\u3cem\u3eRhizobium leguminosarum\u3c/em\u3e CFN42 Genetic Regions Encoding Lipopolysaccharide Structures Essential for Complete Nodule Development on Bean Plants

Eight symbiotic mutants defective in lipopolysaccharide (LPS) synthesis were isolated from Rhizobium leguminosarum biovar phaseoli CFN42. These eight strains elicited small white nodules lacking infected cells when inoculated onto bean plants. The mutants had undetectable or greatly diminished amounts of the complete LPS (LPS I), whereas amounts of an LPS lacking the O antigen (LPS II) greatly increased. Apparent LPS bands that migrated between LPS I and LPS II on sodium dodecyl sulfate-polyacrylamide gels were detected in extracts of some of the mutants. The mutant strains were complemented to wild-type LPS I content and antigenicity by DNA from a cosmid library of the wild-type genome. Most of the mutations were clustered in two genetic regions; one mutation was located in a third region. Strains complemented by DNA from two of these regions produced healthy nitrogen-fixing nodules. Strains complemented to wild-type LPS content by the other genetic region induced nodules that exhibited little or no nitrogenase activity, although nodule development was obviously enhanced by the presence of this DNA. The results support the idea that complete LPS structures, in normal amounts, are necessary for infection thread development in bean plants

Homer Simpson Marches on Washington: Dissent through American Popular Culture

The Simpsons consistently questions what is culturally acceptable, going against the grain of popular culture by showcasing controversial issues like homosexuality, animal rights, the war on terror, and religion. This subtle form of political analysis is entertaining and great for television ratings, but it also can be an effective means of changing opinions and attitudes on a large scale. To consider another example, what does Star Trek teach viewers about feminist politics? Do comedy programs like The Daily Show and Saturday Night Live advance democracy in ways the mainstream news media cannot? Can horror films contribute to a contemporary understanding of environmentalism? Homer Simpson Marches on Washington: Dissent through American Popular Culture explores how popular culture influences political agendas, frames audience perceptions, and changes values and ideals on both the individual and collective level. Editors Timothy M. Dale and Joseph J. Foy have assembled a top-notch team of scholars from the fields of political science, history, women’s and minority studies, film and media studies, communication, music, and philosophy to investigate the full spectrum of popular culture in a democratic society. Homer Simpson Marches on Washington examines television shows such as Star Trek: The Next Generation, The X-Files, All in the Family, The View, and The Colbert Report, as well as movies and popular music, demonstrating how covert political and social messages affect the cultural conversation in America. The contributing authors investigate a wide range of controversial topics, including gender, race, religion, class, the environment, and sexual orientation. Kate Mulgrew, who played Captain Janeway in Star Trek: Voyager, offers her own story in the book’s foreword, describing the societal pressures of being the first female captain in the Star Trek franchise. In today’s fragmented society, audiences are met daily with thousands of messages competing for their attention. Homer Simpson Marches on Washington offers an entertaining and insightful look at how popular culture can break through the clutter and bring about profound changes. Timothy M. Dale, assistant professor of political science at the University of Wisconsin–Green Bay, is coauthor of Political Thinking, Political Theory, and Civil Society. Joseph J. Foy, assistant professor of political science at the University of Wisconsin–Waukesha, is the editor of Homer Simpson Goes to Washington: American Politics through Popular Culture. Popular culture is a growing area of interest, especially given its status as a major U.S. export in this rapidly globalizing world. Homer Simpson Marches on Washington is a useful and interesting work. --Margaret Ferguson, Indiana University–Purdue University Indianapolis Homer Simpson Marches on Washington is essential reading for anyone who believes that mass media can be effective in exposing the oppressive powers the be and inspiring people to resist them. --catapult magazine Both Homer Simpson Goes to Washington and Homer Simpson Marches on Washington look at popular culture as not simply entertainment of the masses. Instead, pop culture can emphasize contemporary societal norms, or introduce new ideas and social constructs....Pop culture reaches a national audience, and as such, is inspiring nationwide conversations about politics, race, marriage, religion, etc. If you want to learn more about the basis for these conversations, these two books are excellent resources. --Annette Aguayo, Voices From the Earthhttps://uknowledge.uky.edu/upk_american_popular_culture/1009/thumbnail.jp

