bluuebunny/crossref_metadata_2025 huggingface dataset:
Baseline FIB‐4 May Be a Risk Factor of Recurrence After SBRT in Patients With HBV‐Related Small HCC
Authors: Zeng Zhan , Han Yifan , Li Wengang , Chen Hongyu , Lin Ning , Yu Yanyan , Xu Xiaoyuan
Published: January 2025

Aims

Exploring fibrosis index‐4 (FIB‐4)'s predictive value for HBV‐related hepatocellular carcinoma (HCC) in assessing recurrence following stereotactic body radiation therapy (SBRT) in patients with HBV‐related HCC.

Methods

HBV‐related HCC patients who underwent SBRT were retrospectively enrolled from March 2012 to March 2020. Patients were divided into recurrence and non‐recurrence groups based on the HCC recurrence situation. Baseline data were collected from all patients before treatment and at 3 and 6 months after treatment, and FIB‐4 was calculated at the corresponding time points. Risk factors were selected using Cox regression. The FIB‐4 was stratified for survival analysis.

Results

One hundred and fifty‐two patients were included. With a mean age of 53.5 years old, 94.1% of them had liver cirrhosis. The median recurrence‐free survival (RFS) time for recurrent patients was 17.5 months. The tumor response rate of SBRT was 94.8%. HCC recurrence rates at 12, 24, 36, 48, and 60 months were 19.7% (30/152), 38.2% (58/152), 48.0% (73/152), 52.0% (79/152), and 53.3% (81/152), respectively. Cox regression showed that baseline FIB‐4 (95% CI: 1.030 ~ 1.144, p = 0.002) and 3 tumor nodules (95% CI: 3.727 ~ 260.663, p = 0.002) are risk factors for HCC recurrence. Patients with a baseline FIB‐4 > 6.55 were at a higher risk of HCC recurrence than those with a baseline FIB‐4 < 6.55 (p < 0.001).

Conclusion

Baseline FIB‐4 is a risk factor for recurrence after SBRT in patients with HBV‐related HCC, and the predictive threshold for FIB‐4 is higher in patients with cirrhosis. For patients who received radiotherapy, postoperative FIB‐4 levels are elevated.
Prognostic Features and Potential for Immune Therapy in Metastatic Mismatch Repair‐Deficient Colorectal Cancer: A Retrospective Analysis of a Large Consecutive Population‐Based Patient Series
Authors: Wirta Erkki‐Ville , Elomaa Hanna , Mecklin Jukka‐Pekka , Seppälä Toni T. , Hyöty Marja , Böhm Jan , Ahtiainen Maarit , Väyrynen Juha P.
Published: January 2025

Background

Immune checkpoint inhibition therapies have provided remarkable results in numerous metastatic cancers, including mismatch repair–deficient (dMMR) colorectal cancer (CRC). To evaluate the potential for PD‐1 blockade therapy in a large population‐based cohort, we analyzed the tumor microenvironment and reviewed the clinical data and actualized treatment of all dMMR CRCs in Central Finland province between 2000 and 2015.

Material and Methods

Of 1343 CRC patients, 171 dMMR tumors were identified through immunohistochemical screening. Histological tumor parameters were evaluated from hematoxylin‐ and eosin‐stained whole‐slide samples. CD3 and CD8 immunohistochemistry were analyzed to calculate T‐cell densities in the tumor center and invasive margin, and G‐cross function values to estimate cancer cell–T‐cell co‐localization. Multiplex immunohistochemistry was used to identify CD68+PD‐L1+ and CD3+PD‐1+ immune cells and PD‐L1 expression on tumor cells.

Results

A total of 35 (20%) patients with dMMR tumors were diagnosed as having a metastatic disease. Twelve patients (34%) were fit enough to be offered oncological treatments at the onset of non‐curable metastatic disease. High proportions of necrosis and stroma were common in metastatic tumors and were associated with worse survival. Crohn's‐like reaction, T‐cell proximity score, and CD68+/PD‐L1+ on the tumor center and invasive margin were independent prognostic immune factors.

Conclusion

As dMMR CRC patients are generally older, with often significant comorbidities, only a limited portion of patients with metastatic dMMR tumors ended up in oncological treatments. Many of the metastatic tumors presented features that may impair response to PD‐1 blockade therapy.
Feeding Comfort: The Role of Humor in Online Food Complaints
Authors: Armstrong Christine , Kulczynski Alicia , Hook Margurite
Published: January 2025

This research examines the impact of tone mirroring in organizational responses to food complaints on social media. Drawing on cognitive appraisal theory, two experiments explore how mirroring—matching the tone of the complaint, whether humorous or non‐humorous—influences consumer emotions and intentions. The findings show that humorous responses to humorous complaints and non‐humorous responses to non‐humorous complaints significantly enhance psychological comfort among virtual observers (VPOs). This psychological comfort, in turn, increases purchase intentions and decreases the likelihood of negative word‐of‐mouth. However, in high‐severity service failures, humorous mirroring is ineffective, as the severity of the service failure moderates the indirect effect of mirroring on consumer outcomes via psychological comfort. By highlighting mirroring—rather than humor alone—as a critical mechanism shaped by the severity of the service failure, this study extends our understanding of the role of humor in complaint management. The results offer both theoretical contributions and practical guidance for organizations managing food complaints on social media.
Plackett‐Burman Design Combined With Response Surface Methodology to Recover Polysaccharides With Cardiovascular Protective Potential From Waste Zizania Latifolia Bract
Authors: Zheng Lixue , Chen Qianfeng , Zhou Xin , Yin Run , Yang Jingchun , Hu Zhenbiao , Shen Yingchao , Zhang Yang
Published: January 2025

Zizania latifolia is the second aquatic vegetable in China. The circular valorization of its waste bracts remains an ongoing concern. In this work, the cellulase‐microwave‐assisted extraction (CMAE) of polysaccharides from waste Z. latifolia bracts (PWZLBs) was explored. Seven parameters were selected via a single‐factor test, of which three significant parameters were screened out using the Plackett‐Burman design, followed by response surface methodology optimization. The optimal CMAE for PWZLBs were: cellulase addition of 0.5%, microwave time of 7 min, and microwave power of 425 W, resulting in a yield of 0.82 ± 0.08%. Four polysaccharide fractions (PWZLBs‐1 ∼ 4) were isolated from PWZLBs, of which PWZLBs‐1 accounted for a major proportion and exerted higher scavenging capacities on diphenyl picrylhydrazyl and hydroxyl radicals. More importantly, PWZLBs‐1 elicited anticoagulation via prolonging thrombin time and prothrombin time, exhibiting potential for cardiovascular protection. Various characterizations confirmed that PWZLBs‐1 is a heteropolysaccharide containing uronic acids and sulfates, with galactose (34.3%) as the predominant monosaccharide, and has a molecular weight of 8061 kDa. This work provides clues for the circular valorization of waste Z. latifolia bracts and offers potential opportunities for the development of new cardiovascular protective drugs.
Microwave‐Assisted Synthesis of Bis‐1,2,3‐Triazole‐Based Benzophenones, In Vitro Antimicrobial Activity, and Molecular Docking Studies
Authors: Dharavath Ravinder , Meena Ravila , Ranjan Amit , Thumma Vishnu
Published: January 2025

In this work, we have adopted an easy route to synthesize bis‐1,2,3‐triazole‐based benzophenone compounds via a 1,3‐dipolar cycloaddition reaction (Click chemistry). All the target compounds achieved better yields through the microwave‐assisted method than the conventional method. Target compound structures were confirmed on the basis of the IR, 1H NMR, 13C NMR, and HR mass analysis. Additionally, we have carried out in vitro antibacterial and antifungal activities with ciprofloxacin and fluconazole standard drugs, respectively. Compounds 5b, 5f, 5i, 5k, and 5n were antibacterial, whereas 5a, 5e, 5g, 5i, and 5k showed promising antifungal activity with respect to standard drugs. Further, a molecular docking study performed against DNA gyrase and lanosterol 14‐alpha demethylase envisioned promising binding interactions with a good docking score.
Persistent Aggressive Behaviour From Childhood to Adolescence: The Influence of Environmental Tobacco Exposure and the Protective Role of Fish Consumption
Authors: Liu Jianghong , Yang Yi , Shi Haoer , Wong Keri Ka‐Yee , Raine Adrian
Published: January 2025

Background

Understanding changes in aggressive behaviour throughout child development is crucial for identifying effective intervention strategies. This study investigates children's aggressive behaviour in a longitudinal cohort and explores the role of environmental tobacco exposure and fish consumption as potential risk and protective factors, respectively, for persistent aggression in children.

Methods

This study involved 452 children from the Chinese Jintan Cohort. Aggressive behaviour was assessed at ages 6 and 12 years using the child behaviour checklist (CBCL) and the Reactive–Proactive Aggression Questionnaire (RPQ), respectively. Information on lifestyle habits and living environment, including parental smoking, was collected via questionnaires. Linear regression was employed to investigate the association between childhood and adolescence aggressive behaviour with relevant covariates adjusted. Subsequently, we conducted interaction analyses to explore the moderating effects of parent smoking and fish consumption on the association.

Results

We identified no significant association between childhood and adolescent aggression in the entire sample. Interaction analysis revealed environmental tobacco exposure as a moderator for the association. Specifically, persistent reactive and total aggression across development was only observed among those with environmental tobacco exposure (reactive: β = 0.549, p = 0.020; total: β = 0.654, p = 0.035). Furthermore, within the parent smoking subgroup, freshwater fish consumption at the age of 12 showed a marginally significant interaction with childhood aggression (reactive: p = 0.061; total: p = 0.095). A significant longitudinal association for aggression was found only among those consuming fish less frequently at the age of 12 years (reactive: β = 0.927, p = 0.002; total: β = 1.082, p = 0.006).

Conclusion

Our findings suggest exposure to environmental tobacco as a contributing factor to the lasting presence of aggressive behaviour during children's development, whereas freshwater fish consumption shows potential protective effects.
The Positive Effect of Psychotherapy in the Treatment of an Erosive Oral and Dermal Lichen Planus Case
Authors: Noori Zana Fuad , Mahmood Mohammed Khalid , Raof Pinar Yaseen , Kurda Handren Ameer , Qadir Balen Hamid , Abdulrahman Didar Anwar , Abdulghafor Mohammed Aso , Fatih Mohammed Taib , Hama Noori Basoz Khalid
Published: January 2025

Lichen planus (LP) is an autoimmune disease that may affect the oral cavity and the skin, and it has the potential to change to malignancy. In this paper we report a LP case in a 42‐year‐old male patient in which anxiety and depression were apparently the only possible risk factors of LP. Due to this apparent comorbidity and the risk of not responding well to conventional medication (topical and systemic corticosteroids) or the risk of relapse in the case of ongoing stress, we decided to integrate psychotherapy (without psychotropic drugs) as an adjunct into the management strategy. Psychotherapy sessions, reassuring the patient and stress alleviation, proved to be a very useful alongside the standard corticosteroid medication.
Pincer–Ruthenium Catalyzed Selective α‐Alkylation of Nitriles
Authors: Vikas  , Pasha Farhan Ahmad , Kumar Akshai
Published: January 2025

The catalytic α‐alkylation of benzyl nitriles with benzyl alcohols has been investigated with NNN pincer–ruthenium (Ru) complexes based on bis(imino)pyridine and 2,6‐bis(benzimidazole‐2‐yl)pyridine ligands. The complex [Cy2NNN(RuCl2(PPh3)] was found to be the most efficient in comparison to other considered catalysts, leading to a 99% yield of α‐alkylated nitrile with 100% selectivity in the presence of 3 mol% KOtBu in 1 mL of toluene at 140 °C within 2 h of reaction. While the release of PPh3 appears to be pivotal, mercury drop experiments point to the well‐defined molecular nature of the pincer–Ru catalyst. The reaction demonstrates first‐order dependence of rate on the concentration of [Cy2NNN(RuCl2(PPh3)], KOtBu, benzyl alcohol, and benzyl nitrile. DFT calculations indicate that the formation of α‐alkylated nitrile via the alcoholysis path with a barrier of 28.7 kcal/mol is the rate‐determining step (RDS) owing to equilibrium‐driven reasons despite the hydrogenolysis path being kinetically comparable (ΔG140‡ = 29.0 kcal/mol). These barriers are in good agreement with the experimentally determined barrier of 29.6 kcal/mol.
Artificial and Algorithmic Screening of Infrared Spectral Feature Bands of Gastrodia elata to Achieve Rapid Identification of Its Species
Authors: Liu Shuai , Liu Honggao , Li Jieqing , Wang Yuanzhong
Published: January 2025

Gastrodia elata is a traditional Chinese medicine with medicinal and edible values. In this paper, two kinds of datasets were acquired: partial spectra (artificially obtained peak segment spectra) and full spectra (4000–400 cm−1). Competitive adaptive reweighted sampling algorithm (CARS) and successive projection algorithm (SPA) were utilized to extract the characteristic variables of the two datasets, and Partial Least Squares Discriminant Analysis (PLS‐DA) models, Support Vector Machines (SVM) models, Random Forests (RF) models, and Residual convolutional neural networks (ResNet) were established. It was found that among the PLS‐DA models whole‐MSC‐CARS‐PLS‐DA was optimal, with a Root Mean Square Error of Prediction (RMSEP) of 0.0658; among the SVM models Partial‐Standard Normal Variable (SNV‐SPA‐SVM was the best, with a kernel parameter of 0.1768 and the lowest number of support vectors; among the RF models Partial‐SNV‐RF is optimal, but not as effective as the first two models. The loss value of the ResNet model built based on effective information is 0.001, and the model building time is short and directly uses the original data. Therefore, the ResNet model based on feature bands is the most suitable for practical application compared with other models.
Synthesis of α,β‐Unsaturated Carbonyl Compounds via Cu/TEMPO/O2 Aerobic Catalytic System
Authors: Wang Yao , Du Zhi‐Hong , Bo Chunbo , Li Min , Chen Fei , Liu Ning
Published: January 2025

An N,N,N‐type Cu(II) complex‐catalyzed desaturation method for converting alcohols, ketones, lactones, and lactams to their α,β‐unsaturated carbonyl compounds is reported. The dehydrogenation reaction can be conducted with a green terminal oxidant O2 without requiring strong acid/base or stoichiometric oxidants. The Cu(II) complex/TEMPO/O2 system uses a non‐noble catalyst, and a green terminal oxidant as well as demonstrates high activity and functional group tolerance. Notably, H2O is the byproduct produced and overoxidation is not observed during the reaction process. The proposed mechanism was investigated via high‐resolution mass spectrometry (HRMS), in situ FT‐IR spectrometry, and GC analysis, and the formation of intermediates of α,β‐unsaturated carbonyl compounds from the aerobic dehydrogenation of α,β‐saturated counterparts was observed.
A Non‐Volatile Pro‐Dicamba Herbicide Inspired by Meclofenoxate
Authors: Haywood Joel , Breese Karen J. , Jordi Muria‐Gonzalez M. , Bernath‐Levin Kalia , Waters Mark , Stubbs Keith A. , Mylne Joshua S.
Published: January 2025

Dicamba is a popular herbicide with rising use but is also notorious for volatility drift. Inspired by meclofenoxate, which we show to be highly herbicidal, we developed a derivative of dicamba with an ester‐bond to 2‐dimethylaminoethanol. It remained herbicidal but is non‐volatile, entering plants intact and hydrolyzing inside leaves to dicamba and 2‐dimethylaminoethanol. This pro‐dicamba is compatible with the relatively novel dicamba monooxygenase tolerance technology, suggesting pro‐dicamba might be a suitable, non‐volatile replacement for dicamba.
Intermolecular 1,2‐Difunctionalization of Nitriles via Redox Gold Catalysis: Synthesis of Benzoxazoles and Benzimidazoles
Authors: Xu Chengzhi , Xu Zhenyan , Chen Yifeng , Chen Ming , Liu Yuanhong
Published: January 2025

The unprecedent gold‐catalyzed intermolecular 1,2‐difunctionalization of nitriles with o‐iodophenols or o‐iodoanilines via Au(I)/Au(III) redox catalysis has been developed, providing an expedient route to the synthesis of benzoxazoles or benzimidazoles with broad substrate scope and high functional compatibility. Mechanistic investigation reveals that the Au(III)‐Ar species generated via oxidative addition of o‐iodophenol to MeDalphosAu+, serves as a key intermediate. Particularly, this annulation is initiated by oxidative addition, rather than the nucleophilic attack of the phenol moiety in o‐iodophenol towards the nitrile. The method was also applied to the synthesis of poly aza‐heterocycles via a cascade Au(I)/Au(III) and Au(I) catalysis relay.
Impact of Standardized Heart Failure Management Center Construction on the Management of Patients With Chronic Heart Failure
Authors: Guo Xiaoxia , Jing Lele , Zhai Changlin , Shen Liang , Hu Huilin
Published: January 2025

Background

Heart failure is extremely harmful to human health and social economics. The purpose of standardized heart failure management center (SHFMC) is to correct the non‐standardization of heart failure treatment.

Hypothesis

SHFMC has a positive impact on the management and prognosis of patients with chronic heart failure (CHF).

Methods

The SHFMC database of Jiaxing First Hospital was retrospectively analyzed. Two hundred sixty‐three patients with CHF who were hospitalized in the cardiovascular medicine department of Jiaxing First Hospital in Zhejiang Province from January 2020 to December 2020 were identified as study subjects. The SHFMC opening day, July 1, 2020, was used as the dividing line around which the patients were divided into Group A (before the completion of SHFMC, n = 137) and Group B (after, n = 126). The baseline data, treatment standardization, long‐term efficacy, 1‐year all‐cause mortality, and readmission rate of the two groups were compared.

Results

The use of angiotensin receptor enkephalinase inhibitors (ARNIs), β‐blockers (β‐Bs), and sodium‐glucose cotransport protein 2 inhibitors (SGLT2is) increased significantly, and the long‐term outcome, readmission rate, and 1‐year all‐cause mortality of patients improved in group B.

Conclusions

The construction of SHFMC has been associated with consistent improvements in the standardization of CHF treatment, long‐term patient outcomes, 1‐year cumulative survival rates, and readmission rates.
Detecting Rising Wildfire Risks for South East England
Authors: Thompson Vikki , Mitchell Dann , Melia Nathanael , Bloomfield Hannah , Dunstone Nick , Kay Gillian
Published: January 2025

In July 2022 southeast England experienced a record breaking heatwave and unprecedented wildfires in urban areas. We investigate fire weather trends since 1960 in southeast England using a large ensemble of initialised climate models. Record smashing temperatures coincided with widespread fires in London, and we find that while wildfire risk was high, it was not record breaking. We show that between the 1960s and 2010s annual maximum daily fire weather has increased. The proportion of summertime days with high and very high fire risk has increased—while medium and low risk days have become less common. These findings show the need to mitigate against the increasing risk of wildfire caused by climate change.
Predictive Methods and Probabilistic Mapping of Subcortical Brain Components in Fossil Carnivora
Authors: Baer Emily , Nguyen Phuoc D. , Lilly Stefan , Song Jiyoon , Yee Mathew , Matz Olivia , Sahasrabudhe Rachna , Hall Douglas R. , La Susan , Merritt Brandon J. , Mahesh Pallavi , Eliacin Christelle , Bitterman Kathleen , Oddes Demi , Bertelsen Mads F. , Tang Cheuk Y. , Cook Peter F. , Mars Rogier B. , Hof Patrick R. , Dunn Rachel , Manger Paul R. , Sherwood Chet C. , Spocter Muhammad A.
Published: January 2025

Paleoneurology reconstructs the evolutionary history of nervous systems through direct observations from the fossil record and comparative data from extant species. Although this approach can provide direct evidence of phylogenetic links among species, it is constrained by the availability and quality of data that can be gleaned from the fossil record. Here, we sought to translate brain component relationships in a sample of extant Carnivora to make inferences about brain structure in fossil species. Using high resolution magnetic resonance imaging on extant canids and felids and 3D laser scanning on fossil Carnivora, spanning some 40 million years of evolution, we derived measurements for select brain components. From these primary data, predictive equations of cortical (gray matter mass, cortical thickness, and gyrification index) and subcortical structures (caudate nucleus, putamen, and external globus pallidus mass) were used to derive estimates for select fossil Carnivora. We found that regression equations based on both extant and simulation samples provided moderate to high predictability of subcortical masses for fossil Carnivora. We also found that using exploratory probabilistic mapping of subcortical structures in extant Carnivora, a reasonable prediction could be made of the 3D subcortical morphospace of fossil endocasts. These results identify allometric departures and establish adult species ranges in brain component size for fossil species. The integrative approach taken in this study may serve as a model to promote further dialog between neurobiologists working on extant Carnivora models and paleoneurologists describing the nervous system of fossils from this understudied group of mammals.
Deciphering the Evolution of Current Distribution in Hybrid Silver Vanadium Oxide / Carbon Monofluoride Cathodes within Lithium Primary Batteries
Authors: Arnot David J. , Vila Mallory N. , Hill Ryan C. , Kingan Arun , Zhong Zhong , Vo Nghia T. , Drakopoulos Michael , Takeuchi Esther S. , Marschilok Amy C. , Takeuchi Kenneth J.
Published: January 2025

For batteries to function effectively all active material must be accessible requiring both electron and ion transport to each particle. A common approach to generating the needed conductive network is the addition of carbon to create a composite electrode. An alternative approach is the electrochemically induced formation of conductive reaction products where the electrochemically generated materials are in intimate contact with the active material contributing to effective connection of each active particle. This study probes silver vanadium oxide (Ag2V4O11, SVO), carbon monofluoride (CFx), and hybrid SVO/CFx electrodes in lithium batteries. Ex situ XRD identifies Ag0 as a reduction product from SVO and LiF from CFx that can be followed as a function of depth‐of‐discharge (DOD). Spatially‐resolved operando energy dispersive x‐ray diffraction reveals that the presence of SVO alleviates reaction heterogeneity in the electrodes which are electron transfer limited in the absence of sufficient Ag0. Synchrotron X‐ray tomography on discharged cathodes reveals the distribution of silver particles where the particles are more closely spaced near the current collector indicating multiple nucleation sites for their formation. Finally, operando isothermal microcalorimetry is used to determine the heat dissipation of the parent and hybrid battery types. Using material enthalpy potentials, we determine the current distribution between the two active materials for the discharging hybrid cathode adding further insight to the diffraction analysis. Taken together, these results provide a comprehensive understanding of hybrid SVO/CFx cathodes and give guidance on optimal compositions that balance power and energy density considerations.
A Simple Protocol for Visualization of RNA–Protein Complexes by Atomic Force Microscopy
Authors: Tripepi Andrea , Shakoor Huma , Klapetek Petr
Published: January 2025

Atomic force microscopy (AFM) has recently received increasing interest in molecular biology. This technique allows quick and reliable detection of biomolecules. However, studying RNA–protein complexes using AFM poses significant challenges. Here, we describe a simple and reliable method to visualize positively charged proteins bound to RNA that does not require metallic cations. This method allowed us to effectively detect and visualize Staufen–RNA complexes by height or logarithmic stiffness. The study of the mechanical properties is particularly important in the case of protein‐coated RNA complexes, where RNA cannot be detected by height channel. In any case, it is necessary to compare AFM data with the data derived from other techniques like nuclear magnetic resonance, X‐ray crystallography, cryogenic electron microscopy, and small‐angle X‐ray scattering. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC.

Basic Protocol: Preparation and visualization of RNA–protein complex
Aligning Investment With Impact: Exploring Social Impact Bonds in Emerging Markets for Sustainable Development
Authors: Velez‐Valencia Cristina , Herrera‐Cano Carolina , Gonzalez‐Perez Maria Alejandra , Alvarez Pilar , Vergara Garavito Judith
Published: January 2025

This article explores investor motivations and the contribution to sustainable development goals of social impact bonds (SIBs) in emerging markets. Through qualitative analysis of in‐depth stakeholder interviews, we identified that SIB investors are primarily driven by organisational learning, social impact generation and strategic alignment with core business objectives rather than financial returns. Our findings reveal that SIBs offer a pathway for achieving corporate social responsibility (CSR) and environmental, social and governance (ESG) objectives by blending private investment with public goals. Drawing on signalling theory, we exhibit how SIBs serve as credible signals of institutional commitment to sustainable development. The study contributes to the literature by identifying the role of SIBs in fostering public–private partnerships via signalling and investors' approaches to environmental and social challenges in emerging economies. This research expands our understanding of SIBs' potential within the CSR and ESG framework and proposes practical implications for businesses seeking to enhance their sustainability impact.
LcProt: Proteomics‐based identification of plasma biomarkers for lung cancer multievent, a multicentre study
Authors: Liang Hengrui , Wang Runchen , Cheng Ran , Ye Zhiming , Zhao Na , Zhao Xiaohong , Huang Ying , Jiang Zhanpeng , Li Wangzhong , Zheng Jianqi , Deng Hongsheng , Jiang Yu , Lin Yuechun , Yan Yun , Song Lei , Li Jie , Xu Xin , Liang Wenhua , Liu Jun , He Jianxing
Published: January 2025

Background

Plasma protein has gained prominence in the non‐invasive predicting of lung cancer. We utilised Zeolite Zotero NaY‐based plasma proteomics to investigate its potential for multiple event predicting, including lung cancer diagnosis (task #1), lymph node metastasis detection (task #2) and tumour‒node‒metastasis (TNM) staging (task #3).

Methods

A total of 4703 plasma proteins were quantified from 241 participants based on a prospective cohort of 2757 participants. An additional 46 participants from external prospective cohort of 735 participants were used for validation. Feature selection was performed using differential expressed protein analysis, area under curve (AUC) evaluation and least absolute shrinkage and selection operator (LASSO) regression. Random forest was used for multitask model construction based on the key proteins. Feature importance was interpreted using Shapley additive explanations (SHAP) algorithm.

Results

For task #1, 10 proteins panel showed an AUC of .87 (.77‒.97) in the external validation. After integrating clinical factors, a significant increase diagnostic accuracy was observed with AUC of .91 (.85‒.98). For task #2, nine proteins panel achieved an AUC of .88 (.80‒.96), integration model showed an increase diagnostic accuracy with AUC of .90 (.85‒.97). For task #3, 10 proteins panel showed an AUC of .88 (.74‒.96) for stage I, .92 (.84‒.97) for stage II, .88 (.76‒.96) for stage III and .99 (.98‒.99) for stage IV in the integration model.

