bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drying of virus-containing aerosol particles: Modelling effects of droplet origin and composition
Authors: Jarvis Michael C. 
Published: March 2021

AbstractBackground and PurposeVirus-containing aerosol droplets emitted by breathing, speech or coughing dry rapidly to equilibrium with ambient relative humidity (RH), increasing in solute concentration with effects on virus survival and decreasing in diameter with effects on sedimentation and respiratory uptake. The aim of this paper is to model the effect of ionic and macromolecular solutes on droplet drying and solute concentration.MethodsDeliquescence-efflorescence concepts and Kohler theory were used to simulate the evolution of solute concentrations and water activity in respiratory droplets, starting from efflorescence data on mixed NaCl/KCl aerosols and osmotic pressure data on respiratory macromolecules.ResultsIn NaCl/KCl solutions supersaturated total salt concentrations were shown to reach 10-15M at the efflorescence RH of 40-55%, depending on the K:Na ratio. Dependence on K:Na ratio implies that the evaporation curves differ between aerosols derived from saliva and from airway surfaces. The direct effect of liquid droplet size through the Kelvin term was shown to be smaller and largely restricted to breath emissions. Modelling the effect of proteins and glycoproteins showed that salts determine drying equilibria down to the efflorescence RH, and macromolecules at lower RH.ConclusionDifferences in drying behaviour are predicted between breathing, speech and coughing emissions and between droplet size fractions within these. High salt concentrations may inactivate some viruses.
Molecular Dynamics Study on the Effects of Charged Amino Acid Distribution Under low pH Condition to the Unfolding of Hen Egg White Lysozyme and Formation of Beta Strands
Authors: Zein Husnul Fuad , Alam Ibra , Asanithi Piyapong , Sutthibutpong Thana 
Published: March 2021

AbstractAggregation of unfolded or misfolded proteins into amyloid fibrils can cause various diseases in humans. However, the fibrils synthesized in vitro can be developed toward useful biomaterials under some physicochemical conditions. In this study, atomistic molecular dynamics simulations were performed to address the mechanism of beta-sheet formation of the unfolded hen egg white lysozyme (HEWL) under a high temperature and low pH. Simulations of the protonated HEWL at pH 2 and the non-protonated HEWL at pH 7 were performed at the highly elevated temperature of 450 K to accelerate the unfolding, followed by the 333 K temperature in some previous in vitro studies. The simulations showed that HEWL unfolded faster and refolded into structures with higher beta-strand contents at pH 2. The mechanism of beta-strand formation at the earlier stage of amyloidosis was addressed in terms of the radial distribution of amino acids, affected by the high protonation level at a low pH.
Phylogenomic discordance suggests polytomies along the backbone of the large genusSolanum
Authors: Gagnon Edeline , Hilgenhof Rebecca , Orejuela Andrés , McDonnell Angela , Sablok Gaurav , Aubriot Xavier , Giacomin Leandro , Gouvêa Yuri , Bragionis Thamyris , Stehmann João Renato , Bohs Lynn , Dodsworth Steven , Martine Christopher , Poczai Péter , Knapp Sandra , Särkinen Tiina 
Published: March 2021

AbstractPremise of the studyEvolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance inSolanum,one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants.MethodsA densely sampled species-level phylogeny ofSolanumis built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS,waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species ofSolanum(Angiosperms353 probe set).Key resultsWhile the taxonomic framework ofSolanumremained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node ofSolanum,could potentially represent a hard polytomy.ConclusionsWe argue that incomplete lineage sorting due to rapid diversification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.
Experimental characterization ofin silicored-shift predicted iLOVL470T/Q489Kand iLOVV392K/F410V/A426Smutants
Authors: Wehler Pierre , Armbruster Daniel , Günter Andreas , Schleicher Erik , Di Ventura Barbara , Öztürk Mehmet Ali 
Published: March 2021

