Analytical methods for bacterial kinetics studies

Methods utilize mathematical equations and models and specialized computer techniques. Techniques apply to food production, complex chemicals production, and polluted water purification

Experimental Comparisons of Derivative Free Optimization Algorithms

In this paper, the performances of the quasi-Newton BFGS algorithm, the NEWUOA derivative free optimizer, the Covariance Matrix Adaptation Evolution Strategy (CMA-ES), the Differential Evolution (DE) algorithm and Particle Swarm Optimizers (PSO) are compared experimentally on benchmark functions reflecting important challenges encountered in real-world optimization problems. Dependence of the performances in the conditioning of the problem and rotational invariance of the algorithms are in particular investigated.Comment: 8th International Symposium on Experimental Algorithms, Dortmund : Germany (2009

Structural evolution drives diversification of the large LRR-RLK gene family

Cells are continuously exposed to chemical signals that they must discriminate between and respond to appropriately. In embryophytes, the leucine‐rich repeat receptor‐like kinases (LRR‐RLKs) are signal receptors critical in development and defense. LRR‐RLKs have diversified to hundreds of genes in many plant genomes. Although intensively studied, a well‐resolved LRR‐RLK gene tree has remained elusive. To resolve the LRR‐RLK gene tree, we developed an improved gene discovery method based on iterative hidden Markov model searching and phylogenetic inference. We used this method to infer complete gene trees for each of the LRR‐RLK subclades and reconstructed the deepest nodes of the full gene family. We discovered that the LRR‐RLK gene family is even larger than previously thought, and that protein domain gains and losses are prevalent. These structural modifications, some of which likely predate embryophyte diversification, led to misclassification of some LRR‐RLK variants as members of other gene families. Our work corrects this misclassification. Our results reveal ongoing structural evolution generating novel LRR‐RLK genes. These new genes are raw material for the diversification of signaling in development and defense. Our methods also enable phylogenetic reconstruction in any large gene family

Magnetic Photon Splitting: Computations of Proper-time Rates and Spectra

The splitting of photons in the presence of an intense magnetic field has recently found astrophysical applications in polar cap models of gamma-ray pulsars and in magnetar scenarios for soft gamma repeaters. Numerical computation of the polarization-dependent rates of this third order QED process for arbitrary field strengths and energies below pair creation threshold is difficult: thus early analyses focused on analytic developments and simpler asymptotic forms. The recent astrophysical interest spurred the use of the S-matrix approach by Mentzel, Berg and Wunner to determine splitting rates. In this paper, we present numerical computations of a full proper-time expression for the rate of splitting that was obtained by Stoneham, and is exact up to the pair creation threshold. While the numerical results derived here are in accord with the earlier asymptotic forms due to Adler, our computed rates still differ by as much as factors of 3 from the S-matrix re-evaluation of Wilke and Wunner, reflecting the extreme difficulty of generating accurate S-matrix numerics for fields below about \teq{4.4\times 10^{13}}Gauss. We find that our proper-time rates appear very accurate, and exceed Adler's asymptotic specializations significantly only for photon energies just below pair threshold and for supercritical fields, but always by less than a factor of around 2.6. We also provide a useful analytic series expansion for the scattering amplitude valid at low energies.Comment: 13 pages, AASTeX format, including 3 eps figures, ApJ in pres

Church-Rosser Systems, Codes with Bounded Synchronization Delay and Local Rees Extensions

What is the common link, if there is any, between Church-Rosser systems, prefix codes with bounded synchronization delay, and local Rees extensions? The first obvious answer is that each of these notions relates to topics of interest for WORDS: Church-Rosser systems are certain rewriting systems over words, codes are given by sets of words which form a basis of a free submonoid in the free monoid of all words (over a given alphabet) and local Rees extensions provide structural insight into regular languages over words. So, it seems to be a legitimate title for an extended abstract presented at the conference WORDS 2017. However, this work is more ambitious, it outlines some less obvious but much more interesting link between these topics. This link is based on a structure theory of finite monoids with varieties of groups and the concept of local divisors playing a prominent role. Parts of this work appeared in a similar form in conference proceedings where proofs and further material can be found.Comment: Extended abstract of an invited talk given at WORDS 201

Potential, core-level and d band shifts at transition metal surfaces

We have extended the validity of the correlation between the surface 3d-core-level shift (SCLS) and the surface d band shift (SDBS) to the entire 4d transition metal series and to the neighboring elements Sr and Ag via accurate first-principles calculations. We find that the correlation is quasilinear and robust with respect to the differencies both between initial and final-state calculations of the SCLS's and two distinct measures of the SDBS's. We show that despite the complex spatial dependence of the surface potential shift (SPS) and the location of the 3d and 4d orbitals in different regions of space, the correlation exists because the sampling of the SPS by the 3d and 4d orbitals remains similar. We show further that the sign change of the SCLS's across the transition series does indeed arise from the d band-narrowing mechanism previously proposed. However, while in the heavier transition metals the predicted increase of d electrons in the surface layer relative to the bulk arises primarily from transfers from s and p states to d states within the surface layer, in the lighter transition metals the predicted decrease of surface d electrons arises primarily from flow out into the vacuum.Comment: RevTex, 22 pages, 5 figures in uufiles form, to appear in Phys.Rev.

