bluuebunny/crossref_metadata_2025 huggingface dataset:
Perspectives, Experiences, and Opportunities of Academic Surgeons in the Era of Healthcare Corporatization
Authors: Sakowitz Sara , Bakhtiyar Syed Shahyan , Sienna Nicholas S. , Mallick Saad , Ali Konmal , Benharash Peyman , Jolly Richard , Donahue Timothy R.
Published: January 2025

Objective:

To characterize contemporary surgeons’ viewpoints and perspectives on the academic mission during healthcare corporatization.

Summary Background Data:

Academic surgery, traditionally driven by the tripartite missions of excellence in clinical care, scientific research, and education, faces increasing challenges from a corporatized healthcare environment. While previous studies have addressed the financial aspects of corporatization, a comprehensive evaluation of academic surgeons’ attitudes and experiences remains lacking.

Methods:

An online survey was distributed to a national sample of academic surgical department chairs and program directors assessing their views, perspectives, and experiences with healthcare corporatization. We also analyzed trends in National Institutes of Health (NIH) funding and abstract submissions to the Academic Surgical Congress.

Results:

Of 105 respondents, 72.9% believe corporatization negatively impacts academic surgery. Among program directors, 79.1% feel corporatization prioritizes clinical productivity over research and teaching. Similarly, 82.8% of department chairs report their faculty often must prioritize clinical duties over other academic responsibilities.

Qualitative analysis reveals that surgeons perceive corporatization as a significant barrier to achieving their goals. Many feel that profit has become “king,” reducing their roles to “cogs in a wheel.”

While overall NIH funding increased, the proportion awarded to surgical departments remained largely unchanged from 2006 to 2023 (2.7% vs. 2.8%, P=0.94). Additionally, the proportion of basic science abstracts submitted to the Academic Surgical Congress declined by 37.9%.

Conclusions:

Corporatization has had a profound impact on surgeons’ perceptions of their roles, responsibilities, and autonomy. Surgical departments must take intentional steps to preserve the multidimensional mission of the academic surgeon.
Hovering hawkmoths exploit unsteady circulation to produce aerodynamic force
Authors: Liu Yun , Li Biao , Zhou Deli
Published: January 2025

This study employs an integrated approach, combining three-dimensional flow visualization and two-dimensional flow measurement to investigate the underlying unsteady aerodynamic mechanisms of hovering hawkmoths. Using a single vortex ring model, three aerodynamic force components, such as aerodynamic force induced by unsteady circulation, vortex loop size variation and added mass, are estimated within a dimensionless time (normalized by one wing beat cycle) range of 0.418 <
T
*
< 0.455, where both the vortex loop circulation and loop size data are available. The force analysis reveals that the unsteady circulation-induced aerodynamic force dominates the overall force production and contributes 67% of the total force while the vortex loop size variation and added mass effect-induced aerodynamic forces only count for 25% and 8%, respectively. These findings suggest the hawkmoth primarily relies on unsteady circulation to generate aerodynamic forces.
Stepwise order in protein complex assembly: approaches and emerging themes
Authors: Brown Michael T. , McMurray Michael A.
Published: January 2025

Protein-based nanomachines drive every cellular process. An explosion of high-resolution structures of multiprotein complexes has improved our understanding of what these machines look like and how they work, but we still know relatively little about how they assemble in living cells. For example, it has only recently been appreciated that many complexes assemble co-translationally, with at least one subunit still undergoing active translation while already interacting with other subunits. One aspect that is particularly understudied is assembly order, the idea that there is a stepwise order to the subunit–subunit associations that underlies the efficient assembly of the quaternary structure. Here, we integrate a review of the methodological approaches commonly used to query assembly order within a discussion of studies of the 20S proteasome core particle, septin protein complexes, and the histone octamer. We highlight shared and distinct properties of these complexes that illustrate general themes applicable to most other multisubunit assemblies.
Description of Veillonella absiana sp. nov., isolated from pig faeces
Authors: Bai Lu , Paek Jayoung , Shin Yeseul , Kim Hongik , Kim Si Hyun , Shin Jeong Hwan , Kook Joong-Ki , Chang Young-Hyo
Published: January 2025

Two Gram-stain-negative cocci anaerobes were isolated from pig faeces and designated as strains YH-vei2232T and YH-vei2233. Phylogenetic analysis using 16S rRNA gene sequences revealed that the isolates were most closely related to Veillonella rogosae KCTC 5967T, with 97.0% similarity. Analysis of housekeeping gene sequences (rpoB) revealed the strain formed a sub-cluster within the genus Veillonella. The average nucleotide identities between the two isolates and the most closely related strains within genus Veillonella were <75.0%. The major fatty acids were Summed Feature 8 and C16 : 1
 ω9c. The cell wall peptidoglycan contained meso-diaminopimelic acid. The major metabolic end products of isolates were propionic and acetic acids. The genomic DNA G+C contents of both strains were 40.1 mol%. The chemotaxonomic, phenotypic and phylogenetic properties of YH-vei2232T (=KCTC 25748T=NBRC 116427T) and YH-vei2233 (=KCTC 25749=NBRC 116428) suggest that they represent a novel species of the genus Veillonella, for which the name Veillonella absiana sp. nov. is proposed.
Super-compensator alleles rescue diverse deleterious substitutions and buffer the effects of mutations
Authors: Jiang Wenhong , Yin Hengchuang , Khan Saad S. , Yiparemu
Published: January 2025

