bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep Learning and Hyperspectral Imaging for Liver Cancer Staging and Cirrhosis Differentiation
Authors: Hang Tianyi , Fan Danfeng , Sun Tiefeng , Chen Zhengyuan , Yang Xiaoqing , Yue Xiaoqing 
Published: January 2025

ABSTRACTLiver malignancies, particularly hepatocellular carcinoma (HCC), pose a formidable global health challenge. Conventional diagnostic techniques frequently fall short in precision, especially at advanced HCC stages. In response, we have developed a novel diagnostic strategy that integrates hyperspectral imaging with deep learning. This innovative approach captures detailed spectral data from tissue samples, pinpointing subtle cellular differences that elude traditional methods. A sophisticated deep convolutional neural network processes this data, effectively distinguishing high‐grade liver cancer from cirrhosis with an accuracy of 89.45%, a sensitivity of 90.29%, and a specificity of 88.64%. For HCC differentiation specifically, it achieves an impressive accuracy of 93.73%, sensitivity of 92.53%, and specificity of 90.07%. Our results underscore the potential of this technique as a precise, rapid, and non‐invasive diagnostic tool that surpasses existing clinical methods in staging liver cancer and differentiating cirrhosis.
Unlocking the Potential of miRNAs in Sepsis Diagnosis and Prognosis: From Pathophysiology to Precision Medicine
Authors: Khidr Emad Gamil , El‐Sayyad Gharieb S. , Abulsoud Ahmed I. , Rizk Nehal I. , Zaki Mohamed Bakr , Raouf Ahmed Amr , Elrebehy Mahmoud A. , Abdel Hady Manal M. M. , Elballal Mohammed S. , Mohammed Osama A. , Abdel‐Reheim Mustafa Ahmed , El‐Dakroury Walaa A. , Abdel Mageed Sherif S. , AL‐Noshokaty Tohada M. , Doghish Ahmed S. 
Published: January 2025

ABSTRACTThe clinical syndrome appears as a dysregulated host response to infection that results in life‐threatening organ dysfunction known as Sepsis. Sepsis is a serious public health concern where for every five deaths in ICU there is one patient who dies with sepsis worldwide. Sepsis is featured as unbalanced inflammation and immunosuppression which is sustained and profound, increasing patient susceptibility to secondary infections and mortality. microRNAs (miRNAs) play a central role in the control of many biological processes, and the deregulation of their expression has been linked to the development of oncological, cardiovascular, neurodegenerative, and metabolic diseases. In this review, we discuss the role of miRNAs in sepsis pathophysiology. Overall, miRNAs are seen as promising biomarkers, and it has been proposed to develop miRNA‐based diagnosis and therapies for sepsis. Yet, the picture is not so straightforward because of miRNAs’ versatile and dynamic features. More research is needed to clarify the expression and role of miRNAs in sepsis and promote the use of miRNAs for sepsis management. This study provides an extensive, current, and thorough analysis of the involvement of miRNAs in sepsis. Its purpose is to encourage future research in this area, as tiny miRNAs have the potential to be used for rapid diagnosis, prognosis, and treatment of sepsis.
Exploring the Role of Epithelial–Mesenchymal Transition During Colorectal Cancer Peritoneal Metastasis: Update on Their Mechanisms
Authors: Long Chenyan , Li Xiang , Liu Jungang , Mo Xianwei , Zhong Huage , Tang Weizhong , Yu Junfeng 
Published: January 2025

