bluuebunny/crossref_metadata_2025_split huggingface dataset:
A unified lattice Boltzmann model and application to multiphase flows
Authors: Luo Kai H. , Fei Linlin , Wang Geng 
Published: August 2021

In this work, we develop a unified lattice Boltzmann model (ULBM) framework that can seamlessly integrate the widely used lattice Boltzmann collision operators, including the Bhatnagar–Gross–Krook or single-relation-time, multiple-relaxation-time, central-moment or cascaded lattice Boltzmann method and multiple entropic operators (KBC). Such a framework clarifies the relations among the existing collision operators and greatly facilitates model comparison and development as well as coding. Importantly, any LB model or treatment constructed for a specific collision operator could be easily adopted by other operators. We demonstrate the flexibility and power of the ULBM framework through three multiphase flow problems: the rheology of an emulsion, splashing of a droplet on a liquid film and dynamics of pool boiling. Further exploration of ULBM for a wide variety of phenomena would be both realistic and beneficial, making the LBM more accessible to non-specialists.This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.
Structure and dynamics of water confined in cylindrical nanopores with varying hydrophobicity
Authors: Tinti Antonio , Camisasca Gaia , Giacomello Alberto 
Published: August 2021

We report a detailed study of the main structural and dynamical features of water confined in model Lennard–Jones nanopores with tunable hydrophobicity and finite length (

L
=
26

Å). The generic model of cylindrical confinement used is able to reproduce the wetting features of a large class of technologically and biologically relevant systems spanning from crystalline nanoporous materials, to mesoporous silica and ion channels. The aim of this work is to discuss the influence of parameters such as wall hydrophobicity, temperature, and pore size on the structural and dynamical features of confined water. Our simulation campaign confirmed the existence of a core domain in which water displays bulk-like structural features even in extreme (

R
=
7.0

Å) confinement, while dynamical properties were shown to depend non-trivially on the size and hydrophobicity of the pores.

This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.
A multiple-relaxation-time collision model by Hermite expansion
Authors: Shan Xiaowen , Li Xuhui , Shi Yangyang 
Published: August 2021

The Bhatnagar–Gross–Krook (BGK) single-relaxation-time collision model for the Boltzmann equation serves as the foundation of the lattice BGK (LBGK) method developed in recent years. The description of the collision as a uniform relaxation process of the distribution function towards its equilibrium is, in many scenarios, simplistic. Based on a previous series of papers, we present a collision model formulated as independent relaxations of the irreducible components of the Hermite coefficients in the reference frame moving with the fluid. These components, corresponding to the irreducible representation of the rotation group, are the minimum tensor components that can be separately relaxed without violating rotation symmetry. For the 2nd, 3rd and 4th moments, respectively, two, two and three independent relaxation rates can exist, giving rise to the shear and bulk viscosity, thermal diffusivity and some high-order relaxation process not explicitly manifested in the Navier–Stokes-Fourier equations. Using the binomial transform, the Hermite coefficients are evaluated in the absolute frame to avoid the numerical dissipation introduced by interpolation. Extensive numerical verification is also provided.
This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.
IgA deficiency destabilizes immunological homeostasis towards intestinal microbiota and increases the risk of systemic immune dysregulation
Authors: Conrey Peyton E. , Denu Lidiya , O’Boyle Kaitlin C. , Green Jamal , Maslanka Jeffrey , Lubin Jean-Bernard , Duranova Tereza , Haltzman Brittany L. , Gianchetti Lauren , Oldridge Derek , Vella Laura A , Allman David , Spergel Jonathan , Tanes Ceylan , Bittinger Kyle , Henrickson Sarah E. , Silverman Michael A. 
Published: August 2021

