bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of a novel immersive Virtual Reality setup with responses of wild-caught freely-moving coral reef fish
Authors: Vidal Manuel , Mills Suzanne C. , Gairin Emma , Bertucci Frédéric , Lecchini David 
Published: November 2022

AbstractVirtual Reality (VR) enables standardised stimuli to invoke behavioural responses in animals, however, in fish studies VR has been limited to either basic virtual stimulation projected below the bowl for freely-swimming individuals or a simple virtual arena rendered over a large field-of-view for head-restrained individuals. We developed a novel immersive VR setup with real-time rendering of animated 3D scenarios, validated in a proof of concept study on the behaviour of coral reef post-larval fish. Fish use a variety of cues to select a habitat during the recruitment stage, and to recognize conspecifics and predators, but which visual cues are used remains unknown. We measured behavioural responses of groups of five convict surgeonfish (Acanthurus triostegus) to simulations of habitats, static or moving shoals of conspecifics, predators, and non-aggressive heterospecifics. Post-larval fish were consistently attracted to virtual corals and conspecifics presented statically, but repulsed by their predators (bluefin jacks,Caranx melampygus). When simulated shoals passed nearby repeatedly, they were again attracted by conspecifics showing a tendency to follow the shoal, whereas they moved repeatedly to the back of the passing predator shoal. They also discriminated between species of similar sizes: they were attracted more to conspecifics than butterflyfish (Forcipiger longirostris), and repulsed more by predators than parrotfish (Scarus psittacus). The quality of visual simulations was high enough to identify between visual cues – size, body shape, colour pattern – used by post-larval fish in species recognition. Despite a tracking technology limited to fish 2D positions in the aquarium, preventing the real-time updating of the rendered viewpoint, we could show that VR and modern tracking technologies offer new possibilities to investigate fish behaviour through the quantitative analysis of their physical reactions to highly-controlled scenarios.
Differential Patterns of Synaptic Plasticity in the Nucleus Accumbens Caused by Continuous and Interrupted Morphine Exposure
Authors: Lefevre Emilia M. , Gauthier Elysia A. , Bystrom Lauren L. , Scheunemann Jordan , Rothwell Patrick E. 
Published: November 2022

ABSTRACTOpioid exposure and withdrawal both cause adaptations in brain circuits that may contribute to abuse liability. These adaptations vary in magnitude and direction following different patterns of opioid exposure, but few studies have systematically manipulated the pattern of opioid administration while measuring neurobiological impact. In this study, we compared cellular and synaptic adaptations in the nucleus accumbens shell caused by morphine exposure that was either continuous, or interrupted by daily bouts of naloxone-precipitated withdrawal. At the behavioral level, continuous morphine administration caused psychomotor tolerance, which was reversed when the continuity of morphine action was interrupted by naloxone-precipitated withdrawal. Usingex vivoslice electrophysiology in female and male mice, we investigated how these patterns of morphine administration altered intrinsic excitability and synaptic plasticity of medium spiny neurons (MSNs) expressing the D1 or D2 dopamine receptor. We found that morphine-evoked adaptations at excitatory synapses were predominately conserved between patterns of administration, but there were divergent effects on inhibitory synapses and the subsequent balance between excitatory and inhibitory synaptic input. Overall, our data suggest that continuous morphine administration produces adaptations that dampen the output of D1-MSNs, which are canonically thought to promote reward-related behaviors. Interruption of otherwise continuous morphine exposure does not dampen D1-MSN functional output to the same extent, which may enhance behavioral responses to subsequent opioid exposure. Our findings support the hypothesis that maintaining continuity of opioid administration could be an effective therapeutic strategy to minimize the vulnerability to opioid use disorders.
AMPKα2 is a skeletal muscle stem cell intrinsic regulator of myonuclear accretion
Authors: Kneppers A , Theret M , Ben Larbi S , Gsaier L , Saugues A , Dabadie C , Ferry A , Sakamoto K , Mounier R 
Published: November 2022

