bluuebunny/crossref_metadata_2025 huggingface dataset:
2-oxoglutarate triggers assembly of active dodecamericMethanosarcina mazeiglutamine synthetase
Authors: Herdering Eva , Reif-Trauttmansdorff Tristan , Kumar Anuj , Habenicht Tim , Hochberg Georg , Bohn Stefan , Schuller Jan , Schmitz Ruth A.
Published: March 2024

Glutamine synthetases (GS) are central enzymes essential for the nitrogen metabolism across all domains of life. Consequently, they have been extensively studied for more than half a century. Based on the ATP dependent ammonium assimilation generating glutamine, GS expression and activity are strictly regulated in all organisms. In the methanogenic archaeonMethanosarcina mazei, it has been shown that the metabolite 2-oxoglutarate (2-OG) directly induces the GS activity. Besides, modulation of the activity by interaction with small proteins (GlnK1and sP26) has been reported. Here, we show that the strong activation ofM. mazeiGS (GlnA1) by 2-OG is based on the 2-OG dependent dodecamer assembly of GlnA1by using mass photometry (MP) and single particle cryo-electron microscopy (cryo-EM) analysis of purified strep-tagged GlnA1. The dodecamer assembly from dimers occurred without any detectable intermediate oligomeric state and was not affected in the presence of GlnK1. The 2.39 Å cryo-EM structure of the dodecameric complex in the presence of 12.5 mM 2-OG demonstrated that 2-OG is binding between two monomers. Thereby, 2-OG appears to induce the dodecameric assembly in a cooperative way. Furthermore, the active site is primed by an allosteric interaction cascade caused by 2-OG-binding towards an adaption of an open active state conformation. In the presence of additional glutamine, strong feedback inhibition of GS activity was observed. Since glutamine dependent disassembly of the dodecamer was excluded by MP, feedback inhibition most likely relies on an allosteric binding of glutamine to the catalytic site.

Based on our findings, we propose that under nitrogen limitation the induction ofM. mazeiGS into a catalytically active dodecamer is not affected by GlnK1and crucially depends on the presence of 2-OG.
Scaled and Efficient Derivation of Loss of Function Alleles in Risk Genes for Neurodevelopmental and Psychiatric Disorders in Human iPSC
Authors: Zhang Hanwen , Peyton Lilia , McCarroll Ada , de León Guerrerro Sol Díaz , Zhang Siwei , Gowda Prarthana , Sirkin David , Achwah Mahmoud El , Duhe Alexandra , Wood Whitney G. , Jamison Brandon , Tracy Gregory , Pollak Rebecca , Hart Ronald P. , Pato Carlos N. , Mulle Jennifer G. , Sanders Alan R. , Pang Zhiping P. , Duan Jubao
Published: March 2024

Translating genetic findings for neurodevelopmental and psychiatric disorders (NPD) into actionable disease biology would benefit from large-scale and unbiased functional studies of NPD genes. Leveraging the cytosine base editing (CBE) system, here we developed a pipeline for clonal loss-of-function (LoF) allele mutagenesis in human induced pluripotent stem cells (hiPSCs) by introducing premature stop-codons (iSTOP) that lead to mRNA nonsense-mediated-decay (NMD) or protein truncation. We tested the pipeline for 23 NPD genes on 3 hiPSC lines and achieved highly reproducible, efficient iSTOP editing in 22 NPD genes. Using RNAseq, we confirmed their pluripotency, absence of chromosomal abnormalities, and NMD. Interestingly, for three schizophrenia risk genes (SETD1A, TRIO,CUL1), despite the high efficiency of base editing, we only obtained heterozygous LoF alleles, suggesting their essential roles for cell growth. We replicated the reported neural phenotypes ofSHANK3-haploinsufficiency and foundCUL1-LoF reduced neurite branches and synaptic puncta density. This iSTOP pipeline enables a scaled and efficient LoF mutagenesis of NPD genes, yielding an invaluable shareable resource.
Unraveling a novel dual-function regulatory element showing epistatic interaction with a variant that escapes genome-wide association studies
Authors: Adjemout Mathieu , Nisar Samia , Escandell Amélie , Huu Hong Thu Nguyen , Torres Magali , Thiam Alassane , Manosalva Iris , Mbengue Babacar , Dieye Alioune , Spicuglia Salvatore , Rihet Pascal , Marquet Sandrine
Published: March 2024

Regulation of gene expression has recently been complexified by the identification of Epromoters, a subset of promoters with enhancer function. Here, we uncovered the first dual cis-regulatory element, "ESpromoter," exhibiting both enhancer and silencer function, as a regulator of the nearby genesATP2B4andLAX1in single human T cells. Through integrative approach, we pinpointed functional rs11240391, a severe malaria risk variant that escapes detection in genome-wide association studies, challenging conventional strategies for identifying causal variants. CRISPR-modified cells demonstrated the regulatory effect of ESpromoter and rs11240391 onLAX1expression and T cell activation. Furthermore, our findings revealed an epistatic interaction between ESpromoter SNPs and rs11240391, impacting severe malaria susceptibility by further reducingLAX1expression. This groundbreaking discovery challenges the conventional enhancer-silencer dichotomy. It highlights the sophistication of transcriptional regulation and argues for an integrated approach combining genetics, epigenetics, and genomics to identify new therapeutic targets for complex diseases.

