bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive Hierarchical Classification of Transposable Elements based on Deep Learning
Authors: Qi Yang , Chen Yiqi , Wu Yingfu , Li Yanyan , Gao Meihong , Zhang Fuhao , Liao Xingyu , Shang Xuequn
Published: January 2024

Transposable elements (TEs) are DNA sequences capable of translocating within a genome. They constitute a substantial portion of eukaryotic genomes and play significant roles in genome evolution and gene regulation. The correct classification of these repetitive elements is essential to investigate their potential impact on genomes. Despite the existence of several tools for TE classification, they often neglect the importance of simultaneously utilizing global and local information for TE-type identification, resulting in suboptimal performance. Furthermore, these tools are not user-friendly due to the complex installation processes and numerous dependencies. In this study, we introduced a novel framework, CREATE, which leverages the strengths ofConvolutional andRecurrent Neural NEtworks, combined withAttention mechanisms, for efficientTEclassification. Given the tree-like structure of TE groups, we separately trained nine models within the class hierarchy. Benchmarking experiments showed that CREATE significantly outperformed other TE classification tools. The source code and demo data for CREATE are available athttps://github.com/yangqi-cs/CREATE. To facilitate TE annotation for researchers, we have developed a web platform, named WebDLTE, based on the CREATE framework. This platform employs GPU-accelerated pre-trained deep learning models for real-time TE classification and offers the most comprehensive collection of TEs for download. The web interface can be accessed athttps://www.webdlte.nwpu.edu.cn.
Adaptive and pleiotropic effects of evolution in synonymous sugar environments
Authors: Ahlawat Neetika , Venkataraman Pavithra , Brajesh Raman Gulab , Saini Supreet
Published: January 2024

Adaptation to an environment is enabled by the accumulation of beneficial mutations. When adapted populations are shifted to other environments, the byproduct or pleiotropic fitness effects of these mutations can be wide-ranged. Since there exists no molecular framework to quantify relatedness of environments, predicting pleiotropic effects based on adaptation has been challenging. In this work, we ask if evolution in highly similar environments elicits correlated adaptive and pleiotropic responses. We evolve replicate populations ofEscherichia coliin non-stressful environments that contain either a mixture of glucose and galactose, lactose, or melibiose as the source of carbon. We term these similar sugars as “synonymous”, since lactose and melibiose are disaccharides made up of glucose and galactose. Therefore, the evolution environments differed only in the way carbon was presented to the bacterial population. After 300 generations of evolution, we see that the adaptive responses of these populations are not predictable. We investigate the pleiotropic effects of adaptation in a range of non-synonymous environments, and show that despite uncorrelated adaptive changes, the nature of pleiotropic effects is largely predictable based on the fitness of the ancestor in the non-home environments. Overall, our results highlight how subtle changes in the environment can alter adaptation, but despite sequence-level variations, pleiotropy is qualitatively predictable.

Lay Summary

In nature, evolution in “similar” environments is believed to elicit identical responses. For example, the arctic fox and ptarmigan, which are two unrelated species living in the arctic, have evolved to turn white in the winters. They did not evolve this ability because they from the common ancestor, but because the environment favoured this trait. In this work, we ask what happens to evolving populations if there are minute changes in the environment, and what are the consequences of adapting in these environments that are “almost identical”, or as we call them, “synonymous”.

We evolve replicate populations of the bacteriaE. coliin three synonymous environments, and quantify their ability to grow in both synonymous and non-synonymous environments. We see that evolution does not proceed in an identical fashion in these populations, and that each environment favours a different trait. However, interestingly, in non-synonymous environments, these three sets of populations perform almost identically, and their growth is qualitatively predictable.

Our results show that even simple and subtle changes in the environment can act as drivers of biodiversity.
Efficient candidate drug target discovery through proteogenomics in a Scottish cohort
Authors: Kuliesius Jurgis , Timmers Paul R.H.J. , Navarro Pau , Klaric Lucija , Wilson James F.
Published: January 2024

Understanding the genomic basis of human proteomic variability provides powerful tools to probe potential causal relationships of proteins and disease risk, and thus to prioritise candidate drug targets. Here, we investigated 6432 plasma proteins (1533 previously unstudied in large-scale proteomic GWAS) using the SomaLogic (v4.1) aptamer-based technology in a Scottish population from the Viking Genes study. A total of 505 significant independent protein quantitative trait loci (pQTL) were found for 455 proteins in blood plasma: 382cis-(P < 5x10-8) and 123trans-(P < 6.6x10-12). Of these, 31cis-pQTL were for proteins with no previous GWAS. We leveraged these pQTL to perform causal inference using bidirectional Mendelian randomisation and colocalisation against complex traits of biomedical importance. We discovered 42 colocalising associations (with a posterior probability >80% that pQTL and complex traits share a causal variant), pointing to plausible causal roles for the proteins. These findings include hitherto undiscovered causal links of leukocyte receptor tyrosine kinase (LTK) to type-2 diabetes and beta-1,3-glucuronyltransferase (B3GAT1) to prostate cancer. These new connections will help guide the search for new or repurposed therapies. Our findings provide strong support for continuing to increase the number of proteins studied using GWAS.
Streamlining Intersectoral Provision of Real-World Health Data: A Service Platform for Improved Clinical Research and Patient Care
Authors: Hoffmann Katja , Nesterow Igor , Peng Yuan , Henke Elisa , Barnett Daniela , Klengel Cigdem , Gruhl Mirko , Bartos Martin , Nüßler Frank , Gebler Richard , Grummt Sophia , Seim Anne , Bathelt Franziska , Reinecke Ines , Wolfien Markus , Weidner Jens , Sedlmayr Martin
Published: January 2024