SUMMARYDue to the post-mitotic nature of skeletal muscle fibers, adult muscle maintenance relies on dedicated muscle stem cells (MuSCs). In most physiological contexts, MuSCs support myofiber homeostasis by contributing to myonuclear accretion, which requires a coordination of cell-type specific events between the myofiber and MuSCs. Here, we addressed the role of the kinase AMPKα2 in the coordination of these events supporting myonuclear accretion. We demonstrate that AMPKα2 deletion impairs skeletal muscle regeneration. Throughin vitroassessments of MuSC myogenic fate and EdU-based cell tracing, we reveal a MuSC-specific role of AMPKα2 in the regulation of myonuclear accretion, which is mediated by phosphorylation of the non-metabolic substrate BAIAP2. Similar cell tracingin vivoshows that AMPKα2 knockout mice have a lower rate of myonuclear accretion during regeneration, and that MuSC-specific AMPKα2 deletion decreases myonuclear accretion in response to myofiber contraction. Together, this demonstrates that AMPKα2 is a MuSC-intrinsic regulator of myonuclear accretion.
Molecular dynamics simulations of the calmodulin-induced α-helix in the SK2 calcium-gated potassium ion channel
Authors: Ramis Rafael , R. Ballesteros Óscar , Muguruza-Montero Arantza , M-Alicante Sara , Núñez Eider , Villarroel Álvaro , Leonardo Aritz , Bergara Aitor 
Published: November 2022

AbstractThe family of small-conductance (SK) ion channels is composed of four members (SK1, SK2, SK3, and SK4) involved in neuron-firing regulation. The gating of these channels depends on the intracellular Ca2+concentration, and their sensitivity to this ion is provided by calmodulin (CaM). This protein binds to a specific region in SK channels known as the calmodulin-binding domain (CaMBD), an event which is essential for their gating. While CaM-binding domains are typically disordered in the absence of CaM, the SK2 channel subtype displays a small pre-folded α-helical region in its CaMBD even if CaM is not present. This small helix is known to turn into a full α-helix upon CaM binding, although the molecular-level details for this conversion are not fully understood yet. In this work, we offer new insights on this physiologically relevant process by means of enhanced sampling, atomistic Hamiltonian replica exchange molecular dynamics simulations, providing a more detailed understanding of CaM binding to this target. Our results show that CaM is necessary for inducing a full α-helix along the SK2 CaMBD through hydrophobic interactions with V426 and L427. However, it is also necessary that W431 does not compete for these interactions; the role of the small pre-folded α-helix in the SK2 CaMBD would be to stabilize W431 so that this is the case.
Co-translational binding of importins to nascent proteins
Authors: Seidel Maximilian , Romanov Natalie , Obarska-Kosinska Agnieszka , Becker Anja , de Azevedo Nayara Trevisan Doimo , Provaznik Jan , Nagaraja Sankarshana R. , Landry Jonathan J. M. , Benes Vladimir , Beck Martin 
Published: November 2022

AbstractVarious cellular quality control mechanisms support proteostasis. While, ribosome-associated chaperones prevent misfolding of nascent chains during translation, importins were shown to prevent the aggregation of specific cargoes in a post-translational mechanism prior the import into the nucleoplasm. Here, we hypothesized that importins may already bind ribosome-associated cargo in a co-translational manner. We systematically measured the nascent chain association of all importins inSaccharomyces cerevisiaeby selective ribosome profiling. We identified a subset of importins that bind to a wide range of nascent, often uncharacterized cargoes. This included ribosomal proteins, chromatin remodelers and RNA binding proteins that are aggregation prone in the cytosol. We show that importins act consecutively with other ribosome-associated chaperones. Thus, the nuclear import system is directly intertwined with nascent chain folding and chaperoning.One-Sentence SummaryWe describe an unanticipated connection between co-translational protein chaperoning and the nuclear import system.
Early endosomes act as local exocytosis hubs to repair endothelial membrane damage
Authors: Raj Nikita , Greune Lilo , Kahms Martin , Mildner Karina , Franzkoch Rico , Psathaki Olympia Ekaterini , Zobel Thomas , Zeuschner Dagmar , Klingauf Jürgen , Gerke Volker 
Published: November 2022