HIGHLIGHTS

Novel dual enhancer-silencer element (ESpromoter) in a single human cell type

Functional SNP for severe malaria risk that escapes genome-wide association studies

Genome editing at the SNP demonstrates a regulatory effect onLAX1and T cell activation

Epistatic interaction between SNPs increases the risk of severe malaria

In brief

Epistatic interaction between common variants within a novel dual enhancer-silencer regulatory element and theLAX1promoter variant is responsible for severe malaria susceptibility through T-cell activation.
Structure and dynamics of the autoantigen GAD65 in complex with the human autoimmune polyendocrine syndrome type 2-associated autoantibody b96.11
Authors: Stander Susanne , Reboul Cyril F , Lee Sarah N , Williams Daniel , Chandler Peter G , Costa Mauricio GS , Hoke David E , Jimma John DT , Fodor James , Fenalti Gustavo , Mannering Stuart I , Porebski Benjamin T , Schofield Peter , Christ Daniel , Buckle Malcolm , McGowan Sheena , Elmlund Dominika , Rand Kasper D. , Buckle Ashley M
Published: March 2024

The enzyme glutamate decarboxylase (GAD) produces the neurotransmitter GABA, using pyridoxal-5'-phosphate. GAD exists as two isoforms, GAD65 and GAD67. Only GAD65 acts as a major autoantigen, with its autoantibodies frequently found in type 1 diabetes and other autoimmune diseases. Here we characterize the structure and dynamics of GAD65 and its interaction with the autoimmune polyendocrine syndrome type 2-associated autoantibody b96.11. Combining hydrogen-deuterium exchange mass spectrometry (HDX), X-ray crystallography, cryo-electron microscopy and computational approaches, we dissect the conformational dynamics of the inactive apo- and the active holo-forms of GAD65, as well as the structure of the GAD65-autoantibody complex. HDX reveals the time-resolved, local dynamics that accompany autoinactivation, with the catalytic loop playing a key role in promoting collective dynamics at the interface between CTD and PLP domains. In the GAD65-b96.11 complex, heavy chain CDRs dominate the interaction, with the relatively long CDRH3 at the interface centre and uniquely bridging the GAD65 dimer via extensive electrostatic interactions with the260PEVKEK265motif. The autoantibody bridges structural elements on GAD65 that contribute to conformational change in GAD65, thus connecting the unique and intrinsic conformational flexibility that governs the autoinactivation mechanism of the enzyme to its autoantigenicity. The intrinsic dynamics, rather than sequence differences within epitopes, appear to be responsible for the contrasting autoantigenicities of GAD65 and GAD67. Our data thus reveal insights into the structural and dynamic differences between GAD65 and GAD67 that dictate their contrasting autoantibody reactivities, provide a new structural rationalisation for the nature of the autoimmune response to GAD65, and may have broader implications for antigenicity in general.
Cardiac Outflow tract septation defects in a DiGeorge syndrome model respond to Minoxidil treatment
Authors: Aurigemma Ilaria , Ferrentino Rosa , Krishnan Varsha Poondi , Lanzetta Olga , Angelini Claudia , Illingworth Elizabeth , Baldini Antonio
Published: March 2024

Background

The T-BOX transcription factor TBX1 is essential for the development of the pharyngeal apparatus and it is haploinsufficient in DiGeorge syndrome (DGS), a developmental anomaly associated with congenital heart disease and other abnormalities. The murine model recapitulates the heart phenotype and showed collagen accumulation.

Methods

We first used a cellular model to study gene expression during cardiogenic differentiation of WT andTbx1-/-mouse embryonic stem cells. Then we used a mouse model of DGS to test whether interfering with collagen accumulation using an inhibitor of lysyl hydroxylase would modify the cardiac phenotype of the mutant.

Results and conclusions

In the cell differentiation model, loss ofTbx1was associated with up regulation of a subset of ECM-related genes, including several collagen genes. In thein vivomodel, early prenatal treatment with Minoxidil, a lysyl hydroxylase inhibitor, ameliorated the cardiac outflow tract septation phenotype inTbx1mutant fetuses, but it had no effect on septation in WT fetuses. We conclude that TBX1 suppresses a subset of ECM-related genes. The partial rescue of the septation phenotype through Minoxidil treatment suggests that inhibiting collagen cross-linking reduces the impact of the phenotypic consequences ofTbx1mutation.
TheCandida aurisHog1 MAP kinase is essential for the colonization of murine skin and intradermal persistence
Authors: Shivarathri Raju , Chauhan Manju , Datta Abhishek , Das Diprasom , Karuli Adela , Jenull Sabrina , Kuchler Karl , Thangamani Shankar , Chowdhary Anuradha , Desai Jigar V. , Chauhan Neeraj
Published: March 2024

