bluuebunny/crossref_metadata_2025 huggingface dataset:
MUSICiAn: Genome-wide Identification of Genes Involved in DNA Repair via Control-Free Mutational Spectra Analysis
Authors: Seale Colm , Barazas Marco , van Schendel Robin , Tijsterman Marcel , Gonçalves Joana P.
Published: January 2025

Motivation

Understanding the factors involved in DNA double-strand break (DSB) repair is crucial for the development of targeted anti-cancer therapies, yet the roles of many genes remain unclear. Recent studies show that perturbations of certain genes can alter the distribution of sequence-specific mutations left behind after DSB repair. This suggests that genome-wide screening could reveal novel DSB repair factors by identifying genes whose perturbation causes the mutational distribution spectra observed at a given DSB site to deviate significantly from the wild-type. However, designing proper controls for a genome-wide perturbation screen could be challenging. We explore the idea that a genome-wide screen might allow us to forgo the use of traditional non-targeting controls by reframing the analysis as an outlier detection problem, assuming that most genes have minimal influence on DSB repair.

Results

We propose MUSICiAn (Mutational Signature Catalogue Analysis), a compositional data analysis method that ranks gene perturbation-specific mutational spectra without controls by measuring deviations from the central tendency in the distributions of all spectra. We show that MUSICiAn can effectively estimate pseudo-controls for the existing Repair-seq dataset, screening 476 genes and 60 non-targeting controls. We further apply MUSICiAn to a genome-wide dataset profiling mutational outcomes induced by CRISPR-Cas9 at three target sites across cells with individual perturbations of 18,406 genes. MUSICiAn successfully recovers known genes, highlights the spliceosome as a lesser-appreciated player in DSB repair, and reveals candidates for further investigation.

Availability

github.com/joanagoncalveslab/MUSICiAn.
The Plankton Imager (Pi-10): An imaging instrument for automated and continuous zooplankton data collection
Authors: Scott James , Pitois Sophie G. , Blackwell Robert , Close Hayden , Culverhouse Phil , Tilbury Julian
Published: January 2025

The Pi-10 is the latest iteration of the Plankton Imager: a high-speed colour line-scan camera that images particles in a flow-through system. The Pi-10 is a cost-effective, easy to install and low maintenance automated instrument that can be used on any platform with access to water and power supply. We tested the Pi-10 on the research vessel Cefas Endeavour, connected to a continuous water supply pumping water at 34 L min-1. The instrument collected images of particles, within the size range of 180 µm - 3.5 cm, automatically and continuously, alongside other vessel operations, in all weathers over a period of 18 days. The Pi-10 successfully captured and saved up 5000 images per minute, translating into a 46 GB of digital storage per day. When particle density exceeded 147 per litre, the instrument stopped saving all images, while still recording the number of particles that passed through the system. This is akin to subsampling, with more sub-sampling required in areas or times of high particle density (e.g at the time of spring plankton bloom or in turbid waters). The Pi-10 collects high volumes of data in a continuous manner, thus providing unprecedented fine spatial data. The high frequency nature of the instrument opens the door to new areas of research. These include, in particular, the observation of fine scale processes, the move towards real-time sampling, and the increased capability to build a digital twin of the oceans. As technologies continue evolving the Pi-10 performance will increase, being able to collect and save more and more images.
Effects of host sex, age and behaviour on co-infection patterns in a wild ungulate
Authors: Berland Florian , Bourret Vincent , Peroz Carole , Malandrin Laurence , Bonsergent Claire , Bailly Xavier , Masseglia Sébastien , Nouvel Laurent-Xavier , Lagrée Anne-Claire , Rouxel Clotilde , Dimeglio Chloé , Izopet Jacques , Ollivier Valentin , Boulinier Thierry , Villena Isabelle , Aubert Dominique , Sluydts Vincent , Le Loc’h Guillaume , Bonnet Arnaud , Chaval Yannick , Merlet Joël , Lourtet Bruno , Gilot-Fromont Emmanuelle , Verheyden Hélène
Published: January 2025

Recent zoonotic disease emergences reveal the importance of studying wildlife parasite communities. As wild hosts frequently harbour diverse parasite species, understanding the drivers of multiple infection patterns in free-ranging hosts is critical for elucidating the ecological and epidemiological dynamics of parasite communities. In this study, we analysed co-infection patterns in European roe deer (Capreolus capreolus) inhabiting a fragmented rural landscape in southwestern France. Using data from 130 GPS-tracked roe deer, we examined the influence of proximity to livestock, host activity levels, age, sex, and between-parasite interactions on the presence of 11 parasitic taxa. Hierarchical modelling of species communities (HMSC) revealed that proximity to livestock significantly increased the likelihood of infection with orofecally transmitted parasites (Toxoplasma gondii, gastrointestinal parasites). Sex and age were other key predictors, with males and juveniles exhibiting a higher frequency of parasite presence, likely influenced by hormonal and immune system differences. Activity levels showed distinct age-related effects, with higher activity levels being positively associated with increased parasite prevalence in yearlings, but not in adults. In contrast, parasite association patterns within individual hosts were weak, suggesting minimal interactions between parasite species. Our findings highlight the interplay between exposure and susceptibility in shaping co-infection patterns and underscore the value of hierarchical modelling approaches in multi-parasite systems.

