bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancer-driven Shh signaling promotes glia-to-mesenchyme transition during bone repair
Authors: Shen Xin , Zhang Hang , Song Zesheng , Dong Yangjiele , Ge Xiao , Jin Shenghao , Guo Songsong , Zhang Ping , Fu Yu , Zhu Yuchi , Xiao Na , Wang Dongmiao , Cheng Jie , Xu Rongyao , Jiang Hongbing
Published: January 2025

Plp1-lineage Schwann cells (SCs) of peripheral nerve play a critical role in vascular remodeling and osteogenic differentiation during the early stage of bone healing, and the abnormal plasticity of SCs would jeopardize the bone regeneration. However, how Plp1-lineage cells respond to injury and initiate the vascularized osteogenesis remains incompletely understood. Here, by employing single-cell transcriptional profiling combined with lineage-specific tracing models, we uncover that Plp1-lineage cells undergoing injury-induced glia-to-MSCs transition contributed to osteogenesis and revascularization in the initial stage of bone injury. Importantly, our data demonstrated that the Sonic hedgehog (Shh) signaling was responsible for the transition process initiation, which was strongly activated by c-Jun/SIRT6/BAF170 complex-driven Shh enhancers. Collectively, these findings depict an injury-specific niche signal-mediated Plp1-lineage cells transition towards Gli1+ MSCs and may be instructive for approaches to promote bone regeneration during aging or other bone diseases.
ZBP1-mediated PANoptosis is a crucial lethal form in diverse keratinocyte death modalities in UVB-induced skin injury
Authors: Bi Xuechan , Li Min , Guo Yiming , Hu Mengyao , Chen Yujie , Lian Ni , Chen Sihan , Li Min , Gu Heng , Chen Xu
Published: January 2025

UVB irradiation induces diverse modalities of regulatory cell death in keratinocytes. Recently, the pattern of coexistence of pyroptosis, apoptosis, and necroptosis has been termed PANoptosis; however, whether PANoptosis occurs in keratinocytes in UVB-induced skin injury remains unclear. We observed that the key molecules of GSDMD-mediated pyroptosis, apoptosis, and necroptosis, which are N-terminal GSDMD, cleaved caspase-3/PARP, and phosphorylated MLKL, respectively, were elevated in keratinocytes of UVB-challenged mice and human skin tissue. Through keratinocyte-specific gene knockout or using corresponding inhibitors, we found that individual inhibition of GSDMD-mediated pyroptosis, caspase-3-mediated apoptosis, or MLKL-mediated necroptosis did not reduce the overall level of keratinocyte death after UVB exposure, and that the other two pathways maintained the activation. However, when the PANoptosome sensor ZBP1 was knocked out, keratinocyte death was reduced and epidermal thickening was alleviated in UVB-challenged mice. In conclusion, our study demonstrated that UVB irradiation induces ZBP1-mediated PANoptosis in keratinocytes, which is a crucial lethal form in diverse keratinocyte death modalities in UVB-induced skin injury. The above findings provide a new insight on the complexity of regulated cell death modalities in keratinocytes exposed to UV irradiation.
MAPK4 inhibits the early aberrant activation of B cells in rheumatoid arthritis by promoting the IRF4-SHIP1 signaling pathway
Authors: Huang Pei , Yang Guangli , Zhang Pingping , Zhu Yin , Guan Yaning , Sun Jian , Li Qian , An Yang , Shi Xiaoqi , Zhao Juanjuan , Liu Chaohong , He Zhixu , Chen Yan , Du Zuochen
Published: January 2025

The involvement of B lymphocytes in the pathogenesis of rheumatoid arthritis (RA) is well-established, with their early and aberrant activation being a crucial factor. However, the mechanisms underlying this abnormal activation in RA remain incompletely understood. In this study, we identified a significant reduction in MAPK4 expression in both RA patients and collagen-induced arthritis (CIA) mouse models, which correlates with disrupted B cell activation. Using MAPK4 knockout (KO) mice, we demonstrated that MAPK4 intrinsically promotes the differentiation of marginal zone (MZ) B cells. Loss of MAPK4 in KO mice enhances proximal BCR signaling and activates the PI3K-AKT-mTOR pathway, leading to heightened B cell proliferation. Notably, B cells from MAPK4 KO mice produce significantly higher levels of IL-6, a key pro-inflammatory cytokine in RA. Furthermore, MAPK4 KO mice exhibit impaired T cell-independent humoral immune responses. Mechanistically, MAPK4 inhibits the activation of the PI3K signaling pathway in B cells by activating the IRF4-SHIP1 pathway. Treatment with the MAPK4 agonist Vacquinol-1 enhances MZ B cell differentiation in WT mice and reduces IL-6 secretion in CIA mouse models. In summary, this study reveals the diverse roles of MAPK4 in regulating of B cell functions, with potential implications for developing therapeutic strategies for RA and related autoimmune diseases.
Mathematical model linking telomeres to senescence in Saccharomyces cerevisiae reveals cell lineage versus population dynamics
Authors: Rat Anaïs , Martinez Fernandez Veronica , Doumic Marie , Teixeira Maria Teresa , Xu Zhou
Published: January 2025

