bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiomics unveils extracellular vesicle-driven mechanisms of endothelial communication in human carotid atherosclerosis
Authors: Raju Sneha , Turner Mandy E , Cao Christian , Abdul-Samad Majed , Punwasi Neil , Blaser Mark C , Cahalane Rachel ME , Botts Steven R , Prajapati Kamalben , Patel Sarvatit , Wu Ruilin , Gustafson Dakota , Galant Natalie J , Fiddes Lindsey , Chemaly Melody , Hedin Ulf , Matic Ljubica , Seidman Michael , Subasri Vallijah , Singh Sasha A , Aikawa Elena , Fish Jason E , Howe Kathryn L
Published: June 2024

Background:Carotid atherosclerosis is orchestrated by cell-cell communication that drives progression along a clinical continuum (asymptomatic to symptomatic). Extracellular vesicles (EVs) are cell-derived nanoparticles representing a new paradigm in cellular communication. Little is known about their biological cargo, cellular origin/destination, and functional roles in human atherosclerotic plaque.

Methods:EVs were enriched via size exclusion chromatography from human carotid endarterectomy samples dissected into paired plaque and marginal zones (symptomatic n=16, asymptomatic n=13). EV cargos were assessed via whole transcriptome miRNA sequencing and mass spectrometry-based proteomics. EV multi-omics were integrated with bulk and single cell RNA-sequencing (scRNA-seq) datasets to predict EV cellular origin and ligand-receptor interactions, and multi-modal biological network integration of EV-cargo was completed. EV functional impact was assessed with endothelial angiogenesis assays.

Results:Carotid plaques contained more EVs than adjacent marginal zones, with differential enrichment for EV-miRNAs and EV-proteins in key atherogenic pathways. EV cellular origin analysis suggested that tissue EV signatures originated from endothelial cells (EC), smooth muscle cells (SMC), and immune cells. Integrated tissue vesiculomics and scRNA-seq indicated complex EV-vascular cell communication that changed with disease progression and plaque vulnerability (i.e., symptomatic disease). Plaques from symptomatic patients, but not asymptomatic patients, were characterized by increased involvement of endothelial pathways and more complex ligand-receptor interactions, relative to their marginal zones. Plaque-EVs were predicted to mediate communication with ECs. Pathway enrichment analysis delineated an endothelial signature with roles in angiogenesis and neovascularization – well-known indices of plaque instability. This was validated functionally, wherein human carotid symptomatic plaque EVs induced sprouting angiogenesis in comparison to their matched marginal zones.

Conclusion:Our findings indicate that EVs may drive dynamic changes in plaques through EV- vascular cell communication and effector functions that typify vulnerability to rupture, precipitating symptomatic disease. The discovery of endothelial-directed angiogenic processes mediated by EVs creates new therapeutic avenues for atherosclerosis.
Analysis of live cell data with G-DNABERT supports a role for G-quadruplexes in chromatin looping
Authors: Konovalov Dmitry , Umerenkov Dmitry , Herbert Alan , Poptsova Maria
Published: June 2024

Alternative DNA conformation formed by sequences called flipons potentially alter the readout of genetic information by directing the shape-specific assembly of complexes on DNA The biological roles of G-quadruplexes formed by motifs rich in guanosine repeats have been investigated experimentally using many different methodologies including G4-seq, G4 ChIP-seq, permanganate nuclease footprinting (KEx), KAS-seq, CUT&Tag with varying degrees of overlap between the results. Here we trained large language model DNABERT on existing data generated by KEx, a rapid chemical footprinting technique performed on live, intact cells using potassium permanganate. The snapshot of flipon state when combined with results from other in vitro methods that are performed on permeabilized cells, allows a high confidence mapping of G-flipons to proximal enhancer and promoter sequences. Using G4-DNABERT predictions,with data from ENdb, Zoonomia cCREs and single cell G4 CUT&Tag experiments, we found support for a model where G4-quadruplexes regulate gene expression through chromatin loop formation.
Breathing modulates network activity in frontal brain regions during anxiety
Authors: Dias Ana L.A. , Drieskens Davi , Belo Joseph A. , Duarte Elis H. , Laplagne Diego A. , Tort Adriano B.L.
Published: June 2024

Anxiety elicits various physiological responses, including changes in respiratory rate and neuronal activity within specific brain regions such as the medial prefrontal cortex (mPFC). Previous research suggests that the olfactory bulb (OB) modulates the mPFC through respiration-coupled neuronal oscillations (RCOs), which have been linked to fear-related freezing behavior. Nevertheless, the impact of breathing on frontal brain networks during other negative emotional responses, such as anxiety-related states characterized by higher breathing rates, remains unclear. To address this, we subjected rats to the elevated plus maze (EPM) paradigm while simultaneously recording respiration and local field potentials in the OB and mPFC. Our findings demonstrate distinct respiratory patterns during EPM exploration: slower breathing frequencies prevailed in the closed arms, whereas faster frequencies were observed in the open arms, independent of locomotor activity, indicating that anxiety-like states are associated with increased respiratory rates. Additionally, we identified RCOs at different frequencies, mirroring the bimodal distribution of respiratory frequencies. RCOs exhibited higher power during open arm exploration, when they showed greater coherence with breathing at faster frequencies. Furthermore, we confirmed that nasal respiration drives RCOs in frontal brain regions, and found a stronger effect during faster breathing. Interestingly, we observed that the frequency of prefrontal gamma oscillations modulated by respiration increased with heightened anxiety levels and breathing frequency. Overall, our study provides evidence for a significant influence of breathing on prefrontal cortex networks during anxious states, shedding light on the complex interplay between respiratory physiology and emotional processing.

