bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the trail-following pheromone receptor in termites
Authors: Diallo Souleymane , Kašparová Kateřina , Šulc Josef , Johny Jibin , Křivánek Jan , Nebesářová Jana , Sillam-Dussès David , Kyjaková Pavlína , Vondrášek Jiří , Machara Aleš , Lukšan Ondřej , Grosse-Wilde Ewald , Hanus Robert 
Published: July 2024

ABSTRACTChemical communication is the cornerstone of eusocial insect societies since it mediates the social hierarchy, division of labor, and concerted activities of colony members. The chemistry of social insect pheromones received considerable attention in both major groups of social insects, the eusocial Hymenoptera and termites. By contrast, current knowledge on molecular mechanisms of social insect pheromone detection by odorant receptors (ORs) is limited to hymenopteran social insects and no OR was yet functionally characterized in termites, the oldest eusocial insect clade. Here, we present the first OR deorphanization in termites. Using the data from antennal transcriptome and genome of the termiteProrhinotermes simplex(Rhinotermitidae), we selected 4 candidate OR sequences, expressed them in Empty NeuronDrosophila, and functionally characterized using single sensillum recording (SSR) and a panel of termite semiochemicals. In one of the selected ORs, PsimOR14, we succeeded in obtaining strong and reliable responses to the main component ofP. simplextrail-following pheromone, the monocyclic diterpene neocembrene. PsimOR14 showed a narrow tuning to neocembrene; only one additional compound out of 72 tested (geranylgeraniol) generated non-negligible responses. Subsequently, we used SSR andP. simplexworkers to identify the olfactory sensillum specifically responding to neocembrene, thus likely expressingPsimOR14. We report on homology-based modelling of neocembrene binding by PsimOR14 and show how different ligands impact the receptor dynamicity using molecular dynamics simulations. Finally, we demonstrate thatPsimOR14is significantly more expressed in workers than in soldiers, which correlates with higher sensitivity of workers to neocembrene.
Evolution of novel mimicry polymorphisms through Haldane’s sieve and rare recombination
Authors: Deshmukh Riddhi , Baral Saurav , Kizhakke Athulya Girish , Kuwalekar Muktai , Kunte Krushnamegh 
Published: July 2024

AbstractOrigins of phenotypic novelty represent a paradox. Maintenance of distinct, canalized morphs usually requires a complex array of polymorphisms, whose co-retention requires a genetic architecture resistant to recombination, involving inversions and master regulators. Here, we reveal how such a constraining architecture can still accommodate novel morphs in evolving polymorphisms using the classic polymorphic Batesian mimicry inPapilio polytes, whose supergene-like genetic architecture is maintained in a large inversion. We show that rapidly evolving alleles of the conserved gene,doublesex, within this inversion underlie the genetic basis of this polymorphism. Using precisely dated phylogeny and breeding experiments, we show that novel adaptive mimetic morphs and underlying alleles evolved in a sequentially dominant manner, undergoing selective sweeps in the mimetic species as predicted under Haldane’s sieve. Furthermore, we discovered that mimetic forms share precise inversion breakpoints, allowing rare exon swaps between the universally dominant and a recessive allele to produce a novel, persistent intermediate phenotype, ultimately facilitating the acquisition of phenotypic novelty. Thus, genetic dominance, selective sweeps, rapid molecular divergence, and rare recombination promote novel forms in this iconic evolving polymorphism, resolving the paradox of phenotypic novelty arising even in highly constrained genetic architectures.
Environmental “Wiggles” as Stabilizers of Species Range Limits Set by Interspecific Competition
Authors: Shirani Farshad , Freeman Benjamin G. 
Published: July 2024

