PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction

Protein Blocks (PBs) are a widely used structural alphabet describing local protein backbone conformation in terms of 16 possible conformational states, adopted by five consecutive amino acids. The representation of complex protein 3D structures as 1D PB sequences was previously successfully applied to protein structure alignment and protein structure prediction. In the current study, we present a new model, PYTHIA (predicting any conformation at high accuracy), for the prediction of the protein local conformations in terms of PBs directly from the amino acid sequence. PYTHIA is based on a deep residual inception-inside-inception neural network with convolutional block attention modules, predicting 1 of 16 PB classes from evolutionary information combined to physicochemical properties of individual amino acids. PYTHIA clearly outperforms the LOCUSTRA reference method for all PB classes and demonstrates great performance for PB prediction on particularly challenging proteins from the CASP14 free modelling category.     

Impact of three different TiO2 morphologies on hydrogen evolution by methanol assisted water splitting: Nanoparticles, nanotubes and aerogels

Increasing the activity of a photocatalyst goes through the improvement of both its absorption (light) and adsorption (reactant) properties. For a given semiconducting material, the charge carrier separation is also a very important step. Properly combining chosen phases is one option to improve this separation (example of the commercial P25) and depositing platinum on the surface of the catalyst, another one. In some cases, coupling both may nevertheless lead to a decrease of photoactivity or at least limit the potentiality of the catalyst. A third option, consisting in modifying the morphology of the photoactive phase, has shown very promising results.In this study, we have elaborated, characterized and evaluated the hydrogen evolution potentiality (through methanol assisted water splitting) of different TiO₂ morphologies: nanoparticles, nanotubes and aerogels. These materials have shown different behaviours depending on both their composition and morphology. Different types of separation processes have been claimed to account for the observed different photoactivities, with more or less pronounced synergetic effects, due to: the use of Pt as a co-catalyst, the mixture of different TiO₂ phases (anatase and TiO₂(B) or rutile) and the specific morphology of the samples (nanotubes or aerogels). Among all the tested samples, the TiO₂ aerogel supported Pt one exhibited very promising performances, three times as active as P25 supported Pt, which is already much more active than pure P25 in our testing conditions.     

Fast Zirconium Oxidation Using Supercritical Water

A novel route for fast zirconium oxidation is reported, using supercritical water, for the case of Zircaloy-4 tubes that are used to clad nuclear fuel pellets in pressurized water reactors. An adherent and dense monoclinic zirconia layer 28 µm thick is obtained after 5 h of supercritical water oxidation at 500 °C. The zirconia crystallites are about 13 ± 2 nm in size. This technique reduces the time needed to oxidize Zircaloy-4 from several weeks to a few hours when standard conditions are being used.     

Clear model fluids to emulate the rheological properties of thickened digested sludge

Optimising flow processes in wastewater treatment plants requires that designers and operators take into account the flow properties of the sludge. Moreover, due to increasingly more stringent conditions on final disposal avenues such as landfill, composting, incineration etc., practitioners need to produce safer sludge in smaller quantities. Anaerobic digestion is a key treatment process for solids treatment and pathogen reduction. Due to the inherent opacity of sludge, it is impossible to visualise the mixing and flow patterns inside an anaerobic digester. Therefore, choosing an appropriate transparent model fluid which can mimic the rheological behaviour of sludge is imperative for visualisation of the hydrodynamic functioning of an anaerobic digester.Digested sludge is a complex material with time dependent non-Newtonian thixotropic characteristics. In steady state, it can be modelled by a basic power-law. However, for short-time processes the Herschel-Bulkley model can be used to model liquid-like properties.The objective of this study was to identify transparent model fluids which will mimic the behaviour of real sludge. A comparison of three model fluids, Carboxymethyl Cellulose (CMC), Carbopol gel and Laponite clay revealed that these fluids could each model certain aspects of sludge behaviour. It is concluded that the rheological behaviour of sludge can be modelled using CMC in steady state flow at high shear rates, Carbopol gel for short-time flow processes and Laponite clay suspension where time dependence is dominant.     