Significance Statement

Understanding how breathing influences brain activity during anxious states could pave the way for novel therapeutic interventions targeting respiratory control to alleviate anxiety symptoms. Our study uncovers a crucial link between respiratory patterns and anxiety-related neural activity in the brain. By investigating the interplay between breathing, neuronal oscillations, and emotional states, we reveal that anxiety induces distinct respiratory patterns, with higher breathing rates correlating with anxious behavior. Importantly, we demonstrate that respiration drives oscillatory activity in the prefrontal cortex, and this effect is potentiated during the fast breathing associated with anxiety. Furthermore, the breathing cycle modulates the emergence of prefrontal gamma oscillations differentially across anxiety levels. This discovery sheds new light on the intricate relationship between respiratory physiology and emotional processing.
ACtnnb1enhancer transcriptionally regulates Wnt signaling dosage to balance homeostasis and tumorigenesis of intestinal epithelia
Authors: Hua Xiaojiao , Zhao Chen , Tian Jianbo , Wang Junbao , Miao Xiaoping , Zheng Gen , Wu Min , Ye Mei , Liu Ying , Zhou Yan
Published: June 2024

The β-catenin-dependent canonical Wnt signaling is pivotal in organ development, tissue homeostasis, and cancer. Here we identified an upstream enhancer ofCtnnb1– the coding gene for β-catenin, named ieCtnnb1 (intestinalenhancer ofCtnnb1), which is crucial for intestinal homeostasis. ieCtnnb1 is predominantly active in the base of small intestinal crypts and throughout the epithelia of large intestine. Knockout of ieCtnnb1 led to a reduction inCtnnb1transcription, compromising the canonical Wnt signaling in intestinal crypts. Single-cell sequencing revealed that ieCtnnb1 knockout altered epithelial compositions and potentially compromised functions of small intestinal crypts. While deletion of ieCtnnb1 hampered epithelial turnovers in physiologic conditions, it prevented occurrence and progression of Wnt/β-catenin-driven colorectal cancers. Human ieCTNNB1 drove reporter gene expression in a pattern highly similar to mouse ieCtnnb1. ieCTNNB1 contains a single-nucleotide polymorphism associated withCTNNB1expression levels in human gastrointestinal epithelia. The enhancer activity of ieCTNNB1 in colorectal cancer tissues was stronger than that in adjacent normal tissues. HNF4αand phosphorylated CREB1 were identified as key trans-factors binding to ieCTNNB1 and regulatingCTNNB1transcription. Together, these findings unveil an enhancer-dependent mechanism controlling the dosage of Wnt signaling and homeostasis in intestinal epithelia.
Muscle Moment Arm–Joint Angle Relations in the Hip, Knee, and Ankle: A Visualization of Datasets
Authors: Chen Ziyu , Franklin David W.
Published: June 2024

Muscle moment arm is a property that associates muscle force with joint moment and is crucial to biomechanical analysis. In musculoskeletal sim-ulations, the accuracy of moment arm is as important as that of muscle force, and moment arm calibration requires data from anatomical measure-ments. Nonetheless, such data are elusive, and the complex relation between moment arm and joint angle can be unclear. Using common techniques in systematic review, we collected a total of 300 moment arm datasets from literature and visualized the muscle moment arm–joint angle relations in the hip, knee, and angle. The findings contribute to the understanding and anal-ysis of musculoskeletal mechanics, as well as providing reference regarding the experimental design for future moment arm measurements.
A proposed newTombusviridaegenus featuring extremely long 5’ untranslated regions and a luteo/polerovirus-like gene block
Authors: Lozier Zachary , Hill Lilyahna , Semmann Elizabeth , Miller W. Allen
Published: June 2024