AbstractWhether interspecific competition is a major contributing factor in setting species’ range limits has been debated for a long time. Evolutionary models have helped propose a possible mechanism: interspecific competition interacts with the disruptive effects of gene flow along an environmental gradient to halt range expansion of species when they meet and compete with each other. However, the stability of such range limits has not previously been well-addressed. Here we use a deterministic evolutionary model to show that, when the environmental gradient varies linearly in space, range limits set by interspecific competition are unlikely to be evolutionarily stable. However, we demonstrate that step-like nonlinearities in the environmental optimum for a fitness-related phenotypic trait, or sharp changes in the steepness of the trait optimum, can stabilize competitively-formed range limits. We show that the stability of the range limits established at such nonlinearities is sufficiently robust against environmental perturbations such as climate change. We note that strong climatic changes can still destabilize the range limits, depending on how the relative dominance of the species changes across the environmental nonlinearities. Therefore, our results further highlight the importance of measuring the competitive ability of species when predicting their response to climate change.
ZIBGLMM: Zero-Inflated Bivariate Generalized Linear Mixed Model for Meta-Analysis with Double-Zero-Event Studies
Authors: Li Lu , Lin Lifeng , Cappelleri Joseph C. , Chu Haitao , Chen Yong 
Published: July 2024

AbstractDouble-zero-event studies (DZS) pose a challenge for accurately estimating the overall treatment effect in meta-analysis. Current approaches, such as continuity correction or omission of DZS, are commonly employed, yet these ad hoc methods can yield biased conclusions. Although the standard bivariate generalized linear mixed model can accommodate DZS, it fails to address the potential systemic differences between DZS and other studies. In this paper, we propose a zero-inflated bivariate generalized linear mixed model (ZIBGLMM) to tackle this issue. This two-component finite mixture model includes zero-inflation for a subpopulation with negligible or extremely low risk. We develop both frequentist and Bayesian versions of ZIBGLMM and examine its performance in estimating risk ratios (RRs) against the bivariate generalized linear mixed model and conventional two-stage meta-analysis that excludes DZS. Through extensive simulation studies and real-world meta-analysis case studies, we demonstrate that ZIBGLMM outperforms the bivariate generalized linear mixed model and conventional two-stage metaanalysis that excludes DZS in estimating the true effect size with substantially less bias and comparable coverage probability.
Rescuing behavioral flexibility in a mouse model for OCD by enhancing reward-cue salience
Authors: van den Boom Bastijn J.G. , Carlo Sara De , van Klaveren Jennifer , Denys Damiaan , Willuhn Ingo 
Published: July 2024

AbstractDeficits in cognitive flexibility are a frequent symptom of obsessive-compulsive disorder (OCD) and have been hypothesized to underlie compulsive behavior. Sign- and goal-tracking behaviors are thought to be related to cognitive flexibility, yet have not been studied in this context. To investigate the relationship between sign- and goal-tracking behavior and cognitive flexibility, we tested SAPAP3 knockout mice (SAPAP3-/-) and wild-type littermate controls in a Pavlovian reversal-learning task with two conditioned stimuli, one predicting reward delivery and the other reward omission. SAPAP3-/-displayed a heterogenous reversal-learning performance: Half of the population failed to acquire the reversed cue-reward contingencies, whereas the other half reversed their approach behavior similar to control mice. Surprisingly, such behavioral inflexibility and compulsive-like grooming were unrelated, suggesting a non-causal relationship between these traits. Importantly, compromised reversal learning in impaired mice was associated with diminished sign-tracking behavior (and therefore presumably with an overreliance on goal-tracking behavior). Administration of the selective serotonin reuptake inhibitor (SSRI) fluoxetine, the first-line pharmacological OCD treatment, ameliorated both anxiety-like behavior and compulsive-like grooming, but did not improve behavioral flexibility in SAPAP3-/-. In contrast, enhancing reward-cue salience by altering conditioned stimuli brightness improved behavioral flexibility through augmenting sign-tracking behavior. These findings suggest that deficits in behavioral flexibility are associated with imbalanced sign- and goal-tracking behaviors in SAPAP3-/-, and enhancing reward-cue salience can rescue behavioral flexibility by restoring the balance. Thus, sign- and goal-tracking behavior might be an underexplored cognitive mechanism that could potentially be exploited to improve cognitive flexibility in OCD patients.
Chemokines Kill Bacteria by Binding Anionic Phospholipids without Triggering Antimicrobial Resistance
Authors: Pontejo Sergio M. , Martinez Sophia , Zhao Allison , Barnes Kevin , de Anda Jaime , Alimohamadi Haleh , Lee Ernest Y. , Dishman Acacia F. , Volkman Brian F. , Wong Gerard C.L. , Garboczi David N. , Ballesteros Angela , Murphy Philip M. 
Published: July 2024

