Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes

We created a simulation based on experimental data from bacteriophage T7 that computes the developmental cycle of the wild-type phage and also of mutants that have an altered genome order. We used the simulation to compute the fitness of more than 105 mutants. We tested these computations by constructing and experimentally characterizing T7 mutants in which we repositioned gene 1, coding for T7 RNA polymerase. Computed protein synthesis rates for ectopic gene 1 strains were in moderate agreement with observed rates. Computed phage-doubling rates were close to observations for two of four strains, but significantly overestimated those of the other two. Computations indicate that the genome organization of wild-type T7 is nearly optimal for growth: only 2.8% of random genome permutations were computed to grow faster, the highest 31% faster, than wild type. Specific discrepancies between computations and observations suggest that a better understanding of the translation efficiency of individual mRNAs and the functions of qualitatively “nonessential” genes will be needed to improve the T7 simulation. In silico representations of biological systems can serve to assess and advance our understanding of the underlying biology. Iteration between computation, prediction, and observation should increase the rate at which biological hypotheses are formulated and tested.

Dreams for Dead Bodies : Blackness, Labor, and the Corpus of American Detective Fiction /

Robinson argues that the detective genre’s lineage lies in experimental works on the margins of what we recognize as classical detective fiction today. Authors like Edgar Allan Poe, Mark Twain, Pauline Hopkins, and Rudolph Fisher drew on detective fiction’s puzzle-elements to wrestle with complicated questions about race and labor in the U.S.

Postural and respiratory activation of the trunk muscles changes with mode and speed of locomotion

Despite the importance of the deep intrinsic spinal muscles for trunk control, few studies have investigated their activity during human locomotion or how this may change with speed and mode of locomotion. Furthermore, it has not been determined whether the postural and respiratory functions, of which these muscles take part, can be coordinated when locomotor demands are increased. EMG recordings of abdominal and paraspinal muscles were made in seven healthy subjects using fine-wire and surface electrodes. Measurements were also made of respiration and gait parameters. Recordings were made for 10s as subjects walked on a treadmill at 1 and 2 ms(-1) and ran at 2, 3, 4 and 5 ms(-1). Unlike the superficial muscles, transversus abdominis was active tonically throughout the gait cycle with all tasks, except running at speeds of 3 ms(-1) and greater. All other muscles were recruited in a phasic manner. The relative duration of these bursts of activity was influenced by speed and/or mode of locomotion. Activity of all abdominal muscles, except rectus abdominis (RA), was modulated both for respiration and locomotor-related functions but this activity was affected by the speed and mode of locomotion. This study provides evidence that the deep abdominal muscles are controlled independently of the other trunk muscles. Furthermore, the pattern of recruitment of the trunk muscles and their respiratory and postural coordination is dependent on the speed and mode of locomotion. (C) 2003 Published by Elsevier B.V.

Some New Classes of Orthogonal Polynomials and Special Functions

In dieser Dissertation präsentieren wir zunächst eine Verallgemeinerung der üblichen Sturm-Liouville-Probleme mit symmetrischen Lösungen und erklären eine umfassendere Klasse. Dann führen wir einige neue Klassen orthogonaler Polynome und spezieller Funktionen ein, welche sich aus dieser symmetrischen Verallgemeinerung ableiten lassen. Als eine spezielle Konsequenz dieser Verallgemeinerung führen wir ein Polynomsystem mit vier freien Parametern ein und zeigen, dass in diesem System fast alle klassischen symmetrischen orthogonalen Polynome wie die Legendrepolynome, die Chebyshevpolynome erster und zweiter Art, die Gegenbauerpolynome, die verallgemeinerten Gegenbauerpolynome, die Hermitepolynome, die verallgemeinerten Hermitepolynome und zwei weitere neue endliche Systeme orthogonaler Polynome enthalten sind. All diese Polynome können direkt durch das neu eingeführte System ausgedrückt werden. Ferner bestimmen wir alle Standardeigenschaften des neuen Systems, insbesondere eine explizite Darstellung, eine Differentialgleichung zweiter Ordnung, eine generische Orthogonalitätsbeziehung sowie eine generische Dreitermrekursion. Außerdem benutzen wir diese Erweiterung, um die assoziierten Legendrefunktionen, welche viele Anwendungen in Physik und Ingenieurwissenschaften haben, zu verallgemeinern, und wir zeigen, dass diese Verallgemeinerung Orthogonalitätseigenschaft und -intervall erhält. In einem weiteren Kapitel der Dissertation studieren wir detailliert die Standardeigenschaften endlicher orthogonaler Polynomsysteme, welche sich aus der üblichen Sturm-Liouville-Theorie ergeben und wir zeigen, dass sie orthogonal bezüglich der Fisherschen F-Verteilung, der inversen Gammaverteilung und der verallgemeinerten t-Verteilung sind. Im nächsten Abschnitt der Dissertation betrachten wir eine vierparametrige Verallgemeinerung der Studentschen t-Verteilung. Wir zeigen, dass diese Verteilung gegen die Normalverteilung konvergiert, wenn die Anzahl der Stichprobe gegen Unendlich strebt. Eine ähnliche Verallgemeinerung der Fisherschen F-Verteilung konvergiert gegen die chi-Quadrat-Verteilung. Ferner führen wir im letzten Abschnitt der Dissertation einige neue Folgen spezieller Funktionen ein, welche Anwendungen bei der Lösung in Kugelkoordinaten der klassischen Potentialgleichung, der Wärmeleitungsgleichung und der Wellengleichung haben. Schließlich erklären wir zwei neue Klassen rationaler orthogonaler hypergeometrischer Funktionen, und wir zeigen unter Benutzung der Fouriertransformation und der Parsevalschen Gleichung, dass es sich um endliche Orthogonalsysteme mit Gewichtsfunktionen vom Gammatyp handelt.

