Exact regularized point particle method for multi-phase flows in the two-way coupling regime

Particulate flows have been largely studied under the simplifying assumptions of one-way coupling regime where the disperse phase do not react-back on the carrier fluid. In the context of turbulent flows, many non trivial phenomena such as small scales particles clustering or preferential spatial accumulation have been explained and understood. A more complete view of multiphase flows can be gained calling into play two-way coupling effects, i.e. by accounting for the inter-phase momentum exchange between the carrier and the suspended phase, certainly relevant at increasing mass loading. In such regime, partially investigated in the past by the so-called Particle In Cell (PIC) method, much is still to be learned about the dynamics of the disperse phase and the ensuing alteration of the carrier flow. In this paper we present a new methodology rigorously designed to capture the inter-phase momentum exchange for particles smaller than the smallest hydrodynamical scale, e.g. the Kolmogorov scale in a turbulent flow. In fact, the momentum coupling mechanism exploits the unsteady Stokes flow around a small rigid sphere where the transient disturbance produced by each particle is evaluated in a closed form. The particles are described as lumped, point masses which would lead to the appearance of singularities. A rigorous regularization procedure is conceived to extract the physically relevant interactions between particles and fluid which avoids any "ah hoc" assumption. The approach is suited for high efficiency implementation on massively parallel machines since the transient disturbance produced by the particles is strongly localized in space around the actual particle position. As will be shown, hundred thousands particles can therefore be handled at an affordable computational cost as demonstrated by a preliminary application to a particle laden turbulent shear flow.Comment: Submitted to Journal of Fluid Mechanics, 56 pages, 15 figure

MSpin‐JCoupling. A modular program for prediction of scalar couplings and fast implementation of Karplus relationships

This is the peer reviewed version of the following article:Navarro-Vázquez, A., Santamaría-Fernández, R., & Sardina, F. (2018). MSpin-JCoupling. A modular program for prediction of scalar couplings and fast implementation of Karplus relationships. Magnetic Resonance In Chemistry, 56(6), 505-512, which has been published in final form at https://doi.org/10.1002/mrc.4667. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived VersionsMSpin‐JCoupling is a modular program for the prediction of scalar couplings using a large variety of Karplus relationships. The program was specially designed for small molecule analysis and can be run in graphical or command‐line mode. The architecture of the program is highly modular, and new equations can be rapidly implemented, through a complete C++ programming interface, and deployed as run‐time loadable pluginsMinisterio de Ciencia e Innovación. Grant Number: PET2008‐074 Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia. Grant Number: Consellería de Educación 2009/071 Spanish Ministerio de Ciencia e Innovación. Grant Number: PET2008‐074 Xunta de Galicia for a Parga Pondal. Grant Number: Consellería de Educación 2009/071S

Whole genome semiconductor based sequencing of farmed European sea bass (Dicentrarchus labrax) Mediterranean genetic stocks using a DNA pooling approach

European sea bass (Dicentrarchus labrax) is an important marine species for commercial and sport fisheries and aquaculture production. Recently, the European sea bass genome has been sequenced and assembled. This resource can open new opportunities to evaluate and monitor variability and identify variants that could contribute to the adaptation to farming conditions. In this work, two DNA pools constructed from cultivated European sea bass were sequenced using a next generation semiconductor sequencing approach based on Ion Proton sequencer. Using the first draft version of the D. labrax genome as reference, sequenced reads obtained a total of about 1.6 million of single nucleotide polymorphisms (SNPs), spread all over the chromosomes. Transition/transversion (Ti/Tv) was equal to 1.28, comparable to what was already reported in Salmon species. A pilot homozygosity analysis across the D. labrax genome using DNA pool sequence datasets indicated that this approach can identify chromosome regions with putative signatures of selection, including genes involved in ion transport and chloride channel functions, amino acid metabolism and circadian clock and related neurological systems. This is the first study that reported genome wide polymorphisms in a fish species obtained with the Ion Proton sequencer. Moreover, this study provided a methodological approach for selective sweep analysis in this species

A One-Step, Versatile Synthesis of Dibenzo [n.2.2] Macrobicyclic Compounds via a Conformation-Directed Macrocyclization Reaction

A series of dibenzo [n.2.2] bicyclic compounds (n = 2–20) were prepared in one step and good yields starting from dimethyl anthracene-9,10-dicarboxylate. Reduction of the aromatic diester using lithium/naphthalene led to a bis-enolate that was cyclized with a variety of bis-electrophiles. The ease of the cyclization is probably due to the puckered conformation of the intermediate formed after the first alkylation step, in which the newly introduced chain that will become the bridge portion occupies a pseudoaxial position, positioning the leaving group close to the enolate nucleophile in the macrocyclization stepThis work was supported by the Ministerio de Economía y Competitividad of Spain (CTQ2011-22436) and Xunta de Galicia (PGIDIT10-PXIB209113PR, 10PXIB209155PR, and 2007/085)S

Garment allergy caused by Disperse Blue 360: A new sensitizer

This is the peer reviewed version of the following article: Pousa-Martínez M, González-Rodríguez C, Rodriguez-Rodriguez M, Sainz-Gaspar L,Sardina FJ, Fernández-Redondo V. Garment allergy caused by Disperse Blue 360: A new sensitizer. Contact Dermatitis. 2018;79:37–38, which has been published in final form at https://doi.org/10.1111/cod.12975. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived VersionsDisperse dyes are some of the most common causes of textile contact dermatitis. Current legislation does not help to identify the colorant used in a garmentS

