bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multi-component lattice Boltzmann approach to study the causality of plastic events
Authors: Kumar Pinaki , Benzi Roberto , Trampert Jeannot , Toschi Federico 
Published: June 2020

Using a multi-component lattice Boltzmann (LB) model, we perform fluid kinetic simulations of confined and concentrated emulsions. The system presents the phenomenology of soft-glassy materials, including a Herschel–Bulkley rheology, yield stress, ageing and long relaxation time scales. Shearing the emulsion in a Couette cell below the yield stress results in plastic topological re-arrangement events which follow established empirical seismic statistical scaling laws, making this system a good candidate to study the physics of earthquakes. One characteristic of this model is the tendency for events to occur in avalanche clusters, with larger events, triggering subsequent re-arrangements. While seismologists have developed statistical tools to study correlations between events, a process to confirm causality remains elusive. We present here, a modification to our LB model, involving small, fast vibrations applied to individual droplets, effectively a macroscopic forcing, which results in the arrest of the topological plastic re-arrangements. This technique provides an excellent tool for identifying causality in plastic event clusters by examining the evolution of the dynamics after ‘stopping’ an event, and then checking which subsequent events disappear.This article is part of the theme issue ‘Fluid dynamics, soft matter and complex systems: recent results and new methods’.
Reviving the local second-order boundary approach within the two-relaxation-time lattice Boltzmann modelling
Authors: Silva Goncalo , Ginzburg Irina 
Published: June 2020

This work addresses the Dirichlet boundary condition for momentum in the lattice Boltzmann method (LBM), with focus on the steady-state Stokes flow modelling inside non-trivial shaped ducts. For this task, we revisit a local and highly accurate boundary scheme, called the local second-order boundary (LSOB) method. This work reformulates the LSOB within the two-relaxation-time (TRT) framework, which achieves a more standardized and easy to use algorithm due to the pivotal parametrization TRT properties. The LSOB explicitly reconstructs the unknown boundary populations in the form of a Chapman–Enskog expansion, where not only first- but also second-order momentum derivatives are locally extracted with the TRT symmetry argument, through a simple local linear algebra procedure, with no need to compute their non-local finite-difference approximations. Here, two LSOB strategies are considered to realize the wall boundary condition, the original one called Lwall and a novel one Lnode, which operate with the wall and node variables, roughly speaking. These two approaches are worked out for both plane and curved walls, including the corners. Their performance is assessed against well-established LBM boundary schemes such as the bounce-back, the local second-order accurate CLI scheme and two different parabolic multi-reflection (MR) schemes. They are all evaluated for 3D duct flows with rectangular, triangular, circular and annular cross-sections, mimicking the geometrical challenges of real porous structures. Numerical tests confirm that LSOB competes with the parabolic MR accuracy in this problem class, requiring only a single node to operate.
This article is part of the theme issue ‘Fluid dynamics, soft matter and complex systems: recent results and new methods’.
Dynamics of a long chain in turbulent flows: impact of vortices
Authors: Picardo Jason R. , Singh Rahul , Ray Samriddhi Sankar , Vincenzi Dario 
Published: June 2020

We show and explain how a long bead–spring chain, immersed in a homogeneous isotropic turbulent flow, preferentially samples vortical flow structures. We begin with an elastic, extensible chain which is stretched out by the flow, up to inertial-range scales. This filamentary object, which is known to preferentially sample the circular coherent vortices of two-dimensional (2D) turbulence, is shown here to also preferentially sample the intense, tubular, vortex filaments of three-dimensional (3D) turbulence. In the 2D case, the chain collapses into a tracer inside vortices. In the 3D case on the contrary, the chain is extended even in vortical regions, which suggests that the chain follows axially stretched tubular vortices by aligning with their axes. This physical picture is confirmed by examining the relative sampling behaviour of the individual beads, and by additional studies on an inextensible chain with adjustable bending-stiffness. A highly flexible, inextensible chain also shows preferential sampling in three dimensions, provided it is longer than the dissipation scale, but not much longer than the vortex tubes. This is true also for 2D turbulence, where a long inextensible chain can occupy vortices by coiling into them. When the chain is made inflexible, however, coiling is prevented and the extent of preferential sampling in two dimensions is considerably reduced. In three dimensions, on the contrary, bending stiffness has no effect, because the chain does not need to coil in order to thread a vortex tube and align with its axis.
This article is part of the theme issue ‘Fluid dynamics, soft matter and complex systems: recent results and new methods’.
Lattice Boltzmann simulations capture the multiscale physics of soft flowing crystals
Authors: Montessori A. , Tiribocchi A. , Bonaccorso F. , Lauricella M. , Succi S. 
Published: June 2020