SummaryMammals produce large quantities of mucosal and systemic antibodies that maintain the intestinal barrier, shape the intestinal microbiome and promote lifelong mutualism with commensal microbes. Here, we developed an integrated host-commensal approach combining microbial flow cytometry and 16s rRNA gene sequencing to define the core microbes that induce mucosal and systemic antibodies in pediatric selective Immunoglobulin A (IgA) deficient and household control siblings with CyTOF analysis to determine the impacts of IgA deficiency on host cellular immune phenotype. In healthy controls, mucosal secretory IgA and IgM antibodies coat an overlapping subset of microbes, predominantly Firmicutes and Proteobacteria. Serum IgG antibodies target a similar consortium of fecal microbes, revealing connections between mucosal and systemic antibody networks. Unexpectedly, IgM provides limited compensation for IgA in children lacking intestinal IgA. Furthermore, we find broad systemic immune dysregulation in a subset of children and mice lacking IgA, including enhanced IgG targeting of fecal microbiota, elevated levels of inflammatory and allergic cytokines and alterations in T cell activation state. Thus, IgA tunes systemic interactions between the host and commensal microbiota. Understanding how IgA tunes baseline immune tone has implications for predicting and preventing autoimmune, inflammatory and allergic diseases broadly, as well as providing improved prognostic guidance to patients with IgA deficiency.One Sentence SummaryIgA deficiency impairs immune homeostasis toward microbiota in children, increasing the risk of immune dysregulation.
Exploring Vaccine Hesitancy in Care Home Employees in North West England: A Qualitative Study
Authors: Dennis Amelia , Robin Charlotte , Jones Leah , Carter Holly 
Published: August 2021

ABSTRACTObjectivesCare homes have experienced a high number of COVID-19 outbreaks, and it is therefore important for care home employees to receive the COVID-19 vaccine. However, there is vaccine hesitancy at a greater rate among this group than in the wider community. We aimed to understand barriers and facilitators to getting the COVID-19 vaccine, as well as views on potential mandatory vaccination policies.DesignSemi-structured interviews.SettingCare home employees in North West England. Interviews conducted in April 2021.Participants10 care home employees (aged 25 to 61 years old) in the North West, who had been invited to have, but had not yet received, the COVID-19 vaccine.ResultsWe analysed the interviews using a framework analysis. Our analysis identified eight themes: perceived risk of COVID-19, efficacy of the vaccine, concerns about the vaccine, mistrust in authorities, facilitators to getting the vaccine, views on potential mandatory COVID-19 vaccination policies, negative experiences of care work during the COVID-19 pandemic, and communication challenges.ConclusionsThe care home employees interviewed at the time of this study reported a low perceived risk of COVID-19, alongside concerns over the efficacy of the vaccine, side effects, and speed of vaccine development, which is exacerbated by mistrust in authorities. Facilitators to getting the vaccine included wanting to protect others, perceived severity of COVID-19, and workplace norms. Making COVID-19 vaccination a condition of deployment may not result in increased willingness to get the COVID-19 vaccination, with most care home employees in this study favouring leaving their job rather than getting vaccinated. At a time when many of the workers already had negative experiences of care work during the pandemic due to perceived negative judgment from others and a perceived lack of support facing care home employees, policies that require vaccination as a condition of deployment were not positively received.
A novel Vascular Leak Index identifies sepsis patients with a higher risk for in-hospital death and fluid accumulation
Authors: Chandra Jay , Ángel Armengol Miguel , Lee Gwendolyn , Lee Alexandria , Thoral Patrick , Elbers Paul , Lee Hyung-Chul , Munger John S. , Celi Leo Anthony , Kaufman David A. 
Published: August 2021

