Assessing the Hierarchical Hamiltonian Splitting Integrator for Collisionless N-body Simulations

The N-body problem has become one of the hottest topics in the fields of computational dynamics and cosmology. The large dynamical range in some astrophysical problems led to the use of adaptive time steps to integrate particle trajectories, however, the search of optimal strategies is still challenging. We quantify the performance of the hierarchical time step integrator Hamiltonian Splitting (HamSp) for collisionless multistep simulations. We compare with the constant step Leap-Frog (LeapF) integrator and the adaptive one (AKDK). Additionally, we explore the impact of different time step assigning functions. There is a computational overhead in HamSp however there are two interesting advantages: choosing a convenient time-step function may compensate and even turn around the efficiency compared with AKDK. We test both reversibility and time symmetry. The symmetrized nature of the HamSp integration is able to provide time-reversible integration for medium time scales and overall deliver better energy conservation for long integration times, and the linear and angular momentum are preserved at machine precision. We address the impact of using different integrators in astrophysical systems. We found that in most situations both AKDK and HamSp are able to correctly simulate the problems. We conclude that HamSp is an attractive and competitive alternative to AKDK, with, in some cases, faster and with better energy and momentum conservation. The use of recently discussed Bridge splitting techniques with HamSp may allow to reach considerably high efficiency.Comment: 13 pages, 16 figure

Evaluating the effectiveness of a sodium butyrate feed additive for the control of Salmonella carriage in finishing pigs

This study aimed to investigate the effectiveness of commercially available sodium butyrate to control the shedding of Salmonella on two Irish pig farms with a history of high Salmonella seroprevalence. On both farms, pens (12-17 pigs/pen) were randomly assigned to a control (finisher feed without additives) or an acid treatment (the same feed supplemented with 0.03% sodium butyrate) for 24-26 days prior to slaughter. On Farm A, Salmonella shedding was reduced in the acid group compared to the control group at the end of the treatment period (30% vs. 57% probability of detecting Salmonella in faeces, respectively; p\u3c0.05). However no effect of treatment was observed on Farm B, which could perhaps be explained by a concomitant infection by Lawsonia intracellularis. No significant differences in Salmonella recovery rates were observed from caecal digesta or ileocaecal/mesenteric lymph nodes collected at slaughter in either of the trials. Furthermore, feed intake, weight gain and feed conversion efficiency did not differ significantly between control and treatment groups on either farm

Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors

Nonlinear control techniques by means of a software sensor that are commonly used in chemical engineering could be also applied to genetic regulation processes. We provide here a realistic formulation of this procedure by introducing an additive white Gaussian noise, which is usually found in experimental data. Besides, we include model errors, meaning that we assume we do not know the nonlinear regulation function of the process. In order to illustrate this procedure, we employ the Goodwin dynamics of the concentrations [B.C. Goodwin, Temporal Oscillations in Cells, (Academic Press, New York, 1963)] in the simple form recently applied to single gene systems and some operon cases [H. De Jong, J. Comp. Biol. 9, 67 (2002)], which involves the dynamics of the mRNA, given protein, and metabolite concentrations. Further, we present results for a three gene case in co-regulated sets of transcription units as they occur in prokaryotes. However, instead of considering their full dynamics, we use only the data of the metabolites and a designed software sensor. We also show, more generally, that it is possible to rebuild the complete set of nonmeasured concentrations despite the uncertainties in the regulation function or, even more, in the case of not knowing the mRNA dynamics. In addition, the rebuilding of concentrations is not affected by the perturbation due to the additive white Gaussian noise and also we managed to filter the noisy output of the biological systemComment: 21 pages, 7 figures; also selected in vjbio of August 2005; this version corrects a misorder in the last three references of the published versio

Transport studies in three-terminal microwave graphs with orthogonal, unitary, and symplectic symmetry