Key Findings

Parasite communities, studied in 130 GPS monitored roe deer, revealed frequent co-infection.

Proximity to livestock increased the risk of infection by parasite taxa shared with domestic animals.

For several parasitic taxa, males and younger roe deer had a higher probability of infection.

The effect of host activity on parasite infection was dependent on roe deer age.

Only slight between-parasite interactions were detected within individual hosts.
Cell-state specific drug-responses are associated with differences in signaling network wiring
Authors: Krämer Niels , van Eijl Roderick , Stohn Tim , Tanis Sabine , Wessels Lodewyk , Bosdriesz Evert , Mulder Klaas W.
Published: January 2025

Intracellular signaling pathways form networks through which information is transmitted, often in the form of kinase-mediated phosphorylation events, to interpret extracellular signals and elicit appropriate cellular responses. Yet, even isogenic cells in a homogenous environment show heterogeneity in their intracellular “cell-state”, as well as their response to extracellular signals. Here, we aimed to better understand this relation between these phenomena by investigating how information flows through the EGF-receptor centered network upon targeted drug treatment, and how this is affected by cell-to-cell-state differences. Using single-cell ID-seq, we profiled the cell-state and signaling activity of primary human epidermal stem cells by measuring 69 (phospho-)proteins upon inhibition of the Erk/MAPK (p90RSK) and Akt/mTOR (p70S6K) routes downstream of the EGF pathway. We found that the effects of drug treatment propagated from the EGF-signaling pathway to other connected parts of the cellular signaling network, indicating altered signaling flow. We identified nine distinct cell-states that show pervasive state-dependent drug-responses for many (phospho-)proteins. Computational modeling of the signaling network using single-cell Comparative Network Reconstruction showed that many interactions between phospho-proteins (i.e. network wiring) were quantitatively different between cell-states. Furthermore, (phospho-)proteins with a cell-state dependent drug response, were more likely to be involved in interactions that showed a cell-state dependent strength. Overall, our results indicate that drug treatment response and signaling interactions between proteins are closely related and modulated by cell-state.
Interactions between motor cortical forelimb regions and their influence on muscles reorganize across behaviors
Authors: Kristl Amy C , Koh Natalie , Agrios Mark , Savya Sajishnu , Ma Zhengyu , Basrai Diya , Hsu Sarah , Miri Andrew
Published: January 2025

It remains unclear how classical models of motor cortical hierarchy align with emerging evidence of behavioral organization in motor cortex. To address this, we combined optogenetic inactivation, Neuropixels recording, and electromyography to quantify the pattern and influence of activity in the mouse analogs of forelimb premotor and primary motor cortex (RFA and CFA) during reaching and climbing. Results revealed that RFA's dominant influence on forelimb muscles and on CFA during reaching is replaced by a dominant influence of CFA on muscles and on RFA during climbing, even when forelimb muscle activity during climbing resembles that during reaching. Short-latency influence between regions on excitatory and inhibitory populations in different cortical laminae also showed behavioral specificity. Simultaneous recordings in both areas during climbing revealed a loss of activity timing differences seen during reaching previously interpreted as reflective of hierarchy. These findings demonstrate that hierarchical interactions between forelimb motor cortical regions are behavior-specific.
Nucleotide-derived bacterial alarmones attenuate the induction of type-I interferon responses in a murine macrophage reporter cell line
Authors: Kilduff Ryan P , Purcell Erin B , Shollenberger Lisa M
Published: January 2025

The stringent response is a well-studied phenomenon in many bacterial systems and regulates resource-consuming activities such as transcription, translation, and replication. The stringent response is a well-conserved signaling framework, as are the nucleotide-derived signaling mediators, collectively referred to as (p)ppGpp or as alarmones. There is a wealth of research evaluating nucleotide-derived alarmone signaling in bacterial models, however, their potential to modulate innate immune signaling has not yet been evaluated. Several common pathogen-synthesized molecules, such as lipopolysaccharide (LPS) and cyclic-di-AMP (c-di-AMP), act as pathogen-associated molecular patterns (PAMPs), which are common patterns that alert the innate immune system of bacterial infection. The goal of this work is to elucidate the impact of (p)ppGpp on innate immune signaling. To explore this, RAW-Dual cells were incubated with guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), two well-studied nucleotide-derived alarmones found in many different pathogenic bacteria, as well as with GTP. Both ppGpp and pppGpp were able to significantly reduce the expression of secreted luciferase in RAW-Dual cells in a dose-dependent manner, indicating a reduction of the interferon-stimulated regulatory elements (ISREs). Neither alarmone impacted secreted embryonic alkaline phosphatase (SEAP) secretion, which reports for NF-kB activation. This is the first work to suggest that nucleotide-derived alarmones produced by bacteria may impact an arm of innate immunity responsible for type-I interferon secretion.

