bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tailoring convolutional neural networks for custom botanical data
Authors: Sykes Jamie R. , Denby Katherine J. , Franks Daniel W. 
Published: October 2024

AbstractPremiseAutomated disease, weed, and crop classification with computer vision will be invaluable in the future of agriculture. However, existing model architectures like ResNet, EfficientNet, and ConvNeXt often underperform on smaller, specialised datasets typical of such projects.MethodsWe address this gap with informed data collection and the development of a new convolutional neural network architecture, PhytNet. Utilising a novel dataset of infrared cocoa tree images, we demonstrate PhytNet's development and compare its performance with existing architectures. Data collection was informed by spectroscopy data, which provided useful insights into the spectral characteristics of cocoa trees. Cocoa was chosen as a focal species due to the diverse pathology of its diseases, which pose significant challenges for detection.ResultsResNet18 showed some signs of overfitting, while EfficientNet variants showed distinct signs of overfitting. By contrast, PhytNet displayed excellent attention to relevant features, almost no overfitting, and an exceptionally low computation cost of 1.19 GFLOPS.ConclusionsWe show that PhytNet is a promising candidate for rapid disease or plant classification and for precise localisation of disease symptoms for autonomous systems. We also show that the most informative light spectra for detecting cocoa disease are outside the visible spectrum and that efforts to detect disease in cocoa should be focused on local symptoms, rather than the systemic effects of disease.
Effects and phenotypic consequences of transient thyrotoxicosis and hypothyroidism at different stages of zebrafish Danio rerio (Teleostei; Cyprinidae) skeleton development
Authors: Borisov Vasily , Shkil Fedor 
Published: October 2024

AbstractThe effects and consequences of changes in thyroid hormones (THs) level are among the actively studied topics in teleost developmental and evolutionary biology. In most of the experimental models used, the altered hormonal status (either hypo‐ or hyperthyroidism) is a stable characteristic of the developing organism, and the observed phenotypic outcomes are the cumulative consequences of multiple TH‐induced developmental changes. Meanwhile, the influence of the transient fluctuations of TH content on skeleton development has been much less studied. Here, we present experimental data on the developmental effects and phenotypic consequences of transient, pharmacologically induced thyrotoxicosis and hypothyroidism at different stages of ossified skeleton patterning in zebrafish. According to the results, the skeleton structures differed in TH sensitivity. Some showed a notable shift in the developmental timing and rate, while other demonstrated little or no response to changes in TH content. The developmental stages also differed in TH sensitivity. We identified a relatively short developmental period, during which changes in TH level significantly increased the developmental instability and plasticity, leading to phenotypic consequences comparable to those in fish with a persistent hypo‐ or hyperthyroidism. These findings allow this period to be considered as a critical developmental window.
Neutrophil Activation Markers and Rheumatoid Arthritis Treatment Response to the JAK1/2 Inhibitor Baricitinib
Authors: Kuley Runa , Duvvuri Bhargavi , Hasnain Sabeeha , Dow Ernst R. , Koch Alisa E. , Higgs Richard E. , Krishnan Venkatesh , Lood Christian 
Published: October 2024