The Landauer-B\"uttiker formalism establishes an equivalence between the electrical conduction through a device, e.g., a quantum dot, and the transmission. Guided by this analogy we perform transmission measurements through three-port microwave graphs with orthogonal, unitary, and symplectic symmetry thus mimicking three-terminal voltage drop devices. One of the ports is placed as input and a second one as output, while a third port is used as a probe. Analytical predictions show good agreement with the measurements in the presence of orthogonal and unitary symmetries, provided that the absorption and the influence of the coupling port are taken into account. The symplectic symmetry is realized in specifically designed graphs mimicking spin 1/2 systems. Again a good agreement between experiment and theory is found. For the symplectic case the results are marginally sensitive to absorption and coupling strength of the port, in contrast to the orthogonal and unitary case.Comment: 6 pages, 6 figure

Characterization and Structure of a Zn2+ and [2Fe-2S]-containing Copper Chaperone from Archaeoglobus Fulgidus

Bacterial CopZ proteins deliver copper to P1B-type Cu+-ATPases that are homologous to the human Wilson and Menkes disease proteins. The genome of the hyperthermophile Archaeoglobus fulgidus encodes a putative CopZ copper chaperone that contains an unusual cysteine rich N-terminal domain of 130 amino acids in addition to a C-terminal copper-binding domain with a conserved CXXC motif. The N-terminal domain (CopZ-NT) is homologous to proteins found only in extremophiles and is the only such protein that is fused to a copper chaperone. Surprisingly, optical, electron paramagnetic resonance, and X-ray absorption spectroscopic data indicate the presence of a [2Fe-2S] cluster in CopZ-NT. The intact CopZ protein binds two copper ions, one in each domain. The 1.8 Å resolution crystal structure of CopZ-NT reveals that the [2Fe-2S] cluster is housed within a novel fold and that the protein also binds a zinc ion at a four cysteine site. CopZ can deliver Cu+ to the A. fulgidus CopA N-terminal metal binding domain and is capable of reducing Cu2+ to Cu+. This unique fusion of a redox-active domain with a CXXC-containing copper chaperone domain is relevant to the evolution of copper homeostatic mechanisms and suggests new models for copper trafficking

Exploración con biomicroscopio ocular : Técnicas y protocolo de intervención

Exploración con biomicroscopio ocular es un libro que puede ser utilizado desde los primeros semestres en los programas de Óptica y Optometría, por su manera clara y sencilla de explicar cada una de las partes del segmento anterior y las diferentes técnicas de iluminación a través del examen de biomicroscopía, entendiendo que éste examen es uno de los más importantes y necesarios para el manejo adecuado de la salud visual y ocular de nuestros pacientes. Es por ello que el libro inicia en su primer capítulo con el tema del “Rol social y profesional del contactólogo”, explicando el porqué debemos como profesionales de la salud visual capacitarnos y prepararnos para hacer de manera adecuada la atención primaria en salud visual. Continúa explicando las técnicas de iluminación paso por paso de manera sencilla y detallada, permitiendo de una manera clara y específica que el lector entienda el cómo utilizarlas de manera adecuada. Los demás capítulos profundizan en la descripción anatómica, fisiológica y patológica de las estructuras del segmento anterior. (del prólogo de Margarita María Ayala Cárdenas)Facultad de Ciencias Exacta

Structure of the pasquí pyroclastic cone from indirect interpretation of gravity data

