Schema Mapper: A Visualization Tool for DL Integration

Schema mapping is a challenging problem. It has come to the fore in recent years; there are important applications like database schema integration and, more recently, digital library merging of heterogeneous data. Previous studies have approached the schema mapping process either from algorithmic or visualization perspectives, with few integrating both. With Schema Mapper we demonstrate a semi-automatic tool for schema integration that combines a novel visual interface with an algorithm-based recommendation engine. Schemas are visualized as hyperbolic trees (see Fig. 1), thus allowing more schema nodes to be displayed at one time. Matches to selections are recommended to the user, which makes the mapping operation easier and faster

Integration of Heterogeneous Digital Libraries with Semi-automatic Mapping and Browsing: From Formalization to Specification to Visualization

In this paper, we formalize the digital library (DL) integration problem and propose an overall approach based on the 5S framework. We apply 5S to domain-specific (archaeological) DLs, illustrating our solutions for key problems in DL integration. We use ETANA-DL as a case study to describe the process of semi-automatically generating a union catalog and a unified browsing service in an archaeological DL. A visual schema mapping tool is developed for union catalog creation. A pilot user study aids tool evaluation. Our approach is further validated through application of a general browsing component to two integrated DLs

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Construction, analysis, and modeling of complex reaction networks with RING

University of Minnesota Ph.D. Thesis. August 2013. Major: Chemical Engineering. Advisors: Prodromos Daoutidis and Aditya Bhan. 1 computer file (PDF); xviii, 210 pages.Complex reaction networks are found in a variety of engineered and natural chemical systems ranging from petroleum processing to atmospheric chemistry and including biomass conversion, materials synthesis, metabolism, and biological degradation of chemicals. These systems comprise of several thousands of reactions and species inter-related through a highly interconnected network. This thesis presents methods, computational tools, and applications that demonstrate that: (a) any complex network can be constructed automatically from a small set of initial reactants and chemical transformation rules, and (b) a given network can be analyzed in terms of identifying topological information such as reaction pathways, determining thermodynamically feasible routes, evaluating the spectrum of plausible and synthetically feasible compounds, exploring dominant routes to form experimentally observed products, and formulating and solving a rigorous kinetic model. A new computational tool called Rule Input Network Generator, or RING, has been developed to construct and analyze complex reaction networks. Given initial reactants of a reaction system (e.g. the components of the feed to a reactor) and reaction rules that describe the possible chemical transformations that can occur, RING first constructs an exhaustive network of reactions and species consistent with the inputs. Inputs into RING are in the form an English-like domain specific language with syntax involving common chemistry parlance. The language compiler further catches erroneous chemistry rules, such as incorrect charge balance in a reaction rule, and heuristically optimizes user-specified instructions to improve the speed of execution. RING, further, accepts "post-processing" instructions that allow for: (i) lumping, or grouping together isomers to reduce the size of the reaction network, (ii) "querying" the network to extract information such as reaction pathways and mechanisms that describe how an initial reactant is transformed into a specific product, (iii) calculating thermochemical properties of species and reactions to evaluate thermochemical feasibility of reaction steps, and (iv) formulating and solving rigorous microkinetic models of complex reaction networks. RING, thus, provides a rule-based" framework to assemble and explore a complex reaction network. RING implements several algorithms, methods, and techniques from computer science, cheminformatics, and graph theory. The language has been developed using SILVER, a meta-language for specifying attribute grammars, and COPPER, a parser generator. The language is extensible in that independent additions can be incorporated to the original language to perform additional analysis without syntactical and semantic conflicts with the existing grammar. Algorithms from chemical graph theory and cheminformatics are adopted to (i) represent molecules as strings externally and as graphs internally, (ii) store reaction rules as graph transformation rules, (iii) identify fragments in molecules that can serve as reaction centers through pattern matching, (iv) determine molecular characteristics such as shape (linear, branched, cyclic, etc.) and aromaticity, and (v) identify isomeric lumps through a new molecular hashing technique. Graph traversal algorithms are further employed by the post-processing modules to identify pathways and mechanisms. This thesis presents several case studies of application of RING in elucidating complex networks of reactions. First, when chemistry alone is known about the system, RING can be used to identify plausible mechanisms for product formation consistent with experimental observations; it can further be used to postulate possible experiments to discriminate between the alternative mechanisms. This has been demonstrated with a case study of glycerol and acetone conversion on solid Bronsted acid catalysts. Second, if molecular properties can be evaluated quickly using semi-empirical methods for a large number of species and compounds, RING can be used to identify species in the network that have desired physical properties and thermochemically favorable synthesis routes to form them. A case study on identifying fatty alcohols, in a spectrum of more than 60,000 compounds, that can potentially be used to make nonionic surfactants with desirable properties and their synthesis routes from biomass-derived oxygenates presents an application of this method. It was found that lauryl alcohol, a fatty alcohol currently used to make surfactants, can be synthesized from biomass-oxygenates using a combination of metal, basic, and acid catalysts. It was also found that some of the intermediate synthesis steps could potentially be coupled to drive the overall reaction forward, or could benefit from using biphasic systems for immediate separation of products from reactants. Third, if activation barriers of each step in the reaction can be reliably predicted using semi-empirical methods, RING can be used to identify dominant reaction mechanisms for converting reactants to experimentally observed products. This was demonstrated by analyzing the energetically favorable mechanisms for glycerol conversion to syn gas or 1,2-propane diol on transition metal catalysts such as Platinum, Palladium, Rhodium, and Ruthenium. It was found that glycerol would decompose to syn gas on Platinum and Palladium, while a significant selectivity to the diol can be obtained on Rhodium and Ruthenium, thus offering insights for designing catalysts for complex biomass conversion systems. Finally, if kinetic parameters and thermochemistry can be estimated apriori, RING can be used to formulate and solve rigorous microkinetic models to get quantitative information such as yield and selectivity. This feature is demonstrated through a model developed for methanol conversion to hydrocarbons (MTH) on Bronsted acid catalyst HZSM-5. RING is generic in terms of chemistries it can handle and flexible in terms of the type of analysis that can be performed. This thesis posits that it can be used in conjunction with experimental and computational chemistry data to elucidate systems with complex reaction networks, especially in hydrocarbon processing and biomass conversion