Candida auris, a multidrug-resistant human fungal pathogen, was first identified in 2009 in Japan. Since then, systemicC. aurisinfections have now been reported in more than 50 countries, with mortality rates of 30-60%. A major contributing factor to its high inter- and intrahospital clonal transmission is thatC. auris,unlike mostCandidaspecies, displays unique skin tropism and can stay on human skin for a prolonged period. However, the molecular mechanisms responsible forC. aurisskin colonization, intradermal persistence, and systemic virulence are poorly understood. Here, we report thatC. aurisHog1 mitogen-activated protein kinase (MAPK) is essential for efficient skin colonization, intradermal persistence, as well as systemic virulence. RNA-seq analysis of wildtype parental andhog1Δ mutant strains revealed marked down-regulation of genes involved in processes such as cell adhesion, cell-wall rearrangement, and pathogenesis inhog1Δ mutant compared to the wildtype parent. Consistent with these data, we found a prominent role for Hog1 in maintaining cell-wall architecture, as thehog1Δ mutant demonstrated a significant increase in cell-surface β-glucan exposure and a concomitant reduction in chitin content. Additionally, we observed that Hog1 was required for biofilm formationin vitroand fungal survival when challenged with primary murine macrophages and neutrophilsex vivo. Collectively, these findings have important implications for understanding theC. aurisskin adherence mechanisms and penetration of skin epithelial layers preceding bloodstream infections.

Importance

Candida aurisis a World Health Organization (WHO) fungal priority pathogen and an urgent public health threat recognized by the Centers for Disease Control and Prevention (CDC).C. aurishas a unique ability to colonize human skin. It also persists on abiotic surfaces in healthcare environments for an extended period of time. These attributes facilitate the inter- and intrahospital clonal transmission ofC. auris. Therefore, understandingC. aurisskin colonization mechanisms are critical for infection control, especially in hospitals and nursing homes. However, despite its profound clinical relevance, the molecular and genetic basis ofC. aurisskin colonization mechanisms are poorly understood. Herein, we present data on the identification of the Hog1 MAP kinase as a key regulator ofC. aurisskin colonization. These findings lay foundation for further characterization of unique mechanisms that promote fungal persistence on human skin.
Structure and Functions of Gesture Sequences in Wild Bonnet Macaques (Macaca radiata)
Authors: Gupta Shreejata , Sinha Anindya
Published: March 2024

Compositionality, a hallmark of human language, involves generating novel meaning by combining existing units. Nonhuman primates (mostly apes) are known to combine gestural units in non-random ways, but they do not make novel meaning with these combinations. What could, however, be the functional roles of these gesture sequences and whether they bear any significance to language evolution is still unclear. Moreover, studies on gesture-sequences in non-ape primate species is almost non-existent. Here, we investigated for the first time, the structure and functions of gesture sequences in the naturally occurring communication of wild bonnet macaques (Macaca radiata), using analyses akin to ape gesture studies (Genty & Byrne, 2010; Hobaiter & Byrne, 2011). Bonnet macaque gesture sequences exhibit non-random combinations of gestures and non-gesture units – certain gestures are significantly more common in sequences, they associate preferentially with specific other components and certain components are more likely to appear either at the beginning or at the end of a sequence. Interplay of these sequences form distinct gestural clusters, corresponding to affiliative/play and agonistic contexts. Although, the overall functions of bonnet macaque gesture sequences remain obscure, as in apes, we found that gesture sequences were specifically used as a persistence strategy, after the initial single gestures have failed to initiate and sustain social interactions. We discuss our findings in the light of a possibility that primate gesture sequences, coordinating the flow of social interactions, may be evolutionary precursors to pragmatic gestures in human language.
Stability and affinity evaluation of aptamers as a biorecognition system for testosterone and its analogs
Authors: Medina-Benítez Ariadna , García-Alonso Claudia A. , Fragoso-Rodríguez Roberto , Torres-Huerta Ana Laura , Antonio-Pérez Aurora
Published: March 2024

The present project results from the need to develop a biosensor for the detection of testosterone and synthetic analogs in nutritional supplements. A biosensor is composed of two systems: (1) the biorecognition system and (2) the transducer system. We propose the use of aptamers as a biorecognition system, given their functional capacities to recognize and “capture” specific small analytes. For this study, eight aptamers sequences with previous reports of interaction with testosterone were evaluated to select the best candidate on regard with the best affinity and structural stability at different ionic concentrations and temperature values.In silicoanalysis involves predicting secondary and tertiary structures in different conditions and molecular docking.In vitroanalysis. tracks the changes in the folded and unfolded aptamer dimensions monitored by dynamic light scattering under the previouslyin silicoconditions, and performs relative capture tests with testosterone and testosterone undecanoate by immobilized aptamers on gold nanoparticles. The outcomes of thein silicoapproach aligned with the experimental data collected, exhibit that the nucleotide composition and aptamers binding structure, intervene in their affinity and biosensor functionality. The aptamers apT5 and P4G13 were discarded as possible candidates because they did not show stability in experimental conditions (temperature and ion plug). TESS2, TESS3, T4, T5.1, and T6 proved to be functional aptamers because they showed good affinity with the three analytes, however, TESS1 turned out to be the best candidate because of its stability and number of interactions, which translates into a greater affinity, compared to the rest.
Multi-substrate specificity shaped the complex evolution of the aminotransferase family across the tree of life
Authors: Koper Kaan , Han Sang-Woo , Kothadia Ramani , Salamon Hugh , Yoshikuni Yasuo , Maeda Hiroshi A.
Published: March 2024

