bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing and manipulating the Mexican hat-shaped valence band of In2Se3
Authors: Felton James , Harknett Jordan , Page Joe , Yang Zhuo , Alghofaili Nada , O’Shea James N. , Eaves Laurence , Kohama Yoshimitsu , Greenaway Mark T. , Patanè Amalia 
Published: January 2025

Abstract
Ferroelectrics based on van der Waals semiconductors represent an emergent class of materials for disruptive technologies ranging from neuromorphic computing to low-power electronics. However, many theoretical predictions of their electronic properties have yet to be confirmed experimentally and exploited. Here, we use nanoscale angle-resolved photoemission electron spectroscopy and optical transmission in high magnetic fields to reveal the electronic band structure of the van der Waals ferroelectric indium selenide (α-In2Se3). This indirect bandgap semiconductor features a weakly dispersed valence band, which is shaped like an inverted Mexican hat. Its form changes following an irreversible structural phase transition of α-In2Se3 into β-In2Se3 via a thermal annealing in ultra-high vacuum. Density functional theory supports the experiments and reveals the critical contribution of spin orbit coupling to the form of the valence band. The measured band structure and its in situ manipulation offer opportunities for precise engineering of ferroelectrics and their functional properties beyond traditional semiconducting systems.
Recombinant production platform for Group A Streptococcus glycoconjugate vaccines
Authors: Ajay Castro Sowmya , Passmore Ian J. , Ndeh Didier , Shaw Helen Alexandra , Ruda Alessandro , Burns Keira , Thomson Sarah , Nagar Rupa , Alagesan Kathirvel , Reglinski Mark , Lucas Kieron , Abouelhadid Sherif , Schwarz-Linek Ulrich , Mawas Fatme , Widmalm Göran , Wren Brendan W. , Dorfmueller Helge C. 
Published: January 2025

Abstract
Group A Streptococcus (Strep A) is a human-exclusive bacterial pathogen killing annually more than 500,000 patients, and no current licensed vaccine exists. Strep A bacteria are highly diverse, but all produce an essential, abundant, and conserved surface carbohydrate, the Group A Carbohydrate, which contains a rhamnose polysaccharide (RhaPS) backbone. RhaPS is a validated universal vaccine candidate in a glycoconjugate prepared by chemical conjugation of the native carbohydrate to a carrier protein. We engineered the Group A Carbohydrate biosynthesis pathway to enable recombinant production using the industry standard route to couple RhaPS to selected carrier proteins within Escherichia coli cells. The structural integrity of the produced recombinant glycoconjugate vaccines was confirmed by Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. Purified RhaPS glycoconjugates elicited carbohydrate-specific antibodies in mice and rabbits and bound to the surface of multiple Strep A strains of diverse M-types, confirming the recombinantly produced RhaPS glycoconjugates as valuable vaccine candidates.
Multiscale footprints reveal the organization of cis-regulatory elements
Authors: Hu Yan , Horlbeck Max A. , Zhang Ruochi , Ma Sai , Shrestha Rojesh , Kartha Vinay K. , Duarte Fabiana M. , Hock Conrad , Savage Rachel E. , Labade Ajay , Kletzien Heidi , Meliki Alia , Castillo Andrew , Durand Neva C. , Mattei Eugenio , Anderson Lauren J. , Tay Tristan , Earl Andrew S. , Shoresh Noam , Epstein Charles B. , Wagers Amy J. , Buenrostro Jason D. 
Published: January 2025

Abstract

Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes in the composition of diverse effector proteins over time1. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here we developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size. Using these multiscale footprints, we created the seq2PRINT framework, which uses deep learning to allow precise inference of transcription factor and nucleosome binding and interprets regulatory logic at CREs. Applying seq2PRINT to single-cell chromatin accessibility data from human bone marrow, we observe sequential establishment and widening of CREs centred on pioneer factors across haematopoiesis. We further discover age-associated alterations in the structure of CREs in murine haematopoietic stem cells, including widespread reduction of nucleosome footprints and gain of de novo identified Ets composite motifs. Collectively, we establish a method for obtaining rich insights into DNA-binding protein dynamics from chromatin accessibility data, and reveal the architecture of regulatory elements across differentiation and ageing.
Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted
Authors: Reina-Campos Miguel , Monell Alexander , Ferry Amir , Luna Vida , Cheung Kitty P. , Galletti Giovanni , Scharping Nicole E. , Takehara Kennidy K. , Quon Sara , Challita Peter P. , Boland Brigid , Lin Yun Hsuan , Wong William H. , Indralingam Cynthia S. , Neadeau Hayley , Alarcón Suzie , Yeo Gene W. , Chang John T. , Heeg Maximilian , Goldrath Ananda W. 
Published: January 2025