Introduction

Obtaining real-world data from routine clinical care is of growing interest for scientific research and personalized medicine. Despite the abundance of medical data across various facilities — including hospitals, outpatient clinics, and physician practices — the intersectoral exchange of information remains largely hindered due to differences in data structure, content, and adherence to data protection regulations. In response to this challenge, the Medical Informatics Initiative (MII) was launched in Germany, focusing initially on university hospitals to foster the exchange and utilization of real-world data through the development of standardized methods and tools, including the creation of a common core dataset. Our aim, as part of the Medical Informatics Research Hub in Saxony (MiHUBx), is to extend the MII concepts to non-university healthcare providers in a more seamless manner to enable the exchange of real-world data among intersectoral medical sites.

Methods

We investigated what services are needed to facilitate the provision of harmonized real-world data for cross-site research. On this basis, we designed a Service Platform Prototype that hosts services for data harmonization, adhering to the globally recognized Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) international standard communication format and the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). Leveraging these standards, we implemented additional services facilitating data utilization, exchange and analysis. Throughout the development phase, we collaborated with an interdisciplinary team of experts from the fields of system administration, software engineering and technology acceptance to ensure that the solution is sustainable and reusable in the long term.

Results

We have developed the pre-built packages “ResearchData-to-FHIR”, “FHIR-to-OMOP” and “Addons”, which provide the services for data harmonization and provision of project-related real-world data in both the FHIR MII Core dataset format (CDS) and the OMOP CDM format as well as utilization and a Service Platform Prototype to streamline data management and use.

Conclusion

Our development shows a possible approach to extend the MII concepts to non-university healthcare providers to enable cross-site research on real-world data. Our Service Platform Prototype can thus pave the way for intersectoral data sharing, federated analysis, and provision of SMART-on-FHIR applications to support clinical decision making.
Elucidating Molecular Networks Underpinning Heterogeneity in Parkinson’s Disease Progression Across Clinical Manifestation Spectrum
Authors: Zhou Manqi , Ke Alison , Wang Xingbo , Chen Kun , Wang Fei , Su Chang
Published: January 2024

In this study, we applied statistical and machine learning techniques to identify molecular mechanisms underlying the heterogeneity in individual Parkinson’s Disease (PD) progression. Leveraging data from the Parkinson’s Progression Markers Initiative (PPMI) cohort, we analyzed genetic and clinical data for patients with PD, focusing on traits including motor symptoms, non-motor symptoms, and biomarkers. Our method identified significant single-nucleotide polymorphisms (SNPs) associated with each PD trait, revealing key genetic factors and their impact on disease progression. Furthermore, through network medicine approaches, we delineated disease modules, uncovering unique gene clusters and their roles in PD pathology. The integration of pathway enrichment analysis further enhanced our understanding of the functional implications of these genetic variations, notably highlighting the significance of cellular stress response and protein aggregation pathways in PD. Overall, our findings offer a comprehensive view of the genetic landscape of PD progression, highlighting the potential of personalized medicine in managing this complex disease.
Specific amygdala and hippocampal subfield volumes in social anxiety disorder and their relation to clinical characteristics – an international mega-analysis
Authors: Ntwatwa Ziphozihle , Spreckelmeyer Jule M. , Bas-Hoogendam Janna Marie , van Honk Jack , Mufford Mary M. , Boraxbekk Carl-Johan , Fouche Jean-Paul , Frick Andreas , Furmark Tomas , Klumpp Heide , Lochner Christine , Phan K Luan , Månsson Kristoffer N.T. , Pannekoek J. Nienke , Peterburs Jutta , Roelofs Karin , Roos Annerine , Straube Thomas , van Steenbergen Henk , Tol Marie-José Van , Veltman Dick J. , van der Wee Nic J.A. , Stein Dan J. , Ipser Jonathan C. , Groenewold Nynke A.
Published: January 2024

