bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interferon-α promotes HLA-B-restricted presentation of conventional and alternative antigens in human pancreatic β-cells
Authors: Carré Alexia , Samassa Fatoumata , Zhou Zhicheng , Perez-Hernandez Javier , Lekka Christiana , Manganaro Anthony , Oshima Masaya , Liao Hanqing , Parker Robert , Nicastri Annalisa , Brandao Barbara , Colli Maikel L. , Eizirik Decio L. , Aluri Jahnavi , Patel Deep , Göransson Marcus , Burgos Morales Orlando , Anderson Amanda , Landry Laurie , Kobaisi Farah , Scharfmann Raphael , Marselli Lorella , Marchetti Piero , You Sylvaine , Nakayama Maki , Hadrup Sine R. , Kent Sally C. , Richardson Sarah J. , Ternette Nicola , Mallone Roberto 
Published: January 2025

Abstract
Interferon (IFN)-α is the earliest cytokine signature observed in individuals at risk for type 1 diabetes (T1D), but the effect of IFN-α on the antigen repertoire of HLA Class I (HLA-I) in pancreatic β-cells is unknown. Here we characterize the HLA-I antigen presentation in resting and IFN-α-exposed β-cells and find that IFN-α increases HLA-I expression and expands peptide repertoire to those derived from alternative mRNA splicing, protein cis-splicing and post-translational modifications. While the resting β-cell immunopeptidome is dominated by HLA-A-restricted peptides, IFN-α largely favors HLA-B and only marginally upregulates HLA-A, translating into increased HLA-B-restricted peptide presentation and activation of HLA-B-restricted CD8+ T cells. Lastly, islets of patients with T1D show preferential HLA-B hyper-expression when compared with non-diabetic donors, and islet-infiltrating CD8+ T cells reactive to HLA-B-restricted granule peptides are found in T1D donors. Thus, the inflammatory milieu of insulitis may skew the autoimmune response toward alternative epitopes presented by HLA-B, hence recruiting T cells with a distinct repertoire that may be relevant to T1D pathogenesis.
Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population
Authors: Jeyaram Kumaraswamy , Lahti Leo , Tims Sebastian , Heilig Hans G. H. J. , van Gelder Antonie H. , de Vos Willem M. , Smidt Hauke , Zoetendal Erwin G. 
Published: January 2025

Abstract
The effect of fermented foods on healthy human gut microbiota structure and function, particularly its seasonal preference and frequent long-term consumption, has been largely uncharacterised. Here, we assess the gut microbiota and metabolite composition of 78 healthy Indian agrarian individuals who differ in the intake of fermented milk and soybean products by seasonal sampling during hot-humid summer, autumn and dry winter. Here we show that, seasonal shifts between the Prevotella- and Bifidobacterium/Ruminococcus-driven community types, or ecological states, and associated fatty acid derivatives, with a bimodal change in Bacteroidota community structure during summer, particularly in fermented milk consumers. Our results associate long-term fermented food consumption with reduced gut microbiota diversity and bacterial load. We identify taxonomic groups that drive the seasonal fluctuation and associated shifts between the two ecological states in gut microbiota. This understanding may pave the way towards developing strategies to sustain a healthy and resilient gut microbiota through dietary interventions.
An In Vitro Study of the Effects of Methotrexate Loaded Biocomposite Beads on MG63 Osteoblast Cells
Authors: Malash A. E. , Al-esnawy A. A. , Ereiba Khairy T. , Bakr Ahmed M. , Abdraboh A. S. 
Published: January 2025

