Network Inference via the Time-Varying Graphical Lasso

Many important problems can be modeled as a system of interconnected entities, where each entity is recording time-dependent observations or measurements. In order to spot trends, detect anomalies, and interpret the temporal dynamics of such data, it is essential to understand the relationships between the different entities and how these relationships evolve over time. In this paper, we introduce the time-varying graphical lasso (TVGL), a method of inferring time-varying networks from raw time series data. We cast the problem in terms of estimating a sparse time-varying inverse covariance matrix, which reveals a dynamic network of interdependencies between the entities. Since dynamic network inference is a computationally expensive task, we derive a scalable message-passing algorithm based on the Alternating Direction Method of Multipliers (ADMM) to solve this problem in an efficient way. We also discuss several extensions, including a streaming algorithm to update the model and incorporate new observations in real time. Finally, we evaluate our TVGL algorithm on both real and synthetic datasets, obtaining interpretable results and outperforming state-of-the-art baselines in terms of both accuracy and scalability

Progress and Research Needs of Plant Biomass Degradation by Basidiomycete Fungi

Peer reviewe

Determination of hydroxyl groups in biorefinery resources via quantitative 31P NMR spectroscopy

The analysis of chemical structural characteristics of biorefinery product streams (such as lignin and tannin) has advanced substantially over the past decade, with traditional wet-chemical techniques being replaced or supplemented by NMR methodologies. Quantitative 31P NMR spectroscopy is a promising technique for the analysis of hydroxyl groups because of its unique characterization capability and broad potential applicability across the biorefinery research community. This protocol describes procedures for (i) the preparation/solubilization of lignin and tannin, (ii) the phosphitylation of their hydroxyl groups, (iii) NMR acquisition details, and (iv) the ensuing data analyses and means to precisely calculate the content of the different types of hydroxyl groups. Compared with traditional wet-chemical techniques, the technique of quantitative 31P NMR spectroscopy offers unique advantages in measuring hydroxyl groups in a single spectrum with high signal resolution. The method provides complete quantitative information about the hydroxyl groups with small amounts of sample (~30 mg) within a relatively short experimental time (~30-120 min)

Simulation of the discharge propagation in a capillary tube in air at atmospheric pressure

International audienceThis paper presents simulations of an air plasma discharge at atmospheric pressure initiated by a needle anode set inside a dielectric capillary tube. We have studied the influence of the tube inner radius and its relative permittivity ε r on the discharge structure and dynamics. As a reference, we have used a relative permittivity ε r = 1 to study only the influence of the cylindrical constraint of the tube on the discharge. For a tube radius of 100 µm and ε r = 1, we have shown that the discharge fills the tube during its propagation and is rather homogeneous behind the discharge front. When the radius of the tube is in the range 300 to 600 µm, the discharge structure is tubular with peak values of electric field and electron density close to the dielectric surface. When the radius of the tube is larger than 700 µm, the tube has no influence on the discharge which propagates axially. For a tube radius of 100 µm, when ε r increases from 1 to 10, the discharge structure becomes tubular. We have noted that the velocity of propagation of the discharge in the tube increases when the front is more homogeneous and then, the discharge velocity increases with the decrease of the tube radius and ε r. Then, we have compared the relative influence of the value of tube radius and ε r on the discharge characteristics. Our simulations indicate that the geometrical constraint of the cylindrical tube has more influence than the value of ε r on the discharge structure and dynamics. Finally, we have studied the influence of photoemission processes on the discharge structure by varying the photoemission coefficient. As expected, we have shown that photoemission, as it increases the number of secondary electrons close to the dielectric surface, promotes the tubular structure of the discharge

Pre-clinical imaging of transgenic mouse models of neuroblastoma using a dedicated 3-element solenoid coil on a clinical 3T platform.