ABSTRACTColorectal cancer is a common malignant tumor worldwide. The prognosis of patients with colorectal cancer peritoneal metastasis is very poor. The study of the specific mechanisms of colorectal cancer peritoneal metastasis plays an important role in the treatment of patients with this disease. The mechanisms of colorectal cancer peritoneal metastasis are mainly pathological and biological. Biologically, the epithelial–mesenchymal transition process is an important precursor to tumor cell metastasis. Therefore, it is necessary to study the mechanisms of colorectal cancer peritoneal metastasis, especially the epithelial–mesenchymal transition, to identify new methods for the prevention and treatment of colorectal cancer peritoneal cancer, reduce the incidence of colorectal cancer peritoneal metastasis, and improve patient prognosis.
PrPC Glycoprotein Is Indispensable for Maintenance of Skeletal Muscle Homeostasis During Aging
Authors: Liu Wenduo , Kieu Thi Thu Trang , Wang Zilin , Sim Hyun‐Jaung , Lee Seohyeong , Lee Jeong‐Chae , Park Yoonjung , Kim Sang Hyun , Kook Sung‐Ho 
Published: January 2025

ABSTRACTBackgroundThe cellular prion protein (PrPC), a glycoprotein encoded by the PRNP gene, is known to modulate muscle mass and exercise capacity. However, the role of PrPC in the maintenance and regeneration of skeletal muscle during ageing remains unclear.MethodsThis study investigated the change in PrPC expression during muscle formation using C2C12 cells and evaluated muscle function in Prnp wild‐type (WT) and knock‐out (KO) mice at different ages (1, 9 and 15 months). To determine the role of PrPC in skeletal muscle homeostasis during ageing, we conducted regeneration experiments via cardiotoxin injection in Prnp mice to assess the effects of PrPC deficiency on the senescence of satellite stem cells (SCs) and regenerative capacity in skeletal muscle.ResultsOur data demonstrate that PrPC expression increased significantly during muscle differentiation (p < 0.01), correlating with myogenin (immunofluorescence at the differentiation stage). PrPC deficiency disrupted muscle homeostasis, leading to age‐associated mitochondrial autophagy (Pink‐1, +180%, p < 0.001; Parkin, +161%, p < 0.01) and endoplasmic reticulum stress (SERCA, −26%, p < 0.05; IRE1α, +195%, p < 0.001) while decreasing the level of mitochondrial biogenesis (SIRT‐1, −50%, p < 0.01; PGC‐1α, −36%, p < 0.05; VDAC, −27%, p < 0.001), and activated oxidative stress (serum myoglobin, +23%, p < 0.001; MDA, +23%, p < 0.05; NFκB, +117%, p < 0.05) during ageing, which accelerated reduced muscle growth or mass accumulation (tibialis anterior muscle mass, −23%, p < 0.001; gastrocnemius muscle mass, −30%, p < 0.001; muscle fibre size, −48%, p < 0.05; MSTN, +160%, p < 0.01; MAFbx, +83%, p < 0.05). Furthermore, PrPC deficiency induced the senescence (β‐galactosidase, +60%, p < 0.05; p16, +103%, p < 0.001) of SCs, which was directly related to the defect in muscle recovery, with the senescence‐mediated enhancement of adipogenesis (PPARγ, +74%, p < 0.05) during the regeneration process after cardiotoxin‐induced muscle injury.ConclusionsOur findings demonstrate that PrPC is indispensable for maintaining skeletal muscle homeostasis during ageing by modulating the functional integrity of mitochondria, ER and SCs.
Risk Factors for Viral Coinfections in Blood Donors in Bahia, Brazil
Authors: Luz Estela , Marques Marinho , Arriaga María B. , Campos Luísa Meireles , Lima Lara , Amaral Sávio , Marques Eduardo Luz , Page Kimberly , Brites Carlos 
Published: January 2025

