bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional annotation of de novo variants found near GWAS loci associated with cleft lip with or without cleft palate
Authors: Curtis Sarah W. , Cook Laura E. , Paraiso Kitt , Visel Axel , Cotney Justin L. , Murray Jeffrey C. , Beaty Terri H. , Marazita Mary L. , Carlson Jenna C. , Leslie-Clarkson Elizabeth J.
Published: February 2025

Orofacial clefts (OFCs) are the most common craniofacial birth defects, affecting 1 in 700 births, and have a strong genetic basis with a high recurrence risk within families. While many of the previous studies have associated common, noncoding genetic loci with OFCs, previous studies onde novovariants (DNVs) in OFC cases have focused on coding variants that could have a functional impact on protein structure, and the contribution of noncoding DNVs to the formation of OFCs has largely been ignored and is not well understood. Therefore, we reanalyzed an existing dataset of DNVs from 1,409 trios with OFCs that had undergone targeted sequencing of known OFC-associated loci. We then annotated these DNVs with information from datasets of predicted epigenetic function during human craniofacial development. Of the 66 DNVs in this cohort, 17 (25.7%) were within a predicted enhancer or promotor region. Two DNVs fell within the same enhancer region (hs1617), which is more than expected by chance (p = 0.0017). The sequence changes caused by these DNVs are predicted to create binding sites not seen in the reference sequence for transcription factors PAX6 and ZBTB7A and to disrupt binding sites for STAT1 and STAT3. This enhancer region is within the same topologically-associated domain asHHAT,SERTAD4, andIRF6, all of which are involved in craniofacial development. All three genes are highly expressed in human neural crest cells. Knockout mice forHhatandIrf6have abnormal embryonic development including a cleft palate, and variants in and aroundIRF6are associated with nonsyndromic and syndromic forms of OFCs in humans. Taken together, this suggests that noncoding DNVs contribute to the genetic architecture of OFCs, with a burden of DNVs in OFC trios in enhancer regions near known OFC-associated genes. Overall, this adds to our understanding of the genetic mechanisms that underly OFC formation.
The Neurocognitive Profile of Post-operative Paediatric Cerebellar Mutism Syndrome: A Systematic Review
Authors: Horne Bethany M. , Attanayake Annisha A. , Aquilina Kristian , Murphy Tara , Malcolm Charlotte P.
Published: February 2025

AIM:To systematically review neurocognitive outcomes associated with Post-operative Paediatric Cerebellar Mutism Syndrome (PPCMS), comparing children with and without PPCMS after posterior fossa tumour surgery, and in relation to moderating demographic and clinical risk factors.METHODSPsycInfo, Medline and Embase databases were systematically searched up to December 2024. Studies of children aged 2-18 years with PPCMS who had undergone standardised neurocognitive assessment were included. Quality was appraised using Institute of Health Economics Quality Appraisal Checklist for Case Series and Quality In Prognosis Studies tools. Synthesis without meta-analysis was conducted.RESULTSSixteen studies (PPCMS+n=252, PPCMS-n=590) met criteria for inclusion. Children who experience PPCMS were found to have pronounced, long-term neurocognitive impairments with severely affected processing speed, psychomotor and executive function, and poorer neurocognitive outcomes generally compared to children without PPCMS. Current literature is limited by small samples, lack of diagnostic clarity or routine prospective screening of PPCMS, and limited investigation of factors that may moderate neurocognitive outcomes.INTERPRETATIONChildren with PPCMS have increased vulnerability to neurocognitive impairments which persist beyond the recovery of initial PPCMS symptoms in the post-operative phase. Dedicated research is needed to further our understanding of PPCMS and associated neurocognitive outcomes to inform clinical care.

What this paper adds

Children who experience PPCMS after surgery experience significant long-term neurocognitive impairment, with most consistent moderate-severe impairments in processing speed, psychomotor function, and executive function.

Children who experience PPCMS have poorer neurocognitive outcomes generally than children treated for posterior fossa tumour without PPCMS, however future research is needed with larger matched samples of children with and without PPCMS.

Prospective screening for PPCMS using formal diagnostic criteria in research and clinical practice is recommended, and cognitive development should be monitored in the long-term when PPCMS is identified.

Future research is needed to understand the role of potential moderating influences on neurocognitive outcomes, such as duration and severity of mutism, age at surgery, and adjuvant oncology treatments.
Stochastic Assembly and Metabolic Network Reorganization Drive Microbial Resilience in Arid Soils
Authors: Ayala-Ortiz Christian , Freire-Zapata Viviana , Tfaily Malak M.
Published: February 2025

Microbial resilience plays a pivotal role in ecosystems as environmental fluctuations impact community functioning and stability. Despite resilience emerging from both individual adaptations and community-level processes, integration of these mechanisms remains enigmatic, particularly in arid environments. These extreme ecosystems, spanning over 45% of Earth’s terrestrial surface, provide a natural laboratory for understanding microbial survival under harsh conditions. Here, we use time-resolved multi-omics to show that resilience results from dynamic microbial network reorganization enabling the coordination between stochastic processes that maintain community stability, and individual stress responses. Additionally, Thermoproteota emerged as a keystone taxon maintaining nitrogen cycling and fostering cross- feeding networks. Its ecological prominence highlights its central role in arid ecosystems, making it an ideal model organism for understanding microbial adaptation to environmental extremes. Our findings bridge the gap between individual adaptations and community-wide resilience, offering a framework for understanding microbial responses to environmental fluctuations and their implications for ecosystem function.
Actin crosslinking is required for force sensing at tricellular junctions
Authors: Taneja Nilay , Moubarak Michael F. , McGovern Meriel J. , Yeoh Kenji , Zallen Jennifer A.
Published: February 2025