Abstract
This study aims to synthesize a new localized drug delivery system of bioglass, polyvinyl alcohol (PVA), cellulose (CNC), and sodium alginate (SA) beads as a carrier for methotrexate (MTX) drugs for the treatment of osteosarcoma. Methotrexate /Bioglass-loaded Polyvinyl/Cellulose/Sodium alginate biocomposite beads were prepared via the dropwise method with different concentrations of (65%SiO2-30%CaO- 5%P2O5) bioglass. Samples were named B0, S0, S1, S2, and S3, respectively. Calcium chloride (CaCl2) was used as a cross-linking agent. The obtained biocomposite beads were investigated by different techniques FTIR, XRD, SEM, etc. The bioactivity of MTX/BG-loaded PVA-CNC-SA biocomposite beads was tested by immersion in simulated body fluid (SBF). The profile release of methotrexate was investigated with UV–vis spectroscopy for 30 days. A cytotoxicity study of the methotrexate was performed by a human osteosarcoma (MG-63) cell line. Results indicated that the formation of a hydroxyapatite layer on the bead’s surface confirmed its biological activity. Bioactivity was directly proportional to the BG content. All samples of B1, S0, S1, S2, and S3 exhibited significant maximum release up to 6 days and were controlled gradually. Cytotoxicity results of biocomposite beads showed that high cell death was detected on the MG-63 cells, with (IC-50 ± SD) of S3 (116.16 ± 1.57) compared with B1 (306.99 ± 2.72) and S1 (204.74 ± 4.55) due to the high release of MTX, which was confirmed by the results of the drug release profile. Results prove that the prepared biocomposite beads can be used as bioactive, drug delivery systems, and anticancer materials.
A hybrid Harris Hawks Optimization with Support Vector Regression for air quality forecasting
Authors: Houssein Essam H. , Mohamed Meran , Younis Eman M. G. , Mohamed Waleed M. 
Published: January 2025

Abstract
This paper proposes a hybridized model for air quality forecasting that combines the Support Vector Regression (SVR) method with Harris Hawks Optimization (HHO) called (HHO-SVR). The proposed HHO-SVR model utilizes five datasets from the environmental protection agency’s Downscaler Model (DS) to predict Particulate Matter (
$$PM_{2.5}$$
) levels. In order to assess the efficacy of the suggested HHO-SVR forecasting model, we employ metrics such as Mean Absolute Percentage Error (MAPE), Average, Standard Deviation (SD), Best Fit, Worst Fit, and CPU time. Additionally, we contrast our methodology with recently created models that have been published in the literature, such as the Grey Wolf Optimizer (GWO), Salp Swarm Algorithm (SSA), Henry Gas Solubility Optimization (HGSO), Barnacles Mating Optimizer (BMO), Whale Optimization Algorithm (WOA), and Manta Ray Foraging Optimization (MRFO). In particular, the proposed HHO-SVR model outperforms other approaches, establishing it as the optimal model based on its superior results.
Modelling the impact of environmental and social determinants on mental health using generative agents
Authors: Kambeitz Joseph , Meyer-Lindenberg Andreas 
Published: January 2025

Abstract
Mental health is shaped by socio-environmental determinants, yet traditional research approaches struggle to capture their complex interactions. This review explores the potential of generative agents, powered by large language models, to simulate human-like behaviour in virtual environments for mental health research. We outline potential applications including the modelling of adverse life events, urbanicity, climate change, discuss potential challenges and describe how generative agents could transform mental health research.
Prenatal inflammation impairs early CD11c-positive microglia induction and delays myelination in neurodevelopmental disorders
Authors: Fuma Kazuya , Iitani Yukako , Imai Kenji , Ushida Takafumi , Tano Sho , Yoshida Kosuke , Yokoi Akira , Miki Rika , Kidokoro Hiroyuki , Sato Yoshiaki , Hara Yuichiro , Ogi Tomoo , Nomaki Kohei , Tsuda Makoto , Komine Okiru , Yamanaka Koji , Kajiyama Hiroaki , Kotani Tomomi 
Published: January 2025

Abstract
Histological chorioamnionitis (HCA) is a form of maternal immune activation (MIA) linked to an increased risk of neurodevelopmental disorders in offspring. Our previous study identified neurodevelopmental impairments in an MIA mouse model mimicking HCA. Thus, this study investigated the role of CD11c+ microglia, key contributors to myelination through IGF-1 production, in this pathology. In the mouse model, the CD11c+ microglial population was significantly lower in the MIA group than in the control group on postnatal day 3 (PN3d). Furthermore, myelination-related protein levels significantly decreased in the MIA group at PN8d. In humans, preterm infants with HCA exhibited higher IL-6 and IL-17A cord-serum levels and lower IGF-1 levels than those without HCA, followed by a higher incidence of delayed myelination on magnetic resonance imaging at the term-equivalent age. In silico analysis revealed that the transient induction of CD11c+ microglia during early development occurred similarly in mice and humans. Notably, a lack of high CD11c+ microglial population has been observed in children with neurodevelopmental disorders. This study reports impaired induction of CD11c+ microglia during postnatal development in a mouse model of MIA associated with delayed myelination. Our findings may inform strategies for improving outcomes in infants with HCA.
A multi-tissue longitudinal proteomics study to evaluate the suitability of post-mortem samples for pathophysiological research
Authors: Beusch Christian M. , Braesch-Andersen Ken , Felldin Ulrika , Sabatier Pierre , Widgren Anna , Bergquist Jonas , Grinnemo Karl-Henrik , Rodin Sergey 
Published: January 2025

Abstract
Recent developments in mass spectrometry-based proteomics have established it as a robust tool for system-wide analyses essential for pathophysiological research. While post-mortem samples are a critical source for these studies, our understanding of how body decomposition influences the proteome remains limited. Here, we have revisited published data and conducted a clinically relevant time-course experiment in mice, revealing organ-specific proteome regulation after death, with only a fraction of these changes linked to protein autolysis. The liver and spleen exhibit significant proteomic alterations within hours post-mortem, whereas the heart displays only modest changes. Additionally, subcellular compartmentalization leads to an unexpected surge in proteome alterations at the earliest post-mortem interval (PMI). Additionally, we have conducted a comprehensive analysis of semi-tryptic peptides, revealing distinct consensus motifs for different organs, indicating organ-specific post-mortem protease activity. In conclusion, our findings emphasize the critical importance of considering PMI effects when designing proteomics studies, as these effects may significantly overshadow the impacts of diseases. Preferably, the samples should be taken in the operation room, especially for studies including subcellular compartmentalization or trans-organ comparison. In single-organ studies, the planning should involve careful control of PMI.
AoI‐optimal path planning for UAV‐assisted data collection with heterogeneous information aging speed
Authors: Xie Chen , Wu Binbin , Pan Zihao , Guo Daoxing , Ma Wenfeng 
Published: January 2025

AbstractThis article investigates a problem involving the collection of data from sensor nodes (SNs) with heterogeneous information aging speed (IAS) by an unmanned aerial vehicle (UAV) in a dense obstacle environment. The objective is to minimize the average age of information (AoI) of the SNs through UAV path planning. The problem is challenging due to the tight coupling of obstacle avoidance, information timeliness, and the heterogeneity of SNs. Directly solving this path planning problem is difficult, and the conventional approach involves planning the access sequence without considering obstacle avoidance and then optimizing the UAV trajectory while incorporating safety constraints. However, optimizing the trajectory for safe flight introduces changes in the flight time cost, resulting in the average AoI not reaching its minimum value. To address this, a UAV safe flight network is first established by generating trajectories using a combination of A*‐based and successive convex approximation (SCA)‐based algorithms. Subsequently, a genetic algorithm (GA)‐based method is employed and compared with the time greedy strategy. The numerical results demonstrate that the time greedy strategy, which aligns with intuitive understanding, can achieve a smaller total UAV flight time, while the proposed method effectively minimizes the average AoI of SNs.
Circularly polarized RABBITT on atomic shells with large orbital momentum
Authors: Kheifets Anatoli S 
Published: January 2025

Abstract
In light atoms, the technique of Reconstruction of Attosecond Bursts by Interference of Two-Photon Transitions (RABBITT), driven by circularly polarized radiation, enables a complete retrieval of ionization amplitudes in the XUV+IR regime, including their relative phases (Kheifets 2024 Phys. Rev. Res.
6 L012002). In this work, we extend this method to heavier atoms by conducting numerical simulations of circularly polarized RABBITT on the Kr 3d and Xe 4d atomic shells. The XUV ionization dynamics in these atoms differ markedly due to the presence of a ‘giant’ shape resonance in the

4
d
→
E
f

ionization channel of Xe, a feature absent in Kr. Nevertheless, when an IR photon is added to the XUV ionization, the results for Kr and Xe are surprisingly similar, with the ratio of absorption/emission matrix elements and their relative phases remaining close in value. Moreover, these ratios and phases show minimal variation even when the Xe atom is encapsulated within a C60 fullerene cage. In search for the Cooper-like minimum in the IR absorption amplitude ratios predicted in Ji et al (2024 J. Phys. B 57 235601), we extend our investigation to the Ce 4f shell where this minimum is indeed present.
Controllable frequency tunability in constriction-based spin Hall nano-oscillators for neuromorphic computing
Authors: TM Arunima , Fulara Himanshu 
Published: January 2025

Abstract
The capability to precisely tune auto-oscillation frequency in spin Hall nano-oscillators (SHNOs) holds great promise across diverse applications, from data communication to neuromorphic computing. This study systematically investigates the controllable frequency tunability of nano-constriction-based SHNOs across distinct operational regimes. Through the independent tuning of critical magnetodynamical parameters-effective magnetization (