ABSTRACTPurposeSepsis is a leading cause of morbidity and mortality worldwide and is characterized by vascular leak syndrome. Treatment for sepsis, specifically intravenous fluids, may worsen deterioration in the context of vascular leak.MethodsWe performed a retrospective cohort study of sepsis patients in four ICU databases in North America, Europe, and Asia. We developed an intuitive vascular leak index (VLI) and determined the relationship between VLI and in-hospital death and 36h-84h fluid balance using generalized additive models (GAM).ResultsUsing GAM, we found that increased VLI is associated with an increased risk of in-hospital death. Patients with a VLI in the highest quartile (Q4), across the four datasets, had a 1.61-2.31 times increased odds of dying in the hospital compared to patients with a VLI in the lowest quartile (Q1). VLI Q2 and Q3 were also associated with increased odds of dying. The relationship between VLI, treated as a continuous variable, and in-hospital death and 36h-84h death was statistically significant in the three datasets with a large number of patients. Specifically, we observed that as VLI increased, there was increase in the risk for in-hospital death and 36h-84h fluid balance. For the few patients with a positive VLI, this relationship differed across databases.ConclusionsOur VLI identifies groups of patients who may be at higher risk for in-hospital death and for fluid accumulation early in the ICU course. This relationship persisted in models developed to control for severity of illness and chronic comorbidity burden.
AEROSOL GENERATION DURING COUGHING - QUANTITATIVE DEFINITION FOR AEROSOL GENERATING PROCEDURES: OBSERVATIONAL STUDY
Authors: Sanmark Enni , Oksanen Lotta-Maria A.H. , Rantanen Noora , Lahelma Mari , Anttila Veli-Jukka , Lehtonen Lasse , Hyvärinen Antti-Pekka , Geneid Ahmed 
Published: August 2021

ABSTRACTAimThe purpose of the study was to determine aerosol exposure generated by coughing in operation room environments to create a quantitative limit value for high-risk aerosol-generating medical procedures.BackgroundCoughing is known to produce a significant amount of aerosols and is thus commonly used as a best reference for high-risk aerosol-generation. Accordingly, procedures during which aerosol generation exceeds the amount of aerosol generated in instances of coughing are seen as high-risk aerosol generating procedures. However, no reliable quantitative values are available for high-risk aerosol-generation.MethodsCoughing was measured from 37 healthy volunteers in the operating room environment. Aerosol particles generated during coughing within the size range of 0.3–10 µm were measured with Optical Particle Sizer from 40cm, 70cm, and 100cm distances. The distances reflected potential exposure distances where personnel are during surgeries.ResultsA total of 306 coughs were measured. Average aerosol concentration during coughing was 1.580 ± 13.774 particles/cm3 (range 0.000 – 195.528).DiscussionThe aerosol concentration measured in this study can be used as a limit for high-risk aerosol generation in the operating room environment when assessing the aerosol generating procedures and the risk of operating room staff’s exposure for aerosol particles.
Optimized extraction method enables quantitative analysis of surface metabolite recovery for exposomics and behavioral studies
Authors: Katemauswa Mitchelle , Hossain Ekram , Liu Zongyuan , Lesani Mahbobeh , Parab Adwaita R. , Dean Danya A. , McCall Laura-Isobel 
Published: August 2021

ABSTRACTWorkplace chemical exposures are a major source of occupational injury. Although over half of these are skin exposures, exposomics research often focuses on chemical levels in the air or in worker biofluids such as blood and urine. Until now, one limitation has been the lack of methods to quantitatively measure surface chemical transfer. Outside the realm of harmful chemicals, the small molecules we leave behind on surfaces can also reveal important aspects of human behavior. In this study, we developed a swab-based quantitative approach to determine small molecule concentrations across common surfaces. We demonstrate its utility using one drug, cyclobenzaprine, and two human-derived metabolites, carnitine and phenylacetylglutamine, on four common surfaces: linoleum flooring, plastified laboratory workbench, metal and Plexiglass. This approach enabled linear small molecule recovery and quantification of molecule abundance on workplace built environment surfaces. Overall, this method paves the way for future quantitative exposomics studies.
Peer teaching as bioinformatics training strategy: incentives, challenges, and benefits
Authors: Rahman Nur-Taz , Meyer Caitlin , Thakral Durga , Cai Wesley L. , Chen Ann T. , Obaid Razib , Garcia-Milian Rolando 
Published: August 2021