Telomere shortening ultimately causes replicative senescence. However, identifying the mechanisms driving replicative senescence in cell populations is challenging due to the heterogeneity of telomere lengths and the asynchrony of senescence onset. Here, we present a mathematical model of telomere shortening and replicative senescence in Saccharomyces cerevisiae which is quantitatively calibrated and validated using data of telomerase-deficient single cells. Simulations of yeast populations, where cells with varying proliferation capacities compete against each other, show that the distribution of telomere lengths of the initial population shapes population growth, especially through the distribution of cells’ shortest telomere lengths. We also quantified how factors influencing cell viability independently of telomeres can impact senescence rates. Overall, we demonstrate a temporal evolution in the composition of senescent cell populations—from a state directly linked to critically short telomeres to a state where senescence onset becomes stochastic. This population structure may promote genome instability and facilitate senescence escape.
Nonlinearity of the post-spinel transition and its expression in slabs and plumes worldwide
Authors: Dong Junjie , Fischer Rebecca A. , Stixrude Lars P. , Brennan Matthew C. , Daviau Kierstin , Suer Terry-Ann , Turner Katlyn M. , Meng Yue , Prakapenka Vitali B.
Published: January 2025

Phase transitions in the mantle control its internal dynamics and structure. The post-spinel transition marks the upper–lower mantle boundary, where ringwoodite dissociates into bridgmanite plus ferropericlase, and its Clapeyron slope regulates mantle flow across it. This interaction has previously been assumed to have no lateral spatial variations, based on the assumption of a linear post-spinel boundary in pressure and temperature. Here we present laser-heated diamond anvil cell experiments with synchrotron X-ray diffraction to better constrain this boundary, especially at higher temperatures. Combining our data with results from the literature, and using a global analysis based on machine learning, we find a pronounced nonlinearity in the post-spinel boundary, with its slope ranging from –4 MPa/K at 2100 K, to –2 MPa/K at 1950 K, and to 0 MPa/K at 1600 K. Changes in temperature over time and space can therefore cause the post-spinel transition to have variable effects on mantle convection and the movement of subducting slabs and upwelling plumes.
LDPC-cat codes for low-overhead quantum computing in 2D
Authors: Ruiz Diego , Guillaud Jérémie , Leverrier Anthony , Mirrahimi Mazyar , Vuillot Christophe
Published: January 2025

The main obstacle to large scale quantum computing are the errors present in every physical qubit realization. Correcting these errors requires a large number of additional qubits. Two main avenues to reduce this overhead are (i) low-density parity check (LDPC) codes requiring very few additional qubits to correct errors (ii) cat qubits where bit-flip errors are exponentially suppressed by design. In this work, we combine both approaches to obtain an extremely low overhead architecture. Assuming a physical phase-flip error probability ϵ ≈ 0.1% per qubit and operation, one hundred logical qubits can be implemented on a 758 cat qubit chip, with a total logical error probability per cycle and per logical qubit ϵ

L
≤ 10−8. Our architecture also features two major advantages. First, the hardware implementation of the code can be realised with short-range qubit interactions in 2D and low-weight stabilizers, under constraints similar to those of the popular surface code architecture. Second, we demonstrate how to implement a fault-tolerant universal set of logical gates with an additional layer of routing cat qubits stacked on top of the LDPC layer, while maintaining the local connectivity. Furthermore, our architecture benefits from a high capacity of parallelization for these logical gates.
Mechano-gated iontronic piezomemristor for temporal-tactile neuromorphic plasticity
Authors: Wei Xiao , Wu Zhixin , Gao Hanfei , Cao Shiqi , Meng Xue , Lan Yuqun , Su Huixue , Qin Zhenglian , Liu Hang , Du Wenxin , Wu Yuchen , Liu Mingjie , Zhao Ziguang
Published: January 2025

In bioneuronal systems, the synergistic interaction between mechanosensitive piezo channels and neuronal synapses can convert and transmit pressure signals into complex temporal plastic pulses with excitatory and inhibitory features. However, existing artificial tactile neuromorphic systems struggle to replicate the elaborate temporal plasticity observed between excitatory and inhibitory features in biological systems, which is critical for the biomimetic processing and memorizing of tactile information. Here we demonstrate a mechano-gated iontronic piezomemristor with programmable temporal-tactile plasticity. This system utilizes a bicontinuous phase-transition heterogel as a stiffness-governed iontronic mechanogate to achieve bidirectional piezoresistive signals, resulting in wide-span dynamic tactile sensing. By micro-integrating the mechanogate with an oscillatory iontronic memristor, it exhibits stiffness-induced bipolarized excitatory and inhibitory neuromorphics, thereby enabling the activation of temporal-tactile memory and learning functions (e.g., Bienenstock–Cooper–Munro and Hebbian learning rules). Owing to dynamic covalent bond network and iontronic features, reconfigurable tactile plasticity can be achieved. Importantly, bridging to bioneuronal interfaces, these systems possess the capacity to construct a biohybrid perception-actuation circuit. We anticipate that such temporal plastic piezomemristor devices for abiotic-biotic interfaces can serve as promising hardware systems for interfacing dynamic tactile behaviors into diverse neuromodulations.
Machine learning Hubbard parameters with equivariant neural networks
Authors: Uhrin Martin , Zadoks Austin , Binci Luca , Marzari Nicola , Timrov Iurii
Published: January 2025