AbstractiLOV is a flavin mononucleotide-binding fluorescent protein used forin vivocellular imaging similar to the green fluorescent protein. To expand the range of applications of iLOV, spectrally tuned red-shifted variants are desirable to have reduced phototoxicity and better tissue penetration. In this report, we experimentally tested two iLOV mutants, iLOVL470T/Q489Kand iLOVV392K/F410V/A426S, which were previously computationally proposed by Khrenova et al. (DOI: 10.1021/acs.jpcb.7b07533) to have red-shifted excitation and emission spectra. We found that mutants bearing the V392K mutation lost the ability to bind FMN. While iLOVL470T/Q489Kis about 20% brighter compared to WT iLOVin vitro, it exhibits a blue shift in contrast to QM/MM predictions. Additionally, both mutants are expressed at low levels and have undetectable fluorescence in living cells, which prevents their utilization in imaging applications. Our results suggest that rational fluorescent protein design efforts can benefit fromin silicoprotein stability and ligand affinity calculations.
Multi-centre, multi-vendor 7 Tesla fMRI reproducibility of hand digit representation in the human somatosensory cortex
Authors: Driver Ian D , Sanchez Panchuelo Rosa M , Mougin Olivier , Asghar Michael , Kolasinski James , Clarke William T , Rua Catarina , Morgan Andrew T , Carpenter Adrian , Muir Keith , Porter David , Rodgers Christopher T , Clare Stuart , Wise Richard G , Bowtell Richard , Francis Susan T 
Published: March 2021

AbstractWhilst considerable progress has been made in using ultra-high field fMRI to study brain function at fine spatial resolution, methods are generally optimized at a single site and do not translate to studies where multiple sites are required for sufficient subject recruitment. With a recent increase in installations of human 7 T systems, there is now the opportunity to establish a framework for multi-site 7 T fMRI studies. However, an understanding of the inter-site variability of fMRI measurements is required for datasets to be combined across sites. To address this, we employ a hand digit localization task and compare across-site and within-site reproducibility of 7 T fMRI to a hand digit localization task which requires fine spatial resolution to resolve individual digit representations. As part of the UK7T Network “Travelling Heads” study, 10 participants repeated the same hand digit localization task at five sites with whole-body 7T MRI systems to provide a measure of inter-site variability. A subset of the participants (2 per site) performed repeated sessions at each site for measurement of intra-site reproducibility. Dice’s overlap coefficient was used to assess reproducibility, with hand region inter-site Dice = 0.70±0.04 significantly lower than intrasite Dice = 0.76±0.06, with similar trends for the individual digit maps. Although slightly lower than intra-site reproducibility, the inter-site reproducibility results are consistent with previous single site reproducibility measurements, providing evidence that multi-site 7 T fMRI studies are feasible. These results can be used to inform sample size calculations for future multi-site somatomotor mapping studies.
Synergy between vesicular and non-vesicular gliotransmission regulates synaptic plasticity and working memory
Authors: Lalo Ulyana , Rasooli-Nejad Seyed , Bogdanov Alexander , More Lorenzo , Koh Wuhyun , Muller Jurgen , Wall Mark , Lee C. Justin , Pankratov Yuriy 
Published: March 2021

SUMMARYAstrocytes are an active element of brain signalling, capable of release of small molecule gliotransmitters by vesicular and channel-mediated mechanisms. However, specific physiological roles of astroglial exocytosis of glutamate and D-Serine remain controversial. Our data demonstrate that cortical astrocytes can release glutamate and D-Serine by combination of SNARE-dependent exocytosis and non-vesicular mechanisms dependent on TREK-1 and Best1 channels. Astrocyte-derived glutamate and D-serine elicited complex multicomponent phasic response in neocortical pyramidal neurons, which is mediated by extra-synaptic GluN2B receptors. Impairment of either pathway of gliotransmission (in the TREK1 KO, Best-1 KO or dnSNARE mice) strongly affected the NMDAR-dependent long-term synaptic plasticity in the hippocampus and neocortex. Moreover, impairment of astroglial exocytosis in dnSNARE mice led to the deficit in the spatial working memory which was rescued by environmental enrichment.We conclude that synergism between vesicular and non-vesicular gliotransmission is crucial for astrocyte-neuron communication and astroglia-driven regulation of synaptic plasticity and memory.HighlightsAstrocytesin siturelease glutamate via exocytosis and channel-mediated release.Astroglia-derived glutamate and D-Serine activate phasic NMDAR currents in neuronsBoth vesicular and non-vesicular gliotransmission are required for synaptic plasticityImpaired exocytosis of gliotransmitters causes deficit in working memory
Interactions among Diameter, Myelination and the Na/K pump Affect Axonal Resilience to High Frequency Spiking
Authors: Zang Yunliang , Marder Eve 
Published: March 2021