Aminotransferases (ATs) are an ancient enzyme family that play central roles in core nitrogen metabolism essential to all organisms. However, many of the AT enzyme functions remain poorly defined, limiting our fundamental understanding of the nitrogen metabolic networks that exist in different organisms. Here we traced the deep evolutionary history of the AT family by analyzing AT enzymes from 90 species spanning the tree of life (ToL). We found that each organism has maintained a relatively small and constant number of ATs. Mapping the distribution of ATs across the ToL uncovered that many essential AT reactions are carried out by taxon-specific AT enzymes due to wide-spread non-orthologous gene displacements. This complex evolutionary history explains the difficulty of homology-based AT functional prediction. Biochemical characterizations of diverse aromatic ATs further revealed their broad substrate specificity, unlike other core metabolic enzymes that evolved to catalyze specific reactions today. Interestingly, however, we found that these AT enzymes that diverged over billion years share common signatures of multi-substrate specificity by employing different non-conserved active site residues. These findings illustrate that AT evolution had leveraged their inherent substrate promiscuity to maintain a small yet distinct set of multi-functional AT enzymes in different taxa. This evolutionary history of versatile ATs likely contributed to the establishment of robust and diverse nitrogen metabolic networks that exist throughout the ToL. The study provides a critical foundation to systematically determine diverse AT functions and underlying nitrogen metabolic networks across the ToL.

Significance Statement

The ToL-wide analyses of the ubiquitous aminotransferases (AT) family revealed that the broad substrate promiscuity of ATs, which is unusual for core metabolic enzymes, allowed recruitment of distinct, non-orthologous ATs to carry out essential AT reactions in different taxa but without increasing their copy numbers. Some distantly related ATs were also found to exhibit a common signature of multi-substrate specificity by employing different non-conserved active site residues. The versatile evolutionary trajectory of the promiscuous AT enzyme family likely led to biochemical diversity of the robust nitrogen metabolic networks that exist among various extant organisms.
Physical forces driveC. elegansembryonic deformation
Authors: Wang Ting , Ben Amar Martine
Published: March 2024

The abnormal development of embryos is closely linked to abnormal cell division and elongation, but the underlying mechanism remains to be elucidated. The embryonic development ofC elegansembryo is different because it occurs without cell proliferation or cell rearrangement. Here, we focus on a spectacular 4-fold elongation that is achieved approximately 3 hours before the egg shell hatches and results from active filament networks. The body shape is represented by an inhomogeneous cylinder, which allows us to assess the active stresses induced by the actomyosin network located in the cortex and the muscles in ventral position near the epidermis. By considering the specific embryo configuration, we can quantitatively obtain the contractile forces induced by actomyosin filaments and muscles for a bending torsion event with defined curvature. We find that the active stress induced by actomyosin molecular motors or muscles increases with elongation and bending curvature, while also varying with radius. Both elongation and torsional deformation contribute to increased moment magnitudes that explain the dynamics of the embryo in the egg. Our results highlight the complex interplay between biomechanical factors in modulating embryonic deformation.
Genomic and phenotypic imprints of microbial domestication on cheese starter cultures
Authors: Somerville Vincent , Thierer Nadine , Schmidt Remo S. , Roetschi Alexandra , Braillard Lauriane , Haueter Monika , Berthoud Hélène , Shani Noam , von Ah Ueli , Mazel Florent , Engel Philipp
Published: March 2024

Domestication – the artificial selection of wild species to obtain variants with traits of human interest– was integral to the rise of civilization. During the neolithic, the oversupply of food enabled by the domestication of crop plants and farm animals was associated with the invention of food preservation strategies through microbial fermentation. However, it remains unclear whether fermented food microbes show similar signs of domestication by humans like plants or animals. Only a few eukaroytic have been studied so far in this respect (e.g., yeasts used in mantou or wine), whereas little is known for bacteria.

Here, we tested if cheese starter cultures harbour typical hallmarks of domestication by characterising over 100 community samples and over 100 individual strains isolated from historical and modern traditional Swiss cheese starter cultures. We find that cheese starter cultures have low genetic diversity both at the species and strain-level and are taxonomically and phenotypically stable. Our analyses further suggest that the evolutionary origin of the bacteria in cheese starter cultures coincided with the start of cheesemaking as reported from archeological records. Finally, we find evidence for ongoing genome decay and pseudogenization via transposon insertion related to a reduction of their niche breadth.