Density-functional theory with extended Hubbard functionals (DFT + U + V) provides a robust framework to accurately describe complex materials containing transition-metal or rare-earth elements. It does so by mitigating self-interaction errors inherent to semi-local functionals which are particularly pronounced in systems with partially-filled d and f electronic states. However, achieving accuracy in this approach hinges upon the accurate determination of the on-site U and inter-site V Hubbard parameters. In practice, these are obtained either by semi-empirical tuning, requiring prior knowledge, or, more correctly, by using predictive but expensive first-principles calculations. Here, we present a machine learning model based on equivariant neural networks which uses atomic occupation matrices as descriptors, directly capturing the electronic structure, local chemical environment, and oxidation states of the system at hand. We target here the prediction of Hubbard parameters computed self-consistently with iterative linear-response calculations, as implemented in density-functional perturbation theory (DFPT), and structural relaxations. Remarkably, when trained on data from 12 materials spanning various crystal structures and compositions, our model achieves mean absolute relative errors of 3% and 5% for Hubbard U and V parameters, respectively. By circumventing computationally expensive DFT or DFPT self-consistent protocols, our model significantly expedites the prediction of Hubbard parameters with negligible computational overhead, while approaching the accuracy of DFPT. Moreover, owing to its robust transferability, the model facilitates accelerated materials discovery and design via high-throughput calculations, with relevance for various technological applications.
Encorafenib, cetuximab and chemotherapy in BRAF-mutant colorectal cancer: a randomized phase 3 trial
Authors: Kopetz Scott , Yoshino Takayuki , Van Cutsem Eric , Eng Cathy , Kim Tae Won , Wasan Harpreet Singh , Desai Jayesh , Ciardiello Fortunato , Yaeger Rona , Maughan Timothy S. , Beyzarov Elena , Zhang Xiaoxi , Ferrier Graham , Zhang Xiaosong , Tabernero Josep
Published: January 2025

Encorafenib + cetuximab (EC) is approved for previously treated BRAF V600E-mutant metastatic colorectal cancer (mCRC) based on the BEACON phase 3 study. Historically, first-line treatment of BRAF V600E-mutant mCRC with chemotherapy regimens has had limited efficacy. The phase 3 BREAKWATER study investigated EC+mFOLFOX6 versus standard of care (SOC) in patients with previously untreated BRAF V600E mCRC. The dual primary endpoint of progression-free survival is event driven; data were not mature at data cutoff. BREAKWATER met the other dual primary endpoint of objective response rate, demonstrating significant and clinically relevant improvement in objective response rate (EC+mFOLFOX6: 60.9%; SOC: 40.0%; odds ratio, 2.443; 95% confidence interval (CI): 1.403–4.253; 99.8% CI: 1.019–5.855; one-sided P = 0.0008). Median duration of response was 13.9 versus 11.1 months. At this first interim analysis of overall survival, the hazard ratio was 0.47 (95% CI: 0.318–0.691; repeated CI: 0.166–1.322). Serious adverse event rates were 37.7% versus 34.6%. The safety profiles were consistent with those known for each agent. BREAKWATER demonstrated a significantly improved response rate that was durable for first-line EC+mFOLFOX6 versus SOC in patients with BRAF V600E mCRC. ClinicalTrials.gov identifier: NCT04607421.
Genomic analysis of three medieval parchments from German monasteries
Authors: Heinrich Felix , Simianer Henner , Bölling Jörg , Röckelein Hedwig , Roos Christian , Reimer Christian , Schmitt Armin O.
Published: January 2025

In the last two decades there has been growing interest in the analysis of ancient DNA obtained from the parchment used in historic documents. The genetic insight that this data provides makes collections of historic documents an invaluable source for studying the development and spread of historical livestock populations. Additionally, the biological data may provide new information for the historical analysis that could be used to determine the provenance as well as the authenticity of these documents. In this study, we extracted DNA from three medieval parchments that were written in German monasteries in the twelfth century. The source animal of the parchments could be identified as cattle and we compared their genome sequences with those of modern populations that are part of the 1000 Bull Genomes Project. The three animals were found to carry mtDNA haplogroup T3 and show a closer genetic relationship to other historic animals than to modern breeds. We further identified 39 haplotypes and 132 SNPs variants, which are rare (

$$<0.1$$

<
0.1

) or even non-existent in modern breeds. Finally, the genetic distances between the parchment samples show a putative association with the dates when the documents were written, indicating the usefulness of genetic analysis for provenance research.
Imaging flow cytometry reveals the mechanism of equine arteritis virus entry and internalization
Authors: Kublicka Agata , Lorek Daria , Mikołajczyk-Martinez Agata , Chodaczek Grzegorz , Chwirot Aleksandra , Bażanów Barbara , Matczuk Anna Karolina
Published: January 2025

The process of viral entry into host cells is crucial for the establishment of infection and the determination of viral pathogenicity. A comprehensive understanding of entry pathways is fundamental for the development of novel therapeutic strategies. Standard techniques for investigating viral entry include confocal microscopy and flow cytometry, both of which provide complementary qualitative and quantitative data. Imaging flow cytometry, which integrates the advantages of both methodologies, offers significant potential in virological studies. In this investigation, we employed imaging flow cytometry coupled with immunostaining to monitor the entry of equine arteritis virus EAV into Vero cells via the endosomal trafficking route. Analysis provided an insight into the early infection dynamics across thousands of cells, revealing statistically significant alterations in internalization and uncoating process. Moreover, we evaluated the effectiveness of two inhibitors targeting cellular factors involved in facilitating viral entry: ammonium chloride, which disrupts endocytosis, and camostat mesylate, which inhibits the activity of serine proteases. The results demonstrated a clear distinction between effective and ineffective inhibitors. This study highlighted the potential of imaging flow cytometry to advance the study of viral entry and the evaluation of antiviral agents.
Lactiplantibacillus plantarum 22 A-3 ameliorates leaky gut in mice through its anti-inflammatory effects
Authors: Kobayashi Takashi , Kessoku Takaomi , Iwaki Michihiro , Nogami Asako , Yoneda Masato , Saito Satoru , Yamana Yoshie , Nishitani Yosuke , Kuwahara Hiroshige , Nakajima Atsushi
Published: January 2025

There are limited studies on the improvement of leaky gut with minor inflammation associated with various diseases. To explore the therapeutic potential of Lactiplantibacillus plantarum 22 A-3, a member of the Lactobacillus species, in addressing a leaky gut. Lactiplantibacillus plantarum 22 A-3 was administered to a leaky gut mice model with low dextran sulfate sodium concentrations. The Lactiplantibacillus plantarum 22 A-3-treated group exhibited amelioration of increased intestinal permeability, as indicated by lower blood fluorescein isothiocyanate-dextran levels compared with that of the control group. Furthermore, the messenger RNA expression of interleukin-10, an anti-inflammatory cytokine, was upregulated in the small intestine of Lactiplantibacillus plantarum 22 A-3-treated mice. Moreover, forkhead box P3 was upregulated in the small intestine and colon following Lactiplantibacillus plantarum 22 A-3 administration. Flow cytometry showed that forkhead box P3-positive regulatory T cells tended to increase in the small intestine and colon; however, this was not significant. Messenger RNA levels for the pro-inflammatory cytokines, interleukin-1 beta, and tumor necrosis factor-alpha showed no significant changes in the small intestine; however, their expressions significantly decreased in the colon. Blood fluorescein isothiocyanate-dextran levels showed that intestinal permeability also decreased in Lactiplantibacillus plantarum 22 A-3-dead bacteria. The bacterial component of Lactiplantibacillus plantarum 22 A-3 ameliorates increased intestinal permeability through its anti-inflammatory effect in the intestinal tract and may be a novel treatment for leaky gut.
Genetic analysis reveals the genetic diversity and zoonotic potential of Streptococcus dysgalactiae isolates from sheep
Authors: Stefańska Ilona , Kwiecień Ewelina , Didkowska Anna , Kizerwetter-Świda Magdalena , Chrobak-Chmiel Dorota , Sałamaszyńska-Guz Agnieszka , Żmuda Piotr , Anusz Krzysztof , Rzewuska Magdalena
Published: January 2025

Streptococcus dysgalactiae (S. dysgalactiae ) is a common pathogen of humans and various animals. However, the phylogenetic position of animal S. dysgalactiae isolates and their zoonotic potential remain unclear. Most molecular epidemiological studies explicate beta-hemolytic streptococci according to their MLST and M protein gene (emm) types. Although human S. dysgalactiae isolates are relatively well characterized, the data concerning animal isolates are scarce. Here, we report the molecular characteristics and antimicrobial resistance of S. dysgalactiae strains recovered from sheep and their genetic relationship with isolates from other animal hosts and humans. Overall, 11 PFGE pulsotypes, five MLST sequence types (STs), and two emm types were distinguished, with ST248 and stL1376 being the most prevalent, indicating genetic diversity among tested 17 ovine isolates. Some isolates exhibited resistance to doxycycline (59%), erythromycin (6%), ciprofloxacin (6%), and trimethoprim/sulfamethoxazole (6%), harboring various resistance determinants. Phylogenetic analysis showed that studied ovine isolates grouped together with human S. dysgalactiae isolates from the cases of zoonotic infections. Moreover, some ovine isolates shared identical STs and emm gene sequences with human non-invasive and invasive S. dysgalactiae strains. These findings suggest a possible link between human and ovine isolates and indicate the zoonotic potential of this pathogen.
Novel transcripts of EMT driving the malignant transformation of oral submucous fibrosis
Authors: Shetty Smitha Sammith , Ram Padam Kanaka Sai , Sharma Mohit , Kudva Adarsh , Patel Pratik , Radhakrishnan Raghu
Published: January 2025

Oral submucous fibrosis (OSF) is a chronic, progressive, and fibrotic condition of the oral mucosa that carries an elevated risk of malignant transformation. We aimed to identify and validate novel genes associated with the regulation of epithelial-to-mesenchymal transition (EMT) in OSF. Genes regulating EMT were identified through differential gene expression analysis, using a LogFC threshold of -1 and + 1 and a padj value < 0.05, based on data from GEO datasets and the TCGA-HNSC datasets. The curated EMT genes were correlated with functional cancer states and subjected to clustering to identify candidate genes. Integration of bioinformatics and proteomics led to the discovery of the EMT genes MMP9, SPARC, and ITGA5 as novel candidates. Comprehensive pathway and immunohistochemical analyses confirmed their roles in regulating EMT in OSF, oral squamous cell carcinoma (OSCC), and OSF-associated squamous cell carcinoma (OSFSCC). The significant roles of MMP9, SPARC, and ITGA5 in fibrosis and malignancy suggest a novel mechanism in which fibrosis-associated type 2 EMT undergoes transition to type 3 EMT, driving OSF towards malignancy.
Asymptomatic female softball pitchers have altered hip morphology and cartilage composition
Authors: Warden Stuart J. , Coburn Sally L. , Fuchs Robyn K. , Surowiec Rachel K. , Carballido-Gamio Julio , Kemp Joanne L. , Jalaie Peter K. , Hanff David F. , Palmer Antony J. R. , Fernquest Scott J. , Crossley Kay M. , Heerey Joshua J.
Published: January 2025

