Point-particle method to compute diffusion-limited cellular uptake

We present an efficient point-particle approach to simulate reaction-diffusion processes of spherical absorbing particles in the diffusion-limited regime, as simple models of cellular uptake. The exact solution for a single absorber is used to calibrate the method, linking the numerical parameters to the physical particle radius and uptake rate. We study configurations of multiple absorbers of increasing complexity to examine the performance of the method, by comparing our simulations with available exact analytical or numerical results. We demonstrate the potentiality of the method in resolving the complex diffusive interactions, here quantified by the Sherwood number, measuring the uptake rate in terms of that of isolated absorbers. We implement the method in a pseudo-spectral solver that can be generalized to include fluid motion and fluid-particle interactions. As a test case of the presence of a flow, we consider the uptake rate by a particle in a linear shear flow. Overall, our method represents a powerful and flexible computational tool that can be employed to investigate many complex situations in biology, chemistry and related sciences.Comment: 13 pages, 13 figure

Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.Comment: 9 pages, 2 figure

Calibration of optimal execution of financial transactions in the presence of transient market impact

Trading large volumes of a financial asset in order driven markets requires the use of algorithmic execution dividing the volume in many transactions in order to minimize costs due to market impact. A proper design of an optimal execution strategy strongly depends on a careful modeling of market impact, i.e. how the price reacts to trades. In this paper we consider a recently introduced market impact model (Bouchaud et al., 2004), which has the property of describing both the volume and the temporal dependence of price change due to trading. We show how this model can be used to describe price impact also in aggregated trade time or in real time. We then solve analytically and calibrate with real data the optimal execution problem both for risk neutral and for risk averse investors and we derive an efficient frontier of optimal execution. When we include spread costs the problem must be solved numerically and we show that the introduction of such costs regularizes the solution.Comment: 31 pages, 8 figure

A new look inside Planetary Nebula LoTr 5: A long-period binary with hints of a possible third component

LoTr 5 is a planetary nebula with an unusual long-period binary central star. As far as we know, the pair consists of a rapidly rotating G-type star and a hot star, which is responsible for the ionization of the nebula. The rotation period of the G-type star is 5.95 days and the orbital period of the binary is now known to be $\sim$2700 days, one of the longest in central star of planetary nebulae. The spectrum of the G central star shows a complex H$\alpha$ double-peaked profile which varies with very short time scales, also reported in other central stars of planetary nebulae and whose origin is still unknown. We present new radial velocity observations of the central star which allow us to confirm the orbital period for the long-period binary and discuss the possibility of a third component in the system at $\sim$129 days to the G star. This is complemented with the analysis of archival light curves from SuperWASP, ASAS and OMC. From the spectral fitting of the G-type star, we obtain a effective temperature of $T_{\rm eff}$ = 5410$\pm$250 K and surface gravity of $\log g$ = 2.7$\pm$0.5, consistent with both giant and subgiant stars. We also present a detailed analysis of the H$\alpha$ double-peaked profile and conclude that it does not present correlation with the rotation period and that the presence of an accretion disk via Roche lobe overflow is unlikely.Comment: 12 pages, 12 figures, accepted for publication in MNRA

Hierarchically nested factor model from multivariate data

We show how to achieve a statistical description of the hierarchical structure of a multivariate data set. Specifically we show that the similarity matrix resulting from a hierarchical clustering procedure is the correlation matrix of a factor model, the hierarchically nested factor model. In this model, factors are mutually independent and hierarchically organized. Finally, we use a bootstrap based procedure to reduce the number of factors in the model with the aim of retaining only those factors significantly robust with respect to the statistical uncertainty due to the finite length of data records.Comment: 7 pages, 5 figures; accepted for publication in Europhys. Lett. ; the Appendix corresponds to the additional material of the accepted letter

Acute kidney injury and extrarenal organ dysfunction - A randomized experimental study

Indexación: Web of Science; ScieloIntroducción: La insuficiencia renal aguda (IRA) es una enfermedad grave y causante de disfunciones de órganos distantes que incrementan su mortalidad. Objetivo: Identificar disfunción hemodinámica y respiratoria gatillada por IRA en un modelo pediátrico animal de isquemia-reperfusión renal. Método: Doce cerdos anestesiados (11,9 ± 1,0 kg). En seis animales se indujo lesión renal bilateral por isquemia-reperfusión: 45 min de isquemia y 240 min de reperfusión, mientras que los seis animales restantes fueron grupo control. En condiciones basales y posterior a lesión renal se realizó monitorización hemodinámica convencional y termodilución transpulmonar. Paralelamente se midió gasometría arterial y análisis de mecánica pulmonar. Resultados: Hubo un incremento de la precarga volumétrica en 29% (221 ± 22 ml/m2 vs 286 ± 16 ml/m2, p = 0,04) y de la presión arterial media en 58% (71 ± 6 mmHg vs 112 ± 17 mmHg, p = 0,04) respecto a controles, sin cambios en frecuencia cardíaca, presión venosa central ni gasto cardíaco. Además ocurrió un aumento del agua extravascular pulmonar en 86% (7,6 ± 0,6 ml/kg vs 14,1 ± 1,4 ml/kg, p = 0,02), sin cambios en intercambio gaseoso ni mecánica pulmonar. Simultáneamente hubo un leve deterioro de la creatinina sérica (1,12 ± 0,07 mg/dL vs 1,45 ± 0,10 mg/dL, p = 0,03). Discusión: En este modelo experimental se pudo apreciar el desarrollo temprano de disfunción hemodinámica y pulmonar. Se evidenció un aumento de la precarga volumétrica y de la presión arterial, asociado a un incremento substancial del agua extravascular pulmonar. Creemos que es fundamental monitorizar de forma seriada la función hemodinámica y respiratoria en sujetos con una lesión renal aguda, aún sin una IRA urémica.Acute kidney injury (AKI) is a serious disease that can cause distant organ injuries and is associated with high mortality rates. Objective: To identify the hemodynamic and respiratory dysfunction triggered by AKI, in an animal model of renal ischemia-reperfusion. Method: Twelve anesthetized juvenile pigs (11.9 ± 1.0 kg). Six animals underwent ischemia/reperfusion-induced AKI: 45 min of ischemia and 240 minutes of reperfusion, while the remaining six animals were the control group. In basal conditions and after AKI, a conventional hemodynamic monitoring and transpulmonary thermodilution were performed. At the same time, arterial blood gases and lung mechanics were measured. Results: There was a 29% increase in volumetric preload (221 ± 22 ml/m2 vs 286 ± 16 ml/m2, p = 0.04) and a 58% mean arterial pressure increase (71 ± 6 mmHg vs 112 ± 17 mmHg, p = 0.04) compared to controls, without changes in heart rate, central venous pressure and cardiac output. In addition, an increase of 86% in extravascular lung water (7.6 ± 0.6 ml/kg vs 14.1 ± 1.4 ml/ kg, p = 0.02) was reported, without changes in gas exchange and lung mechanics. Simultaneously, a slight increase in serum creatinine (1.12 ± 0.07 mg/dl vs 1.45 ± 0.10 mg/dl, p = 0.03) was described. Discussion: An early development of hemodynamic and pulmonary dysfunction was observed in this experimental reperfusion model. An increase in volumetric preload and blood pressure associated with a substantial increase in the extravascular lung water were also reported. It is essential serially monitor the hemodynamic and respiratory functions in AKI, including nonuremic subjects.http://www.scielo.cl/pdf/rcp/v84n3/art04.pd