Mechanical forces are essential for tissue morphogenesis, but risk causing ruptures that could compromise tissue function. In epithelial tissues, adherens junctions withstand the forces that drive morphogenesis by recruiting proteins that stabilize cell adhesion and reinforce connections to the actin cytoskeleton under tension. However, how junctional actin networks respond to forcesin vivois not well understood. Here we show that the actin crosslinker Fimbrin is recruited to tricellular junctions under tension and plays a central role in amplifying actomyosin contractility and stabilizing cell adhesion. Loss of Fimbrin results in a failure to reorganize actin under tension and an inability to enhance myosin-II activity and recruit junction-stabilizing proteins in response to force, disrupting cell adhesion. Conversely, increasing Fimbrin activity constitutively activates force-response pathways, aberrantly stabilizing adhesion. These results demonstrate that Fimbrin-mediated actin crosslinking is an essential step in modulating actomyosin dynamics and reinforcing cell adhesion under tension during epithelial remodeling.
DINASTY in NSCLC – a multicenter retrospective study on real-world data using federated analysis
Authors: Öjlert Å. , Bhatnagar P. , Hendriks L.E.L. , Ogliari F.R. , Acker F. , Bolton E. , Bouissou O. , Brash J. , Bynens A.-L. , Cheeseman S. , Fenton H. , Banduge P. Galgane , Gomes A. Lobo , McDonald R. , Mahon P. , Ross E. , Gomez L. Sanchez , Theophanous S. , Zhovannik I. , Helland Å.
Published: February 2025

Real-world data is an important complement to randomized controlled trials and can be used to assess whether study results translate well to routine clinical practice and to groups of patients that are often excluded from clinical trials. The aim of thisdiseasenatural history and care qualityassessment (DINASTY) study is to describe treatments, outcomes and care quality for patients with metastatic non-small cell lung cancer using real-world data. The study is a retrospective observational multicenter study conducted within DIGICORE, a non-profit European Economic Interest Grouping, formed to facilitate real-world evidence studies. The study will make use of methods developed within the network. Forty essential variables to describe patients with cancer, treatments and outcomes have been defined within DIGICORE and mapped to the Observational Medical Outcomes Partnership (OMOP) common data model (CDM). The study uses data that is drawn directly from the electronic patient health records at the patient’s local hospital and mapped to OMOP. Data are analyzed using a federated approach, meaning that patient-level data is analyzed locally, and only aggregated results are shared across centers and combined to present results for the full cohort. This method enables the delivery of multicenter studies and the presentation of results in a privacy-preserving way.
Oral microbiome profiles relate to periodontal disease and brain health - a microbiome network analysis in the Hamburg City Health Study
Authors: Petersen Marvin , Walther Carolin , Borof Katrin , Heydecke Guido , Beikler Thomas , Alawi Malik , Müller Christian , Nägele Felix L. , Zyriax Birgit-Christiane , Fiehler Jens , Gallinat Jürgen , Kühn Simone , Twerenbold Raphael , Bang Corinna , Thomalla Götz , Cheng Bastian , Aarabi Ghazal
Published: February 2025

The relationship between oral microbiome composition and brain health in the general population remains poorly understood. In this study, we inferred a microbiome similarity network based on 16S rRNA sequencing data of crevicular fluid collected from 1,026 participants in the Hamburg City Health Study, which revealed a continuous disease gradient mirroring the microbial pathogenicity spectrum of periodontitis. Leveraging this network, we systematically examined associations between periodontal microbiome profiles and 37 brain health-related phenotypes, including cognitive function, brain structure, mental health, inflammatory biomarkers, diet, vascular risk factors, and demographics. We found that higher abundance of periodontitis-related microbial taxa was linked to poorer cognitive performance, lower cortical thickness and subcortical volumes, and elevated leukocyte counts, after adjusting for covariates. Notably, we identified both, previously known as well as novel microbial associations with brain health phenotypes. These findings advance the understanding of the oral microbiome-brain axis, suggesting mechanistic links between periodontal health and brain function with potential implications for future causal and interventional studies.
Evaluation of Progesterone Resistance and the Role of Downregulation Protocols in Endometrial Preparation for Frozen Embryo Transfer in Patients with Recurrent Implantation Failure—A Retrospective Study
Authors: Luo Yuxing , Cen Changshuang , Liu Huaicong , Mo Dan , Fu Pingfang , Liu Xin , Liu Lidan , Wei Lansi , Gan Qiuying , Bi Yin , Yang Yihua , Liang Ting
Published: February 2025