Understanding loss-of-function mutations and their potential compensatory mechanisms is crucial for elucidating the complexities of gene expression. Here, we investigate whether additional mutations can rescue non-functional alleles and their evolutionary significance. To achieve this, we conducted an extensive analysis of 372,867 amino acid sequence variants of the imidazole glycerol-phosphate dehydratase (IGPD, PDB: 6ezm) protein, which is over 1000 times greater than previously examined. We discovered that one or more additional substitutions located in loop and interface regions could easily restore function for each of the 10,019 of 31,701 (31.6%) non-functional missense allele. We further identified a small set of super-compensatory substitutions that can increase the function of many diverse alleles and flatten the fitness landscape, that is, buffer the fitness effects of both beneficial and deleterious substitutions. We also found that the protein structures of rescuable variants are more stable than those of non-rescuable variants. This suggests that restoring the stability of protein structures is a key part of compensation. These findings offer new insights into the understanding of protein function loss and its adaptive compensatory evolution.
Building an atlas of mechanobiology: high-throughput contractility screen of 2418 kinase inhibitors in five primary human cell types reveals selective divergent responses among related cell types
Authors: Shpak Anton , Wan Jeremy , Huang Ricky , Cortes Enrico , Wang Yao , Damoiseaux Robert , Pushkarsky Ivan
Published: January 2025

Cellular mechanical forces play crucial roles in both normal physiology and disease, yet drug discovery efforts targeting mechanobiology have been limited in part by assumptions about the conservation of contractile pathways across cell types. Here, we present the first high-throughput contractility screen of an annotated kinase inhibitor library, evaluating 2,418 compounds across five primary human cell types using the FLECS (Fluorescent Elastomer Contractility Sensors) platform. Quantification of contractile responses revealed selective divergent responses among related cell types. Clustering analysis identified distinct mechanobiological profiles and novel pathway associations that challenge the assumption that contractile pathways are too highly conserved for selective targeting. This systematic approach supports wider adoption of mechanical phenotypic screening as a viable strategy for discovering cell-type specific contractile pathway modulators for a broad range of mechanically-driven disease indications.
Whole-genome duplication increases genetic diversity and load in outcrossingArabidopsis
Authors: Vlček Jakub , Hämälä Tuomas , Cobo Cristina Vives , Curran Emma , Šrámková Gabriela , Slotte Tanja , Schmickl Roswitha , Yant Levi , Kolář Filip
Published: January 2025

Genetic variation underpins evolutionary change, but accumulation of slightly deleterious mutations also increases mutation load. There are multiple factors affecting the extent of load such as population size and breeding system, yet other potential determinants remain unexplored. A common macromutation, whole-genome duplication (WGD) occurs broadly across Eukaryotes, yet we lack a clear understanding of how WGD impacts neutral and selective processes within a population. Using forward simulations and empirical analysis of 632 short- and 16 long-read sequenced individuals ofArabidopsis arenosa(23 diploid and 42 natural autotetraploid populations), we test for the effects of WGD on genome-wide diversity and mutation load. Our simulations show how genetic variation gradually rises in autotetraploids due to increase of mutational target size. Moreover, mutation load increases due to relaxed purifying selection when deleterious mutations are masked by additional chromosome copies. Empirical data confirm these patterns, showing significant increase in nucleotide diversity, ratios of non-synonymous to synonymous SNPs, and number of indels and large structural variants inA. arenosaautotetraploids. However, a rather modest increase in load proxies together with a broad distribution and niche of autotetraploids suggests load accumulation has not (yet) limited their successful expansion. Overall, we demonstrate a complex interplay between neutral processes and purifying selection in shaping genetic variation following WGD and highlight ploidy as an important determinant of genetic diversity and mutation load in natural populations.
SFCalculator: connecting deep generative models and crystallography
Authors: Li Minhuan , Dalton Kevin , Hekstra Doeke
Published: January 2025

Proteins drive biochemical transformations by transitioning through distinct conformational states. Understanding these states is essential for modulating protein function. Although X-ray crystallography has enabled revolutionary advances in protein structure prediction by machine learning, this connection was made at the level of atomic models, not the underlying data. This lack of connection to crystallographic data limits the potential for further advances in both the accuracy of protein structure prediction and the application of machine learning to experimental structure determination. Here, we present SFCalculator, a differentiable pipeline that generates crystallographic observables from atomistic molecular structures with bulk solvent correction, bridging crystallographic data and neural network-based molecular modeling. We validate SFCalculator against conventional methods and demonstrate its utility by establishing three important proof-of-concept applications. First, SFCalculator enables accurate placement of molecular models relative to crystal lattices (known as phasing). Second, SFCalculator enables the search of the latent space of generative models for conformations that fit crystallographic data and are, therefore, also implicitly constrained by the information encoded by the model. Finally, SFCalculator enables the use of crystallographic data during training of generative models, enabling these models to generate an ensemble of conformations consistent with crystallographic data. SFCalculator, therefore, enables a new generation of analytical paradigms integrating crystallographic data and machine learning.
Metabolic implications for dual substrate growth in “CandidatusAccumulibacter”
Authors: Páez-Watson Timothy , Jansens Casper , van Loosdrecht Mark C.M. , Roy Samarpita
Published: January 2025

