Development of a high-order parallel solver for direct and large eddy simulations of turbulent flows

Turbulence is inherent in fluid dynamics, in that laminar flows are rather the exception than the rule, hence the longstanding interest in the subject, both within the academic community and the industrial R&D laboratories. Since 1883, much progress has been made, and statistics applied to turbulence have provided understanding of the scaling laws which are peculiar to several model flows, whereas experiments have given insight on the structure of real-world flows, but, soon enough, numerical approaches to the matter have become the most promising ones, since they lay the ground for the solution of high Reynolds number unsteady Navier-Stokes equations by means of computer systems. Nevertheless, despite the exponential rise in computational capability over the last few decades, the more computer technology advances, the higher the Reynolds number sought for test-cases of industrial interest: there is a natural tendency to perform simulations as large as possible, a habit that leaves no room for wasting resources. Indeed, as the scale separation grows with Re, the reduction of wall clock times for a high-fidelity solution of desired accuracy becomes increasingly important. To achieve this task, a CFD solver should rely on the use of appropriate physical models, consistent numerical methods to discretize the equations, accurate non-dissipative numerical schemes, efficient algorithms to solve the numerics, and fast routines implementing those algorithms. Two archetypal approaches to CFD are direct and large-eddy simulation (DNS and LES respectively), which profoundly differ in several aspects but are both “eddy-resolving” methods, meant to resolve the structures of the flow-field with the highest possible accuracy and putting in as little spurious dissipation as possible. These two requirements of accurate resolution of scales, and energy conservation, should be addressed by any numerical method, since they are essential to many real-world fluid flows of industrial interest. As a consequence, high order numerical schemes, and compact schemes among them, have received much consideration, since they address both goals, at the cost of a lower ease of application of the boundary condition, and a higher computational cost. The latter problem is tackled with parallel computing, which also allows to take advantage of the currently available computer power at the best possible extent. The research activity conducted by the present author has concerned the development, from scratch, of a three-dimensional, unsteady, incompressible Navier-Stokes parallel solver, which uses an advanced algorithm for the process-wise solution of the linear systems arising from the application of high order compact finite difference schemes, and hinges upon a three-dimensional decomposition of the cartesian computational space. The code is written in modern Fortran 2003 — plus a few features which are unique to the 2008 standard — and is parallelized through the use of MPI 3.1 standard’s advanced routines, as implemented by the OpenMPI library project. The coding was carried out with the objective of creating an original CFD high-order parallel solver which is maintainable and extendable, of course within a well-defined range of possibilities. With this main priority being outlined, particular attention was paid to several key concepts: modularity and readability of the source code and, in turn, its reusability; ease of implementation of virtually any new explicit or implicit finite difference scheme; modern programming style and avoidance of deprecated old legacy Fortran constructs and features, so that the world wide web is a reliable and active means to the quick solution of coding problems arising from the implementation of new modules in the code; last but not least, thorough comments, especially in critical sections of the code, explaining motives and possible expected weak links. Design, production, and documentation of a program from scratch is almost never complete. This is certainly true for the present effort. The method and the code are verified against the full three-dimensional Lid-Driven Cavity and Taylor-Green Vortex flows. The latter test is used also for the assessment of scalability and parallel efficiency

Preliminary results of geological characterization and geochemical monitoring of Sulcis Basin (Sardinia), as a potential CCS site

The Sulcis Basin is an area situated in SW Sardinia (Italy) and is a potential site for the development of CCS in Italy. This paper illustrates the preliminary results of geological characterization of fractured carbonate reservoir (Miliolitico Fm.) and the sealing sequence, composed by clay, marl and volcanic rocks, with a total thickness of more than 900 m. To characterize the reservoircaprock system an extensive structural-geological survey at the outcrop was conducted. It was also performed a study of the geochemical monitoring, to define the baseline conditions, measuring CO2 concentrations and flux in the study site

Differential redox state contributes to sex disparities in the response to influenza virus infection in male and female mice