Abstract
Tissue-resident memory CD8 T (TRM) cells provide protection from infection at barrier sites. In the small intestine, TRM cells are found in at least two distinct subpopulations: one with higher expression of effector molecules and another with greater memory potential1. However, the origins of this diversity remain unknown. Here we proposed that distinct tissue niches drive the phenotypic heterogeneity of TRM cells. To test this, we leveraged spatial transcriptomics of human samples, a mouse model of acute systemic viral infection and a newly established strategy for pooled optically encoded gene perturbations to profile the locations, interactions and transcriptomes of pathogen-specific TRM cell differentiation at single-transcript resolution. We developed computational approaches to capture cellular locations along three anatomical axes of the small intestine and to visualize the spatiotemporal distribution of cell types and gene expression. Our study reveals that the regionalized signalling of the intestinal architecture supports two distinct TRM cell states: differentiated TRM cells and progenitor-like TRM cells, located in the upper villus and lower villus, respectively. This diversity is mediated by distinct ligand–receptor activities, cytokine gradients and specialized cellular contacts. Blocking TGFβ or CXCL9 and CXCL10 sensing by antigen-specific CD8 T cells revealed a model consistent with anatomically delineated, early fate specification. Ultimately, our framework for the study of tissue immune networks reveals that T cell location and functional state are fundamentally intertwined.
An updated reference genome of Barbatula barbatula (Linnaeus, 1758)
Authors: Laczkó Levente , Nagy Nikoletta Andrea , Nagy Ágnes , Maroda Ágnes , Sály Péter 
Published: January 2025

Abstract
The stone loach Barbatula barbatula is a benthic fish species widely distributed throughout Europe, primarily inhabiting stony upper sections of stream networks. This study presents an updated genome assembly of B. barbatula, contributing to the species’ available genomic resources for downstream applications such as conservation genetics. The draft assembly was 550 Mbp in size, with an N50 of 11.21 Mbp. We used the species’ available chromosome scaffolds to finish the genome. The final assembly had a BUSCO score of 96.7%. We identified 23270 protein-coding genes, and the proteome exhibited high completeness with BUSCO (93.1%) and OMArk (90.81%). Despite using multiple approaches to reduce duplicate contigs, we observed a relatively high duplicate ratio of 6.1% (BUSCO) and 8.52% (OMArk) in the annotations. We aimed to find microsatellite loci present in both the species’ publicly available genome and the new assembly to aid marker development for downstream analyses. This dataset serves as a reference for genomic analysis and is useful for developing markers to study the species’ biodiversity and support conservation efforts.
Evaluating survival outcomes and treatment recommendations in resectable gastric cancer
Authors: Sabbagh Saad , Jabbal Iktej Singh , Herrán María , Mohanna Mohamed , Iska Sindu , Itani Mira , Dominguez Barbara , Sarna Kaylee , Nahleh Zeina , Nagarajan Arun 
Published: January 2025

