bluuebunny/crossref_metadata_2025 huggingface dataset:
Dengue virus replicative-form dsRNA is recognized by RIG-I and MDA5 cooperatively to activate innate immunity
Authors: Ye Sichao , Liang Yisha , Chang Yu , Lai Bailiang , Zhong Jin
Published: October 2024

RIG-I like receptors (RLRs) are a family of cytosolic RNA sensors that sense RNA virus infection to activate innate immune response. It is generally believed that different RNA viruses are recognized by either RIG-I or MDA5, two important RLR members, depending on the nature of pathogen-associated molecular patterns (PAMPs) that are generated by RNA virus replication. Dengue virus (DENV) is an important RNA virus causing serious human diseases. Despite extensive investigations, the molecular basis of the DENV PAMP recognized by the host RLR has been poorly defined, and which RLR is involved in sensing the DENV PAMP remains controversial. Here, we demonstrated that the DENV infection-induced interferon response is dependent upon both RIG-I and MDA5, with RIG-I playing a predominant role. Next we purified the DENV PAMP RNA from the DENV-infected cells, and demonstrated that the purified DENV PAMP is viral full-length double-stranded RNA bearing 5’ppp modifications, likely representing the viral replicative-form RNA. Finally, we confirmed the nature of the DENV PAMP by reconstituting the viral replicative-form RNA fromin vitrosynthesized DENV genomic RNA. In conclusion, our work not only defined the molecular basis of the RLR-PAMP interaction during DENV infection, but also revealed the previously underappreciated recognition of the distinct moiety of same PAMP by different RLRs in innate immunity against RNA viruses.

Importance

The molecular interaction between PAMPs and RLRs plays a crucial role in innate immune response against the RNA virus infection. To our knowledge, the exact molecular basis of the DENV PAMPs and which RLR member (RIG-I or MDA5) is involved in this recognition remain controversial. In this study, we demonstrated that the DENV PAMP is likely DENV replicative-form RNA, a double-stranded RNA. RIG-I and MDA5 can sense different moieties of this DENV PAMP to active innate immune response. Our work not only clarified which RLR and what viral PAMP are involved in innate immune sensing of DENV infection, but also revealed previously underappreciated recognition of the same PAMPs by different RLRs in innate immunity against RNA viruses.
FtsZ of wall-less bacteria forms ring-like structures
Authors: Kasai Taishi , Tahara Yohei O , Miyata Makoto , Shiomi Daisuke
Published: October 2024

The FtsZ protein is involved in bacterial cell division. In cell-walled bacteria, such asBacillus subtilis, FtsZ forms a ring-like structure, called the Z ring, at the cell division site and acts as a scaffold for cell wall synthesis. The inhibition of cell wall synthesis inB. subtilishas been shown to interfere with the function of the Z ring, causing a loss in cell division control.Spiroplasma, a cell wall-less bacterium, lacks most of the genes involved in cell division; however, theftsZgene remains conserved. The function ofSpiroplasma eriocheirisFtsZ (SeFtsZ) remains to be determined. In the present study, we analyzed the biochemical characteristics of SeFtsZ. Purified SeFtsZ demonstrated lower polymerization capacity and GTPase activity than FtsZ fromE. coliandB. subtilis. We also investigated the relationship between SeFtsZ and SeSepF, which anchors FtsZ to the cell membrane, and found that SeSepF did not contribute to the stability of FtsZ filaments, unlike theB. subtilisSepF. SeFtsZ and SeSepF were produced inE. coliL-forms, where cell wall synthesis was inhibited. SeFtsZ formed ring-like structures in cell wall-lessE. colicells, suggesting that SeFtsZ forms Z rings and is involved in cell division independently of cell wall synthesis.
DDX3 regulates the cap-independent translation of the Japanese encephalitis virus via its interactions with PABP1 and the untranslated regions of the viral genome
Authors: Li Chenxi , Zhang Linjie , Tang Chenyang , Chen Xuan , Shi Jing , Li Qingyu , Jiao Xue , Guo Jinyao , Wang Bin , Bu Kefan , Wahaab Abudl , Yuan Yuguo , Sun Ming-an , Li Yanhua
Published: October 2024