μ
0

M

eff

) and magnetic damping (α)-we unveil varying impacts on frequency tunability with changes in out-of-plane (OOP) field strengths and constriction widths. At large OOP fields,

μ
0

M

eff

predominantly governs frequency tunability, yielding a current tunability of 1 GHz/mA-four times greater than observed at the lowest

μ
0

M

eff

. At low OOP fields, although we observe a remarkably high frequency-tunability of 4 GHz mA−1,

μ
0

M

eff

alters the onset of transition from a linear-like mode to a spin-wave bullet mode. In contrast, α primarily affects the threshold current with less impact on frequency tunability. Moreover, we demonstrate that M
eff-driven frequency tuning enables control over the mutual synchronization of SHNOs, mimicking synaptic-like interactions between artificial neurons. Our findings greatly extend the versatility of SHNOs for oscillator-based neuromorphic computing and provide key insights into the intricate auto-oscillation dynamics under varying OOP fields.
Role of spin–orbit coupling for the band splitting in α-Sb and α-Bi on SiC(0001)
Authors: Yaegashi Ken , Sugawara Katsuaki , Takahashi Takashi , Sato Takafumi 
Published: January 2025

Abstract
Monolayer atomic thin films of group-V elements have a high potential for application in spintronics and valleytronics because of their unique crystal structure and strong spin–orbit coupling. We fabricated Sb and Bi monolayers on a SiC(0001) substrate by the molecular-beam-epitaxy method and studied the electronic structure by angle-resolved photoemission spectroscopy (ARPES) and first-principles calculations. The fabricated Sb film shows the (√3 × √3)R30° superstructure associated with the formation of α-Sb, and exhibits a semiconducting nature with a band gap of more than 1.8 eV. Spin-resolved ARPES measurements of isostructural α-Bi revealed the in-plane spin polarization for the topmost valence band, demonstrating its Rashba-splitting nature due to the space-inversion-symmetry breaking. We discuss the origin of observed characteristic band structure and its similarity and difference between Sb and Bi.
Anomalous pumping in the non-Hermitian Rice–Mele model
Authors: Kumar Abhishek , Mazumdar Sarbajit , Mahanti S D , Saha Kush 
Published: January 2025

Abstract
We study topological charge pumping in the Rice–Mele (RM) model with irreciprocal hopping. The non-Hermiticity gives rise to interesting pumping physics, owing to the presence of skin effect and exceptional points. In the static one-dimensional (1D) RM model, we find two independent tuning knobs that can drive the topological transition, namely, non-Hermitian parameter γ and system size N. To elucidate the system-size dependency, we use a finite-size generalized Brillouin zone scheme to show that the edge modes can be distinguished from the non-hermiticity induced skin modes. Moreover, this scheme can capture the state pumping of topological edge modes as a function of γ in the static 1D RM model and it further provides insight into engineering novel gapless exceptional edge modes with the help of adiabatic drive. Furthermore, we show that the standard topological pumping due to the adiabatic and periodic variation of the model parameters survives even with finite γ. However, we observe that it depends upon the driving protocols and strength of the non-Hermiticity (γ). With increasing γ, the adiabatic pumping for non-trivial protocols is destroyed first and then re-emerges as an anomalous pumping which does not have any Hermitian counterpart. Additionally, we observe that even a trivial adiabatic protocol can give rise to pumping as opposed to the Hermitian system. This is attributed to the inherent point gap physics of non-Hermitian system which we explain by reformulating a non-Bloch topological invariant for the 1+1D RM model. This invariant explains the number of pumped charges (in each period) for all the driving protocols.
Combined feature of enhanced stability and multi-level switching observed in TiN/Ta2O5/Ag-NPs/ITO/PET structure
Authors: Hu Su , Jiang Kang’an , He Yunyang , Bao Peng , Su Nan , Zhao Xinhui , Wang Hui 
Published: January 2025