This study explores the metabolic implications of dual substrate uptake in“Candidatus Accumulibacter”, focusing on the co-consumption of volatile fatty acids and amino acids under conditions typical of enhanced biological phosphorus removal (EBPR) systems. Combining batch tests from highly enriched “Ca.Accumulibacter” cultures with conditional flux balance analysis (cFBA) predictions, we demonstrated that co-consumption of acetate and aspartate leads to synergistic metabolic interactions, lowering ATP loss compared to individual substrate consumption. The metabolic synergy arises from the complementary roles of acetate and aspartate uptake: acetate uptake provides acetyl-CoA to support aspartate metabolism, while aspartate conversion generates NADH, reducing the need for glycogen degradation during acetate uptake. We termed this type of metabolic interaction as reciprocal synergy. We further expanded our predictions to uncover three types of interactions between catabolic pathways when substrates are co-consumed by “Ca.Accumulibacter”: (i) neutral, (ii) one-way synergistic and (iii) reciprocal synergistic interactions. Our results highlight the importance of network topology in determining metabolic interactions and optimizing resource use. These findings provide new insights into the metabolism “Ca.Accumulibacter” and suggest strategies for improving EBPR performance in wastewater treatment plants, where the influent typically contains a mixture of organic carbon compounds.

Synopsis

This research demonstrates how dual substrate uptake by “Ca.Accumulibacter” enhances metabolic efficiency in EBPR by reducing global ATP losses through optimization of storage polymer usage.
Transmission Dynamics of Eastern Equine Encephalitis Infection Rates: The Role of Avian Host Stage and Differential Mosquito Exposure
Authors: Ounsinegad Aurod , Mitchell Christopher , Komar Nicholas
Published: January 2025

The Eastern equine encephalitis virus (EEEV) is a neurological mosquito-borne disease that spans the northeastern coast of the United States and Canada. Prior studies have focused on how mosquitoes prefer to take blood meals from hatch-year avian hosts rather than adult avian hosts to determine the rate at which the virus is spread between the Black-Tailed Mosquito (Culiseta melanura) and select avian species. In these studies, it was found that mosquito blood meal preference correlated well with avian brooding seasons for certain avian species such as the European Starling (Sturnus vulgaris) and the American Robin (Turdus migratorius). In this study, a host stage-structured model is developed where the avian host group is split into two categories: adult avians and hatch-year avians. The system of ordinary differential equations (ODEs) used to create this model are analyzed to better understand the transmission dynamics of EEEV between the two host classes. The extent to which fluctuations occurred in transmission rates according to host/vector abundances, mosquito biting rate, and host stage was explored. By utilizing the model, it was found that when hatch-year avians are more exposed to the virus, a cyclic outbreak can be observed. Since hatch-year avians lack defensive mechanisms, unlike their adult counterpart, they are more readily exposed to the mosquito vector.

Author Summary

In this study, researchers developed a host stage-structured model to investigate how Eastern equine encephalitis virus (EEEV) transmission dynamics vary between adult and hatch-year avian hosts along the northeastern coast of North America. Previous research established that the primary vector, Black-Tailed Mosquito (Culiseta melanura), preferentially feeds on hatch-year (hatchling and fledgling) avians rather than adults, with blood meal patterns aligning with breeding seasons of species like European Starlings and American Robins. The authors constructed a system of ordinary differential equations to analyze transmission patterns between these two distinct host classes. Their model revealed that higher virus exposure in hatch-year avians, which lack the defensive capabilities of adults, can trigger cyclic disease outbreaks. Key factors examined included host/vector populations, mosquito biting rates, and host life stage. The findings suggest that the increased vulnerability of hatch-year avians to mosquito feeding can be one of the factors that significantly influences EEEV transmission dynamics in the region.
Developmentally cascading structures do not lose evolutionary potential, but compound developmental instability in rat molars
Authors: Vitek Natasha S. , Saks Ella , Dong Amy , Burroughs Robert W. , Ward Devin L , Pomeroy Emma , Martin-Gronert Malgorzata , Ozanne Susan E.
Published: January 2025

Increasing variability down serially segmented structures, such as mammalian molar teeth and vertebrate limb segments, is a much-replicated pattern. The same phenotypic pattern has conflicting interpretations at different evolutionary scales. Macroevolutionary patterns are thought to reflect greater evolutionary potential in later-forming segments, but microevolutionary patterns are thought to reflect less evolutionary potential and greater phenotypic plasticity. We address this conflict by recalculating evolutionary potential (evolvability) from published mammalian molar data and directly measuring phenotypic plasticity from a controlled feeding experiment. Effects on lengths and widths are discordant in a way that suggests general growth pathways have a role in phenotypically plastic dental responses to nutrition. Effects on successive trait means do not necessarily increase downstream, contrary to long-standing hypotheses. We confirm prior findings of increasing non-inherited variance downstream, showing decoupling between effects on trait mean and variance. These patterns can be explained by a cascading model of tooth development compounding the effect of anatomically hyper-local developmental instability as an influence separate from general environmental effects on the developing embryo. When evaluated in terms of evolvability, not heritability, later-developing molars are equally or more evolvable than earlier-developing molars, aligning their microevolutionary potential with macroevolutionary patterns in other serially segmented structures.
Performance of o1 pro and GPT-4 in self-assessment questions for nephrology board renewal
Authors: Noda Ryunosuke , Yuasa Chiaki , Kitano Fumiya , Ichikawa Daisuke , Shibagaki Yugo
Published: January 2025

Background

Large language models (LLMs) are increasingly evaluated in medical education and clinical decision support, but their performance in highly specialized fields, such as nephrology, is not well established. We compared two advanced LLMs, GPT-4 and the newly released o1 pro, on comprehensive nephrology board renewal examinations.