Lessons from the organization of a proficiency testing program in food microbiology by interlaboratory comparison: analytical methods in use, impact of methods on bacterial counts and measurement uncertainty of bacterial counts

The proficiency testing program in food microbiology RAEMA (Réseau d'Analyses et d'Echanges en Microbiologie des Aliments), created in 1988, currently includes 450 participating laboratories. This interlaboratory comparison establishes proficiency in detection of Salmonella and Listeria monocytogenes, as well as enumeration of aerobic micro-organisms, Enterobacteriaceae, coliforms, beta-glucuronidase-positive Escherichia coli, anaerobic sulfito-reducing bacteria, Clostridium perfringens, coagulase-positive staphylococci, and L. monocytogenes. Twice a year, five units samples are sent to participants to assess their precision and trueness for enumeration and detection of micro-organisms. Most of participating laboratories use standard or validated alternative methods, they were 50-70% in 1994 and, for 5 years, they are 95%. An increasing use of alternative methods was also observed. This phenomenon is all the more significant as standard methods are laborious and time consuming; thus, 50% of the laboratories use alternative methods for the detection of Salmonella and L. monocytogenes. More and more laboratories use ready-to-use media and although the percentage is variable according to the microflora, we can consider that, today, 50-60% of the laboratories participating to the proficiency program only use ready-to-use media. The internal quality assurance programs lead also to an increasing use of media quality controls. The impact of analytical methods on bacterial counts was assessed by grouping together the results obtained by participating laboratories during the 10 last testing schemes from 1999 to 2003. The identified significant factors influencing enumeration results are variable from one microflora to another. Some of them significantly influence many microflora: the plating method (spiral plating or not) is influential for aerobic micro-organisms, Enterobacteriaceae, coliforms, and staphylococci, the type of culture medium and the medium manufacturer is influential for aerobic micro-organisms, Enterobacteriaceae, coliforms, E. coli, anaerobic sulfito-reducing bacteria, staphylococci, and L. monocytogenes. Others are specific of some micro-organisms: the resuscitation broth for L. monocytogenes, the mode of medium preparation for staphylococci and the incubation temperature for C. perfringens. These effects lead generally to small differences of about 0.1 log10 cfu g(-1), except for the enumeration of anaerobic sulfito-reducing bacteria, where the difference reaches 0.7 log10 cfu g(-1). These results, although difficult to extrapolate to all actual situations, which associate numerous food constituents and physiological states of bacteria to detect or numerate, allow nevertheless the quantification of interlaboratory variations linked to the methods in use. The analysis of bacterial counts obtained by the laboratories participating to the RAEMA proficiency testing program allowed also to validate a formula to calculate the repeatability of bacterial counts and to estimate the between-laboratory uncertainties for the majority of micro-organisms enumerated in food microbiology. The repeatability uncertainty is only indirectly affected by the method in use but depends essentially on the number of counted colonies. On the other hand, the between-laboratory uncertainty varies with the enumeration method in use, this variability is relatively small for the enumerations calling for methods without colony confirmation, i.e. for the enumeration of aerobic micro-organisms, Enterobacteriaceae, 'total' and thermotolerant coliforms, beta-glucuronidase-positive E. coli and coagulase-positive staphylococci with the technique using the rabbit-plasma fibrinogen agar. For these methods, the average between-laboratory standard deviation is 0.17 log10 cfu g(-1). The between-laboratory uncertainty is, on the contrary, larger for more complex techniques. For the enumeration of coagulase-positive staphylococci with the Baird-Parker agar, the between-laboratory standard deviation is equal to 0.23 log10 cfu g(-1), it is equal to 0.28 log10 cfu g(-1) for the enumeration of L. monocytogenes, to 0.34 log10 cfu g(-1) for the enumeration of C. perfringens, and to 0.47 log10 cfu g(-1) for the enumeration of anaerobic sulfito-reducing bacteria.     