Summary

Tombusviridaeis a large family of single-stranded, positive-sense RNA plant viruses with uncapped, non-polyadenylated genomes encoding 5-7 open reading frames (ORFs). Previously, we discovered, by high-throughput sequencing of maize and teosinte RNA, a novel genome of a virus we call Maize-associated tombusvirus (MaTV). Here we determined the precise termini of the MaTV genome by using 5’ and 3’ rapid amplification of cDNA ends (RACE). In GenBank, we discovered eleven other nearly complete viral genomes with MaTV-like genome organizations and related RNA-dependent RNA polymerase (RdRp) sequences. These genomes came from diverse plant, fungal, invertebrate and vertebrate organisms, and some have been found in multiple organisms across the globe. The available 5’ untranslated regions (UTRs) of these genomes are remarkably long: at least 438 to 727 nucleotides (nt), in contrast to those of other tombusvirids, which are <150 nt. Moreover these UTRs contain 6 to 12 AUG triplets that are unlikely to be start codons, because - with the possible exception of MaTV - there are no large or conserved ORFs in the 5’ UTRs. Such features suggest an internal ribosome entry site (IRES), but we found no conserved secondary structures. In the 50 nt upstream of and adjacent to the ORF1 start codon, the 5’ UTR was cytosine-rich and guanosine-poor. As in most tombusvirids, ORF2 (RdRp gene) appears to be translated by in-frame ribosomal readthrough of the ORF1 stop codon. Indeed, in all twelve genomes we identified RNA structures known in other tombusviruses to facilitate this readthrough. ORF5 is predicted to be translated by readthrough of the ORF3 (coat protein gene) stop codon as in genusLuteovirus. The resulting readthrough domains are highly divergent. ORF4 overlaps with ORF3 and may initiate with a non-AUG start codon. We also found no obvious 3’ cap-independent translation elements, which are present in other tombusvirids. The twelve genomes diverge sufficiently from other tombusvirids to warrant classification in a new genus. Because they contain two leaky stop codons and a potential leaky start codon, we propose to name this genusRimosavirus(rimosa= leaky in Latin).
Single and combined effect of salinity, heat, cold, and drought in Arabidopsis at metabolomics and photosynthetic levels
Authors: Secomandi Elena , De Gregorio Marco Armando , Castro-Cegrí Alejandro , Lucini Luigi
Published: June 2024

Ensuring food security is one of the main challenges related to a growing global population under climate change conditions. The increasing soil salinity levels, drought, heatwaves, and late chilling severely threaten crops and often co-occur in field conditions. This work aims to provide deeper insight into the impact of single vs combined abiotic stresses at the growth, biochemical and photosynthetic levels inArabidopsis thalianaL. By studying single and combined stresses, stress interactions and synergic effects have been highlighted. Lower photosynthetic efficiency was recorded from the beginning in all the conditions that included salinity. Consistently, membrane stability and ROS production, combined with a targeted metabolomic quantification of glycine, GABA, proline, and glycine-betaine molecular markers, highlighted the hierarchically stronger impact of salinity and its combinations on plant biochemistry. Untargeted metabolomics coupled with multivariate statistics pointed out distinct metabolic reprogramming triggered by the different stress conditions, either alone or in combination, differentiating the impact of salinity, drought, and their combination with cold and heat. These results contribute to delving into the impact of various stress combinations, hierarchically highlighting the stress-specific effects and pointing out different interactions.

HIGHLIGHTS

Combined stresses highlighted synergic and stronger impact on Arabidopsis secondary metabolism, redox imbalance and photosynthetic performance compared to individual stresses. Overall, salinity and its combination were the most impactful.
Development, validation and application of an LC-MS/MS method quantifying free forms of the micronutrients queuine and queuosine in human plasma using a surrogate matrix approach
Authors: Pan Xiaobei , Chandrasekaran Swathine , Woodside Jayne V. , Riedel-Heller Steffi G. , Scherer Martin , Wagner Michael , Ramirez Alfredo , Green Brian D.
Published: June 2024

Queuosine (Q) is a hypermodified 7-deaza-guanosine nucleoside exclusively synthesized by bacteria. This micronutrient and its respective nucleobase form queuine (q) are salvaged by humans either from gut microflora, or digested food. Depletion of Q-tRNA in human or mouse cells causes protein misfolding that triggers endoplasmic reticular stress and activation of the unfolded protein responses. In vivo, this reduces neuronal architecture of the mouse brain affecting learning and memory. Herein, a sensitive method for quantifying free q and Q in human blood was developed, optimised and validated.

After evaluating q/Q extraction efficiency in several different solid-phase sorbents, Bond Elut PBA (phenylboronic acid) cartridges were found to have the highest extraction recovery for q (82%) and Q (71%) from pooled human plasma. PBS with 4% BSA was used as surrogate matrix for method development and validation. An LC-MS/MS method was validated across the concentration range of 0.0003 – 1 µM for both q and Q, showing excellent: linearity (r2= 0.997 (q) and r2= 0.998 (Q)), limit of quantification (0.0003 µM), accuracy (100.39% - 125.71%) and precision (CV% < 15.68%). In a sampling of healthy volunteers (n = 44) there was no significant difference in q levels between male (n = 14; mean = 0.0068 µM) and female (n = 30; mean = 0.0080 µM) participants (p = 0.50). Q was not detected in human plasma. This validated method can now be used to further our understanding of the role of q/Q in nutrition, physiology and pathology.
Magnesium modulates phospholipid metabolism to promote bacterial phenotypic resistance to antibiotics
Authors: Li Hui , Yang Jun , Kuang Su-fang , Fu Huan-zhe , Lin Hui-ying , Peng Bo
Published: June 2024

