bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation and application of the lattice Boltzmann algorithm for a turbulent immiscible Rayleigh–Taylor system
Authors: Tavares H. S. , Biferale L. , Sbragaglia M. , Mailybaev A. A. 
Published: August 2021

We develop a multicomponent lattice Boltzmann (LB) model for the two-dimensional Rayleigh–Taylor turbulence with a Shan–Chen pseudopotential implemented on GPUs. In the immiscible case, this method is able to accurately overcome the inherent numerical complexity caused by the complicated structure of the interface that appears in the fully developed turbulent regime. The accuracy of the LB model is tested both for early and late stages of instability. For the developed turbulent motion, we analyse the balance between different terms describing variations of the kinetic and potential energies. Then we analyse the role of the interface in the energy balance and also the effects of the vorticity induced by the interface in the energy dissipation. Statistical properties are compared for miscible and immiscible flows. Our results can also be considered as a first validation step to extend the application of LB model to three-dimensional immiscible Rayleigh-Taylor turbulence.This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.
Lattice Boltzmann method investigation of a reactive electro-kinetic flow in porous media: towards a phenomenological model
Authors: Li Haijing , Clercx Herman J. H. , Toschi Federico 
Published: August 2021

A model based on the Lattice Boltzmann method is developed to study the flow of reactive electro-kinetic fluids in porous media. The momentum, concentration and electric/potential fields are simulated via the Navier–Stokes, advection–diffusion/Nernst–Planck and Poisson equations, respectively. With this model, the total density and velocity fields, the concentration of reactants and reaction products, including neutral and ionized species, the electric potential and the interaction forces between the fields can be studied, and thus we provide an insight into the interplay between chemistry, flow and the geometry of the porous medium. The results show that the conversion efficiency of the reaction can be strongly influenced by the fluid velocity, reactant concentration and by porosity of the porous medium. The fluid velocity determines how long the reactants stay in the reaction areas, the reactant concentration controls the amount of the reaction material and with different dielectric constant, the porous medium can distort the electric field differently. All these factors make the reaction conversion efficiency display a non-trivial and non-monotonic behaviour as a function of the flow and reaction parameters. To better illustrate the dependence of the reaction conversion efficiency on the control parameters, based on the input from a number of numerical investigations, we developed a phenomenological model of the reactor. This model is capable of capturing the main features of the causal relationship between the performance of the reactor and the main test parameters. Using this model, one could optimize the choice of reaction and flow parameters in order to improve the performance of the reactor and achieve higher production rates.This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.
Molecular dynamics lattice gas equilibrium distribution function for Lennard–Jones particles
Authors: Pachalieva Aleksandra , Wagner Alexander J. 
Published: August 2021

The molecular dynamics lattice gas (MDLG) method maps a molecular dynamics (MD) simulation onto a lattice gas using a coarse-graining procedure. This is a novel fundamental approach to derive the lattice Boltzmann method (LBM) by taking a Boltzmann average over the MDLG. A key property of the LBM is the equilibrium distribution function, which was originally derived by assuming that the particle displacements in the MD simulation are Boltzmann distributed. However, we recently discovered that a single Gaussian distribution function is not sufficient to describe the particle displacements in a broad transition regime between free particles and particles undergoing many collisions in one time step. In a recent publication, we proposed a Poisson weighted sum of Gaussians which shows better agreement with the MD data. We derive a lattice Boltzmann equilibrium distribution function from the Poisson weighted sum of Gaussians model and compare it to a measured equilibrium distribution function from MD data and to an analytical approximation of the equilibrium distribution function from a single Gaussian probability distribution function.
This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.
Linear and brute force stability of orthogonal moment multiple-relaxation-time lattice Boltzmann methods applied to homogeneous isotropic turbulence
Authors: Simonis Stephan , Haussmann Marc , Kronberg Louis , Dörfler Willy , Krause Mathias J. 
Published: August 2021

