bluuebunny/crossref_metadata_2025_split huggingface dataset:
Birch (Betula pubescens Ehrh.) Encroachment Alters Contribution of Plant Functional Groups to Ecosystem Carbon Cycling in a Rewetted Bog
Authors: Welpelo Carla , Dubbert Maren , Tiemeyer Bärbel , Knohl Alexander , Piayda Arndt 
Published: December 2024

ABSTRACTRewetted bogs with high water levels (WL) and mire‐specific vegetation are crucial carbon (C) sinks, but their function might be threatened by tree encroachment, a phenomenon widespread in the northern hemisphere that often coincides with low WL. This might impact C cycling both at the ecosystem and microform scale in multiple ways, but so far, data are lacking. We established two sites in the same former peat extraction area, one showing permanently high WL and mire‐specific vegetation (open site, OS), while the other one has more fluctuating WL and a dense birch (Betula pubescens Ehrh.) population (tree site, TS). We measured the carbon dioxide (CO2) exchange at ecosystem (eddy covariance) and plot scale (chamber measurements) for 1 year to clarify the differences between the sites and the impact of birch encroachment on the contribution of the different bog‐specific microforms and the trees to the ecosystem's CO2 balance. Overall, the OS had a CO2 balance of −262.4 ± 7.8 g CO2‐C m−2 year−1 indicating CO2 uptake, while the TS was close to neutral (−28 ± 5.1 g CO2‐C m−2 year−1). The smaller uptake at the TS was caused by higher (151%) ecosystem respiration, while gross primary production was 14% higher. However, the microform contributions to C uptake strongly differed: At the OS, both hummocks and hollows showed net uptake, while at the TS, most C (52%) was assimilated by the birches and the understory was a net CO2 source. This indicates a loss of peat C from the TS, while the successfully rewetted site was accumulating new peat. Accounting for plot‐scale CH4 fluxes, both sites were a weak source of greenhouse gases, but a distinctly stronger C sink occurred at the OS. Our data show the possibility of increasing C removal from the atmosphere by full rewetting and the establishment of mire‐specific vegetation.
Subject‐Level Segmentation Precision Weights for Volumetric Studies Involving Label Fusion
Authors: Chen Christina , Das Sandhitsu R. , Tisdall M. Dylan , Hu Fengling , Chen Andrew A. , Yushkevich Paul A. , Wolk David A. , Shinohara Russell T. ,   for the Alzheimer's Disease Neuroimaging Initiative
Published: December 2024

ABSTRACTIn neuroimaging research, volumetric data contribute valuable information for understanding brain changes during both healthy aging and pathological processes. Extracting these measures from images requires segmenting the regions of interest (ROIs), and many popular methods accomplish this by fusing labels from multiple expert‐segmented images called atlases. However, post‐segmentation, current practices typically treat each subject's measurement equally without incorporating any information about variation in their segmentation precision. This naïve approach hinders comparing ROI volumes between different samples to identify associations between tissue volume and disease or phenotype. We propose a novel method that estimates the variance of the measured ROI volume for each subject due to the multi‐atlas segmentation procedure. We demonstrate in real data that weighting by these estimates markedly improves the power to detect a mean difference in hippocampal volume between controls and subjects with mild cognitive impairment or Alzheimer's disease.
Approximating R1 and R2: A Quantitative Approach to Clinical Weighted MRI
Authors: Moskovich Shachar , Shtangel Oshrat , Mezer Aviv A. 
Published: December 2024