AbstractAxons reliably conduct action potentials between neurons and/or other targets. Axons have widely variable diameters and can be myelinated or unmyelinated. Although the effect of these factors on propagation speed is well studied, how they constrain axonal resilience to high frequency spiking is incompletely understood. Maximal firing frequencies range from ~ 1 Hz to > 300 Hz across neurons, but the process by which Na/K pumps counteract Na+influx is slow, and it is unclear the extent to which slow Na+removal is compatible with high frequency spiking. Modeling the process of Na+removal shows that large diameter axons are more resilient to high frequency spikes than small diameter axons, because of their slow Na+accumulation. In myelinated axons, the myelinated compartments between nodes of Ranvier act as a ‘reservoir’ to slow Na+accumulation and increase the reliability of axonal propagation. We now find that slowing the activation of K+current can increase the Na+influx rate, and the effect of minimizing the overlap between Na+- and K+-currents on spike propagation resilience depends on complex interactions among diameter, myelination and the Na/K pump density. Our results suggest that, in neurons with different channel gating kinetic parameters, different strategies may be required to improve the reliability of axonal propagation.Significance StatementThe reliability of spike propagation in axons is determined by complex interactions among ionic currents, ion pumps and morphological properties. We use compartment-based modeling to reveal that interactions of diameter, myelination and the Na/K pump determine the reliability of high frequency spike propagation. By acting as a ‘reservoir’ of nodal Na+influx, myelinated compartments efficiently increase propagation reliability. Although spike broadening was thought to oppose fast spiking, its effect on spike propagation is complicated, depending on the balance of Na+channel inactivation gate recovery, Na+influx and axial charge. Our findings suggest that slow Na+removal influences axonal resilience to high frequency spike propagation, and that different strategies may be required to overcome this constraint in different neurons.
Temporal attention selectively enhances target features
Authors: Ramirez Luis D. , Foster Joshua J. , Ling Sam 
Published: March 2021

AbstractHow does directing attention to a moment in time augment vision? Here, we examined the computations by which temporal attention – the allocation of attention to a moment in time – improves perception, under a divisive normalization framework. Under this framework, attention can improve perception of a target signal in three ways:stimulus enhancement(increasing gain across all sensory channels),signal enhancement(selectively increasing gain in channels that encode the target stimulus), orexternal noise exclusion(reducing the gain in channels that encode irrelevant features). These mechanisms make diverging predictions when a target is embedded in varying levels of noise: stimulus enhancement improves performance only when noise is low, signal enhancement improves performance at all noise intensities, and external noise exclusion improves performance only when noise is high. To date, temporal attention studies have used noise-free displays. Therefore, it is unclear whether temporal attention acts via stimulus enhancement (amplifying both target features and noise) or signal enhancement (selectively amplifying target features) because both mechanisms predict improved performance in the absence of noise. To tease these mechanisms apart, we manipulated temporal attention using an auditory cue while parametrically varying external noise in a fine-orientation discrimination task. Temporal attention improved performance across all noise levels. Formal model comparisons revealed that this cueing effect was best accounted for by a combination of signal enhancement and stimulus enhancement, suggesting that temporal attention improves perceptual performance, in part, by selectively increasing gain for target features.
Quantifying isolation-by-resistance and connectivity in dendritic ecological networks
Authors: Chafin Tyler K. , Mussmann Steven M. , Douglas Marlis R. , Douglas Michael E. 
Published: March 2021