ObjectiveNeutrophils play an important role in regulating immune and inflammatory responses in patients with rheumatoid arthritis (RA). We assessed whether baricitinib, a JAK1/JAK2 inhibitor, could reduce neutrophil activation and whether a neutrophil activation score could predict treatment response.MethodsMarkers of neutrophil activation, calprotectin, and neutrophil extracellular traps (NETs) were analyzed using enzyme‐linked immunosorbent assay in plasma from patients with RA (n = 271) and healthy controls (n = 39). For patients with RA, neutrophil activation markers were measured at baseline, 12 weeks, and 24 weeks after receiving placebo and 2 and 4 mg baricitinib. Whole‐blood RNA analyses from multiple randomized baricitinib RA trials were performed to study neutrophil‐related transcripts (n = 1,651).ResultsBaseline levels of plasma neutrophil markers were elevated in patients with RA compared to healthy controls (P < 0.001). Receiving baricitinib reduced levels of soluble calprotectin at 12 and 24 weeks, especially in patients with RA responding to treatment, as determined by American College of Rheumatology 20% improvement criteria. Whole‐blood RNA analysis revealed similar changes in the predominant neutrophil markers calprotectin and Fcα receptor I upon reception of baricitinib in three randomized clinical trials involving patients with at various stages of disease‐modifying therapy. Clustering analysis of plasma activation markers showed elevated levels of calprotectin and NETs (eg, a neutrophil activation score, at baseline, could predict treatment response to baricitinib). In contrast, C‐reactive protein levels could not distinguish between responders and nonresponders.ConclusionNeutrophil activation markers may add clinical value in predicting treatment response to baricitinib and other drugs targeting RA. This study supports personalized medicine in treating patients with RA, not only based on symptoms but also based on immunophenotyping.
Alkaline Synthesis of Pure Silica ITH Zeolite for Vapor Phase Beckmann Rearrangement of Cyclohexanone Oxime
Authors: Luan Huimin , Zai Tianming , Wu Qinming , Meng Xiangju , Wu Jianping , Liu Weiliao , Sheng Na , Wang Han , Xiao Feng‐Shou 
Published: October 2024

AbstractPure silica ITH zeolite is normally synthesized under neutral or acidic conditions in the presence of HF, but it is challenging for synthesis of this zeolite under alkaline conditions. In this work, it is successful for alkaline synthesis of pure silica ITH in the absence of HF using a designed organic template containing F species, showing that the sample obtained has high crystallinity associated with ITH structure, nanosheet morphology, and rich silanol nests. Very importantly, this ITH zeolite exhibited better performance in vapor phase Beckmann rearrangement of cyclohexanone oxime than that of Silicalite‐1 zeolite, one of the best catalysts for this reaction. This work might offer a new opportunity for preparation of pure silica zeolites as efficient catalysts in the Beckmann rearrangement in the future.
Producing aromatic‐rich oil through microwave‐assisted catalytic pyrolysis of low‐density polyethylene over Ni/Co/Cu‐doped Ga/ZSM‐5 catalysts
Authors: Islam K. M. Oajedul , Ahmad Nabeel , Ahmed Usama , Siddiqui Mohammad Nahid , Ummer Aniz Chennampilly , Abdul Jameel Abdul Gani 
Published: October 2024

AbstractMicrowave (MW)‐assisted catalytic pyrolysis represents a promising method for transforming petroleum‐based plastic waste into valuable chemicals, offering a pathway towards more sustainable circular economy. In this study, catalytic pyrolysis of low‐density polyethylene (LDPE) was conducted under MW irradiation. The influence of various catalyst types (HZSM‐5, Ga/ZSM‐5, Ga/Ni/ZSM‐5, Ga/Co/ZSM‐5, and Ga/Cu/ZSM‐5) on product yield and distribution was examined. The results revealed that the Ga/ZSM‐5 catalyst yielded the maximum liquid oil, approximately 41%. Ga/Ni/ZSM‐5 performed excellently in the production of long‐chain olefins, constituting about 27% of the liquid fraction. However, Ga/Co/ZSM‐5 led to the production of heavy pyrolysis oil containing nearly 25% long‐chain paraffins, rendering it unsuitable for producing high‐value chemicals. Conversely, the Ga/Cu/ZSM‐5 catalyst yielded an aromatic‐rich pyrolysis oil, with benzene derivatives constituting approximately 90% of the liquid oil fraction, thus proving to be a suitable catalyst for the intended application. The liquid product distribution was compared with a petroleum assay by SimDist, and this suggested that utilizing the HZSM‐5 catalyst could yield an 86.4% naphtha fraction. The study also revealed that the Ga/Cu/ZSM‐5 catalyst generated the largest amounts of hydrogen and syngas, as determined by a MicroGC analysis of the gas products. This catalyst also exhibited the maximum coke deposition (1.35%) postreaction, which was attributed to its high aromatic hydrocarbon content in the pyrolysis oil and maximal hydrogen release. A comparison of fresh and spent catalyst properties was conducted to gain insights into catalyst activity and to correlate the effects of metal doping on product distribution. These findings underscore the potential of MW‐assisted catalytic pyrolysis, particularly with the Ga/Cu/ZSM‐5 catalyst, for the efficient conversion of plastic waste into valuable chemicals, thereby contributing to sustainable resource utilization and environmental conservation.
CXC chemokine receptor 4 ‐ mediated immune modulation and tumor microenvironment heterogeneity in gastric cancer: Utilizing multi‐omics approaches to identify potential therapeutic targets
Authors: Tang Jing , Wei Wei , Xu Yaoqing , Chen Kexin , Miao Yaping , Fan Weining , Huang Zhi , Liu Jie , Chen Ping , Luo Honghao , Wang Lexin 
Published: October 2024