Asymptotic behavior at infinity of solutions of multidimensional second kind integral equations

We consider second kind integral equations of the form x(s) - (abbreviated x - K x = y ), in which Ω is some unbounded subset of Rn. Let Xp denote the weighted space of functions x continuous on Ω and satisfying x (s) = O(|s|-p ),s → ∞We show that if the kernel k(s,t) decays like |s — t|-q as |s — t| → ∞ for some sufficiently large q (and some other mild conditions on k are satisfied), then K ∈ B(XP) (the set of bounded linear operators on Xp), for 0 ≤ p ≤ q. If also (I - K)-1 ∈ B(X0) then (I - K)-1 ∈ B(XP) for 0 < p < q, and (I- K)-1∈ B(Xq) if further conditions on k hold. Thus, if k(s, t) = O(|s — t|-q). |s — t| → ∞, and y(s)=O(|s|-p), s → ∞, the asymptotic behaviour of the solution x may be estimated as x (s) = O(|s|-r), |s| → ∞, r := min(p, q). The case when k(s,t) = к(s — t), so that the equation is of Wiener-Hopf type, receives especial attention. Conditions, in terms of the symbol of I — K, for I — K to be invertible or Fredholm on Xp are established for certain cases (Ω a half-space or cone). A boundary integral equation, which models three-dimensional acoustic propaga-tion above flat ground, absorbing apart from an infinite rigid strip, illustrates the practical application and sharpness of the above results. This integral equation mod-els, in particular, road traffic noise propagation along an infinite road surface sur-rounded by absorbing ground. We prove that the sound propagating along the rigid road surface eventually decays with distance at the same rate as sound propagating above the absorbing ground.

Wages of interned merchant seamen, disability and other benefits to merchant seamen. Hearings before the Committee on the merchant marine and fisheries, House of representatives, Seventy-eighth Congress, second session, on H. R. 3262, a bill to amend section 2 (B) of Public law 17, Seventy-eighth Congress, relating to functions of War shipping administration, and for other purposes; and H. R. 2652, a bill to amend section 222 (E) of subtitle--Insurance of title II of the Merchant marine act, 1936, as amended. December 9, 1943, and February 10, 1944

Mode of access: Internet.

Group theory and quasiprobability integrals of Wigner functions

The integral of the Wigner function of a quantum-mechanical system over a region or its boundary in the classical phase plane, is called a quasiprobability integral. Unlike a true probability integral, its value may lie outside the interval [0, 1]. It is characterized by a corresponding selfadjoint operator, to be called a region or contour operator as appropriate, which is determined by the characteristic function of that region or contour. The spectral problem is studied for commuting families of region and contour operators associated with concentric discs and circles of given radius a. Their respective eigenvalues are determined as functions of a, in terms of the Gauss-Laguerre polynomials. These polynomials provide a basis of vectors in a Hilbert space carrying the positive discrete series representation of the algebra su(1, 1) approximate to so(2, 1). The explicit relation between the spectra of operators associated with discs and circles with proportional radii, is given in terms of the discrete variable Meixner polynomials.