The translation of global cellular proteins is almost completely repressed in cells with flavivirus infection, while viral translation remains efficient. The mechanisms of flaviviruses evade host translational shutoff are largely unknown. Here, we identified viral elements and host factors associated with JEV evasion of host shutoff. JEV 5′UTR lacked IRES or IRES-like activity, while noncapped 5′UTR initiated translation in the presence of 3′UTR. Furthermore, the elements DB2 and sHP-SL within 3′UTR were involved in the regulation of cap-independent translation, which is conserved in the genusOrthoflavivirus. By RNA affinity purification and mass spectrometry analysis, cellular DDX3 and PABP1 were identified as key factors in regulating cap-independent translation of JEV via their interactions with DB2 and sHP-SL RNA structures. Mechanistically, we revealed that DDX3 could bind to both 5′UTR and 3′UTR of the JEV genome to establish a closed-loop architecture, recruit eIF4G/eIF4A to form the DDX3/PABP1/eIF4G/eIF4A tetrameric complex via its interaction with PABP1, thereby recruiting 43S PIC to the 5′-end of the JEV genome to start translation. Our findings demonstrated a noncanonical translation strategy employed by JEV and further revealed the regulatory roles of DDX3 and PABP1 in this mechanism. These results expand our knowledge of the translation initiation regulation in flaviviruses under the state of host translational shutoff, which provides a conserved antiviral target againstorthoflavivirus.
Role of a single MCP in evolutionary adaptation ofShewanella putrefaciensfor swimming in planktonic and structured environments
Authors: Edelmann Daniel B , Jakob Anna M , Wilson Laurence G , Colin Remy , Brandt David , Eck Frederik , Kalinowski Joern , Thormann Kai M
Published: October 2024

Bacteria can adapt to their environments by changing phenotypic traits by mutations. However, improving one trait often results in deterioration of another one, a trade-off which limits the degree of adaption. The gammaproteobacteriumShewanella putrefaciensCN-32 has an elaborate motility machinery comprising two distinct flagellar systems and an extensive chemotaxis array with 36 methyl-accepting chemotaxis sensor proteins (MCPs). In this study we performed experimental selection on S. putrefaciens for increased spreading through a porous environment. We readily obtained a mutant that showed a pronounced increase in covered distance. This phenotype was almost completely caused by a deletion of 24 bp from the chromosome, which leads to a moderately enhanced production of a single MCP. Accordingly, chemotaxis assays under planktonic conditions and cell tracking in soft agar showed that the mutation improved navigation through nutritional gradients. The study demonstrates how differences in the abundance of a single MCP can lead to an efficient upgrade of directed flagella-mediated motility in specific environments at a low expense of cellular resources.
Pathogenic mechanisms ofPlasmodium falciparumegress unveiled by a microvascular 3D blood-brain barrier model
Authors: Piatti Livia , Batzilla Alina , Nakaki Fumio , Fleckenstein Hannah , Korbmacher François , Long Rory K.M. , Schraivogel Daniel , Hawkins John A. , Romero-Uruñuela Tais , López-Gutiérrez Borja , Sanz Silvia , Schwab Yannick , Steinmetz Lars M. , Sharpe James , Bernabeu Maria
Published: October 2024

Cerebral malaria is a severe neurovascular complication ofPlasmodium falciparumwith high mortality, even after treatment with effective antimalarials. A better understanding of pathogenic mechanisms could help future development of adjunctive therapies, yet limitations in current experimental models have hindered our knowledge of the disease. We developed a 3D blood-brain barrier model with enhanced barrier properties using primary brain endothelial cells, astrocytes and pericytes. Exposure to parasite egress products increased microvascular permeability, likely due to transcriptional downregulation of junctional and vascular development genes in endothelial cells. In addition, it increased the expression of ferroptosis markers, antigen presentation and type I interferon genes across all BBB cell types. Incubation with cytoadherent schizont-stageP. falciparum-infected erythrocytes induced a similar, but highly localized transcriptional shift, along with inter-endothelial gaps at sites of parasite egress, significantly increasing permeability. These findings provide key insights into the parasite-mediated mechanisms driving brain microvascular pathogenesis in cerebral malaria.
Simultaneous production of lipopeptide and rhamnolipid biosurfactants byPseudomonas aeruginosa: A promising blend for biosurfactant-enhanced bioremediation
Authors: del Rosario Jacoby Maria , Iustman Laura J. Raiger
Published: October 2024

Oil contamination is an environmental issue worldwide, and bioremediation has emerged as a preferred strategy to address this challenge. One of the limiting factors in oil biodegradation is its bioavailability, which can be solved by the addition of tensioactive compounds. Given the increasing demand for environmentally friendly surfactants, this study aimed to obtain cell-free biosurfactant extracts as additives in surfactant enhanced remediation (SER) protocols. Diesel-degrading, surfactant-producing strains were isolated to obtain biosurfactant extracts with minimal post-production purification cost. The most promising extracts were tested for SER assays using diesel-contaminated microcosms. One of these showed a significant enhancement in diesel degradation compared with the controls. This extract was obtained from aPseudomonas aeruginosastrain and consisted of a blend of rhamnolipids and lipopeptides. This is the first work reporting the co-production of both kinds of surfactants by aP. aeruginosastrain and its potential for application in surfactant-enhanced bioremediation strategies.

HIGHLIGHTS

Pseudomonas aeruginosaMM and ML were isolated as diesel-degrading surfactant-producing strains.