Manual Therapy Facilitates Homeostatic Adaptation to Bone Microstructural Declines Induced by a Rat Model of Repetitive Forceful Task

The effectiveness of manual therapy in reducing the catabolic effects of performing repetitive intensive force tasks on bones has not been reported. We examined if manual therapy could reduce radial bone microstructural declines in adult female Sprague–Dawley rats performing a 12-week high-repetition and high-force task, with or without simultaneous manual therapy to forelimbs. Additional rats were provided 6 weeks of rest after task cessation, with or without manual therapy. The control rats were untreated or received manual therapy for 12 weeks. The untreated TASK rats showed increased catabolic indices in the radius (decreased trabecular bone volume and numbers, increased osteoclasts in these trabeculae, and mid-diaphyseal cortical bone thinning) and increased serum CTX-1, TNF-α, and muscle macrophages. In contrast, the TASK rats receiving manual therapy showed increased radial bone anabolism (increased trabecular bone volume and osteoblast numbers, decreased osteoclast numbers, and increased mid-diaphyseal total area and periosteal perimeter) and increased serum TNF-α and muscle macrophages. Rest, with or without manual therapy, improved the trabecular thickness and mid-diaphyseal cortical bone attributes but not the mineral density. Thus, preventive manual therapy reduced the net radial bone catabolism by increasing osteogenesis, while rest, with or without manual therapy, was less effective.     

IL-17A in Human Liver: Significant Source of Inflammation and Trigger of Liver Fibrosis Initiation

IL-17A is considered to guide liver inflammation and fibrosis. From twenty-two human liver samples of different fibrosis stages (F0 to F4), IL-17A, IL-22, and TGFβ1 protein expression in liver tissue lysates were analyzed. Ten paired samples of liver tissue (F0–F1 stage) and blood from the same patient were used to analyze intrahepatic and blood T-lymphoid IL-17A⁺ cells by flow cytometry. The analyses have been performed regardless of pathology, considering the stage of fibrosis. Human liver tissue was used for the primary human liver slice cultures, followed by subsequent cytokine stimulation and fibrotic markers’ analysis by ELISA. IL-17A production in human liver tissue was significantly higher in the early fibrotic stage compared with the advanced stage. Th17 T cells and, to a lesser extent, MAIT cells were the main sources of IL-17A in both compartments, the liver and the blood. Moreover, the presence of liver Th17IL-17A⁺INFγ⁺ cells was detected in the liver. IL-17A stimulation of human liver slice culture increased the expression of profibrotic and pro-inflammatory markers. IL-17A, secreted by Th17 and MAIT cells in the liver, triggered fibrosis by inducing the expression of IL-6 and profibrotic markers and could be a target for antifibrotic treatment. Further amplitude studies are needed to confirm the current results.     

One-Piece Stainless-Steel 3D Printed Minichannel Evaporators using Flow Boiling Carbon Dioxide

New concepts are required for high-performance minichannel evaporators with low mass and reduced size involved in the cooling of cylindrical or conical surfaces. The development of one-piece stainless-steel evaporators using flow boiling CO₂ for the cooling of conical copper test specimens heated by a foil heater element is presented. The specimens mimic a mobile cooling device used in high-energy and particle physics. The stainless-steel evaporators were manufactured with a state-of-the-art 3D stainless-steel printer via selective laser melting. The computer-aided design and the construction of this new type of evaporators are described. A dedicated two-phase accumulator controlled loop filled with liquid CO₂ was developed, it allowed for operating four parallel connected evaporators. Cooling efficiency and manufacture reproducibility were experimentally investigated by applying different thermal loads and refrigerant mass flows.     

Investigation of microstructure-property relantionships of magnesia-hercynite refractory composites by a refined digital image correlation technique

Industrial magnesia-spinel bricks destined for thermal shock applications often show more flexibility and improved crack growth resistance. Components from the spinel structure group are usually added to promote microcracking coming from thermal expansion mismatch. This leads to the development of toughening mechanisms that are very effective in improving the crack propagation resistance.Magnesia-hercynite composites were investigated in order to highlight their fracture process, with regard to their microstructure, by using Digital Image Correlation (DIC). The direct measurement of displacement fields between digital images of the reference state and the deformed one has provided valuable information on material deformation during loading. The aim of this work was to investigate the fracture behaviour of refractories through the coupling of the Wedge Splitting Test (WST) and DIC. By using a refined DIC process transformation taking into account a discontinuity of displacement, called 2P-DIC, a more effective characterisation of the fracture behaviour was achieved.