Abstract
No consensus exists on the optimal therapy for resectable gastric cancer (GC) and gastroesophageal junction (GEJ) tumors, including the effectiveness of chemoradiotherapy versus perioperative chemotherapy (PC). Our study aimed to compare overall survival (OS) outcomes associated with the recommended treatment modalities for GC and GEJ tumors and evaluate treatment trends from 2010 to 2020. A national registry cohort identified patients with ≥ cT2 nonmetastatic GC and GEJ cancer. Treatment modalities were classified as neoadjuvant chemotherapy (NC), neoadjuvant chemoradiotherapy (NCR), PC, adjuvant chemotherapy (AC), and adjuvant chemoradiation (ACR). Kaplan-Meier curve and multivariable Cox regression models evaluated factors associated with OS. A cohort of 7665 patients were included. Patients who received PC had the highest OS (median 86.80 months, 95% CI 73.40-NE), while chemoradiotherapy in the neoadjuvant and adjuvant settings had worse OS than PC and NC (NCR median 47.15 months, 95% CI 44.58–52.27, and ACR median 52.67 months, 95%CI 42.78–63.93). The Cox proportional hazards model showed that NCR and NC had worse survival than PC (HR 1.74, 95% CI 1.50–2.02, p < 0.001 and HR 1.26, 95% CI 1.10–1.44, p = 0.0008, respectively). Additionally, the most utilized modality during 2020 was NC (35.8%), followed by PC (28.0%) and NCR (24.9%). The utilization of PC and NC had the most substantial rise between 2010 and 2020, increasing by 11.0%. The study demonstrates the association of PC with improved OS outcomes for nonmetastatic GC and GEJ tumors. Therapies combining radiation with chemotherapy and extended lymph node dissection correlated with a worse prognosis compared to PC and NC. Despite the association with improved outcomes, national data reveals low utilization rates for PC.
Field switching of microfabricated metamagnetic FeRh MRI contrast agents
Authors: Dodd Stephen , Gudino Natalia , Zadorozhnii Oleksii , Staňo Michal , Hajduček Jan , Arregi Jon Ander , Morris H. Douglas , Uhlíř Vojtěch , Barbic Mladen , Koretsky Alan P. 
Published: January 2025

Abstract
In a step towards generating switchable MRI cellular labels, we demonstrate in-situ field switching of micron scale metamagnetic Iron-Rhodium (FeRh) thin film particles. A thin-film (200 nm) FeRh sample was fabricated and patterned into an array of progressively smaller squares with sizes ranging from 500 μm down to 1 μm. The large first order phase change from antiferromagnetic to ferromagnetic state was characterized using vibrating sample magnetometry, magnetic force microscopy, and MRI. Room temperature MRI experiments sensitive to the local magnetic field surrounding the particles demonstrated the low moment state (OFF MRI contrast) at 4.7T and high moment state (ON MRI contrast) at 11.7T for the array where sizes down to 2–3 μm were observed in MRI at 50 μm resolution. The expected temperature dependent MRI contrast change was seen at 4.7T, where 10 μm particles could be observed at 150 μm resolution in the ON state. A shielded MRI insert, used to temporarily increase or decrease the magnetic field up to 0.77T amplitude, was used to reversibly switch the particle array at constant temperature and blink the particles ON and OFF at 4.7T. This work demonstrates the MRI contrast switching potential for FeRh particles with biological cell dimensions, and the use of magnetic field pulses for reversible MRI label contrast control.
An in silico analysis of heart rate impact on wall shear stress hemodynamic parameters in aortic coarctation
Authors: Wang Jie , Manchester Emily , Skillen Alex , Ngoepe Malebogo , Keavney Bernard , Revell Alistair 
Published: January 2025

Abstract
This study examines how heart rate (HR) affects hemodynamics in a South African infant with Coarctation of the Aorta. Computed tomography angiography segments aortic coarctation anatomy; Doppler echocardiography derives inlet flow waveforms. Simulations occur at 100, 120, and 160 beats per minute, representing reduced, resting, and elevated HR levels. Turbulence was analyzed over time and space using turbulence-resolving and pulsatile large-eddy simulations. Specifically, a 60% reduction in HR led to a reduction in maximum velocity by 45%, and a 57% decrease in pressure drop. The reduction in turbulence-related metrics was less significant. The ratio of turbulent kinetic energy to total kinetic energy decreased by 2%, while turbulent wall shear stress decreased by 3%. These results demonstrate that HR significantly affects velocity and pressure drop, while turbulence arising from the coarctation region is relatively unaffected. The balance between turbulent kinetic energy and total kinetic energy shows minimal enhancement due to the complex interplay among HR, turbulence, and geometry. This complexity prompts discussion on how HR-slowing medications, such as beta-blockers or ivabradine, could positively influence hemodynamic stresses. In particular, the results indicate that while HR modulation can influence flow dynamics, it may not significantly reduce turbulence-induced shear stresses within the coarctation zone. Therefore, further investigation is necessary to understand the potential impact of HR modulation in the management of CoA, and whether interventions targeting the anatomical correction of the coarctation may be more effective in improving hemodynamic outcomes.
Investigation of sensory attenuation in the somatosensory domain using EEG in a novel virtual reality paradigm
Authors: Giannini Gianluigi , Nierhaus Till , Blankenburg Felix 
Published: January 2025