Influenza virus replicates intracellularly exploiting several pathways involved in the regulation of host responses. The outcome and the severity of the infection are thus strongly conditioned by multiple host factors, including age, sex, metabolic, and redox conditions of the target cells. Hormones are also important determinants of host immune responses to influenza and are recently proposed in the prophylaxis and treatment. This study shows that female mice are less susceptible than males to mouse-adapted influenza virus (A/PR8/H1N1). Compared with males, PR8-infected females display higher survival rate (+36%), milder clinical disease, and less weight loss. They also have milder histopathological signs, especially free alveolar area is higher than that in males, even if pro-inflammatory cytokine production shows slight differences between sexes; hormone levels, moreover, do not vary significantly with infection in our model. Importantly, viral loads (both in terms of viral M1 RNA copies and tissue culture infectious dose 50%) are lower in PR8-infected females. An analysis of the mechanisms contributing to sex disparities observed during infection reveals that the female animals have higher total antioxidant power in serum and their lungs are characterized by increase in (i) the content and biosynthesis of glutathione, (ii) the expression and activity of antioxidant enzymes (peroxiredoxin 1, catalase, and glutathione peroxidase), and (iii) the expression of the anti-apoptotic protein Bcl-2. By contrast, infected males are characterized by high expression of NADPH oxidase 4 oxidase and phosphorylation of p38 MAPK, both enzymes promoting viral replication. All these factors are critical for cell homeostasis and susceptibility to infection. Reappraisal of the importance of the host cell redox state and sex-related effects may be useful in the attempt to develop more tailored therapeutic interventions in the fight against influenza

Hyperbaric exposure and oxidative Stress in occupational activities (HEOxS): the study protocol

Background: Hyperbaric exposure (HE) is proven to be a stressor to several mechanisms in living cells. Even if after homeostasis restoration, harmful effects are expected, in particular a presence of free radicals. These latter are the stimulus to negative phenomenon as inflammation or cancer. In Italy, with 7500 km of sea shores, a large quantity of workers is exposed to HE during occupational activities. A deep knowledge of HE and bodily effects is not well defined; hence a multidisciplinary assessment of risk is needed. To detect one or more indicators of HE a research group is organised, under the INAIL sponsorship. The research project focused on the oxidative stress (OxS) and this paper details on the possible protocol to estimate, with a large amount of techniques on several human liquids, the relationship between OxS and HE. Specific attention will be paid to identify confounding factors and their influence. Methods: Blood and urine will be sampled. Several lab techniques will be performed on samples, both targeted, to measure the level of well-known biomarkers, and untargeted. Regard the formers: products of oxidation of DNA and RNA in urine; inflammation and temperature cytokines and protein carbonyles in blood. Untargeted evaluation will be performed for a metabolomics analysis in urine. Confounding factors: temperature, body fat, fitness, allergies and dietary habits. These factors will be assessed, directly or indirectly, prior and after HE. The final scope of the project is to determine one or more indicators that relates to HE in hits twofold nature: depth and duration. Conclusion: The relationship between OxS and HE is not deeply investigated and literature proposes diverging results. The project aims to define the time dependence of biomarkers related to OxS, to rise knowledge in risk assessment in workers exposed to HE

Study of the neutron-rich region in the vicinity of 208Pb via multinucleon transfer reactions

The multinucleon transfer reaction mechanism was employed to populate isotopes around the doubly- magic 208 Pb nucleus. We used an unstable 94 Rb beam on 208 Pb targets of different thickness. Transfer channels were studied via the fragment-γ and γ-γ coincidences, by using MINIBALL γ spectrometer coupled to a particle detector. Gamma transitions associated to the different Pb isotopes, populated by the neutron transfers, are discussed in terms of excitation energy and spin. Fragment angular distributions were extracted, andcompared with the reaction model

Unilateral Pelvic Lymph Node Dissection in Prostate Cancer Patients Diagnosed in the Era of Magnetic Resonance Imaging-targeted Biopsy: A Study That Challenges the Dogma

PURPOSE Bilateral extended pelvic lymph node dissection at the time of radical prostatectomy is the current standard of care if pelvic lymph node dissection is indicated; often, however, pelvic lymph node dissection is performed in pN0 disease. With the more accurate staging achieved with magnetic resonance imaging-targeted biopsies for prostate cancer diagnosis, the indication for bilateral extended pelvic lymph node dissection may be revised. We aimed to assess the feasibility of unilateral extended pelvic lymph node dissection in the era of modern prostate cancer imaging. MATERIALS AND METHODS We analyzed a multi-institutional data set of men with cN0 disease diagnosed by magnetic resonance imaging-targeted biopsy who underwent prostatectomy and bilateral extended pelvic lymph node dissection. The outcome of the study was lymph node invasion contralateral to the prostatic lobe with worse disease features, ie, dominant lobe. Logistic regression to predict lymph node invasion contralateral to the dominant lobe was generated and internally validated. RESULTS Overall, data from 2,253 patients were considered. Lymph node invasion was documented in 302 (13%) patients; 83 (4%) patients had lymph node invasion contralateral to the dominant prostatic lobe. A model including prostate-specific antigen, maximum diameter of the index lesion, seminal vesicle invasion on magnetic resonance imaging, International Society of Urological Pathology grade in the nondominant side, and percentage of positive cores in the nondominant side achieved an area under the curve of 84% after internal validation. With a cutoff of contralateral lymph node invasion of 1%, 602 (27%) contralateral pelvic lymph node dissections would be omitted with only 1 (1.2%) lymph node invasion missed. CONCLUSIONS Pelvic lymph node dissection could be omitted contralateral to the prostate lobe with worse disease features in selected patients. We propose a model that can help avoid contralateral pelvic lymph node dissection in almost one-third of cases