Few studies have explored hip morphology and cartilage composition in female athletes or the impact of asymmetric repetitive loading, such as occurs during softball pitching. The current cross-sectional study assessed bilateral bony hip morphology on computed tomography imaging in collegiate-level softball pitchers (‘Pitch1’, n = 25) and cross-country runners (‘Run’, n = 13). Magnetic resonance imaging was used to assess cartilage relaxation times in a second cohort of pitchers (‘Pitch2’, n = 10) and non-athletic controls (‘Con’, n = 4). Pitch1 had 52% greater maximum alpha angle than Run (p < 0.001) and were 21.3 (95% CI 2.4 to 192.0) times more likely to have an alpha angle ≥ 60° within at least one hip. Pitch2 had longer T2 relaxation times in the superior femoral cartilage of the drive leg (same side as the throwing arm) and stride leg than Con (all p < 0.02). The drive leg in Pitch2 had longer T1ρ and T2 relaxation times in the superior femoral cartilage compared to the stride leg (all p ≤ 0.03). Asymptomatic softball pitchers exhibit altered bony hip morphology and cartilage composition compared to cross-country runners and non-athletic controls, respectively. They also exhibit asymmetry in cartilage composition. Further studies with larger sample sizes are warranted and any potential long-term consequences of the changes in terms of symptom and osteoarthritis development requires investigation.
Shifted dominant flood drivers of an alpine glacierized catchment in the Tianshan region revealed through interpretable deep learning
Authors: Liang Wenting , Duan Weili , Chen Yaning , Fang Gonghuan , Zou Shan , Li Zhi , Qiu Zewei , Lyu Haodong
Published: January 2025

The Kumalak River, a typical alpine glacierized catchment in the Tianshan region, experiences complex flooding driven by glacier meltwater, snowmelt, and rainfall. However, the mechanisms driving these processes under climate change remain unclear. To address this, a SWAT-Glacier hydrological model and a degree–day factor model were used for snowmelt, glacier meltwater, and rainfall calculations. Two Long Short-Term Memory (LSTM) models (LSTM-SG and LSTM-DDF) were developed using these inputs, and additive decomposition and integrated gradient methods were applied to interpret flood mechanisms. Glacier meltwater was found to dominate annual maximum flood (AMF) events, while snowmelt drove annual spring maximum flood (AMFSp) events. For AMF events (1960–2018), contributions were 10.01–12.21% from snowmelt, 60.49–60.92% from glacier meltwater, and 26.86–29.50% from rainfall. For AMFSp events (1961–2018), contributions were 48.49–56.08% from snowmelt, 16.12–22.08% from glacier meltwater, and 27.79–29.42% from rainfall. These findings provide critical insights for enhancing flood prediction and optimizing water resource management.
Challenges and opportunities for statistical power and biomarker identification arising from rhythmic variation in proteomics
Authors: Spick Matt , Isherwood Cheryl M. , Gethings Lee A. , Hughes Christopher J. , Daly Matthew E. , Hassanin Hana , van der Veen Daan R. , Skene Debra J. , Johnston Jonathan D.
Published: January 2025

Time-of-day variation in the molecular profile of biofluids and tissues is a well-described phenomenon, but—especially for proteomics—is rarely considered in terms of the challenges this presents to reproducible biomarker identification. We provide a case study analysis of human circadian and ultradian rhythmicity in proteins, including in the complement and coagulation cascades and apolipoproteins, with PLG, CFAH, ZA2G and ITIH2 demonstrated as rhythmic for the first time. We also show that rhythmicity increases the risk of Type II errors due to the reduction in statistical power from increased variance, and that controlling for rhythmic time-of-day variation improves statistical power and reduces the chances of Type II errors. We recommend that best practice in proteomics study design should account for temporal variation and that time of sampling be reported as part of study metadata. These simple steps can mitigate against both false and missed discoveries, as well as improving reproducibility.
Tailoring nanomaterials towards global One Health: a promising nano-strategy against antibiotic resistance
Authors: Chen Feiran , Zhang Shuhan , Wang Xi , Wang Zhenyu
Published: January 2025

Engineering nanomaterials to combat plant-associated antibiotic resistance for global One Health.
3D medical image segmentation using the serial–parallel convolutional neural network and transformer based on cross‐window self‐attention
Authors: Yu Bin , Zhou Quan , Yuan Li , Liang Huageng , Shcherbakov Pavel , Zhang Xuming
Published: January 2025

Convolutional neural network (CNN) with the encoder–decoder structure is popular in medical image segmentation due to its excellent local feature extraction ability but it faces limitations in capturing the global feature. The transformer can extract the global information well but adapting it to small medical datasets is challenging and its computational complexity can be heavy. In this work, a serial and parallel network is proposed for the accurate 3D medical image segmentation by combining CNN and transformer and promoting feature interactions across various semantic levels. The core components of the proposed method include the cross window self‐attention based transformer (CWST) and multi‐scale local enhanced (MLE) modules. The CWST module enhances the global context understanding by partitioning 3D images into non‐overlapping windows and calculating sparse global attention between windows. The MLE module selectively fuses features by computing the voxel attention between different branch features, and uses convolution to strengthen the dense local information. The experiments on the prostate, atrium, and pancreas MR/CT image datasets consistently demonstrate the advantage of the proposed method over six popular segmentation models in both qualitative evaluation and quantitative indexes such as dice similarity coefficient, Intersection over Union, 95% Hausdorff distance and average symmetric surface distance.
A combined aperture‐coupled membrane microstrip patch antenna array
Authors: Wang Zhao‐rui , Wang Nan , Zhang Kai‐lun
Published: January 2025

