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Background: The association between microbes and cancer has been reported repeatedly; however, it is not clear if molecular tumour properties are connected to specific microbial colonisation patterns. This is due mainly to the current technical and analytical strategy limitations to characterise tumour-associated bacteria. Methods: Here, we propose an approach to detect bacterial signals in human RNA sequencing data and associate them with the clinical and molecular properties of the tumours. The method was tested on public datasets from The Cancer Genome Atlas, and its accuracy was assessed on a new cohort of colorectal cancer patients. Results: Our analysis shows that intratumoural microbiome composition is correlated with survival, anatomic location, microsatellite instability, consensus molecular subtype and immune cell infiltration in colon tumours. In particular, we find Faecalibacterium prausnitzii, Coprococcus comes, Bacteroides spp., Fusobacterium spp. and Clostridium spp. to be strongly associated with tumour properties. Conclusions: We implemented an approach to concurrently analyse clinical and molecular properties of the tumour as well as the composition of the associated microbiome. Our results may improve patient stratification and pave the path for mechanistic studies on microbiota-tumour crosstalk. [ABSTRACT FROM AUTHOR]

Polyclonal antibodies against abaca bunchy top virus (ABTV) and banana bunchy top virus (BBTV) proteins are necessary for immuno-based detection of these two viruses in abaca (Musa textilis Nee). In this study, recombinant bunchy top viral coat proteins fused with a 6xHis tag at the N-terminus were expressed in E. coli BL21StarTM(DE3)pLysS strain and purified under denaturing conditions. Purified recombinant ABTV and BBTV coat proteins were used as antigens for the production of rabbit polyclonal antibodies. IgG was purified and evaluated by Direct Antigen Coating (DAC)-ELISA and further optimized by testing primary to secondary antibody dilution combinations. Analysis of ABTV and BBTV-infected abaca samples using the optimized DAC-ELISA assay showed that the anti-ABTV CP IgG can react to BBTV and that anti-BBTV CP IgG can react to ABTV, hence, a cross-reaction. The study demonstrates the advantage of using recombinant DNA technology for mass production of antigens for antibody production. Although specificity of the polyclonal antibodies may have been compromised when renatured recombinant proteins were used as immunogens, the ability of the purified IgGs to detect positive abaca samples reveals that the DAC-ELISA can be routinely used for screening disease-free abaca planting materials. [ABSTRACT FROM AUTHOR]

The nonlinear dynamics of a buoyant air flow in the gap formed by a horizontal cylindrical heat source and a concentric isothermally cooled square enclosure have been recently studied, in the limits of a two-dimensional approximation, for different values of the system aspect ratio, defined as the ratio between the cavity side length and the minimum gap width. Accurate analyses have revealed that, for low values of the aspect ratio, the dominant pattern is the swaying motion of a buoyant plume, which undergoes a period-doubling cascade for increasing values of the Rayleigh number. On the other hand, a substantially different behaviour has been preliminarily observed for higher values of the aspect ratio, since, in a thinner gap, the flow exhibits Rayleigh-Bénard-like cellular patterns above the cylinder. The aim of this communication is to describe the peculiar route to chaos which has been detected for this second type of geometry. The scenario consists in the progressive winding of a periodic limit cycle on an attractor whose topology resembles that of a French horn, which is a typical signature of the codimension-2 Shilnikov bifurcation from periodic dynamics to chaos. A similar feature, known as the blue-sky catastrophe, has never been reported so far for confined convection of pure fluids. [ABSTRACT FROM AUTHOR]