Author Summary

Many different disease-causing bacteria use a similar signaling network to help them survive in environments with low resources; this network is called “the stringent response.” All bacteria that use this network also produce signaling molecules, called alarmones, that help coordinate their response to resource deprivation. Interestingly, the human immune system recognizes molecules that are made by many pathogens. As such, our team decided to evaluate whether these bacterially-produced alarmones are able to affect our immune system. We discovered, rather than stimulating our immune system, that high concentrations of these alarmone compounds are able to turn off an important arm of the immune system that is essential in combating viral infections. This suggests another mechanism that bacteria may use to hide from the immune system during infection. In addition, there are potential clinical uses for a molecule that is selectively turn off arms of the immune system, and these molecules may have potential as future anti-inflammatory drugs after further research is able to explore their mechanism of action.
Diet links gut chemistry with cancer risk in C57Bl/6 mice and human colorectal cancer patients
Authors: Cohen Ziv , Choi Jiahn , Peregrina Karina , Khan Saad , Wolfson Sarah , Sherman Cherrie , Augenlicht Leonard , Kelly Libusha
Published: January 2025

Background & Aims

Western-style diets, characterized by higher fat and protein, and low micronutrient levels, promote the development of colorectal cancer (CRC). Here, we investigate the role of a Western diet on microbiome composition, sulfide production, and intestinal epithelial damage in pre-CRC mice, and validate taxonomic changes in a meta-analysis of human CRC patients.

Methods

NWD1 is a purified Western-style diet that produces sporadic intestinal and colon tumors in wild-type C57BL/6 mice in the absence of genetic or carcinogen exposure. To determine how this diet influences cancer risk by shaping microbial composition and sulfide chemistry, mice were fed NWD1 or a purified control diet for 24 weeks. Microbiome composition, sulfide production, and intestinal stem cell mRNA expression were assessed. Observed microbiome changes were validated in a human CRC meta-analysis.

Results

Fecal sulfide levels were tripled in NWD1-fed mice (P< 0.00001), concurrent with increased abundance of the sulfidogenicErysipelotrichaceaefamily. NWD1-fed mice had increased expression of mitochondrial sulfide oxidation genes in Lgr5hiintestinal stem cells, demonstrating an adaptive response to elevated sulfide. In a meta-analysis of human CRC studies, we observed thatErysipelotrichaceaewere associated with CRC, validating both canonical CRC microbes such asSolobacterium mooreiand highlighting the potential contribution of previously unrecognized, disease-associated microbes.

Conclusions

Our analyses connect the risk factors of Western diet, sulfide, and epithelial damage in a pre-cancer mouse model to microbiome changes observed in human CRC patients and suggest that microbial signatures of CRC and gut ecosystem alteration may manifest long before disease development.
Histopathologic Evaluation and Single-Cell Spatial Transcriptomics of the Colon Reveal Cellular and Molecular Abnormalities Linked to J-Pouch Failure in Patients with Inflammatory Bowel Disease
Authors: Olivas Andrea D. , Ngai Paul Chak Mou , Schahrer Emily , Olortegui Kinga S. , Cursio John F. , Akiyama Shintaro , Chang Eugene B. , Shen Le , Umanskiy Konstantin , Rubin David T. , Zemmour David , Weber Christopher R.
Published: January 2025

Background and Aims

Total abdominal colectomy (TAC) with a staged ileal pouch-anal anastomosis (IPAA) is a common surgical treatment for ulcerative colitis (UC). However, a significant percentage of patients experience pouch failure, leading to morbidity. This retrospective case-control study identified histopathological features of the TAC specimen associated with pouch failure and investigated the molecular mechanisms of this susceptibility using single-cell spatial transcriptomics.

Methods

We analyzed a cohort of 417 patients who underwent IPAA between 2000-2010 at the University of Chicago Medical Center for up to 18 years. Histological examination of TAC specimens focused on disease activity, depth of inflammation, and specific features, including granulomas and deep ulcers. A subset of patients was profiled using single-cell spatial transcriptomics to map gene expression and immune cell interactions in relation to the risk of pouch failure.

Results

The 18-year pouch failure risk was 23%, with post-procedure diagnosis of CD as a major risk factor (HR = 4.3, 95% CI: 2.3–8.1) as well as high-risk histologic features, including deep chronic inflammation (HR = 21, 95% CI: 11-41) and severe disease activity (HR = 14, 95% CI: 5.7-32) in TAC specimens. Spatial transcriptomics showed immune infiltration of T and myeloid cells, reduced myocyte-glial interactions, and cytokine signaling pathways such as IL-10, IL-1β, and type I/II interferons, associated with an increased risk of pouch failure.