Homer Simpson Ponders Politics: Popular Culture as Political Theory

It is often said that the poet Homer “educated” ancient Greece. Joseph J. Foy and Timothy M. Dale have assembled a team of notable scholars who argue, quite persuasively, that Homer Simpson and his ilk are educating America and offering insights into the social order and the human condition. Following Homer Simpson Goes to Washington (winner of the John G. Cawelti Award for Best Textbook or Primer on American and Popular Culture) and Homer Simpson Marches on Washington, this exceptional volume reveals how books like J. R. R. Tolkien’s The Hobbit and J. K. Rowling’s Harry Potter, movies like Avatar and Star Wars, and television shows like The Office and Firefly define Americans’ perceptions of society. The authors expand the discussion to explore the ways in which political theories play out in popular culture. Homer Simpson Ponders Politics includes a foreword by fantasy author Margaret Weis (coauthor/creator of the Dragonlance novels and game world) and is divided according to eras and themes in political thought: The first section explores civic virtue, applying the work of Plato and Aristotle to modern media. Part 2 draws on the philosophy of Hobbes, Locke, Rousseau, and Smith as a framework for understanding the role of the state. Part 3 explores the work of theorists such as Kant and Marx, and the final section investigates the ways in which movies and newer forms of electronic media either support or challenge the underlying assumptions of the democratic order. The result is an engaging read for undergraduate students as well as anyone interested in popular culture. Joseph J. Foy, associate campus dean and associate professor of political science at the University of Wisconsin–Waukesha, is the editor of Homer Simpson Goes to Washington: American Politics through Popular Culture and coeditor of Homer Simpson Marches on Washington: Dissent through American Popular Culture. Timothy M. Dale, assistant professor of political science at the University of Wisconsin–La Crosse, is coeditor of Homer Simpson Marches on Washington: Dissent through American Popular Culture. “Today, film, fiction, and television reflect our notions of civic virtue, morality, and the human condition—or at least help us to struggle with understanding and defining these. The ubiquitous nature of popular culture means that it will have an effect upon us, whether one likes that or not. The authors argue that, given this fact, even those who doubt the ‘seriousness’ of popular culture would do well to pay attention to it.”—Margaret Ferguson, Assistant Vice President for Statewide Academic Relations at Indiana University Since ancient times myths and stories have been used to convey our deepest thoughts about how to live together in community. With this book we now have a fun and engaging way to learn and think about political theory through the myths and stories of our time, popular culture. -- William Irwin, author of Black Sabbath and Philosophy: Mastering Reality Foy and Dale have done it again, this time with political theory! Political theory is one of the most difficult subjects that political science undergraduates encounter and Homer Simpson Ponders Politics opens up an avenue for students to engage many of the broad theories through some of the cultural artifacts with which they are most familiar: popular culture. These important theories bubble up through all areas of popular culture from Machiavelli and The Godfather to Plato and Star Wars— there is much to learn from this compendium. This is a useful book for students of political theory of any age or training and for those who are intrigued by the many political concepts popular culture teaches us. --Lilly J. Goren, coeditor of Women and the White House: Gender, Popular Culture, and Presidential Politics Most essays in this collection employ their philosophical guides in ways that can...disabuse undergraduates of the notion that political theory can better address the sterile and obsolete concerns of forgotten eras than fundamental questions about contemporary political life. -- Choicehttps://uknowledge.uky.edu/upk_american_popular_culture/1013/thumbnail.jp

On-Orbit Validation of a Framework for Spacecraft-Initiated Communication Service Requests with NASA's SCaN Testbed

We design, analyze, and experimentally validate a framework for demand-based allocation of high-performance space communication service in which the user spacecraft itself initiates a request for service. Leveraging machine-to-machine communications, the automated process has potential to improve the responsiveness and efficiency of space network operations. We propose an augmented ground station architecture in which a hemispherical-pattern antenna allows for reception of service requests sent from any user spacecraft within view. A suite of ground-based automation software acts upon these direct-to-Earth requests and allocates access to high-performance service through a ground station or relay satellite in response to immediate user demand. A software-defined radio transceiver, optimized for reception of weak signals from the helical antenna, is presented. Design and testing of signal processing equipment and a software framework to handle service requests is discussed. Preliminary results from on-orbit demonstrations with a testbed onboard the International Space Station are presented to verify feasibility of the concept