Methods

We administered 209 Japanese Self-Assessment Questions for Nephrology Board Renewal from 2014–2023 to o1 pro and GPT-4 using ChatGPT pro. Each question, including images, was presented in separate chat sessions to prevent contextual carryover. Questions were classified by taxonomy (recall/interpretation/problem-solving), question type (general/clinical), image inclusion, and nephrology subspecialty. We calculated the proportion of correct answers and compared performances using chi-square or Fisher’s exact tests.

Results

Overall, o1 pro scored 81.3% (170/209), significantly higher than GPT-4’s 51.2% (107/209; p<0.001). o1 pro exceeded the 60% passing criterion every year, while GPT-4 achieved this in only two out of the ten years. Across taxonomy levels, question types, and the presence of images, o1 pro consistently outperformed GPT-4 (p<0.05 for multiple comparisons). Performance differences were also significant in several nephrology subspecialties, such as chronic kidney disease, confirming o1 pro’s broad superiority.

Conclusion

o1 pro substantially outperformed GPT-4 in a comprehensive nephrology board renewal examination, demonstrating advanced reasoning and integration of specialized knowledge. These findings highlight the potential of next-generation LLMs as valuable tools in specialty medical education and possibly clinical support in nephrology, warranting further and careful validation.
Age-associated B-cells are expanded in early arthritis linked to atherosclerosis and immune circuits - a potential role as a biomarker for risk stratification
Authors: Miranda-Prieto Daniel , Alperi-López Mercedes , Pérez-Álvarez Ángel I. , Alonso-Castro Sara , Suárez Ana , Rodríguez-Carrio Javier
Published: January 2025

Objective

immune dysregulation may play a role in cardiovascular (CV) risk excess in rheumatoid arthritis (RA). However, exact mediators are unknown. Age-associated B cells (ABCs) have emerged as multi-faceted pro-inflammatory mediators, also in the atherosclerosis microenvironment, but their role in autoimmunity is ill-defined. Our aim was to evaluate ABCs levels in the earliest stages of inflammatory arthritis and their potential role as biomarkers of atherosclerosis.

Methods

ABCs were quantified by flow cytometry in 58 early RA patients, 11 individuals with clinical-suspect arthralgia (CSA) and 33 healthy controls (HC). Atherosclerosis occurrence was measured by Doppler-ultrasound. Cytokines were measured by multiplex immunoassays. Cardiometabolic-related proteins were evaluated using high-throughput targeted proteomics.

Results

Circulating ABCs were increased in RA patients compared with HC within the CD19+ and PBMCs pools (p=0.013 and p<0.001, respectively). Numerically higher ABCs levels were found in CSA. ABCs frequency was unrelated to disease features and traditional CV risk factors but negatively associated with good therapeutic outcomes upon csDMARD at 6 and 12 months. ABCs frequency was positively correlated with proinflammatory cytokines (IFNg, TNF, IL-6 and IL-21) and proteomic signatures related to B- and T-cell responses as well as cellular pathways linked to atherosclerosis.

ABCs were independently associated with atherosclerosis occurrence and extent in RA patients. Furthermore, adding ABCs levels significantly improved risk stratification over conventional instruments.

Conclusions

ABCs expansion is an early event along arthritis course, linked to therapeutic outcomes, inflammatory milieu and atherosclerosis burden. ABCs may be a missing link between humoral responses and atherosclerosis in autoimmunity.
Unraveling the network signatures of oncogenicity in virus-human protein-protein interactions
Authors: Zambelli Francesco , Pancaldi Vera , De Domenico Manlio
Published: January 2025

Climate change, increasing urbanization and global human mobility have increased the risk of emergent infectious diseases and the risk for their pandemic potential. Consequently, there is a pressing need for methods that can provide rapid insights about the potential enduring effects on the human hosts. In-silico methods can be more suitable than in-vitro and in-vivo methods to identify effects potentially manifesting after a long time, under the hypothesis that the underlying causes can be ascribed to perturbed biomolecular processes. Here we focus on oncogenicity, i.e., the risk of developing cancer subsequent to a viral infection, a phenomenon estimated to account for approximately 15 of global cancer prevalence. We characterize viruses in terms of their oncogenic potential by analyzing a multilayer representation of protein-protein interaction networks reconstructed from the human interactome. Our framework facilitates classification and allows us to identify sub-sets of proteins involved in oncogenesis, highlighting the mechanisms underpinning viral oncogenicity, including factors like chromatin structure. Our framework serves as a foundational resource for medical research, paving the way for the study of other potential long-term effects associated with emerging viruses.
Dissociation of SYNGAP1 Enzymatic and Structural Roles: Intrinsic Excitability and Seizure Susceptibility
Authors: Brill Julia , Clarke Blaise , Hong Ingie , Huganir Richard L.
Published: January 2025