AbstractThe plasma membrane of a cell is subject to stresses causing ruptures that must be repaired immediately to preserve membrane integrity and ensure cell survival. Yet, the spatio-temporal membrane dynamics at the wound site and the source of membrane required for wound repair are poorly understood. Here, we show that early endosomes, previously only known to function in the uptake of extracellular material and its endocytic transport, are involved in plasma membrane repair in human endothelial cells. Using live-cell imaging and correlative light and electron microscopy, we demonstrate that membrane injury triggers a previously unknown exocytosis of early endosomes that is induced by Ca2+entering through the wound. This exocytosis is restricted to the vicinity of the wound site and mediated by the endosomal SNARE VAMP2, which is crucial for efficient membrane repair. Thus, the here identified Ca2+-evoked and localized exocytosis of early endosomes supplies the membrane material required for rapid resealing of a damaged plasma membrane, thereby providing the first line of defense against damage in mechanically challenged endothelial cells.
Loss of the centrosomal protein ALMS1 alters lipid metabolism and the regulation of extracellular matrix-related processes
Authors: Bea-Mascato Brais , Gómez-Castañeda Eduardo , Sánchez-Corrales Yara E. , Castellano Sergi , Valverde Diana 
Published: November 2022

ABSTRACTBackgroundAlström syndrome (ALMS) is a rare autosomal recessive disease that is associated with mutations inALMS1gene. The main clinical manifestations of ALMS are retinal dystrophy, obesity, type 2 diabetes mellitus, dilated cardiomyopathy and multi-organ fibrosis, characteristic in kidneys and liver. Depletion of the protein encoded byALMS1has been associated with the alteration of different processes regulatedviathe primary cilium, such as the NOTCH or TGF-β signalling pathways. However, the cellular impact of these deregulated pathways in the absence of ALMS1 remains unknown.MethodsIn this study, we integrated RNA-seq and proteomic analysis to determine the gene expression profile of hTERT-BJ-5ta ALMS1 knockout fibroblasts after TGF-β stimulation. In addition, we studied alterations in cross-signalling between the TGF-β pathway and the AKT pathway in this cell line.ResultsWe found that ALMS1 depletion affects the TGF-β pathway and its cross-signalling with other pathways such as PI3K/AKT, EGFR1 or p53. In addition, alterations associated with ALMS1 depletion clustered around the processes of extracellular matrix regulation and lipid metabolism in both the transcriptome and proteome. By studying the enriched pathways of common genes differentially expressed in the transcriptome and proteome, collagen fibril organisation, β-oxidation of fatty acids and eicosanoid metabolism emerged as key processes altered by the absence of ALMS1. Finally, an overactivation of the AKT pathway was determined in the absence of ALMS1 that could be explained by a decrease inPTENgene expression.ConclusionALMS1 deficiency disrupts cross-signalling between the TGF-β pathway and other dependent pathways in hTERT-BJ-5ta cells. Furthermore, altered cross-signalling impacts the regulation of extracellular matrix-related processes and fatty acid metabolism, and leads to over-activation of the AKT pathway.
Primordial germ cells adjust their protrusion type while migrating in different tissue contextsin vivo
Authors: Truszkowski Lukasz , Batur Dilek , Long Hongyan , Tarbashevich Katsiaryna , Vos Bart E. , Trappmann Britta , Raz Erez 
Published: November 2022