These characteristics suggest that cheese starter cultures were domesticated by humans before knowing about microbes, potentially starting as early as the neolithics Future work documenting the prevalence of these hallmarks across diverse fermented food systems and geographic regions will be key to unveiling the joint history of humanity with fermented food microbes.
NFATC2IP is a mediator of SUMO-dependent genome integrity
Authors: Cho Tiffany , Hoeg Lisa , Setiaputra Dheva , Durocher Daniel
Published: March 2024

The post-translational modification of proteins by SUMO is crucial for cellular viability and mammalian development in part due to the contribution of SUMOylation to genome duplication and repair. To investigate the mechanisms underpinning the essential function of SUMO, we undertook a genome-scale CRISPR/Cas9 screen probing the response to SUMOylation inhibition. This effort identified 130 genes whose disruption reduces or enhances the toxicity of TAK-981, a clinical-stage inhibitor of the SUMO E1-activating enzyme. Among the strongest hits, we validated and characterized NFATC2IP, an evolutionarily conserved protein related to the fungal Esc2 and Rad60 proteins that harbors tandem SUMO-like domains. Cells lacking NFATC2IP are viable but are hypersensitive to SUMO E1 inhibition, likely due to the accumulation of mitotic chromosome bridges and micronuclei. NFATC2IP primarily acts in interphase and associates with nascent DNA, suggesting a role in the postreplicative resolution of replication or recombination intermediates. Mechanistically, NFATC2IP interacts with the SMC5/6 complex and UBC9, the SUMO E2, via its first and second SUMO-like domains, respectively. AlphaFold-Multimer modeling suggests that NFATC2IP positions and activates the UBC9–NSMCE2 complex, the SUMO E3 ligase associated with SMC5/SMC6. We conclude that NFATC2IP is a key mediator of SUMO-dependent genomic integrity that collaborates with the SMC5/6 complex.
Protein domains of low sequence complexity—dark matter of the proteome
Authors: McKnight Steven L.
Published: March 2024

This perspective begins with a speculative consideration of the properties of the earliest proteins to appear during evolution. What did these primitive proteins look like, and how were they of benefit to early forms of life? I proceed to hypothesize that primitive proteins have been preserved through evolution and now serve diverse functions important to the dynamics of cell morphology and biological regulation. The primitive nature of these modern proteins is easy to spot. They are composed of a limited subset of the 20 amino acids used by traditionally evolved proteins and thus are of low sequence complexity. This chemical simplicity limits protein domains of low sequence complexity to forming only a crude and labile type of protein structure currently hidden from the computational powers of machine learning. I conclude by hypothesizing that this structural weakness represents the underlying virtue of proteins that, at least for the moment, constitute the dark matter of the proteome.
Viscosity bounds in liquids with different structure and bonding types
Authors: Withington M. , Devereux H. L. , Cockrell C. , Elena A. M. , Todorov I. T. , Liu Z. K. , Shang S. L. , McCloy J. S. , Bingham P. A. , Trachenko K.
Published: March 2024

Recently, it was realized that liquid viscosity has a lower bound which is nearly constant for all liquids and is governed by fundamental physical constants. This was supported by experimental data in noble and molecular liquids. Here, we perform large-scale molecular dynamics simulations to ascertain this bound in two other important liquid types: the ionic molten salt system LiF and metallic Pb. We find that these ionic and metallic systems similarly have lower viscosity bounds corresponding to the minimum of kinematic viscosity of ∼10−7m2/s. We show that this agrees with experimental data in other systems with different structures and bonding types, including noble, molecular, metallic, and covalent liquids. This expands the universality of viscosity bounds into the main system types known.

Published by the American Physical Society
2024
Crossover from string to cluster dynamics following a field quench in spin ice
Authors: Pal Sukla , Powell Stephen
Published: March 2024

We investigate quench dynamics of spin ice after removal of a strong magnetic field along the [100] crystal direction, using Monte Carlo simulations and theoretical arguments. We show how the early time relaxation of the magnetization can be understood in terms of nucleation and growth of strings of flipped spins, in agreement with an effective stochastic model that we introduce and solve analytically. We demonstrate a crossover at longer times to a regime dominated by approximately isotropic clusters, which we characterize in terms of their morphology, and present evidence for a percolation transition as a function of magnetization.

Published by the American Physical Society
2024
Revisiting the Vashishta-Singwi dielectric scheme for the warm dense uniform electron fluid
Authors: Tolias Panagiotis , Lucco Castello Federico , Kalkavouras Fotios , Dornheim Tobias
Published: March 2024

The finite temperature version of the Vashishta-Singwi (VS) dielectric scheme for the paramagnetic warm dense uniform electron fluid is revisited correcting for an earlier thermodynamic derivative error. The VS scheme handles quantum mechanical effects at the level of the random phase approximation and treats correlations via the density expansion of a generalized Singwi-Tosi-Land-Sjölander (STLS) closure that inserts a parameter determined by enforcing the compressibility sum rule. Systematic comparison with quasiexact results, based on quantum Monte Carlo simulations, reveals a structural superiority of the VS scheme towards strong coupling and a thermodynamic superiority of the STLS scheme courtesy of a favorable cancellation of errors. Guidelines are provided for the construction of dielectric schemes that are expected to be more accurate but computationally costly.