SYNGAP1 is a key Ras-GAP protein enriched at excitatory synapses, with mutations causing intellectual disability and epilepsy in humans. Recent studies have revealed that in addition to its role as a negative regulator of G-protein signaling through its GAP enzymatic activity, SYNGAP1 plays an important structural role through its interaction with post-synaptic density proteins. Here, we reveal that intrinsic excitability deficits and seizure phenotypes in heterozygous Syngap1 knockout (KO) mice are differentially dependent on Syngap1 GAP activity. Cortical excitatory neurons in heterozygous KO mice displayed reduced intrinsic excitability, including lower input resistance, and increased rheobase, a phenotype recapitulated in GAP-deficient Syngap1 mutants. However, seizure severity and susceptibility to pentylenetetrazol (PTZ)-induced seizures were significantly elevated in heterozygous KO mice but unaffected in GAP-deficient mutants, implicating the structural rather than enzymatic role of Syngap1 in seizure regulation. These findings highlight the complex interplay between SYNGAP1 structural and catalytic functions in neuronal physiology and disease.

Significance Statement

Mutations in theSYNGAP1gene are a major cause of intellectual disability, autism, and epilepsy. The SYNGAP1 protein is an important constituent of postsynaptic specializations, and two distinct functions have been characterized: a structural function, carried by its C-terminal PDZ domain, that organizes the composition of the postsynaptic density, and an enzymatic function, in which its GAP domain negatively regulates small GTPases. So far, no electrophysiological/behavioral phenotype of SYNGAP1 has been directly linked to the GAP catalytic activity. Here, we describe that while the GAP catalytic activity does not contribute to the increased seizure susceptibility seen in SYNGAP1 haploin-sufficiency, it does regulate the intrinsic excitability of upper lamina pyramidal cells.
Different artificial light modalities during daytime have all positive effects on attention and alertness
Authors: Bjerrum Louise Bruland , Visted Endre , Nordhus Inger Hilde , Osnes Berge , Bjorvatn Bjorn , Bugge Kambestad Oda , Hansen Malika Elise , Sorensen Lin , Flo-Groeneboom Elisabeth
Published: January 2025

Light exposure during the day exerts acute effects on attention, such as how alert and ready a person is for solving problems and goal-oriented behavior. However, to increase the understanding of how different light modalities during daytime affect our attention, there is a need for more studies. The current study tested the acute effects of daytime exposure to four artificial light modalities on attention and alertness with the Psychomotor Vigilance Task (PVT). Healthy, young adults (N = 39; mean age: 21.7, 61.5% females) performed the PVT three times in four light modalities presented on separate days at the same time-of-day (09:00-11:00): short-wavelength light [SWL, 'blue'], long-wavelength light [LWL, 'red'], bright white light [BWL], and dim light [DL] as control. Attention and alertness measures included fluctuations in attention, quantified as the number of lapses and Reaction Time (RT) variability, mean RT, and optimum response capability (10% fastest RTs). Compared to DL, participants had significantly fewer lapses and faster mean RT during all three light conditions and enhanced optimum response capability during SWL and LWL. Light did not appear to have effects on intra-individual RT variability. Results suggest that 2 hours of exposure to artificial light during daytime can induce alerting effects and fewer attentional lapses in young, healthy adults. Surprisingly, neither SWL, LWL, nor BWL were significantly superior to one another.
Dynamical phases of a Bose-Einstein condensate in a bad optical cavity at optomechanical resonance
Authors: Harmon Gage W. , Morigi Giovanna , Jäger Simon B.
Published: January 2025

We study the emergence of dynamical phases of a Bose-Einstein condensate that is optomechanically coupled to a dissipative cavity mode and transversally driven by a laser. We focus on the regime close to the optomechanical resonance, where the atoms' refractive index shifts the cavity into resonance, assuming fast cavity relaxation. We derive an effective model for the atomic motion, where the cavity degrees of freedom are eliminated using perturbation theory in the atom-cavity coupling and benchmark its predictions using numerical simulations based on the full model. Away from the optomechanical resonance, perturbation theory in the lowest order (adiabatic elimination) reliably describes the dynamics and predicts chaotic phases with unstable oscillations. Interestingly, the dynamics close to the optomechanical resonance are qualitatively captured only by including the corrections to next order (nonadiabatic corrections). In this regime we find limit-cycle phases that describe stable oscillations of the density with a well-defined frequency. We further show that such limit-cycle solutions are metastable configurations of the adiabatic model. Our work sheds light on the mechanisms that are required to observe dynamical phases and predict their existence in atom-cavity systems where a substantial timescale separation is present.