Conclusions

This study comprehensively profiled the NaY‐based plasma proteome biomarker, laying the foundation for a high‐performance blood test for predicting multiple events in lung cancer.

Key points

Our study developed an innovative nanomaterial, Zeolite NaY, which addressed the masking effect and improved the depth of the proteome.

The performance of NaY‐based plasma proteomics as a preclinical diagnostic tool was validated through both internal and external cohort.

Furthermore, we explored the different patterns of plasma protein changes during the progression of lung cancer and used the explanations method to elucidate the roles of proteins in the multitask predictive model.
Immunoregulatory programs in anti‐N‐methyl‐D‐aspartate receptor encephalitis identified by single‐cell multi‐omics analysis
Authors: Li Xinhui , Xu Yicong , Zhang Weixing , Chen Zihao , Peng Dongjie , Ren Wenxu , Tang Zhongjie , Li Huilu , Xu Jin , Shu Yaqing
Published: January 2025

Background

Anti‐N‐methyl‐D‐aspartate receptor encephalitis (anti‐NMDARE) is a prevalent type of autoimmune encephalitis caused by antibodies targeting the NMDAR's GluN1 subunit. While significant progress has been made in elucidating the pathophysiology of autoimmune diseases, the immunological mechanisms underlying anti‐NMDARE remain elusive. This study aimed to characterize immune cell interactions and dysregulation in anti‐NMDARE by leveraging single‐cell multi‐omics sequencing technologies.

Methods

Peripheral blood mononuclear cells (PBMCs) from patients in the acute phase of anti‐NMDARE and healthy controls were sequenced using single‐cell joint profiling of transcriptome and chromatin accessibility. Differential gene expression analysis, transcription factor activity profiling, and cell‐cell communication modeling were performed to elucidate the immune mechanisms underlying the disease. In parallel, single‐cell B cell receptor sequencing (scBCR‐seq) and repertoire analysis were conducted to assess antigen‐driven clonal expansion within the B cell population.

Results

The study revealed a significant clonal expansion of B cells, particularly plasma cells, in anti‐NMDARE patients. The novel finding of type I interferon (IFN‐I) pathway activation suggests a regulatory mechanism that may drive this expansion and enhance antibody secretion. Additionally, activation of Toll‐like receptor 2 (TLR2) in myeloid cells was noted, which may connect to tumor necrosis factor‐alpha (TNF‐α) secretion. This cytokine may contribute to the activation of B and T cells, thereby perpetuating immune dysregulation.

Conclusions

This study presents a comprehensive single‐cell multi‐omics characterization of immune dysregulation in anti‐NMDARE, highlighting the expansion of B cell and the activation of the IFN‐I and TLR2 pathways. These findings provide deeper insights into the molecular mechanism driving the pathogenesis of anti‐NMDARE and offer promising targets for future therapeutic intervention.

Key points

Significant B cell clonal expansion, particularly in plasma cells, driven by antigen recognition.

IFN‐I pathway activation in plasma cells boosts their antibody production and potentially exacerbates immune dysregulation.

TLR2 pathway activation in myeloid cells contributes to TNF‐α secretion and could influence adaptive immune responses.
Transmit Antenna Selection for Full‐Duplex Relay Millimeter‐Wave Communications Employing Rate‐Splitting Multiple Access
Authors: Hung Dinh Cong , Nghia Pham Xuan , Thi Thanh Huyen Le , Tan Tran Dinh , Cao Nguyen Ba
Published: January 2025

This article suggests using rate‐splitting multiple access (RSMA) and transmit antenna selection (TAS) within a full‐duplex relay (FDR) system that operates at high millimeter‐wave (MW) frequencies. We perform a mathematical analysis to derive closed‐form formulas for the outage probabilities (OPs) and throughputs for two users in the proposed RSMA‐MW system with TAS, taking into account the effects of residual self‐interference (RSI) at the FDR. Additionally, we consider practical system and channel parameters in our analysis. The numerical results indicate that the OPs in the RSMA‐MW system are significantly lower than those in a conventional nonorthogonal multiple access (NOMA)‐MW system. Importantly, high MW frequencies have a considerable impact on the OPs and throughputs of the RSMA‐MW system. In this context, using multiple antennas at the base station with TAS can greatly enhance the performance of the RSMA‐MW system. Furthermore, we thoroughly assess the effects of RSI caused by FDR, the distances between transmitters and receivers, transmit power, common and private rates, power allocation coefficients, and frequencies. Based on the observed behaviors of the RSMA‐MW system, several strategies are proposed to reduce OPs and increase throughputs. Finally, Monte Carlo simulations are performed to validate the derived formulas.
Sparse Code Multiple Access With Time Spreading and Repetitive Transmissions
Authors: Ülgen Oğuz , Kagan Tufekci Tolga , Sadi Yalcin , Erkucuk Serhat , Anpalagan Alagan , Baykaş Tunçer
Published: January 2025

For the next‐generation communication systems, to improve spectral efficiency and increase the data rate, new multiple access techniques have been investigated. Orthogonal multiple access techniques are widely used in traditional communication systems while nonorthogonal multiple access (NOMA), proposed in 5G, has been a promising technology for satisfying the demand for future wireless communication networks. Sparse code multiple access (SCMA) is a code‐domain NOMA method that provides diversity gain with signal constellation coding. However, to increase the performance of SCMA, there are only limited works provided in the literature in terms of codebook design and receiver design. In this paper, a new multiple‐access model is proposed by applying various diversity techniques for downlink SCMA. The performance of the proposed model is evaluated with both computer simulations and theoretical analysis. Results show that the proposed model provides a 1.6 dB gain in terms of the bit error rate (BER) under the Rayleigh fading channel.
Serous Cystadenoma of the Pancreas: An Easily Missed Cytological Diagnosis and Clues to Diagnosis
Authors: Cuber Alicia , Chopra Shefali
Published: January 2025