Published by the American Physical Society
2024
Exploring the impact of high-precision top-quark pair production data on the structure of the proton at the LHC
Authors: Ablat Alim , Guzzi Marco , Xie Keping , Dulat Sayipjamal , Hou Tie-Jiun , Sitiwaldi Ibrahim , Yuan C.-P.
Published: March 2024

The impact of recent LHC top-quark pair production single differential cross section measurements at 13 TeV collision energy on the structure of the proton is explored. In particular, the impact of these high-precision data on the gluon and other parton distribution functions (PDFs) of the proton at intermediate and large partonic momentum fraction x is analyzed. This study extends the CT18 global analysis framework to include these new data. The interplay between top-quark pair and inclusive jet production as well as other processes at the LHC, is studied. In addition, a study of the impact of scale choice on the theory description of the new 13 TeV tt¯ measurements is performed.

Published by the American Physical Society
2024
Quark masses and low-energy constants in the continuum from the tadpole-improved clover ensembles
Authors: Hu Zhi-Cheng , Hu Bo-Lun , Wang Ji-Hao , Gong Ming , Liu Guoming , Liu Liuming , Sun Peng , Sun Wei , Wang Wei , Yang Yi-Bo , Zhao Dian-Jun ,   CLQCD Collaboration
Published: March 2024

We present the light-flavor quark masses and low-energy constants using the 2+1 flavor full-QCD ensembles with stout smeared-clover fermion action and Symanzik gauge action. Both the fermion and gauge actions are tadpole improved self-consistently. The simulations are performed on 11 ensembles at three lattice spacings a∈[0.05,0.11]  fm, four spatial sizes L∈[2.5,5.1]  fm, seven pion masses mπ∈[135,350]  MeV, and several values of the strange quark mass. The quark mass is defined through the partially conserved axial current relation and renormalized to MS¯(2 GeV) through the intermediate regularization independent momentum subtraction scheme. The systematic uncertainty of using the symmetric momentum subtraction scheme is also included. Eventually, we predict mu=2.45(22)(20)  MeV, md=4.74(11)(09)  MeV, and ms=98.8(2.9)(4.7)  MeV with the systematic uncertainties from lattice spacing determination, continuum extrapolation and renormalization constant included. We also obtain the chiral condensate Σ1/3=268.6(3.6)(0.7)  MeV and the pion decay constant F=86.6(7)(1.4)  MeV in the Nf=2 chiral limit, and the next-to-leading order low-energy constants ℓ3=2.43(54)(05) and ℓ4=4.322(75)(96).

Published by the American Physical Society
2024
Mutually elusive: Vectorlike antileptons and leptoquarks
Authors: Bigaran Innes , Dobrescu Bogdan A. , Russo Alessandro
Published: March 2024

We study the properties of vectorlike fermions that have the same gauge charges as the Standard Model lepton doublets, but opposite lepton number. These antileptons undergo decays mediated by heavier scalar leptoquarks, while the symmetries of this renormalizable model protect the vectorlike fermions and the leptoquarks from standard decays probed so far at colliders. We derive upper limits on the new Yukawa couplings imposed by flavor-changing processes, including B→Kνν¯ and Bs−B¯s mixing, and show that they are compatible with prompt antilepton decays at the LHC for wide parameter ranges. If the new particles couple predominantly to second-generation quarks, then their collider probes involve multiple jets and two taus or neutrinos, and are hampered by large backgrounds. If couplings to third-generation quarks are large, then the collider signals involve top quarks, and can be probed more efficiently at the LHC. Even in that case, both the vectorlike fermion doublet and the leptoquarks remain more elusive than in models with standard decays.

Published by the American Physical Society
2024
Searching for exotic spin-dependent interactions with diamond-based vector magnetometer
Authors: Guo Aolong , Kang Runqi , Jiao Man , Rong Xing
Published: March 2024

We propose a new method to search for exotic spin-spin interactions between electrons and nucleons using a diamond-based vector magnetometer. The vector magnetometer can be constructed from ensembles of nitrogen-vacancy centers along different axes in a diamond. The N14 nuclear spins of nitrogen-vacancy centers in the same diamond can be polarized through the dynamic nuclear polarization method to serve as spin sources. With the vector magnetometer, the sought-after exotic interactions can be distinguished from the magnetic dipole-dipole interaction. For the axion-mediated interaction VPP, new upper bounds of the coupling |gPegPN| are expected within the force range from 10 nm to 100  μm. For the Z′-mediated interaction VAA, new upper bounds of the coupling

|

g

A

e

g

A

N

|

are expected within the force range from 10 nm to 1 cm. The new upper bounds for VPP and VAA are both expected to be more than 5 orders of magnitude more stringent than existing constraints at the force range of 1  μm with the total measurement time of 1 day.

Published by the American Physical Society
2024
Dynamical tidal response of Kerr black holes from scattering amplitudes
Authors: Saketh M. V. S. , Zhou Zihan , Ivanov Mikhail M.
Published: March 2024

We match scattering amplitudes in point particle effective field theory (EFT) and general relativity to extract low frequency dynamical tidal responses of rotating (Kerr) black holes to all orders in spin. In the conservative sector, we study local worldline couplings that correspond to the time-derivative expansion of the black hole tidal response function. These are dynamical (frequency-dependent) generalizations of the static Love numbers. We identify and extract couplings of three types of subleading local worldline operators: the curvature time derivative terms, the spin-curvature time derivative couplings, and quadrupole-octupole mixing operators that arise due to the violation of spherical symmetry. The first two subleading couplings are nonzero and exhibit a classical renormalization group running; we explicitly present their scheme-independent beta functions. The conservative mixing terms, however, vanish as a consequence of vanishing static Love numbers. In the nonconservative sector, we match the dissipation numbers at next-to-leading and next-to-next-to leading orders in frequency. In passing, we identify terms in the general relativity absorption probabilities that originate from tails and short-scale logarithmic corrections to the lowest order dissipation contributions.