A novel lightweight L‐band combined aperture‐coupled microstrip antenna has been proposed for synthetic aperture radar (SAR) applications. The proposed antenna element is composed of only two membranes. This design innovatively integrates the coupling aperture with the radiating patch, significantly reducing the number of required dielectric layers to achieve a simplified and lightweight structure. The feed line is placed on the front side to facilitate integration with the transmit/receive (T/R) module. Simulation results demonstrate that the antenna element exhibits excellent radiation pattern performance and bandwidth. A passive antenna array utilising polyimide as the dielectric material was fabricated and measured to validate its performance. This array employs a 4‐stage Wilkinson power divider network. Measurements show that S1,1 is below −15 dB in the frequency range from 1.15 to 1.49 GHz, with a maximum efficiency of 72.87%. Additionally, an phased array antenna was fabricated and tested. This array demonstrated stable radiation pattern performance over an azimuthal scan range of and an elevation scan of . This design offers a new option for antenna modules in spaceborne SAR applications.
Discontinuation of anticoagulants and occurrence of bleeding and thromboembolic events in vitamin K antagonist users with a life-limiting disease
Authors: Kempers Eva , Visser Chantal , Geijteman Eric , Goedegebuur Jamilla , Portielje Johanneke , Søgaard Mette , Ording Anne , van den Dries Carline , Abbel Denise , Geersing GJ , Aldridge Sarah , Lifford Kate , Akbari Ashley , van de Leur Sjef , Nierman Melchior , Mahé Isabelle , Mooijaart Simon , Szmit Sebastian , Edwards Michelle , Noble Simon , Klok Frederikus A. , Chen Qingui , Cannegieter Suzanne C , Kruip Marieke J.H.A.
Published: January 2025

Background: Data on risks and benefits of long-term anticoagulants in patients with a life-limiting disease are limited. This cohort study aims to describe (dis)continuation of anticoagulants and incidences of bleeding and thromboembolic events in vitamin K antagonist (VKA) users with a life-limiting disease.
Methods: Data from five Dutch anticoagulation clinics were linked to data from Statistics Netherlands and the Netherlands Cancer registry. Prevalent VKA users diagnosed with a pre-specified life-limiting disease between 01/01/2013 and 31/12/2019 were included and followed until 31/12/2019. Hospitalization data were used to identify bleeding and thromboembolic events. Cumulative incidences of anticoagulant discontinuation were calculated, accounting for death as competing risk, and event rates were determined for both anticoagulant exposed and unexposed person-years (PYs).
Results: Among 18,145 VKA users (median age 81 years, 49% females, median survival time 2.03 years), the most common life-limiting diseases were heart disease (60.0%), hip fracture (18.1%), and cancer (13.5%). One year after diagnosis, the cumulative incidence of anticoagulant discontinuation was 14.0% (95%CI: 13.5-14.6). Over 80% of patients continued anticoagulant therapy until the last month before death, with median 14 days between discontinuation and death. Event rates per 100 PYs (95%CI) were comparable during anticoagulant use and after discontinuation for bleeding 2.6 (2.4-2.8) versus 2.1 (1.5-2.8); venous thromboembolism 0.2 (0.1-0.2) versus 0.4 (0.2-0.7); and arterial thromboembolism 3.1 (2.9-3.3) versus 3.3 (2.6-4.2).
Conclusion: Most VKA users with a life-limiting disease continued anticoagulant treatment during their last phase of life, with similar rates of bleeding and thromboembolic events during use and after discontinuation.
To label or not? A choice experiment testing whether labelled green bonds matter to retail investors
Authors: Saravade Vasundhara , Weber Olaf , Vitalis Adam
Published: January 2025

Green bonds are an important sustainable finance tool that can help reorient financial flows and influence public policy in addressing climate action across the global financial markets. However, this market is still in its infancy for the retail investor segment, and it has not been sufficiently examined from a behavioural policy lens. We fill this research gap by examining whether labelling and environmental benefits framing of a green bond can influence retail investor decision-making. By employing 1105 Amazon Mechanical Turk workers across three choice scenarios, we test whether alignment of pro-environmental personal norms or having specific personal traits can have a mediating effect on their green bond preferences. Using a mix of quantitative analyses, we find that most retail investors are influenced by the presence of a ‘green label effect’. For most retail investors, we find that the presence of a green label matters more than the ‘greenness’ of a green bond or the higher financial return of a non-green bond. However, for a very small sub-set of our sample, the alignment of environmental performance-related framing with their pro-environmental personal norms, enables greater investment into enhanced performance green bonds, even at the cost of losing financial returns. Finally, personal traits like individual risk tolerance (high), or previous investment experience with investment products (bonds, stocks), gender (non-binary individuals) and those having employment experience with financial industry, are more likely to invest in a labelled green bond. Our findings have timely implications for sustainable finance public policy, as it relates to regulating the growth of such products through labelling schemes like green taxonomies as well as addressing greenwashing risks through improved regulatory oversight.
Order and disorder in solid oxygen: Neutron scattering investigations
Authors: Dunstetter F. , Duparc O. Hardouin , Plakhty V. P. , Schweizer J. , Delapalme A.
Published: January 2025

