Mercury Optoelectronics Research Institute

Python package for imputing missing CpG methylation data at the read level

Drug discovery is usually focused on a single protein target; in this process, existing compounds that bind to related proteins are often ignored. We describe ProBiS plugin, extension of our earlier ProBiS-ligands approach, which for a given protein structure allows prediction of its binding sites and, for each binding site, the ligands from similar binding sites in the Protein Data Bank. We developed a new database of precalculated binding site comparisons of about 290000 proteins to allow fast prediction of binding sites in existing proteins. The plugin enables advanced viewing of predicted binding sites, ligands' poses, and their interactions in three-dimensional graphics. Using the InhA query protein, an enoyl reductase enzyme in the Mycobacterium tuberculosis fatty acid biosynthesis pathway, we predicted its possible ligands and assessed their inhibitory activity experimentally. This resulted in three previously unrecognized inhibitors with novel scaffolds, demonstrating the plugin's utility in the early drug discovery process.

<div class="section abstract"><div class="htmlview paragraph">In the investigation of a collision involving recreational watercraft, analytical methods are generally limited when compared to incidents involving land-based vehicles. As is indicated in previous publications, investigators often rely on time/distance relationships, human factors, the matching of damage to determine vessel positioning at impact, and the recollections of witnesses. When applicable, speed estimates are generally based on the boat engine's revolutions. By considering the engine speed, the drive gear ratio, the propeller pitch, and the likely slip of the propeller, an estimation of the boat's travel speed can be made.</div><div class="htmlview paragraph">In more recent publications, it has been recognized that Event Data Recorder (EDR) technology incorporated into various Electronic Control Units (ECUs) used in automotive applications can be beneficial to collision investigation and reconstruction. These devices record data surrounding diagnostic occurrences, airbag deployments, and, with respect to some heavy vehicles, “last stop” and/or “sudden deceleration” events. Formal testing of these devices has shown their accuracy and use in collision analysis.</div><div class="htmlview paragraph">This research examines event data as recorded by specific Mercury Marine ECUs in combination with external data acquisition devices. Specifically, the study focused on validating engine speed data. In addition, recording parameters were researched, as were the effects of a powerloss condition on data files. The results of this research suggest that marine ECUs can be beneficial to accident investigation by recording specific engine parameters and operator inputs immediately prior to a collision incident.</div></div>

<div class="section abstract"><div class="htmlview paragraph">When designing a connecting rod, one needs to pay attention to the buckling strength of the rod. The buckling strength is heavily affected by the beam section, and Johnson's buckling equation is used to estimate the buckling strength of a given beam section. This approach is acceptable if the beam section geometry is constant from the small end to the big end. But, recent expectations for light weight, low NVH, and low fuel consumption engines require optimizing the connecting rod section geometries to be progressively changing from the small end to the big end.</div><div class="htmlview paragraph">Finite Element Analysis (FEA) is often used to evaluate the buckling strength of a rod that has complex changes in beam section. There are two primary FEA methods to do this. One is an eigenvalue method and the other is an explicit dynamic method.</div><div class="htmlview paragraph">The eigenvalue method can obtain stable results without satisfying Courant-Friedrichs-Lewy condition that is required to control the size of the time step in the explicit dynamic method. The eigenvalue method is meant for analyzing the static (or quasi-static) problem, and is comparable to a static load test that can be done in a structural test lab. To get proper analysis results, this method requires geometry, modal analysis, interpretation of results to include a certain number of mode shapes in the buckling analysis, as well as an imperfection value.</div><div class="htmlview paragraph">In the case of the explicit dynamic method, the time step size must satisfy Courant-Friedrichs-Lewy condition in order to obtain stable calculation results. This method can analyze quasi-static and dynamic problems, and is useful for calculating the in-situ buckling strength of a rod. An advantage of the explicit dynamic method is that simultaneous equations do not have to be solved, so memory size requirements are reduced and less computation time is used than in the eigenvalue method. Furthermore, the explicit dynamic method requires only the geometry and an input force (or velocity) to get proper analysis results.</div><div class="htmlview paragraph">This paper shows analysis results from the eigenvalue method and the explicit dynamic method, as well as physical test results. Then, the paper discusses the pros and cons of the two methods for rod buckling analysis.</div></div>