Abstract
We are not only passively immersed in a sensorial world, but we are active agents that directly produce stimulations. Understanding what is unique about sensory consequences can give valuable insight into the action-perception-cycle. Sensory attenuation is the phenomenon that self-produced stimulations are perceived as less intense compared to externally-generated ones. Studying this phenomenon, however, requires considering a plethora of factors that could otherwise interfere with its interpretation, such as differences in stimulus properties, attentional resources, or temporal predictability. We therefore developed a novel Virtual Reality (VR) setup which allows control over several of these confounding factors. Furthermore, we modulated the expectation of receiving a somatosensory stimulation across self-production and passive perception through a simple probabilistic learning task, allowing us to test to what extent the electrophysiological correlates of sensory attenuation are impacted by stimulus expectation. Therefore, the aim of the present study was twofold: first we aimed validating a novel VR paradigm during electroencephalography (EEG) recoding to investigate sensory attenuation in a highly controlled setup; second, we tested whether electrophysiological differences between self- and externally-generated sensations could be better explained by stimulus predictability factors, corroborating the validity of sensory attenuation. Results of 26 participants indicate that early (P100), mid-latency (P200) and later negative contralateral potentials were significantly attenuated by self-generated sensations, independent of the stimulus expectation. Moreover, a component around 200 ms post-stimulus at frontal sites was found to be enhanced for self-produced stimuli. The P300 was influenced by stimulus expectation, regardless of whether the stimulation was actively produced or passively attended. Together, our results demonstrate that VR opens up new possibilities to study sensory attenuation in more ecological valid yet well-controlled paradigms, and that sensory attenuation is not significantly modulated by stimulus predictability, suggesting that sensory attenuation relies on motor-specific predictions about their sensory outcomes. This not only supports the phenomenon of sensory attenuation, but is also consistent with previous research and the concept that action actually plays a crucial role in perception.
FABP4 as a therapeutic host target controlling SARS-CoV-2 infection
Authors: Baazim Hatoon , Koyuncu Emre , Tuncman Gürol , Burak M Furkan , Merkel Lea , Bahour Nadine , Karabulut Ezgi Simay , Lee Grace Yankun , Hanifehnezhad Alireza , Karagoz Zehra Firat , Földes Katalin , Engin Ilayda , Erman Ayse Gokce , Oztop Sidika , Filazi Nazlican , Gul Buket , Ceylan Ahmet , Cinar Ozge Ozgenc , Can Fusun , Kim Hahn , Al-Hakeem Ali , Li Hui , Semerci Fatih , Lin Xihong , Yilmaz Erkan , Ergonul Onder , Ozkul Aykut , Hotamisligil Gökhan S 
Published: January 2025

Abstract
Host metabolic fitness is a critical determinant of infectious disease outcomes. Obesity, aging, and other related metabolic disorders are recognized as high-risk disease modifiers for respiratory infections, including coronavirus infections, though the underlying mechanisms remain unknown. Our study highlights fatty acid-binding protein 4 (FABP4), a key regulator of metabolic dysfunction and inflammation, as a modulator of SARS-CoV-2 pathogenesis, correlating strongly with disease severity in COVID-19 patients. We demonstrate that loss of FABP4 function, by genetic or pharmacological means, reduces SARS-CoV-2 replication and disrupts the formation of viral replication organelles in adipocytes and airway epithelial cells. Importantly, FABP4 inhibitor treatment of infected hamsters diminished lung viral titers, alleviated lung damage and reduced collagen deposition. These findings highlight the therapeutic potential of targeting host metabolism in limiting coronavirus replication and mitigating the pathogenesis of infection.
Evaluation of Masseteric Vestibular Evoked Myogenic Potentials: A Comparative Study Between Children and Adults
Authors: Somani Sejal , Neupane Anuj Kumar 
Published: January 2025

Purpose:
The present study examined masseteric vestibular evoked myogenic potential (mVEMP) responses in children and compared these results with those of adults, using both air- and bone-conduction modes of stimulation.