The study of the underlying physics of soft flowing materials depends heavily on numerical simulations, due to the complex structure of the governing equations reflecting the competition of concurrent mechanisms acting at widely disparate scales in space and time. A full-scale computational modelling remains a formidable challenge since it amounts to simultaneously handling six or more spatial decades in space and twice as many in time. Coarse-grained methods often provide a viable strategy to significantly mitigate this issue, through the implementation of mesoscale supramolecular forces designed to capture the essential physics at a fraction of the computational cost of a full-detail description. Here, we review some recent advances in the design of a lattice Boltzmann mesoscale approach for soft flowing materials, inclusive of near-contact interactions (NCIs) between dynamic interfaces, as they occur in high packing-fraction soft flowing crystals. The method proves capable of capturing several aspects of the rheology of soft flowing crystals, namely, (i) a 3/2 power-law dependence of the dispersed phase flow rate on the applied pressure gradient, (ii) the structural transition between an ex-two and ex-one (bamboo) configurations with the associated drop of the flow rate, (iii) the onset of interfacial waves once NCI is sufficiently intense.This article is part of the theme issue ‘Fluid dynamics, soft matter and complex systems: recent results and new methods’.
Efficient supersonic flow simulations using lattice Boltzmann methods based on numerical equilibria
Authors: Latt Jonas , Coreixas Christophe , Beny Joël , Parmigiani Andrea 
Published: June 2020

A double-distribution-function based lattice Boltzmann method (DDF-LBM) is proposed for the simulation of polyatomic gases in the supersonic regime. The model relies on a numerical equilibrium that has been extensively used by discrete velocity methods since the late 1990s. Here, it is extended to reproduce an arbitrary number of moments of the Maxwell–Boltzmann distribution. These extensions to the standard 5-constraint (mass, momentum and energy) approach lead to the correct simulation of thermal, compressible flows with only 39 discrete velocities in 3D. The stability of this BGK-LBM is reinforced by relying on Knudsen-number-dependent relaxation times that are computed analytically. Hence, high Reynolds-number, supersonic flows can be simulated in an efficient and elegant manner. While the 1D Riemann problem shows the ability of the proposed approach to handle discontinuities in the zero-viscosity limit, the simulation of the supersonic flow past a NACA0012 aerofoil confirms the excellent behaviour of this model in a low-viscosity and supersonic regime. The flow past a sphere is further simulated to investigate the 3D behaviour of our model in the low-viscosity supersonic regime. The proposed model is shown to be substantially more efficient than the previous 5-moment D3Q343 DDF-LBM for both CPU and GPU architectures. It then opens up a whole new world of compressible flow applications that can be realistically tackled with a purely LB approach.
This article is part of the theme issue ‘Fluid dynamics, soft matter and complex systems: recent results and new methods’.
Risk of SARS-CoV-2 infection from contaminated water systems
Authors: Shutler Jamie , Zaraska Krzysztof , Holding Tom , Machnik Monika , Uppuluri Kiranmai , Ashton Ian , Migdał Łukasz , Dahiya Ravinder 
Published: June 2020

AbstractFollowing the outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV-2) in China, airborne water droplets (aerosols) have been identified as the main transmission route, although other transmission routes are likely to exist. We quantify SARS-CoV-2 virus survivability within water and the risk of infection posed by faecal contaminated water within 39 countries. We identify that the virus can remain stable within water for up to 25 days, and country specific relative risk of infection posed by faecal contaminated water is related to the environment. Faecal contaminated rivers, waterways and water systems within countries with high infection rates can provide infectious doses >100 copies within 100 ml of water. The implications for freshwater systems, the coastal marine environment and virus resurgence are discussed.
Clozapine treatment and risk of COVID-19
Authors: Govind Risha , de Freitas Daniela Fonseca , Pritchard Megan , Hayes Richard D. , MacCabe James H. 
Published: June 2020