Social anxiety disorder (SAD) has been associated with alterations in amygdala and hippocampal volume but there is mixed evidence for the direction of volumetric alterations. Additionally, little is known about the involvement of the distinct subfields in the pathophysiology of SAD. Volumetric data from a large multi-centre sample of 107 adult individuals with SAD and 140 healthy controls (HCs) was segmented using FreeSurfer to produce 9 amygdala and 12 hippocampal subfield volumes. Volumes were compared between groups using linear mixed-effects models adjusted for age, age-squared, sex, site and whole amygdala and hippocampal volumes. Subgroup analyses examined subfield volumes in relation to comorbid anxiety disorder, and comorbid major depressive disorder (MDD), psychotropic medication status, and symptom severity. In the full sample, SAD was associated with smaller amygdala volumes in the basal (d=-0.32, pFDR=0.022), accessory basal (d=-0.42, pFDR=0.005) and corticoamygdaloid transition area (d=-0.37, pFDR=0.014), and larger hippocampal volume in the CA3 (d=0.34, pFDR=0.024), CA4 (d=0.44, pFDR=0.007), dentate gyrus (d=0.35, pFDR=0.022) and molecular layer (d=0.28, pFDR= 0.033), compared to HCs. SAD without comorbid anxiety, in addition, demonstrated smaller lateral amygdala (d=-0.30, pFDR=0.037) and hippocampal amygdala transition area (d=-0.33, pFDR=0.027) relative to HCs. In SAD without comorbid MDD, only the smaller accessory basal amygdala remained significant (d=-0.41, pFDR=0.017). No association was found between subfield volume and medication status or symptom severity. In conclusion, we observed distinct patterns of volumetric differences across specific amygdala and hippocampal subfields, regions that are associated with sensory information processing, threat evaluation and fear generalization. These findings suggest a possible disruption in information flow between the amygdala and hippocampal formation for fear processing in SAD.
Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens
Authors: Jiang Longda , Dalgarno Carol , Papalexi Efthymia , Mascio Isabella , Wessels Hans-Hermann , Yun Huiyoung , Iremadze Nika , Lithwick-Yanai Gila , Lipson Doron , Satija Rahul
Published: January 2024

Recent advancements in functional genomics have provided an unprecedented ability to measure diverse molecular modalities, but learning causal regulatory relationships from observational data remains challenging. Here, we leverage pooled genetic screens and single cell sequencing (i.e. Perturb-seq) to systematically identify the targets of signaling regulators in diverse biological contexts. We demonstrate how Perturb-seq is compatible with recent and commercially available advances in combinatorial indexing and next-generation sequencing, and perform more than 1,500 perturbations split across six cell lines and five biological signaling contexts. We introduce an improved computational framework (Mixscale) to address cellular variation in perturbation efficiency, alongside optimized statistical methods to learn differentially expressed gene lists and conserved molecular signatures. Finally, we demonstrate how our Perturb-seq derived gene lists can be used to precisely infer changes in signaling pathway activation for in-vivo and in-situ samples. Our work enhances our understanding of signaling regulators and their targets, and lays a computational framework towards the data-driven inference of an ‘atlas’ of perturbation signatures.
Mechanism of bacterial predation via ixotrophy
Authors: Lien Yun-Wei , Amendola Davide , Lee Kang Soo , Bartlau Nina , Xu Jingwei , Furusawa Go , Polz Martin F. , Stocker Roman , Weiss Gregor L. , Pilhofer Martin
Published: January 2024

Predation allows bacteria to access alternative substrates in low-nutrient conditions. Ixotrophy has been proposed as a predatory lifestyle of multicellular filamentous bacteria in aquatic environments; however, the molecular mechanism remains unknown.

Here we uncover by a multidisciplinary approach that ixotrophy requires the interplay of multiple cellular machineries and a regulatory mechanism. Attacker-prey contacts are established by gliding motility and extracellular grappling hook-like structures that bind prey flagella. Cryo-electron microscopy identifies the grappling hooks as a heptameric assembly of a Type 9 Secretion System substrate. Cryo-electron tomography and functional assays show that killing is mediated by puncturing of the prey cell using a Type 6 Secretion System, possibly triggered by extracellular antennae. Single-cell analyses with stable isotope-labeled prey demonstrate that prey components are taken up by the attacker. Depending on nutrient availability, ixotrophy is switched off by endogenous Insertion Sequence Elements and re-activated through their excision. A marine metagenomic time series provides evidence for coupled dynamics of ixotrophic bacteria and their prey.

Our study reveals the complex mechanism of a conserved microbial predatory lifestyle and indicates the need for its regulation in conditions where the expression of costly pathways is dispensable.
Nutrient Abundance Signals the Changing of the Seasons by Phosphorylating PER2
Authors: Levine Daniel C. , Reeh Rasmus H. , McMahon Thomas , Mandrup-Poulsen Thomas , Fu Ying-Hui , Ptáček Louis J.
Published: January 2024

The circadian clock synchronizes metabolic and behavioral cycles with the rotation of the Earth by integrating environmental cues, such as light. Nutrient content also regulates the clock, though how and why this environmental signal affects the clock remains incompletely understood. Here, we elucidate a role for nutrient in regulating circadian alignment to seasonal photoperiods. High fat diet (HFD) promoted entrainment to a summer light cycle and inhibited entrainment to a winter light cycle by phosphorylating PER2 on serine 662. PER2-S662 phospho-mimetic mutant mice were incapable of entraining to a winter photoperiod, while PER2-S662 phospho-null mutant mice were incapable of entraining to a summer photoperiod, even in the presence of HFD. Multi-omic experimentation in conjunction with isocaloric hydrogenated-fat feeding, revealed a role for polyunsaturated fatty acids in nutrient-dependent seasonal entrainment. Altogether, we identify the mechanism whereby nutrient content shifts circadian rhythms to anticipate seasonal photoperiods in which that nutrient state predominates.