ABSTRACTHuman Immunodeficiency Virus (HIV), Human T Lymphotropic Virus (HTLV), Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) coinfection may lead to disease progression or worsen its clinical presentation. Viral coinfections screening during blood donation is critical. To identify risk factors for coinfection among blood donors, we assessed the blood donations at the Fundação de Hematologia e Hemoterapia da Bahia, from 2008 to 2017. We compared serological/molecular evidence of single infection versus two or more viral blood‐borne infections—BBI). A multivariable logistic regression model was performed to evaluate independent associations between characteristics of donors with single infection and multiple infection using “non‐infection” category as reference. Among 777,446 collected blood donations, 27 358 (3.5%) were reactive, most (n = 26 677, 97.6%) for a single infection and 681 (2.4%) for coinfection. The most frequent coinfections were HBV‐HIV (30.6%), HBV‐HCV (30.4%), and HBV‐HTLV (24.4%). Male sex, lower education, being single, and being a first‐time donor were independently associated with both single and coinfections. Nevertheless, the adjusted odds for risk factors of coinfections were much higher than those for single infection. Donors with single and coinfection for BBI shared identical risks, but they were significantly higher for coinfection. Preventive strategies addressing the identified risks can decrease transmission of viral BBI by blood transfusion.
Antioxidant, antidiabetic, and antimicrobial efficacy of germinated Ocimum gratissimum and Ocimum basilicum seed
Authors: B Neeharika , K G Vijayalaxmi , V Chavannavar Suvarna , Chavan Mohan 
Published: January 2025

AbstractBACKGROUNDThe edible seeds of Ocimum gratissimum and Ocimum basilicum were found to be a potent source of phytochemicals with noteworthy antioxidant, antidiabetic, and antimicrobial properties. This study aimed to investigate the impact of germination and extraction solvents (ethanol (EtOH), distilled water) on the therapeutic properties exhibited and the ability of seed extracts to act as natural food preservatives.RESULTSThe EtOH extracts of germinated O. gratissimum and O. basilicum seeds exhibited more phytoconstituents content with significantly higher phenols (21.03 ± 0.01 mg gallic acid equivalent (GAE)/g and 21.46 ± 0.01 mg GAE/g respectively) and flavonoids (11.92 ± 0.03 mg quercetin equivalent (QE)/g and 14.45 ± 0.04 mg QE/g respectively) than other extracts did. Thus, they exhibited superior antioxidant potential with substantially lower half‐maximal inhibitory concentration (IC50) values for scavenging 2,2′‐azino‐bis(3‐ethylbenzothiazoline‐6‐sulfonic acid) cation radical (0.013 ± 0.00 mg mL−1 and 0.007 ± 0.00 mg mL−1 respectively) and superoxide anion radical (4.33 ± 0.01 mg mL−1 and 4.14 ± 0.00 mg mL−1 respectively) and for inhibiting lipid oxidation (2.57 ± 0.00 mg mL−1 and 2.33 ± 0.00 mg mL−1 respectively) compared with other extracts. Further, they exhibited better antidiabetic potential with substantially lower IC50 values for inhibiting α‐amylase activity (0.93 ± 0.01 mg mL−1 and 1.01 ± 0.01 mg mL−1 respectively) and α‐glucosidase activity (0.60 ± 0.01 mg mL−1 and 0.51 ± 0.01 mg mL−1 respectively). Also, they showed superior antimicrobial potential with higher inhibition zones for Bacillus subtilis (13.98 ± 0.18 mm, 17.02 ± 0.18 mm respectively), Vibrio parahaemolyticus (19.00 ± 0.20 mm, 22.58 ± 0.45 mm respectively), Salmonella enterica (24.98 ± 0.18 mm, 22.17 ± 0.15 mm respectively), and Escherichia coli (23.50 ± 0.50 mm, 27.00 ± 0.20 mm respectively) and better inhibition of Aspergillus flavus growth (93.28% and 81.77% respectively) compared with other extracts.CONCLUSIONBoth the O. gratissimum and O. basilicum seed extracts can be utilized efficiently as therapeutic agents to manage inflammation‐driven diseases and diabetes, or as natural preservatives in foods and in edible films or coatings. © 2025 Society of Chemical Industry.
Stabilization of blackberry extract by interaction with bovine sodium caseinate in the presence of tara gum
Authors: Ferreyra Ornella N. , Lionello Melina E. , Ingrassia Romina , Hidalgo María Eugenia , dos Santos Ferreira Cristina , del Pilar Buera María , Risso Patricia 
Published: January 2025