Solid oxygen exists at zero pressure in three crystallographic phases, denoted α, β, γ. Various results have been obtained by neutron scattering in the two disordered β and γ phases. Plastic γ–O2 has an Al5 structure with 8 molecules per unit cell. The molecules, located at 2a and 6c sites, exhibit two different types of disorder of molecular axes: a spherical-like disorder for the 6c molecules, and a disk-like disorder for the 6c molecules. A precise diffraction analysis on large single crystals shows that the disorder of molecular axis of the molecules can be interpreted in terms of localized forbidden orientations, or orientational holes, with a wide disorder among the other orientations. An important contribution of the translation-rotation coupling must be taken into account for the 6c molecules. Analysis of diffuse scattering by both an approximate analytical model and molecular dynamics simulation shows an important contribution to the orientational correlations between 6c-6c and 2a-6c molecules. Magnetic disorder can be investigated by neutron polarization analysis of the paramagnetic scattering. The 3D long range antiferromagnetic order of the α phase becomes a 2D short range helicoidal order in the β phase, with a very short 0.5 nm correlation range. In the γ phase, one observes, as in the liquid, a strong antiferromagnetic correlation, with a suggestion of a ID order along the linear chains of 6c molecules. In all the measured phases, the variation of the scattering intensity with scattering vector q cannot be reproduced at high q by the known magnetic form factor. This suggests the need for a better description of the π orbital and the theoretical magnetic form factor of the molecule.
Wetting phenomena in films of molecular hydrogen isotopes
Authors: Albrecht U. , Conradt R. , Herminghaus S. , Leiderer P.
Published: January 2025

We have investigated various aspects of the wetting behavior of hydrogen films (including the heavier isotopes) using surface plasmon resonance, light scattering, and photoelectron emission. Studies in the vicinity of the triple point (T3(H2)= 13.96 K) confirmed the known “triple point wettings,” and gave no indications for a prewetting transition in this range. At low temperatures (T<T3/3) the equilibrium film thickness reaches only a few monolayers. Thicker films, prepared by quench-condensation of H2 gas at 1.5 K, undergo a dewetting process during annealing: most of the film material contracts to clusters, and in between the films thin down to its equilibrium thickness. This surface diffusion process is thermally activated, with an activation energy of 23 K (in the case of H2). The dewetting kinetics have not revealed any indication for a surface-molten layer on the solid films at low temperatures, or for a superfluid component.
Approximation of static fluctuations for Hubbard’s model
Authors: Loskutov V. V. , Mironov G. I. , Nigmatullin R. R.
Published: January 2025

The application of statistical fluctuation method to Hubbard’s model is demonstrated. Expressions for anticommutator Green’s function, magnetization, and concentration are derived. The results are compared with the exact solution in the atomic limit and the exact solution in one-dimensional model for T=0.
Size-effect of Kondo scattering by Fe impurities in Cu point contacts
Authors: van der Post N. , Mettes F. , Mydosh J. A. , van Ruitenbeek J. M. , Yanson I. K.
Published: January 2025

The low temperature dV/dI(V) characteristics are investigated for point contacts of various sizes (d ≈ 2–35 nm) using a mechanically controlled breakjunction of a Kondo alloy CuFe (0.1 at. %). A size effect, being manifested in an increase in the effective Kondo temperature with decreasing contact size, is found both on voltage and magnetic field dV/dl dependences. In accordance with the prediction of the Zarand–Udvardi theory the enhancement of the Kondo temperature in the CuFe alloy appears to be quantitatively much smaller than in CuMn alloy of the same concentration. This enhancement is due to the strong fluctuations of the local electron density of states in the ultrasmall metallic contacts. The Kondo temperature of a magnetic impurity provides a local probe of these fluctuations.
Dynamics of transformation of conduction electrons into a charge-density-wave soliton at low temperatures
Authors: Kovalev A. S. , Pershin Yu. V. , Rozhavsky A. S.
Published: January 2025

The analytical model which describes the dynamics of transformation of conduction electrons into nonlinear charge-carrying excitations of CDW in quasi-one-dimensional Peierls–Fröhlich conductors is formulated and studied by the inverse scattering transformation method. The pair of self-trapped conduction electrons transform into a charged 2π-kink localized in a single conducting chain and surrounded by dipoles in neighboring chains.
Peculiarities of electron weak localization and interaction in disordered platinum films with magnetic impurities
Authors: Belevtsev B. I. , Kashirin V. Yu. , Komnik Yu. F. , Bobkov V. V.
Published: January 2025

The effects of weak localization (WL) and electron–electron interaction (EEI) in the conductivity of disordered platinum films with Cr impurities are investigated. The films are prepared by vacuum deposition. The crystal lattice disorder is enhanced by bombardment with Ar+ ions. It is found that electron spin-flip due to scattering by magnetic impurities dominates in electron phase relaxation processes in the films under investigation. The magnitude and temperature dependence of spin-spin relaxation time are determined. Magnetic impurities are also responsible for a significant contribution of the Kondo effect to the film conductivity at low temperatures (< 10 K). The obtained results permit to separate quite accurately the contributions of the WL and EEI effects to the conductivity from the contribution of the Kondo effect. It is shown that the relative contribution of the Kondo effect to resistance is suppressed upon an enhancement of film disorder. The magnitude of the Kondo correction to resistivity does not depend on the film thickness or disorder.
Multipetal anisotropic structure of the gap parameter in high-temperature superconductors as a consequence of strong anisotropy of the band spectrum
Authors: Pashitskiĭ È. A. , Pentegov V. I. , Semenov A. V.
Published: January 2025