AbstractG‐protein‐coupled receptors (GPRs) are critical regulators of various biological behaviors, and their role in gastric cancer (GC) progression is gaining increasing attention. Among them, the immune regulatory mechanisms mediated by chemokine receptor 4 (CXCR4) remain insufficiently understood. This study aims to explore the immune regulatory functions of CXCR4 and the heterogeneity of the tumor microenvironment (TME) by examining GPR‐related gene expression in GC. Through multi‐omics approaches, including spatial transcriptomics and single‐cell RNA sequencing, we investigated the oncogenic mechanisms of CXCR4, particularly its role in T cell immune exhaustion. In vitro experiments, including ELISA, PCR, CCK8 assays, cell scratch assays, and colony formation assays, were used to validate the role of CXCR4 in the migration and invasion of AGS and SNU‐1 cell lines. CXCR4 silencing using siRNA further demonstrated its regulatory effects on these cellular processes. Our results revealed a strong correlation between elevated CXCR4 expression and increased exhaustion of regulatory T cells (Tregs) in the TME. Furthermore, heightened CXCR4 expression was linked to increased TME heterogeneity, driven by oxidative stress and activation of the NF‐κB pathway, promoting immune evasion and tumor progression. Silencing CXCR4 significantly inhibited the invasive and proliferative abilities of AGS and SNU‐1 cells, while also reducing the expression of pro‐inflammatory cytokines IL‐1β and interleukin‐6, thus alleviating chronic inflammation and improving TME conditions. In conclusion, our comprehensive investigation highlights CXCR4 as a key mediator of TME dynamics and immune modulation in GC. Targeting CXCR4 presents a promising therapeutic strategy to slow tumor progression by reducing Tregs‐mediated immune exhaustion and TME heterogeneity, positioning it as a novel therapeutic target in GC treatment.
Delphinidin or α‐amyrin attenuated liver steatosis and metabolic disarrangement in rats fed a high‐fat diet
Authors: Ali Bassam Mohamed , Elbaz Eman M. , Al‐Mokaddem Asmaa K. , El‐Emam Soad Z. , Awny Magdy M. 
Published: October 2024

AbstractNon‐alcoholic fatty liver disease (NAFLD) is a liver pathology concomitant with metabolic disarrangement. This study assessed the therapeutic impacts of delphinidin, an anthocyanin, or α‐amyrin, a pentacyclic triterpenoid, on NAFLD in rats and the underlying mechanisms involved. NAFLD was established by feeding a high‐fat diet (HFD) for 10 weeks, either alone or in combination with delphinidin (40 mg/kg, oral) or α‐amyrin (20 mg/kg, oral). Delphinidin or α‐amyrin ameliorated the metabolic and histopathological perturbations induced by HFD. These compounds markedly attenuated NAFLD‐induced hepatic steatosis, as evidenced by a substantial decrease in body weight, insulin resistance, and liver and adipose tissue indices. Alongside normalization of the atherogenic index, both improved HFD‐mediated abnormalities in serum lipids, liver enzymes, leptin, and ghrelin levels. Moreover, their intervention activated the NFE2 like bZIP transcription factor 2 and heme oxygenase 1 pathways and abrogated HFD‐triggered activation of mitogen‐activated protein kinase 1 signaling. These remedies inhibited hepatic apoptosis and modulated the gene expression of lipogenic enzymes. Furthermore, histological analysis corroborated the suppression of lipid accumulation and amelioration of hepatic architecture in the treated rats. Our findings highlight the hepatoprotective value of delphinidin or α‐amyrin against NAFLD and related metabolic diseases through their insulin‐sensitizing, anti‐inflammatory, antioxidant, and antiapoptotic effects.
CH25H Promotes Autophagy and Regulates the Malignant Progression of Laryngeal Squamous Cell Carcinoma Through the PI3K‐AKT Pathway
Authors: Xiang Zhenfei , Yu Senquan , Xu Yuxin , Xiong Huacai , Hu Danfei , Li Qun , Wu Zhenhua 
Published: October 2024