AbstractIn both physiological processes and disease contexts, migrating cells have the ability to adapt to conditions in their environment. As anin vivomodel for this process, we use zebrafish primordial germ cells that migrate throughout the developing embryo. When migrating within an ectodermal environment, the germ cells form fewer and smaller blebs as compared with their behavior within mesodermal environment. We find that cortical tension of neighboring cells is a parameter that affects blebbing frequency. Interestingly, the change in blebbing activity is accompanied by the formation of more actin-rich protrusions. These alterations in cell behavior that correlate with changes in RhoA activity could allow the cells to maintain dynamic motility parameters, such as migration speed and track straightness, in different settings. In addition, we find that the polarity of the cells can be affected by stiff structures positioned in their migration path.
Aircraft route optimization with simulated annealing for a mixed airspace composed of free and fixed route structures
Authors: Aydoğan Emre , Cetek Cem 
Published: November 2022

Purpose
The purpose of this paper is to create a flight route optimization for all flights that aims to minimize the total cost consists of fuel cost, ground delay cost and air delay cost over the fixed route and free route airspaces.

Design/methodology/approach
Efficient usage of current available airspace capacity becomes more and more important with the increasing flight demands. The efficient capacity usage of an airspace is generally in contradiction to optimum flight efficiency of a single flight. It can only be achieved with the holistic approach that focusing all flights over mixed airspaces and their routes instead of single flight route optimization for a single airspace. In the scope of this paper, optimization methods were developed to find the best route planning for all flights considering the benefits of all flights not only a single flight. This paper is searching for an optimization to reduce the total cost for all flights in mixed airspaces. With the developed optimization models, the determination of conflict-free optimum routes and delay amounts was achieved with airway capacity and separation minimum constraints in mixed airspaces. The mathematical model and the simulated annealing method were developed for these purposes.

Findings
The total cost values for flights were minimized by both developed mathematical model and simulated annealing algorithm. With the mathematical model, a reduction in total route length of 4.13% and a reduction in fuel consumption of 3.95% was achieved in a mixed airspace. The optimization algorithm with simulated annealing has also 3.11% flight distance saving and 3.03% fuel consumption enhancement.

Research limitations/implications
Although the wind condition can change the fuel consumption and flight durations, the paper does not include the wind condition effects. If the wind condition effect is considered, the shortest route may not always cause the least fuel consumption especially under the head wind condition.

Practical implications
The results of this paper show that a flight route optimization as a holistic approach considering the all flight demand information enhances the fuel consumption and flight duration. Because of this reason, the developed optimization model can be effectively used to minimize the fuel consumption and reduce the exhaust emissions of aircraft.

Originality/value
This paper develops the mathematical model and simulated annealing algorithm for the optimization of flight route over the mixed airspaces that compose of fixed and free route airspaces. Each model offers the best available and conflict-free route plan and if necessary required delay amounts for each demanded flight under the airspace capacity, airspace route structure and used separation minimum for each airspace.
Corporate social responsibility and firm market performance: the role of product market competition and firm life cycle
Authors: Al-Dhamari Redhwan , Al-Gamrh Bakr , Farooque Omar Al , Moses Elaigwu 
Published: November 2022

PurposeThis study empirically investigates the role of product market competition and mature-stage firm life cycle on the relation between corporate social responsibility (CSR) and market performance in an emerging market context – Malaysia.Design/methodology/approachThe authors construct a comprehensive CSR index toward the economy, environment and society (EES) and apply both Ordinary Least Squares (OLS) and Two-Stage Least Squares (2SLS) instrumental variables (IV) approaches to test the hypotheses of the study.FindingsThe authors find that EES-based CSR generally enhances firms' market performance; however, the level of product market competition undermines the market performance of socially and economically responsible firms. In addition, the study results indicate that mature-stage firm life cycle with more involvement in CSR activities shows better market performance. However, the endogeneity check of CSR suggests that both CSR and mature-stage firms are mutually exclusive in influencing market performance. The study findings are robust to alternative measures and different identifications of high and low default risk situations of sample firms.Practical implicationsThis study carries practical policy implications for the listed firms, regulators and stakeholders in general. For example, regulatory bodies may promote greater involvement in CSR activities by listed companies in the Malaysian stock market. Investors and other market participants should be aware of factors influencing socially responsible firms' market performance such as the corporate life cycle and the level of competition in product markets.Originality/valueThis research work responds to the call of regulatory bodies in Malaysia at a time when the Malaysian economy is under threat of environmental distraction practices by the palm oil industry and import ban by the largest export market, i.e. the European Union by 2030. The study also contributes to the theoretical literature by refining the moderating role of product market competition and mature-stage life cycle on the relationship between CSR and market performance from the perspectives of resource-based and stakeholder theories in emerging economy settings.
Acceleration of structural topology optimization using symmetric element-by-element strategy for unstructured meshes on GPU
Authors: Ratnakar Shashi Kant , Kiran Utpal , Sharma Deepak 
Published: November 2022