Non-inheritable antibiotic or phenotypic resistance ensures bacterial survival during antibiotic treatment. However, exogenous factors promoting phenotypic resistance are poorly defined. Here, we demonstrate thatVibrio alginolyticusare recalcitrant to killing by a broad spectrum of antibiotics under high magnesium. Functional metabolomics demonstrated that magnesium modulates fatty acid biosynthesis by increasing saturated fatty acid biosynthesis while decreasing unsaturated fatty acid production. Exogenous supplementation of unsaturated and saturated fatty acids increased and decreased bacterial susceptibility to antibiotics, respectively, confirming the role of fatty acids in antibiotic resistance. Functional lipidomics revealed that glycerophospholipid metabolism is the major metabolic pathway remodeled by magnesium, where phosphatidylethanolamine (PE) biosynthesis is reduced and phosphatidylglycerol (PG) production is increased. This process alters membrane composition, increasing membrane polarization, and decreasing permeability and fluidity, thereby reducing antibiotic uptake byV. alginolyticus. These findings suggest the presence of a previously unrecognized metabolic mechanism by which bacteria escape antibiotic killing through the use of an environmental factor.
Dynamic HSF2 regulation drives breast cancer progression by steering the balance between proliferation and invasion
Authors: Pessa Jenny C. , Paavolainen Oona , Puustinen Mikael C. , Hästbacka Hendrik S. E. , Da Silva Alejandro J. , Pihlström Sandra , Gramolelli Silvia , Boström Pia , Hartiala Pauliina , Peuhu Emilia , Joutsen Jenny , Sistonen Lea
Published: June 2024

Phenotypic plasticity is a hallmark of breast carcinogenesis that facilitates the acquisition of invasive propertiesviaepithelial-mesenchymal transition (EMT). Transforming growth factor-beta (TGF-β), a key EMT-inducing cytokine, drives pro-metastatic gene programs through downstream transcription factors. Among mammalian stress-protective transcription factors, heat shock factor 2 (HSF2) has been associated with cancer progression, but the mechanisms regulating HSF2 expression and activity are unknown. Here, we demonstrate that TGF-β stimulation downregulates HSF2 to enable activation of an invasive phenotype. Remarkably, ectopic expression of HSF2 in breast cancer cells inhibited TGF-β-mediated effects on gene expression and cellular properties. By using bothin vitrocell models andin vivozebrafish xenografts, we found that a temporal downregulation of HSF2 is a prerequisite for EMT activation, while ectopically sustained HSF2 promotes rapid cell proliferation and survival. Analyses of human patient tissues corroborated our results by showing that HSF2 is dynamically regulated during breast cancer progression. Specifically, HSF2 expression and nuclear co-localization with the proliferation marker Ki67 are dramatically increased already in ductal carcinomain situ. Altogether, our findings expand the pathological landscape of HSF2, demonstrating that dynamic regulation of HSF2 is an inherent property of malignant progression and characterizes the distinct stages of breast cancer.
The Aggregated Gut Viral Catalogue (AVrC): A Unified Resource for Exploring the Viral Diversity of the Human Gut
Authors: Galperina Anastasia , Lugli Gabriele Andrea , Milani Christian , De Vos Willem M. , Ventura Marco , Salonen Anne , Hurwitz Bonnie , Ponsero Alise J.
Published: June 2024

Despite the growing interest in the role of the gut virome in human health and disease, identifying viral sequences from human gut metagenomes remains computationally challenging due to underrepresentation of viral genomes in reference databases. Several recent large-scale efforts have mined human gut metagenomes to establish viral sequence catalogues, using varied computational tools and quality control criteria. However, there has been no consistent comparison of these catalogues’ quality, diversity, and completeness, nor unification into a comprehensive resource. Here, we systematically surveyed nine previously published human gut viral catalogues, assessing their quality and the overlap of the viral sequences retrieved. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy. We further expanded representation by mining 7,867 infant gut metagenomes, retrieving 1,205,739 additional putative viral sequences. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Detailed annotations were generated for sequence quality, taxonomy, predicted lifestyle, and putative host. The AVrC reveals the gut virome’s substantial unexplored diversity, providing a pivotal resource for viral discovery. The AVrC is accessible as a relational database and through a web interface allowing customized querying and subset retrieval, enabling streamlined utilization by the research community and future expansions as novel data becomes available.

Author summary

The human gut is home to a vast array of viruses, collectively known as the gut virome, which play a crucial role in human health and disease. Recently, several research groups aiming at providing an overview of the Human gut viral diversity, have created catalogues of viral sequences found in the human gut by analyzing a large number of fecal samples from different individuals. In this study, we compared nine of these existing catalogues and found that there was surprisingly little overlap between them, with 82% of the viral sequences being unique to a single catalogue. To further expand the available data, we analyzed nearly 8,000 additional fecal samples from infants. By combining all this ressources, we created a unified resource called the Aggregated Gut Viral Catalogue (AVrC), which contains more than a million distinct viral sequences, representing nearly 450,000 different viral species. This catalogue, which is easily accessible to the scientific community through a user-friendly web interface, provides a valuable tool for exploring the vast diversity of the human gut virome and its potential implications for human health.
An efficient method for visualizing the plaques ofBdellovibrio bacteriovorus
Authors: Zhao Qian , Xu Jiangong , Zhu Kui
Published: June 2024