This work represents the second part of a twofold study aiming at a detailed characterisation of the low order dynamics of a buoyant plume arising from an enclosed horizontal cylindrical heat source, for which chaos unfolds through a period doubling cascade preluded by a window of quasiperiodicity. In part I, this behaviour has been found to be related to the inherent bimodal nature of the flow, and an analytical characterisation of the asymptotic flows in the vicinity of the bifurcation points has been carried out. In this second part, the thermo-fluid dynamic origin of this bimodal flow is investigated. A novel approach is proposed based on the observation of the existing correspondences between the recurrent formation of cellular flow structures, and the global structure of the system dynamics, as described by the attractor in an appropriate state space. In particular, the two modes are shown to correspond to the existence of two alternate and distinct sequences of flow patterns, and the locking between them corresponds to the synchronisation of analogous events in the evolution of the flow structures. Moreover, reported results show that, within the same framework, the period doubling cascade generated by the extinction of the quasiperiodic flow can be seen as a consequence of the modulation of the cellular flow structures. In light of the remarkable similarities with experimental evidences of other buoyancy-driven flows, the proposed approach may represent a useful paradigm for the analysis of transitional, confined convection problems. [ABSTRACT FROM AUTHOR]

The series of bifurcations leading a confined thermal plume from stationary behaviour to deterministic chaos has been recently reported for the case of a horizontal cylindrical heat source within an air-filled, isothermally cooled square cavity. A refined sampling of the bifurcation parameter range revealed that, in the limit of the 2D approximation, transition unfolds through a period doubling cascade; however, a peculiarity of the observed scenario resides in the occurrence of a window of quasiperiodic behaviour at the beginning of the period doubling cascade. In particular, the quasiperiodic range splits the regions of stability of the period-1 and period-2 limit cycles, hinting at the bimodal nature of the subsequent subharmonic cascade. Within this frame, new analyses are presented here, to achieve of a deeper insight on the birth, evolution and disappearance of quasiperiodic flow. Particular attention has been given to the study of the transient dynamics leading to the asymptotic flows, especially in the vicinity of the bifurcation points. [ABSTRACT FROM AUTHOR]

Long road and railway tunnels necessitate of a fine-tuned control of the ventilation system to be activated, for both safety and air quality maintenance reasons. This, in turn, requires that the main fluid-dynamic parameters of the tunnel are known with sufficient accuracy, so that the system behaviour can be predicted with reasonable confidence under standard and emergency operative conditions. As a first step in the modelling of the complex system embodying the 11,611 m long Mont Blanc road tunnel, and its ventilation facilities, a movable 5-point survey rake was designed and built-up, for detecting the distribution of the axial velocity on the tunnel cross-section. Two extensive experimental campaigns were carried out, where the airflow-rates were either measured at different stations along the tunnel length (C1), or at a fixed location, under purely axial main-flow conditions and varying the number of the activated axial fan pairs (C2). A simplified dynamic model of the tunnel was developed, and the airflow data from the experiments were used for the model fine-tuning, additional CFD analyses having provided extra information on concentrated pressure losses connected with air inlet and discharge through the tunnel ends. The Mont Blanc tunnel was finally characterised in terms of friction factors and jet-fans installation efficiency. [ABSTRACT FROM AUTHOR]

• Numerical simulations of a Heavy Liquid Metal cooled bundle. • Direct Numerical Simulation of an experimental test. • Detailed comparison of DNS and RANS approaches to the same test case. • General comparison of numerical results and experimental data. One of the requirements for achieving high levels of safety in fourth generation nuclear power plants, is that core thermal-hydraulics can be simulated numerically at a good level of accuracy. To this aim, detailed validation of turbulent heat transfer models needs to be carried out and discussed, in relevant flow and heat transfer configurations, and for low Prandtl-number fluids. The focus of this research is the turbulent, fully developed convection in a heated rod bundle with a triangular arrangement, and a pitch-to-diameter ratio P / D = 1.4. Statistics derived from a set of Direct Numerical Simulations (DNS) at the moderate Reynolds number of Re = 8290 are compared to Reynolds Averaged Navier-Stokes (RANS) solutions where the closure is provided by the two-equation model SST k - ω and by the Reynolds-Stress Model. Comparisons are drawn for forced flow and in mixed convection conditions (Ri ≈ 0.25). Global quantities extracted from experiments performed in very similar conditions are also compared against the numerical results. Profiles of the turbulent Prandtl number about the unit flow cell are also displayed and discussed. This work clarifies through detailed comparison that if, on the one hand, only the Reynolds-Stress model is able to reasonably capture important flow features like secondary flow components, on the other hand also the SST k - ω two-equation model considered is acceptably accurate in predicting the integral quantities of interest. [ABSTRACT FROM AUTHOR]