ABSTRACTClassically, chemokines coordinate leukocyte trafficking during immune responses; however, many chemokines have also been reported to possess direct antibacterial activity in vitro. Yet, the bacterial killing mechanism of chemokines and the biochemical properties that define which members of the chemokine superfamily are antimicrobial remain poorly understood. Here we report that the antimicrobial activity of chemokines is defined by their ability to bind phosphatidylglycerol and cardiolipin, two anionic phospholipids commonly found in the bacterial plasma membrane. We show that only chemokines able to bind these two phospholipids killEscherichia coliandStaphylococcus aureusand that they exert rapid bacteriostatic and bactericidal effects againstE. coliwith a higher potency than the antimicrobial peptide beta-defensin 3. Furthermore, our data support that bacterial membrane cardiolipin facilitates the antimicrobial action of chemokines. Both biochemical and genetic interference with the chemokine-cardiolipin interaction impaired microbial growth arrest, bacterial killing, and membrane disruption by chemokines. Moreover, unlike conventional antibiotics,E. colifailed to develop resistance when placed under increasing antimicrobial chemokine pressure in vitro. Thus, we have identified cardiolipin and phosphatidylglycerol as novel binding partners for chemokines responsible for chemokine antimicrobial action. Our results provide proof of principle for developing chemokines as novel antibiotics resistant to bacterial antimicrobial resistance mechanisms.
Assessing the Relative Contributions of Mosaic and Regulatory Developmental Modes from Single-Cell Trajectories
Authors: Song Solène , Villoutreix Paul 
Published: July 2024

AbstractDevelopment is a highly complex process consisting of coordinated cell proliferation, cell differentiation and spatial organization. Classically, two ways to specify cell types during development are hypothesized : mosaic and regulative modes. In the mosaic mode, a particular cell isolated from the rest of the embryo will nevertheless give rise to cells with a fate identical to the ones expected in normal development, thus relying on lineage-inherited factors. In the regulative mode, the fate of a cell depends on its interactions with its environment, and thus relies on space-dependant factors. Both modes often coexist in the development of a given animal. We propose to quantify their respective contributions from single-cell trajectories.C. elegansdevelopment provides a unique opportunity to elaborate such an approach. Indeed, its invariant lineage enables the integration of spatial positions, lineage relationships and protein expression data. Using the single cell protein expression profile as a readout of the cell state, we relate the contributions of the mosaic and the regulative modes to the following measurable quantities. The contribution of the mosaic mode, or lineage-inherited contribution is quantified by the strength of the relationship between the cell-celllineage distanceand the cell-cellexpression distance. Similarly, the contribution of the regulative mode, or context-dependent contribution is quantified by the strength of the relationship between the cell-cellcontext distanceand the cell-cellexpression distance. The cell-cellcontext distancemeasures the similarity between the spatial neighborhoods of two cells based on the gene expression profiles of their neighbours. We assess the significance of these contributions by comparing the empirical results obtained onC. elegansdata to artificial models generated using simple rules. With these measures, we show the co-existence of mosaic and regulative modes in the development ofC. elegans. The relative contribution of these two modes varies across the different tissues and in time. In particular, we see in the skin tissue that during early development, the mosaic mode dominates while at later stages, regulative mode dominates, suggesting a convergence of single cell trajectories. These measures are general and can be applied to other datasets that will be made available with the progress of spatial transcriptomics and lineage-tracing, paving the way for a quantitative, unbiased and perturbation-free study of fundamental concepts in developmental biology.
Advancing Liver Gene Therapy: Enhanced Transduction with GalNAc-Bioconjugated rAAV Capsids
Authors: Lalys Pierre-Alban , Bourdon Audrey , Bouzelha Mohammed , Alvarez-Dorta Dimitri , Pavageau Karine , Girard Tiphaine , Peumery Roxane , Bouchouireb Zakaria , Marchand Maia , Mellet Anthony , Ledevin Mireille , Depienne Sébastien , Guilbaud Mickaël , Croyal Mikaël , Gouin Sébastien G. , Roubinet Benoit , Landemarre Ludovic , Adjali Oumeya , Ayuso Eduard , Larcher Thibaut , Le Guiner Caroline , Mével Mathieu , Deniaud David 
Published: July 2024