HIGHLIGHTS

High fat diet promotes entrainment to summer but inhibits entrainment to winter.

Calorie restriction promotes entrainment to winter but inhibits entrainment to summer.

PER2-S662 phosphorylation is required for nutritional regulation of seasonal circadian entrainment.

Dietary polyunsaturated fatty acids regulate seasonal circadian entrainment.
Adult sex change leads to extensive forebrain reorganization in clownfish
Authors: Parker Coltan G. , Gruenhagen George W. , Hegarty Brianna E. , Histed Abigail R. , Streelman Jeffrey T. , Rhodes Justin S. , Johnson Zachary V.
Published: January 2024

Sexual differentiation of the brain occurs in all major vertebrate lineages but is not well understood at a molecular and cellular level. Unlike most vertebrates, sex-changing fishes have the remarkable ability to change reproductive sex during adulthood in response to social stimuli, offering a unique opportunity to understand mechanisms by which the nervous system can initiate and coordinate sexual differentiation. This study explores sexual differentiation of the forebrain using single nucleus RNA-sequencing in the anemonefishAmphiprion ocellaris, producing the first cellular atlas of a sex-changing brain. We uncover extensive sex differences in cell type-specific gene expression, relative proportions of cells, baseline neuronal excitation, and predicted inter-neuronal communication. Additionally, we identify the cholecystokinin, galanin, and estrogen systems as central molecular axes of sexual differentiation. Supported by these findings, we propose a model of neurosexual differentiation in the conserved vertebrate social decision-making network spanning multiple subtypes of neurons and glia, including neuronal subpopulations within the preoptic area that are positioned to regulate gonadal differentiation. This work deepens our understanding of sexual differentiation in the vertebrate brain and defines a rich suite of molecular and cellular pathways that differentiate during adult sex change in anemonefish.

Significance Statement

This study provides key insights into brain sex differences in sex-changing anemonefish (Amphiprion ocellaris), a species that changes sex in adulthood in response to the social environment. Using single nucleus RNA-sequencing, the study provides the first brain cellular atlas showing sex differences in two crucial reproductive areas: the preoptic area and telencephalon. The research identifies notable sex-differences in cell-type proportions and gene expression, particularly in radial glia and glutamatergic neurons that co-express the neuropeptide cholecystokinin. It also highlights differences in preoptic area neurons likely involved in gonadal regulation. This work deepens our understanding of sexual differentiation of the brain in vertebrates, especially those capable of adult sex change, and illuminates key molecular and cellular beginning and endpoints of the process.
Protein sequence landscapes are not so simple: on reference-free versus reference-based inference
Authors: Dupic Thomas , Phillips Angela M. , Desai Michael M.
Published: January 2024

In a recent preprint, Park, Metzger, and Thornton reanalyze 20 empirical protein sequence-function landscapes using a “reference-free analysis” (RFA) method they recently developed. They argue that these empirical landscapes are simpler and less epistatic than earlier work suggested, and attribute the difference to limitations of the methods used in the original analyses of these landscapes, which they claim are more sensitive to measurement noise, missing data, and other artifacts. Here, we show that these claims are incorrect. Instead, we find that the RFA method introduced by Park et al. is exactly equivalent to the reference-based least-squares methods used in the original analysis of many of these empirical landscapes (and also equivalent to a Hadamard-based approach they implement). Because the reanalyzed and original landscapes are in fact identical, the different conclusions drawn by Park et al. instead reflect different interpretations of the parameters describing the inferred landscapes; we argue that these do not support the conclusion that epistasis plays only a small role in protein sequence-function landscapes.
Complex Hybridization in a Clade of Polytypic Salamanders (Plethodontidae:Desmognathus) Uncovered by Estimating Higher-Level Phylogenetic Networks
Authors: Pyron R. Alexander , O’Connell Kyle A. , Myers Edward A. , Beamer David A. , Baños Hector
Published: January 2024

Hybridization between incipient lineages is a common feature of ecomorphological diversification. We examine these phenomena in the Pisgah clade ofDesmognathussalamanders from the southern Appalachian Mountains of the eastern United States. The group contains four to seven species exhibiting two discrete phenotypes, aquatic “shovel-nosed” and semi-aquatic “black-bellied” forms. These ecomorphologies are ancient and have apparently been transmitted repeatedly between lineages through introgression. Geographically proximate populations of both phenotypes exhibit admixture, and at least two black-bellied lineages have been produced via reticulations between shovel-nosed parentals, suggesting complex transmission dynamics. However, computational constraints currently limit our ability to reconstruct network radiations from gene-tree data. Available methods are limited to level-1 networks wherein reticulations do not share edges, and higher-level networks may be non-identifiable in many cases. We present a heuristic approach to recover information from higher-level networks across a range of potentially identifiable empirical scenarios, supported by theory and simulation. When extrinsic information indicating the location and direction of hybridization events is available, our method can yield successful estimates of non-level-1 networks, or at least a reduced possible set thereof. Phylogenomic data strongly support a single backbone topology with up to five overlapping hybrid edges. These results suggest an unusual mechanism of ecomorphological hybrid speciation, wherein a binary threshold trait causes hybrids to shift between two microhabitat niches, promoting ecological divergence between sympatric hybrids and parentals. This contrasts with other well-known systems in which hybrids exhibit intermediate, novel, or transgressive phenotypes. Finally, the genetic basis of these phenotypes is unclear and further data are needed to clarify the evolutionary basis of morphological changes with ecological consequences.
Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
Authors: Kelly Richard D.W. , Stengel Kristy R. , Chandru Aditya , Johnson Lyndsey C. , Hiebert Scott W. , Cowley Shaun M.
Published: January 2024

