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Summary InterMine is a data integration warehouse and analysis software system developed for large and complex biological data sets. Designed for integrative analysis, it can be accessed through a user-friendly web interface. For bioinformaticians, extensive web services as well as programming interfaces for most common scripting languages support access to all features. The web interface includes a useful identifier look-up system, and both simple and sophisticated search options. Interactive results tables enable exploration, and data can be filtered, summarized, and browsed. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other entities. InterMine databases have been developed for the major model organisms, budding yeast, nematode worm, fruit fly, zebrafish, mouse, and rat together with a newly developed human database. Here, we describe how this has facilitated interoperation and development of cross-organism analysis tools and reports. InterMine as a data exploration and analysis tool is also described. All the InterMine-based systems described in this article are resources freely available to the scientific community. genesis 53:547–560, 2015. © 2015 Wiley Periodicals, Inc.

Summary: InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of ‘widgets’ performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. Availability: Freely available from http://www.intermine.org under the LGPL license. Contact: ku.ca.mac.neg@melkcim.g Supplementary information: Supplementary data are available at Bioinformatics online.

Experiments have been conducted to observe fragmentation events in a model alloy (succinonitrile and acetone) solidifying in the presence of forced convection in the superheated melt. Measurements of fragmentation rates have been made, and an attempt was made to relate the results to the controllable parameters of the system. A microscope-video system recorded the mushy zone-melt interface, and the fragmentation process and fragmentation rates could be determined from a frame-by-frame analysis of the video images. Experiments were conducted for varying cooling rates, overall temperature differences, melt flow rates, and for two different concentrations of acetone (1.3 and 6.1 wt pct). Significant dendritic fragmentation occurred for all runs. In addition, the influence of buoyancy forces is clearly evident from particle motion near the mushy zone-melt interface. Fragmentation rates appear to correlate well with the magnitude of particle velocities near the interface, with increasing fragmentation being associated with higher particle velocity magnitude (either in the same or the opposite direction to the mean flow) for the 1.3 wt pct acetone mixture. However, the correlation is quite different for the higher concentration. The relationship between these results and the possible mechanisms for fragmentation are discussed. Although it appears that either constitutional remelting or capillary pinching are likely of importance, hydrodynamic shear forces or some other mechanism as yet undiscovered cannot be completely discounted, although circumstantial evidence suggests that mechanical shearing is inconsistent with observations made both here and already in published literature. The results provide a step in the development of solidification models that incorporate fragmentation processes in the mushy zone as an important mechanism of grain refinement and a potential source of macrosegregation in ingots and large castings.

CORRIGENDUM: InterMOD: integrated data and tools for the unification of model organism research

Model organisms are widely used for understanding basic biology and have significantly contributed to the study of human disease. In recent years, genomic analysis has provided extensive evidence of widespread conservation of gene sequence and function amongst eukaryotes, allowing insights from model organisms to help decipher gene function in a wider range of species. The InterMOD consortium is developing an infrastructure based around the InterMine data warehouse system to integrate genomic and functional data from a number of key model organisms, leading the way to improved cross-species research. So far including budding yeast, nematode worm, fruit fly, zebrafish, rat and mouse, the project has set up data warehouses, synchronized data models and created analysis tools and links between data from different species. The project unites a number of major model organism databases, improving both the consistency and accessibility of comparative research, to the benefit of the wider scientific community.

Precision adiabatic recalescence experiments on both pure and binary undercooled melts have been conducted. The adiabatic constraint limits the amount of net phase transformation from the metastable under-cooled state (creating a mushy zone) and also sets bounds on the microstructural parameters of the mushy zone, namely the volume fraction of the phases, their length scales, and the interfacial compositions. As many as three distinct kinetic time scales are observed in these experiments: a short time scale (less than ∼1 s) of rapidly increasing temperature from the initial nucleation temperature, associated with the propagation of the dendrites and release of latent heat; an intermediate time scale (∼103–104 s) of slowly rising temperature, associated with coarsening of the mushy zone; and a long time scale (days) of steadily falling temperature, associated with solid-state diffusional adjustments near the solid-liquid interface.

In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium has generated an enormous library of genomic data along with detailed, structured information on all aspects of the experiments. The modMine database (http://intermine.modencode.org) described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data sets of interest among the thousands generated by modENCODE; (ii) access the data in an integrated form together with non-modENCODE data sets; and (iii) facilitate fine-grained analysis of the above data. The sophisticated search features are possible because of the collection of extensive experimental metadata by the consortium. Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine.

The model organism Encyclopedia of DNA Elements (modENCODE) project is a National Human Genome Research Institute (NHGRI) initiative designed to characterize the genomes of Drosophila melanogaster and Caenorhabditis elegans. A Data Coordination Center (DCC) was created to collect, store and catalog modENCODE data. An effective DCC must gather, organize and provide all primary, interpreted and analyzed data, and ensure the community is supplied with the knowledge of the experimental conditions, protocols and verification checks used to generate each primary data set. We present here the design principles of the modENCODE DCC, and describe the ramifications of collecting thorough and deep metadata for describing experiments, including the use of a wiki for capturing protocol and reagent information, and the BIR-TAB specification for linking biological samples to experimental results. modENCODE data can be found at http://www.modencode.org. Database URL: http://www.modencode.org.