Bdellovibrio bacteriovoruspreys upon other Gram-negative bacteria. This obligate predator is recognized as a living antibiotic to control the rising problem of antibiotic resistance. Plaque forming units (PFU) counting is commonly used to determine the viable numbers ofB. bacteriovorus. However, nearly 3-days incubation is always necessary for getting the single, obvious plaques on the double layer agar plate. This time-consuming procedure greatly impedes the purification and enumeration efficiency ofB. bacteriovorus. In this work, we evaluated the advantages of fluorescent prey on the plaque visualization of the predator. Our study reveals that plaques of theB. bacteriovorushave already formed before they could be monitored by eyes on the double layer agar plate. The regular single plaques are easily observed under the enhanced background of fluorescent prey lawn in 1.5 days, reducing nearly half of the time consumption in the purification and enumeration ofB. bacteriovorus. In addition, it also provides some paradigms for modeling and testing the subtle predation process on the solid medium.

IMPORTANCE

The viability of predatorBdellovibrio bacteriovorusis typically suggested by the lysis of the prey bacteria on the double layer agar plate. However, long period incubation is necessary to get single obvious plaques ofB. bacteriovorus. Here, we found that plaques are already generated before it can be monitored by eyes. The plaques are obvious on the enhanced background of the double layer agar plate in the presence of fluorescent prey under UV light. We confirmed that the utilization of fluorescence labeled prey bacteria reduces the time spent on the isolation, purification, and enumeration of the predatorB. bacteriovoruson the double layer agar plate.
Polarity sorting of actin filaments by motor-driven cargo transport
Authors: Akenuwa Oghosa H. , Abel Steven M
Published: June 2024

During the active transport of cellular cargo, forces generated by cargo-associated molecular motors propel the cargo along cytoskeletal tracks. However, the forces impact not only the cargo, but also the underlying cytoskeletal filaments. To better understand the interplay between cargo transport and the organization of cytoskeletal filaments, we employ coarse-grained computer simulations to study actin filaments interacting with cargo-anchored myosin motors in a confined domain. We show that cargo transport can lead to the segregation of filaments into domains of preferred filament polarity separated by clusters of aggregated cargoes. The formation of polarity-sorted filament domains is enhanced by larger numbers of cargoes, more motors per cargo, and longer filaments. Analysis of individual trajectories reveals dynamic and heterogeneous behavior, including locally stable aggregates of cargoes that undergo rapid coalescence into larger clusters when sufficiently close. Our results provide insight into the impact of motor-driven organelle transport on actin filaments, which is relevant both in cells and in synthetic environments.
Tensing Flipper: Photosensitized manipulation of membrane tension, lipid phase separation and raft protein sorting in biological membranes
Authors: Torra Joaquim , Campelo Felix , Garcia-Parajo Maria F.
Published: June 2024

The lateral organization of proteins and lipids in the plasma membrane is fundamental to regulating a wide range of cellular processes. Compartmentalized ordered membrane domains enriched with specific lipids, often termed lipid rafts, have been shown to modulate the physicochemical and mechanical properties of membranes and to drive protein sorting. Novel methods and tools enabling the visualization, characterization and/or manipulation of membrane compartmentalization are crucial to link the properties of the membrane with cell functions. Flipper, a commercially-available fluorescent membrane tension probe, has become a reference tool for quantitative membrane tension studies in living cells. Here, we report on a so far unidentified property of Flipper, namely, its ability to photosensitize singlet oxygen (1O2) under blue light when embedded into lipid membranes. This in turn results in the production of lipid hydroperoxides that increase membrane tension and trigger phase separation. In biological membranes, the photo-induced segregated domains retain the sorting ability of intact phase-separated membranes, directing raft and non-raft proteins into ordered and disordered regions, respectively, in contrast to radical-based photo-oxidation reactions that disrupt raft protein partitioning. The dual tension reporting and photosensitizing abilities of Flipper enable simultaneous visualization and manipulation of the mechanical properties and lateral organization of membranes, providing a powerful tool to optically control lipid raft formation and to explore the interplay between membrane biophysics and cell function.
Giant caloric effects in spin-chain materials
Authors: Zvyagin A. A. , Slavin V. V.
Published: June 2024

The giant electro- and elastocaloric effects in spin-chain materials are predicted. The theory is based on the exact quantum mechanical solution of the problem. It is shown that the giant jumps in the entropy and the temperature caused by the caloric effect are weakly affected by the initial temperature. The effect can be used for the cooling of new quantum devices (like systems of qubits in quantum computers). On the other hand, since large changes are predicted in the narrow neighborhood of the critical point, the predicted effect can be used in ultrasensitive electric and stress sensors for modern microelectronics.