Machine learning methods for metabolic pathway prediction

<p>Abstract</p> <p>Background</p> <p>A key challenge in systems biology is the reconstruction of an organism's metabolic network from its genome sequence. One strategy for addressing this problem is to predict which metabolic pathways, from a reference database of known pathways, are present in the organism, based on the annotated genome of the organism.</p> <p>Results</p> <p>To quantitatively validate methods for pathway prediction, we developed a large "gold standard" dataset of 5,610 pathway instances known to be present or absent in curated metabolic pathway databases for six organisms. We defined a collection of 123 pathway features, whose information content we evaluated with respect to the gold standard. Feature data were used as input to an extensive collection of machine learning (ML) methods, including naïve Bayes, decision trees, and logistic regression, together with feature selection and ensemble methods. We compared the ML methods to the previous PathoLogic algorithm for pathway prediction using the gold standard dataset. We found that ML-based prediction methods can match the performance of the PathoLogic algorithm. PathoLogic achieved an accuracy of 91% and an F-measure of 0.786. The ML-based prediction methods achieved accuracy as high as 91.2% and F-measure as high as 0.787. The ML-based methods output a probability for each predicted pathway, whereas PathoLogic does not, which provides more information to the user and facilitates filtering of predicted pathways.</p> <p>Conclusions</p> <p>ML methods for pathway prediction perform as well as existing methods, and have qualitative advantages in terms of extensibility, tunability, and explainability. More advanced prediction methods and/or more sophisticated input features may improve the performance of ML methods. However, pathway prediction performance appears to be limited largely by the ability to correctly match enzymes to the reactions they catalyze based on genome annotations.</p

A systematic study of genome context methods: calibration, normalization and combination

<p>Abstract</p> <p>Background</p> <p>Genome context methods have been introduced in the last decade as automatic methods to predict functional relatedness between genes in a target genome using the patterns of existence and relative locations of the homologs of those genes in a set of reference genomes. Much work has been done in the application of these methods to different bioinformatics tasks, but few papers present a systematic study of the methods and their combination necessary for their optimal use.</p> <p>Results</p> <p>We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor. We find that for most organisms the gene neighbor method outperforms the phylogenetic profile method by as much as 40% in sensitivity, being competitive with the gene cluster method at low sensitivities. Gene fusion is generally the worst performing of the four methods. A thorough exploration of the parameter space for each method is performed and results across different target organisms are presented.</p> <p>We propose the use of normalization procedures as those used on microarray data for the genome context scores. We show that substantial gains can be achieved from the use of a simple normalization technique. In particular, the sensitivity of the phylogenetic profile method is improved by around 25% after normalization, resulting, to our knowledge, on the best-performing phylogenetic profile system in the literature.</p> <p>Finally, we show results from combining the various genome context methods into a single score. When using a cross-validation procedure to train the combiners, with both original and normalized scores as input, a decision tree combiner results in gains of up to 20% with respect to the gene neighbor method. Overall, this represents a gain of around 15% over what can be considered the state of the art in this area: the four original genome context methods combined using a procedure like that used in the STRING database. Unfortunately, we find that these gains disappear when the combiner is trained only with organisms that are phylogenetically distant from the target organism.</p> <p>Conclusions</p> <p>Our experiments indicate that gene neighbor is the best individual genome context method and that gains from the combination of individual methods are very sensitive to the training data used to obtain the combiner's parameters. If adequate training data is not available, using the gene neighbor score by itself instead of a combined score might be the best choice.</p

Effect of Surface Patterning and Presence of Collagen I on the Phenotypic Changes of Embryonic Stem Cell Derived Cardiomyocytes

Embryonic stem cell derived cardiomyocytes have been widely investigated for stem cell therapy or in vitro model systems. This study examines how two specific biophysical stimuli, collagen I and cell alignment, affect the phenotypes of embryonic stem cell derived cardiomyocytes in vitro. Three phenotypic indicators are assessed: sarcomere organization, cell elongation, and percentage of binucleation. Murine embryonic stem cells were differentiated in a hanging drop assay and cardiomyocytes expressing GFP-α-actinin were isolated by fluorescent sorting. First, the effect of collagen I was investigated. Addition of soluble collagen I markedly reduced binucleation as a result of an increase in cytokinesis. Laden with a collagen gel layer, myocyte mobility and cell shape change were impeded. Second, the effect of cell alignment by microcontact printing and nanopattern topography was investigated. Both patterning techniques induced cell alignment and elongation. Microcontact printing of 20 μm line pattern accelerated binucleation and nanotopography with 700 nm ridges and 3.5 μm grooves negatively regulated binucleation. This study highlights the importance of biophysical cues in the morphological changes of differentiated cardiomyocytes and may have important implications on how these cells incorporate into the native myocardium.Singapore-MIT Alliance for Research and TechnologyNational Science Foundation (U.S.) ((Science and Technology Center (EBICS): Emergent Behaviors of Integrated Cellular Systems, Grant CBET-0939511)Charles Stark Draper Laboratory (Internal Research and Development Program