Multiple-relaxation-time (MRT) lattice Boltzmann methods (LBM) based on orthogonal moments exhibit lattice Mach number dependent instabilities in diffusive scaling. The present work renders an explicit formulation of stability sets for orthogonal moment MRT LBM. The stability sets are defined via the spectral radius of linearized amplification matrices of the MRT collision operator with variable relaxation frequencies. Numerical investigations are carried out for the three-dimensional Taylor–Green vortex benchmark at Reynolds number 1600. Extensive brute force computations of specific relaxation frequency ranges for the full test case are opposed to the von Neumann stability set prediction. Based on that, we prove numerically that a scan over the full wave space, including scaled mean flow variations, is required to draw conclusions on the overall stability of LBM in turbulent flow simulations. Furthermore, the von Neumann results show that a grid dependence is hardly possible to include in the notion of linear stability for LBM. Lastly, via brute force stability investigations based on empirical data from a total number of 22 696 simulations, the existence of a deterministic influence of the grid resolution is deduced.
This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.
Microscale modelling of dielectrophoresis assembly processes
Authors: Tiribocchi A. , Montessori A. , Lauricella M. , Bonaccorso F. , Brown K. A. , Succi S. 
Published: August 2021

This work presents a microscale approach for simulating the dielectrophoresis assembly of polarizable particles under an external electric field. The model is shown to capture interesting dynamical and topological features, such as the formation of chains of particles and their incipient aggregation into hierarchical structures. A quantitative characterization in terms of the number and size of these structures is also discussed. This computational model could represent a viable numerical tool to study the mechanical properties of particle-based hierarchical materials and suggest new strategies for enhancing their design and manufacture.
This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.
Molecular dynamics of ionic polymer-metal composites
Authors: Truszkowska A. , Porfiri M. 
Published: August 2021

Ionic polymer-metal composites (IPMCs) constitute a promising class of soft, active materials with potentially ubiquitous use in science and engineering. Realizing the full potential of IPMCs calls for a deeper understanding of the mechanisms underpinning their most intriguing characteristics: the ability to deform under an electric field and the generation of a voltage upon mechanical deformation. These behaviours are tightly linked to physical phenomena at the level of atoms, including rearrangements of ions and molecules, along with the formation of sub-nanometre thick double layers on the surface of the metal electrodes. Several continuum theories have been developed to describe these phenomena, but their experimental and theoretical validation remains incomplete. IPMC modelling at the atomistic scale could beget valuable support for these efforts, by affording granular analysis of individual atoms. Here, we present a simplified atomistic model of IPMCs based on classical molecular dynamics. The three-dimensional IPMC membrane is constrained by two smooth walls, a simplified analogue of metal electrodes, impermeable only to counterions. The electric field is applied as an additional force acting on all the atoms. We demonstrate the feasibility of simulating counterions’ migration and pile-up upon the application of an electric field, similar to experimental observations. By analysing the spatial configuration of atoms and stress distribution, we identify two mechanisms for stress generation. The presented model offers new insight into the physical underpinnings of actuation and sensing in IPMCs.This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.
Intramuscular SARS-CoV-2 vaccines elicit varying degrees of plasma and salivary antibody responses as compared to natural infection
Authors: Nahass George Ronald , Salomon-Shulman Rachel E. , Blacker Grace , Haider Kazim , Brotherton Rich , Teague Kristine , Yiu Ying Ying , Brewer Rachel E. , Galloway Sarah Danielle , Hansen Paige , Marquez-Arreguin Gabriel , Sheikh-Mohamed Salma , Chao Gary Y.C. , Isho Baweleta , Do Evan , Chang Iris , Snow Theo , Lee Alexandra S. ,   STANFORD COVID-19 BIOBANK, Manohar Monali , Yang Samuel , Blomkalns Andra L. , Rogers Angela J , McGeer Allison , Gingras Anne-Claude , Straus Sharon , Grant Phillip , Nadeau Kari C. , Blish Catherine A. , Gommerman Jennifer L. , Sanders Erin C. , Weissman Irving L. , Tal Michal Caspi 
Published: August 2021