ABSTRACTWeighted MRI images are widely used in clinical as well as open‐source neuroimaging databases. Weighted images such as T1‐weighted, T2‐weighted, and proton density‐weighted (T1w, T2w, and PDw, respectively) are used for evaluating the brain's macrostructure; however, their values cannot be used for microstructural analysis, as they lack physical meaning. Quantitative MRI (qMRI) relaxation rate parameters (e.g., R1 and R2) do contain microstructural physical meaning. Nevertheless, qMRI is rarely done in large‐scale clinical databases. Currently, the weighted images ratio T1w/T2w is used as a quantifier to approximate the brain's microstructure. In this paper, we test three additional quantifiers that approximate quantitative maps, which can help bring quantitative MRI to the clinic for easy use. Following the signal equations and using simple mathematical operations, we combine the T1w, T2w, and PDw images to estimate the R1 and R2 maps. We find that two of these quantifiers (T1w/PDw and T1w/ln(T2w)) can approximate R1, and that (ln(T2w/PDw)) can approximate R2, in 3 datasets that were tested. We find that this approach also can be applied to T2w scans taken from widely available DTI (Diffusion Tensor Imaging) datasets. We tested these quantifiers on both in vitro phantom and in vivo human datasets. We found that the quantifiers accurately represent the quantitative parameters across datasets. Finally, we tested the quantifiers within a clinical context, and found that they are robust across datasets. Our work provides a simple pipeline to enhance the usability and quantitative accuracy of MRI weighted images.
Innovative public strategies in response to COVID‐19: A review of practices from China
Authors: Wu You , Cao Zijian , Yang Jing , Bi Xinran , Xiong Weiqing , Feng Xiaoru , Yan Yue , Zhang Zeyu , Zhang Zongjiu 
Published: December 2024

AbstractThe COVID‐19 pandemic presented unparalleled challenges to prompt and adaptive responses from nations worldwide. This review examines China's multifaceted approach to the crisis, focusing on five key areas of response: infrastructure and system design, medical care and treatment, disease prevention and control, economic and social resilience, and China's engagement in global health. This review demonstrates the effectiveness of a top‐down command system at the national level, intersectoral coordination, a legal framework, and public social governance. This study also examines medical care and treatment strategies, highlighting the importance of rapid emergency response, evidence‐based treatment, and well‐planned vaccination rollout. Further discussion on disease prevention and control measures emphasizes the importance of adaptive measures, timely infection control, transmission interruption, population herd immunity, and technology applications. Socioeconomic impact was also assessed, detailing strategies for disease prevention, material supply, livelihood preservation, and social economy revival. Lastly, we examine China's contributions to the global health community, with a focus on knowledge‐sharing, information exchange, and multilateral assistance. While it is true that each nation's response must be tailored to its own context, there are universal lessons to be drawn from China's approach. These insights are pivotal for enhancing global health security, especially as the world navigates evolving health crises.
Expression of Major Basic Protein and Endothelial Adhesion Molecules in Chronically Inflamed Mucosa of the Ethmoid Labyrinth
Authors: Vukadinović Tijana , Đurđević Biserka Vukomanović , Perić Aleksandar 
Published: December 2024

ABSTRACTBackground/ObjectivesTissue remodeling, including dense eosinophil infiltration, is essential for forming inflammatory nasal polyps (NPs) and the pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP). Toxic eosinophil major basic protein (MBP) damages the sinus mucosa epithelium and lamina propria, which initiates reparative processes leading to tissue remodeling. MBP specifically binds to BMK‐13 antibodies allowing immunohistochemical (IHC) tissue staining for eosinophils. This study evaluated the association between NP stromal BMK‐13 and endothelial adhesion molecule staining, and clinical parameters of NP patients compared to IHC expression and clinical parameters in subjects with healthy nasal mucosa.MethodsWe included 30 patients with bilateral NPs who were selected for endoscopic ethmoidectomy. The control group was of 30 subjects with non‐inflamed nasal mucosa but with middle turbinate aeration, chosen for surgery. All participants were clinically scored before surgery, according to quality of life (QoL) outcome and symptoms. The degree of disease extension on computed tomography scans of the paranasal sinuses was also evaluated. Tissue samples after surgery were IHC stained for BMK‐13 and endothelial proliferation markers CD31 and CD34.ResultsExpression of BMK‐13, CD31, and CD34 in tissues of NPs was higher than in healthy nasal mucosa. Positive correlations were observed between BMK‐13 expression, impaired QoL, and radiologically assessed extension of inflammation in NP patients.ConclusionApart from the fact that the NP tissue has, as expected, more intense eosinophilic infiltration, the proliferation of blood vessels is more pronounced in the NP tissue than in the tissue of healthy nasal mucosa. Expression of MBP in the tissue of ethmoidal NPs could serve as a potential marker of the degree of expansion of CRSwNP and indicate the severity of the disease.Clinical Trial RegistrationNone, because it was a cross‐sectional study.
Research Progress on the Correlation Between Atmospheric Particulate Matter and Autism
Authors: Xiao Yaqian , Xiang Wang , Ma Xuerui , Zheng Aijia , Rong Dechang , Zhang Nimeng , Yang Ning , Bayram Hasan , Lorimer George H. , Wang Jun 
Published: December 2024