ABSTRACTBackgroundClozapine, an antipsychotic with unique efficacy in treatment resistant psychosis, is associated with increased susceptibility to infection, including pneumonia.AimsTo investigate associations between clozapine treatment and increased risk of COVID-19 in patients with schizophrenia-spectrum disorders who are receiving antipsychotic medications, using electronic health records data, in a geographically defined population in London.MethodUsing information from South London and Maudsley NHS Foundation Trust (SLAM) clinical records, via the Clinical Record Interactive Search system, we identified 6,309 individuals who had an ICD-10 diagnosis of schizophrenia-spectrum disorders and were taking antipsychotics at the time on the COVID-19 pandemic onset in the UK. People who were on clozapine treatment were compared with those on any other antipsychotic treatment for risk of contracting COVID-19 between 1 March and 18 May 2020. We tested associations between clozapine treatment and COVID-19 infection, adjusting for gender, age, ethnicity, BMI, smoking status, and SLAM service use.ResultsOf 6,309 patients, 102 tested positive for COVID-19. Individuals who were on clozapine had increased risk of COVID-19 compared with those who were on other antipsychotic medication (unadjusted HR = 2.62 (95% CI 1.73 - 3.96), which was attenuated after adjusting for potential confounders, including clinical contact (adjusted hazard ratio HR=1.76, 95% CI 1.14 - 2.72).ConclusionsThese findings provide support for the hypothesis that clozapine treatment is associated with an increased risk of COVID-19. Further research will be needed in other samples to confirm this association. Potential clinical implications are discussed.
Determinants of HIV-1 late presentation in a cohort of Portuguese HIV-1 patients
Authors: Cláudia Miranda Ana , Miranda Mafalda , Pingarilho Marta , Pimentel Victor , Torres João , Peres Susana , Alberto Teresa Baptista , Gomes Perpetua , Abecasis Ana , Mansinho Kamal 
Published: June 2020

AbstractBackgroundUndiagnosed HIV-1 patients still account for 25% of worldwide HIV patients. Studying late presenters for HIV care may help to identify characteristics of such patients.ObjectiveThe present study aims to identify factors associated with late presentation (LP) and late presentation with advanced disease (LPAD) based on a population of patients followed in a Portuguese hospital between 1984 and 2017.MethodsSociodemographic and clinical data from infected patients with HIV-1 aged 18 years and older, followed in Egas Moniz Hospital, in Portugal were collected.ResultsOf the 907 patients included in this study, 68.7% were males and the median age was 37 years (IQR 30-47). 459 patients (50.6%) were LP and, of these, 284 patients (61.9%) were LPAD. The LP population mostly originated from Portugal and Sub-Saharan Africa (64.4% and 28.8%; p=0.004) and the HIV exposure category mainly heterosexuals and MSM (57.0% and 24.9%; p<0.001). The stage of disease and viral load at diagnosis were significantly associated with both LP and LPAD (p<0.001). Factors associated with LP in the logistic regression included age at diagnosis lower than 30y (aOR 0.34; 0.17-0.68; p=0.002) and origin from Sub-Saharan Africa (aOR 2.24; 1.44-3.50; p<0.001).ConclusionLate presentation is a major obstacle to halt the HIV epidemic. In this population, the majority of newly diagnosed HIV-infected individuals were late presenters. Our results characterize vulnerable populations that should be frequently tested for HIV.
Hospital based autonomous pre-clinical screening of COVID-19: An emergency triage using a vital signs recording system, Paris-Ile de France region
Authors: Brizio Albert , Faure Valérie , Baudino Franck , Wilmet Arnaud , Gonzalez Jean-Paul 
Published: June 2020