The speciation of mercury (Hg) in Minamata Bay (Japan) was studied over a 2-year period (2006–2008). Concentrations of dissolved total Hg, dissolved methylmercury (MeHg), particulate total Hg, and suspended solids were 0.43 ± 0.14 ng/l (mean ± standard deviation), 0.10 ± 0.06 ng/l, 3.04 ± 2.96 ng/l, and 5.94 ± 2.10 mg/l, respectively. Correlations between concentrations of particulate total Hg and suspended solids at four depths (surface: 0 m; mid-depth: −6 m, −10 m; and bottom +1 m layer) were only significant in the bottom +1 m layer. The mean dissolved MeHg concentration and the ratio of dissolved MeHg to dissolved total Hg were considerably higher in summer compared to other seasons. The data suggest that bottom sediment was not the sole source of MeHg, and that MeHg may be produced in the water column by the conversion of divalent Hg eluted from resuspended bottom sediment. The correlation between seawater characteristics such as salinity, temperature, dissolved oxygen (DO), and dissolved MeHg concentration indicates that Hg methylation could be influenced by the heterotrophic activity of microorganisms in the seawater. In particular, inverse correlations were observed between DO, salinity, and MeHg concentration. However, dissolved MeHg concentrations did not correlate with seawater characteristics such as pH or chlorophyll-a.

<div class="htmlview paragraph">High-pressure die casting is a highly productive process that yields near net-shape castings at a relatively low cost. One disadvantage of die casting, however, is residual porosity that is inherently present in the castings. Semi-solid die casting is a method that is superior to die casting as it relates to porosity but has historically been a more expensive process. This is due to the higher cost of the billet feed material and the inability to easily recycle billets and runners. Slurry-on-Demand is a new semi-solid casting process that develops the semi-solid slurry directly from the liquid, thereby eliminating the cost penalties intrinsic to the billet semi-solid process. This paper will describe the Slurry-on-Demand process in detail and present case studies comparing the casting of large components using both Slurry-on Demand and conventional high-pressure die casting. It will also provide examples of quality improvements achievable by the Slurry-on-Demand process.</div>

<div class="htmlview paragraph">The Oil Certification Committee of the National Marine Manufacturers Association has developed FC-W<sup>®</sup>, a new standard for crankcase lube oil used in four-stroke cycle inboard, outboard, and sterndrive marine engines. A sub-committee representing the marine engine industry, the oil industry, oil testing laboratories, and the NMMA engineering standards group was formed to study the lubrication and corrosion prevention needs of four-stroke cycle engines. The sub-committee developed a rust test and an engine test as well as adopting 3 industry standard bench tests. These tests, together with formulation restrictions are used to identify oils that meet the requirements for use in four-stroke cycle marine engines. This paper gives an overview of the development of the new tests, formulation restrictions, and product approval system.</div>

PreviousNext No AccessSEG Technical Program Expanded Abstracts 19973‐D seismic survey design and linear v(z)Authors: Christopher L. LinerRalph GobeliChristopher L. LinerUniversity of Tulsa and Ralph GobeliMercury International Technologyhttps://doi.org/10.1190/1.1885927 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1885927FiguresReferencesRelatedDetailsCited ByReferences26 September 2016 SEG Technical Program Expanded Abstracts 1997ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1997 Pages: 2067 publication data© 1997 Copyright © 1997 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 10 Feb 2005 CITATION INFORMATION Christopher L. Liner and Ralph Gobeli, (1997), "3‐D seismic survey design and linear v(z)," SEG Technical Program Expanded Abstracts : 43-46. https://doi.org/10.1190/1.1885927 Plain-Language Summary PDF DownloadLoading ...

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1996Bin size and linear v(z)Authors: Christopher L. LinerRalph GobeliChristopher L. LinerUniversity of Tulsa and Ralph GobeliMercury International Technologyhttps://doi.org/10.1190/1.1826680 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1826680FiguresReferencesRelatedDetailsCited ByReferences26 September 20163-D seismic survey design for linear v ( z ) mediaGEOPHYSICS, Vol. 64, No. 23‐D seismic survey design and linear v(z)Christopher L. Liner and Ralph Gobeli10 February 2005 SEG Technical Program Expanded Abstracts 1996ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1996 Pages: 2106 publication data© 1996 Copyright © 1996 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 10 Feb 2005 CITATION INFORMATION Christopher L. Liner and Ralph Gobeli, (1996), "Bin size and linear v(z)," SEG Technical Program Expanded Abstracts : 47-50. https://doi.org/10.1190/1.1826680 Plain-Language Summary PDF DownloadLoading ...