Addressing mechanism bias in model-based impact forecasts of new tuberculosis vaccines

In tuberculosis (TB) vaccine development, multiple factors hinder the design and interpretation of the clinical trials used to estimate vaccine efficacy. The complex transmission chain of TB includes multiple routes to disease, making it hard to link the vaccine efficacy observed in a trial to specific protective mechanisms. Here, we present a Bayesian framework to evaluate the compatibility of different vaccine descriptions with clinical trial outcomes, unlocking impact forecasting from vaccines whose specific mechanisms of action are unknown. Applying our method to the analysis of the M72/AS01E vaccine trial -conducted on IGRA+ individuals- as a case study, we found that most plausible models for this vaccine needed to include protection against, at least, two over the three possible routes to active TB classically considered in the literature: namely, primary TB, latent TB reactivation and TB upon re-infection. Gathering new data regarding the impact of TB vaccines in various epidemiological settings would be instrumental to improve our model estimates of the underlying mechanisms

Spreading of Persistent Infections in Heterogeneous Populations

Up to now, the effects of having heterogeneous networks of contacts have been studied mostly for diseases which are not persistent in time, i.e., for diseases where the infectious period can be considered very small compared to the lifetime of an individual. Moreover, all these previous results have been obtained for closed populations, where the number of individuals does not change during the whole duration of the epidemics. Here, we go one step further and analyze, both analytically and numerically, a radically different kind of diseases: those that are persistent and can last for an individual's lifetime. To be more specific, we particularize to the case of Tuberculosis' (TB) infection dynamics, where the infection remains latent for a period of time before showing up and spreading to other individuals. We introduce an epidemiological model for TB-like persistent infections taking into account the heterogeneity inherent to the population structure. This sort of dynamics introduces new analytical and numerical challenges that we are able to sort out. Our results show that also for persistent diseases the epidemic threshold depends on the ratio of the first two moments of the degree distribution so that it goes to zero in a class of scale-free networks when the system approaches the thermodynamic limit.Comment: 12 pages and 2 figures. Revtex format. Submitted for publication

Proteomic characterization of the porcine neutrophil response to LPS from Salmonella Typhimurium by 2D-Gel electrophoresis and mass spectrometry

Comunicaciones a congreso

Bioinformatics tools for inferring immune-relatedfunctions from proteomic data

Comunicaciones a congreso

Nanoscopic surface inspection by analyzing the linear polarization degree of the scattered light

We present an optical method for the nanoscopic inspection of surfaces. The method is based on the spectral and polarization analysis of the light scattered by a probe nanoparticle close to the inspected surface. We explore the sensitivity to changes either in the probe–surface distance or in the refractive index of the surface

Pressure-Induced Phase-Transition Sequence In Cof 2 : An Experimental And First-Principles Study On The Crystal, Vibrational, And Electronic Properties

We report a complete structural study of CoF2 under pressure. Its crystal structure and vibrational and electronic properties have been studied both theoretically and experimentally using first-principles density functional theory (DFT) methods, x-ray diffraction, x-ray absorption at Co K-edge experiments, Raman spectroscopy, and optical absorption in the 0–80 GPa range. We have determined the structural phase-transition sequence in CoF2 and corresponding transition pressures. The results are similar to other transition-metal difluorides such as FeF2 but different to ZnF2 and MgF2, despite that the Co2+ size (ionic radius) is similar to Zn2+ and Mg2+. We found that the complete phase-transition sequence is tetragonal rutile (P42/mnm) → CaCl2 type (orthorhombic Pnnm) → distorted PdF2 (orthorhombic Pbca)+PdF2 (cubic Pa3¯) in coexistence → fluorite (cubic Fm3¯m) → cotunnite (orthorhombic Pnma). It was observed that the structural phase transition to the fluorite at 15 GPa involves a drastic change of coordination from sixfold octahedral to eightfold cubic with important modifications in the vibrational and electronic properties. We show that the stabilization of this high-pressure cubic phase is possible under nonhydrostatic conditions since ideal hydrostaticity would stabilize the distorted-fluorite structure (tetragonal I4/mmm) instead. Although the first rutile → CaCl2-type second-order phase transition is subtle by Raman spectroscopy, it was possible to define it through the broadening of the Eg Raman mode which is split in the CaCl2-type phase. First-principles DFT calculations are in fair agreement with the experimental Raman mode frequencies, thus providing an accurate description for all vibrational modes and elastic properties of CoF2 as a function of pressure

Data-driven model for the assessment of mycobacterium tuberculosis transmission in evolving demographic structures

In the case of tuberculosis (TB), the capabilities of epidemic models to produce quantitatively robust forecasts are limited by multiple hindrances. Among these, understanding the complex relationship between disease epidemiology and populations’ age structure has been highlighted as one of the most relevant. TB dynamics depends on age in multiple ways, some of which are traditionally simplified in the literature. That is the case of the heterogeneities in contact intensity among different age strata that are common to all airborne diseases, but still typically neglected in the TB case. Furthermore, while demographic structures of many countries are rapidly aging, demographic dynamics are pervasively ignored when modeling TB spreading. In this work, we present a TB transmission model that incorporates country-specific demographic prospects and empirical contact data around a data-driven description of TB dynamics. Using our model, we find that the inclusion of demographic dynamics is followed by an increase in the burden levels predicted for the next decades in the areas of the world that are most hit by the disease today. Similarly, we show that considering realistic patterns of contacts among individuals in different age strata reshapes the transmission patterns reproduced by the models, a result with potential implications for the design of age-focused epidemiological interventions

Evaluation of on-line solid-phase extraction capillary electrophoresis-mass spectrometry with a nanoliter valve for the analysis of peptide biomarkers

On-line solid-phase extraction capillary electrophoresis-mass spectrometry (SPE-CE-MS) is a powerful technique for high throughput sample clean-up and analyte preconcentration, separation, detection, and characterization. The most typical design due to its simplicity and low cost is unidirectional SPE-CE-MS. However, in this configuration, the sample volumes introduced by pressure depend on the dimensions of the separation capillary and some matrix components could be irreversibly adsorbed in its inner walls. Furthermore, in many cases, the requirements of on-line preconcentration are incompatible with the background electrolyte necessary for an efficient separation and sensitive MS detection. Here, we present SPE-CE-MS with a nanoliter valve (nvSPE-CE-MS) to overcome these drawbacks while keeping the design simple. The nvSPE-CE-MS system is operated with a single CE instrument and two capillaries for independent and orthogonal SPE preconcentration and CE separation, which are interfaced through an external and electrically isolated valve with a 20 nL sample loop. The instrumental setup is proved for the analysis of opioid and amyloid beta peptide biomarkers in standards and plasma samples. NvSPE-CE-MS allowed decreasing the limits of detection (LODs) 200 times with regard to CE-MS. Compared to unidirectional SPE-CE-MS, peak efficiencies were better and repeatabilities similar, but total analysis times longer and LODs for standards slightly higher due to the heart-cut operation and the limited volume of the valve loop. This small difference on the LODs for standards was compensated for plasma samples by the improved tolerance of nvSPE-CE-MS to complex sample matrices. In view of these results, the presented setup can be regarded as a promising versatile alternative to avoid complicated matrix samples entering the separation capillary in SPE-CE-MS