Published by the American Physical Society
2024
Integrable symplectic maps with a polygon tessellation
Authors: Zolkin T. , Kharkov Y. , Nagaitsev S.
Published: June 2024

Identifying integrable dynamics remains a formidable challenge, and despite centuries of research, only a handful of examples are known to date. In this article, we explore a distinct form of area-preserving (symplectic) mappings derived from the stroboscopic Poincaré cross section of a kicked rotator—an oscillator subjected to an external force periodically switched on in short pulses. The significance of this class of problems extends to various applications in physics and mathematics, including particle accelerators, crystallography, and studies of chaos. Notably, Suris's theorem constrains the integrability within this category of mappings, outlining potential scenarios with analytic invariants of motion. In this paper, we challenge the assumption of the analyticity of the invariant by exploring piecewise linear transformations on a torus (T2) and associated systems on the plane (R2), incorporating arithmetic quasiperiodicity and discontinuities. Introducing a new automated technique, we discovered previously unknown scenarios featuring polygonal invariants that form perfect tessellations and, moreover, fibrations of the plane or torus. This work reveals a novel category of planar tilings characterized by discrete symmetries that emerge from the invertibility of transformations and are intrinsically linked to the presence of integrability. Our algorithm relies on the analysis of the Poincaré rotation number and its piecewise monotonic nature for integrable cases, contrasting with the noisy behavior in the case of chaos, thereby allowing for clear separation. Some of the newly discovered systems exhibit the peculiar behavior of “integrable diffusion,” characterized by infinite and quasirandom hopping between tiles while being confined to a set of invariant segments. Finally, through the implementation of a smoothening procedure, all mappings can be generalized to quasi-integrable scenarios with suppressed volume occupied by chaotic trajectories, thereby opening doors to potential practical applications.

Published by the American Physical Society
2024
Nuclear deformation effects in the spectra of highly charged ions
Authors: Sun Zewen , Valuev Igor A. , Oreshkina Natalia S.
Published: June 2024

With the increasing precision of spectroscopic measurements, there is a growing demand for more accurate theoretical predictions, which requires the estimation of various higher-order effects, such as the nuclear deformation effect. Here, we present the results for nuclear deformation correction for the widest range of nuclei. The effects are investigated in terms of electronic transition energies, g factors, and hyperfine splitting constants, by implementing the deformed Fermi nuclear model to the Dirac equation. Based on the improved methodology and appropriate data classification, we present the results for over 1100 nuclei on figures, showing the general trends and anomalies. Moreover, it can serve as a simple tool providing estimations for specific planned research. In addition, we examine the connections and significance of deformation effects in the search of new physics with singly charged ions.

Published by the American Physical Society
2024
Coherent Transfer of Lattice Entropy via Extreme Nonlinear Phononics in Metal Halide Perovskites
Authors: Liu Z. , Shi Y. , Jiang T. , Luo L. , Huang C. , Mootz M. , Song Z. , Yan Y. , Yao Y. , Zhao J. , Wang J.
Published: June 2024

Entropy transfer in metal halide perovskites, characterized by significant lattice anharmonicity and low stiffness, underlies the remarkable properties observed in their optoelectronic applications, ranging from solar cells to lasers. The conventional view of this transfer involves stochastic processes occurring within a thermal bath of phonons, where the lattice arrangement and energy flow from higher- to lower-frequency modes. Here, we unveil a comprehensive chronological sequence detailing a conceptually distinct coherent transfer of entropy in a prototypical perovskite CH3NH3Pbl3. The terahertz periodic modulation imposes vibrational coherence into electronic states, leading to the emergence of mixed (vibronic) quantum beat between approximately 3 and 0.3 THz. We highlight a well-structured bidirectional time-frequency transfer of these diverse phonon modes, each developing at different times and transitioning from high to low frequencies from 3 to 0.3 THz, before reversing direction and ascending to around 0.8 THz. First-principles molecular dynamics simulations disentangle a complex web of coherent-phononic coupling pathways and identify the salient roles of the initial modes in shaping entropy evolution at later stages. Capitalizing on coherent entropy transfer and dynamic anharmonicity presents a compelling opportunity to exceed the fundamental thermodynamic (Shockley-Queisser) limit of photoconversion efficiency and to pioneer novel optoelectronic functionalities.

Published by the American Physical Society
2024
GIWAXS experimental methods at the NFPS-BL17B beamline at Shanghai Synchrotron Radiation Facility
Authors: Zhu Zhongjie , Lu Lanlu , Li Chunyu , Xiao Qingjie , Wu Tingting , Tang Jianchao , Gu Yijun , Bao Kangwen , Zhang Yupu , Jiang Luozhen , Liu Yang , Zhang Weizhe , Zhou Shuyu , Qin Wenming
Published: June 2024

The BL17B beamline at the Shanghai Synchrotron Radiation Facility was first designed as a versatile high-throughput protein crystallography beamline and one of five beamlines affiliated to the National Facility for Protein Science in Shanghai. It was officially opened to users in July 2015. As a bending magnet beamline, BL17B has the advantages of high photon flux, brightness, energy resolution and continuous adjustable energy between 5 and 23 keV. The experimental station excels in crystal screening and structure determination, providing cost-effective routine experimental services to numerous users. Given the interdisciplinary and green energy research demands, BL17B beamline has undergone optimization, expanded its range of experimental methods and enhanced sample environments for a more user-friendly testing mode. These methods include single-crystal X-ray diffraction, powder crystal X-ray diffraction, wide-angle X-ray scattering, grazing-incidence wide-angle X-ray scattering (GIWAXS), and fully scattered atom pair distribution function analysis, covering structure detection from crystalline to amorphous states. This paper primarily presents the performance of the BL17B beamline and the application of the GIWAXS methodology at the beamline in the field of perovskite materials.
Category–level drivers of the market share–rank power law relationship
Authors: Bae Young Han , Gruca Thomas S. , Lim Hyunwoo , Russell Gary J.
Published: June 2024

Purpose

This paper aims to analyze variations in the parameters of the market share–rank power law across consumer packaged goods (CPG) categories.

