Three-Body Capture of Irregular Satellites: Application to Jupiter

We investigate a new theory of the origin of the irregular satellites of the giant planets: capture of one member of a ~100-km binary asteroid after tidal disruption. The energy loss from disruption is sufficient for capture, but it cannot deliver the bodies directly to the observed orbits of the irregular satellites. Instead, the long-lived capture orbits subsequently evolve inward due to interactions with a tenuous circumplanetary gas disk. We focus on the capture by Jupiter, which, due to its large mass, provides the most stringent test of our model. We investigate the possible fates of disrupted bodies, the differences between prograde and retrograde captures, and the effects of Callisto on captured objects. We make an impulse approximation and discuss how it allows us to generalize capture results from equal-mass binaries to binaries with arbitrary mass ratios. We find that at Jupiter, binaries offer an increase of a factor of ~10 in the capture rate of 100-km objects as compared to single bodies, for objects separated by tens of radii that approach the planet on relatively low-energy trajectories. These bodies are at risk of collision with Callisto, but may be preserved by gas drag if their pericenters are raised quickly enough. We conclude that our mechanism is as capable of producing large irregular satellites as previous suggestions, and it avoids several problems faced by alternative models.Comment: 39 pages, 12 figures, 1 table, submitted to Icaru

Progressives at War

Craig's study of McAdoo and Baker illuminates the aspirations and struggles of two prominent southern Democrats.In this dual biography, Douglas B. Craig examines the careers of two prominent American public figures, Newton Diehl Baker and William Gibbs McAdoo, whose lives spanned the era between the Civil War and World War II.Both Baker and McAdoo migrated from the South to northern industrial cities and took up professions that had nothing to do with staple-crop agriculture. Both eventually became cabinet officers in the presidential administration of another southerner with personal memories of defeat and Reconstruction: Woodrow Wilson. A Georgian who practiced law and led railroad tunnel construction efforts in New York City, McAdoo served as treasury secretary at a time when Congress passed an income tax, established the Federal Reserve System, and funded the American and Allied war efforts in World War I. Born in the eastern panhandle of West Virginia, Baker won election as mayor of Cleveland in the early twentieth century and then, as Wilson's secretary of war, supervised the dramatic build-up of the U.S. military when the country entered the Great War in Europe.This is the first full biography of McAdoo and the first since 1961 of Baker. Craig points out similarities and differences in their backgrounds, political activities, professional careers, and family lives.Craig's approach in Progressives at War illuminates the shared struggles, lofty ambitions, and sometimes conflicted interactions of these figures. Their experiences and perspectives on public and private affairs (as insiders who nonetheless were, in some sense, outsiders) make their lives, work, and thought especially interesting. Baker and McAdoo, in league with Wilson, offer Craig the opportunity to deliver a fresh and insightful study of the period, its major issues, and some of its leading figures

Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins

Abstract Background Disulfide engineering is an important biotechnological tool that has advanced a wide range of research. The introduction of novel disulfide bonds into proteins has been used extensively to improve protein stability, modify functional characteristics, and to assist in the study of protein dynamics. Successful use of this technology is greatly enhanced by software that can predict pairs of residues that will likely form a disulfide bond if mutated to cysteines. Results We had previously developed and distributed software for this purpose: Disulfide by Design (DbD). The original DbD program has been widely used; however, it has a number of limitations including a Windows platform dependency. Here, we introduce Disulfide by Design 2.0 (DbD2), a web-based, platform-independent application that significantly extends functionality, visualization, and analysis capabilities beyond the original program. Among the enhancements to the software is the ability to analyze the B-factor of protein regions involved in predicted disulfide bonds. Importantly, this feature facilitates the identification of potential disulfides that are not only likely to form but are also expected to provide improved thermal stability to the protein. Conclusions DbD2 provides platform-independent access and significantly extends the original functionality of DbD. A web server hosting DbD2 is provided at http://cptweb.cpt.wayne.edu/DbD2/

Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny

Abstract Background The rabbit is an important model organism used in a wide range of biomedical research. However, the rabbit genome is still sparsely annotated, thus prohibiting extensive functional analysis of gene sets derived from whole-genome experiments. We developed a web-based application that provides augmented annotation and orthologue analysis for rabbit genes. Importantly, the application allows comprehensive functional analysis through the use of orthologous relationships. Results Using data extracted from several public bioinformatics repositories we created Better Bunny, a database and query tool that extensively augments the available functional annotation for rabbit genes. Using the complete set of target genes from a commercial rabbit gene expression microarray as our benchmark, we are able to obtain functional information for 88 % of the genes on the microarray. Previously, functional information was available for fewer than 10 % of the rabbit genes. Conclusions We have developed a freely available, web-accessible bioinformatics tool that enables investigators to quickly and easily perform extensive functional analysis of rabbit genes (http://cptweb.cpt.wayne.edu). The software application fills a critical void for a wide range of biomedical research that relies on the rabbit model and requires characterization of biological function for large sets of genes

A New Algorithm for Detecting Central Apnea in Neonates

Apnea of prematurity is an important and common clinical problem, and is often the rate-limiting process in NICU discharge. Accurate detection of episodes of clinically important neonatal apnea using existing chest impedance (CI) monitoring is a clinical imperative. The technique relies on changes in impedance as the lungs fill with air, a high impedance substance. A potential confounder, however, is blood coursing through the heart. Thus, the cardiac signal during apnea might be mistaken for breathing. We report here a new filter to remove the cardiac signal from the CI that employs a novel resampling technique optimally suited to remove the heart rate signal, allowing improved apnea detection. We also develop an apnea detection method that employs the CI after cardiac filtering. The method has been applied to a large database of physiological signals, and we prove that, compared to the presently used monitors, the new method gives substantial improvement in apnea detection

Intelligent fracture creation for shale gas development

Shale gas represents a major fraction of the proven reserves of natural gas in the United States and a collection of other countries. Higher gas prices and the need for cleaner fuels provides motivation for commercializing shale gas deposits even though the cost is substantially higher than traditional gas deposits. Recent advances in horizontal drilling and multistage hydraulic fracturing, which dramatically lower costs of developing shale gas fields, are key to renewed interest in shale gas deposits. Hydraulically induced fractures are quite complex in shale gas reservoirs. Massive, multistage, multiple cluster treatments lead to fractures that interact with existing fractures (whether natural or induced earlier). A dynamic approach to the fracturing process so that the resulting network of reservoirs is known during the drilling and fracturing process is economically enticing. The process needs to be automatic and done in faster than real-time in order to be useful to the drilling crews

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

BACKGROUND: Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species. METHODOLOGY/PRINCIPAL FINDINGS: We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences. CONCLUSIONS/SIGNIFICANCE: Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them