ABSTRACTAutism spectrum disorder (ASD) is a neurodevelopmental disorder caused by the interaction of genetic and complex environmental factors. The prevalence of autism has dramatically increased in countries and regions undergoing rapid industrialization and urbanization. Recent studies have shown that particulate matter (PM) in air pollution affects the development of neurons and disrupts the function of the nervous system, leading to behavioral and cognitive problems and increasing the risk of ASD. However, research on the mechanism of environmental factors and ASD is still in its infancy. On this basis, we conducted a literature search and analysis to review epidemiological studies on the correlation between fine particulate matter (PM2.5) and inhalable particulate matter (PM10) and ASD. The signaling pathways and pathogenic mechanisms of PM in synaptic injury and neuroinflammation are presented, and the mechanism of the ASD candidate gene SHANK3 was reviewed. Additionally, the different sites of action of different particles in animal models and humans were highlighted, and the differences of their effects on the pathogenesis of ASD were explained. We summarized the aetiology and mechanisms of PM‐induced autism and look forward to future research breakthroughs in improved assessment methods, multidisciplinary alliances and high‐tech innovations.
A Construction of a 3/2‐Tough Plane Triangulation With No 2‐Factor
Authors: Shan Songling 
Published: December 2024

ABSTRACTIn 1956, Tutte proved the celebrated theorem that every 4‐connected planar graph is Hamiltonian. This result implies that every more than ‐tough planar graph on at least three vertices is Hamiltonian and so has a 2‐factor. Owens in 1999 constructed non‐Hamiltonian maximal planar graphs of toughness arbitrarily close to and asked whether there exists a maximal non‐Hamiltonian planar graph of toughness exactly . In fact, the graphs Owens constructed do not even contain a 2‐factor. Thus the toughness of exactly is the only case left in asking the existence of 2‐factors in tough planar graphs. This question was also asked by Bauer, Broersma, and Schmeichel in a survey. In this paper, we close this gap by constructing a maximal ‐tough plane graph with no 2‐factor, answering the question asked by Owens as well as by Bauer, Broersma, and Schmeichel.
Strong approximation of special functions of bounded variation functions with prescribed jump direction
Authors: Lazzaroni Giuliano , Wozniak Piotr , Zeppieri Caterina Ida 
Published: December 2024

AbstractIn this note, we show that special functions of bounded variation ( functions with jump normal lying in a prescribed set of directions can be approximated by sequences of functions whose jump set is essentially closed, polyhedral, and preserves the orthogonality to , moreover the functions are smooth away from their jump set.
Cysteinyl‐tRNA synthetase is involved in damage of renal tubular cells in ischemia–reperfusion‐induced acute kidney injury via pyroptosis
Authors: Yang Hongsha , Song Pan , Yu Meidie , Huang Liming , Tang Yun , Li Guisen , Li Yi , Feng Yunlin 
Published: December 2024