Conclusion

Histological features and spatial molecular profiling are predictive of IPAA failure. These findings support the use of histologic evaluation and targeted molecular analysis of the TAC specimen to identify high-risk patients and improve IPAA outcomes.
Distinctive associations between plasma p-tau181 levels and hippocampal subfield volume across the Alzheimer’s disease continuum
Authors: Rich Adea , Oh Hwamee ,   Alzheimer’s Disease Neuroimaging Initiative
Published: January 2025

Background

Plasma p-tau181 is a promising diagnostic marker of Alzheimer’s disease (AD) pathology, reflecting amyloid accumulation, tau deposition, and downstream neurodegeneration that leads to cognitive impairment. However, the specificity of plasma p-tau181 to AD-related tau pathology remains unclear.

Objective

To assess whether plasma p-tau181 is differentially associated with volumetric changes in distinct hippocampal subfields and whether they mediate the relationship between plasma p-tau181 and cognition across the AD continuum.

Methods

213 participants with normal cognition (N=57), mild cognitive impairment (N=109), and AD (N=47) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) were included for cross-sectional analyses of hippocampal subfield volume that was quantified using the Automatic Segmentation of Hippocampal Subfields (ASHS) software. A subset (n=89) was evaluated for one-year longitudinal changes in hippocampal subfield volume.

Results

Higher plasma p-tau181 levels (pg/mL) were associated with decreased volumes in the CA1 and dentate gyrus, bilaterally, and right entorhinal cortex (ps< 0.05). Additionally, volumes of these subfields partially mediated the relationship between plasma p-tau181 and ADNI memory and executive function composite scores. Baseline plasma p-tau181, however, did not predict longitudinal atrophy of hippocampal subfields across diagnostic groups.

Conclusions

Plasma p-tau181 is differentially associated with hippocampal subfields that are closely related to both age- and AD-related neurodegeneration. Elevated plasma p-tau181 levels may reflect tau accumulation, and volumetric changes in CA1 and DG may mediate the detrimental effect of tau pathology on cognition.
Alpha-frequency stimulation strengthens coupling between temporal fluctuations in alpha oscillation power and default mode network connectivity
Authors: Ma Yijia , Brown Joshua A , Chen Chaowen , Ding Mingzhou , Wu Wei , Li Wen
Published: January 2025

Alpha (8-12 Hz) oscillations and default mode network (DMN) activity dominate the brain's intrinsic activity in the temporal and spatial domains, respectively. They are thought to play crucial roles in the spatiotemporal organization of the complex brain system. Relatedly, both have been implicated, often concurrently, in diverse neuropsychiatric disorders, with accruing electroencephalogram/magnetoencephalogram (EEG/MEG) and functional magnetic resonance imaging (fMRI) data linking these two neural activities both at rest and during key cognitive operations. Prominent theories and extant findings thus converge to suggest a mechanistic relationship between alpha oscillations and the DMN. Here, we leveraged simultaneous EEG-fMRI data acquired before and after alpha-frequency transcranial alternating current stimulation (α-tACS) and observed that α-tACS tightened the dynamic coupling between spontaneous fluctuations in alpha power and DMN connectivity (especially, in the posterior DMN, between the posterior cingulate cortex and the bilateral angular gyrus). In comparison, no significant changes were observed for temporal correlations between power in other oscillatory frequencies and connectivity in other major networks. These results thus suggest an inherent coupling between alpha and DMN activity in humans. Importantly, these findings highlight the efficacy of alpha-tACS in regulating the DMN, a clinically significant network that is challenging to target directly with non-invasive methods.
Agonistic interactions between slender mudskippers (Periophthalmus gracilis) in Singapore
Authors: Saleh Soroush , Yan Ying Tan Alyssa , Wei Jie Edmund Chow , Jun Chee Koi , Neville Sean , Johns Philip
Published: January 2025

Mudskippers engage in frequent territorial interactions. Few studies of mudskipper agonistic behavioral sequences exist. The slender mudskipper (Periophthalmus gracilis) inhabits intertidal zones of mangrove forests across Southeast Asia. Here, we describe common behavioral sequences of winners and losers among unmanipulated, wild slender mudskipper interactions in Singapore. Winning mudskippers showed more approach behaviors than losers, such as “Crawl towards”, and more behaviors that may indicate aggression, such as “Pectoral wave”, “Flag”, and “Head up”. Losers showed more evasive behaviors, like “Jump” and “Crawl away”. We found evidence of agonistic behavioral matching. Larger mudskippers won contests more frequently than smaller mudskippers.
Spatial profiling of central nervous system cellular markers in murine breast cancer to brain metastases
Authors: Hogg Karen , Calder Grant , Droop Alastair , Yang Ming , Simon Anna , Hunt Mark J , Kaye Paul M , Whittington Miles , Chawla Sangeeta , Brackenbury William J
Published: January 2025

Background

Brain metastasis occurs in approximately 16% of metastatic breast cancer patients, and incidence is increasing. Patients with breast cancer brain metastases frequently develop neurological problems including cognitive impairments and seizures. We previously demonstrated accumulation of activated microglia around the tumour site in a breast cancer brain metastasis model, which co-localised with spontaneously occurring local field potential events that resembled interictal epileptic discharges. However, the mechanisms underlying these spatially restricted effects on neuronal excitability are poorly understood.