Design/methodology/approach

The authors use a two-level hierarchical linear model to examine the relationships between category-level variables and the parameters of the market share–rank power law in 790 CPG categories.

Findings

The slope of the market share–rank power law is shallower – indicating more equal market shares – in categories of high importance to retailers and those with high levels of promotional activity or high-volume purchases. Higher levels of market share inequality are associated with categories with high overall prices.

Research limitations/implications

To the best of the authors’ knowledge, this is the first research to show the systematic influence of category characteristics on the relationship between brands’ market shares and their ranks, thus, identifying a key moderator for this important empirical generalization in marketing.

Practical implications

While market leadership may be a desirable goal for many brands, the corresponding market share at the top brand does vary. Moreover, the share premium for being number one in the category (gap between the top and other highly ranked brands) can be greatly affected by retailers’ strategies. In addition, the slope of the power law has desirable qualities as a measure of market concentration. However, the empirical study shows that category characteristics must be considered when analyzing differences in concentration across categories or time.

Originality/value

While other studies document variations in the market share–rank power law relationship, to the best of the authors’ knowledge, this is the first that models these variations as a function of observable category characteristics. The comprehensive nature of the data demonstrates the universality of the market share–rank power law relationship across CPG categories in the USA.
A comparative analysis of supply chain management between Portugal and Ireland
Authors: Dominique-Ferreira Sérgio , Brophy Richard , Prentice Catherine
Published: June 2024

Purpose

This study investigates how insurance intermediaries in Portugal and Ireland evaluate supply chain management (SCM) practices within the insurance industry, specifically focusing on potential regional variations in their assessments.

Design/methodology/approach

A comparative research design was employed, collecting data through surveys administered to insurance brokers in Portugal and Ireland. These countries were chosen due to their well-developed intermediary-based insurance markets.

Findings

The results show that some dimensions of supply chain management are significantly different between Portugal and Ireland. Nevertheless, the insurance brokers from the two countries also share similar views on key aspects of supply chain management.

Practical implications

This study offers valuable insights for insurance industry management, particularly regarding the dynamics of the insurer-intermediary relationship and the importance of catering to intermediary needs. The findings also highlight potential areas for European Union policy consideration, such as addressing potential asymmetries within the insurance sector across member states.

Social implications

Improved relationships and collaboration within the insurance supply chain can lead to enhanced access to insurance products and more tailored services for consumers.

Originality/value

This research addresses two key gaps in the literature. Firstly, it examines the insurer-intermediary relationship from the intermediary perspective, a viewpoint often neglected in prior research. Secondly, the study investigates and confirms the existence of regional variations in insurance SCM practices across two European countries.
Compared predictions of a consumption and a normative criterion of housing affordability in two mid-sized Canadian cities over time
Authors: Phipps Alan G.
Published: June 2024

Purpose

The purpose of this study is to theorize and measure a consumption criterion of housing affordability and then to compare its predictions with those of a normative criterion over time. The new consumption criterion of housing affordability is quantified with predicted compensatory expenditures that a resident would pay to upgrade to their most preferred home. Its predictions are compared with those of the most popular normative criterion that predicts unaffordability if a resident spends more than a proportion such as 30% of their income on housing.

Design/methodology/approach

This study uses census and experimental data for owner-occupiers in two mid-sized Canadian cities between 1987 or 2001 and 2020 or 2021. These data are mapped and statistically analysed for comparing the predictions of the two criteria.

Findings

The study’s primary finding is that both criteria predict improved affordability of owned homes over time. Secondarily, however, the consumption criterion predicts worse unaffordability for the minority experiencing this. It furthermore clarifies their budgets for housing as more constraining than their social utilities that they may have already revised toward affordable home attributes. Indisputable unaffordability after the end of the study period may have nullified the originally recommended sacrifices for residents upgrading to their most preferred owned home.

Originality/value

The study is original because it demonstrates that a new consumption criterion of housing affordability subsumes the popular normative criterion if plausible assumptions are made about a homeowner’s choices. It then proceeds to speculate how this new criterion might refine the normative criterion with predicted compensatory expenditures for a resident’s affordable preferred homes.
International retailers as a main force for sustainability
Authors: Elg Ulf
Published: June 2024

Purpose

This study investigates how global retailers develop sustainability through network interactions that influence institutionalized sustainability perceptions. The findings enable retailers to drive sustainability systematically and understand the critical internal and external issues.

Design/methodology/approach

The study investigates how retailers can work to increase support for sustainability through the normative, cognitive, and regulative institutional pillars. The network perspective suggests the need to offer relevant resources, involve influential actors and perform supporting activities to mobilise stakeholders. Empirically, qualitative case studies of IKEA and Hennes & Mauritz were conducted.