AbstractAcute kidney injury (AKI) is a significant global healthcare burden but lacks specific and effective treatment. Renal tubular cells damage is central to ischemia‐reperfusion injury (IRI) induced AKI. It is critical to clarify the initiation mechanisms of renal IRI and develop early intervention targets of AKI. This study used label‐free quantification proteomic analysis to identify new targets in AKI‐related renal tubular injury and investigate the potential mechanisms. We discovered significant changes in cysteinyl‐tRNA synthetase (CARS) in renal tubular cell during IRI. Considering the involvement of CARS in ATP metabolism and the close correlation between ATP and pyroptosis, we further explored pyroptosis phenotype with and without CARS intervention as well as the expression of CARS during pyroptosis activation and inhibition. Our findings suggest that CARS expression decreased over time and is linked to pyroptosis. Modifying CARS affects ATP metabolism and alters the expression of pyroptosis‐related proteins during H/R and IRI treatments. Regulating pyroptosis may influence CARS expression during IRI treatment. Overall, CARS is associated with renal tubular damage from ischemia‐reperfusion injury, possibly involving pyroptosis, though the regulatory mechanism remains unclear.
Multilevel network for large deformation image registration based on feature consistency and flow normalization
Authors: Huang Xingyu , Zhang Jian , Tang Kun , Cheng Xinyu , Ye Chen , Wang Lihui 
Published: December 2024

AbstractBackgroundDeformable image registration is an essential technique of medical image analysis, which plays important roles in several clinical applications. Existing deep learning‐based registration methods have already achieved promising performance for the registrations with small deformations, while it is still challenging to deal with the large deformation registration due to the limits of the image intensity‐similarity‐based objective function.PurposeTo achieve the image registration with large‐scale deformations, we proposed a multilevel network architecture FCNet to gradually refine the registration results based on semantic feature consistency constraint and flow normalization (FN) strategy.MethodsAt each level of FCNet, the architecture is mainly composed to a FeaExtractor, a FN module, and a spatial transformation module. FeaExtractor consists of three parallel streams which are used to extract the individual features of fixed and moving images, as well as their joint features, respectively. Using these features, the initial deformation field is estimated, which passes through a FN module to refine the deformation field based on the difference map of deformation filed between two adjacent levels. This allows the FCNet to progressively improve the registration performance. Finally, a spatial transformation module is used to get the warped image based on the deformation field. Moreover, in addition to the image intensity‐similarity‐based objective function, a semantic‐feature consistency constraint is also introduced, which can further promote the alignments by imposing the similarity between the fixed and warped image features. To validate the effectiveness of the proposed method, we compared our method with the state‐of‐the‐art methods on three different datasets. In EMPIRE10 dataset, 20, 3, and 7 fixed and moving 3D computer tomography (CT) image pairs were used for training, validation, and testing respectively; in IXI dataset, atlas to individual image registration task was performed, with 3D MR images of 408, 58, and 115 individuals were used for training, validation, and testing respectively; in the in‐house dataset, patient to atlas registration task was implemented, with the 3D MR images of 94, 3, and 15 individuals being training, validation, and testing sets, respectively.ResultsThe qualitative and quantitative comparison results demonstrated that the proposed method is beneficial for handling large deformation image registration problems, with the DSC and ASSD improved by at least 1.0% and 25.9% on EMPIRE10 dataset. The ablation experiments also verified the effectiveness of the proposed feature combination strategy, feature consistency constraint, and FN module.ConclusionsOur proposed FCNet enables multiscale registration from coarse to fine, surpassing existing SOTA registration methods and effectively handling long‐range spatial relationships.
The mechanistic role of curcumin and its analogs in NSCLC: An evaluation of cell death in preclinical studies
Authors: Kesen Boztas Ela , Demiroz Sevki Mustafa , Onen Hacer Ilke 
Published: December 2024