Histone acetylation is a dynamic modification regulated by the opposing actions of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Deacetylation of histone tails results in chromatin tightening, and therefore, HDACs are generally regarded as transcriptional repressors. Counterintuitively, simultaneous deletion ofHdac1andHdac2in embryonic stem cells (ESCs) reduces expression of the pluripotency-associated transcription factorsPou5f1,Sox2, andNanog(PSN). By shaping global histone acetylation patterns, HDACs indirectly regulate the activity of acetyl-lysine readers, such as the transcriptional activator BRD4. Here, we use inhibitors of HDACs and BRD4 (LBH589 and JQ1, respectively) in combination with precision nuclear run-on and sequencing (PRO-seq) to examine their roles in defining the ESC transcriptome. Both LBH589 and JQ1 cause a marked reduction in the pluripotent gene network. However, although JQ1 treatment induces widespread transcriptional pausing, HDAC inhibition causes a reduction in both paused and elongating polymerase, suggesting an overall reduction in polymerase recruitment. Using enhancer RNA (eRNA) expression to measure enhancer activity, we find that LBH589-sensitive eRNAs are preferentially associated with superenhancers and PSN binding sites. These findings suggest that HDAC activity is required to maintain pluripotency by regulating the PSN enhancer network via the recruitment of RNA polymerase II.
Optically induced umklapp shift currents in striped cuprates
Authors: Dolgirev Pavel E. , Michael Marios H. , Curtis Jonathan B. , Parker Daniel E. , Nicoletti Daniele , Buzzi Michele , Fechner Michael , Cavalleri Andrea , Demler Eugene
Published: January 2024

Motivated by recent experiments that observed low-frequency second-order optical responses in doped striped superconductors, here we investigate the nonlinear electrodynamics of systems exhibiting a charge density wave (CDW) order parameter. Due to the Bragg scattering off the CDW order, an incoming spatially homogeneous electric field in addition to zero momentum current generates umklapp currents that are modulated in space at momenta of the reciprocal CDW lattice. In particular, here we predict and microscopically evaluate the umklapp shift current, a finite momentum analog of the regular shift current which represents the second-order optical process that downconverts homogeneous AC electric field into low-frequency, zero momentum current. Specifically, we evaluate real-time response functions within mean-field theory via the Keldysh technique and use the Peierls substitution to compute observables at finite momenta in lattice models. We find that systems with certain lattice symmetries (such as inversion symmetry), where the regular shift current is disallowed, may give rise to the umklapp one. We apply our framework to investigate lattice symmetries in layered materials with helical-like stripes and show that both types of shift currents provide insight into the nature of intertwined phases of matter. Finally, we discuss the relation of our findings to recent experiments in striped superconductors.

Published by the American Physical Society
2024
Light baryon spatial correlators at short distances
Authors: Han Chao , Zhang Jialu
Published: January 2024

To study the light baryon light cone distribution amplitudes (LCDAs), the spatial correlator of the light baryon has been calculated up to one-loop order in coordinate space. They reveal certain identities that do not appear in the study of mesons DAs and parton distribution functions. Subsequently, it was renormalized using the ratio renormalization scheme involving division by a 0-momentum matrix element. Then through the matching in the coordinate space, the light baryon light cone correlator can be extracted out from the spatial correlator. These results provide insights into both the ultraviolet and infrared structures of the light baryon spatial correlator, which is valuable for further exploration in this field. Furthermore, the employed ratio scheme is an efficient and lattice-friendly renormalization approach suitable for short-distance applications. These can be used for studying the light baryon LCDAs using lattice techniques.