ABSTRACTBackgroundLaryngeal squamous cell carcinoma (LSCC) is a type of cancer of the respiratory tract that often presents with subtle symptoms at the early stage and is susceptible to recurrence and metastasis.Materials and MethodsTo find out key regulatory genes involved in LSCC development, we downloaded LSCC‐related sequencing datasets for bioinformatics analysis. WGCNA was performed on GSE142083 and differential analysis was conducted on GSE51985 and TCGA‐HNSC. Intersection genes were taken from the above three datasets. To confirm the function of genes, we overexpressed and knocked down genes in cells and treated them with autophagy agonist Rapamycin and PI3K‐AKT pathway inhibitor. At the cellular level, the expression of CH25H, autophagy‐related proteins (LC3 I, LC3 II, p62, and Beclin 1), and PI3K‐AKT pathway‐related proteins (PI3K, AKT, and p‐AKT) were assessed via Western blot; the mRNA level of CH25H was evaluated through qRT‐PCR; the cell activity was examined by CCK8; the apoptosis was assessed through flow cytometry; and the cell migration and invasion were assessed through wound healing and Transwell assays.ResultsThrough bioinformatics analysis, we screened 7 genes (CH25H, NELL2, STC2, TMEM158, ZIC2, HOXD11, and HOXD10). Ultimately, CH25H was selected for follow‐up experiments. By detecting CH25H expression in human immortalized keratinocytes (HaCaT) and LSCC cells (Tu‐686, SNU899, and AMC‐HN‐8), it was found out that CH25H expression was higher in HaCaT cells than in LSCC cells. To elucidate the role of CH25H in LSCC development, we overexpressed CH25H in Tu‐686 cells and downregulated its expression in AMC‐HN‐8 cells. CH25H was revealed to reduce the proliferation, activity, invasion, and migration of LSCC cells while increasing their apoptosis levels. Significant changes were also observed in the expressions of autophagy‐ and PI3K‐AKT pathway‐related proteins. To further investigate the roles of autophagy and the PI3K‐AKT pathway in LSCC development, we respectively employed autophagy agonists and inhibitors targeting the PI3K‐AKT pathway to intervene the cells, and found that CH25H regulated the PI3K‐AKT pathway to promote autophagy, thus enhancing the apoptosis of LSCC cells. We further investigated CH25H's impact on tumor growth, autophagy, and the PI3K‐AKT pathway at the animal level and found that CH25H promoted autophagy of LSCC cells and inhibited the PI3K‐AKT pathway, and ultimately inhibiting the progression of LSCC.ConclusionsIn summary, CH25H promotes autophagy and affects the malignant progression of LSCC through the PI3K‐AKT pathway.
Anti‐Inflammatory Activities of New Compounds Isolated from the Fruits of Foeniculum Vulgare Mill
Authors: Dong Wei‐Mao , Zhang Yun‐Tao , Wang Hai‐Ming , Deng Mao‐Xin , Chen Zhang‐Xian , He Hong‐Ping , Dong Fa‐Wu 
Published: October 2024