Methods

To better understand the underlying cellular changes and potential mechanisms, we used digital spatial profiling of brain cell subtype-specific markers to chart the spatial organisation of neurons, oligodendrocytes, astrocytes, and microglia in relation to metastatic lesion site. We developed a novel chordline-based approach to analyse these spatial changes in biomarker distribution.

Results

Several protein markers associated with proliferation (Ki67), astrocytes (GFAP) and microglia (CD11b, IBA1, CD45, MSR1) were upregulated in the tumour compared to healthy contralateral brain parenchyma. In contrast, some neuroglial markers (MAP2, Neurofilament light, NeuN, S100B and TMEM119) were lower in the lesion compared to normal tissue.

Conclusions

Overall, the protein marker changes in the lesion are indicative of neuronal cell loss and changes in the immune microenvironment of the metastatic lesion involving activated microglia, astrocytes and recruitment of peripheral immune cells. Such cellular changes may contribute to the changes in electrical activity resulting from brain metastases observed in mice and patients.
Ion-kinetic-energy sampling in a 22-pole trap using ring-electrode evaporation
Authors: Jiménez-Redondo Miguel , Gerlich Dieter , Caselli Paola , Jusko Pavol
Published: January 2025

We present an experimental method for the characterization of the kinetic energies of ions confined in a 22-pole radio frequency trap by inducing a small potential barrier using the surrounding ring electrodes, allowing the selective extraction of ions. Energy sampling experiments have been performed on buffer-gas thermalized He+ ions at trap temperatures between 10 and 180 K, resulting in distinct extraction curves as a function of the potential barrier, and a differentiated behavior depending on the escape time from the trap. The experiments are complemented by Monte Carlo simulations of the ion trajectories inside the calculated trap potential and allow us to investigate the properties of the sampling method, the role of ion motion coupling, and the impact of residual buffer-gas collisions on the observed results. The technique has also been successfully applied to identify energetic H3+ ions produced in an exothermic reaction inside the trap. Upon calibration, this method can provide relative kinetic energy distributions or be used to filter the maximum desired kinetic energy of the ions inside the trap.

Published by the American Physical Society
2025
Quantitative modeling of spintronic terahertz emission due to ultrafast spin transport
Authors: Foggetti Francesco , Oppeneer Peter M.
Published: January 2025

In spintronic terahertz (THz) emitters, THz radiation is generated by exciting an ultrafast spin current through femtosecond laser excitation of a ferromagnetic-nonmagnetic metallic heterostructure. Although an extensive phenomenological knowledge has been built up during the last decade, a solid theoretical modeling that connects the generated THz signal to the laser induced-spin current is still incomplete. Here, starting from general solutions to Maxwell’s equations, we model the electric field generated by a superdiffusive spin current in spintronic emitters, taking Co/Pt as a typical example. We explicitly include the detector shape, which is shown to significantly influence the detected THz radiation. Additionally, the electron energy dependence of the spin Hall effect is taken into account, as well as the duration of the exciting laser pulse and the thickness of the detector crystal. Our modeling leads to realistic emission profiles and highlights the role of the detection method for distinguishing key features of the spintronic THz emission.

Published by the American Physical Society
2025
First-principles calculation of alloy scattering and
n
-type mobility in strained
Ge−Sn
Authors: Sewell K. , Murphy-Armando F.
Published: January 2025

We use first-principles electronic-structure theory to determine the intra- and intervalley electron-alloy scattering parameters in -type Ge−Sn alloys. These parameters are used to determine the alloy scattering contributions to the -type electron mobility of Ge−Sn at 300 and 15K using a first iteration of the Boltzmann transport equation in the relaxation-time approximation. For unstrained Ge−Sn, we find that an Sn concentration of at least 13.5% is needed to achieve an electron mobility greater than that of Ge. Our results show that the mobility of Ge−Sn can be over 25 times that of Ge, or 105cm2/(Vs). At 15K, incorporation of less than 6% Sn into Ge quadruples its mobility, which suggests that Ge−Sn has potential applications as a high-mobility 2D electron gas. Applying biaxial tensile strain to Ge−Sn further increases the mobility and achieves this improvement at lower Sn content than in unstrained Ge−Sn.