P. aeruginosaMM synthesizes rhamnolipids and lipopeptides simultaneously

This surfactant blend enhances diesel degradation in soil microcosm assays
Temporal Prediction through Integration of Probability Distributions of Event Timings at Multiple Levels
Authors: Huang Yiyuan Teresa , Chao Zenas C.
Published: October 2024

Our brain uses prior experience to anticipate the timing of upcoming events. This dynamical process can be modeled using a hazard function derived from the probability distribution of event timings. However, the contexts of an event can lead to various probability distributions for the same event, and it remains unclear how the brain integrates these distributions into a coherent temporal prediction. In this study, we create a local-global foreperiod paradigm consisting of a sequence of paired trials, where in each trial, participants respond to a target signal after a specified time interval (i.e. foreperiod) following a warning cue. The prediction of the target onset in the second trial can be based on the probability distribution of the second foreperiod (local level) and its conditional probability given the foreperiod in the first trial (global level). These probability distributions are then transformed into hazard functions to represent the local and global temporal predictions. Reaction times to the target signal are best explained by incorporating both local and global predictions, indicating that both levels of temporal information contribute to making predictions. We further show that electroencephalographic source signals are best reconstructed when integrating both predictions. Specifically, the local and global predictions are separately encoded in the posterior and anterior brain regions, and to achieve synergy between both predictions, a third region—particularly the right posterior cingulate area—is needed. Our study reveals brain networks that integrate multilevel temporal information, providing a comprehensive view of hierarchical predictive coding of time.
Meta-analysis: Purity of extracted human blood DNA,E. coligDNA, and plasmid using magnetic nanoparticle
Authors: Tjoa Stanley Evander Emeltan , Mudasir Mudasir , Suharyadi Edi , Daryono Budi Setiadi
Published: October 2024

DNA extraction technology continues to evolve along with the need for a fast and simple process. The DNA extraction with magnetic nanoparticles accommodates these demands by providing a method that is safe, simple, and yet able to give good purity. The purity parameter of the extracted DNA is based on the A260/280 value. This meta-analysis aims to find variables that can affect the purity of extracted DNA using magnetic nanoparticles, based on its extraction and particle synthesis procedure. The information to be analyzed is from DNA extraction from human blood, plasmid extraction, andE. coligDNA extraction. The research begins with a systematic review to collect appropriate studies and analysis will be carried out using Minitab to find variables that affect the purity of DNA, either positive or negative. Here we show, that no variables have been found significant to the purity of the extracted DNA in both the DNA extraction procedure steps and reagents. For the magnetic nanoparticle synthesis method, for extraction ofE. coligDNA, coating agent TEOS/TiO2; CoZnFe3O4magnetic nanoparticles, and the interaction between CoZnFe3O4and TEOS are found to be variables that influence the purity of the extracted DNA based on A260/280. Hopefully, this information can be used as a development idea, either for the magnetic nanoparticle synthesis procedure or the selection of reagents and DNA extraction procedures. In addition, the results of this analysis can also be used for consideration in an in-house magnetic nanoparticle-based DNA extraction assembly.
Domain Specific AI Segmentation of IMPDH2 Rod/Ring Structures in Mouse Embryonic Stem Cells
Authors: Ball Samuel T.M. , Hennessy Meagan J. , Tan Yuhan , Hoettges Kai F. , Perkins Neil D. , Wilkinson David J. , White Michael R.H. , Zheng Yalin , Turner David A.
Published: October 2024

Background

Inosine monophosphate dehydrogenase 2 (IMPDH2) is an enzyme that catalyses the rate limiting step of guanine nucleotides. In mouse embryonic stem cells (ESCs) IMPDH2 is held as large multi-protein complexes known as rod-ring (RR) structures that dissociate when ESCs differentiate. Manual analysis of RR structures from confocal microscopy images, although possible, is not feasible on a large scale due to the quantity of RR structures present in each field of view. To address this analysis bottleneck, we have created a fully automatic RR image classification pipeline to segment, characterise and measure feature distributions of these structures in ESCs.

Results

We find that this model can automatically segment images with a Dice score of over 80% for both rods and rings for in-domain images compared to expert annotation, with a slight drop to 70% for datasets out of domain. Important feature measurements derived from these segmentations show high agreement with the measurements derived from expert annotation, achieving anR2score of over 90% for counting the number of rings and rods over the dataset.

Conclusions

We have established for the first time a quantitative baseline for RR distribution in pluripotent ESCs and have made a pipeline available for training to be applied to other models in which RR remain an open topic of study.
About bacteriophage tail terminator and tail completion proteins: structure of the proximal extremity of siphophage T5 tail
Authors: Linares Romain , Breyton Cécile
Published: October 2024

Bacteriophages are viruses infecting bacteria. The vast majority of them bear a tail, allowing host recognition, cell wall perforation and DNA injection into the host cytoplasm. Using electron cryo-microscopy (cryo-EM) and single particle analysis, we determined the organisation of the tail proximal extremity of siphophage T5 that possess a long flexible tail, and solved the structure of its tail terminator protein (TrP) p142 (TrP142). It allowed to confirm the common evolutionary origin between T5 TrPp142and other known or putative TrPs from siphophages, myophages and bacterial tail-like machines, despite very poor sequence conservation. By also determining the structure of T5 tail proximal extremity after interaction with T5 bacterial receptor FhuA, we showed that no conformational changes occur in TrPp142and confirmed that the infection signal transduction is not carried by the tube itself. We also investigated the location of T5 tail completion protein (TCP) p143 (TCPp143) and showed, thanks to a combination of cryo-EM and structure prediction using Alphafold2, that it is not located at the capsid-to-tail interface as suggested by its position in the genome, but instead, very unexpectedly, on the side of T5 tail tip, and that it appears to be monomeric. Based on structure comparison with other putative TCPs predicted structures, this feature could not be shared by other TCPs. The stoichiometry of the Tape Measure Protein is also discussed.