ABSTRACTThe COVID-19 pandemic, has had a dramatic toll worldwide on the populations but also has been essentially supported by the existing public health system, particularly hospital-based emergency wards and intensive care units.In France, the first cases were identified on the 24th of January 2020. The first epidemic sprout emerged in the Eastern part of the country and spread in two weeks towards the center to the Paris-region where it peaked on the 14th of April 2020. In Paris and the region around it, the intensity of the epidemic has increased significantly to have a strong impact on all public and private hospital systems in a few weeks.During France’s 2020 COVID-19 epidemic, a private hospital went into a major organizational change of its Emergency Department which mainly included the use of a Telemedicine Booth for vitals automatic recording during triage procedures.The present study describes the organizational scheme adopted by the hospital and discusses the data of 1,844 patients that attended the facility over a month. While among them, 766 patients were engaged in a automated triage process supported by a Telemedicine Booth. Patients’ clinical characteristics are comparable to those found in international literature during the COVID-19 pandemic.The use of the Telemedicine Booth as a screening process facilitated patients’ flow. It usefully participated in the patient rapid orientation, relieving the hospital emergency department, actively contributes in a safe and secure environment highly trusted by the hospital staff and health workers. To our nowledge, the Telemedicine Booth use as a screening process during an epidemic constitutes the first contribution to such an innovative approach.
Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic
Authors: Petrone Mary E. , Earnest Rebecca , Lourenço José , Kraemer Moritz U.G. , Paulino-Ramirez Robert , Grubaugh Nathan D. , Tapia Leandro 
Published: June 2020

ABSTRACTMosquito-borne viruses pose a perpetual public health threat to countries and territories in the Carribean due to the region’s tropical climate and seasonal reception of international tourists. Outbreaks of the emerging viruses chikungunya and Zika in 2014 and 2016, respectively, demonstrated the rapidity with which these viruses can spread between islands. At the same time, the number of reported dengue fever cases, caused by the endemic dengue virus, has steadily climbed over the past decade, and a large dengue outbreak that began sweeping through this region in 2019 continues in 2020. Sustainable disease and mosquito control measures are urgently needed to quell virus transmission in the long term and prevent future outbreaks from occurring. To improve upon current surveillance methods, we analyzed temporal and spatial patterns of chikungunya, Zika, and dengue outbreaks reported in the Dominican Republic between 2012 and 2018. The viruses that caused these outbreaks are transmitted by Aedes mosquitoes, which are sensitive to seasonal climatological variability. In this study, we evaluated whether climate and the spatio-temporal dynamics of past dengue outbreaks could inform when and where future emerging disease outbreaks might occur. We found that the temporal and spatial distribution of emerging disease outbreaks did not conform to those of seasonal dengue outbreaks. Rather, the former occurred when climatological conditions were suboptimal for Aedes activity. Provincial dengue attack rates did not correspond to those of emerging diseases. Our study also provides evidence for under-reporting of dengue cases, especially following the 2016 Zika outbreak. We advocate for the implementation of a sustainable and long-term surveillance system to monitor the spread of known mosquito-borne viruses and to identify emerging threats before they cause outbreaks. Specifically, we recommend the use of febrile illness incidence, ca se fatality rates, and serosurveys during inter-outbreak periods to better understand rates of transmission and asymptomatic infection.
Reconstructing the course of the COVID-19 epidemic over 2020 for US states and counties: results of a Bayesian evidence synthesis model
Authors: Chitwood Melanie H. , Russi Marcus , Gunasekera Kenneth , Havumaki Joshua , Klaassen Fayette , Pitzer Virginia E. , Salomon Joshua A. , Swartwood Nicole A. , Warren Joshua L. , Weinberger Daniel M. , Cohen Ted , Menzies Nicolas A. 
Published: June 2020