Published by the American Physical Society
2025
Fermi-liquid behavior of nonaltermagnetic
RuO2
Authors: Wenzel Maxim , Uykur Ece , Rößler Sahana , Schmidt Marcus , Janson Oleg , Tiwari Achyut , Dressel Martin , Tsirlin Alexander A.
Published: January 2025

The presence of magnetism in potentially altermagnetic RuO2 has been a subject of intense debate. Using broadband infrared spectroscopy combined with density-functional band-structure calculations, we show that the optical conductivity of RuO2, the bulk probe of its electronic structure, is best described by a nonmagnetic model. The sharp Pauli edge demonstrates the presence of a Dirac nodal line lying 45 meV below the Fermi level. An excellent match between the experimental and plasma frequencies underpins the weakness of electronic correlations. The intraband part of the optical conductivity indicates Fermi-liquid behavior with two distinct scattering rates below 150 K. Fermi-liquid theory also accounts for the temperature-dependent magnetic susceptibility of RuO2 and allows a consistent description of this material as a paramagnetic metal.

Published by the American Physical Society
2025
Quantum circuit for
Z3
lattice gauge theory at nonzero baryon density
Authors: Hidaka Yoshimasa , Yamamoto Arata
Published: January 2025

Z3 lattice gauge theory is the simplest discrete gauge theory with three-quark bound states, i.e., baryons. Since it has a finite-dimensional Hilbert space, it can be used for testing quantum simulation of lattice gauge theory at nonzero baryon density. We discuss global and local gauge symmetries and their importance in quantum simulation. We perform quantum emulator calculation and demonstrate how to study the ground state property of baryonic matter.

Published by the American Physical Society
2025
Bounds on Lorentz and
CPT
violation from the
1S−2P
transition in antihydrogen
Authors: Vargas Arnaldo J.
Published: January 2025

A model for the Lorentz- and CPT-violating frequency shift for the antihydrogen 1S−2P transition in the presence of an external magnetic field is derived. Using the recent measurement of the 1S−2P transition frequency in antihydrogen by the ALPHA collaboration, which they demonstrated agrees with predictions from the Standard Model of particle physics, we establish the first constraints on 26 effective coefficients for Lorentz and CPT violation. Also, this work uses these results to underscore the value of measuring multiple transition frequencies to test CPT symmetry through antihydrogen spectroscopy, emphasizing the advantages of transitions involving states with higher angular momentum.

Published by the American Physical Society
2025
Black hole from entropy maximization
Authors: Yokokura Yuki
Published: January 2025

One quantum characterization of a black hole motivated by (local) holography and thermodynamics is that it maximizes thermodynamic entropy for a given surface area. In the context of quantum gravity, this could be more fundamental than the classical characterization by a horizon. As a step, we explore this possibility by solving the 4D semiclassical Einstein equation with many matter fields. For highly excited spherically symmetric static configurations, we apply local typicality and estimate the entropy including self-gravity to derive its upper bound. The saturation condition uniquely determines the entropy-maximized configuration: self-gravitating quanta condensate into a radially uniform dense configuration with no horizon, where the self-gravity and a large quantum pressure induced by the curvatures are balanced and no singularity appears. The interior metric is a self-consistent and nonperturbative solution in Planck’s constant. The maximum entropy, given by the volume integral of the entropy density, agrees with the Bekenstein-Hawking formula through self-gravity, deriving the Bousso bound for thermodynamic entropy. Finally, 10 future prospects are discussed, leading to a speculative view that the configuration represents a quantum-gravitational condensate in a semiclassical manner.

Published by the American Physical Society
2025
Investigation of anisotropy in the collective dynamics and thermal diffusivity in the phenyl pyrimidine liquid crystal
Authors: Ryu Meguya , Kurose Shu-hei , Yoshida Koji , Uchiyama Hiroshi , Morikawa Junko
Published: January 2025

Liquid crystals (LCs) are unique heat transfer media that exhibit large anisotropy in thermal properties depending on the direction of the director (n) of the LC state. This phenomenon is the basis of thermal conduction in ordered soft materials, and has been extensively studied to understand thermal conduction in soft materials. In this study, we used inelastic x-ray scattering (IXS) to investigate the anisotropic thermal diffusivity and collective dynamics in the terahertz region of a pyrimidine-type LC (PYP8O8). The dispersion relations at several frequencies corresponding to the LC state were analyzed in the directions parallel and perpendicular to n. The results showed that there was a significant difference between the anisotropy of the sound velocity and that of the attenuation coefficient (Γ) estimated from the shape parameter of the IXS spectrum. The results for the linewidth of inelastic excitation show Q2 dependence that is far beyond the viscoelastic relaxation of the system, and the anisotropy in the collective dynamics predicted by Forster . [] in the hydrodynamic region can be extensively applied to the more localized collective motion of LC systems.