Importance

Bacteriophages, viruses infecting bacteria, are the most abundant living entities on Earth. They are present in all ecosystems where bacteria develop and are instrumental in the regulation, diversity, evolution and pathogeny of microbial populations. Moreover, with the increasing number of pathogenic strains resistant to antibiotics, virulent phages are considered as a serious alternative or complement to classical treatments. 96% of all phages present a tail that allows host recognition and safe channelling of the DNA to the host cytoplasm. We present the atomic model of the proximal extremity of siphophage T5 tail, confirming structural similarities with other phages. This structure, combined to results previously published further explored, also allowed a review and a discussion on the role and localisation of a mysterious tail protein, the Tail Completion Protein, which is known to be present in the phage tails, but that was never identified in a phage structure.
A lipid signature of BAK-driven apoptotic pore formation
Authors: Uren Rachel T. , Ritchie Matthew E. , Wong Agnes W. , Ludeman Justin P. , Uno Etsuko , Narayana Vinod K. , De Souza David P. , Sviridov Dmitri , Kluck Ruth M.
Published: October 2024

Apoptotic cell death is regulated by the BCL-2 protein family, with clusters of BAK or BAX homodimers driving pore formation in the mitochondrial outer membrane via a poorly understood process. There is growing evidence that, in addition to BAK and BAX, lipids play an important role in pore formation. Towards a better understanding of the lipidic drivers of apoptotic pore formation in isolated mitochondria, two complementary approaches were taken. Firstly, the lipids released during BAK-mediated pore formation were measured with targeted lipidomics, revealing enrichment of long chain polyunsaturated lysophospholipids (LPLs) in the released fraction. In contrast, the BAK protein was not released suggesting that BAK and LPLs locate to distinct microdomains. Secondly, added cholesterol not only prevented pore formation but prevented the clustering of BAK homodimers. Our data lead us to a model in which BAK clustering triggers formation of a separate microdomain rich in LPLs that can progress to lipid shedding and the opening of a lipid-lined pore. Pore stabilisation and growth may be due to BAK dimers then moving to the pore edge. Our BAK-lipid microdomain model supports the heterogeneity of BAK assemblies, and the observed lipid-release signature gives new insight into the genesis of the apoptotic pore.
Intra-manchette transport employs both microtubule and actin tracks
Authors: Judernatz Jo H. , Pañeda Laura Pérez , Kadavá Tereza , Heck Albert J. R. , Zeev-Ben-Mordehai Tzviya
Published: October 2024

The manchette is a transient microtubule based structure that plays a vital role in nuclear shaping during spermio-genesis. It comprises thousands of microtubules (MTs) that build a scaffold around the distal half of the nucleus. The manchette distributes proteins and vesicles during spermio-genesis in a process called intra-manchette transport (IMT). The current hypothesis is that IMT shares many similarities with intra-flagellar transport (IFT) and utilizes both MTs and filamentous actin (F-actin). However, IMT is still poorly understood as direct visualization of IMT complexes is missing, and the presence of F-actin has not been experimentally shown. Here, we use proteomics and cryogenic-electron tomography (cryo-ET) to identify and visualize IMT components. We find that F-actin is an integral part of the manchette with two different spatial organizations, namely bundles and single filaments, providing tracks for transport as well as having structural and mechanical roles. We further uncover that IMT on MTs is mediated by two distinct transport machineries: a dynein-mediated transport of soluble cargo and a dynein-independent transport for vesicles. Our results provide new insights into the manchette’s function as a transport scaffold, highlighting its significance for the polarization of spermatids during spermiogenesis.
HSV-1 Infection AltersMAPTSplicing and Promotes Tau Pathology in Neural Models of Alzheimer’s Disease
Authors: Ijezie Emmanuel C , Miller Michael J , Hardy Celine , Jarvis Ava R. , Czajka Timothy F , D’Brant Lianna , Rugenstein Natasha , Waickman Adam , Murphy Eain , Butler David C
Published: October 2024

INTRODUCTION

Herpes simplex virus 1 (HSV-1) infection alters critical markers of Alzheimer’s Disease (AD) in neurons. One key marker of AD is the hyperphosphorylation of Tau, accompanied by altered levels of Tau isoforms. However, an imbalance in these Tau splice variants, specifically resulting from altered 3R to 4RMAPTsplicing of exon 10, has yet to be directly associated with HSV-1 infection

METHODS

To this end, we infected 2D and 3D human neural models with HSV-1 and monitoredMAPTsplicing and Tau phosphorylation. Further, we transduced SH-SY5Y-neurons with HSV-1 ICP27 which alters RNA splicing to analyze if ICP27 alone is sufficient to induce alteredMAPTexon 10 splicing.