AbstractAs biomedical research becomes more data-intensive, bioinformatics is becoming essential to understanding biological processes, systems, and diseases. In this paper we describe the use of a series of peer teaching workshops as a strategy to respond to the bioinformatics training needs at a research-intensive institution. In addition to the data collected from the workshops, we also used personal experiences of researchers who participated as peer teachers to understand the incentives, challenges, and benefits of peer teaching. Developing communication skills such as confidence in teaching, explaining complex concepts, and better understanding of the topic emerged as primary benefits that the teachers obtained from this experience. Lack of time for teaching and the struggles of classroom management were identified as two major challenges. We suggest that peer teaching can be beneficial not only to train researchers in bioinformatics, but also as a professional development opportunity for graduate students and postdoctoral trainees.
Risk of Serious Infections in Patients with Psoriasis on Biologic Therapies: An Updated Systematic Review and Meta-Analysis
Authors: Manounah L. , Yiu Z.Z.N. , Mahil S.K. , Exton L.S. , Ezejimofor M.C. , Burden A.D. , Murphy R. , Owen C.M. , Parslew R. , Woolf R.T. , Smith C.H. , Mohd Mustapa M.F. 
Published: August 2021

ABSTRACTBackgroundThe increase in the number of available biologic agents for psoriasis has led to an urgent need to evaluate their associated risk of serious infections to help inform clinical decisions.MethodologyWe systematically searched PubMed, Medline, Embase, and Cochrane databases for biologics targeting TNF (adalimumab, etanercept, infliximab, certolizumab pegol), interleukin (IL)-12/23 (ustekinumab), IL-17A (secukinumab, ixekizumab), IL-17RA (brodalumab) and IL-23p19 (guselkumab, risankizumab, and tildrakizumab) for the primary outcome serious infections, at 10– 16 weeks, 1 year and 3 years. Peto’s method (fixed effect model) was used to estimate the pooled odds ratio (OR) in meta-analyses comparing biologics with one another, methotrexate, or placebo.ResultsForty-three publications (49 trials) consisting of 29,724 participants met our inclusion criteria. Serious infections across all studies were low (n=97) at 10–16 weeks and did not show an increased risk with biologic therapies compared with placebo. Seven head-to-head RCTs were identified, most of which showed no significant difference in the risk of serious infections at 10–16 weeks and at 1 year. Adalimumab was not associated with a significant increased risk of serious infections compared with methotrexate in children at 10–16 weeks.ConclusionsBiologics for psoriasis were not associated with an increased risk of serious infections compared with placebo or one another at 10–16 weeks. Longer-term, real-world data with larger sample sizes are warranted.
Accuracy of mutual predictions of plant and microbe communities varies along a successional gradient in an alpine glacier forefield
Authors: He Xie , Hanusch Maximilian , Ruiz-Hernández Victoria , Junker Robert R. 
Published: August 2021

SummaryDue to climate warming, recently deglaciated glacier forefields create virtually uninhabited substrates waiting for initial colonization of bacteria, fungi and plants and serve as an ideal ecosystem for studying transformations in community composition and diversity over time and the interactions between taxonomic groups.In this study, we investigated the composition and diversity of bacteria, and fungi, plants and environmental factors (pH, temperature, plot age and soil nutrients) along a 1.5km glacier forefield. We used random forest analysis to detect how well the composition and diversity of taxonomic groups and environmental factors can be mutually predicted.Community composition and diversity of taxonomic groups predicted each other more accurately than environmental factors predicted the taxonomic groups; within the taxonomic groups bacteria and fungi predicted each other best and the taxa’s composition was better predicted than diversity indices. Additionally, accuracy of prediction among taxonomic groups and environmental factors considerably varied along the successional gradient.Although our results are no direct indication of interactions between the taxa investigated and the environmental conditions, the accurate predictions among bacteria, fungi, and plants do provide insights into the concerted community assembly of different taxa in response to changing environments along a successional gradient.
Cell tip growth underlies injury response of marine macroalgae
Authors: Shirae-Kurabayashi Maki , Edzuka Tomoya , Suzuki Masahiro , Goshima Gohta 
Published: August 2021