This study investigates the impact of progesterone resistance on endometrial receptivity and evaluates the efficacy of pituitary downregulation combined with hormone replacement therapy (HRT) in improving pregnancy outcomes following frozen embryo transfer (FET). A retrospective analysis was conducted on 147 patients with recurrent implantation failure (RIF) who underwent secretory-phase endometrial biopsy and subsequent FET treatments at the Reproductive Center of the First Affiliated Hospital of Guangxi Medical University between April 2019 and May 2022. Based on biopsy results and endometrial preparations, patients were categorized into four groups: secretory phase + non-downregulated protocol group (n=29), secretory phase + GnRH-a + HRT Protocol group (n=20), proliferative phase + non-downregulated protocol group (n=59), proliferative Phase + GnRH-a + HRT Protocol group (n=39). Endometrial preparation regimens and pregnancy outcomes during the first FET cycle after biopsy were compared. The results showed that there was no statistical difference in the outcome of assisted pregnancy between the different endometrial preparation protocols in the four groups. These findings suggest that the prioritization of down-regulation protocols may not be essential for FET in patients with RIF, even when endometrial biopsy during the implantation window reveals proliferative-phase characteristics.
The aging human brain exhibits reduced cerebrospinal fluid flow during sleep due to both neural and vascular factors
Authors: Bailes Sydney M. , Williams Stephanie D. , Ashenagar Baarbod , Licata Joseph , Bosli Massinissa Y. , Dormes Brandon J. , Yun Hannah J. , Zimmerman Dabriel , Hernandez Moyers Alejandra , Salat David H. , Lewis Laura D.
Published: February 2025

Aging reduces the quality and quantity of sleep, and greater sleep loss over the lifespan is predictive of neurodegeneration and cognitive decline. One mechanism by which sleep loss could contribute to impaired brain health is through disruption of cerebrospinal fluid (CSF) circulation. CSF is the primary waste transport system of the brain, and in young adults, CSF waves are largest during NREM sleep. However, whether sleep-dependent brain fluid physiology changes in aging is not known, due to the technical challenges of performing neuroimaging studies during sleep. We collected simultaneous fast fMRI and EEG data to measure large-scale CSF flow in healthy young and older adults and tested whether there were age-related changes to CSF dynamics during nighttime sleep. We found that sleep-dependent CSF flow was reduced in older adults, and this reduction was linked to impaired frontal EEG delta power and global hemodynamic oscillations during sleep. To identify mechanisms underlying reduced CSF flow, we used sensory and vasoactive stimuli to drive CSF flow in daytime task experiments, and found that both neural and cerebrovascular physiological changes contributed to the disruption of CSF flow during sleep. Finally, we found that this reduction in CSF flow was associated with gray matter atrophy in aging. Together, these results demonstrate that the aging human brain has reduced CSF flow during sleep, and identifies underlying neurovascular mechanisms that contribute to this age-related decline, suggesting targets for future interventions.
Structural basis for the midnolin-proteasome pathway and its role in suppressing myeloma
Authors: Nardone Christopher , Gao Jingjing , Seo Hyuk-Soo , Mintseris Julian , Ort Lucy , Yip Matthew C. J. , Negasi Milen , Besschetnova Anna K. , Kamitaki Nolan , Gygi Steven P. , Dhe-Paganon Sirano , Munshi Nikhil , Fulciniti Mariateresa , Greenberg Michael E. , Shao Sichen , Elledge Stephen J. , Gu Xin
Published: February 2025

The midnolin-proteasome pathway degrades many nuclear proteins without ubiquitination, but how it operates mechanistically remains unclear. Here, we present structures of the midnolin-proteasome complex, revealing how established proteasomal components are repurposed to enable a unique form of proteolysis. While the proteasomal subunit PSMD2/Rpn1 binds to ubiquitinated or ubiquitin-like proteins, we discover that it also interacts with the midnolin nuclear localization sequence, elucidating how midnolin’s activity is confined to the nucleus. Likewise, PSMD14/Rpn11, an enzyme that normally cleaves ubiquitin chains, surprisingly functions non-enzymatically as a receptor for the midnolin ubiquitin-like (Ubl) domain, positioning the substrate-binding Catch domain directly above the proteasomal entry site to guide substrates into the proteasome. Moreover, we demonstrate that midnolin downregulation is critical for the survival of myeloma cells by promoting the expression of its transcription factor substrate IRF4. Our findings uncover the mechanisms underlying the midnolin-proteasome pathway and midnolin downregulation as a driver of multiple myeloma.
Treatment outcome is associated with pre-treatment connectome measures across psychiatric disorders - evidence for connectomic reserve?
Authors: Vriend Chris , Fitzsimmons Sophie M.D.D. , Aarts Inga , Broekhuizen Aniek , van der Werf Ysbrand D. , Douw Linda , Visser Henny A. D. , Thomaes Kathleen , van den Heuvel Odile A.
Published: February 2025

Background

Predicting treatment efficacy in psychiatric disorders remains challenging, despite the availability of effective interventions. Previous studies suggest a link between brain network topology and treatment efficacy in individual disorders, but cross-disorder investigations are lacking.

Methods

We analyzed pre-treatment MRI data from 177 individuals (113 females) with either obsessive-compulsive disorder (OCD) or post-traumatic stress disorder with comorbid personality disorders (PTSD) that received different non-pharmacological treatments. Using diffusion and resting-state MRI, we constructed structural, functional, and multilayer connectomes and calculated network measures at the global and mesoscale for network integration (global efficiency, eccentricity), segregation (modularity) and their balance (small-worldness). We assessed the relationship between these pre-treatment network measures and treatment improvement using mixed-model and Bayesian analyses and compared them to healthy controls. We also investigated associations between response and treatment-induced changes in network measures.