Serous cystadenoma (SCA) of the pancreas is a benign nonmucinous cystic pancreatic neoplasm and the second most common type of pancreatic cystic neoplasm. Conservative management is advocated in asymptomatic cases as they have indolent clinical behavior and risk for postoperative morbidity, making an exact diagnosis essential. Morphologically, serous cystadenoma has a prominent subepithelial capillary meshwork causing the aspirate to be paucicellular and nondiagnostic. Therefore, cytologic diagnosis can be challenging, resulting in repeat aspirations or even unnecessary surgical resections. Since this is a diagnosis that is often overlooked, herein we offer a concise review of SCA along with characteristic radiology findings, diagnostic criteria including ancillary studies and possible differential considerations.
Advances in precise cell manipulation
Authors: Ma Yuan , Liang Zhenwei , Chen Yiqing , Wang Jiadao
Published: January 2025

Research on cells and organ‐like tissues is critical in the fields of molecular biology, genetic analysis, proteomics analysis, tissue engineering, and others. In recent years, advancements in precise cell manipulation technologies have made precise positioning and batch processing of cells feasible. Various methods are used for cell recognition, positioning, manipulation, and assembly, often introducing external fields such as electric, magnetic, acoustic, or optical fields into the liquid environment to interact with cells, applying forces to induce cell movement and rearrangement. Alternatively, three‐dimensional (3D) bioprinting technology is employed for precise cell positioning and assembly. This review will comprehensively assess the status, principles, advantages, disadvantages, and prospects of these precise cell manipulation technologies, covering single‐cell manipulation, multicellular assembly, and biological 3D printing techniques.
Linking Functional Traits To Trophic Roles In Scavenger Assemblages
Authors: Marie Montenegro Violeta , Mateo‐Tomás Patricia , Schneider Jessica , Dent Daisy H. , Crowther Tom , Bello Carolina
Published: January 2025

Scavenging is a widespread feeding strategy involving a diversity of taxa from different trophic levels, from apex predators to obligate scavengers. Scavenger species play a crucial role in ecosystem functioning by removing carcasses, recycling nutrients and preventing disease spread. Understanding the trophic roles of scavenger species can help identify specialized species with unique roles and species that may be more vulnerable to ecological changes. To identify species with specialized roles, we studied three scavenger networks (one in north temperate Spain and two in central‐south Mediterranean Spain) that comprised 25 scavenger species (65% birds and 35% mammals), consuming carcasses of four wild ungulate species. We characterized the trophic role of a species by combining four species‐level network metrics (normalized degree, specialization, closeness, and betweenness centrality) into a single centrality metric, quantifying how scavenger species interact with carcass species within their ecological network. Higher centrality indicates the species feeds on a greater variety of carcasses and may contribute more to carrion consumption than species with lower centrality, which have more peripheral and specialized roles. The griffon vulture (Gyps fulvus) and the azure‐winged magpie (Cyanopica cyanus) had the highest centrality. In contrast, the red kite (Milvus milvus) in the northern site had the lowest centrality, and the Egyptian vulture (Neophron percnopterus) was among the most peripheral species for all three networks. In general, scavengers with large home ranges and nocturnal or crepuscular activity patterns tended to have more central roles, whereas species that forage silently tended to have more peripheral roles. Changes in species' centrality between sites and the high centrality of species with large home ranges suggest that management strategies in one location can have implications that extend beyond, highlighting the need to implement coordinated transboundary protection efforts to ensure the resilience and functionality of scavenger networks and derived ecosystem services.
Uncovering Diversity within the Glomeromycota: Novel Clades, Family Distributions, and Land Use Sensitivity
Authors: Delavaux Camille S. , Aellen Alexis , Stürmer Sidney L. , Primieri Silmar , Schütte Ursel M. E. , Drown Devin M. , Ramos Robert J. , Crowther Thomas W. , Bever James D.
Published: January 2025

Arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are essential to plant community diversity and ecosystem functioning. However, increasing human land use represents a major threat to native AMF globally. Characterizing the loss of AMF diversity remains challenging because many taxa are undescribed, resulting in poor documentation of their biogeography and family‐level disturbance sensitivity. We survey sites representing native and human‐altered ecosystems across the American continents—in Alaska, Kansas, and Brazil—to shed light on these gaps. Using a recently developed pipeline for phylogenetic placement of eDNA, we find evidence for three putative novel clades within the Glomeromycota, sister to Entrophosporaceae, Glomeraceae, and Archaeosporaceae, with evidence for geographic structuring. We further find that taxa in the Diversisporaceae, Glomeraceae, and Entrophosporaceae relatively high families are overrepresented and more diverse in temperate samples. By contrast, the diversity of taxa that cannot be placed into a family is higher in tropical samples, suggesting that tropical sites harbor relatively high undescribed AMF diversity. Moreover, we find evidence that Entrophosporaceae is more tolerant, while Glomeraceae is more sensitive to disturbance. These results underscore the vast undescribed diversity of AMF while highlighting a way forward to systematically improve our understanding of AMF biogeography and response to human disturbance.
How Does Landscape Structure Affect Dung Beetle Assemblages in Amazon Cities?
Authors: Mesquita Vanessa Pontes , Bernardino Glenda Vanessa dos Santos , Bobrowiec Paulo Estefano Dineli , Salomão Renato Portela , Cornelius Cintia
Published: January 2025