On the permutation behaviour of Dickson polynomials of the second kind

The known permutation behaviour of the Dickson polynomials of the second kind in characteristic 3 is expanded and simplified. (C) 2002 Elsevier Science (USA).

A cellulose liquid crystal motor: a steam engine of the second kind

The salient feature of liquid crystal elastomers and networks is strong coupling between orientational order and mechanical strain. Orientational order can be changed by a wide variety of stimuli, including the presence of moisture. Changes in the orientation of constituents give rise to stresses and strains, which result in changes in sample shape. We have utilized this effect to build soft cellulose-based motor driven by humidity. The motor consists of a circular loop of cellulose film, which passes over two wheels. When humid air is present near one of the wheels on one side of the film, with drier air elsewhere, rotation of the wheels results. As the wheels rotate, the humid film dries. The motor runs so long as the difference in humidity is maintained. Our cellulose liquid crystal motor thus extracts mechanical work from a difference in humidity.

Theory of mind tasks and executive functions: A systematic review of group studies in neurology.

A growing number of studies have been addressing the relationship between theory of mind (TOM) and executive functions (EF) in patients with acquired neurological pathology. In order to provide a global overview on the main findings, we conducted a systematic review on group studies where we aimed to (1) evaluate the patterns of impaired and preserved abilities of both TOM and EF in groups of patients with acquired neurological pathology and (2) investigate the existence of particular relations between different EF domains and TOM tasks. The search was conducted in Pubmed/Medline. A total of 24 articles met the inclusion criteria. We considered for analysis classical clinically accepted TOM tasks (first- and second-order false belief stories, the Faux Pas test, Happe's stories, the Mind in the Eyes task, and Cartoon's tasks) and EF domains (updating, shifting, inhibition, and access). The review suggests that (1) EF and TOM appear tightly associated. However, the few dissociations observed suggest they cannot be reduced to a single function; (2) no executive subprocess could be specifically associated with TOM performances; (3) the first-order false belief task and the Happe's story task seem to be less sensitive to neurological pathologies and less associated to EF. Even though the analysis of the reviewed studies demonstrates a close relationship between TOM and EF in patients with acquired neurological pathology, the nature of this relationship must be further investigated. Studies investigating ecological consequences of TOM and EF deficits, and intervention researches may bring further contributions to this question.

Understanding deep architectures and the effect of unsupervised pre-training

Cette thèse porte sur une classe d'algorithmes d'apprentissage appelés architectures profondes. Il existe des résultats qui indiquent que les représentations peu profondes et locales ne sont pas suffisantes pour la modélisation des fonctions comportant plusieurs facteurs de variation. Nous sommes particulièrement intéressés par ce genre de données car nous espérons qu'un agent intelligent sera en mesure d'apprendre à les modéliser automatiquement; l'hypothèse est que les architectures profondes sont mieux adaptées pour les modéliser. Les travaux de Hinton (2006) furent une véritable percée, car l'idée d'utiliser un algorithme d'apprentissage non-supervisé, les machines de Boltzmann restreintes, pour l'initialisation des poids d'un réseau de neurones supervisé a été cruciale pour entraîner l'architecture profonde la plus populaire, soit les réseaux de neurones artificiels avec des poids totalement connectés. Cette idée a été reprise et reproduite avec succès dans plusieurs contextes et avec une variété de modèles. Dans le cadre de cette thèse, nous considérons les architectures profondes comme des biais inductifs. Ces biais sont représentés non seulement par les modèles eux-mêmes, mais aussi par les méthodes d'entraînement qui sont souvent utilisés en conjonction avec ceux-ci. Nous désirons définir les raisons pour lesquelles cette classe de fonctions généralise bien, les situations auxquelles ces fonctions pourront être appliquées, ainsi que les descriptions qualitatives de telles fonctions. L'objectif de cette thèse est d'obtenir une meilleure compréhension du succès des architectures profondes. Dans le premier article, nous testons la concordance entre nos intuitions---que les réseaux profonds sont nécessaires pour mieux apprendre avec des données comportant plusieurs facteurs de variation---et les résultats empiriques. Le second article est une étude approfondie de la question: pourquoi l'apprentissage non-supervisé aide à mieux généraliser dans un réseau profond? Nous explorons et évaluons plusieurs hypothèses tentant d'élucider le fonctionnement de ces modèles. Finalement, le troisième article cherche à définir de façon qualitative les fonctions modélisées par un réseau profond. Ces visualisations facilitent l'interprétation des représentations et invariances modélisées par une architecture profonde.