RESULTS

We show that HSV-1 infection induces altered splicing ofMAPTexon 10, increasing 4R-Tau protein levels, Tau hyperphosphorylation, and Tau oligomerization.

DISCUSSION

Our experiments reveal a novel link between HSV-1 infection and the development of cytopathic phenotypes linked with AD progression.

HIGHLIGHTS

HSV-1 infection in forebrain organoids reduces the neurite length of MAP2-positive neurons.

HSV-1 infection increases Tau hyperphosphorylation in both two-month-old and four-month-old forebrain organoids.

HSV-1 infection increases Exon 10 containing (4R)MAPTmRNA and 4R-Tau protein expression in both forebrain organoids and human SH-SY5Y-neurons.

HSV-1 ICP27 is both necessary and sufficient to induce increased 4RMAPTmRNA and 4R-Tau protein expression in SH-SY5Y-neurons.

HSV-1 infection increases Tau oligomerization in both forebrain organoids and SH-SY5Y-neurons.
An Update on Active and Passive Surveillance for African Swine Fever in the Dominican Republic
Authors: Schambow Rachel A. , Carrasquillo Nianet , Kreindel Silvia , Perez Andres M.
Published: October 2024

African Swine Fever (ASF) is a viral, hemorrhagic disease of swine that is reportable to the World Organisation for Animal Health. Since 2007, ASF has been expanding globally and caused severe disruption to the global swine industry. In 2021, ASF was detected in the Dominican Republic, prompting an emergency response from local and international officials. Nearly three years later, ASF is still present in the country despite control efforts. This study used data from January 2023-March 2024 from government-mandated sampling of commercial farms, a newly initiated active surveillance program of backyard farms, and passive reports to provide a comprehensive and descriptive assessment of ASF in the Dominican Republic. The attack rate for each region was calculated, and the reproductive ratio (R0) was estimated using the doubling time method. ASF continues to be distributed throughout the Dominican Republic with lower attack rates in central regions and R0nearing 1. These results suggest that ASF in the country is reaching a stable state that does not resemble an epidemic situation. This may suggest the need to change from an approach of emergency response to one of sustained and progressive control, ultimately for the long-term goal of ASF eradication in the Dominican Republic.
Transcriptomic bases of within- and trans-generational predator-induced plasticity in the freshwater snailPhysa acuta
Authors: Dejeux Léo , Saclier Nathanaëlle , Tariel-Adam Juliette , Hoareau Maxime , Lefébure Tristan , Konecny Lara , Plénet Sandrine , Luquet Emilien
Published: October 2024

Inducible defences in response to predation risk are a well-known example of adaptive phenotypic plasticity. While inducible defences have been mainly studied within a generation (within-generational plasticity), there is now clear evidence that the ancestral exposure to predation risk can influence the defences expressed by the offspring, even if they have not been exposed themselves (transgenerational plasticity). The molecular mechanisms allowing the transmission of environmental information across generations are still misunderstood. In this study, we combined measures of anti-predator responses (behavioural and morphological) with transcriptomic investigations across two generations in the freshwater snailPhysa acuta. We hypothesised that both within- and transgenerational plasticity would induce phenotypic changes associated with differential gene expression. Our results confirmed within- and transgenerational plasticity: F1 snails have responded to predator-cue exposure by increasing escape behaviour, reducing shell length, and developing thicker and slender shells and F2 from exposed parents have shown similar responses. Within- and transgenerational plasticity were accompanied by the differential expression of 78 genes (77 up- and 1 down-regulated) and 14 differentially expressed genes (13 up- and 1 down-regulated), respectively. Within- and transgenerational plasticity did not share common differentially expressed genes but some differentially expressed genes in F1 are also highly expressed in F2 and overall, the molecular functions were similar, involving metabolism and transcription regulation. The quantitatively low molecular response associated with transgenerational plasticity suggests that gene expression changes induced by parental exposure may have occurred early in development and have decreased at adult stage.
GRASP55 Regulates Sorting and Maturation of the Lysosomal Enzyme β-Hexosaminidase A
Authors: Akaaboune Sarah Reem , Javed Aadil , Bui Sarah , Wierenga Alissa , Wang Yanzhuang
Published: October 2024