ABSTRACTVaccination induced antibody and T-cell immune responses are important for systemic protection from COVID-19. Because SARS-CoV-2 infects and is transmitted by oral-pharyngeal mucosa, we wished to test mucosal antibodies elicited by natural infection or intramuscular vaccine injection. In a non-randomized observational study, we measured antibodies against the SARS-CoV-2 RBD in plasma and saliva from convalescent or vaccinated individuals and tested their neutralizing potential using a replication competent rVSV-eGFP-SARS-CoV-2. We found IgG and IgA anti-RBD antibodies as well as neutralizing activity in convalescent plasma and saliva. Two doses of mRNA vaccination (BNT162b2 or mRNA-1273) induced high levels of IgG anti-RBD in saliva, a subset of whom also had IgA, and significant neutralizing activity. We detected anti-RBD IgG and IgA with significant neutralizing potential in the plasma of single dose Ad26.COV2.S vaccinated individuals, and we detected slight amounts of anti-RBD antibodies in matched saliva. The role of salivary antibodies in protection against SARS-CoV-2 infection is unknown and merits further investigation. This study was not designed to, nor did it study the full kinetics of the antibody response or protection from infection, nor did it address variants of SARS-CoV-2.
The Association Between Platelet Transfusion and Mortality Rate Among Preterm Neonates in the Eastern Province, Saudi Arabia
Authors: Alhamad Fatimah Abdullah , Hussien Ahlam Mohammed , Alqahtani Friyal Mubarak 
Published: August 2021

AbstractPlatelet transfusion is the main mode of management of thrombocytopenia. However, some studies link frequent and high-threshold platelet transfusions with an incremental increase of mortality rate.AimThis study aims to assess the association between the frequency and the threshold of platelet transfusions, with the mortality rate among preterm neonates.MethodsA retrospective cohort study design was used. This study was conducted at maternity and children’s hospitals in Al-Ahasa, Saudi Arabia. The sample size includes 154 preterm neonates, included in the study by the use of the convenience sampling technique.ResultThere is a significant relationship found between the gestational age and the birth weight of the preterm neonates with the survival rates among both groups. In contrast, there is no significant relationship found between transfusion frequency, transfusion threshold, and the survival rates of the group which received platelet transfusion.Implications for Practice and ResearchThe current study found that mortality is mainly associated with lower gestational ages, and not platelet transfusions. More studies are needed to fill the remaining gaps of knowledge, and to optimise platelet transfusion practices among preterm neonates.
Whole-genome analysis of monozygotic twins discordant for type 1 narcolepsy
Authors: Campos João H. , Aguilar Ana C. R. , Antoneli Fernando , Truzzi Giselle , Briones Marcelo R. S. , Ferreira Renata C. , Coelho Fernando M. S. 
Published: August 2021

SummaryNarcolepsy type 1 (NT1) is a rare and chronic neurological disease characterized by sudden sleep attacks, overwhelming daytime drowsiness, and cataplexy. To contribute to the understanding of NT1 genetic causes, here we describe a whole-genome analysis of a monozygotic twin pair discordant for NT1. Our study revealed that although both twins have the same pathogenic mutations in NT1 associated genes (such as HLA-DQB1*06:02:01, HLA-DRB1*11:01:02/*15:03:01) the unaffected twin has mutations in genes outside the HLA loci that could be suppressing the NT1 phenotype. These results support the notion that NT1 has an immunological basis but that protective mutations in non-HLA might interfere with the clinical manifestation of the disease.
Expansion, persistence and efficacy of donor memory-like NK cells for the treatment of post-transplant relapse
Authors: Shapiro Roman M. , Birch Grace , Vergara Juliana , Hu Guangan , Nikiforow Sarah , Baginska Joanna , Ali Alaa , Tarannum Mubin , Rambaldi Benedetta , Arihara Yohei , Reynolds Carol , Halpern Max , Rodig Scott , Cullen Nicole , Lane Andrew A. , Lindsley R. Coleman , Cutler Corey S. , Antin Joseph H. , Ho Vincent T. , Koreth John , Gooptu Mahasweta , Kim Haesook T. , Malmberg Karl-Johan , Wu Catherine J. , Chen Jianzhu , Soiffer Robert J. , Ritz Jerome , Romee Rizwan 
Published: August 2021