The growth of cities is one of the main direct and indirect factors responsible for the loss of native vegetation cover. Urbanization directly affects the biological communities inhabiting forest remnants inserted in cities, compromising the maintenance of urban and natural ecosystems. By understanding the effects of landscape transformation due to urbanization, we can have insights regarding the distribution of land uses that allow a proper maintenance of the urban ecosystems. This work assessed the effects of landscape structure variables (forest cover, agricultural area, edge density, and number of forest patches) on dung beetle assemblages and functional groups (i.e., diet and resource removal strategy) sampled in 38 sites located along an urban–rural gradient of six cities belonging to the metropolitan area of Manaus in Central Amazonia. Losses of forest cover were the most determining factor, negatively affecting species richness, abundance, and body size. The increases in agriculture cover negatively affected dung beetle abundance, while edge density positively affected their abundance. The number of forest patches positively affected dung beetle abundances—except for dweller species—and negatively affected the body size of diet‐generalist species. These results demonstrate that changes in ecological diversity caused by urbanization are driven mostly by forest cover loss, although forest configuration is important for dung beetle abundance. This study contributes to the understanding of how changes in the amount and distribution of forest cover in tropical cities affect the taxonomic diversity of dung beetle assemblages.
Gyrfalcon Prey Abundance and Their Habitat Associations in a Changing Arctic
Authors: Gustafson Michaela , McCabe Jennifer D. , Rolek Brian W. , Booms Travis L. , Henderson Michael T. , Dunn Leah , Anderson David L. , Cruz Jennyffer
Published: January 2025

Arctic habitats are changing rapidly and altering trophic webs and ecosystem functioning. Understanding how species' abundances and distributions differ among Arctic habitats is important in predicting future species shifts and trophic‐web consequences. We aimed to determine the habitat–abundance relationships for three small herbivores on the Seward Peninsula of Alaska, USA by fitting data from 983 point counts (collected during 2019, 2021, and 2022) with N‐mixture models that account for imperfect detection. These herbivore species, Willow Ptarmigan (Lagopus lagopus), Rock Ptarmigan (L. muta), and Arctic ground squirrels (Urocitellus parryii), are fundamental to tundra food webs, and primary prey for Arctic raptors including Gyrfalcons (Falco rusticolus). Second, we aimed to map herbivore densities within Gyrfalcon breeding territories. Third, we aimed to evaluate whether Gyrfalcons were more likely to occupy territories with higher prey densities using a multi‐season occupancy model coupled with occupancy observations from helicopter surveys conducted during 2016–2022 at 97 Gyrfalcon territories. We found that male Willow Ptarmigan were more abundant in areas with greater cover of tundra, tall shrubs, and tussock tundra. Conversely, male Rock Ptarmigan were more abundant in areas with greater cover of sparse vegetation and tundra. Arctic ground squirrels were more abundant at higher elevations with greater cover of sparse vegetation and low shrubs. Willow Ptarmigan were widespread within Gyrfalcon breeding territories, whereas Rock Ptarmigan and Arctic ground squirrels had patchier distributions with few areas of high abundance. Lastly, Gyrfalcons were more likely to occupy territories with higher densities of Willow Ptarmigan and Arctic ground squirrels. As the Artic continues to warm, Rock Ptarmigan and Arctic ground squirrels may be vulnerable to ongoing shrub encroachment, whereas Willow Ptarmigan may benefit. By tying abundances of three prey to Gyrfalcon occupancy, our results contribute to understanding potential impacts on higher levels of this Arctic trophic web.
Development of SNP for Sebastes Species Identification With Special Focus on the Cryptic Species Complex of Sebastes norvegicus
Authors: Johansen Torild , Hanebrekke Tanja , Besnier Francois , Westgaard Jon Ivar , Bruvold Ingrid Marie , Dahle Geir , Unneland Laila , Torp Christensen Helle , Saha Atal
Published: January 2025

The genus Sebastes in the North Atlantic comprises of long lived deep‐waters species that have been extensively fished upon, and many stocks are severely depleted across the Atlantic. This is particularly evident for the species Sebastes norvegicus. In recent papers, cryptic species have been indicated within this genus and molecular markers are therefore needed to provide identification for the Sebastes species, including the cryptic species as a basis for advice regarding management and rebuilding of the stocks. A suite of 2800 Single Nucleotide Polymorphism (SNP) markers were identified from ddRAD sequencing data, of which 56 SNPs were organized in two multiplex reactions and tested on 191 Sebastes spp. from different sampling locations from Norway and Greenland. Good‐quality amplification products were successfully obtained from 49 SNP markers for Sebastes species ID, and 3 TaqMan probes were designed to successfully assign S. mentella, S. viviparus, and the two cryptic species S. norvegicus types A and B. A total 47 SNPs were biallelic, with averaged HE per locus ranging between 0.053 and 0.50. This SNP‐based method establishes a foundation for genetically identifying the Northeast Atlantic Sebastes species. The findings presented should be followed by an effort to look for morphological characters to recognize the S. norvegicus cryptic species on site. In general, the SNP markers are a proper tool for monitoring the distribution of the species from a management perspective.