AbstractBACKGROUNDThe antioxidant capacity of anthocyanins (AC) rapidly degrades during storage, highlighting the need for their stabilization. The conformational properties and high proline content of sodium caseinate (NaCAS), combined with the formation of NaCAS microgels in the presence of tara gum (TG) and acid gelation, suggest its potential as an effective stabilizing or encapsulating agent of AC.RESULTSSpectrofluorimetric results suggest the formation of a complex between NaCAS and AC. Fourier transform infrared spectroscopy demonstrated that the presence of TG and blackberry extract (BEX) modifies the NaCAS spectra in the analyzed range. These results validated the presence of hydrogen bonding and hydrophobic interactions between NaCAS and AC. The impact of the AC–NaCAS complex on the stability of the antioxidant capacity was assessed. After 43 days of storage, the lyophilized complex with an optimal BEX concentration retained 70% of its iron‐reducing power. Additionally, the results indicate that, at the tested concentrations of BEX, the radical scavenging capacity of NaCAS is minimally affected.CONCLUSIONThe present study demonstrates that the bioactive properties of the aqueous extract of blackberry are effectively stabilized through the formation of complexes with NaCAS in the presence of TG. Both AC and TG interact with NaCAS, but in different ways. The antioxidant capacity of these mixtures, demonstrated through both reducing power and free radical capture, is preserved to a high degree after storage. © 2025 Society of Chemical Industry.
Multivariate Controls of Water–Carbon Coupling Relationship Under Various Land Use Types in the Thick Loess Deposits
Authors: Li Ruifeng , Zhang Xuanhua , Ji Wangjia , Li Bingbing , Li Zhi 
Published: January 2025

ABSTRACTPrior studies have conducted extensive investigations of the water–carbon coupling relationship for aboveground vegetation and shallow soils, but the characteristics and multivariate controls in deep soils have not been fully explored. This has important implications for better understanding the water and carbon cycles of ecosystems. In this study, we attempted to examine the water–carbon coupling relationship in 18 m profiles under farmland (F), grassland (G), willow (SP), and poplar (P) in China's Loess Plateau. Specially, the multivariate controls of the water–carbon coupling relationship at diverse depths and scales were explored via the wavelet analysis. Individually, the conversion from F to G, SP, and P decreased the soil water storage within the 0–15 m by 553 (22% of F), 557 (22%), and 943 mm (38%). Land use change had little impact on soil organic or inorganic carbon. Even so, the poplar, compared with the willow, resulted in higher vertical variations in deep water and carbon. Furthermore, land use conversion increased the coherence between soil water and carbon in the whole layer. In comparison to F, which was dominated by water retention, G, SP, and P exhibited dominant carbon sequestration. The poplar reduced the root‐mean‐square deviation between soil water and organic carbon from 0.29 (F) to 0.13 in the 6‐ to 15‐m layer and between soil water and inorganic carbon from 0.32 (F) to 0.20 in the 0‐ to 2‐m layer. Sand content and electrical conductivity both played negative roles in maintaining water and carbon in the 6‐ to 15‐m and 0‐ to 15‐m layers at different scales, respectively. This study endeavors to present a novel viewpoint on land use management, with the potential to enhance ecosystem services in water‐limited and land‐degradation regions.
Ontogenetic shifts by juvenile fishes highlight the need for habitat heterogeneity and connectivity in river restoration
Authors: Stoffers Twan , Buijse Anthonie D. , Poos Jan Jaap , Verreth Johan A. J. , Nagelkerke Leopold A. J. 
Published: January 2025