Published by the American Physical Society
2025
Design of a resonant slow extraction from low-emittance electron booster rings using transverse resonance island buckets
Authors: Cortés García E. C. , Agapov I. V. , Hillert W.
Published: January 2025

In this contribution, we present the design of a resonant slow extraction based on the radio-frequency knockout (rf-KO) scheme, where we make use of the transverse resonance islands bucket (TRIB) optics. The generation of the TRIB optics is presented in two example lattices, which are considered for the potential upgrade of the current booster at DESY. The slow extraction studies are motivated to potentially supply high energy electron beams to the high energy physics beamline users. Simulations show an extraction efficiency in excess of 90% with a septum blade thickness of 100  μm.

Published by the American Physical Society
2025
Cs-
O2
-Li as enhanced NEA surface layer with increased lifetime for GaAs photocathodes
Authors: Herbert Maximilian , Eggert Tobias , Enders Joachim , Engart Markus , Fritzsche Yuliya , Meier Maximilian , Schulze Julian , Wende Vincent
Published: January 2025

GaAs-based photocathodes are the only viable source capable of providing spin-polarized electrons for accelerator applications. This type of photocathode requires a thin surface layer, in order to achieve negative electron affinity (NEA) for efficient photoemission. However, this layer is vulnerable to environmental and operational effects, leading to a decay of the quantum efficiency η characterized by a decay constant or lifetime τ. In order to increase τ, additional agents can be introduced during the activation procedure to improve the chemical robustness of the surface layer. This paper presents the results of recent research on Li as an enhancement agent for photocathode activation using Cs and O2, forming Cs-O2-Li as an enhanced NEA layer. Measurements yielded an increase in lifetime by a factor of up to 19±2 and an increase in extracted charge by a factor of up to 16.5±2.4, without significant reduction of η. This performance is equal to or better than that reported for other enhanced NEA layers so far.

Published by the American Physical Society
2025
Krylov complexity and Trotter transitions in unitary circuit dynamics
Authors: Suchsland Philippe , Moessner Roderich , Claeys Pieter W.
Published: January 2025

We investigate many-body dynamics where the evolution is governed by unitary circuits through the lens of “Krylov complexity,” a recently proposed measure of complexity and quantum chaos. We extend the formalism of Krylov complexity to unitary circuit dynamics and focus on Floquet circuits arising as the Trotter decomposition of Hamiltonian dynamics. For short Trotter steps the results from Hamiltonian dynamics are recovered, whereas a large Trotter step results in different universal behavior characterized by the existence of local : operators with vanishing autocorrelation functions, as exemplified in dual-unitary circuits. These operators exhibit maximal complexity growth, act as a memoryless bath for the dynamics, and can be directly probed in current quantum computing setups. These two regimes are separated by a crossover in chaotic systems. Conversely, we find that free integrable systems exhibit a nonanalytic transition between these different regimes, where maximally ergodic operators appear at a critical Trotter step.

Published by the American Physical Society
2025
Light dark matter constraints from SuperCDMS HVeV detectors operated underground with an anticoincidence event selection
Authors: Albakry M. F. , Alkhatib I. , Alonso-González D. , Amaral D. W. P. , Anczarski J. , Aralis T. , Aramaki T. , Arnquist I. J. , Ataee Langroudy I. , Azadbakht E. , Bathurst C. , Bhattacharyya R. , Biffl A. J. , Brink P. L. , Buchanan M. , Bunker R. , Cabrera B. , Calkins R. , Cameron R. A. , Cartaro C. , Cerdeño D. G. , Chang Y.-Y. , Chaudhuri M. , Chen J.-H. , Chen R. , Chott N. , Cooley J. , Coombes H. , Cushman P. , Cyna R. , Das S. , De Brienne F. , Dharani S. , di Vacri M. L. , Diamond M. D. , Elwan M. , Fascione E. , Figueroa-Feliciano E. , Fouts K. , Fritts M. , Germond R. , Ghaith M. , Golwala S. R. , Hall J. , Harms S. A. S. , Harris K. , Hassan N. , Hong Z. , Hoppe E. W. , Hsu L. , Huber M. E. , Iyer V. , Jardin D. , Kashyap V. K. S. , Keller S. T. D. , Kelsey M. H. , Kennard K. T. , Kubik A. , Kurinsky N. A. , Lee M. , Leyva J. , Liu J. , Liu Y. , Loer B. , Lopez Asamar E. , Lukens P. , MacFarlane D. B. , Mahapatra R. , Mammo J. S. , Mast N. , Mayer A. J. , Meyer zu Theenhausen H. , Michaud É. , Michielin E. , Mirabolfathi N. , Mirzakhani M. , Mohanty B. , Monteiro D. , Nelson J. , Neog H. , Novati V. , Orrell J. L. , Osborne M. D. , Oser S. M. , Pandey L. , Pandey S. , Partridge R. , Pedreros D. S. , Peng W. , Perna L. , Perry W. L. , Podviianiuk R. , Poudel S. S. , Pradeep A. , Pyle M. , Rau W. , Reid E. , Ren R. , Reynolds T. , Rios M. , Roberts A. , Robinson A. E. , Ryan J. L. , Saab T. , Sadek D. , Sadoulet B. , Sahoo S. P. , Saikia I. , Sander J. , Sattari A. , Schmidt B. , Schnee R. W. , Scorza S. , Serfass B. , Simchony A. , Sincavage D. J. , Sinervo P. , Street J. , Sun H. , Tanner E. , Terry G. D. , Toback D. , Verma S. , Villano A. N. , von Krosigk B. , Watkins S. L. , Wen O. , Williams Z. , Wilson M. J. , Winchell J. , Wykoff K. , Yellin S. , Young B. A. , Yu T. C. , Zatschler B. , Zatschler S. , Zaytsev A. , Zhang E. , Zheng L. , Zuniga A. , Zurowski M. J.
Published: January 2025