The Golgi apparatus plays a crucial role in the delivery of lysosomal enzymes. Golgi Reassembly Stacking Proteins, GRASP55 and GRASP65, are vital for maintaining Golgi structure and function. GRASP55 depletion results in the missorting and secretion of the lysosomal enzyme Cathepsin D (Xianget al., 2013), though the mechanisms remain unclear. In this study, we conducted secretomic analyses of GRASP55 knockout (KO) cells and found a significant increase in lysosome-associated proteins in the extracellular medium. Using the lysosomal beta-hexosaminidase subunit alpha (HEXA) as a model, we found that GRASP55 depletion disrupted normal trafficking and processing of HEXA, resulting in increased secretion of the immature (pro-form) HEXA into the extracellular milieu, along with decreased levels of the mature form and enzymatic activity within the cell. GRASP55 depletion significantly reduced the complex formation between HEXA and mannose-6-phosphate (M6P) receptors (MPR), despite no overall change in MPR expression. And finally, we found there was a notable reduction in the expression of GNPTAB, leading to a reduction in M6P modification of HEXA, hindering its efficient targeting to lysosomes. These findings reveal the role of GRASP55 in regulating lysosomal enzyme dynamics, emphasizing its role in the sorting and trafficking of lysosomal proteins.
Quantum-limited superresolution of two arbitrary incoherent point sources: Beating the resurgence of Rayleigh's curse
Authors: Li Junyan , Pang Shengshi
Published: October 2024

Superresolution has been demonstrated to overcome the limitation of Rayleigh's criterion and achieve significant precision improvement in resolving the separation of two incoherent optical point sources. However, in recent years, it was found that, if the photon numbers of two incoherent optical sources are unknown, the precision of superresolution vanishes when the photon numbers are actually different. In this work, we first analyze in detail the estimation precision of the separation for two incoherent optical sources with the same point-spread functions and show that, when the two photon numbers are different but sufficiently close, the superresolution can still be realized but with different precisions. We find the condition on how close the photon numbers need to be to realize the superresolution and derive the precision of superresolution in different regimes of the photon number difference. We further consider the superresolution for two incoherent optical sources with different point-spread functions and show that the competition between the difference of photon numbers, the difference of point-spread functions, and the separation of source locations determines the precision of superresolution. The results exhibit precision limits distinct from that of two identical point-spread functions with equal photon numbers and extend the realizable regimes of quantum superresolution. Finally, the results are illustrated by Gaussian point-spread functions.

Published by the American Physical Society
2024
Coherent synchrotron radiation instability in low-emittance electron storage rings
Authors: Dastan Sara , Zhou Demin , Ishibashi Takuya , Karantzoulis Emanuel , Di Mitri Simone , Lindberg Ryan
Published: October 2024

High-frequency longitudinal impedances, particularly at wavenumbers k≫1/σz (where σz is the bunch length), can drive microwave instability and potentially limit the performance of modern low-emittance electron storage rings. In such rings, the coherent synchrotron radiation (CSR) emerges as a prominent contributor to these high-frequency impedances. This paper undertakes a systematic investigation into the effects of CSR on electron rings, utilizing the fourth-generation storage ring light source Elettra 2.0 and the low-energy ring of the SuperKEKB e+e− circular collider as illustrative examples. Our work revisits theories of microwave instability driven by CSR impedance, extending the analysis to encompass other high-frequency impedances, such as resistive wall and coherent wiggler radiation. Through instability analysis and numerical simulations conducted on the two aforementioned rings, the study explored the impact of high-frequency impedances and their combined effects with broadband impedances caused by discontinuities in vacuum chambers.

Published by the American Physical Society
2024
Significant contributions of the Higgs mode and impurity-scattering self-energy corrections to the low-frequency complex conductivity in dc-biased superconducting devices
Authors: Kubo Takayuki
Published: October 2024

We investigate the complex conductivity of superconductors under a direct-current (dc) bias based on the well-established Keldysh-Eilenberger formalism of nonequilibrium superconductivity. This robust framework allows us to account for the Higgs mode and impurity-scattering self-energy corrections, which are now known to significantly impact the complex conductivity under a bias dc, especially near the resonance frequency of the Higgs mode. The purpose of this paper is to explore the effects of these contributions on the low-frequency complex conductivity relevant to superconducting device technologies. We begin by nonperturbatively calculating the equilibrium Green’s functions under a bias dc, followed by an analysis of the time-dependent perturbative components. This approach enables us to derive the complex conductivity formula for superconductors ranging from clean to dirty limits, applicable to any bias dc strength. We validate our theoretical approach by reproducing known results and experimentally observed features, such as the characteristic peak in σ1 and the dip in σ2 attributed to the Higgs mode. Our calculations reveal that the Higgs mode and impurity-scattering self-energy corrections significantly affect the complex conductivity even at low frequencies (ℏω≪Δ), relevant to superconducting device technologies. Specifically, we find that the real part of the low-frequency complex conductivity, σ1, exhibits a bias-dependent reduction up to ℏω∼0.1, a much higher frequency than previously considered. This finding allows for the suppression of dissipation in devices by tuning the bias dc. Additionally, through the calculation of the imaginary part of the complex conductivity, σ2, we evaluate the bias-dependent kinetic inductance for superconductors ranging from clean to dirty limits. The bias dependence becomes stronger as the mean free path decreases. Our dirty-limit results coincide with previous studies based on the oscillating superfluid density (the so-called slow experiment) scenario. This widely used scenario can be understood as a phenomenological implementation of the Higgs mode into the kinetic inductance calculation, now justified by our calculation based on the robust theory of nonequilibrium superconductivity, which microscopically treats the Higgs-mode contribution. These results highlight the importance of considering the Higgs mode and impurity-scattering self-energy corrections in the design and optimization of superconducting devices under a bias dc.