Published by the American Physical Society
2025
3D Reconstruction of a Nuclear Reactor by Muon Tomography: Structure Validation and Anomaly Detection
Authors: Lefevre Baptiste , Vogel Julien , Gomez Héctor , Attié David , Gallego Laurent , Gonzales Philippe , Lesage Bertrand , Mas Philippe , Pomarède Daniel
Published: January 2025

Muon tomography is a consolidated technique to investigate the internal components of high-opacity objects. With the use of detectors with high angular and spatial resolution (usually referred to as “muon telescopes”), the track reconstruction of the atmospheric muons after they have crossed the object provides muography images, also called “muon radiographs.” This work presents the muography (or muon radiography) reconstruction of a French historical UNGG (natural-uranium, graphite, and gas) nuclear reactor: the G3 reactor, located at CEA Marcoule. A measurement campaign involving 46 points of view below the reactor was conducted, providing a set of muography images. The method to analyze these muographies is detailed here. Besides, a method to combine these images to provide three-dimensional (2D) tomography of the reactor is also presented. After a general description of the project, all the methods performed to reconstruct and analyze muographies and the 3D reconstruction are presented. It comprises different tools based on data augmentation and machine learning, which proved to be very efficient on simulated data and increase the quality of the experimental data analysis. All these methods were evaluated with a set of synthetic data, providing a precise evaluation for better identification of the associated systematics. Finally, all the described methods were applied to the experimental data, leading to a full characterization of the reactor, in both two dimensions and three dimensions, and the identification of some discrepancies between the reactor actual structure and the original model. These anomalies are discussed, showing the potential of the technique to evaluate the internal structure of a nuclear reactor. This could have potential applications during the decommissioning phase and the dismantling phase of different kinds of nuclear installation.

Published by the American Physical Society
2025
Efficient Learning of Quantum States Prepared With Few Fermionic Non-Gaussian Gates
Authors: Mele Antonio Anna , Herasymenko Yaroslav
Published: January 2025

The experimental realization of increasingly complex quantum states underscores the pressing need for new methods of state learning and verification. In one such framework, quantum state tomography, the aim is to learn the full quantum state from data obtained by measurements. Without prior assumptions on the state, this task is prohibitively hard. Here, we present an efficient algorithm for learning states on n fermion modes prepared by any number of Gaussian and at most t non-Gaussian gates. By Jordan-Wigner mapping, this also includes n-qubit states prepared by nearest-neighbor matchgate circuits with at most t gates. Our algorithm is based exclusively on single-copy measurements and produces a classical representation of a state, guaranteed to be close in trace distance to the target state. The sample and time complexity of our algorithm is poly(n,2t); thus if t=O(log﻿(n)), it is efficient. We also show that, if t scales more than logarithmically, any learning algorithm to solve the same task must be inefficient, under common cryptographic assumptions. We also provide an efficient property-testing algorithm that, given access to copies of a state, determines whether such a state is far or close to the set of states for which our learning algorithm works. In addition to the outputs of quantum circuits, our tomography algorithm is efficient for some physical target states, such as those arising in time dynamics and low-energy physics of impurity models. Beyond tomography, our work sheds light on the structure of states prepared with few non-Gaussian gates and offers an improved upper bound on their circuit complexity, enabling an efficient circuit-compilation method.

Published by the American Physical Society
2025
Measuring organisational legitimacy in Haute Cuisine restaurants: perceptions of customers, experts and news media
Authors: Dönmez Semiha Deniz , Blanco-González Alicia
Published: January 2025

Purpose

Legitimacy is the perceived appropriateness of an organisation to a social system in terms of values, norms and definitions. This research analyses how customer reviews, news media and experts’ opinions influence the legitimacy perception of high-end restaurants. The aim is to understand how collective evaluators’ opinions impact the individual legitimacy perception, linking the micro and macro levels of legitimacy. This study measures and analyses the relationships and impacts of individual (customers) and collective (experts and news media) judgments to rationalise these differences in legitimacy perceptions.

Design/methodology/approach

This research was conducted through a combined analysis of the reviews published in news media, online customer review platforms and experts’ publications. This study elaborates a theoretical model using partial least squares structural equation modelling analysing 246 Michelin-starred restaurants in Spain.

Findings

Our findings indicate that individual legitimacy judgments are impacted by news media but not by experts. On the contrary, experts’ evaluations positively impact news media’s evaluations. The individual legitimacy perception of the Haute Cuisine restaurant is influenced by the collective judgments of news media.

Originality/value

The novelty of this research states the application of the multi-level legitimacy theory to analyse the relationship between news media, online customer reviews and expert evaluations, thus the individual and collective legitimacy perceptions of Haute Cuisine restaurants. Additionally, this study adds to legitimacy theory by revealing the relationships of legitimacy judgments on micro and macro levels and analysing which and how audiences perceive organisational legitimacy.
Unified integration approach for bridging BIM model to 3D construction printing and scale prototyping
Authors: Sangiorgio Valentino , Floris Ignazio , Duran Dayan
Published: January 2025

Purpose

This work aims to develop a multi-step approach for the unified integration of 3D construction printing (3DCP) and building information modeling (BIM), allowing users to easily and automatically outline the instructions for 3D printing of buildings starting from BIM model and ensuring the wide spread of this new technology in Civil Engineering sector.

Design/methodology/approach

The proposed methodology exploits Revit for 3D modeling and BIM, using Dynamo as a programming interface for generating G-code.