AbstractLarge‐scale anthropogenic river modifications have caused the loss of critical floodplain nursery habitats for riverine fish, leading to population declines. Restoration efforts have been implemented to recover these habitats, but with varying success. Understanding how larval and juvenile fish use habitats in dynamic river environments is essential for improving restoration strategies. We assessed ontogenetic shifts in habitat use by young‐of‐the‐year fishes in the lower Rhine, analyzing 2167 samples across 18 restored floodplains over three growing seasons (2018–2020). Five distinct nursery habitats were identified: (1) exposed, fast‐flowing habitats with coarse substrate; (2) turbid, nonflowing areas with high turbidity and chlorophyll; (3) shallow, vegetated habitats with macrophytes and shoreline vegetation; (4) deeper, sheltered habitats with structural complexity; and (5) shallow, slow‐flowing areas. Habitat use shifted significantly with ontogeny across species. Larvae generally preferred shallow habitats (< 50‐cm depth), either in slow‐flowing areas (e.g., asp, ide, monkey goby, nase, and whitefin gudgeon) or vegetated zones with macrophytes (e.g., bleak, bitterling, bream, round goby, and zander). Juveniles increasingly used deeper habitats (> 50‐cm depth), favoring fast‐flowing areas (e.g., asp, barbel, ide), or deeper, nonflowing habitats (e.g., bream, zander). Our findings thus highlight the critical importance of habitat heterogeneity and connectivity for riverine fish biodiversity. Restoration strategies should prioritize the creation of a mosaic of shallow, low‐velocity habitats for larvae, alongside deeper, fast‐flowing, or sheltered areas for juveniles. Additionally, the movement of rheophilic species from floodplain habitats to the main river channel emphasizes the need for maintaining continuous connectivity between floodplains and the river.
Epiphyton phenology determines the persistence of submerged macrophytes: Exemplified in temperate shallow lakes
Authors: Gsell Alena S. , Teurlincx Sven , Alirangues Nuñez Marta M. , Hilt Sabine 
Published: January 2025

AbstractSubmerged macrophytes are key components in many freshwater and marine ecosystems, contributing to ecosystem functions and services. In temperate shallow lakes, spring epiphyton shading can be decisive for submerged macrophyte development, potentially leading to macrophyte collapse and a shift to undesired, turbid conditions. Global change can alter epiphyton phenology; however, the consequences for submerged macrophytes and their stabilizing effects on clear‐water conditions remain to be elucidated. Based on field data, we propose a general epiphyton shading phenology for submerged macrophytes in temperate shallow lake ecosystems. We express the temporal dynamics of epiphyton shading in terms of onset and relative increase (slope) of epiphyton development as well as epiphyton grazing impacts (onset, duration) using a Boltzmann function. This function is added to the ecosystem model PCLake+ as a customizable, macrophyte‐specific shading factor. We then assess how changes in the epiphyton phenology and the presence of grazing on epiphyton affects submerged macrophyte biomass in a generic temperate shallow model lake under control and warm winter scenarios. The results from the model provide a proof‐of‐concept that epiphyton shading can provoke macrophyte loss and shifts between alternative equilibria. Threshold values for critical shifts depend on epiphyton shading phenology. Earlier onset and longer duration of grazing can maintain macrophytes in nutrient or climate conditions under which they would otherwise collapse. Our results show the pivotal importance of epiphyton phenology in determining lake ecosystem‐wide responses stressing the need for better incorporation of epiphyton into both models and monitoring.
Approaching the Quantum‐Limited Precision in Frequency‐Comb‐Based Spectral Interferometric Ranging
Authors: Jang Yoon‐Soo , Ahn Heulbi , Eom Sunghoon , Park Jungjae , Jin Jonghan 
Published: January 2025