A series of experiments were performed to investigate the effects of a thick wall on the freezing process occurring inside a cylindrical container. Two cylinders with different thermal diffusivity (k/ϱc) values were compared. To isolate the effects of the wall sensible energy, experiments were run for both a subcooled wall and the wall initially at the phase change material (PCM) fusion temperature. The PCM was initially at its fusion temperature for all cases. The base of the cylinder was maintained at a constant temperature in all but one case, where the lower boundary was approximately adiabatic. At several time steps, the mass fraction solidified and the phase front profile were determined. Measurements of the base heat flux and mean cylinder temperature were also obtained as functions of time. The fraction frozen vs time curves and the shape of the phase front profiles are compared for each set of conditions. The energy content of the wall can significantly affect both results. The data are presented in such a way as to encourage comparison with numerical computations of a similar complex-boundary freezing problem.

A key element of mushy zone modeling is the description of the microscopic evolution of the lengthscales within the mushy zone and the influence of macroscopic transport processes. This article describes some recent progress in developing a mean-field statistical theory of phase coarsening in adiabatic mushy zones. The main theoretical results are (1) temporal scaling laws that indicate that the average lengthscale increases as time1/3, (2) a self-similar distribution of mushy zone lengthscales based on spherical solid particle shapes, and (3) kinetic rate constants which provide the dependences of the coarsening process on material parameters and the volume fraction of the solid phase. High precision thermal decay experiments are described which verify aspects of the theory in pure material mushy zones held under adiabatic conditions. The microscopic coarsening theory is then integrated within a simple macroscopic heat-transfer model of one-dimensional alloy solidification. The method demonstrates an ability to predict the influence of macroscopic heat transfer on the evolution of primary and secondary dendrite arm spacings in Al-Cu alloys.

Three-dimensional measurement of dental morphology is providing new variables and shape information not available previously, and the reliability of these data has proved to be substantial. Accurate superimposition of 2D and 3D data-sets has several applications in dental research when making comparisons of similar structures. For example, two data-sets of the same object can be superimposed to highlight differences apparent in limited region(s) of the tooth crown. When significant regions represented by the two data-sets are identical, registration of the images can be achieved by standard superimposition methods. However, for comparisons of crown morphologies between monozygotic and dizygotic co-twins, the data sets are similar but not identical so a new approach to superimposition has been developed.To develop a non 'best fit' (Synetic) method for the 3D superimposition of non-similar objects that forms one comparable interface providing enhanced methodology for the analysis of differences within the dentition of twins.A minimised least-squares registration approach is followed by diffusion based registration to provide global minimisation between points that is not based on a best fit algorithm. This process is linear and therefore the method ensures uniqueness of the superimposition.Initial results indicate a reliable method producing only one output as opposed to best fit approaches that may generate a different output each time.Diffusion-based registration offers a more reliable approach to superimposing non-identical objects, such as the tooth crowns of monozygotic co-twins, than conventional best-fit methods.

The potential inhibitory effect of chlorhexidine digluconate on the intergeneric coaggregation of 11 pairs of Gram-positive organisms was compared to its ability to inhibit coaggregations of 14 pairs comprised of both a Gram-positive and a Gram-negative cell type. Dramatic differences in the inhibitory effectiveness of the antimicrobial compound on the two kinds of coaggregation pairs were found. Gram-positive pairs were not inhibited at a concentration of 0.25%, whereas the coaggregations involving a Gram-negative partner were usually completely blocked at concentrations as low as 0.01%. Similar effects to chlorhexidine digluconate were found with octenidine dihydrochloride and cetylpyridinium chloride, while sodium dodecylsulfate was inhibitory only at 10- to 50-fold higher concentrations. These results suggest that chlorhexidine digluconate, octenidine dihydrochloride, and cetylpyridinium chloride may be effective inhibitors of later microbial colonizers of dental plaque but may not disturb a normal healthy indigenous flora.