PurposeStructural topology optimization is computationally expensive due to the involvement of high-resolution mesh and repetitive use of finite element analysis (FEA) for computing the structural response. Since FEA consumes most of the computational time in each optimization iteration, a novel GPU-based parallel strategy for FEA is presented and applied to the large-scale structural topology optimization of 3D continuum structures.Design/methodology/approachA matrix-free solver based on preconditioned conjugate gradient (PCG) method is proposed to minimize the computational time associated with solution of linear system of equations in FEA. The proposed solver uses an innovative strategy to utilize only symmetric half of elemental stiffness matrices for implementation of the element-by-element matrix-free solver on GPU.FindingsUsing solid isotropic material with penalization (SIMP) method, the proposed matrix-free solver is tested over three 3D structural optimization problems that are discretized using all hexahedral structured and unstructured meshes. Results show that the proposed strategy demonstrates 3.1× –3.3× speedup for the FEA solver stage and overall speedup of 2.9× –3.3× over the standard element-by-element strategy on the GPU. Moreover, the proposed strategy requires almost 1.8× less GPU memory than the standard element-by-element strategy.Originality/valueThe proposed GPU-based matrix-free element-by-element solver takes a more general approach to the symmetry concept than previous works. It stores only symmetric half of the elemental matrices in memory and performs matrix-free sparse matrix-vector multiplication (SpMV) without any inter-thread communication. A customized data storage format is also proposed to store and access only symmetric half of elemental stiffness matrices for coalesced read and write operations on GPU over the unstructured mesh.
Enduring buyer–supplier relationship and buyer performance: the mediating role of buyer–supplier dyadic embeddedness and supplier external embeddedness
Authors: Li Xun , Wu Qun , Goldsby Thomas J. , Holsapple Clyde W. 
Published: November 2022

PurposeThe purpose of this research is to investigate the causal mechanisms that explain the relationship between the long-term buyer–supplier relationship and buyer performance. Building on the growing body of research on social capital in supply chain management (SCM), the authors examine how a buyer achieves superior performance in forming the enduring partnership with a supplier through two different forms of supplier embeddedness: buyer–supplier dyadic embeddedness and supplier external embeddedness.Design/methodology/approachThe bootstrapping method is utilized in data analysis to examine the mediating effects of the two different forms of supplier embeddedness simultaneously on the linkage between the duration of buyer–supplier relationships and buyer performance outcomes.FindingsThe authors find that the two forms of supplier embeddedness serve as distinct conduits for the buyer to translate the long-term buyer–supplier relationship into performance effectiveness. Notably, dyadic embeddedness only mediates the linkage between the duration of buyer–supplier relationships and buyer economic performance, while supplier external embeddedness solely mediates the linkage between the duration of buyer–supplier relationships and buyer innovation performance.Originality/valueThis study empirically demonstrates that different forms of supplier embeddedness may benefit a buyer differentially when directed at distinct performance goals. If a buyer can leverage both buyer–supplier dyadic embeddedness and supplier external embeddedness, the buyer will overcome value creation limitations of social capital from a single source, obtaining more comprehensive performance benefits sought by developing long-term buyer–supplier relationships.