Background The use of clinical MRI scanners to conduct pre-clinical research facilitates comparisons with clinical studies. Here the utility and sensitivity of anatomical and functional MRI data/biomarkers acquired from transgenic mouse models of neuroblastoma using a dedicated radiofrequency (RF) coil on a clinical 3T scanner was evaluated.Methods Multiparametric MRI of transgenic mice bearing abdominal neuroblastomas was performed at 3T, and data cross-referenced to that acquired from the same mice on a pre-clinical 7T MRI system. T2-weighted imaging, quantitation of the native longitudinal relaxation time (T1) and the transverse relaxation rate (R2*), and dynamic contrast-enhanced (DCE)-MRI, was used to assess tumour volume, phenotype and response to cyclophosphamide or cabozantinib.Results Excellent T2-weighted image contrast enabled clear tumour delineation at 3T. Significant correlations of tumour volume (R=0.98, P2* (R=0.87, P2* (Ptrans for each tumour (median Ktrans values of 0.202, 0.168 and 0.114 min-1). Cyclophosphamide elicited a significant reduction in both tumour burden (P1 (P<0.01), whereas cabozantinib induced significant (P<0.01) tumour growth delay.Conclusions Simultaneous multiparametric MRI of multiple tumour-bearing animals using this coil arrangement at 3T can provide high efficiency/throughput for both phenotypic characterisation and evaluation of novel therapeutics, and facilitate the introduction of functional MRI biomarkers into aligned imaging-embedded clinical trials

In Situ UV-Visible Assessment of Iron-Based High-Temperature Water-Gas Shift Catalysts Promoted with Lanthana: An Extent of Reduction Study

The extent of reduction of unsupported iron-based high-temperature water-gas shift catalysts with small (&lt;5 wt %) lanthana contents was studied using UV-visible spectroscopy. Temperature- programmed reduction measurements showed that lanthana content higher than 0.5 wt % increased the extent of reduction to metallic Fe, while 0.5 wt % of lanthana facilitated the reduction to Fe3O4. In situ measurements on the iron oxide catalysts using mass and UV-visible spectroscopies permitted the quantification of the extent of reduction under temperature-programmed reduction and high-temperature water-gas shift conditions. The oxidation states were successfully calibrated against normalized absorbance spectra of visible light using the Kubelka-Munk theory. The normalized absorbance relative to the fully oxidized Fe2O3 increased as the extent of reduction increased. XANES suggested that the average bulk iron oxidation state during the water-gas shift reaction was Fe+2.57 for the catalyst with no lanthana and Fe+2.54 for the catalysts with 1 wt % lanthana. However, the UV-vis spectra suggest that the surface oxidation state of iron would be Fe+2.31 for the catalyst with 1 wt % lanthana if the oxidation state of iron in the catalyst with 0 wt % lanthana were Fe+2.57. The findings of this paper emphasize the importance of surface sensitive UV-visible spectroscopy for determining the extent of catalyst reduction during operation. The paper highlights the potential to use bench-scale UV-visible spectroscopy to study the surface chemistry of catalysts instead of less-available synchrotron X-ray radiation facilities

Dual ¹⁹F/¹H MR Gene Reporter Molecules for <i>in Vivo</i> Detection of β-Galactosidase

Increased emphasis on personalized medicine and novel therapies requires the development of noninvasive strategies for assessing biochemistry <i>in vivo</i>. The detection of enzyme activity and gene expression <i>in vivo</i> is potentially important for the characterization of diseases and gene therapy. Magnetic resonance imaging (MRI) is a particularly promising tool, since it is noninvasive and has no associated radioactivity, yet penetrates deep tissue. We now demonstrate a novel class of dual ¹H/¹⁹F nuclear magnetic resonance (NMR) <i>lacZ</i> gene reporter molecule to specifically reveal enzyme activity in human tumor xenografts growing in mice. We report the design, synthesis, and characterization of six novel molecules and evaluation of the most effective reporter in mice <i>in vivo</i>. Substrates show a single ¹⁹F NMR signal and exposure to β-galactosidase induces a large ¹⁹F NMR chemical shift response. In the presence of ferric ions, the liberated aglycone generates intense proton MRI T₂ contrast. The dual modality approach allows both the detection of substrate and the imaging of product enhancing the confidence in enzyme detection