AbstractThis study investigates novel approaches to improve targeted gene delivery to the liver, a crucial organ for metabolic processes that faces vulnerabilities from various pathologies. Adeno-associated virus (AAV)-based gene therapy has emerged as a promising approach for liver targeting, with numerous investigational avenues. However, administration of high doses of AAV vectors present safety concerns, often requiring the use of corticosteroids and immunosuppression to mitigate immune adverse events. To address this, substantial efforts are underway to engineer optimized capsids to enhance the efficiency and specificity of recombinant AAV (rAAV) targeting hepatocytes, aiming to reduce required dosages. In this study, we employed bioconjugation chemistry to target the Asialoglycoprotein receptor (ASGPR), a C-type lectin abundantly expressed at the surface of hepatocyte membranes. We demonstrated that covalently attaching carbohydrates derived from GalNAc (a known ASGPR ligand) to lysine amino-acids on the rAAV2 capsid significantly enhancedin vivoliver transduction efficiency in mice. These optimized vectors present a promising avenue for the treatment of a spectrum of liver diseases, providing an alternative solution within the framework of liver gene therapy.
A Rose by any Other Name: Towards a quantitative theory of memory in neuroimmune memories
Authors: Fadai Nabil T. , Turcanu Victor , Nicolau Dan V. 
Published: July 2024

AbstractHumanity has known about – and been fascinated by – the connection between mind and body since time immemorial, yet we have only been able to begin to quantitatively explore their interactions in recent years. Even so, the field of neuroimmunology is categorically in its infancy. Despite myriad and diverse experimental reports, no coherent theoretical approach to the neuroimmune system has been even attempted, which makes it difficult to make sense of the emerging body of empirical findings. Here, we take the first steps towards this goal by introducing a mathematical framework that describes the triggering and control of neurological memories (engrams) of immune challenges. Using peanut allergies as a model system, we show how a simple differential equation model of coupled ‘immune-engram’ responses can explain a number of key observations regarding putative neurological control of focal inflammatory responses and failures thereof. Simulations of our model identify four areas of the parameter regime corresponding to distinct consequences of ‘fake’ immune stimulation: a) resolution b) finite oscillations of inflammation, followed by resolution c) sustained, self-amplifying oscillations (cytokine storm-like phenomena) and d) resolution followed by the permanent establishment of a chronic higher-baseline inflammatory state. Importantly, we then show how our model recapitulates the key qualitative features of a recent experimental description of immune engram encoding and re-activation (respectively, suppression) in a mouse model of colitis. We conclude with remarks around clinical implications as well as directions for future work in theoretical neuroimmunology.Abstract Figure
Mass and decay width of
Tccs
from symmetries
Authors: Tanaka Mitsuru , Yamaguchi Yasuhiro , Harada Masayasu 
Published: July 2024

We analyze the mass and width of the doubly heavy tetraquark Tccs composed of a heavy diquark and a light-quark cloud with strangeness with assuming that a color antitriplet heavy diquark is a dominant component of the doubly charmed tetraquarks Tcc and Tccs. We construct an effective Lagrangian for masses of heavy hadrons based on the superflavor symmetry between the doubly heavy tetraquarks and the singly heavy baryons by including the terms that simultaneously break the heavy-quark and light-flavor symmetries, and predict the mass of Tccs as M(Tccs)=4047±11  MeV. The comparison of this prediction with future experimental observation will give a clue to understand the color structure of the heavy diquark. We also predict the mass of Ωcc as M(Ωcc)=3706−15+14  MeV. We next calculate the decay width of Tccs, based solely on the light-flavor symmetry, as Γ(Tccs)=42±24  MeV.