• DNS data of a low-Pr flow in a loosely-spaced triangular rod bundle are presented. • Forced and mixed convection conditions are analyzed. • Aiding buoyancy determines an impairment of overall heat transfer. • Presented data might be used as benchmark for advanced turbulence modeling. In this work, reference data obtained by means of Direct Numerical Simulations of fully-developed flow and heat transfer around a vertical rod bundle are presented. Finite-Volume computations are performed by an original discretization technique based on the representation of arbitrarily-shaped cylindrical boundaries on a non-uniform Cartesian grid. A periodic domain consisting of four subchannels of a triangular lattice of rods with a pitch-to-diameter ratio P / D = 1.4 is considered as the reference geometry. A Prandtl number Pr = 0.031 is chosen to represent Liquid Lead-Bismuth Eutectic (LBE) as the working fluid. A single friction Reynolds number value is simulated, namely Re τ = 550. Both forced and mixed convection regimes are investigated, buoyancy effects being introduced by imposing a Rayleigh number Ra = 5 × 10 5 , corresponding to a Richardson number Ri = 0.22. Instantaneous snapshots and relevant statistics of the velocity and thermal fields are reported and discussed for the considered cases, focusing on the effect of aiding buoyancy on turbulent flow and heat transfer. Integral results are also compared against available literature data. [ABSTRACT FROM AUTHOR]

• The three jets undergo intense mixing within the entrance region (x < 10H). • Far from the inlet a single, non-buoyant stream is observed. • It displays typical self-preserving characteristics of purely mechanical jets. • Despite the low-Prandtl number heat transfer is mainly due to turbulent transport. Mixing of buoyant streams is a phenomenon of relevance in many practical cases like pollutant emission in the atmosphere, discharges from marine outfalls and cooling of fuel rods in nuclear reactors to name a few. A canonical configuration for this class of flows consists in three buoyant jets at different temperatures vertically entering a pool from the bottom. This work reports a Direct Numerical Simulation study performed on the triple jet configuration. The Reynolds number based on the average jet centerline velocity and jet width is set to Re = 5000 and mixed convection regime is established at a Richardson number, Ri = 0.25. In order to represent flows occurring inside liquid metal fast reactors, the selected Prandtl number is Pr = 0.031. Statistics computed show that in the first stages of development, the three jets undergo a strong interaction. In that same region the shedding of large-scale vortices is originated accompanied by low-frequency undulations. Further from the inlet, the three jets are observed to coalesce in a single, isothermal stream. The analysis of momentum fluxes clarifies the mutual entrainment mechanism behind coalescence, which is commonly known as Coandă effect. At distances larger than ten times the jet width the self-similar characteristics of single and isothermal planar jets are recovered. The flow configuration presented includes several peculiar features, namely buoyancy effects at low Prandtl number, interaction between jets and the presence of multiple shear layers. This leads to an irregular behaviour of the turbulent diffusivity of momentum and heat as well as the misalignment between the temperature gradient and turbulent heat flux. Therefore the flow can be considered very complex and might constitute a demanding test bench for the development and validation of turbulence models. [ABSTRACT FROM AUTHOR]

