of contractions/ expansions disposed in symmetric and asymmetric arrangements. The real porous medium is in reality, a complex combination of the two arrangements of particles simulated with the microchannels, which can be considered as limiting ideal configurations. The results show that both configurations are able to mimic well the pressure drop variation with flow rate for Newtonian fluids. However, due to the intrinsic differences in the deformation rate profiles associated with each microgeometry, the symmetric configuration is more suitable for studying the flow of viscoelastic fluids at low De values, while the asymmetric configuration provides better results at high De values. In this way, both microgeometries seem to be complementary and could be interesting tools to obtain a better insight about the flow of viscoelastic fluids through a porous medium. Such model systems could be very interesting to use in polymer-flood processes for enhanced oil recovery, for instance, as a tool for selecting the most suitable viscoelastic fluid to be used in a specific formation. The selection of the fluid properties of a detergent for cleaning oil contaminated soil, sand, and in general, any porous material, is another possible application

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

BACKGROUND: Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes. RESULTS: Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued. CONCLUSIONS: The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. THE ONTOLOGY RELEASE FILES ASSOCIATED WITH THE ONTOLOGY MERGE DESCRIBED IN THIS MANUSCRIPT ARE AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ CURRENT ONTOLOGY RELEASE FILES ARE AVAILABLE ALWAYS AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases