bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vespids from the mid-Cretaceous with club-shaped antennae provide new evidence about the intrafamiliar relationships of Vespidae
Authors: Wu Qiong , Yang Hongru , Shih Chungkun , Ren Dong , Zhao Yunyun , Gao Taiping 
Published: September 2020

AbstractThree new species of wasps (Hymenoptera: Vespidae) from mid-Cretaceous Myanmar (Burmese) amber, with club-shaped antennae, are assigned to Archaeovespa gen. nov. and provide morphological information for new phylogenetic analyses of Vespidae. Phylogenetic results suggest that Archaeovespa has more affinities with Masarinae than with Protovespinae and, along with Masarinae, composes the sister clade to Polistinae, Eumeninae, Vespinae and Stenogastrinae. New findings indicate that the antennal morphologies of Vespidae diversified significantly during or before the mid-Cretaceous.
What does success look like for air quality policy? A perspective
Authors: Monks Paul S. , Williams Martin L. 
Published: September 2020

This paper explores the drivers and role of science in air quality policy over the last 100 years or so. Case studies on the smogs of Los Angeles and London, acid rain, health impacts of particulate matter, diesel and lead in fuel are used to explore the drivers and models for the interaction of science, evidence and air quality policy. It suggests there are two phases to air quality mitigation, the first driven by the air quality emergency as the pollution is visible and the effects can be relatively obvious and the second driven by science that is directed towards continuous improvement. A critical element of the ‘science phase’ is the evidence base, the models of evidence-based and -informed policy-making are explored with the conclusion that it is optimal when guided by the ideal of co-creation of knowledge and policy options between scientists and policy-makers. The future and wider drivers for air quality are detailed with a number of key areas for ‘success’ indicated as important for air quality policy development such as continuous improvement. Overall, we find there is tension between two factors: the ambition to reduce emissions, improve air quality and reduce the impacts on public health and the environment on one hand, and questions of cost, technical feasibility and societal acceptability on the other.
This article is part of a discussion meeting issue ‘Air quality, past present and future’.
Action imitation via trajectory-based or posture-based planning
Authors: Barhorst-Cates Erica M. , Isaacs Mitchell W. , Buxbaum Laurel J. , Wong Aaron L. 
Published: September 2020

AbstractImitation is a significant daily activity involved in social interaction and motor learning. Imitation has been theorized to be performed in at least two ways. In posture-based imitation, individuals reproduce how the body should look and feel, and are sensitive to the relative positioning of body parts. In trajectory imitation, individuals mimic the spatiotemporal motion path of the end effector. There are clear anecdotal situations in which one might benefit from imitating postures (when learning ballet) or trajectories (when learning to reach around objects). However, whether these are in fact distinct methods of imitation, and if so, whether they may be applied interchangeably to perform the same task, remain unknown. If these are indeed separate mechanisms that rely on different computational and neural resources, a cost should be incurred when switching from using one mechanism to the other within the context of a single task. Therefore observing a processing cost would both provide evidence that these are indeed two distinct mechanisms, and that they may be used interchangeably when trying to imitate the same stimulus. To test this, twenty-five healthy young adults performed a sequential multitasking imitation task. Participants were first instructed to pay attention to the limb postures or the hand path of a video-recorded model, then performed a neutral, congruent, or incongruent intervening motor task. Finally, participants imitated the modeled movement. Spatiotemporal imitation accuracy was greatest after a neutral intervening task, and worst after posture matching. When the primary task involved imitating trajectories, the data suggested a processing cost: movements following the posture-matching intervening task were less consistent with baseline (neutral) performance, suggesting performance may be disrupted by the incongruence. This effect was not observed when imitating limb postures. In summary, we present initial evidence of a partial dissociation between posture matching and trajectory imitation as a result of instructions and intervening tasks that is consistent with the existence of two computationally distinct imitation mechanisms.
Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion
Authors: Woodward Xinxin , Javanainen Matti , Fábián Balázs , Kelly Christopher V. 
Published: September 2020

AbstractThe precise spatiotemporal control of nanoscale membrane shape and composition is the result of complex interplay of individual and collective molecular behaviors. Here, we employed single-molecule localization microscopy and computational simulations to observe single-lipid diffusion and sorting in model membranes with varying compositions, phase, temperature, and curvature. Supported lipid bilayers were created over 50-nm radius nanoparticles to mimic the size of naturally occurring membrane buds, such as endocytic pits and the formation of viral envelopes. The curved membranes recruited liquid-disordered lipid phases while altering the diffusion and sorting of tracer lipids. Disorder-preferring fluorescent lipids sorted to and experienced faster diffusion on the nanoscale curvature only when embedded in a membrane capable of sustaining lipid phase separation at low temperatures. The curvature-induced sorting and faster diffusion even occurred when the sample temperature was above the miscibility temperature of the planar membrane, implying that the nanoscale curvature could induce phase separation in otherwise homogeneous membranes. Further confirmation and understanding of these results are provided by continuum and coarse-grained molecular dynamics simulations with explicit and spontaneous curvature-phase coupling, respectively. The curvature-induced membrane compositional heterogeneity and altered dynamics were achieved only with a coupling of the curvature with a lipid phase separation. These cross-validating results demonstrate the complex interplay of lipid phases, molecular diffusion, and nanoscale membrane curvature that are critical for membrane functionality.SignificanceNanoscopic membrane organization and dynamics are critical for cellular function but challenging to experimentally measure. This work brings together super-resolution optical methods with multiscale computational approaches to reveal the interplay between curvature, composition, phase, and diffusion in model membranes. We report that curvature can induce phase separation in otherwise homogeneous membranes and that the phase-curvature coupling has a direct implication on lipid mobility. This discovery advances our understanding of the fundamental membrane biophysics that regulate membrane activities such as endocytosis and viral budding.
Predicting the Key Regulators of Cell Identity in Human Adult Pancreas
Authors: Vanheer Lotte , Fantuzzi Federica , To San Kit , Schiavo Andrea Alex , Van Haele Matthias , Haesen Tine , Yi Xiaoyan , Janiszewski Adrian , Chappell Joel , Rihoux Adrien , Sawatani Toshiaki , Roskams Tania , Pattou Francois , Kerr-Conte Julie , Cnop Miriam , Pasque Vincent 
Published: September 2020

SUMMARYCellular identity during development is under the control of transcription factors that form gene regulatory networks. However, the transcription factors and gene regulatory networks underlying cellular identity in the human adult pancreas remain largely unexplored. Here, we integrate multiple single-cell RNA-sequencing datasets of the human adult pancreas, totaling 7393 cells, and comprehensively reconstruct gene regulatory networks. We show that a network of 142 transcription factors forms distinct regulatory modules that characterize pancreatic cell types. We present evidence that our approach identifies regulators of cell identity in the human adult pancreas. We predict that HEYL, BHLHE41 and JUND are active in acinar, beta and alpha cells, respectively, and show that these proteins are present in the human adult pancreas as well as in human induced pluripotent stem cell (hiPSC)-derived islet cells. Using single-cell transcriptomics, we found that JUND represses beta cell genes in hiPSC-alpha cells. Both BHLHE41 and JUND depletion seemed to increase the number of sc-enterochromaffin cells in hiPSC-derived islets. The comprehensive gene regulatory network atlas can be explored interactively online. We anticipate our analysis to be the starting point for a more sophisticated dissection of how transcription factors regulate cell identity in the human adult pancreas. Furthermore, given that transcription factors are major regulators of embryo development and are often perturbed in diseases, a comprehensive understanding of how transcription factors work will be relevant in development and disease.HIGHLIGHTSReconstruction of gene regulatory networks for human adult pancreatic cell typesAn interactive resource to explore and visualize gene expression and regulatory statesPrediction of putative transcription factors that drive pancreatic cell identityBHLHE41 depletion in primary islets induces apoptosis
Treeline ecotones shape the distribution of avian species richness and functional diversity in south temperate mountains
Authors: Altamirano Tomás A. , de Zwaan Devin R. , Ibarra José Tomás , Wilson Scott , Martin Kathy 
Published: September 2020

AbstractMountains produce distinct environmental gradients that may constrain or facilitate both the presence of avian species and/or specific combinations of functional traits. We addressed species richness and functional diversity to understand the relative importance of habitat structure and elevation in shaping avian diversity patterns in the south temperate Andes, Chile. During 2010-2018, we conducted 2,202 point-counts in four mountain habitats (successional montane forest, old-growth montane forest, subalpine, and alpine) from 211 to 1,768 m in elevation and assembled trait data associated with resource use for each species to estimate species richness and functional diversity and turnover. We detected 74 species. Alpine specialists included 16 species (22%) occurring only above treeline with a mean elevational range of 298 m, while bird communities below treeline (78%) occupied a mean elevational range of 1,081 m. Treeline was an inflection line, above which species composition changed by 91% and there was a greater turnover in functional traits (2–3 times greater than communities below treeline). Alpine birds were almost exclusively migratory, inhabiting a restricted elevational range, and breeding in rock cavities. We conclude that elevation and habitat heterogeneity structure avian trait distributions and community composition, with a diverse ecotonal sub-alpine and a distinct alpine community.
Multi-scale Modeling Toolbox for Single Neuron and Subcellular Activity under (repetitive) Transcranial Magnetic Stimulation
Authors: Shirinpour Sina , Hananeia Nicholas , Rosado James , Galanis Christos , Vlachos Andreas , Jedlicka Peter , Queisser Gillian , Opitz Alexander 
Published: September 2020

AbstractTranscranial Magnetic Stimulation (TMS) is a non-invasive brain stimulation technique widely used in research and clinical applications. However, its mechanism of action and the neural response to TMS are still poorly understood. Multi-scale modeling can complement experimental research and provide a framework between the physical input parameters and the subcellular neural effects of TMS. At the macroscopic level, sophisticated numerical models exist to estimate the induced electric fields in whole-brain volume conductor models. However, multi-scale computational modeling approaches to predict TMS cellular and subcellular responses, crucial to understanding TMS plasticity inducing protocols, are not available so far. Here, we develop a multi-scaleNeuron Modeling for TMStoolbox (NeMo-TMS) that enables researchers to easily generate accurate neuron models from morphological reconstructions, couple them to the external electric fields induced by TMS, and to simulate the cellular and subcellular responses of the neurons. Both single-pulse and rTMS protocols can be simulated and results visualized in 3D. We openly share our toolbox and provide example scripts and datasets for the user to explore.NeMo-TMStoolbox (https://github.com/OpitzLab/NeMo-TMS) allows researchers a previously not available level of detail and precision in realistically modeling the physical and physiological effects of TMS.
Measuring Protein Insertion Areas in Lipid Monolayers by Fluorescence Correlation Spectroscopy
Authors: Auerswald Jan , Ebenhan Jan , Schwieger Christian , Scrima Andrea , Meister Annette , Bacia Kirsten 
Published: September 2020