The present paper reports a numerical study of the aerodynamic properties for a novel disc-shaped airship. Different configurations are considered, some of which present a circular opening connecting the bottom and top surface of the airship. The aim of the study is to understand the flow dynamics, in order to define the aerodynamic efficiency and the stability properties of the flying vehicle. Such information is crucial for the design of the propulsion system and of the mission profile of these innovative airships. Results show that, in general, disc-shaped airships are characterized by large values of drag and small levels of lift. Interestingly, it appears that lift keeps increasing up to very high angles of attack. This feature is found to be related with strong tip effects, which induce a significant flow of air from the high-pressure region at the bottom surface to the low-pressure region at the top surface. This air flow energizes the upper boundary layer, thus contrasting the flow separation on the top surface. This phenomenon is found to be useful for the stability properties of the airship: in fact, it shifts the center of pressure closer to the geometrical center of the airship, hence implying a reduction of the aerodynamic moment. The role of openings is also addressed and found to positively contribute to the stability properties of the airship, by further reducing the levels of aerodynamic moment. [ABSTRACT FROM AUTHOR]

Selective seed consumption by harvester ants may be affected by several seed attributes, amongst which seed size and environmental availability play a prominent role. In the present study, we considered the effects of seed size and seed availability on the coexistence and diet preference of twoMessorspecies (Messor wasmanniandMessor minor).M. wasmannicolonies collected the most abundant resource in the environment, grass seeds (Poaceae), according to their availability whilstM. minorshowed a nonselective process. In addition, the two ant species showed a different seed size preference, withM. wasmanniadopting a selective strategy andM. minora generalist strategy. However, competition for foraging resources between the two ant species (assessed by null model algorithms) seems not to affect their foraging behaviour. The lack of a competitive structure within the ant assemblage suggests, in fact, that resources are not a limiting factor for species coexistence. [ABSTRACT FROM AUTHOR]

The transition mechanisms of natural convection flows ensuing in a fluid layer between two differentially heated vertical plates at Prandtl number Pr = 0.71 are investigated by means of Direct Numerical Simulations. In accordance with several previous studies, results show a first bifurcation from the so-called laminar conduction regime to steady convection at Rayleigh number Ra = 5708. On the other hand, the subsequent transition to turbulence appears to be accompanied by a great sensitivity to some fundamental numerical choices such as domain size, accuracy, resolution and amplitude of the imposed perturbations. Results reveal the occurrence of a bifurcation branch which leads the system to chaos via a second bifurcation to a steady-state, a Hopf bifurcation and, seemingly, a period-doubling cascade. Although the described scenario compares well with previous findings, some doubts persist upon the possible pitfalls in the use of numerical simulation for the study of transition in this kind of systems. Indeed, several numerical aspects are found to become of crucial importance for the prediction of the dynamical behaviour and heat transfer rate of the system. [ABSTRACT FROM AUTHOR]

Direct numerical simulation data of the separating and reattaching flow around a blunt bluff body are used for the assessment of the combined role played by the numerical resolution and subgrid turbulence closure in large eddy simulation. The ability of the large-scale resolved field to capture the main flow features is first analyzed. The behavior of the intensity of the resolved fluctuations as a function of the filter lengths reveals a higher sensitivity of the resolved flow on a reduction of resolution in the streamwise direction rather than in the spanwise one. On the other hand, the analysis of the subgrid stresses shows the presence of two challenging phenomena, a reversal of flow of energy from the fluctuating to the mean field in the leading-edge shear layer and a backward energy transfer from small to large scale within the main recirculating bubble. These two phenomena challenge for subgrid closures that should be able to reproduce a flow of energy from the space of small unknown subgrid scales to drive the resolved mean and fluctuating motion. In particular, it is found that the formalism of subgrid viscosity models allows us to capture neither the negative turbulence production of the leading-edge shear layer nor the backward energy transfer within the main flow recirculation. On the other hand, the subgrid similarity models are able to capture both these two phenomena but, from a quantitative point of view, the intensity of the reproduced stresses is very weak. In conclusion, the need of subgrid closures based on a mixed modeling approach for the solution of the flow is envisaged. [ABSTRACT FROM AUTHOR]

Abstract The analysis of Direct Numerical Simulation data of the separating and reattaching flow over a blunt bluff body with sharp edges, reveals the presence of negative turbulence production mechanisms in the leading-edge shear layer. Contrary to what is commonly observed in fully developed turbulent flows, this phenomenon represents flow reversal of energy from the fluctuating field to the mean flow. The detailed study of the data reveals that at the origin of such mechanisms is a statistically positive relation between Reynolds shear stresses and vertical shear. We argue that such a positive relation is a result of large-scale interactions of the fluctuating field with the streamwise inhomogeneity. The analysis of time cospectra confirms this picture by highlighting the presence of a net separation of scales consisting in a range of small scales positively contributing to turbulence production in opposition to a range of large scales giving to a reversal of flow energy from the fluctuating to the mean field. By means of a reduced description of the interactions of the fluctuating field with the mean field given by a generalized mixing length hypothesis, we finally also provide conceptual arguments for the modelling of turbulence production in the transitional shear layer. A model for the mixing length is also proposed which is found to work nicely in shear flows. The simplicity of the formulation supports its use especially in experiments of wall-bounded turbulence. Highlights • We provide evidence of negative turbulence production phenomena in the leading-edge shear layer of separating flows. • The nature of the reversal of flow energy is investigated. • The presence of large-scale interaction phenomena of the fluctuating field with the streamwise inhomogeneity is found at the basis of negative production. • Based on conceptual arguments we provide some modelling insights of negative turbulence production. • A simplified model for the shear scale is also provided. [ABSTRACT FROM AUTHOR]

In this work, four key design parameters of cycloidal rotors, namely the airfoil section, number of blades, chord-to-radius ratio, and pitching axis location, are addressed. The four parameters, which have a strong effect on rotor aerodynamic efficiency, are analyzed with an analytical model and a numerical approach. The numerical method, which is based on a finite-volume discretization of two-dimensional unsteady Reynolds averaged Navier-Stokes equations on a multiple sliding mesh, is proposed and validated against experimental data. A parametric analysis is then carried out considering a large-scale cyclogyro, suitable for payloads above 100 kg, in hovering conditions. Results demonstrate that the airfoil thickness significantly affects the rotor performance; such a result is partly in contrast with previous findings for small-scale and microscale configurations. Moreover, it will be shown that increasing the number of blades could result in a decrease of the rotor efficiency. The effect of chord-to-radius will demonstrate that values of around 0.5 result in higher efficiency. Finally it is found out that for these large systems, in contrast with microscale cyclogyros, the generated thrust increases as the pitching axis is located away from the leading edge, up to 35% of chord length. Furthermore, the shortcomings of using simplified analytical tools in the prediction of thrust and power in nonideal flow conditions are discussed. [ABSTRACT FROM AUTHOR]

Accelerator Driven Systems (ADS) are extensively investigated for the transmutation of high-level nuclear waste within many worldwide research programs. The first advanced design of an ADS system is currently developed in SCK•CEN, Mol, Belgium: the Multi-purpose hYbrid Research Reactor for High-tech Applications (MYRRHA). Many European research programs support the design of MYRRHA. In the framework of the Euratom project ‘Thermal Hydraulics of Innovative nuclear Systems (THINS)’ a liquid-metal free-surface experiment is performed at the Karlsruhe Liquid Metal Laboratory (KALLA) of Karlsruhe Institute of Technology (KIT). The experiment investigates a full-scale model of the concentric free-surface spallation target of MYRRHA using Lead Bismuth Eutectic (LBE) as coolant. In parallel, numerical free surface models are developed and tested which are reviewed in the article. A volume-of-fluid method, a moving mesh model, a free surface model combining the Level-Set method with Large-Eddy Simulation model and a smoothed-particle hydrodynamics approach are investigated. Verification of the tested models is based on the experimental results obtained within the THINS project and on previous water experiments performed at the University Catholic de Louvain (UCL) within the Euratom project ‘EUROpean Research Programme for the TRANSmutation of High Level Nuclear Waste in Accelerator Driven System (EUROTRANS)’. The design of the target enables a high fluid velocity and a stable surface at the beam entry. The purpose of this paper is to present an overview of both experimental and numerical results obtained for free surface target characterization. Without entering in technical details, the status, the major achievements and lessons for the future with respect to model development are described as well as some applications, which were carried out within the work package ‘multi-phase flow’ of THINS. [ABSTRACT FROM AUTHOR]