Numerical studies of the multi-cavity free-electron laser

Consideration is made of a free-electron laser with many optical cavities where the cavities communicate with each other, not optically, but through the electron beam. Numerical simulation results in the one-dimensional approximation, but including nonlinearities, are presented. The multi-cavity free-electron laser (MC/FEL) can be employed to avoid the slippage phenomena, and thus to make pico-second pulses of infrared radiation. Three examples of this application are presented

DFT Insights into the Competitive Adsorption of Sulfur- and Nitrogen-Containing Compounds and Hydrocarbons on Co-Promoted Molybdenum Sulfide Catalysts

The adsorption of 20 nitrogen-/sulfur-containing and hydrocarbon compounds on the sulfur edge of cobalt-promoted molybdenum sulfide (CoMoS) catalyst was studied using density functional theory, accounting for van der Waals interactions, to elicit comparative structure–property trends across different classes of molecules relevant to hydrotreating. Unhindered organosulfur compounds preferentially adsorb on a “CUS-like” site formed by the dimerization of two neighboring sulfur atoms on the edge to create a vacancy. Nitrogen-containing compounds and 4,6-dimethyldibenzothiophene, however, prefer the brim sites. Binding energy trends indicate that nitrogen-containing compounds will inhibit hydrodesulfurization on the brim sites and, relatively weakly, on the CUS-like sites. Edge vacancies are, therefore, likely to be essential for hydrodesulfurization of unhindered organosulfur compounds. Further, van der Waals forces contribute significantly to the binding energy of compounds (up to 1.0 eV for large compounds such as alkyl-substituted acridines) on CoMoS