On the Sets of Real Numbers Recognized by Finite Automata in Multiple Bases

This article studies the expressive power of finite automata recognizing sets of real numbers encoded in positional notation. We consider Muller automata as well as the restricted class of weak deterministic automata, used as symbolic set representations in actual applications. In previous work, it has been established that the sets of numbers that are recognizable by weak deterministic automata in two bases that do not share the same set of prime factors are exactly those that are definable in the first order additive theory of real and integer numbers. This result extends Cobham's theorem, which characterizes the sets of integer numbers that are recognizable by finite automata in multiple bases. In this article, we first generalize this result to multiplicatively independent bases, which brings it closer to the original statement of Cobham's theorem. Then, we study the sets of reals recognizable by Muller automata in two bases. We show with a counterexample that, in this setting, Cobham's theorem does not generalize to multiplicatively independent bases. Finally, we prove that the sets of reals that are recognizable by Muller automata in two bases that do not share the same set of prime factors are exactly those definable in the first order additive theory of real and integer numbers. These sets are thus also recognizable by weak deterministic automata. This result leads to a precise characterization of the sets of real numbers that are recognizable in multiple bases, and provides a theoretical justification to the use of weak automata as symbolic representations of sets.Comment: 17 page

Sensitivity and specificity of a competitive enzyme immunoassay in the serodiagnosis of bovine brucellosis

O trabalho teve por objetivo avaliar a sensibilidade e a especificidade de um teste imunoenzimático competitivo, empregando como conjugado os anticorpos monoclonais BM-38 e BM-40, no diagnóstico sorológico da brucelose bovina. Foram examinados 74 soros de bovinos dos quais havia sido isolada Brucella abortus e 2.118 soros de bovinos procedentes de rebanhos livres de brucelose e que apresentaram resultado negativo quando submetidos ao teste Rosa Bengala. O teste imunoenzimático competitivo, usando qualquer dos dois conjugados, foi capaz de revelar a presença de anticorpos contra o lipopolissacáride bacteriano em todos os soros de bovinos infectados, o que resulta em uma sensibilidade de 100%. A especificidade do teste usando o conjugado BM-38 foi de 98.82% e usando o conjugado BM-40 foi de 99,95%. Estes resultados indicam que o teste imunoenzimático competitivo, principalmente ao se empregar o conjugado BM-40, consiste em um método bastante útil para ser usado como teste confirmatório no diagnóstico sorológico da brucelose bovina.The purpose of this work was to evaluate the sensitivity and the specificity of a competitive enzyme immunoassay, using as conjugate the monoclonal antibodies BM-38 and BM-40, in the serodiagnosis of bovine brucellosis. Seventy-four sera from culture-positive cattle and 2,118 cattle sera from herds free from brucellosis and negative to the Rose Bengal plate test were examined. The competitive enzyme immunoassay, using any of the two conjugates, was able to reveal the presence of antibodies to Brucella lipopolysaccharide in all of the 74 sera of the infected cattle, resulting in a sensitivity of 100%. The specificity of the test using the conjugate BM-38 was 98.82% and using the conjugate BM-40 was 99.95%. These results indicated that the competitive enzyme immunoassay, mainly when using the conjugate BM-40, consists in a technique very useful in the confirmation of the serological diagnosis of bovine brucellosis

Approach Direction Prior to Landing Explains Patterns of Colour Learning in Bees

Gaze direction is closely coupled with body movement in insects and other animals. If movement patterns interfere with the acquisition of visual information, insects can actively adjust them to seek relevant cues. Alternatively, where multiple visual cues are available, an insect’s movements may influence how it perceives a scene. We show that the way a foraging bumblebee approaches a floral pattern could determine what it learns about the pattern. When trained to vertical bicoloured patterns, bumblebees consistently approached from below centre in order to land in the centre of the target where the reward was located. In subsequent tests, the bees preferred the colour of the lower half of the pattern that they predominantly faced during the approach and landing sequence. A predicted change of learning outcomes occurred when the contrast line was moved up or down off-centre: learned preferences again reflected relative frontal exposure to each colour during the approach, independent of the overall ratio of colours. This mechanism may underpin learning strategies in both simple and complex visual discriminations, highlighting that morphology and action patterns determines how animals solve sensory learning tasks. The deterministic effect of movement on visual learning may have substantially influenced the evolution of floral signals, particularly where plants depend on fine-scaled movements of pollinators on flowers