AbstractOver the last two decades, frequency combs have brought breakthroughs in length metrology with traceability to length standards. In particular, frequency‐comb‐based spectral interferometry is regarded as a promising technology for next‐generation length standards. However, to achieve this, the nanometer‐level precision inherent in a laser interferometer is required. Here, distance measurements are reported by frequency‐comb‐based spectral interferometry with sub‐nm precision close to a standard quantum limit. The measurement precision is confirmed as 0.67 nm at an average time of 25 µs. The measurement sensitivity is found to be 4.5·10−12m/Hz1/2, close to the quantum‐limit. As a practical example of observing precise physical phenomena, remote sound sensing is demonstrated through measuring vibrations induced by acoustic waves. The study will be an important step toward the practical realization of upcoming length standards.
Deep learning‐based Monte Carlo dose prediction for heavy‐ion online adaptive radiotherapy and fast quality assurance: A feasibility study
Authors: He Rui , Wang Jian , Wu Wei , Zhang Hui , Liu Yinuo , Luo Ying , Zhang Xinyang , Ma Yuanyuan , Liu Xinguo , Li Yazhou , Peng Haibo , He Pengbo , Li Qiang 
Published: January 2025

AbstractBackgroundOnline adaptive radiotherapy (OART) and rapid quality assurance (QA) are essential for effective heavy ion therapy (HIT). However, there is a shortage of deep learning (DL) models and workflows for predicting Monte Carlo (MC) doses in such treatments.PurposeThis study seeks to address this gap by developing a DL model for independent MC dose (MCDose) prediction, aiming to facilitate OART and rapid QA implementation for HIT.Methods and MaterialsA MC dose prediction DL model called CAM‐CHD U‐Net for HIT was introduced, based on the GATE/Geant4 MC simulation platform. The proposed model improved upon the original CHD U‐Net by adding a Channel Attention Mechanism (CAM). Two experiments were conducted, one with CHD U‐Net (Experiment 1) and another with CAM‐CHD U‐Net (Experiment 2), and involved data from 120 head and neck cancer patients. Using patient CT images, three‐dimensional energy matrices, and ray‐masks as inputs, the model completed the entire MC dose prediction process within a few seconds.ResultsIn Experiment 2, within the Planned Target Volume (PTV) region, the average gamma passing rate (3%/3 mm) between the predicted dose and true MC dose reached 99.31%, and 96.48% across all body voxels. Experiment 2 demonstrated a 46.15% reduction in the mean absolute difference in in organs at risk compared to Experiment 1.ConclusionsBy extracting relevant parameters of radiotherapy plans, the CAM‐CHD U‐Net model can directly and accurately predict independent MC dose, and has a high gamma passing rate with the ground truth dose (the dose obtained after a complete MC simulation). Our workflow enables the implementation of heavy ion OART, and the predicted MCDose can be used for rapid QA of HIT.
DFT Study on Mechanism and Regioselectivity in Pd(II)‐Catalyzed Dehydrogenative Heck Olefination of Selenophenes
Authors: Wang Dongmei , Yang Xiaojiao , Fang Ran 
Published: January 2025

AbstractThe present study deals with the theoretical investigation of mechanistic and regiochemical aspects of the Pd(II)‐catalyzed dehydrogenative Heck olefination of selenophenes. The detailed reaction mechanism was established, and the roles of the catalyst and regioselectivity were well rationalized. Our results clearly showed that the whole reaction involves a concerted metalation‐deprotonation (CMD) process between the C2 site of selenophene and Pd(OAc)2 in the first catalytic cycle. Afterward, the olefin coordinates to the palladium, followed by a regioselective 1,2‐migratory insertion to form a C─C bond. Then, β‐hydride elimination would give the final 2‐monoolefinated product. Subsequently, the second catalytic cycle generates the symmetrical 2,5‐diolefinated selenophene product. Another key finding of this study is that selenophene and its monoolefinated product act as nucleophiles, while the catalyst behaves as an electrophile. A global reactivity index (GRI) analysis revealed that the nucleophilicity (Nk) of C2, C3, C4, and C5 atoms in selenophene plays an important role in controlling the reaction selectivity at these sites. However, the distortion energies play a more important role in controlling the selectivity of reactions at the olefin C sites.