Military doctrine, command philosophy and the generation of fighting power: genesis and theory

Military doctrine is one of the conceptual components of war. Its raison d’être is that of a force multiplier. It enables a smaller force to take on and defeat a larger force in battle. This article’s departure point is the aphorism of Sir Julian Corbett, who described doctrine as ‘the soul of warfare’. The second dimension to creating a force multiplier effect is forging doctrine with an appropriate command philosophy. The challenge for commanders is how, in unique circumstances, to formulate, disseminate and apply an appropriate doctrine and combine it with a relevant command philosophy. This can only be achieved by policy-makers and senior commanders successfully answering the Clausewitzian question: what kind of conflict are they involved in? Once an answer has been provided, a synthesis of these two factors can be developed and applied. Doctrine has implications for all three levels of war. Tactically, doctrine does two things: first, it helps to create a tempo of operations; second, it develops a transitory quality that will produce operational effect, and ultimately facilitate the pursuit of strategic objectives. Its function is to provide both training and instruction. At the operational level instruction and understanding are critical functions. Third, at the strategic level it provides understanding and direction. Using John Gooch’s six components of doctrine, it will be argued that there is a lacunae in the theory of doctrine as these components can manifest themselves in very different ways at the three levels of war. They can in turn affect the transitory quality of tactical operations. Doctrine is pivotal to success in war. Without doctrine and the appropriate command philosophy military operations cannot be successfully concluded against an active and determined foe.

A fast two-grid and finite section method for a class of integral equations on the real line with application to an acoustic scattering problem in the half-plane

We consider the numerical treatment of second kind integral equations on the real line of the form ∅(s) = ∫_(-∞)^(+∞)▒〖κ(s-t)z(t)ϕ(t)dt,s=R〗 (abbreviated ϕ= ψ+K_z ϕ) in which K ϵ L_1 (R), z ϵ L_∞ (R) and ψ ϵ BC(R), the space of bounded continuous functions on R, are assumed known and ϕ ϵ BC(R) is to be determined. We first derive sharp error estimates for the finite section approximation (reducing the range of integration to [-A, A]) via bounds on (1-K_z )^(-1)as an operator on spaces of weighted continuous functions. Numerical solution by a simple discrete collocation method on a uniform grid on R is then analysed: in the case when z is compactly supported this leads to a coefficient matrix which allows a rapid matrix-vector multiply via the FFT. To utilise this possibility we propose a modified two-grid iteration, a feature of which is that the coarse grid matrix is approximated by a banded matrix, and analyse convergence and computational cost. In cases where z is not compactly supported a combined finite section and two-grid algorithm can be applied and we extend the analysis to this case. As an application we consider acoustic scattering in the half-plane with a Robin or impedance boundary condition which we formulate as a boundary integral equation of the class studied. Our final result is that if z (related to the boundary impedance in the application) takes values in an appropriate compact subset Q of the complex plane, then the difference between ϕ(s)and its finite section approximation computed numerically using the iterative scheme proposed is ≤C_1 [kh log⁡〖(1⁄kh)+(1-Θ)^((-1)⁄2) (kA)^((-1)⁄2) 〗 ] in the interval [-ΘA,ΘA](Θ<1) for kh sufficiently small, where k is the wavenumber and h the grid spacing. Moreover this numerical approximation can be computed in ≤C_2 N log⁡N operations, where N = 2A/h is the number of degrees of freedom. The values of the constants C1 and C2 depend only on the set Q and not on the wavenumber k or the support of z.

Laguerre polynomials as Jensen polynomials of Laguerre-Polya entire functions

We prove that the only Jensen polynomials associated with an entire function in the Laguerre-Polya class that are orthogonal are the Laguerre polynomials. (C) 2009 Elsevier B.V. All rights reserved.

Laguerre moments and generalized functions

Here we explore the link between the moments of the Laguerre polynomials or Laguerre moments and the generalized functions (as the Dirac delta-function and its derivatives), presenting several interesting relations. A useful application is related to a procedure for calculating mean values in quantum optics that makes use of the so-called quasi-probabilities. One of them, the P-distribution, can be represented by a sum over Laguerre moments when the electromagnetic field is in a photon-number state. Consequently, the P-distribution can be expressed in terms of Dirac delta-function and derivatives. More specifically, we found a direct relation between P-distributions and the Laguerre factorial moments.