Parametric inference of recombination in HIV genomes

Recombination is an important event in the evolution of HIV. It affects the global spread of the pandemic as well as evolutionary escape from host immune response and from drug therapy within single patients. Comprehensive computational methods are needed for detecting recombinant sequences in large databases, and for inferring the parental sequences. We present a hidden Markov model to annotate a query sequence as a recombinant of a given set of aligned sequences. Parametric inference is used to determine all optimal annotations for all parameters of the model. We show that the inferred annotations recover most features of established hand-curated annotations. Thus, parametric analysis of the hidden Markov model is feasible for HIV full-length genomes, and it improves the detection and annotation of recombinant forms. All computational results, reference alignments, and C++ source code are available at http://bio.math.berkeley.edu/recombination/.Comment: 20 pages, 5 figure

Avoiding Wireheading with Value Reinforcement Learning

How can we design good goals for arbitrarily intelligent agents? Reinforcement learning (RL) is a natural approach. Unfortunately, RL does not work well for generally intelligent agents, as RL agents are incentivised to shortcut the reward sensor for maximum reward -- the so-called wireheading problem. In this paper we suggest an alternative to RL called value reinforcement learning (VRL). In VRL, agents use the reward signal to learn a utility function. The VRL setup allows us to remove the incentive to wirehead by placing a constraint on the agent's actions. The constraint is defined in terms of the agent's belief distributions, and does not require an explicit specification of which actions constitute wireheading.Comment: Artificial General Intelligence (AGI) 201

Effects of static equilibrium and higher-order nonlinearities on rotor blade stability in hover

The equilibrium and stability of the coupled elastic lead/lag, flap, and torsion motion of a cantilever rotor blade in hover are addressed, and the influence of several higher-order terms in the equations of motion of the blade is determined for a range of values of collective pitch. The blade is assumed to be untwisted and to have uniform properties along its span. In addition, chordwise offsets between its elastic, tension, mass, and aerodynamic centers are assumed to be negligible for simplicity. The aerodynamic forces acting on the blade are modeled using a quasi-steady, strip-theory approximation

Crisis and the Emergence of Illicit Markets: A Pragmatist View on Economic Action outside the Law

Although illicit exchange has also been an organized, silent, and ever-present response to harsh economic crisis, only protest and social movements have captured scholars’ attention. In order to fill this void, this paper analyzes the emergence of illegal markets under situations of social breakdown. I claim that an illicit market emerging under socio-economic crisis conditions might be understood as the result of a constant valuation process and the intervention of what Herbert Mead called “generalized others.” In the new arena of exchange, individuals are able to anticipate the reactions of others, inhibit undesirable impulses, and guide their conduct accordingly by visualizing their own line of action from a generalized standpoint. This approach to illicit markets is based on a critical reading of two other approaches: the anomie theory and the field of organized-crime studies. Both perspectives, according to the argument, operate with a model of action characterized by fixed ends and means, a priori assumptions that hinder the ability to perceive the gradual and transforming dynamics of a crisis situation. The paper also offers empirical evidence on the process of the emergence of an illicit market under a crisis situation. By referring to La Salada market, an arena of exchange which emerged during the 1990s in Argentina, I describe a process characterized by an intensification of communicative activities, the adjustment of mutual expectations, the search for definitions that legitimate expectations, and role-taking in the market.Illegaler Markttausch ist oft die leise, aber organisierte und stets präsente Antwort auf ökonomische Krisen. Trotzdem waren bisher nur Protest- und soziale Bewegungen als Krisenreaktionen Gegenstand soziologischer Forschung. Diese Studie soll die Lücke füllen und analysiert das Aufkommen illegaler Märkte in Zeiten sozialen Zusammenbruchs. Der Autor argumentiert, illegaler Markttausch unter den Bedingungen einer sozioökonomischen Krise könne als Ergebnis eines konstanten Bewertungsprozesses und als die Intervention der von Herbert Mead so bezeichneten „generalized others“ verstanden werden. Die neu entstandene Marktarena versetzt Akteure in die Lage, Reaktionen anderer zu antizipieren, unerwünschte Impulse zu unterbinden und ihr Verhalten anzupassen, indem sie ihr Vorgehen von einem allgemeinen Standpunkt aus betrachten. Diese Herangehensweise an illegale Märkte beruht auf einer kritischen Lesart zweier bestehender Ansätze: der Anomietheorie und der Studien zu organisierter Kriminalität, die beide auf einem Akteurmodell mit vom Handlungsprozess losgelösten Zielen und Mitteln basieren. Solche vorweggenommenen Einschätzungen, so die Argumentation, schränken die Fähigkeit ein, graduelle und sich transformierende Dynamiken einer Krisensituation wahrzunehmen. Am Beispiel von La Salada, einer Marktarena, die während der 1990er-Jahre in Argentinien entstanden ist, beschreibt der Autor die Entstehung eines illegalen Marktes in einer Krisensituation. Er untersucht einen Prozess, der von einer Intensivierung kommunikativer Aktivitäten, von der Korrektur gegenseitiger Erwartungen und der Suche nach legitimierenden Definitionen sowie dem role-taking im Markt geprägt ist.1 Introduction 2 Anomie theory and markets after crisis 3 Illegal markets and the rational actor 4 From a portfolio to a problem-solving model of action outside the law 5 The illegal market as a successful end-in-view 6 Crisis, appraisals, and exchanges Searching for definitions Experiencing generalized others 7 A great opportunity: Emerging frames in La Salada Mutual adjustment, definitions, and role-taking The emergence of a generalized other: The market is a chain Generalized others’ specifics and the role of the state 8 Conclusion Reference