Results

Across disorders and treatments, psychiatric cases showed a 41.6±29.6% symptom improvement (62% response rate) after treatment and pre-treatment differences in functional and multilayer network topology compared to healthy controls. Symptom improvement was associated with pre-treatment functional (P=0.04) and structural small-worldness (P=0.01), and multilayer eccentricity (P=0.01), while responders had higher functional modularity (P=0.02). Results were robust across trials and treatments, when adjusting for medication status and showed high credibility in Bayesian analyses. Network change associations with treatment response were only modest.

Conclusions

Pre-treatment connectome characteristics are related to treatment response, regardless of treatment and psychiatric disorder, and suggest that individual differences in intrinsic features of the human connectome underlie amenability to treatment.
A distinctive subset of microglia positioned at the paraventricular zone are dedicated to cleaning the cerebrospinal fluid
Authors: Zhou Guoyang , He Jian , Mao Baojie , Cheng Guo , Zhang Rui , Wang Qiang , Liu Xiaoli , Zheng Jiaxin , Wang Ming , Zhao Li , Shi Peng , Shen Xiao Z , Wan Shu
Published: February 2025

The interconnected ventricles in the central nervous system are filled with cerebrospinal fluid (CSF) which serves multifaceted roles including bring away metabolic wastes. However, whether there is an inherent “dislodging” mechanism, in addition to CSF drainage and reabsorption, at play for the removal of microparticles in the CSF is unclear. In this study, we identified a subset of microglia distributed in close proximity to the ependymal wall of ventricles. They differed from parenchymal microglia in morphology, behaviors and transcriptomes. In particular, the paraventricular microglia extended transependymal dendrites into the lumen of ventricles and were proficient in sequestering and phagocytosing intraventricular exogenous particles when present. A specific removal of the paraventricular microglia led to an acute ventriculomegaly due to an increased colloid osmotic pressure in the CSF resulting from protein accumulation. Thus, we identified the paraventricular microglia as specific guardians in monitoring and cleaning the CSF.
Bridging Gaps in Antibody Responses and Animal Welfare: Assessing Blood Collection Methods and Vaginal Immunity in Mice Immunized with Intranasal Gonococcal Vaccines
Authors: Chanda Abhishek , Song Yujuan , Nazir Junaid , Lin Chenwei , Cheng Alicia , Sargent Jennifer , Sikora Aleksandra E.
Published: February 2025

Assessing antibody titers and functional responses is essential for evaluating vaccine efficacy, yet the impact of blood collection methods on these immunological assessments remains unclear. Retro-orbital (RO) blood collection is commonly used but significant complications can occur. Increasingly, investigators have adopted alternative blood collection approaches, such as saphenous vein (SV) sampling to improve laboratory animal welfare. This study compared RO and SV sampling in the development of aNeisseria gonorrhoeae(Ng) vaccine, evaluating Adhesin Complex Protein (ACP) and multiple transferable resistance (Mtr) E protein (MtrE) as antigen candidates. Epitope mapping revealed that ACP and MtrE possess multiple, highly accessible B-cell and T-cell epitope clusters, reinforcing their immunological potential. Following intranasal immunization with rACP, rACP+CpG, and rMtrE+CpG, we assessed the specificity, magnitude, kinetics, and functional quality of immune responses elicited by the immunization regimens. Out of 45 comparisons, only eight significant differences were detected in antibody titers, while the human serum bactericidal assays revealed no differences between RO and SV in antigen-immunized groups. However, antibodies elicited by rACP alone or ACP+CpG in SV samples restored 30.05% and 75.2% of human lysozyme hydrolytic activity compared to 19.3 and 59.9 % in RO, respectively suggesting that SV sampling may be more reliable for assessing functional antibody responses. Beyond its immunological advantages, SV sampling reduces stress, minimizes ocular trauma, and improves animal welfare, making it a viable alternative to RO collection. Given its widespread use in vaccine research, standardizing SV sampling could improve data reliability, ethical compliance, and translational relevance in preclinical studies.
Processes of Spatial Stratification: A Scoping Review Protocol
Authors: Dmitrzak Dominika
Published: February 2025

Abstract

Objective

The objective of this scoping review is to understand what is known and theorised about the processes of spatial stratification.

Introduction

Regional inequalities, commonly termed the North-South divide, have been an feature in England for years(1). Whilst there is research on the different areas affected, these include, but not limited to, income(2), education(3), and health(4), there is a lack of research on the processes that lead to the differentiation of regions, in other words, on spatial stratification. The aim of this scoping review is, therefore, to identify and synthesise what is known about the processes and factors involved in spatial stratification, bringing together research from separate fields such as economics, sociology, and geography.

EligibilityCriteria

In line with standard scoping review approaches, Population, Concept, Context (PCC)(5) will be used as a guide for eligibility. Population: anyone; Concept: spatial or socio-spatial stratification; Context: any country, any level. Articles and papers written in English, published after 1970, and meeting the inclusion criteria outlines will be included in the review.