Published by the American Physical Society
2024
B
meson anomalies within the triplet vector boson model to the light of recent measurements from LHCb
Authors: Cabarcas J. M. , Muñoz J. H. , Quintero-Poveda Néstor , Rojas Eduardo
Published: January 2024

The triplet vector boson (TVB) is a simplified new physics model involving massive vector bosons transforming as a weak triplet vector. Such a model has been proposed as a combined explanation of the anomalous b→sμ+μ− and b→cτν¯τ data (the so-called B meson anomalies). In this work, we carry out a revamped view of the TVB model by incorporating the most recent 2022 and 2023 LHCb measurements on the lepton-flavor universality ratios R(D(*))=BR(B→D(*)τν¯τ)/BR(B→D(*)ℓ′ν¯ℓ′), R(Λc)=BR(Λb→Λcτν¯τ)/BR(Λb→Λcμν¯μ), and RK(*)=BR(B→K(*)μ+μ−)/BR(B→K(*)e+e−). We perform a global fit to explore the allowed parameter space by the new data and all relevant low-energy flavor observables including the recent experimental progress from Belle, Belle II, and LHCb. Our results are confronted with the recent high-mass dilepton searches at the LHC. We find that for a heavy TVB mass of 1 TeV a common explanation of the B meson anomalies is possible for all data with the recent LHCb measurements on R(D(*)), consistent with LHC constraints. However, this framework is in strong tension with LHC bounds when one considers all data along with the world average values reported by the Heavy Flavor Averaging Group (, Belle, and LHCb) on R(D(*)). Future measurements will be required in order to clarify such a situation.

Published by the American Physical Society
2024
Revisiting
K1(1270)−K1(1400)
mixing with QCD sum rules
Authors: Shi Yu-Ji , Zeng Jun , Deng Zhi-Fu
Published: January 2024

We investigate the K1(1270)−K1(1400) mixing induced by the flavor SU(3) symmetry breaking. The mixing angle is calculated in a purely theoretical manner, where it is expressed by a K1A→K1B transition matrix element of the operators that break flavor SU(3) symmetry. The QCD contribution to this matrix element is assumed to be dominated and calculated with QCD sum rules. A three-point correlation function is defined and handled both at the hadron and quark-gluon levels. The quark-gluon level calculation is based on operator product expansion up to dimension-five condensates. A detailed numerical analysis is performed to determine the Borel parameters, and the obtained mixing angle is θK1=21.4°±9° or θK1=68.6°±9°.

Published by the American Physical Society
2024
Dark dimension and the standard model landscape
Authors: Anchordoqui Luis A. , Antoniadis Ignatios , Cunat Jules
Published: January 2024

We study the landscape of lower-dimensional vacua of the standard model (SM) coupled to gravity in the presence of the so-called “dark dimension” of size R⊥ in the micron range, focusing on the validity of the swampland conjecture forbidding the presence of nonsupersymmetric anti–de Sitter (AdS) vacua in a consistent quantum gravity theory. We first adopt the working assumption that right-handed neutrinos propagate in the bulk, so that neutrino Yukawa couplings become tiny due to a volume suppression, leading to naturally light Dirac neutrinos. We show that the neutrino Kaluza-Klein (KK) towers compensate for the graviton tower to maintain stable de Sitter (dS) vacua found in the past, but neutrino oscillation data set restrictive bounds on R⊥ and therefore the first KK neutrino mode is too heavy to alter the shape of the radion potential or the required maximum mass for the lightest neutrino to carry dS rather than AdS vacua found in the absence of the dark dimension, m1,max≲7.63  meV. We also show that a very light gravitino (with mass in the meV range) could help relax the neutrino mass constraint m1,max≲50  meV. The differences for the predicted total neutrino mass ∑mν among these two scenarios are within reach of next-generation cosmological probes that may measure the total neutrino mass with an uncertainty σ(∑mν)=0.014  eV. We also demonstrate that the KK tower of a very light gravitino can compensate for the graviton tower to sustain stable dS vacua and thus right-handed neutrinos can (in principle) be locked on the brane. For this scenario, Majorana neutrinos could develop dS vacua, which is not possible in the SM coupled to gravity. Finally, we investigate the effects of bulk neutrino masses in suppressing oscillations of the zero modes into the first KK modes to relax the oscillation bound on R⊥.

Published by the American Physical Society
2024
Pseudoentropy for descendant operators in two-dimensional conformal field theories
Authors: He Song , Yang Jie , Zhang Yu-Xuan , Zhao Zi-Xuan
Published: January 2024

We study the late-time behaviors of pseudo-(Rényi) entropy of locally excited states in rational conformal field theories. To construct the transition matrix, we utilize two nonorthogonal locally excited states that are created by the application of different descendant operators to vacuum. We show that when two descendant operators are generated by a single Virasoro generator acting on the same primary operator, the late-time excess of pseudoentropy and pseudo-Rényi entropy corresponds to the logarithm of the quantum dimension of the associated primary operator, in agreement with the case of entanglement entropy. However, for linear combination operators generated by the generic summation of Virasoro generators, we obtain a distinct late-time excess formula for the pseudo-(Rényi) entropy compared to that for (Rényi) entanglement entropy. As the mixing of holomorphic and antiholomorphic generators enhances the entanglement, in this case, the pseudo-(Rényi) entropy can receive an additional contribution. The additional contribution can be expressed as the pseudo-(Rényi) entropy of an effective transition matrix in a finite-dimensional Hilbert space.