The eEF1γ Subunit Contacts RNA Polymerase II and Binds Vimentin Promoter Region

Here, we show that the eukaryotic translation elongation factor 1 gamma (eEF1γ) physically interacts with the RNA polymerase II (pol II) core subunit 3 (RPB3), both in isolation and in the context of the holo-enzyme. Importantly, eEF1γ has been recently shown to bind Vimentin mRNA. By chromatin immunoprecipitation experiments, we demonstrate, for the first time, that eEF1γ is also physically present on the genomic locus corresponding to the promoter region of human Vimentin gene. The eEF1γ depletion causes the Vimentin protein to be incorrectly compartmentalised and to severely compromise cellular shape and mitochondria localisation. We demonstrate that eEF1γ partially colocalises with the mitochondrial marker Tom20 and that eEF1γ depletion increases mitochondrial superoxide generation as well as the total levels of carbonylated proteins. Finally, we hypothesise that eEF1γ, in addition to its role in translation elongation complex, is involved in regulating Vimentin gene by contacting both pol II and the Vimentin promoter region and then shuttling/nursing the Vimentin mRNA from its gene locus to its appropriate cellular compartment for translation

Unilateral Pelvic Lymph Node Dissection in Prostate Cancer Patients Diagnosed in the Era of Magnetic Resonance Imaging-targeted Biopsy: A Study That Challenges the Dogma

PURPOSE: Bilateral extended pelvic lymph node dissection at the time of radical prostatectomy is the current standard of care if pelvic lymph node dissection is indicated; often, however, pelvic lymph node dissection is performed in pN0 disease. With the more accurate staging achieved with magnetic resonance imaging-targeted biopsies for prostate cancer diagnosis, the indication for bilateral extended pelvic lymph node dissection may be revised. We aimed to assess the feasibility of unilateral extended pelvic lymph node dissection in the era of modern prostate cancer imaging. MATERIALS AND METHODS: We analyzed a multi-institutional data set of men with cN0 disease diagnosed by magnetic resonance imaging-targeted biopsy who underwent prostatectomy and bilateral extended pelvic lymph node dissection. The outcome of the study was lymph node invasion contralateral to the prostatic lobe with worse disease features, ie, dominant lobe. Logistic regression to predict lymph node invasion contralateral to the dominant lobe was generated and internally validated. RESULTS: Overall, data from 2,253 patients were considered. Lymph node invasion was documented in 302 (13%) patients; 83 (4%) patients had lymph node invasion contralateral to the dominant prostatic lobe. A model including prostate-specific antigen, maximum diameter of the index lesion, seminal vesicle invasion on magnetic resonance imaging, International Society of Urological Pathology grade in the nondominant side, and percentage of positive cores in the nondominant side achieved an area under the curve of 84% after internal validation. With a cutoff of contralateral lymph node invasion of 1%, 602 (27%) contralateral pelvic lymph node dissections would be omitted with only 1 (1.2%) lymph node invasion missed. CONCLUSIONS: Pelvic lymph node dissection could be omitted contralateral to the prostate lobe with worse disease features in selected patients. We propose a model that can help avoid contralateral pelvic lymph node dissection in almost one-third of cases

The LIFE TRIAD of emergency general surgery

Emergency General Surgery (EGS) was identified as multidisciplinary surgery performed for traumatic and non-traumatic acute conditions during the same admission in the hospital by general emergency surgeons and other specialists. It is the most diffused surgical discipline in the world. To live and grow strong EGS necessitates three fundamental parts: emergency and elective continuous surgical practice, evidence generation through clinical registries and data accrual, and indications and guidelines production: the LIFE TRIAD.Peer reviewe