Abstract
Both stability and multi-level switching are crucial performance aspects for resistive random-access memory (RRAM), each playing a significant role in improving overall device performance. In this study, we successfully integrate these two features into a single RRAM configuration by embedding Ag-nanoparticles (Ag-NPs) into the TiN/Ta2O5/ITO structure. The device exhibits substantially lower switching voltages, a larger switching ratio, and multi-level switching phenomena compared to many other nanoparticle-embedded devices. We attribute it to the embedded Ag-NPs effectively switching the mechanism of conductive filaments and the controlled distribution of Ag-NPs facilitates the occurrence of multi-level switching. Additionally, the fabricated structure demonstrated an impressive optical transmittance of nearly 85%. Undoubtedly, this combined feature of RRAM not only enhances stability but also enables multi-level switching, thereby demonstrating an approach to fabricating versatile and practical electronic devices aimed at boosting storage capacity and speed.
Infrared photoresponse of GeSiSn p–i–n photodiodes based on quantum dots, quantum wells, pseudomorphic and relaxed layers
Authors: Timofeev V A , Skvortsov I V , Mashanov V I , Bloshkin A A , Loshkarev I D , Kirienko V V , Zalyalov T M , Lozovoy K A 
Published: January 2025

Abstract
Structural and photoelectric properties of p–i–n photodiodes based on GeSiSn/Si multiple quantum dots (QDs) both on Si and silicon-on-insulator substrates were investigated. Elastic strained state of grown films was demonstrated by x-ray diffractometry. Annealing of p–i–n structures before the mesa fabrication can improve the ideality factor of current–voltage characteristics. The lowest dark current density of p–i–n photodiodes based on QDs at the reverse bias of 1 V reaches the value of 0.8 mA cm−2. The cutoff wavelength shifts to the long-wavelength region with the Sn content increase. Maximum cutoff wavelength value is found to be 2.6 μm. Moreover, multilayer periodic structures with GeSiSn/Ge quantum wells and GeSiSn relaxed layers on Ge substrates were obtained. Reciprocal space maps were used to study the strained state of GeSiSn layers. The optimal growth parameters were determined to obtain slightly relaxed GeSiSn layers. Designed p–i–n photodiodes based on these structures demonstrated the minimal dark current density of 0.7 mA cm−2 and the cutoff wavelength of about 2 μm.
Generative adversarial networks with fully connected layers to denoise PPG signals
Authors: Avila Castro Itzel A , Oliveira Helder P , Correia Ricardo , Hayes-Gill Barrie , Morgan Stephen P , Korposh Serhiy , Gomez David , Pereira Tania 
Published: January 2025

Abstract

Objective.The detection of arterial pulsating signals at the skin periphery with Photoplethysmography (PPG) are easily distorted by motion artifacts. This work explores the alternatives to the aid of PPG reconstruction with movement sensors (accelerometer and/or gyroscope) which to date have demonstrated the best pulsating signal reconstruction. Approach. A generative adversarial network with fully connected layers is proposed for the reconstruction of distorted PPG signals. Artificial corruption was performed to the clean selected signals from the BIDMC Heart Rate dataset, processed from the larger MIMIC II waveform database to create the training, validation and testing sets. Main results. The heart rate (HR) of this dataset was further extracted to evaluate the performance of the model obtaining a mean absolute error of 1.31 bpm comparing the HR of the target and reconstructed PPG signals with HR between 70 and 115 bpm. Significance. The model architecture is effective at reconstructing noisy PPG signals regardless the length and amplitude of the corruption introduced. The performance over a range of HR (70–115 bpm), indicates a promising approach for real-time PPG signal reconstruction without the aid of acceleration or angular velocity inputs.
Characterization of a radiofrequency storage ion source using numerical simulations
Authors: Kumar Nanditha Sunil , N Vignesh , Kumar S Sunil 
Published: January 2025

Abstract
A radiofrequency ion source routinely employed for laboratory astrophysics and astrochemistry experiments designated as the storage ion source was characterized using numerical simulations. The present work focuses on optimizing the storage and extraction of ions of astrophysical relevance having the m / z range 3 − 330, which covers most of the molecular ions detected in the interstellar medium and circumstellar envelopes. The crucial parameters for the storage of ions: radiofrequency signal frequency, f

RF
and amplitude, V

RF
were optimized, and the range of radiofrequency parameters that can be used to store ions inside the source is presented. The lifetimes of ions inside the source were estimated for various radiofrequency parameters. The difference in the lifetimes of ions of different m / z was explained based on the ions’ thermalization characteristics and the source’s effective potential. The extraction of ions from the source was optimized, and a new design called the T-source was proposed to improve the extraction efficiency. We show that the T-source has better extraction efficiency than the original design, which is further enhanced by maintaining the source at a floating potential. Finally, we investigated the transmission characteristics of the extracted ions through a quadrupole ion guide, which may serve as an ion guide or a mass filter, leading to an ion storage device such as an ion trap or an ion storage ring.