AbstractBackgroundResponses to conventional donor lymphocyte infusion (DLI) for post-allogeneic hematopoietic cell transplantation (HCT) relapse are typically poor. Natural killer (NK) cell-based therapy is a promising modality to treat post-HCT relapse.MethodsWe initiated this ongoing phase 1 trial of adoptively transferred cytokine induced memory-like (CIML) NK cells in patients with myeloid malignancies relapsed after haploidentical HCT. All patients received a donor-derived NK cell dose of 5-10 × million cells/kg after lymphodepleting chemotherapy, followed by systemic IL-2 for 7 doses. High resolution profiling with mass cytometry and single cell RNA sequencing characterized the expanding and persistent NK cells subpopulations in a longitudinal manner after infusion. In vitro functional studies of infused CIML NK cells were complemented with in vivo evaluation of NK trafficking to disease sites using multiparameter immunofluorescence.ResultsIn the first 5 patients on the trial, infusion of CIML NK cells led to a rapid 10 to 50-fold in vivo expansion that was sustained over months. The infusion was well-tolerated, with fever and pancytopenia as the most common adverse events. Responses were attained in 4 of 5 patients at day +28. Immunophenotypic and transcriptional profiling revealed a dynamic evolution of the activated CIML NK cell phenotype, superimposed on the natural variation in donor NK cell repertoires. AML relapse after initial response to CIML NK cell therapy was associated with low transcript expression of CD2 ligands, including CD48/SLAMF2 and CD58/LFA3.ConclusionGiven their rapid expansion and long-term persistence in an immune compatible environment, CIML NK cells serve as a promising platform for the treatment of post-transplant relapse of myeloid disease. Further characterization of their unique in vivo biology and interaction with both T-cells and tumor targets will lead to the development of novel cell-based immunotherapies.
Timing and magnitude of climate driven range shifts in transboundary fish stocks challenge their management
Authors: Palacios-Abrantes Juliano , Frölicher Thomas L. , Reygondeau Gabriel , Rashid Sumaila U. , Tagliabue Alessandro , Wabnitz Colette C.C. , Cheung William W.L. 
Published: August 2021

AbstractClimate change is shifting the distribution of shared fish stocks between neighboring countries’ Exclusive Economic Zones (EEZ) and the high seas. The timescale of these transboundary shifts determines how climate change will affect international fisheries governance. Coupling a large ensemble simulation of an Earth system model to a species distribution model, we show that by 2030, 23% of transboundary stocks would have shifted and 78% of the world EEZs will experience at least one shifting stock under a high emission climate change scenario. By the end of this century, 81% of EEZ waters will see at least one shifting stock with a total of 45% of stocks shifting globally, under a high emissions scenario. Importantly, many countries that are highly dependent on fisheries for income, food and nutrition security, as well as livelihoods emerge as hotspots for transboundary shifts showing early, and sometimes past shifts. Existing fisheries agreements need to be assessed for their capacity in addressing transboundary shifts, and strengthened where necessary to limit conflict over these fish stocks while new agreements are urged to considere this problematic in order to be resilient to global change.
Time In Range, as measured by continuous glucose monitor, as a predictor of microvascular complications in type 2 diabetes– A systemic review
Authors: Raj Rishi , Mishra Rahul , Jha Nivedita , Joshi Vivek , Correa Riccardo , Kern Philip A. 
Published: August 2021