Published by the American Physical Society
2024
Study of net-baryon higher moments in PNJL model and their expectation for net-proton using the subensemble acceptance method for the search of QCD critical point
Authors: Sarkar A. , Deb P. , Mandal Bidhan , Varma R.
Published: October 2024

The critical point is one of the most important aspects of the QCD phase diagram of strongly interacting matter. The nonmonotonic behavior of the higher-order moments of conserved quantities like net-baryon (ΔB), net-charge (ΔQ), and net-strangeness (ΔS) are believed to be the signatures of the QCD critical point as a function of energy. We study the effect of the QCD critical point on moments of net-baryon in the Polyakov loop enhanced Nambu-Jona-Lasinio (PNJL) model of QCD with six-quark and eight-quark interactions for finite and infinite volume systems. The study is performed at energies similar to Relativistic Heavy-Ion Collider beam energy scan. Experimentally measuring conserved quantities is difficult due to systematic limitations. Therefore, net-proton, net-pion, and net-kaon are measured as the proxy of ΔB, ΔQ, and

Δ

S

. Recent studies in the subensemble acceptance method on the hadron resonance gas (HRG) model show the dependency of the measured higher-order moment on the experimental acceptance. We applied the subensemble acceptance method to analyze the behavior of κσ2 of net-baryon distribution within the subvolume system for various acceptance fractions. These results can be directly mapped to the subvolume (particle) percentage of the total volume (conserved quantities). Our findings are compared to the solenoidal tracker at RHIC (STAR) net-proton and proton data with different energies to investigate the presence of the critical point. Additionally, these results are also compared with the ultrarelativistic quantum molecular dynamics (UrQMD), HRG model, and available lattice data.

Published by the American Physical Society
2024
High-energy neutrinos from millicharged dark matter annihilation in the Sun
Authors: Berlin Asher , Hooper Dan
Published: October 2024

Millicharged dark matter particles can be efficiently captured by the Sun, where they annihilate into tau leptons, leading to the production of high-energy neutrinos. In contrast to the Earth, the high temperature of the Sun suppresses the fraction of millicharged particles that are bound to nuclei, allowing for potentially high annihilation rates. We recast existing constraints from the IceCube Neutrino Observatory and use this information to place new limits on the fraction of the dark matter that is millicharged. This analysis excludes previously unexplored parameter space for masses of mχ∼(5–100)  GeV, charges of qχ∼10−3–10−2, and fractional abundances as small as fDM∼10−5.

Published by the American Physical Society
2024
Spontaneous symmetry breaking, gauge hierarchy, and electroweak vacuum metastability
Authors: Benevedes Sean , Steingasser Thomas , Trifinopoulos Sokratis
Published: October 2024

The so-called metastability bound asserts that an unnaturally small Higgs mass is a necessary condition for electroweak vacuum metastability, offering a new approach toward solving the hierarchy problem. So far, this result relies on the assumption of a negative Higgs mass parameter, or equivalently, on electroweak spontaneous symmetry breaking. We derive a new, corresponding bound for the case of a positive mass parameter. When the new bound is significantly more restrictive than or comparable to its established counterpart, it may offer an explanation for the sign of the Higgs mass parameter, and thus, spontaneous symmetry breaking itself. New physics at scales O(1–10)  TeV can lower these bounds as far as the TeV scale. As an illustration, we consider vacuum stability in the presence of additional TeV-scale fermions with Yukawa couplings to the Higgs, as well as a dimension-six term parametrizing new physics in the UV. This scenario requires new physics that couples strongly to the Higgs, and can potentially be probed at future colliders. Finally, to allow for comparison with concrete mechanisms predicting metastability, we provide the mass-dependent lifetime of the electroweak vacuum for this model.

Published by the American Physical Society
2024
H graph with unequal masses in quantum field theory
Authors: Kreer Philipp Alexander , Weinzierl Stefan
Published: October 2024

We compute the family of Feynman integrals related to the H graph with unequal masses in relativistic quantum field theory. We present an ϵ-factorized differential equation for the 40 master integrals. The alphabet consists of 29 dlog forms with algebraic arguments, involving six square roots. As these square roots are not simultaneously rationalizable, we express the master integrals in terms of iterated integrals. In addition, we express the H graph with unit powers of the propagators up to weight 4 in terms of multiple polylogarithms in compact form.