Published by the American Physical Society
2024
Testing the nonunitarity of the leptonic mixing matrix at
FASERv
and
FASERv2
Authors: Celestino-Ramírez Jesús Miguel , Escrihuela F. J. , Flores L. J. , Miranda O. G.
Published: January 2024

The FASERν experiment has detected the first neutrino events coming from LHC. Near future high-statistic neutrino samples will allow us to search for new physics within the neutrino sector. Motivated by the forthcoming promising FASERν neutrino data, and its successor, FASERν2, we study its potential for testing the unitarity of the neutrino lepton mixing matrix. Although it would be challenging for FASERν and FASERν2 to have strong constraints on this kind of new physics, we discuss its role in contributing to a future improved global analysis.

Published by the American Physical Society
2024
Chirality-Induced Selectivity of Phonon Angular Momenta in Chiral Quartz Crystals
Authors: Ohe Kazuki , Shishido Hiroaki , Kato Masaki , Utsumi Shoyo , Matsuura Hiroyasu , Togawa Yoshihiko
Published: January 2024

A generation, propagation, and transfer of phonon angular momenta are examined on thermal transport in chiral insulative and diamagnetic crystals of α-quartz. We found that thermally driven phonons carry chirality-dependent angular momenta in the quartz crystals and they could be extracted from the quartz as a spin signal. Namely, chirality-induced selectivity of phonon angular momenta is realized in the chiral quartz. We argue that chiral phonons available in chiral materials could be a key element in triggering or enhancing chirality-induced spin selectivity with robust spin polarization and long-range spin transport found in various chiral materials.

Published by the American Physical Society
2024
Polarization-Sensitive Photoluminescence from Aligned Carbon Chains Terminated by Gold Clusters
Authors: Kucherik A. , Osipov A. , Samyshkin V. , Hartmann R. R. , Povolotskiy A. V. , Portnoi M. E.
Published: January 2024

We synthesize a thin film composed of long carbyne chains terminated by gold clusters and study its optical properties. The presence of gold particles stabilizes longer chains and leads to their alignment. We show that the gold clusters also act as a source of electron doping, thus, changing the intensity of photoluminescence from quadratic dependence on the pumping intensity without gold to linear with gold. We also observe that the excitation of the film at the gold plasmon frequency causes the blue shift of photoluminescence and estimate, on the basis of this effect, the minimum length of the carbyne chains. The high degree of alignment of the gold-terminated carbyne chains results in strongly anisotropic light absorption characterized by a distinctive cosine dependence on the angle between the carbyne molecule and polarization plane of the excitation. This paves the way for a new class of ultimately thin polarization sensitive emitters to be used in future integrated quantum photonics devices.

Published by the American Physical Society
2024
Life cycle analysis results for engine blisk LCA
Authors: Fricke Kilian , Bergs Thomas , Ganser Philipp , Seimann Martin
Published: January 2024

Purpose

The aviation industry has seen consistent growth over the past few decades. To maintain its sustainability and competitiveness, it is important to have a comprehensive understanding of the environmental impacts across the entire life cycle of the industry, including materials, processes and resources; manufacturing and production; lifetime services; reuse; end-of-life; and recycling. One important component of aircraft engines, integral rotors known as Blisks, are made of high-value metallic alloys that require complex and resource-intensive manufacturing processes. The purpose of this paper is to assess the ecological and economical impacts generated through Blisk production and thereby identify significant ‘hot-spots’.

Design/methodology/approach

This paper focuses on the methodology and approach for conducting a full-scale Blisk life cycle assessment (LCA) based on ISO 14040/44. Unlike previous papers in the European Aerospace Science Network series, which focused on the first two stages of LCA, this publication delves into the “life cycle impact assessment” and “interpretation” stages, providing an overview of the life cycle inventory modeling, impact category selection and presenting preliminary LCA results for the Blisk manufacturing process chain.

Findings

The result shows that the milled titanium Blisk has a lower CO2 footprint than the milled nickel Blisk, which is less than half of the global warming potential (GWP) of the milled nickel Blisk. A main contributor to GWP arises from raw material production. However, no recycling scenarios were included in the analysis, which will be the topic of further investigations.

Originality/value

The originality of this work lies in the detailed ecological assessment of the manufacturing for complex engine components and the derivation of hot spots as well as potential improvements in terms of eco-footprint reduction throughout the products cradle-to-gate cycle. The LCA results serve as a basis for future approaches of process chain optimisation, use of “greener” materials and individual process improvements.
An LLC resonant converter with wide output range fixed frequency PWM control for PEV charging applications
Authors: Wang Dangshu , Chang Menghu , Zhao Licong , Yang Yuxuan , Guan Zhimin
Published: January 2024

Purpose

This study aims to regarding the application of traditional pulse frequency modulation control full-bridge LLC resonant converters in wide output voltage fields such as on-board chargers, there are issues with wide frequency adjustment ranges and low conversion efficiency.

Design/methodology/approach

To address these issues, this paper proposes a fixed-frequency pulse width modulation (PWM) control strategy for a full-bridge LLC resonant converter, which adjusts the gain by adjusting the duty cycle of the switches. In the full-bridge LLC converter, the two switches of the lower bridge arm are controlled by a fixed-frequency and fixed duty cycle, with their switching frequency equal to the resonant frequency, whereas the two switches of the upper bridge arm are controlled by a fixed-frequency PWM to adjust the output voltage. The operation modes of the converter are analyzed in detail, and a mathematical model of the converter is established. The gain characteristics of the converter under the fixed-frequency PWM control strategy are deeply analyzed, and the conditions for implementing zero-voltage switching (ZVS) soft switching in the converter are also analyzed in detail. The use of fixed-frequency PWM control simplifies the design of resonant parameters, and the fixed-frequency control is conducive to the design of magnetic components.