Published by the American Physical Society
2024
Synthesis of organotin(IV) heterocycles containing a xanthenyl group by a Barbier approach via ultrasound activation: synthesis, crystal structure and Hirshfeld surface analysis
Authors: García-González J. Viridiana , Alvarado-Rodríguez José G. , Andrade-López Noemí , Zamora-Martínez Esmeralda , Jancik Vojtech , Martínez-Otero Diego 
Published: July 2024

A series of organotin heterocycles of general formula [{Me2C(C6H3CH2)2O}SnR
2] [R = methyl (Me, 4), n-butyl (n-Bu, 5), benzyl (Bn, 6) and phenyl (Ph, 7)] was easily synthesized by a Barbier-type reaction assisted by the sonochemical activation of metallic magnesium. The 119Sn{1H} NMR data for all four compounds confirm the presence of a central Sn atom in a four-coordinated environment in solution. Single-crystal X-ray diffraction studies for 17,17-dimethyl-7,7-diphenyl-15-oxa-7-stannatetracyclo[11.3.1.05,16.09,14]heptadeca-1,3,5(16),9(14),10,12-hexaene, [Sn(C6H5)2(C17H16O)], 7, at 100 and 295 K confirmed the formation of a mononuclear eight-membered heterocycle, with a conformation depicted as boat–chair, resulting in a weak Sn...O interaction. The Sn and O atoms are surrounded by hydrophobic C—H bonds. A Hirshfeld surface analysis of 7 showed that the eight-membered heterocycles are linked by weak C—H...π, π–π and H...H noncovalent interactions. The pairwise interaction energies showed that the cohesion between the heterocycles are mainly due to dispersion forces.
A thermo-mechanical fully coupled model for high-speed machining of Ti6Al4V
Authors: Zhou Zeyuan , Wang Ying , Xia Zhijie 
Published: July 2024

Purpose
This study aims to further refine the model, explore the influence of cutting parameters on the machining process, and apply it to practical engineering to improve the efficiency and quality of titanium alloy machining.

Design/methodology/approach
This paper establishes a comprehensive thermo-mechanical fully coupled orthogonal cutting model. This paper aims to couple the modified Johnson–Cook constitutive model, damage model and contact model to construct a two-dimensional orthogonal cutting thermo-mechanical coupling model for high-speed cutting of Ti6Al4V. The model considers the evolution of microstructures such as plastic deformation, grain dislocation rearrangement, dynamic recrystallization, as well as stress softening and hardening occurring continuously in Ti6Al4V metal during high-speed cutting. Additionally, the model incorporates friction and contact between the tool and the workpiece. It can be used to predict parameters such as cutting process, cutting force, temperature distribution, stress and strain in titanium alloy machining. The study establishes the model and implements corresponding functions by writing Abaqus VUMAT and VFRICTION subroutines.

Findings
The use of different material constitutive models can significantly impact the prediction of the cutting process. Some models may more accurately describe the mechanical behavior of the material, thus providing more reliable prediction results, while other models may exhibit larger deviations. Compared to the Tanh model, the proposed model achieves a maximum improvement of 8.9% in the prediction of cutting force and a maximum improvement of 20.9% in the prediction of chip morphology parameters. Compared to experiments, the proposed model achieves a minimum prediction error of 2.8% for average cutting force and a minimum error of 0.57% for sawtooth parameters. This study provides a comprehensive theoretical foundation and practical guidance for orthogonal cutting of titanium alloys. The model not only helps engineers and researchers better understand various phenomena in the cutting process but also serves as an important reference for optimizing cutting processes.

Originality/value
The originality of this research is guaranteed, as it has not been previously published in any journal or publication.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-05-2024-0168/