Method:
Fifteen children and fifteen adults with hearing thresholds below 15 dB HL were considered for the study. Ipsilateral 500-Hz narrow-band chirp (NB CE-chirp) evoked mVEMP responses were elicited via a zygomatic montage through both air- and bone-conduction modes of stimulation. Therefore, the recorded responses were analyzed for various mVEMP parameters, namely, absolute P11 and N21 peak latencies, the peak-to-peak amplitude of the P11–N21 complex, and the interaural asymmetry ratio.

Results:
NB CE-chirp–evoked mVEMPs were 100% present at 500 Hz using both air- and bone-conduction modes of stimulation. No significant differences were found in mVEMP parameters between ears, genders, or modes of stimulation in both children and adults. However, a significant P11–N21 amplitude difference was observed between the two groups.

Conclusion:
The findings of the study highlighted the need to incorporate age-appropriate reference values for interpreting mVEMP responses for children and adults across air- and bone-conduction modes.
Active voltage balancing by turn‐off delays regulation for multiple series‐connected SiC MOSFETs
Authors: Mathieu de Vienne Cédric , Lefranc Pierre , Jeannin Pierre‐Olivier , Lefebvre Bruno , Asllani Besar 
Published: January 2025

AbstractSiC MOSFETs are currently the most appropriate solution for high‐efficiency conversions at low kilovolts (). For higher voltages, the series connection of SiC MOSFETs shows great promise. However, voltage sharing remains a significant technical challenge. This article proposes an active voltage balancing approach for a stack of N SiC MOSFETs, achieved through precise adjustment of turn‐off delays based on real‐time voltage feedback. Using an analytical model tailored to describe voltage sharing, a control method is designed, configured, and evaluated. Control behavior is experimentally validated on hard switching converters.
Pulmonary Embolism and Obstructive Sleep Apnea
Authors: García-Ortega Alberto , Pedro-Tudela Ana , Taberner-Lino Laura , Barreiro Esther , Martínez-García Miguel Ángel , Oscullo Grace 
Published: January 2025

AbstractPulmonary embolism (PE) and obstructive sleep apnea (OSA) remain a major health issue worldwide with potential overlapping pathophysiological mechanisms. PE, the most severe form of venous thromboembolism, is associated with high morbidity and mortality, presenting challenges in management and prevention, especially in high-risk populations. OSA is a prevalent condition characterized by repeated episodes of upper airway closure resulting in intermittent hypoxia and sleep fragmentation. Although the understanding of epidemiological and pathogenic relationships between OSA and PE is still limited, current data suggest that interactions between these two conditions appear to be relevant. OSA is emerging as a novel risk factor for PE, potentially affecting all components of Virchow's triad: hypercoagulability, endothelial dysfunction, and venous stasis. Epidemiological studies indicate a high prevalence of undiagnosed OSA in acute PE patients. Moderate-to-severe OSA has been linked to worse clinical presentations and outcomes. Furthermore, OSA has been associated with increased risks of PE recurrence and mortality. Future research directions should include clarifying the bidirectional relationship between these conditions and evaluating the effectiveness and safety of continuous positive airway pressure therapy in improving outcomes in patients with concurrent acute PE and OSA.
Fluctuations and correlations in causal set theory
Authors: Moradi Heidar , Yazdi Yasaman K , Zilhão Miguel 
Published: January 2025

Abstract
We study the statistical fluctuations (such as the variance) of causal set quantities, with particular focus on the causal set action. To facilitate calculating such fluctuations, we develop tools to account for correlations between causal intervals with different cardinalities. We present a convenient decomposition of the fluctuations of the causal set action into contributions that depend on different kinds of correlations. This decomposition can be used in causal sets approximated by any spacetime manifold

M

. Our work paves the way for investigating a number of interesting discreteness effects, such as certain aspects of the Everpresent Λ cosmological model.