• A wide range of reference database has been generated low-Prandtl number flows. • This includes 3-experiment and numerical data of 7 different flow configurations. • This database has been used to assess/validate different turbulent heat flux models. • Some current challenges and perspectives of these models are also highlighted. This article reports the experimental and DNS database that has been generated, within the framework of the EU SESAME and MYRTE projects, for various low-Prandtl flow configurations in different flow regimes. This includes three experiments: confined and unconfined backward facing steps with low-Prandtl fluids, and a forced convection planar jet case with two different Prandtl fluids. In terms of numerical data, seven different flow configurations are considered: a wall-bounded mixed convection flow at low-Prandtl number with varying Richardson number (Ri) values; a wall-bounded mixed and forced convection flow in a bare rod bundle configuration; a forced convection confined backward facing step (BFS) with conjugate heat transfer; a forced convection impinging jet for three different Prandtl fluids corresponding to two different Reynolds numbers of the fully developed planar turbulent jet; a mixed-convection cold-hot–cold triple jet configuration corresponding to Ri = 0.25; an unconfined free shear layer for three different Prandtl fluids; and a forced convection infinite wire-wrapped fuel assembly. This wide range of reference data is used to evaluate, validate and/or further develop different turbulent heat flux modelling approaches, namely simple gradient diffusion hypothesis (SGDH) based on constant and variable turbulent Prandtl number; explicit and implicit algebraic heat flux models; and a second order turbulent heat flux model. Lastly, this article will highlight the current challenges and perspectives of the available turbulence models, in different codes, for the accurate prediction of flow and heat transfer in low-Prandtl fluids. [ABSTRACT FROM AUTHOR]

• The reference numerical database generated within the SESAME and MYRTE projects. • This includes various liquid metal flow configurations in different flow regimes. • In total, seven different flow configurations are considered. • This database will serve the further development of turbulent heat transfer model. Turbulent heat transfer is a complex phenomenon that has challenged turbulence modellers over various decades. In this regard, in the recent past, several attempts have been made for the assessment and further development/calibration of the available turbulent heat flux modelling approaches. One of the main hampering factors with respect to the further assessment of these modelling approaches is the lack of reference data. In the framework of the EU SESAME and MYRTE projects, an extensive effort has been put forward to generate a wide range of reference data, both experimental and numerical, to fill this gap. In that context, this article reports the numerical database that has been generated within these projects for various liquid metal flow configurations in different flow regimes. These high fidelity numerical data include seven different flow configurations: a wall-bounded mixed convection flow at low Prandtl number with varying Richardson number ( R i ) values; a wall-bounded mixed and forced convection flow in a bare rod bundle configuration; a forced convection confined backward facing step (BFS) with conjugate heat transfer; a forced convection impinging jet for three different Prandtl fluids corresponding to two different Reynolds numbers of the fully developed planar turbulent jets; a mixed-convection cold-hot-cold triple jet configuration corresponding to R i = 0.25 ; an unconfined free shear layer for three different Prandtl fluids; and a forced convection infinite wire-wrapped fuel assembly. These high-fidelity numerical databases will serve the further development of turbulent heat transfer models by providing unique, new and detailed data for the thermal-hydraulic behaviour of liquid metals in various flow configurations. [ABSTRACT FROM AUTHOR]