This article presents constraints on dark-matter-electron interactions obtained from the first underground data-taking campaign with multiple SuperCDMS HVeV detectors operated in the same housing. An exposure of 7.63  g−days is used to set upper limits on the dark-matter-electron scattering cross section for dark matter masses between 0.5 and 1000  MeV/c2, as well as upper limits on dark photon kinetic mixing and axionlike particle axioelectric coupling for masses between 1.2 and 23.3  eV/c2. Compared to an earlier HVeV search, sensitivity was improved as a result of an increased overburden of 225 meters of water equivalent, an anticoincidence event selection, and better pile-up rejection. In the case of dark-matter-electron scattering via a heavy mediator, an improvement by up to a factor of 25 in cross section sensitivity was achieved.

Published by the American Physical Society
2025
Real-time scattering in the lattice Schwinger model
Authors: Papaefstathiou Irene , Knolle Johannes , Bañuls Mari Carmen
Published: January 2025

Tensor network methods have demonstrated their suitability for the study of equilibrium properties of lattice gauge theories, even close to the continuum limit. We use them in an out-of-equilibrium scenario, much less explored so far, by simulating the real-time collisions of composite mesons in the lattice Schwinger model. Constructing wave-packets of vector mesons at different incoming momenta, we observe the opening of the inelastic channel in which two heavier mesons are produced and identify the momentum threshold. To detect the products of the collision in the strong coupling regime we propose local quantitites that could be measured in current quantum simulation platforms.

Published by the American Physical Society
2025
Emergent quasicrystal in fermionic superradiance
Authors: Wu Bo-Hao , Yang Xin-Xin , Zhang Wei , Chen Yu
Published: January 2025

Quasicrystal is state of matter with multiple crystalline orders, displaying a short-range density-wave order and a long-range disorder. As an exotic state lying in between crystals and Anderson insulators, its dynamical formation is little discussed. Here, we study the emergence of quasicrystalline order in fermionic superradiance, where Fermi statistics plays a crucial role, being distinct from its bosonic counterpart where interaction is the stabilizer. Owing to quasicrystalline orders, there exist multiple energy gaps opening at different quasicrystalline order strength, which can modify the density of states in excitation spectrum. As a result, the effective ground-state energy is strongly modified and the superradiant quasicrystal transition becomes first order and density dependent. This new mechanism leads to a linear V-shape kink of the fermionic superradiance transition line near a filling which uniquely relates to the quasicrystalline order. Our findings demonstrate that quasicrystal can be realized in fermionic superradiance as a result of Fermi statistics and be verified by characteristic density-dependent phenomena.

Published by the American Physical Society
2025
Modeling kinetic effects of charged vacancies on electromechanical responses of ferroelectrics: Rayleighian approach
Authors: Kumar Rajeev , Zhang Shuaifang , Ganesh P.
Published: January 2025

Understanding the time-dependent effects of charged vacancies on the electromechanical responses of materials is at the forefront of research for designing materials exhibiting metal-insulator transitions and memristive behavior. A Rayleighian approach is used to develop a model for studying the nonlinear kinetics of the reaction leading to generation of vacancies and electrons via the dissociation of vacancy-electron pairs. Also, diffusion and elastic effects of charged vacancies are considered to model polarization-electric potential and strain-electric potential hysteresis loops. The model captures multiphysics phenomena by introducing couplings among polarization, the electric potential, stress, strain, and concentrations of charged (multivalent) vacancies and electrons (treated as classical negatively charged particles), where the concentrations can vary due to association-dissociation reactions. A derivation of coupled time-dependent equations based on the Rayleighian approach is presented. Three limiting cases of the governing equations are considered, highlighting the effects of (1) nonlinear reaction kinetics on the generation of charged vacancies and electrons, (2) Vegard's law (i.e., the concentration-dependent local strain) on asymmetric strain-electric potential relations, and (3) coupling between a fast component and the slow component of the net polarization on the polarization-electric-field relations. The Rayleighian approach discussed in this work should pave the way for developing a multiscale modeling framework in a thermodynamically consistent manner while capturing multiphysics phenomena in ferroelectric materials.

Published by the American Physical Society
2025
Generalized Cycle Benchmarking Algorithm for Characterizing Midcircuit Measurements
Authors: Zhang Zhihan , Chen Senrui , Liu Yunchao , Jiang Liang
Published: January 2025

Midcircuit measurements (MCMs) are crucial ingredients in the development of fault-tolerant quantum computation. While there have been rapid experimental progresses in realizing MCMs, a systematic method for characterizing noisy MCMs is still under exploration. In this work, we develop a cycle benchmarking (CB)-type algorithm to characterize noisy MCMs. The key idea is to use a joint Fourier transform on the classical and quantum registers and then estimate parameters in the Fourier space, analogous to Pauli fidelities used in CB-type algorithms for characterizing the Pauli-noise channel of Clifford gates. Furthermore, we develop a theory of the noise learnability of MCMs, which determines what information can be learned about the noise model (in the presence of state preparation and terminating measurement noise) and what cannot, which shows that all learnable information can be learned using our algorithm. As an application, we show how to use the learned information to test the independence between measurement noise and state-preparation noise in an MCM. Finally, we conduct numerical simulations to illustrate the practical applicability of the algorithm. Similar to other CB-type algorithms, we expect the algorithm to provide a useful toolkit that is of experimental interest.