ABSTRACTA central theme in landscape ecology is the translation of individual movements within a population by deconstructing/interpreting the components of its topographical environment. Most such endeavors rely heavily on the concept of ’landscape resistance’ – a composite of an arbitrary number of features/covariates that, when identified/compiled, yield a ‘surface’ inversely related to net movement. However, the statistical methodologies underlying this compilation have limited applicability when applied to dendritic ecological networks (DENs), including riverscapes.Herein we provide an analytical framework (ResistNet) that more appropriately annotates DEN segments by first aligning individual genetic distances with environmental covariates within a graph structure, then employing a genetic algorithm to optimise a composite model.We evaluated the efficacy of our method by first testing itin silicoacross an array of sampling designs, spatial trajectories, and levels of complexity, then applying it in an empirical case study involving 13,218 ddRAD loci from N=762 Speckled Dace (Leuciscidae:Rhinichthys osculus), sampled across N=78 Colorado River localities. By doing so, we underscored the utility of ResistNet within a large-scale conservation study, as well as identified prerequisites for its appropriate application.Our contemporary framework not only allows an interpretation of meta-population/meta-community structure across DENs, but also highlights several innovative applications. These are: (a) Expanding an ongoing study design, and thus its hypotheses, into yet unsampled temporal and/or spatial arenas, and; (b) Promoting multi-species management through comparative analyses that extend across species and/or drainages.
Prevalence, incidence and risk factors for myopia among urban and rural children in southern China: protocol for a school-based cohort study
Authors: Chen Xin , Ye Guofang , Zhong Yuxin , Jin Ling , Liang Xiaoling , Zeng Yangfa , Zheng Yingfeng , Morgan Ian , Liu Yizhi 
Published: March 2021

ABSTRACTIntroductionMyopia is the common cause of reduced uncorrected visual acuity among school-age children. It is more prevalent in urban than in rural areas. Although many myopia studies have focused on the effect of urbanization, it remains unclear how visual experience in urban regions could affect childhood myopia. This study aims to investigate the incidence and prevalence of myopia among school-age children in urban and rural settings, thereby identifying the environmental factors that affect the onset and progression of myopia.Methods and analysisA school-based cohort study will be conducted. We will enroll all first-grade students from an urban (10 primary schools) and a rural (10 primary schools) regions of Zhaoqing City, China. Over the 3-year follow-up period, students will receive detailed eye examinations annually and complete questionnaires about living habits and environment. In a 5% random subsample of the cohort, physical activity, light intensity, and eye-tracking data will be obtained using wearable devices. The primary outcome is incident myopia, defined as myopia detected during follow up among those without myopia at baseline.Ethics and DisseminationEthics approval was obtained from the ethics committee of the Zhongshan Ophthalmic Center (number: 2019KYPJ171). Study findings will be published in a peer-reviewed journal.Trial registration numberNCT04219228ARTICLE SUMMARYStrengths and limitations of this studyThis is a longitudinal, school-based cohort study to assess the incidence and prevalence of myopia among school-age children in both urban and rural settings.Large sample size and the representative study population.Light exposure and daily activities will be measured using wearable devices in a random subsample of the cohort.A myopia prediction model will be established using a deep learning algorithm based on the collected data.
Increased angiotensin-converting enzyme 2, sRAGE and immune activation, but lowered calcium and magnesium in COVID-19: association with chest CT abnormalities and lowered peripheral oxygen saturation
Authors: Al-Hakeim Hussein Kadhem , Al-Jassas Hawraa Kadhem , Morris Gerwyn , Maes Michael 
Published: March 2021