Findings

The paper demonstrates how the proposed methodology can extract information from a BIM model to support building construction using digital fabrication techniques. This code guides the printer’s movements and operations, specifying the path, speed, layers and essential parameters to construct concrete structures layer by layer. It transforms digital designs into precise and efficient physical structures.

Practical implications

This work allows overcoming some of the current limitations associated with bridging BIM models to 3D construction printing. The proposed approach integrates BIM and 3DCP. If the model undergoes changes in the BIM model, the proposed system allows for automatic updates in the 3D printing files. Furthermore, the possibility offered by the proposed methodology to test the G-code on a scaled model allows for the correction of any errors before printing on a large-scale machine.

Originality/value

The novelty of the proposed approach is threefold: i) A new unified integration methodology for BIM and 3D construction printing is defined; ii) An example of a 3D printed building unit is modeled with BIM, incorporating various discipline models such as Architecture, Structure, and Mechanical, Electrical, Plumbing (MEP) systems; iii) The proposed approach allows for testing the G-code at scale before printing with a full-scale machine.
How to sustain a competent and committed aging workforce: The age-differential effects of development human resource practices
Authors: Yue Lin-Yang , Huang Wei-De
Published: January 2025

Purpose

This paper aims to reveal the nonlinear moderating effect of age on the inverted U-shaped relationship between perceived development human resource practices (DHRPs) and work-related learning with affective commitment being the mediator.

Design/methodology/approach

Regression models combined with the bootstrap method and multigroup analysis, and two-wave survey data from 780 Chinese employees were used to test hypotheses.

Findings

The results revealed that perceived DHRPs related to affective commitment in an inverted U pattern and affective commitment further related to work-related learning positively, which resulted in an inverted U-shaped relationship between perceived DHRPs and work-related learning. Age moderated the nature of the relationships between perceived DHRPs and both the outcomes, such that they were related negatively among younger employees but inverted U-shaped among older employees.

Originality/value

This study reveals inverted U-shaped rather than linear relationships between perceived DHRPs and employee outcomes and shows that age moderates the nature instead of the strength of the relationships.
Understanding the emerging success factors gap of accounting information systems in developing countries – a systematic literature review
Authors: Sultana Reajmin , Alam Mohammad Zahedul , Hasan Najmul
Published: January 2025

Purpose

While the adoption of accounting information systems (AIS) is crucial in developing countries owing to the rapidly changing business environment, the emerging factors in its successful implementation continue to be inconsistent. This systematic literature review (SLR) aims to understand the emerging factors of underlying successful AIS implementation, with a specific focus on developing countries.

Design/methodology/approach

A total of 70 empirical studies from 2017 to 2024 were analysed using an SLR technique. Studies including the search term “accounting information systems” OR “AIS” AND “developing countries” in their titles, keywords or abstracts were retrieved from five digital databases. The articles were analysed and synthesised using thematic analysis.

Findings

The findings revealed six key themes: (1) AIS literacy, (2) automation in AIS, (3) cloud-based AIS, (4) cultural factors, (5) environmental factors and (6) mobile accessibility and 25 subthemes.

Practical implications

A comprehensive understanding of these gaps will enable academics, policymakers and AIS professionals to make well-informed decisions and enhance the efficacy and efficiency of AIS operations.

Originality/value

The thematic analysis highlights the theoretical gaps and exposes areas where the connection between factors may be inadequate to indicate future study avenues.
Identifying categories of patient-driven health services innovation: insights from Taiwan’s health services sector
Authors: Yang Chen-Wei
Published: January 2025

Purpose

This study aims to build a typology of patient-driven health services innovation (PDHSI) and propose their relationships with healthcare quality.

Design/methodology/approach

Guided by value co-creation theory (VCC), this study adopted in-depth interviews and focus groups to collect qualitative data in Taiwan’s health services sector. The collected data were analyzed using manual thematic analysis, following the standard procedures for transcribing, encoding and identifying themes. This approach allowed for a comprehensive identification of unique types of PDHSI.

Findings

This study found four types of PDHSI. They are Human-Computer Interaction Mode (HCIM), Online Social Network Mode (OSNM), Co-created Decision-Making Mode (CDM) and Channel Complementarity Mode (CCM). This study defines these typologies and explains their fundamental properties, key outcomes and important determinants. Finally, through qualitative analysis, four propositions on the relationship between health services innovation and health service quality are put forward.

Practical implications

By constructing a patient-driven typology of health services innovation, this study helps medical institutions understand the strategic behavior of the doctor–patient relationship, to improve the quality of medical service and contribute to patient education and consulting practice.

Originality/value

This study contributes to the theoretical understanding of PDHSI by identifying and categorizing the types of such innovations. It provides a comprehensive typology that is useful for both academic research and practical application in healthcare management. This typology offers new insights into the roles of patients in co-creating healthcare services, addressing a gap in the existing literature regarding PDHSI and supporting the development of patient-centered approaches to healthcare.