Findings

Based on the network and institutional perspectives, the study identified nine fields that retailers can use to develop sustainability internally and in their networks. The study shows that they can mobilise actors, resources, and activities to change institutionalised values and practices.

Originality/value

The developed model provides guidelines on how to systematically work with sustainability. The broad view developed is particularly relevant considering that most of the existing research on global firms and sustainability focuses on a narrow research problem without relating it to sustainability as a complex and overarching phenomenon.
Cashbacks “In the nick of time”: consumers’ sensitivity to promotion delays and impact on promotion judgments
Authors: Kumari Rashmi , Tatavarthy Aruna Divya , Sahay Arvind
Published: June 2024

Purpose

Given the growing acceptance of cashback offers (e.g. $10 PayPal cashback within 24 hours of the transaction) among retailers, this paper aims to understand how consumers evaluate them vis-à-vis traditional price-discounts and their subsequent impact on retailers’ promotional strategies.

Design/methodology/approach

Six experimental studies examine if and when consumers can discern differences in the time-of-reward-accrual (i.e. the waiting time associated with receiving promotional savings) of cashbacks and price-discounts. Building on evaluability theory, we propose that the time-of-reward-accrual of promotion is hard-to-evaluate. Put simply, consumers find it hard to assess the duration of waiting time associated with receiving promotions. Consequently, consumers’ perceptions of cashbacks vis-à-vis price-discounts can be influenced by whether they evaluate both promotions simultaneously [joint-evaluation (JE) mode] or independently [single-evaluation (SE) mode].

Findings

The initial four studies show that the time-of-reward-accrual of promotions is hard-to-evaluate. Cashbacks appear just as appealing as price-discounts when consumers evaluate them independently (SE-mode) but lose their appeal when consumers view them alongside price-discounts (JE-mode). The next two studies further enhance the generalizability of our findings by replicating the observed effects for different purchase types (hedonic vs utilitarian) and varying promotional benefit levels (high vs low).

Originality/value

By shedding light on evaluations of time-of-reward-accrual of promotion, this paper adds a new dimension to research on promotions. The paper also extends the application of evaluability theory beyond domains such as hiring, fairness judgments and product bundle assessments. The paper presents evaluation mode as a boundary condition to explain contradictory predictions from prior research for consumers’ preferences for delayed vs immediate promotions.
A model to access the productivity of an agricultural implements consortium: a case study
Authors: Anand Balakrishnan , P.G. Saleeshya , M. Thenarasu , S. Naren Karthikeyan
Published: June 2024

Purpose

This work presents the results of a case study aimed at revitalizing an agricultural equipment manufacturing consortium facing prolonged losses. The purpose of this paper is to enhance productivity and profitability by identifying and eliminating waste within the manufacturing processes. The study uses lean principles and tools to achieve this objective.

Design/methodology/approach

The study begins with the creation of a questionnaire, administered to the consortium to gather insights. The questionnaire responses serve as a foundation for pinpointing critical areas in need of immediate attention. To tackle the challenge of demand forecasting without customer data, a demand forecasting model is introduced. Value stream mapping (VSM) is used to identify and highlight process inefficiencies and waste. The findings are further analyzed using a Pareto chart to prioritize waste reduction efforts. Based on these insights, the study proposes alternative manufacturing methods and waste elimination strategies. A multiphase lean framework is developed as a step-by-step roadmap for implementing lean manufacturing.

Findings

The study identifies a broken process flow within the consortium’s manufacturing processes and highlights areas of waste through VSM. The Pareto chart analysis reveals the most significant waste areas requiring immediate intervention. Recommendations for process improvements and waste reduction strategies are provided to the consortium.

Originality/value

This study contributes to the field by applying lean principles and tools to address the unique challenges faced by an agricultural equipment manufacturing consortium. The integration of a demand forecasting model and the development of a multiphase lean framework offer innovative approaches to enhancing productivity and profitability in this context.
Mediation of integrations in supply chain information management and supply chain performance: an empirical study from a developing economy
Authors: Rashid Aamir , Rasheed Rizwana , Tanveer Umair , Ishaq Shamaila , Amirah Noor Aina
Published: June 2024

Purpose

This study aims to investigate how the management of supply chain information impacts the performance of the supply chain. This relationship is explored by considering the mediating influence of internal and external integration, which is underpinned by the principles of resource-based theory.

Design/methodology/approach

Data was collected from 144 supply chain professionals across different manufacturing companies. The proposed hypotheses were subjected to quantitative analysis using partial least squares structural equation modeling, and the validity of the measurement model was assessed with the assistance of SmartPLS software.

Findings

This study identified that information management (IM) significantly and positively affects internal integration (II), customer integration (CI) and supply chain performance (SCP). Similarly, the results showed that II significantly and positively affects SCP. Likewise, CI positively and significantly affected SCP. At the same time, II found a positive yet significant mediating role in the relationship between IM and SCP. CI was found to play a positive but insignificant mediating role in the relationship between IM and SCP.

Originality/value

This research evaluated a second-order model and tested the SCP in conjunction with the resource-based view in the manufacturing industry. This research could be beneficial for researchers, manufacturers and policymakers to attain organizational objectives by implementing an efficient IM system for better integration and SCP.