Methods

Searches will be conducted in Scopus, Web of Science, JSTOR, Embase, and ProQuest Social Science Premium Collection. The time frame for the searches will be set from 1970 onwards. All titles and abstracts will be screened against the inclusion criteria in Rayyan. Reference lists of all eligible papers will be searched for further relevant literature. Full-text versions of eligible literature will be reviewed and data relating to theories, concepts, and where relevant, findings, will be extracted. Papers meeting the inclusion criteria will be tabulated, grouped thematically, and written up to form a narrative describing what is currently known and theorised about the processes that lead to spatial stratification.
Revisiting light-flavor diquarks in the inverse matrix method of QCD sum rules
Authors: Mutuk Halil
Published: February 2025

This study reexamines the spectroscopic parameters of light-flavor diquarks within the framework of quantum chromodynamics sum rules (QCDSR) using the inverse matrix method. Conventional QCDSR analyses are based on assumptions such as quark-hadron duality and continuum models, which introduce a degree of systematic uncertainty. The inverse matrix method circumvents these assumptions by reformulating the problem as an inverse integral equation and expanding the unknown spectral density using orthogonal Laguerre polynomials. This method allows for a direct determination of spectral densities, thereby enhancing the precision of predictions regarding resonance masses and decay constants. By employing this methodology with regard to light-flavor diquarks (sq and ud), it is possible to extract the associated masses and decay constants. The results indicate that the masses of diquarks with quantum numbers JP=0+ and JP=0− are nearly degenerate. We compare our results regarding masses and decay constants with those of other theoretical predictions, which could prove a useful complementary tool in interpretation. Our results are consistent with those in the literature and can be shown as evidence for the consistency of the method. The results achieved in this study highlight the potential of the inverse matrix method as a robust tool for exploring nonperturbative QCD phenomena and elucidating the internal structure of exotic hadronic systems.

Published by the American Physical Society
2025
Near-threshold states in coupled
DD*−D*D*
scattering from lattice QCD
Authors: Whyte Travis , Wilson David J. , Thomas Christopher E. ,   for the Hadron Spectrum Collaboration
Published: February 2025

The first determination of doubly charmed isospin-0 coupled-channel DD*−D*D* scattering amplitudes from lattice quantum chromodynamics (QCD) is presented. The finite-volume spectrum is computed for three lattice volumes with a light-quark mass corresponding to mπ≈391  MeV and is used to extract the scattering amplitudes in JP=1+ via the Lüscher quantization condition. By analytically continuing the scattering amplitudes to complex energies, a Tcc pole corresponding to a virtual bound state is found below DD* threshold. We also find a second pole, Tcc′, corresponding to a resonance pole below the kinematically closed D*D* channel, to which it has a strong coupling. A nonzero coupling is robustly found between the S-wave DD* and D*D* channels producing a clear cusp in the DD* amplitude at the D*D* threshold energy. This suggests that the experimental Tcc′ should be observable in DD* and D*D* final states at ongoing experiments.

Published by the American Physical Society
2025
Weak nuclear decays deep-underground as a probe of axion dark matter
Authors: Alda Jorge , Broggini Carlo , Di Carlo Giuseppe , Di Luzio Luca , Piatti Denise , Rigolin Stefano , Toni Claudio
Published: February 2025

We investigate the time modulation of weak nuclear decays as a method to probe axion dark matter. To this end, we develop a theoretical framework to compute the θ dependence of weak nuclear decays, including electron capture and β decay, which enables us to predict the time variation of weak radioactivity in response to an oscillating axion dark matter background. As an application, we recast old datasets, from the weak nuclear decays of K40 and Cs137 taken at the underground Gran Sasso Laboratory, in order to set constraints on the axion decay constant, specifically in the axion mass range from few 10−23 up to 10−19  eV. We finally propose a new measurement at the Gran Sasso Laboratory, based on the weak nuclear decay of K40 via electron capture, in order to explore even shorter timescales, thus reaching sensitivities to axion masses up to 10−9  eV.

Published by the American Physical Society
2025
SU(3)F
sum rules for
CP
asymmetries of
D(s)
decays
Authors: Iguro Syuhei , Nierste Ulrich , Overduin Emil , Schüßler Maurice
Published: February 2025

Charge-parity (CP) asymmetries in charm decays are extremely suppressed in the Standard Model and may well be dominated by new-physics contributions. The LHCb Collaboration reported the results of direct CP asymmetry measurements in D0→K+K− and D0→π+π− decays with unprecedented accuracy: aCP(K+K−)=(7.7±5.7)×10−4 and aCP(π+π−)=(23.2±6.1)×10−4, with the latter quantity inferred from the precise measurement of ΔaCP=aCP(K+K−)−aCP(π+π−)=(−15.7±2.9)×10−4. When interpreted within the Standard Model, these values indicate a breakdown of the approximate U-spin symmetry of QCD. If, however, this symmetry holds and the data stem from new physics, other CP asymmetries should be enhanced as well. We derive CP asymmetry sum rules based on SU(3) flavor symmetry for D meson decays into a pair of pseudoscalar mesons as well as a pair of a pseudoscalar and a vector meson for two generic scenarios, with ΔU=0 and |ΔU|=1 interactions, respectively. The correlations implied by the sum rules can be used to check the consistency between different measurements and to discriminate between these scenarios with future data. For instance, we find aCP(π+K*0)+aCP(K+K¯*0)=0 for ΔU=0 new physics and the opposite relative sign for the |ΔU|=1 case. One sum rule, connecting four decay modes, holds in both scenarios. We further extend our sum rules to certain differences of CP asymmetries from which the D production asymmetries drop out.