Published by the American Physical Society
2024
Framework to generate hypergraphs with community structure
Authors: Ruggeri Nicolò , Battiston Federico , De Bacco Caterina
Published: March 2024

In recent years hypergraphs have emerged as a powerful tool to study systems with multibody interactions which cannot be trivially reduced to pairs. While highly structured methods to generate synthetic data have proved fundamental for the standardized evaluation of algorithms and the statistical study of real-world networked data, these are scarcely available in the context of hypergraphs. Here we propose a flexible and efficient framework for the generation of hypergraphs with many nodes and large hyperedges, which allows specifying general community structures and tune different local statistics. We illustrate how to use our model to sample synthetic data with desired features (assortative or disassortative communities, mixed or hard community assignments, etc.), analyze community detection algorithms, and generate hypergraphs structurally similar to real-world data. Overcoming previous limitations on the generation of synthetic hypergraphs, our work constitutes a substantial advancement in the statistical modeling of higher-order systems.

Published by the American Physical Society
2024
Topological dualities via tensor networks
Authors: Wille C. , Eisert J. , Altland A.
Published: March 2024

The ground state of the toric code, that of the two-dimensional class D superconductor, and the partition sum of the two-dimensional Ising model are dual to each other. This duality is remarkable in as much as it connects systems commonly associated to different areas of physics—that of long-range entangled topological order, (topological) band insulators, and classical statistical mechanics, respectively. Connecting fermionic and bosonic systems, the duality construction is intrinsically nonlocal, a complication that has been addressed in a plethora of different approaches, including dimensional reduction to one dimension, conformal field theory methods, and operator algebra. In this paper, we propose a unified approach to this duality, whose main protagonist is a tensor network (TN) assuming the role of an intermediate translator. Introducing a fourth node into the net of dualities offers several advantages: the formulation is integrative in that all links of the duality are treated on an equal footing, (unlike in field theoretical approaches) it is formulated with lattice precision, a feature that becomes key in the mapping of correlation functions, and their possible numerical implementation. Finally, the passage from bosons to fermions is formulated entirely within the two-dimensional TN framework where it assumes an intuitive and technically convenient form. We illustrate the predictive potential of the formalism by exploring the fate of phase transitions, point and line defects, topological boundary modes, and other structures under the mapping between system classes. Having condensed-matter readerships in mind, we introduce the construction pedagogically in a manner assuming only minimal familiarity with the concept of TNs.

Published by the American Physical Society
2024
Photon condensation, Van Vleck paramagnetism, and chiral cavities
Authors: Mercurio Alberto , Andolina Gian Marcello , Pellegrino Francesco M. D. , Di Stefano Omar , Jarillo-Herrero Pablo , Felser Claudia , Koppens Frank H. L. , Savasta Salvatore , Polini Marco
Published: March 2024

We introduce a gauge-invariant model of planar, square molecules coupled to a quantized spatially varying cavity electromagnetic vector potential Â(r). Specifically, we choose a temporally cavity hosting a uniform magnetic field B̂, as this is the simplest instance in which a transverse spatially varying Â(r) is at play. We show that when the molecules are in the Van Vleck paramagnetic regime, an equilibrium quantum phase transition to a photon condensate state occurs.

Published by the American Physical Society
2024
Crystal structure and Hirshfeld surface analysis of 4,4′-dimethoxybiphenyl-3,3′,5,5′-tetracarboxylic acid dihydrate
Authors: Hanauer Thomas , Seichter Wilhelm , Mazik Monika
Published: March 2024

In the crystal of the title compound, C18H14O10·2H2O, the arene rings of the biphenyl moiety are tilted at an angle of 24.3 (1)°, while the planes passing through the carboxyl groups are rotated at angles of 8.6 (1) and 7.7 (1)° out of the plane of the benzene ring to which they are attached. The crystal structure is essentially stabilized by O—H...O bonds. Here, the carboxyl groups of neighbouring host molecules are connected by cyclic R
2
2(8) synthons, leading to the formation of a three-dimensional network. The water molecules in turn form helical supramolecular strands running in the direction of the crystallographic c-axis (chain-like water clusters). The second H atom of each water molecule provides a link to a methoxy O atom of the host molecule. A Hirshfeld surface analysis was performed to quantify the contributions of the different intermolecular interactions, indicating that the most important contributions to the crystal packing are from H...O/O...H (37.0%), H...H (26.3%), H...C/C...H (18.5%) and C...O/O...C (9.5%) interactions.
Integrating three theories of 21st-century capitalism
Authors: Windsor Duane
Published: March 2024

Purpose

This study aims to help develop “business principles for stakeholder capitalism” in two steps. First, the study defines internal logic of three theories of capitalism and two variants within each theory. Second, it examines approaches to integration into modern democratic capitalism. Treating the three theories as substitutes identifies relative strengths and weaknesses; complementarity and partial overlap approaches to integration study the institutional settings within which stakeholder capitalism operates. Empirical outcomes reflect competition between market and stakeholder businesses for participants, with institutional conditions determining the scope of collective action.