AbstractBackgroundThe characterization of new biomarkers of COVID-19 is extremely important. Few studies measured the soluble receptor for advanced glycation end product (sRAGE), angiotensin-converting enzyme 2 (ACE2), calcium and magnesium in COVID-19.AimsTo measure sRAGE, ACE2, interleukin (IL) -6, IL-10, CRP, calcium, magnesium, and albumin in COVID-19 patients in association with peripheral oxygen saturation (SpO2) and chest CT scan abnormalities (CCTA) including ground glass opacities.MethodsThis study measured sRAGE, ACE2, IL-6, IL-10, CRP using ELISA techniques, and calcium, magnesium, and albumin using a spectrophotometric method in 60 COVID-19 patients and 30 healthy controls.ResultsCOVID-19 is characterized by significantly increased IL-6, CRP, IL-10, sRAGE, ACE2, and lowered levels of SpO2, albumin, magnesium and calcium. Neural networks showed that a combination of calcium, IL-6, CRP, and sRAGE yielded an accuracy of 100% in detecting COVID-19 patients with calcium being the most important predictor followed by IL-6, and CRP. COVID-19 patients with CCTAs showed lower SpO2 and albumin levels than those without CCTAs. SpO2 was significantly and inversely correlated with IL-6, IL-10, CRP, sRAGE, and ACE2, and positively with albumin, magnesium and calcium. Patients with positive IgG results showed a significant elevation in the serum level of IL-6, sRAGE, and ACE2 compared to the negatively IgG patient subgroup.ConclusionThe results show that immune-inflammatory and RAGE pathway biomarkers may be used as external validating criterion for the diagnosis COVID-19. Those pathways coupled with lowered SpO2, calcium and magnesium are drug targets that may help to reduce the consequences of COVID-19.
Positive selection on mitochondria may eliminate heritable microbes from arthropod populations
Authors: Fenton Andy , Camus M Florencia , Hurst Gregory D D 
Published: March 2021

AbstractThe majority of arthropod species carry facultative heritable microbes, bacteria that are passed from mother to offspring, and which may contribute to host function. These symbionts are coinherited down the maternal line with mitochondria, and selection favouring either new symbionts, or new symbiont variants, is known to drive loss of mitochondrial diversity as a correlated response. More recently, evidence has accumulated of episodic directional selection on mitochondria. We therefore examined the reciprocal interaction and model the impact of selection on mitochondrial DNA (mtDNA) on symbiont frequency. We performed this for three generic scenarios: a fixed benefit to the host carrying the symbiont, a benefit that decreased with symbiont frequency, and a benefit that increased with symbiont frequency. We find that direct selection on mtDNA can drive symbionts out of the population under some circumstances. Symbiont extinction occurs where the positively selected mtDNA mutation occurs initially in an individual that is uninfected with the symbiont, and the symbiont is initially at low frequency. When, in contrast, the positively selected mtDNA mutation occurs in a symbiont infected individual, the mutation becomes fixed and in doing so removes symbiont variation from the population. Given low frequency symbiont infections are common in natural populations, and selection on mtDNA is also considered to occur frequently, we conclude that mtDNA driven loss of symbionts represents a novel mechanism driving loss of facultative heritable microbes. We conclude further that the molecular evolution of symbionts and mitochondria, which has previously been viewed from a perspective of selection on symbionts driving the evolution of a neutral mtDNA marker, should be reappraised in the light of positive selection on mtDNA. Where low mtDNA and symbiont genetic diversity are observed, it should not be assumed to be a consequences of selection acting on the symbiont.
Spatial-frequency features of radiation produced by a step-wise tapered undulator
Authors: Trebushinin Andrei , Serkez Svitozar , Veremchuk Mykola , Rakshun Yakov , Geloni Gianluca 
Published: March 2021

A scheme to generate wide-bandwidth radiation using a step-wise tapered undulator with a segmented structure is proposed. This magnetic field configuration allows to broaden the undulator harmonic spectrum by two orders of magnitude, providing 1 keV bandwidth with spectral flux density exceeding 1016 photons s−1 mm−2 (0.1% bandwidth)−1 at 5 keV on the sample. Such a magnetic setup is applicable to superconducting devices where magnetic tapering cannot be arranged mechanically. The resulting radiation with broadband spectrum and flat-top shape may be exploited at a multipurpose beamline for scanning over the spectrum at time scales of 10–100 ms. The radiation from a segmented undulator is described analytically and derivations with numerical simulations are verified. In addition, a start-to-end simulation of an optical beamline is performed and issues related to the longitudinally distributed radiation source and its image upon focusing on the sample are addressed.