Published by the American Physical Society
2025
Leptonic
CP
violation in the sneutrino sector of the BLSSM with an inverse seesaw mechanism
Authors: Basu Arindam , Chakraborty Amit , Liu Yi , Moretti Stefano , Waltari Harri
Published: February 2025

We study CP violation (CPV) in the sneutrino sector within the B-L extension of the minimal supersymmetric Standard Model, wherein an inverse seesaw mechanism has been implemented. CPV arises from the new superpotential couplings in the (s)neutrino sector, which can be complex and the mixing of CP eigenstates induced by those couplings. CPV leads to asymmetries in so-called T-odd observables, but we argue that such asymmetries also lead to a wider distribution of those observables. We look at a final state where a sneutrino decays to a lepton, two jets, and missing transverse momentum at the Future Circular Collider operating in hadron-hadron mode at 100 TeV and with a luminosity of 3  ab−1. In order to exclude the CP conserving scenario we need to improve traditional analysis by introducing boosted decision trees using both standard kinematic variables and T-odd observables and we need Z′ boson not too much above current bounds as a portal to produce sneutrinos efficiently.

Published by the American Physical Society
2025
Impact of LHC precision measurements of inclusive jet and dijet production on the CTEQ-TEA global PDF fit
Authors: Ablat Alim , Dulat Sayipjamal , Hou Tie-Jiun , Huston Joey , Nadolsky Pavel , Sitiwaldi Ibrahim , Xie Keping , Yuan C.-P. ,   CTEQ-TEA Collaboration
Published: February 2025

In this study, we investigate the impact of new Large Hadron Collider (LHC) inclusive jet and dijet measurements on parton distribution functions (PDFs) that describe the proton structure, with a particular focus on the gluon distribution at large momentum fraction, x, and the corresponding partonic luminosities. We assess constraints from these datasets using next-to-next-to-leading-order (NNLO) theoretical predictions, accounting for a range of uncertainties from scale dependence and numerical integration. From the scale choices available for the calculations, our analysis shows that the central predictions for inclusive jet production show a smaller scale dependence than dijet production. We examine the relative constraints on the gluon distribution provided by the inclusive jet and dijet distributions, and also explore the phenomenological implications for inclusive H, tt¯, and tt¯H production at the LHC at 14 TeV.

Published by the American Physical Society
2025
Following marginal stability manifolds in quasilinear dynamical reductions of multiscale flows in two space dimensions
Authors: Ferraro Alessia , Chini Gregory P. , Schneider T. M.
Published: February 2025

We derive a two-dimensional (2D) extension of a recently developed formalism for slow-fast quasilinear (QL) systems subject to fast instabilities. The emergent dynamics of these systems is characterized by a slow evolution of (suitably defined) mean fields coupled to marginally stable, fast fluctuation fields. By exploiting this scale separation, an efficient hybrid fast-eigenvalue/slow-initial-value solution algorithm can be developed in which the amplitude of the fast fluctuations is slaved to the slowly evolving mean fields to ensure marginal stability—and temporal scale separation—is maintained. For 2D systems, the fluctuation eigenfunctions are labeled by their Fourier wave numbers characterizing spatial variability in that extended spatial direction, and the marginal mode(s) must coincide with the fastest-growing mode(s) over all admissible Fourier wave numbers. Here we derive an ordinary differential equation governing the slow evolution of the wave number of the fastest-growing fluctuation mode that simultaneously must be slaved to the mean dynamics to ensure the mode has zero growth rate. We illustrate the procedure in the context of a 2D model partial differential equation that shares certain attributes with the equations governing strongly stratified shear flows and other strongly constrained forms of geophysical turbulence in extreme parameter regimes. The slaved evolution follows one or more marginal stability manifolds, which constitute select state-space structures that are not invariant under the full flow dynamics yet capture quasicoherent structures in physical space in a manner analogous to invariant solutions identified in, e.g., transitionally turbulent shear flows. Accordingly, we propose that marginal stability manifolds are central organizing structures in a dynamical systems description of certain classes of multiscale flows in which scale separation justifies a QL approximation of the dynamics.

Published by the American Physical Society
2025
Coupling a high-Q resonator to a spin qubit with all-electrical control
Authors: Eggli Rafael S. , Patlatiuk Taras , Kelly Eoin G. , Orekhov Alexei , Salis Gian , Warburton Richard J. , Zumbühl Dominik M. , Kuhlmann Andreas V.
Published: February 2025

Building a practical quantum processor involves integrating millions of physical qubits along with the necessary components for individual qubit manipulation and readout. Arrays of gated silicon spins offer a promising route toward achieving this goal. Optimized radio frequency resonators with high internal quality factor are based on superconducting inductors and enable fast spin readout. All-electrical spin control and gate-dispersive readout remove the need for additional device components and simplify scaling. However, superconducting high-Q tank circuits are susceptible to crosstalk-induced ringup from electrical qubit control pulses, which causes fluctuations of the quantum dot potential and is suspected to degrade qubit performance. Here, we report on the coherent and all-electrical control of a hole spin qubit at 1.5K, integrated into a silicon fin field-effect transistor and connected to a niobium nitride nanowire inductor gate-sensor. Our experiments show that qubit control pulses with their broad range of higher harmonics ring up the tank when the control pulse spectrum overlaps with the tank resonance. This can cause a reduction of the readout visibility if the tank ringing amplitude exceeds the excited state splitting of the quantum dot, lifting Pauli spin blockade and thus leading to state preparation and measurement errors. We demonstrate how to circumvent these effects by engineering control pulses around the tank resonances. Importantly, we find that the ringup does not limit the spin coherence time, indicating that efficient high-Q resonators in gate-sensing are compatible with all-electrical spin control.