AbstractReported COVID-19 cases and deaths provide a delayed and incomplete picture of SARS-CoV-2 infections in the United States (US). Accurate estimates of both the timing and magnitude of infections are needed to characterize viral transmission dynamics and better understand COVID- 19 disease burden. We estimated time trends in SARS-CoV-2 transmission and other COVID-19 outcomes for every county in the US, from the first reported COVID-19 case in January 13, 2020 through January 1, 2021. To do so we employed a Bayesian modeling approach that explicitly accounts for reporting delays and variation in case ascertainment, and generates daily estimates of incident SARS-CoV-2 infections on the basis of reported COVID-19 cases and deaths. The model is freely available as thecovidestimR package. Nationally, we estimated there had been 49 million symptomatic COVID-19 cases and 400,718 COVID-19 deaths by the end of 2020, and that 27% of the US population had been infected. The results also demonstrate wide county-level variability in the timing and magnitude of incidence, with local epidemiological trends differing substantially from state or regional averages, leading to large differences in the estimated proportion of the population infected by the end of 2020. Our estimates of true COVID-19 related deaths are consistent with independent estimates of excess mortality, and our estimated trends in cumulative incidence of SARS-CoV-2 infection are consistent with trends in seroprevalence estimates from available antibody testing studies. Reconstructing the underlying incidence of SARS-CoV-2 infections across US counties allows for a more granular understanding of disease trends and the potential impact of epidemiological drivers.
Prolonged low-dose methylprednisolone in patients with severe COVID-19 pneumonia
Authors: Salton Francesco , Confalonieri Paola , Santus Pierachille , Harari Sergio , Scala Raffaele , Lanini Simone , Vertui Valentina , Oggionni Tiberio , Caminati Antonella , Patruno Vincenzo , Tamburrini Mario , Scartabellati Alessandro , Parati Mara , Villani Massimiliano , Radovanovic Dejan , Tomassetti Sara , Ravaglia Claudia , Poletti Venerino , Vianello Andrea , Gaccione Anna Talia , Guidelli Luca , Raccanelli Rita , Lucernoni Paolo , Lacedonia Donato , Foschino Barbaro Maria Pia , Centanni Stefano , Mondoni Michele , Davì Matteo , Fantin Alberto , Cao Xueyuan , Torelli Lucio , Zucchetto Antonella , Montico Marcella , Casarin Annalisa , Romagnoli Micaela , Gasparini Stefano , Bonifazi Martina , D’Agaro Pierlanfranco , Marcello Alessandro , Licastro Danilo , Ruaro Barbara , Volpe Maria Concetta , Umberger Reba , Meduri Umberto , Confalonieri Marco 
Published: June 2020

AbstractBackgroundIn hospitalized patients with COVID-19 pneumonia, progression to acute respiratory failure requiring invasive mechanical ventilation (MV) is associated with significant morbidity and mortality. Severe dysregulated systemic inflammation is the putative mechanism. We hypothesize that early prolonged methylprednisolone (MP) treatment could accelerate disease resolution, decreasing the need for ICU and mortality.MethodsWe conducted a multicenter, observational study to explore the association between exposure to prolonged, low-dose, MP treatment and need for ICU referral, intubation or death within 28 days (composite primary endpoint) in patients with severe COVID-19 pneumonia admitted to Italian respiratory high-dependency units. Secondary outcomes were invasive MV-free days and changes in C-reactive protein (CRP) levels.ResultsFindings are reported as MP (n=83) vs. control (n=90). The composite primary endpoint was met by 19 vs. 40 [adjusted hazard ratio (HR) 0.41; 95% confidence interval (CI): 0.24-0.72]. Transfer to ICU and need for invasive MV was necessary in 15 vs. 27 (p=0.07) and 14 vs. 26 (p=0.10), respectively. By day 28, the MP group had fewer deaths (6 vs. 21, adjusted HR=0.29; 95% CI: 0.12-0.73) and more days off invasive MV (24.0 ± 9.0 vs. 17.5 ± 12.8; p=0.001). Study treatment was associated with rapid improvement in PaO2:FiO2 and CRP levels. The complication rate was similar for the two groups (p=0.84).ConclusionIn patients with severe COVID-19 pneumonia, early administration of prolonged MP treatment was associated with a significantly lower hazard of death (71%) and decreased ventilator dependence. Randomized controlled studies are needed to confirm these findings.RegistrationClinicalTrials.gov. Identifier: NCT04323592