Variable-delay Polarization Modulators for Cryogenic Millimeter-wave Applications

We describe the design, construction, and initial validation of the variable-delay polarization modulator (VPM) designed for the PIPER cosmic microwave background polarimeter. The VPM modulates between linear and circular polarization by introducing a variable phase delay between orthogonal linear polarizations. Each VPM has a diameter of 39 cm and is engineered to operate in a cryogenic environment (1.5 K). We describe the mechanical design and performance of the kinematic double-blade flexure and drive mechanism along with the construction of the high precision wire grid polarizers.Comment: 8 pages, 10 Figures, Submitted to Review of Scientific Instrument

Scientific teaching targeting faculty from diverse institutions

We offered four annual professional development workshops called STAR (for Scientific Teaching, Assessment, and Resources) modeled after the National Academies Summer Institute (SI) on Undergraduate Education in Biology. In contrast to the SI focus on training faculty from research universities, STAR\u27s target was faculty from community colleges, 2-yr campuses, and public and private research universities. Because of the importance of community colleges and 2-yr institutions as entries to higher education, we wanted to determine whether the SI model can be successfully extended to this broader range of institutions. We surveyed the four cohorts; 47 STAR alumni responded to the online survey. The responses were separated into two groups based on the Carnegie undergraduate instructional program categories, faculty from seven associate\u27s and associate\u27s-dominant institutions (23) and faculty from nine institutions with primarily 4-yr degree programs (24). Both groups expressed the opinion that STAR had a positive impact on teaching, student learning, and engagement. The two groups reported using techniques of formative assessment and active learning with similar frequency. The mix of faculty from diverse institutions was viewed as enhancing the workshop experience. The present analysis indicates that the SI model for training faculty in scientific teaching can successfully be extended to a broad range of higher education institutions. © 2013 C. S. Gregg et al

A Phase II Randomized, Double-Blind, Placebo-Controlled Safety and Efficacy Study of Lenalidomide in Lumbar Radicular Pain with a Long-Term Open-Label Extension Phase.

OBJECTIVE: This phase II study assessed lenalidomide efficacy and safety. DESIGN: Three-phase core study: 14-day prerandomization, 12-week treatment, and 52-week open-label extension. SETTING: Fourteen US centers from July 2005 to July 2007. SUBJECTS: Chronic lumbar radicular pain patients without history of nerve injury or deficit. METHODS: Subjects were randomized (1:1) to double-blind treatment with lenalidomide 10 mg or placebo once daily for 12 weeks, followed by a 52-week open-label extension. A 12-week, single-center, randomized-withdrawal (1:2, lenalidomide:placebo), exploratory study with open-label extension was undertaken in 12 subjects from the core extension who were naïve to neuropathic medications and with at least a two-point decrease from baseline average daily Pain Intensity-Numerical Rating Scale score. RESULTS: Of 180 subjects enrolled, 176 had at least one postbaseline measure; 132 completed the 12-week treatment phase. In the core study, no statistically significant difference in Pain Intensity-Numerical Rating Scale mean change (-0.02, P = 0.958) was observed at week 12 between lenalidomide and placebo; proportions achieving pain reduction at week 12 and other secondary measures were comparable between lenalidomide and placebo. In the exploratory study, week 12 mean changes in Pain Intensity-Numerical Rating Scale scores were -0.05 (lenalidomide: N = 3) and 2.11 (placebo: N = 8). Mean changes in Brief Pain Inventory-short form interference scores were -3.33 and 8.38, respectively; scores at six months were maintained or decreased in 10 of 12 subjects. CONCLUSIONS: While this study does not support lenalidomide use in an unselected lumbar radicular pain population, an immunomodulating agent may relieve pain in select subjects naïve to neuropathic pain medications.ClinicalTrials.gov identifier: NCT00120120