Published by the American Physical Society
2025
Chaperone-Driven Entropic Separation of Amyloid Nanofilament Bundles
Authors: Vilar Jose M. G. , Rubi J. Miguel , Saiz Leonor
Published: February 2025

The disassembly of misfolded protein aggregates is a requirement for the proper functioning of cells. It has implications in multiple neuropathologies, such as Alzheimer’s and Parkinson’s diseases. The active unbundling of fibrillar aggregates has recently been identified as a key rate-limiting step in the disassembly process. However, the nature of the underlying molecular mechanism remains an outstanding question. Here, we develop a coarse-grained computational approach from the atomistic structural information and show that the interactions of molecules tethered to fibrils lead to entropic forces consistent with the unbundling process observed in amyloid α-synuclein disaggregation by Hsp70. We uncover two main types of entropic effects, categorized as intraprotofilament and interprotofilament, which are differentially affected by the system parameters and conditions. Our results show that only highly efficient chaperone systems can overcome the free-energy cost of the lateral association between two protofilaments. Through the analysis of cryoelectron tomography and high-speed atomic force microscopy data, we find that the conditions for highly efficient entropic force generation are those typically achieved with cochaperone networks and ATP hydrolysis, which require energy expenditure but do not provide an enthalpic component to the separation force. We highlight the implications of these results for the design of targeted therapies for the underlying neuropathologies.

Published by the American Physical Society
2025
Evaluating container terminal competitiveness in the Hamburg – Le Havre range
Authors: Martinez-Moya Julian , Vanelslander Thierry , Feo-Valero María , Sala-Garrido Ramón
Published: February 2025

Purpose

The present research aims to develop a Terminal Competitiveness Index (TCI) applied to the container terminals located in the Hamburg – Le Havre range, which is an area characterised for its intense container activity. The main components of the TPCI are productivity, foreland connectivity and infrastructure.

Design/methodology/approach

To construct the index, the Benefit-of-the-Doubt and the Common Set of Weights methods in Data Envelopment Analysis are used to obtain a common weighting scheme for the evaluation of container terminals.

Findings

Results show that connectivity and terminal efficiency are the most important factors for terminal competitiveness. The TCI has identified that APM Terminals Maavslakte II (Rotterdam), ECT Delta (Rotterdam) and MPET (Antwerp) turned out with the highest competitiveness score.

Originality/value

Container terminals play a key role in today’s marketplace since they are the main infrastructure responsible for loading and unloading the containers full of intermediate and final goods. Therefore, the competitiveness of such terminals is crucial for shipping lines and importing and exporting companies, influencing their cost and schedule reliability. However, there is scarce literature studying the competitiveness of container terminals, since the focus to date has been on ports as units of analysis. The terminal-approach used allows the analysis of the competitiveness of terminals belonging to different ports, but also between those located in the same port.
Co‐Existence Slows Diversification in Experimental Populations of E. coli and P. fluorescens
Authors: Howells Gareth , Sezmis Aysha L. , Blake Christopher , McDonald Michael J.
Published: February 2025

Microbes grown in heterogeneous laboratory environments can rapidly diversify into multiple, coexisting variants. While the genetic and evolutionary mechanisms of laboratory adaptive radiations are well studied, how the presence of other species alters the outcomes of diversification is less well understood. To test the effect of co‐culture growth on the Pseudomonas fluorescens SBW25 adaptive radiation, Escherichia coli and P. fluorescens were cultured in monoculture and co‐culture for 8 weeks. In P. fluorescens monoculture, Wrinkly and Smooth Spreader types rapidly evolved and were maintained over 8 weeks, while E. coli monocultures evolved two colony types, a big and a small colony variant. In contrast, we found that in co‐culture, E. coli did not evolve small colony variants. Whole genome sequencing revealed the genetic basis of possible co‐culture specific adaptations in both E. coli and P. fluorescens. Altogether, our data support that the presence of multiple species changed the outcome of adaptive radiation.
Immunoassay Detection of SARS‐CoV‐2 Using Monoclonal Antibody Binding to Viral Nucleocapsid Protein
Authors: Hnasko Robert M. , Lin Alice V. , McGarvey Jeffery A. , Jackson Eric S.
Published: February 2025