AbstractThe insertion of protein domains into membranes is an important step in many membrane remodeling processes, for example in vesicular transport. The membrane area taken up by the protein insertion influences the protein binding affinity as well as the mechanical stress induced in the membrane and thereby its curvature. Total area changes in lipid monolayers can be measured on a Langmuir film balance. Finding the area per inserted protein however proves challenging for two reasons: The number of inserted proteins must be determined without disturbing the binding equilibrium and the change in the film area can be very small. Here we address both issues using Fluorescence Correlation Spectroscopy (FCS): Firstly, by labeling a fraction of the protein molecules fluorescently and performing FCS experiments directly on the monolayer, the number of inserted proteins is determinedin situwithout having to rely on invasive techniques, such as collecting the monolayer by aspiration. Secondly, by using another FCS color channel and adding a small fraction of fluorescent lipids, the reduction in fluorescent lipid density accompanying protein insertion can be monitored to determine the total area increase. Here, we use this method to determine the insertion area per molecule of Sar1, a protein of the COPII complex, which is involved in transport vesicle formation, in a lipid monolayer. Sar1 has an N-terminal amphipathic helix, which is responsible for membrane binding and curvature generation. An insertion area of (3.4 ± 0.8) nm2was obtained for Sar1 in monolayers from a lipid mixture typically used in reconstitution, in good agreement with the expected insertion area of the Sar1 amphipathic helix. By using the two-color approach, determining insertion areas relies only on local fluorescence measurements. No macroscopic area measurements are needed, giving the method the potential to be applied also to laterally heterogeneous monolayers and bilayers.Statement of SignificanceWe show that two color Fluorescence Correlation Spectroscopy (FCS) measurements can be applied to the binding of a protein to a lipid monolayer on a Langmuir film balance in order to determine the protein insertion area. One labelling color was used to determine the number of bound proteins and the other one to monitor the area expansion of the lipid monolayer upon protein binding. A strategy for the FCS data analysis is provided, which includes focal area calibration by raster image correlation spectroscopy and a framework for applying z-scan FCS and including free protein in the aqueous subphase. This approach allows determining an area occupied by a protein in a quasi-planar model membrane from a local, non-invasive, optical measurement.
Understanding the emergence of contingent and deterministic exclusion in multispecies communities
Authors: Song Chuliang , Uricchio Lawrence H. , Mordecai Erin A. , Saavedra Serguei 
Published: September 2020

AbstractCompetitive exclusion can be classified as deterministic or as historically contingent. While competitive exclusion is common in nature, it has remained unclear when multispecies communities should be dominated by deterministic or contingent exclusion. Here, we provide a general theoretical approach to explain both the emergence and sources of competitive exclusion in multispecies communities. We illustrate our approach on an empirical competition system between annual and perennial plant species. First, we find that the life-history of perennial species increases the probability of observing contingent exclusion by increasing their effective intrinsic growth rates. Second, we find that the probability of observing contingent exclusion increases with weaker intraspecific competition, and not with the level of hierarchical competition. Third, we find a shift from contingent exclusion to dominance with increasing numbers of competing species. Our work provides a heuristic framework to increase our understanding about the predictability of species persistence within multispecies communities.
Hamilton’s rule, gradual evolution, and the optimal (feedback) control of phenotypically plastic traits
Authors: Avila Piret , Priklopil Tadeas , Lehmann Laurent 
Published: September 2020

AbstractMost traits expressed by organisms, such as gene expression profiles, developmental trajectories, behavioural sequences and reaction norms are function-valued traits (colloquially “phenotypically plastic traits”), since they vary across an individual’s age and in response to various internal and/or external factors (state variables). Furthermore, most organisms live in populations subject to limited genetic mixing and are thus likely to interact with their relatives. We here formalise selection on genetically determined function-valued traits of individuals interacting in a group-structured population, by deriving the marginal version of Hamilton’s rule for function-valued traits. This rule simultaneously gives a condition for the invasion of an initially rare mutant function-valued trait and its ultimate fixation in the population (invasion thus implies substitution). Hamilton’s rule thus underlies the gradual evolution of function-valued traits and gives rise to necessary first-order conditions for their uninvadability (evolutionary stability). We develop a novel analysis using optimal control theory and differential game theory, to simultaneously characterise and compare the first-order conditions of (i) open-loop traits - functions of time (or age) only, and (ii) closed-loop (state-feedback) traits - functions of both time and state variables. We show that closed-loop traits can be represented as the simpler open-loop traits when individuals do no interact or when they interact with clonal relatives. Our analysis delineates the role of state-dependence and interdependence between individuals for trait evolution, which has implications to both life-history theory and social evolution.
Antimicrobial efficacy of neem and liquorice with chlorhexidine on Streptococcus sanguis, Streptococcus mutans, Lactobacillus and Actinomyces naeslundii – An In Vitro Study
Authors: Alqahtani Saad M 
Published: September 2020