El volcán Irazú presenta, en sus cuadrantes sur y oeste, numerosas estructuras relacionadas con antiguos focos de emisión de lavas y piroclastos fuera de su foco cuspidal. Una serie de estas estructuras se encuentra asociada a una zona de deformación extensional que incluye conos piroclásticos como los cerros Nochebuena, Gurdián, Dussan-Quemados y Pasquí. Este último es un cono piroclástico aportillado con coladas, con evidencias de actividad en un espacio temporal más reciente que 40 000 años. En este trabajo, se estudia la estructura interna del cono piroclástico Pasquí mediante la creación de modelos de densidad a partir de datos de gravedad. Los datos de anomalía de Bouguer a un nivel de reducción de 2 389 m muestran la correlación espacial del cono Pasquí con una anomalía negativa local de corta longitud de onda y amplitud de aproximadamente 5 mGal. Esta anomalía indica la presencia de material menos denso que el entorno del cerro. Se infiere a partir de la geología local y los resultados de los modelos de densidad, que existe un espesor de al menos 300 m de material piroclástico asociado con el cono. Este material de relativa baja densidad contrasta con el entorno de mayor densidad compuesto por lavas andesíticas y andesítico-basálticas de la Formación Reventado y lavas asociadas a actividad fisural originadas en focos como el complejo Dussan-Quemados.Irazú volcano shows several structures on its southern and western flank that are associated with ancient vents of lava and pyroclastic material outside of its summit caldera. A set of these type of structures is related to an extensional deformation zone that includes pyroclastic cones such as Nochebuena, Gurdián, Dussan-Quemados and Pasquí.This last structure is an eroded cone with lava flows which shows record of activity within the last 40 000 years. In this work, we study the internal structure of the Pasquí pyroclastic cone by creating density model from gravity data. The Bouguer anomaly data reduced to an altitude of 2,389 m, show a spatial correlation of the Pasquí cone with a local negative gravity anomaly with a short wavelength and an amplitude of approximately 5 mGal. This anomaly is indicative of the presence of material with a lower density than its sorroundings. From the density models, we infer the presence of pyroclastic material associated with the cone with a thickness of at least 300 m.This material of relative lower density, contrasts with the surroundings of the cone composed of andesitic and andesitic-basaltic lavas of the ReventadoFormation and lavas originated by fissures from vents such as the Dussan-Quemados complexUniversidad de Costa Rica/[113-B5-A00]/UCR/Costa RicaUniversidad de Costa Rica/[113-B9-911]/UCR/Costa RicaUCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela Centroamericana de GeologíaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Ciencias Geológicas (CICG

Frecuencia de genes que codifican factores de virulencia en Staphylococcus aureus aislados de niños que concurrieron al Hospital General Pediátrico Niños de Acosta Ñú, durante el año 2010

Staphylococcus aureus es un microorganismo con habilidad de infectar diferentes tejidos celulares, por portar genes que le confieren resistencia a antibióticos, factores de virulencia y su plasticidad genética, que podrían contribuir a una progresión rápida y complicada de la enfermedad. El Paraguay no cuenta con datos epidemiológicos que indiquen los factores de virulencia que presentan las cepas de S. aureus, por lo que el objetivo del trabajo fue determinar un perfil de virulencia detectando los genes codificantes de: hemolisinas α y β, enterotoxinas A, B, C, D, H y toxinas exfoliativas A y B. Este estudio observacional descriptivo de corte transverso, con muestreo no probabilístico de casos consecutivos, incluyó 50 aislados de S. aureus obtenidos a partir de muestras clínicas de secreciones de piel, partes blandas o líquidos corporales de pacientes menores de 17 años que concurrieron al Hospital General Pediátrico Niños de Acosta Ñú durante el año 2.010. Las reacciones de PCR incluyeron la detección de los genes: sea+seb+sec+ADNr16S, hlA+hlB, eta+etb, sed y seh. El 82% de los aislados provenía de niños que presentaron cuadros clínicos compatibles con infecciones de piel y partes blandas y el 18% de cuadros clínicos graves como sepsis, osteomielitis y neumonías. Los aislados contaban con datos de portación de Leucocidina de Panton-Valentine, el cual fue el factor de virulencia más frecuentemente detectado (58%), seguido de las hemolisinas alfa (16%) y beta (8%). Las enterotoxinas y las toxinas exfoliativas fueron menos frecuentes (0-2%), y no se detectaron genes codificantes de las enterotoxinas C y D