It is shown that multipetal asymmetric structure of the anisotropic superconducting gap parameter observed by H. Ding et al. [H. Ding et al., Phys. Rev. Lett. 74, 2784 (1995)] in the plane of CuO2 layers in Bi2Sr2CaCu2O8+x single crystal can be a consequence of the superposition of two effects: hybridization of the wide and narrow 2D bands, leading to the emergence of saddle anomalies in the energy—momentum relation on one hand and the formation of a superlattice and a dielectric pseudogap along a diagonal of a primitive cell in a 2D layer on the other hand. A simple two-component model proposed for describing the gap anisotropy predicts the sign reversal for the gap parameter upon a transition from symmetric directions of the Brillouin zone to other symmetric directions, which is not connected with the d-wave type of Cooper pairing. The possibility of observation of a phase shift for Josephson currents in interference tunnel experiments on Bi2Sr2CaCu2O8+x single crystals is discussed.
Peculiarities of superconductivity in 2D metals: transition from Cooper pairing to local pairing
Authors: Loktev V. M.
Published: January 2025

An attempt is made to analyze the state-of-the-art in the description of the superconducting phase in 2D metals with an arbitrary carrier density. It is shown that a decrease in the density leads to a nontrivial equation for chemical potential μ, in particular, to the inequality μ ≠ εF including μ < 0 (εF is the Fermi energy). In this case, the region of μ ≃ 0 corresponds to a transition (crossover) from Cooper pairing (with strongly overlapping pairs) and from the description of superconductivity in terms of the BCS–Bogoliubov theory to local (nonoverlapping) pairs and their Bose–Einstein condensation. Some examples of such a crossover are discussed.
Temperature dependence of the magnetic field penetration depth in YBa2Cu3O7–δ: effect of impurity scattering
Authors: Golubov A. A. , Trunin M. R. , Zhukov A. A. , Dolgov O. V. , Shulga S. V.
Published: January 2025

Temperature dependence of the anisotropic magnetic field penetration depth of a two-band superconductor is calculated in the model of strong s-wave pairing interaction in one of the bands (S band) and induced superconductivity in the second band (N band). The results of the calculations are compared with experimental data on the (ab) plane and c axis penetration depth in YBa2Cu3O7–δ. It is shown that all recent measurements over the entire temperature range are consistent with the two-band model.
Phonon and magnon mediated d-wave superconductivity in cuprates
Authors: Sherman A. , Schreiber M.
Published: January 2025

We use the Eliashberg formalism for calculating Tc in the 2D t-J model supplemented by an interaction with fully-symmetric apex-oxygen vibrations. It is shown that in this model holes form an anomalous 2D Fermi liquid with a Fermi surface which is also two-dimensional in a certain range of hole concentrations x. This Fermi surface is a part of a large nearly flat region around the boundaries of the magnetic Brillouin zone. Extended saddle points, analogous to those observed in angle-resolved photoemission spectra, form the main part of this region. It produces a pronounced maximum in the density of states near the Fermi level. However, in spite of this favorable condition for superconductivity, created by the hole-magnon interaction, we found this interaction alone to be unable to yield high Tc. Only together with a moderate hole-phonon interaction does it lead to d-wave superconductivity at temperatures and hole concentrations observed in cuprates. High Tc are connected with a large density of states in the nearly flat region, a conformity of the two interactions for the dx2−y2 symmetry, and a high phonon frequency Ω. The obtained dependences of Tc on x and on Ω are in close agreement with observations in cuprates.
Dielectric instabilities and phase transitions in pseudospin-electron model of HTSC systems
Authors: Stasyuk I. V. , Shvaika A. M.
Published: January 2025

The possible dielectric instabilities and phase transitions in high-Tc superconductors are analyzed within the pseudospin-electron model involving Hubbard type electron correlations as well as their interaction with local anharmonic vibrational modes. The calculation of the dynamic dielectric susceptibility χ(ω,q) is performed in the generalized random phase approximation. The instabilities with respect to the polarization and/or charge fluctuations are obtained from the temperature dependences of χ(ω,q). The behavior of low-frequency modes in the vicinity of these instabilities is investigated. The case of the infinity narrow electron band is considered in details.
On possible Bose-liquid mechanism of emergence of the SC state in HTS compounds
Authors: Amelin I. I.
Published: January 2025

An analysis of the electron structure of clusters in a YBaCuO crystal by the CNDO method shows that a decrease in the Coulomb repulsion g between d-electrons of copper ions by 0.2 eV causes a rearrangement in the electron structure of ions in CuO2 planes of the type Cu2+, O2− → Cu1 + , O, O2−. The reason behind the emergence of a charge density wave (CDW) is apparently associated with the disproportionality reaction 2O1−→ O+O2−, the fulfillment of the Shubin–Vonsovskii condition, an insignificant difference between the parameters a and b of the unit cell, and the low degeneracy of orbitals of the CuO2 plane. The formation of the CDW is accompanied by a decrease in the forbidden band width to ΔE ≃0.04 eV. This value of ΔE corresponds to the state of the CuO2 plane with local pairs. The small value of the cluster gap suggests that CuO2 planes of crystals in the metal state contain CDW in the p-subsystem. Thus, electron–electron interactions ensuring high values of Tc play a certain role in the formation of the SC state in HTS compounds.
Fine structure in electron density of states, paramagnetic impurities, and anomalous isotopic effect for T
c in LSCO:Fe systems
Authors: Zhernov A. P.
Published: January 2025

A superconductor with a sharp peak in the electron density of states and paramagnetic impurities is considered. The values of the critical temperature Tc and the isotopic shift factor are analyzed as functions of the position of the Fermi level relative to the center of the peak and impurity concentration. The developed theory is used to analyze experimental data on the isotopic effect for Tc in LSCO:Fe systems.