AbstractThe study was to formulate 2% neem and 2% liquorice mouthwashes and to compare the antimicrobial efficacy of these mouthwashes with the standard 0.2% chlorhexidine mouthwash. Alcoholic solution was prepared and added to neem mixture and liquorice mixture separately and made up to a volume of 16000 ml with purified water. Nine dilutions of each drug were done with Brain heart infusion broth (BHI) for MIC. Culture suspension was added in each serially diluted tube of 200 μl. The tubes were incubated for 24 hours and observed for turbidity. Minimum inhibitory concentration (MIC) of 2% neem, 2% liquorice and 0.2% chlorhexidine against Lactobacillus, Actinomyces naeslundii, Streptococcus sanguis, Streptococcus mutans is determined by serial dilution analysis. Streptococcus mutans shows sensitivity to all three mouthwashes at a concentration starting from 0.2 μg/ml. Lactobacillus shows sensitivity to neem and chlorhexidine mouthwashes at a concentration starting from 1.6 μg/ml, whereas liquorice is effective at a concentration starting from 3.125 μg/ml. Streptococcus sanguis shows sensitivity to chlorhexidine and liquorice mouthwashes at a concentration starting from 25 μg/ml, whereas it shows sensitivity to neem at a concentration starting from 50 μg/ml. Actinomyces naeslundii shows sensitivity to chlorhexidine and neem mouthwashes at a concentration starting from 1.6 μg/ml, whereas it shows sensitivity to liquorice at a concentration starting from 3.125μg/ml. Analysis showed an inhibition of all the four strains by the mouthwashes. The MIC for the studied mouthwashes was found to be similar to that of 0.2% chlorhexidine.
Decoding representations of discriminatory and hedonic information during appetitive and aversive touch
Authors: Kryklywy James H. , Ehlers Mana R. , Beukers Andre O. , Moore Sarah R. , Todd Rebecca M. , Anderson Adam K. 
Published: September 2020

AbstractEmotion is typically understood to be an internal subjective experience originating in the brain. Yet in the somatosensory system hedonic information is coded by mechanoreceptors at the point of sensory contact before it reaches the central nervous system. It remains unknown, however, how these distinct peripheral channels for tactile hedonic information contribute to representations of interoceptive states relative to exteroceptive experience. In this fMRI study we applied representational similarity analyses with pattern component modeling, a technique that deconstructs representational states into a weighted set of distinct predefined constructs, to dissociate how discriminatory vs. hedonic tactile information, carried by A- and C-/CT-fibers respectively, contributes to population code representations in the human brain. Results demonstrated that information about appetitive and aversive tactile sensation is represented separately from non-hedonic tactile information across cortical structures. Specifically, although hedonic touch originates as a peripheral signal, labeled at the point of contact, representations in somatosensory cortices are guided by experiences of non-hedonic touch, By contrast, representations in regions associated with interoception and affect encode signals of hedonic touch. This provides evidence of complex tactile encoding that involves both external-exteroceptive and internal-interoceptive dimensions. Importantly, hedonic touch contributes to representations of internal state as well as those of externally generated stimulation.
Novelty is not Surprise: Human exploratory and adaptive behavior in sequential decision-making
Authors: Xu He A. , Modirshanechi Alireza , Lehmann Marco P. , Gerstner Wulfram , Herzog Michael H. 
Published: September 2020

AbstractClassic reinforcement learning (RL) theories cannot explain human behavior in response to changes in the environment or in the absence of external reward. Here, we design a deep sequential decision-making paradigm with sparse reward and abrupt environmental changes. To explain the behavior of human participants in these environments, we show that RL theories need to include surprise and novelty, each with a distinct role. While novelty drives exploration before the first encounter of a reward, surprise increases the rate of learning of a world-model as well as of model-free action-values. Even though the world-model is available for model-based RL, we find that human decisions are dominated by model-free action choices. The world-model is only marginally used for planning but is important to detect surprising events. Our theory predicts human action choices with high probability and allows us to dissociate surprise, novelty, and reward in EEG signals.