Published by the American Physical Society
2024
Fundamental tests of
P
and
CP
symmetries using octet baryons at the
J/ψ
threshold
Authors: Du Yong , He Xiao-Gang , Ma Jian-Ping , Du Xin-Yu
Published: October 2024

We systematically investigate tests of the parity P and the combined parity and charge-conjugate CP symmetries from differential angular distributions of J/ψ decaying into the lowest-lying baryon pairs at BESIII and the next-generation super tau-charm facilities (STCFs). Large corrections from Z and W exchange induced parity-violating effects are found for J/ψ decays with large logarithms resummed up to O(αs). The parity-violating asymmetries on the production and the decay sides of J/ψ are both estimated to be of O(10−4), thus barely observable with the 10 billion J/ψ events currently collected at BESIII. Nevertheless, these asymmetries utilizing the current BESIII data already permit a measurement of the weak mixing angle with an absolute uncertainty δsw2≈0.09, corresponding to the first determination of sw2 at the J/ψ threshold. In the future, STCFs are estimated to improve this bound by a factor of ∼20 to δsw2≈0.005 within one year based on luminosity rescaling. We also obtain the 95% confidence level upper bounds on the electric dipole moments of the octet baryons, which are of O(10−18)  e cm for BESIII and O(10−19)  e cm for STCFs. These bounds are improved by 2 to 3 orders of magnitude in comparison with the only existing one on Λ from Fermilab. The method discussed in this work also paves a way for a first and direct measurement of the Ξ and Σ electric dipole moments.

Published by the American Physical Society
2024
Enhancing search pipelines for short gravitational-wave transients with Gaussian mixture modeling
Authors: Smith Leigh , Ghosh Sayantan , Sun Jiyoon , Gayathri V. , Heng Ik Siong , Pai Archana
Published: October 2024

We present an enhanced method for the application of Gaussian mixture modeling (GMM) to the coherent WaveBurst (cWB) algorithm in the search for short-duration gravitational wave (GW) transients. The supervised machine learning method of GMM allows for the multidimensional distributions of noise and signal to be modeled over a set of representative attributes, which aids in the classification of GW signals against noise transients (glitches) in the data. We demonstrate that updating the approach to model construction eliminates bias previously seen in the GMM analysis, increasing the robustness and sensitivity of the analysis over a wider range of burst source populations. The enhanced methodology is applied to the generic burst all-sky short search in the LIGO-Virgo full third observing run (O3), marking the first application of GMM to the 3 detector Livingston-Hanford-Virgo network. For both 2- and 3- detector networks, we observe comparable sensitivities to an array of generic signal morphologies, with significant sensitivity improvements to waveforms in the low quality factor parameter space at false alarm rates of 1 per 100 years. This proves that GMM can effectively mitigate blip glitches, which are one of the most problematic sources of noise for unmodeled GW searches. The cWB-GMM search recovers similar numbers of compact binary coalescence (CBC) events as other cWB postproduction methods, and concludes on no new gravitational wave detection after known CBC events are removed.

Published by the American Physical Society
2024
Neophobia of private labels “Won’t buy it, never tried it!”
Authors: Younis Riham Hassan , Elmeniawy Aiesha
Published: October 2024

Purpose

This research aims to offer and empirically examine a research model that includes extrinsic cues, attitudes and purchasing intentions for non-private-label (PL) buyers from a developing economy perspective. It also seeks to test the moderating role of neophobia along with gender.

Design/methodology/approach

Data were received from 640 non-PL buyers via a cross-sectional online questionnaire. The study utilised structural equation modelling to examine the relationships among the study constructs.

Findings

Extrinsic cues, particularly perceived price and store image, along with attitudes, impact the intention to buy PLs. Furthermore, the moderating role of neophobia was supported.

Research limitations/implications

This study is limited to the Egyptian retail sector, so its findings reflect the degree of development of PLs in Egypt. Practical implications should be adopted for contexts with identical development levels.

Practical implications

Retail managers should focus on pricing promotions and enhancing their store image to appeal to non-PL shoppers. They should also consolidate their efforts to counteract neophobic tendencies among non-PL shoppers by maximising exposure to PLs and encouraging their trials.

Originality/value

This research offers empirical evidence of the role of neophobia, further enriching our understanding of Middle Eastern consumer behaviour and supporting the implications of extrinsic cues on PL purchase intention for non-PL buyers in developing economies. It supplements earlier research, which mainly focused on developed economies.
“You’re fired”: the influence of heuristic-systematic processing in communication and termination decisions in organizational environments
Authors: Atkins Aaron , Lancaster Alexander L. , Ault Michael K.
Published: October 2024

Purpose

Decisions regarding the termination of organizational members are not only common but also represent difficult actions for managers. Despite their importance and frequency, managers often make or avoid them based on incomplete or faulty decision-making criteria. Previous research suggests that decision-makers are subject to internal influences that play significant roles in their decision-making.

Design/methodology/approach

Using a controlled between-groups experimental design, this study, guided by the heuristic-systematic model, tested to what extent decision-makers rely on heuristic cues versus the systematic processing of more relevant information when making termination decisions.

Findings

Findings suggest the order in which information is presented influences participants’ decision-making and influences the information-processing structure.

Practical implications

Findings suggest practical considerations for managers, management trainees and others who engage in termination decisions as to potential influencing factors.

Originality/value

This research adds to the understanding of the decision-making process in organizational contexts.