AbstractRegeneration is a widely observed phenomenon by which the integrity of an organism is recovered after damage. So far, studies on the molecular and cellular mechanisms of regeneration have been limited to a handful of model multicellular organisms. Here, we systematically surveyed the regeneration ability of marine macroalgae (Rhodophyta, Phaeophyceae, Chlorophyta) after thallus severing and applied live cell microscopy on them to uncover the cellular response to the damage. We observed three types of responses – budding, rhizoid formation and/or sporulation – in 25 species among 66 examined, demonstrating the high potential of regeneration of macroalgae. In contrast, callus formation, which often accompanies plant regeneration, was never observed. We monitored the cellular and nuclear dynamics during cell repair or rhizoid formation of four phylogenetically diverged Rhodophyta and Chlorophyta species (Colaconemasp.,Dasya sessilis, Cladophora albida, Codium fragile). We observed tip growth of the cells near the damaged site as a common response, despite the difference in the number of nuclei and cells across species. Nuclear translocation follows tip growth, enabling overall uniform distribution of multinuclei (Dasya sessilis, Cladophora albida, Codium fragile) or central positioning of the mononucleus (Colaconemasp.). In contrast, the control of cell cycle events, such as nuclear division and septation, varied in these species. InDasya sessilis, the division of multinuclei was synchronised, whereas it was not the case inCladophora albida. Septation was tightly coupled with nuclear division inColaconemaandDasyabut not in others. These observations show that marine macroalgae utilise a variety of regeneration pathways, with some common features. This study also provides a novel methodology of live cell biology in macroalgae, offering a foundation for the future of this under-studied taxon.
The pigtail macaque (Macaca nemestrina) model of COVID-19 reproduces diverse clinical outcomes and reveals new and complex signatures of disease
Authors: Melton Alexandra , Doyle-Meyers Lara A , Blair Robert V , Midkiff Cecily , Melton Hunter J , Russell-Lodrigue Kasi , Aye Pyone P , Schiro Faith , Fahlberg Marissa , Szeltner Dawn , Spencer Skye , Beddingfield Brandon J , Goff Kelly , Golden Nadia , Penney Toni , Picou Breanna , Hensley Krystle , Chandler Kristin E , Plante Jessica A , Plante Kenneth S , Weaver Scott C , Roy Chad J , Hoxie James A , Gao Hongmei , Montefiori David C , Mankowski Joseph L , Bohm Rudolf P , Rappaport Jay , Maness Nicholas J 
Published: August 2021

AbstractThe novel coronavirus SARS-CoV-2, the causative agent of COVID-19 disease, has killed over four million people worldwide as of July 2021 with infections rising again due to the emergence of highly transmissible variants. Animal models that faithfully recapitulate human disease are critical for assessing SARS-CoV-2 viral and immune dynamics, for understanding mechanisms of disease, and for testing vaccines and therapeutics. Pigtail macaques (PTM, Macaca nemestrina) demonstrate a rapid and severe disease course when infected with simian immunodeficiency virus (SIV), including the development of severe cardiovascular symptoms that are pertinent to COVID-19 manifestations in humans. We thus proposed this species may likewise exhibit severe COVID-19 disease upon infection with SARS-CoV-2. Here, we extensively studied a cohort of SARS-CoV-2-infected PTM euthanized either 6- or 21-days after respiratory viral challenge. We show that PTM demonstrate largely mild-to-moderate COVID-19 disease. Pulmonary infiltrates were dominated by T cells, including CD4+ T cells that upregulate CD8 and express cytotoxic molecules, as well as virus-targeting T cells that were predominantly CD4+. We also noted increases in inflammatory and coagulation markers in blood, pulmonary pathologic lesions, and the development of neutralizing antibodies. Together, our data demonstrate that SARS-CoV-2 infection of PTM recapitulates important features of COVID-19 and reveals new immune and viral dynamics and thus may serve as a useful animal model for studying pathogenesis and testing vaccines and therapeutics.