There are significant transport issues that arise in the development, assembly, qualification, and manufacturing of organic packages. These issues include diverse areas like chemical processing of printed wiring boards (PWBs) during etching, plating and rinsing, lamination of cores, drilling of plated through holes, profiling (the separation of individual chip carriers or PWBs from a large panel) and adhesive curing, all of which occur during the manufacturing of the PWBs and chip carriers. During assembly and rework, transport issues arise in solder reflow during module attach and re-work, adhesive cure during heat-sink attach, and under-fill and curing processes in flip chip packages. Similar, but more complex, processes are encountered in wafer level packaging. During reliability stress testing, concerns arise about establishment of appropriate stress and acceleration factors that relate the accelerated tests to actual field conditions. During shipping and handling, similar concerns arise in simulating potential temperature excursions that may occur. In addition to these thermal and transport issues, manufacturing processes may induce interfacial de-lamination due to surface conditions resulting from process history, residual stresses in the package that impact the thermal performance of the package and manufacturing tolerances that inherently affect the thermal performance. Additionally, ever reducing time-to-market demands novel methods of package manufacture and reliability qualification. Experimentally validated modeling and simulation must play an important role towards this goal. The methodologies and tools must continuously be upgraded to achieve true concurrent engineering. In spite of the wide spread use of numerical simulation, there is much that remains to be done to make simulation truly useful to the practicing engineer in the electronics cooling and packaging area. Among the important shortcomings are: (i) restriction to disciplinary boundaries — electronics cooling and packaging is inherently interdisciplinary, but nearly all simulation tools are discipline-specific; (ii) an emphasis on analysis rather than on synthesis — there are few tools to translate insights from detailed component-level simulations into a broader systemic view; and (iii) long lead times and, consequently, an inability to impact the short time-scale design processes inherent to the electronics manufacturing/ packaging area. The purpose of this panel session is to initiate discussion and idea exchange related to some of these topics. The tone of the panel is set by presentations by panelists addressing the technology aspects of packaging, processes and materials covering three broad issues: substrates, assembly and system-level packaging. The emerging technology challenges in each of these areas will be addressed with attendant examples mainly from computer, automotive electronics. Technology roadmaps will be discussed with special reference to the needs of the automotive electronics of the future. These needs will be translated into the required technology solutions in the substrate, assembly, and packaging arenas. The presentations will also identify future areas of research in modeling and simulation that address the technology broadly related to the technology needs identified above. Such modeling and simulation topics are multi-disciplinary in nature enveloping design, materials selection, and manufacturability. While these topics are of great interest to industry from a concurrent engineering point of view, they also present a great challenge to the academic community to integrate multi-disciplinary nature of this problem and develop truly predictive methods and tools for pervasive use in the industry. The panelists are a combination of industrial and academic researchers as can be seen from their attached biographies below and they will share their vision for long term resolution of this vision.

We present a new approach to teaching the core thermal/fluids curriculum for undergraduate programs in engineering. Traditional thermodynamics, fluid mechanics, and heat transfer classes are being replaced with two integrated courses and a laboratory in which the three disciplines are taught simultaneously to show interconnections and transferability of concepts and ideas, with an emphasis on the way they occur in engineering practice. This approach seeks to improve both the context and manner in which the subject matter is covered. Our goals are to enhance the physical intuition of our students, to stimulate their ability to think critically and synthesize information, and to make clearer the relevance of the fundamentals to advanced analytical and computational tools.

Two computer LAN's, linked by the ACTS satellite, were configured. SCPS-TP and SCPS-NP protocol software was installed on the LAN's. The protocols were tested using various BER's and data rates. This report documents the test results.

Contamination of blood by bowel contents has been generally assumed as an absolute contraindication to autotransfusion. Since abdominal trauma is frequently accompanied by bowel injury and massive blood loss, a potential major use for autotransfusion has thus been precluded. To test this presumption, autologous blood grossly contaminated with feces was incubated in the peritoneal cavity and then autotransfused in dogs. The animals were hemorrhaged 20, 30, or 40% of their estimated blood volume, producing mild to severe hypovolemic shock. Reinfusion of contaminated blood had little effect on survival with 20 or 30% hemorrhage, but contamination markedly decreased survival with 40% hemorrhage:90% survived without contamination while only 30% survived with contamination. The use of antibiotics in a similar group of dogs subjected to 40% hemorrhage essentially eliminated the risk of autotransfusion: 90% of these dogs survived autotransfusion of contaminated blood.

A chart review of 130 patients with colonic injuries treated between the years 1968 and 1976 were reviewed. Types of operative procedure, complication rate, mortality and hospital stay were tabulated. The patients treated by primary closure and exteriorized primary repair had a 2% mortality, while various staged procedures used in the remaining patients resulted in a 6% mortality. Complications were common in all types of repair and correlated with the severity of the injury. Primary closure of the injured colon can safely be accomplished in carefully selected patients. Staged procedures necessitate a secondary operation which we found to be relatively benign, and we continue to use staged operations in the majority of our patients with colonic injuries. This management protocol has resulted in a 4 to 6% over-all mortality.

Description d'un systeme specialement concu pour le prelevement et l'analyse automatique par chromatographie en phase gazeuse. Les performances de prelevement et de recuperation sont de 100±5%

Uremic pericarditis that is unresponsive to intensive hemodialysis may culminate in pericardial tamponade. This complication occurred in 15 of 179 patients in long-term hemodialysis. Echocardiography was employed in 14 of 15 patients and proved to be the single most helpful diagnostic procedure. All were managed surgically, some with generous pericardiectomy, others with "pericardial window." All patients tolerated these surgical procedures well, and there were no deaths related to the surgery. Follow-up done up to four years later demonstrated that a "pericardial window" has the same efficacy as a more extensive procedure. There have been no long-term complications.