Published by the American Physical Society
2025
What factors influence the individual’s behavior in engaging in income tax evasion? An investigation using SEM and fsQCA
Authors: Kumar Jitender , Rani Garima , Rani Manju , Rani Vinki
Published: January 2025

Purpose

The substantial rise in tax evasion raises concerns about its adverse impact on the tax system’s integrity. This article aims to empirically investigate the factors affecting income tax evasion behavior among individuals in India’s National Capital Region (NCR).

Design/methodology/approach

A cross-sectional design was applied to gather primary data from (N = 548) taxpayers using a “self-administered survey questionnaire.” The hybrid “partial least squares structural equation modeling (PLS-SEM) and fuzzy-set qualitative comparative analysis (fsQCA)” approach was applied to analyze the data.

Findings

This research presents a comprehensive model that explains 53.4% of the variance in behavioral intention and accounts for 51.4% in the actual behavior of individuals who participate in income tax evasion. The outcomes show that high tax burden, corruption and complexity of the tax system significantly influence behavioral intention. On the contrary, digitalization and tax morale insignificantly influence behavioral intention. Notably, behavioral intention is significantly associated with the actual behavior of individuals engaging in income tax evasion.

Practical implications

The outcomes offer valuable implications for practitioners, including policymakers, governments and tax authorities, to effectively curb income tax evasion behavior and help them make informed decisions.

Originality/value

The innovative research model enhances prevailing knowledge by providing empirical insights into the effect of income tax evasion behavior among individuals in India. This study also contributes methodologically by combining PLS (linear) and fsQCA (nonlinear) techniques, demonstrating that both methodologies offer a deeper comprehension of the factors affecting individual behavior to engage in income tax evasion.
Researching children’s physical environment: a systematic review of research methods
Authors: El-Husseiny Sara , Mansour Yasser , Elrefaie Mohab , El Antably Ahmed
Published: January 2025

Purpose

The aim is to examine, critique, and synthesize commonly used methodological approaches that capture middle-aged children’s experiences of their physical environments.

Design/methodology/approach

The systematic review identified 174 empirical studies from peer-reviewed journals published in English between 2014 and 2023. Fifty-two studies met the inclusion criteria. A thematic analysis (1) identified study characteristics and common methodological approaches, (2) synthesized the literature to reveal major themes and trends, and (3) pointed out significant research gaps.

Findings

Qualitative methods, combining traditional and participatory approaches, are most effective in capturing children’s spatial experiences. Participatory methods offer more authentic insights and reduce power imbalances compared to traditional methods. Place-based methods, such as child-led walks and participant observations, are particularly valuable for capturing the multidimensional and sensory aspects of children’s interactions with their environments.

Research limitations/implications

The choice of keywords, selected databases, and the English-language criterion restricted the number of captured reviewed articles that might contribute to the topic.

Originality/value

This systematic review contributes to a deeper understanding of the methodological approaches used in researching middle-aged children’s experiences of their physical environments. It highlights common strategies used with children to communicate their experience of place, identifying the strengths and limitations of each method. Additionally, the review discusses the various aspects of space revealed by different methods.
On the hidden layer-to-layer topology of the representations of reality realised within neural networks
Authors: Gafvert Oliver , Grindrod Peter , Harrington Heather A. , Higham Catherine F. , Higham Desmond J. , Yim Ka Man
Published: January 2025

Purpose

Consider an information processing algorithm that is designed to process an input data object onto an output data object via a number of successive internal {\it layers} and mappings between them. The possible activation state within each layer can be represented as a cube within Euclidean space of a high dimension (e.g. equal to the number of artificial neurons at that level). Multiple instances of such input objects produce a point cloud within each layer’s cube: this is the “representation of the reality” at that layer, as sampled by the set of input objects.

Design/methodology/approach

Most neural networks reduce the dimension of each layer’s cube from layer to successive layer. This gives the false impression of refining the inner representations of reality, distilling it down to fewer dimensions from which to discriminate or to infer outcomes (whatever is the aim). However, the representation of reality realised within each layer’s cube is a manifold, a curved subset embedded within it and of much lower dimension. Investigations show that such manifolds may not always be reducing in their local dimension. Instead, the manifold may become folded over and over, filling up further dimensions and creating non-realistic (unforeseeable) proximities.

Findings

We discuss some of the likely consequences of these relatively unforeseen characteristics and, in particular, the possible vulnerability of such algorithms to non-realistic perturbations. We consider a possible response to this issue.

Practical implications

New forms of calibration are necessary, using geometric/topological loss functions, as opposed to simple (variation-limiting) regularisation terms.

Originality/value

We apply persistent homology methods to understand how the images of the point cloud (representing the sampled reality) change as they pass from layer to layer.