Findings

According to the fixed-frequency PWM control strategy proposed in this paper, the correctness of the control strategy is verified through simulation and the development and testing of a 500-W experimental prototype. Test results show that the primary side switches of the converter achieve ZVS and the secondary side rectifier diodes achieve zero-current switching, effectively reducing the switching losses of the converter. In addition, the control strategy reduces the reactive circulating current of the converter, and the peak efficiency of the experimental prototype can reach 95.2%.

Originality/value

The feasibility of the fixed-frequency PWM control strategy was verified through experiments, which has significant implications for improving the efficiency of the converter and simplifying the design of resonant parameters and magnetic components in wide output voltage fields such as on-board chargers.
Climate change exposure and dividend policy: evidence from textual analysis
Authors: Ongsakul Viput , Chintrakarn Pandej , Papangkorn Suwongrat , Jiraporn Pornsit
Published: January 2024

Purpose

Taking advantage of distinctive text-based measures of climate policy uncertainty and firm-specific exposure to climate change, this study aims to examine the impact of firm-specific vulnerability on dividend policy.

Design/methodology/approach

To mitigate endogeneity, the authors apply an instrumental-variable analysis based on climate policy uncertainty as well as use additional analysis using propensity score matching and entropy balancing.

Findings

The authors show that an increase in climate policy uncertainty exacerbates firm-specific exposure considerably. Exploiting climate policy uncertainty to generate exogenous variation in firm-specific exposure, the authors demonstrate that companies more susceptible to climate change are significantly less likely to pay dividends and those that do pay dividends pay significantly smaller dividends. For instance, a rise in firm-specific exposure by one standard deviation weakens the propensity to pay dividends by 5.11%. Climate policy uncertainty originates at the national level, beyond the control of individual firms and is thus plausibly exogenous, making endogeneity less likely.

Originality/value

To the best of the authors’ knowledge, this study is the first attempt in the literature to investigate the effect of firm-specific exposure on dividend policy using a rigorous empirical framework that is less vulnerable to endogeneity and is more likely to show a causal influence, rather than a mere correlation.
Effect of corporate social irresponsibility on organizational workplace deviant behaviour: the meditating role of moral disengagement
Authors: Abbasi Munir A. , Amran Azlan , Sahar Noor e , Lim Chia Yon
Published: January 2024

Purpose

This study aims to investigate the effects of both internal and external corporate social irresponsibility (CSI) on organizational workplace deviant behaviours (OWDB) by using social cognitive theory. The study also explores the role of moral disengagement as a mediator in this relationship.

Design/methodology/approach

Data was collected from a sample of 321 individuals employed in the textile industry of Pakistan. The study used partial least square-structural equation modelling (PLS-SEM) to estimate the relationships within the model.

Findings

The findings indicate that both internal and external CSI have a positive impact on moral disengagement. Secondly, moral disengagement drives OWDB positively. Thirdly, moral disengagement is a significant mediator that mediates between both internal and external CSI and OWDB positively.

Practical implications

This research offers novel perspectives to organizational leaders, highlighting the significance of addressing CSI in conjunction with sustainability endeavours. It is imperative for business managers to prioritize the morality of their employees.

Originality/value

This study’s novelty lies in its confirmation of the mediating role of moral disengagement in the relationship between internal and external CSI and OWDB.
Financial technology and banking market discipline in Indonesia banking
Authors: Yudaruddin Rizky
Published: January 2024

Purpose

This study aims to assess the effectiveness of the banking market discipline in relation to the development of Financial Technology (FinTech) startups.

Design/methodology/approach

Using panel data collected from 144 banks in Indonesia from 2004 to 2018, this study’s regression models were estimated using fixed effects with robust standard errors.

Findings

This study finds that FinTech startups disturb bank deposits. Meanwhile, market discipline exists in Indonesian banks, as indicated by depositors’ behavior with higher credit and liquidity risks. However, market discipline does not exist for bank insolvency risk, which is indicated by a significant and positive relationship with the dependent variable. Therefore, the higher the number of FinTech startups, the more effective the market discipline. Empirical findings also revealed that the joint impact between FinTech startups and bank risk is also important in explaining the difference in the effectiveness of banking market discipline.

Practical implications

This study has policy implications for banks in mitigating risk associated with market discipline and instability of financial intermediation.

Originality/value

This study offers a significant contribution to the empirical literature because it specifically explores the effectiveness of the banking market discipline by focusing on the joint impact of FinTech startups and bank risk on deposits. Furthermore, this study contributes to providing empirical evidence that links between FinTech startups and bank risk affect depositor behavior at government-owned, private, large and small, as well as nonmobile and mobile adoption banks.