Immunoassays represent sensitive, easy‐to‐use, and cost‐effective tests useful for the detection of the SARS‐CoV‐2 virus. In this manuscript, we report on the binding specificity of a pair of novel monoclonal antibodies (MAbs) generated against the SARS‐CoV‐2 nucleocapsid protein (NP) and their development into sensitive sandwich enzyme‐linked immunosorbent assays (sELISA) and a lateral flow immunoassay (LFIA). Binding of these MAbs to hCoVs is limited to variants of SARS‐CoV‐2 and SARS‐CoV NP. Chemiluminescent and absorbance spectroscopy sELISAs report a limit of detection (LOD) for the SARS‐CoV‐2 B.1.1.529 NP variant at 15 pg/mL, and the LFIA using a red‐dyed 200 nm particle at 10 ng/mL. The sELISA exhibits broad SARS‐CoV‐2 viral variant detection with assay LOD for SARS‐CoV‐2 B.1.1.529 virus at 1.4 × 105 genome copies per mL (p ≤ 0.001). The availability of these MAbs should facilitate continued investment in the commercial development of immunoassays to increase global SARS‐CoV‐2 detection technologies.
Investigation of the printability of ethyl 2‐[4‐(1,3,4‐oxadiazol‐2(3H)‐thion‐5‐yl)phenylhydrazono]‐3‐oxobutyrate on coated and uncoated papers
Authors: Akgül Ahmet , Küçükgüzel Ş. Güniz , Oktav Mehmet , Rollas Sevim
Published: February 2025

There is a growing demand in the printing industry for pigment‐based inks with excellent lightfastness and rub resistance qualities. In this work, a novel ink with the formulation ethyl 2‐[4‐(1,3,4‐oxadiazole‐2(3H)‐thione‐5‐yl)phenylhydrazono]‐3‐oxobutyrate (OXKT) was prepared as a pigment and its printability was investigated for use in printing. The OXKT was synthesised, characterised then printed on uncoated and gloss‐coated papers and Bristol cardboard. Physical tests and spectrophotometric measurements were carried out to determine the technical characteristics of the printed ink. Additionally, print quality, ink density and gloss were evaluated. The results showed that the proposed ink with the OXKT compound had acceptable rub resistance. Also, the gloss and light fastness values exceeded the acceptable rates for the printing industry because of their colour differences. However, more research needs to be conducted to improve light performance. Nevertheless, it is still possible for use in applications that do not stipulate strict light fastness values.
Alcohol use in Iraq: Perceptions of interviewed students at three Iraqi universities
Authors: Al Ansari Mustafa , Dawson Angela , AbdulZahra Mohammed S. , Conigrave Katherine M.
Published: February 2025

Introduction

Iraq has faced decades of conflict and increased exposure to alcohol use. While the majority (60%) of Iraq's population is under the age of 24, there is no research examining their views on alcohol use and related factors. This study explores how the individual, interpersonal and social contexts of university students may influence their experiences and perceptions of alcohol use.

Methods

We undertook a qualitative study underpinned by a socio‐ecological framework and the alcohol use motivational model. Forty students from 11 disciplines at three universities across Iraq were interviewed (45% female). Interviews were conducted in English (n = 3) or Arabic (n = 37). Template analysis was used to examine the data.

Results

Perceptions of the prevalence of alcohol use varied among participants. Perceived motives for drinking included using alcohol to cope with grief, loss, poverty and unemployment; as well as peer pressure, thrill‐seeking and social approval. Abstinence was perceived to be associated with knowledge of the adverse effects of alcohol and a commitment to faith. Students reported alcohol use as a clandestine activity. Students suggested education, open communication and employment opportunities as preventative strategies.

Discussion and Conclusion

This is the first study to explore young Iraqi perceptions and experiences of peers' alcohol use in the current context of conflict, political instability and globalisation. Young Iraqis are a vulnerable population who may be at risk of alcohol‐related harm. Iraq should consider multidimensional preventive approaches that include evidence‐based and culturally appropriate interventions that reflect young people's real‐life experiences and challenges.
A Systematic Review on the Prevalence of Tick‐Borne Encephalitis Virus in Milk and Milk Products in Europe
Authors: Tomassone Laura , Martello Elisa , Mannelli Alessandro , Vicentini Aurora , Gossner Céline M. , Leonardi‐Bee Jo
Published: February 2025

Background

Tick‐borne encephalitis virus (TBEV) is one of the most significant zoonotic diseases in Europe. It primarily spreads through the bites of infected ticks and, less frequently, through consumption of raw milk and dairy products from viremic domestic ruminants.

Aims

Assess the prevalence of TBEV or anti‐TBEV antibodies in milk and milk products from domestic ruminants in Europe.

Materials and Methods

Systematic literature review adhering to the JBI methodology, and reported following the PRISMA framework.

Results

From the 16 included scientific articles, we extracted 35 data collections (31 on raw milk and 4 on raw milk cheese); studies focused on cow (n = 15), goat (n = 11) and sheep milk (n = 5), goat (n = 3) and cow/goat cheese (n = 1). Fifteen data collections involved individual milk and 16 bulk milk samples. The estimated prevalence of TBEV in individual raw milk and cheese was 6% and 3%, respectively. TBEV prevalence in bulk milk was very heterogeneous, with most values either 0% or 100%.

Discussion

Although published research on TBEV transmission to humans through milk and dairy products in the EU countries is limited, our results highlight the potential infection risk for consumers. The variable prevalence reported in the studies may reflect the focal nature of TBEV.

Conclusion

Studies on unpasteurised dairy products from domestic ruminants can be valuable for the detection of TBEV presence in a geographic area, even when human cases are not reported. Thanks to the ease of sample collection, their testing could be adopted in monitoring plans on TBEV.