ABSTRACTAimContinuous glucose monitoring (CGM) derived times in range (TIR) correlates with hemoglobin A1c (A1c) among patients with type 2 diabetes mellitus (T2DM); however, there is a paucity of data evaluating its association with microvascular complications. We conducted this systematic review to examine the association between TIR and microvascular complications of diabetic retinopathy (DR), diabetic nephropathy (DN) and peripheral diabetic neuropathy (DPN).MethodWe conducted a comprehensive literature search on online database of PubMed, Scopus, and Web of Science following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Full texts original articles that evaluated association between CGM-derived TIR and risk of microvascular complications which were published between 2010 and June 2021, were included in our systematic review. The quality of included studies were evaluated using National Heart, Lung, and Blood Institute Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies. Data were analyzed using qualitative synthesis.ResultEleven studies were included in the systematic review. The mean sample size, baseline A1c, and diabetes duration were 1271 (105-5901), 8.2 % (SD 0.5 %) and 11.3 years, respectively. Majority of studies were conducted in Asia (10 out 11). Four studies evaluated the relationship between CGM-derived TIR and DR and CGM-derived TIR and DN, while seven studies evaluated the relationship between CGM-derived TIR and DPN. A 10 % increase in TIR was associated with a reduction in albuminuria, severity of diabetic retinopathy, and prevalence of diabetic peripheral nephropathy and cardiac autonomic neuropathy. In addition, an association was observed between urinary albumin-to-creatinine ratio but not with estimated glomerular filtration rate.ConclusionThis review summarizes recent evidence supporting an association between CGM-derived TIR and microvascular complications among patients with T2DM. A larger□scale multi-center investigation that includes more diverse participants is warranted to further validate the utility of TIR as a predictor for diabetic microvascular complications.
Resting-state network topology characterizing callous-unemotional traits in adolescence
Authors: Winters Drew E. , Sakai Joseph T. , Carter R. McKell 
Published: August 2021

AbstractBackgroundCallous-unemotional (CU) traits, a youth antisocial phenotype, are hypothesized to associate with aberrant connectivity (dis-integration) across the salience (SAL), default mode (DMN), and frontoparietal (FPN) networks. However, CU traits have a heterogeneous presentation and previous research has not modeled individual heterogeneity in resting-state connectivity amongst adolescents with CU traits. The present study models individual-specific network maps and examines topological features of individual and subgroup maps in relation to CU traits.MethodsParticipants aged 13-17 completed resting-state functional connectivity and the inventory of callous-unemotional traits as part of the Nathan Klein Rockland study. A sparse network approach (GIMME) was used to derive individual-level and subgroup maps of all participants. We then examined heterogeneous network features associated with CU traits.ResultsHigher rates of CU traits increased probability of inclusion in one subgroup, which had the highest mean level of CU traits. Analysis of network features reveals less density within the FPN and greater density between DMN-FPN associated with CU traits.DiscussionFindings indicate heterogeneous person-specific connections and some subgroup connections amongst adolescents associate with CU traits. Higher CU traits associate with lower density in the FPN, which has been associated with attention and inhibition, and higher density between the DMN-FPN, which have been linked with cognitive control, social working memory, and empathy. Our findings suggest less efficiency in FPN function which, when considered mechanistically, could result in difficulty suppressing DMN when task positive networks are engaged. This is an area for further exploration but could explain cognitive and socio-affective impairments in CU traits.
Mussel memory: bivalves learn to fear parasites
Authors: Selbach Christian , Marchant Loïc , Mouritsen Kim N. 
Published: August 2021

AbstractFear plays a crucial role in predator-prey interactions and can have cascading impacts on the structure of whole ecosystems. Comparable fear effects have recently been described for hosts and their parasites but our understanding of the underlying mechanisms remains limited by the lack of empirical examples. Here, we experimentally tested if bivalvesMytilus eduliscan ‘learn to fear’ the infective transmission stages (cercariae) of the trematodeHimasthla elongataand if experienced mussels change their parasite-avoidance behaviour accordingly. Our results show that previous experience with parasites, but not infection per se, lead to a reduced filtration activity in mussels in the presence of cercariae compared to parasite-naïve conspecifics. This reduction in filtration activity resulted in lower infection rates in mussels. Since parasite avoidance comes at the cost of lower feeding rates, mussels likely benefit from the ability to adjust their defence behaviour when infection risks are high. Overall, these dynamic learning processes of avoidance behaviour can be expected to play a significant role in regulating the bivalves’ ecosystem engineering function in coastal habitats.