Design/methodology/approach

The approach aligns three typologies in a unique conceptual arrangement defining the three theories of capitalism: forms of capitalism, potential failures of each form and associated types of goods. The first method examines the internal logic of each theory of capitalism. The second draws on traditional narrative review of references documenting each theory of capitalism and variants together with modern Marxist anti-capitalism.

Findings

Three typologies align uniquely with the theories of capitalism, each having two variants. Both variants of stakeholder capitalism are compatible with compassionate capitalism, constitutional government or polycentric governance but not with self-interest capitalism, dictatorship or Marxism. A theory of modern democratic capitalism allocates roles for private, club and social goods with empirically variable mixes occurring across countries. Competition among different types of enterprises provides an empirical test for comparative advantages of stakeholder capitalism. Future research should consider approaches for testing the proposed conceptual scheme in practice concerning capacity to deal with grand challenges, wicked problems and black swan events.

Research limitations/implications

Research approach is limited to logical examination of theories and literature documentation without direct empirical confirmation. The study does not address practical implications for managers and public officials or social implications concerning private incentives, stakeholder cooperation or collective action.

Originality/value

Originality lies in shifting terms of debate about stakeholder capitalism from advocacy of substitute theories to understanding of its relationship to market capitalism and collective action capitalism. Value lies in explaining desirability of theoretical integration of three types of capitalism into a comprehensive framework for modern democratic capitalism.
Predicting structure performance of urban critical infrastructure: an augmented attention-based LSTM model
Authors: Yu Gang , Li Zhiqiang , Zeng Ruochen , Jin Yucong , Hu Min , Sugumaran Vijayan
Published: March 2024

Purpose

Accurate prediction of the structural condition of urban critical infrastructure is crucial for predictive maintenance. However, the existing prediction methods lack precision due to limitations in utilizing heterogeneous sensing data and domain knowledge as well as insufficient generalizability resulting from limited data samples. This paper integrates implicit and qualitative expert knowledge into quantifiable values in tunnel condition assessment and proposes a tunnel structure prediction algorithm that augments a state-of-the-art attention-based long short-term memory (LSTM) model with expert rating knowledge to achieve robust prediction results to reasonably allocate maintenance resources.

Design/methodology/approach

Through formalizing domain experts' knowledge into quantitative tunnel condition index (TCI) with analytic hierarchy process (AHP), a fusion approach using sequence smoothing and sliding time window techniques is applied to the TCI and time-series sensing data. By incorporating both sensing data and expert ratings, an attention-based LSTM model is developed to improve prediction accuracy and reduce the uncertainty of structural influencing factors.

Findings

The empirical experiment in Dalian Road Tunnel in Shanghai, China showcases the effectiveness of the proposed method, which can comprehensively evaluate the tunnel structure condition and significantly improve prediction performance.

Originality/value

This study proposes a novel structure condition prediction algorithm that augments a state-of-the-art attention-based LSTM model with expert rating knowledge for robust prediction of structure condition of complex projects.
Evaluation of forecasting models for improved passenger market management and rolling stock planning on Indian railways
Authors: Bhatia Vinod , Kalaivani K.
Published: March 2024

Purpose

Indian railways (IR) is one of the largest railway networks in the world. As a part of its strategic development initiative, demand forecasting can be one of the indispensable activities, as it may provide basic inputs for planning and control of various activities such as coach production, planning new trains, coach augmentation and quota redistribution. The purpose of this study is to suggest an approach to demand forecasting for IR management.

Design/methodology/approach

A case study is carried out, wherein several models i.e. automated autoregressive integrated moving average (auto-ARIMA), trigonometric regressors (TBATS), Holt–Winters additive model, Holt–Winters multiplicative model, simple exponential smoothing and simple moving average methods have been tested. As per requirements of IR management, the adopted research methodology is predominantly discursive, and the passenger reservation patterns over a five-year period covering a most representative train service for the past five years have been employed. The relative error matrix and the Akaike information criterion have been used to compare the performance of various models. The Diebold–Mariano test was conducted to examine the accuracy of models.

Findings

The coach production strategy has been proposed on the most suitable auto-ARIMA model. Around 6,000 railway coaches per year have been produced in the past 3 years by IR. As per the coach production plan for the year 2023–2024, a tentative 6551 coaches of various types have been planned for production. The insights gained from this paper may facilitate need-based coach manufacturing and optimum utilization of the inventory.

Originality/value

This study contributes to the literature on rail ticket demand forecasting and adds value to the process of rolling stock management. The proposed model can be a comprehensive decision-making tool to plan for new train services and assess the rolling stock production requirement on any railway system. The analysis may help in making demand predictions for the busy season, and the management can make important decisions about the pricing of services.