AbstractLung cancer is the leading malignancy among males and ranks the second in females, with an estimated two million new diagnoses annually. It ranks the first in cancer‐related deaths among men and the second, following breast cancer, among women. The most significant risk factor for lung cancer is smoking. There are two main types of lung cancer: non‐small cell lung cancer (NSCLC) and small cell lung cancer (SCLC), with about 85% of cases falling into the NSCLC category. Even with a combination of treatments for NSCLC, such as surgical intervention, chemotherapy, radiation therapy, and immunotherapy, the 5‐year survival rates for those diagnosed with advanced NSCLC have not reached satisfactory levels, with chemotherapy continuing to be the main therapeutic approach. In advanced NSCLC treatment, gemcitabine and platinum‐based agents are applied as first‐line therapy. However, acquired or pre‐existing drug resistance can prevent chemotherapeutic agents from achieving the expected effect on patients and increasing the drug dose can lead to an increase in side effects. In recent years, for these reasons, there has been an increased interest in phytochemicals to enhance the cytotoxic effects of therapeutic agents on cancer cells while minimizing their toxic effects on healthy tissues. One of the most studied phytochemicals is curcumin. Despite its anticancer effects on NSCLC cells, its low stability and poor pharmacokinetics have led to unsatisfactory results in studies. Therefore, a variety of analogs have been synthesized. This review explores the impact of curcumin and its analogs on the pathways of cell death in NSCLC.
Synthesis of β‐Alanine From Isoleucine and Propionate Catabolism via Aminotransferases
Authors: Goldfarb Margo H. , Boesel Joseph , Wilczewski‐Shirai Kai C. , Reinhart Peter , Scherger Trenton , Webb Chloe , Newlun Morgan , Rouhier Kerry A. 
Published: December 2024

ABSTRACTIn plants, the nonproteinogenic amino acid β‐alanine plays a role in response to hypoxia, flooding, drought, heat, and heavy metal stress conditions. It is also a key intermediate in the synthesis of essential molecules including vitamin B5 and coenzyme A (CoA) through the condensation reaction with pantoate. While the syntheses of pantoate, vitamin B5, and CoA appear to be conserved across plants and bacteria, the synthesis of β‐alanine is not. Bacteria and fungi use aspartate, whereas plants can use uracil, spermidine, or propionate to synthesize β‐alanine. Given that these three precursors can be formed from the metabolism of glutamine, arginine, isoleucine, and valine, the synthesis of β‐alanine could be linked to numerous pathways. Studies of valine catabolism in Arabidopsis suggested that some branched‐chain amino acids could in fact serve as precursors for the synthesis of β‐alanine. Using GC–MS and isotopically labeled isoleucine and propionate, we linked their metabolism to the synthesis of β‐alanine via a proposed transamination of malonate semialdehyde. We then identified three aminotransferases that each catalyzed this final reversible transamination reaction. These results affirm our hypothesis that isoleucine metabolism is also linked to the synthesis of β‐alanine via the transamination of metabolic intermediates.
Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification
Authors: Muneer Gul , Chen Ciao‐Syuan , Chen Yu‐Ju 
Published: December 2024

ABSTRACTProtein phosphorylation introduces post‐genomic diversity to proteins, which plays a crucial role in various cellular activities. Elucidation of system‐wide signaling cascades requires high‐performance tools for precise identification and quantification of dynamics of site‐specific phosphorylation events. Recent advances in phosphoproteomic technologies have enabled the comprehensive mapping of the dynamic phosphoproteomic landscape, which has opened new avenues for exploring cell type‐specific functional networks underlying cellular functions and clinical phenotypes. Here, we provide an overview of the basics and challenges of phosphoproteomics, as well as the technological evolution and current state‐of‐the‐art global and quantitative phosphoproteomics methodologies. With a specific focus on highly sensitive platforms, we summarize recent trends and innovations in miniaturized sample preparation strategies for micro‐to‐nanoscale and single‐cell profiling, data‐independent acquisition mass spectrometry (DIA‐MS) for enhanced coverage, and quantitative phosphoproteomic pipelines for deep mapping of cell and disease biology. Each aspect of phosphoproteomic analysis presents unique challenges and opportunities for improvement and innovation. We specifically highlight evolving phosphoproteomic technologies that enable deep profiling from low‐input samples. Finally, we discuss the persistent challenges in phosphoproteomic technologies, including the feasibility of nanoscale and single‐cell phosphoproteomics, as well as future outlooks for biomedical applications.