Persistent, symptomless, systemic, and seed-borne infection of lettuce by Botrytis cinerea

Experiments are presented which show that Botrytis cinerea, the cause of gray mould disease, is often present in symptomless lettuce plants as a systemic, endophytic, infection which may arise from seed. The fungus was isolated on selective media from surface sterilized sections of roots, stem pieces and leaf discs from symptomless plants grown in a conventional glasshouse and in a spore-free air-flow provided by an isolation propagator. The presence of B. cinerea was confirmed by immuno-labelling the tissues with the Botrytis-specific monoclonal antibody BC-12.CA4. As plants grew, infection spread from the roots to stems and leaves. Surface sterilization of seeds reduced the number of infected symptomless plants. Artificial infection of seedlings with dry conidia increased the rate of infection in some experiments. Selected isolates were genetically finger-printed using microsatellite loci. This confirmed systemic spread of the inoculating isolates but showed that other isolates were also present and that single plants hosted multiple isolates. This shows that B. cinerea commonly grows in lettuce plants as an endophyte, as has already been shown for Primula. If true for other hosts, the endophytic phase may be as important a component of the species population as the aggressive necrotrophic phase

Dewey Beegle ARC1996 -004 - Finding Aid

https://place.asburyseminary.edu/findingaids/1004/thumbnail.jp

Replicating Success: Developing an Educational Process for Improving Nursing Accuracy When Using a Patient Classification System

The use of patient classification systems (PCS), within hospitals has been and still is utilized primarily for determining staffing requirements, based upon the projected needs of the patient. Since its conception in the 1950\u27s, health care management has worked to develop a system that accurately depicts those needs to provide good patient care. Recently, a major tertiary health care center located in the Midwest region of the United States implemented a revised patient classification system within its acute care setting. Nurses were provided various levels of education regarding its use. Because of this, accuracy by nurses using the patient classification system varied. This project is designed to identify care areas which have been successful in utilizing the patient classification system, determine how their nursing staff were trained, and synthesize an educational process which will improve their accuracy using the system

Spectral element methods: Algorithms and architectures

Spectral element methods are high-order weighted residual techniques for partial differential equations that combine the geometric flexibility of finite element methods with the rapid convergence of spectral techniques. Spectral element methods are described for the simulation of incompressible fluid flows, with special emphasis on implementation of spectral element techniques on medium-grained parallel processors. Two parallel architectures are considered: the first, a commercially available message-passing hypercube system; the second, a developmental reconfigurable architecture based on Geometry-Defining Processors. High parallel efficiency is obtained in hypercube spectral element computations, indicating that load balancing and communication issues can be successfully addressed by a high-order technique/medium-grained processor algorithm-architecture coupling