Numerical simulations of aggregate breakup in bounded and unbounded turbulent flows

Breakup of small aggregates in fully developed turbulence is studied by means of direct numerical simulations in a series of typical bounded and unbounded flow configurations, such as a turbulent channel flow, a developing boundary layer, and homogeneous isotropic turbulence. Aggregate breakup occurs when the local hydrodynamic stress $\sigma\sim \varepsilon^{1/2}$, where $\varepsilon$ is the energy dissipation at the position of the aggregate, overcomes a given threshold $\sigma_\mathrm{cr}$, characteristic for a given type of aggregates. Results show that the breakup rate decreases with increasing threshold. For small thresholds, it develops a universal scaling among the different flows. For high thresholds, the breakup rates show strong differences among the different flow configurations, highlighting the importance of non-universal mean-flow properties. To further assess the effects of flow inhomogeneity and turbulent fluctuations, results are compared with those obtained in a smooth stochastic flow. Furthermore, we discuss limitations and applicability of a set of independent proxies

Applications of Monte Carlo methods to special radiotherapeutic techniques

Monte Carlo (MC) methods are considered one of the most powerful and precise approaches to study and solve medical physics issues. They, indeed, can be applied in all the situations where to use deterministic algorithms is infeasible or impossible. Surprising improvements in computer technology have promoted a wide diffusion of this technique, giving rise to the born of several Monte Carlo codes, such as the GEANT4 toolkit. In this paper we show some of the applications we developed using GEANT4. In particular, the simulation of two different radiotherapy techniques, such as proton/ion therapy and stereotactic radiosurgery will be discussed. In the first case we show the main features of our last public version of the GEANT4 Hadrontherapy program, also discussing the issues related to the nuclear fragmentation. In the second case, we show the procedures followed for the simulation of a Gamma Knife device, in order to validate the Treatment Planning System (TPS) used for the dose computation

PNPLA3 and TLL-1 Polymorphisms as Potential Predictors of Disease Severity in Patients With COVID-19

Albeit the pathogenesis of COVID-19 remains unclear, host’s genetic polymorphisms in genes involved in infection and reinfection, inflammation, or immune stimulation could play a role in determining the course and outcome. We studied in the early phase of pandemic consecutive patients (N = 383) with SARS-CoV-2 infection, whose subsequent clinical course was classified as mild or severe, the latter being characterized by admission to intensive therapy unit or death. Five host gene polymorphisms (MERTK rs4374383, PNPLA3 rs738409, TLL-1 rs17047200, IFNL3 rs1297860, and INFL4 rs368234815) were assessed by using whole nucleic acids extracted from nasopharyngeal swabs. Specific protease cleavage sites of TLL-1 on the SARS-CoV-2 Spike protein were predicted in silico. Male subjects and older patients were significantly at higher risk for a severe outcome (p = 0.02 and p < 0.001, respectively). By considering patients ≤65 years, after adjusting for potential confounding due to sex, an increased risk of severe outcome was found in subjects with the GG genotype of PNPLA3 (adj-OR: 4.69; 95% CI = 1.01–22.04) or TT genotype of TLL-1 (adj-OR=9.1; 95% CI = 1.45–57.3). In silico evaluation showed that TLL-1 is potentially involved in the Spike protein cleavage which is essential for viral binding and entry into the host cells using the host receptor angiotensin-converting enzyme 2 (ACE2). Subjects carrying a GG genotype in PNPLA3 gene might have a constitutive upregulation of the NLRP3 inflammasome and be more prone to tissue damage when infected by SARS-CoV-2. The TT genotype in TLL-1 gene might affect its protease activity on the SARS-CoV-2 Spike protein, enhancing the ability to infect or re-infect host’s cells. The untoward effect of these variants on disease course is evident in younger patients due to the relative absence of comorbidities as determinants of prognosis. In the unresolved pathogenetic scenery of COVID-19, the identification of genetic variants associates with more prolonged course or with a severe outcome of infection would support the development of predictive tools useful to stratify subjects by risk class at presentation. Moreover, the individuation of key genes could contribute to a better understanding of the pathways involved in the pathogenesis, giving the basis for rational therapeutic approaches

The genome-wide structure of two economically important indigenous Sicilian cattle breeds

Genomic technologies, such as high-throughput genotyping based on SNP arrays, provided background information concerning genome structure in domestic animals. The aim of this work was to investigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (Ne), and the patterns of linkage disequilibrium (LD) in two economically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. In order to understand the genetic relationship and to place both Sicilian breeds in a global context, genotypes from others 134 domesticated bovid breeds were used. Principal component analysis showed that the Sicilian cattle breeds were closer to individuals of B. t. taurus from Eurasia and formed non-overlapping clusters with other breeds. Between the Sicilian cattle breeds, MOD was the most differentiated, whereas the animals belonging to CIN breed showed a lower value of assignment, the presence of substructure and genetic links with MOD breed. The average molecular inbreeding and coancestry coefficients were moderately high, and the current estimates of Ne were low in both breeds. These values indicated a low genetic variability. Considering levels of LD between adjacent markers, the average r2 in MOD breed was comparable to those reported for others cattle breeds, whereas CIN showed a lower value. Therefore, these results support the need of more dense SNP arrays for a high power association mapping and genomic selection efficiency in particular for CIN cattle breed. Controlling molecular inbreeding and coancestry would restrict inbreeding depression, the probability of losing beneficial rare alleles, and therefore, the risk of extinction. The results generated from this study have important implications for the development of conservation and/or selection breeding programs in these two local cattle breeds