AbstractForty‐nine compounds, including six previously unknown together with forty‐three known ones, were isolated from the fruits of Foeniculum vulgare Mill. Their structures were elucidated using high‐resolution electrospray ionization mass spectrometry (HR‐ESI‐MS), infrared spectroscopy (IR), ultraviolet‐visible spectroscopy (UV), nuclear magnetic resonance (NMR), and electronic circular dichroism (ECD) methods. All isolates were evaluated their anti‐inflammatory activity. The results indicated that compounds 1 and 6 inhibit lipopolysaccharide (LPS)‐induced nitric oxide production in RAW 264.7 macrophages with IC50 values of 41.77±1.80, 46.72±1.75 μmol/L, respectively. Moreover, the potential targets of the four active ingredients were explored through network pharmacology, revealing that SRC, TP53, AKT1, and PIK3CA may serve as key anti‐inflammatory targets. Additionally, the anti‐inflammatory activities of compounds 1–6 were first observed in this experiment.
Loureirin B Ameliorates Glycolipid Metabolism Disorders in Ob/ob Mice by Regulating Bile Acid Levels and Modulating Gut Microbiota Composition
Authors: Zhang Junyang , Zhang Xiaoyan , Li Gen , Ge Jun , Feng Xinchi 
Published: October 2024

AbstractLoureirin B (LB), an active component of Resina Draconis, exhibits hypoglycemic and hypolipidemic effects; however, its mode of action remains unclear. Here, ob/ob mice were utilized to investigate the effects of LB on the regulation of glucolipid metabolism disorders. Non‐targeted metabolomics and 16S rDNA sequencing were performed to elucidate the potential mechanisms involved. Results indicated that LB treatment (45 mg/kg) significantly improved glucose intolerance and insulin resistance, reduced lipid levels, and alleviated hepatic steatosis. Non‐targeted metabolomics analysis revealed that LB treatment regulated bile acid levels. Quantification of liver bile acids demonstrated that LB treatment significantly decreased the ratio of 12α‐OH to non‐12α‐OH bile acids in the liver. 16S rDNA sequencing results showed that LB treatment increased the abundance of short‐chain fatty acid‐producing microbiota while decreasing the abundance of bile salt hydrolase (BSH) enzyme‐producing microbiota. In conclusion, LB ameliorates glucolipid metabolism disorders by regulating liver bile acid levels and modulating the composition of the gut microbiota.
Identification of Potential Inhibitors of TGFβR1 for the Treatment of Cancer through Structure‐Based Virtual Screening and Molecular Dynamics Simulations
Authors: Rastogi Saumya , Shekher Mishra Shashank , Singh Lakhveer , Kumar Neeraj 
Published: October 2024

AbstractGlobally, cancer is one of the leading causes of death. Resistance to conventional medications, such as chemotherapy and radiation, continues to be a significant challenge in the treatment of cancer despite the availability of numerous medicines. Therefore, the highest priority is to hunt for new therapeutic agents. Transforming growth factor‐beta is a pivotal regulatory cytokine that exerts significant influence over cellular processes, particularly emphasizing its role in facilitating and modulating cell proliferation. TGF‐β receptor 1, identified as the most promising active site of the TGF‐β signaling, is a potent drug target site that has garnered wide attention for developing new anticancer agents. The present investigation investigates the potential natural products as TGFβR1 inhibitors. The SB431542 complexed TGFβR1 protein model was used to screen the natural product database to obtain a compound with high binding potential. NPC247629 has emerged as the best‐scored compound among all the screened compounds, demonstrating the highest affinity towards the TGFβR1 regarding docking score −17.54 kcal/mol. The all‐atoms MD simulation study indicated that all proposed hits are retained inside the receptor in dynamic states. Additionally, principal component and free energy landscape analysis were performed to explore the binding mechanism of top‐hit natural products. The best‐screened hits, NPC247629 and NPC60735, have excellent binding affinity and hold a massive potential for TGFβR1 inhibition, paving the way for promising future investigations in cancer treatment.
Synthesis, Biological Activities, and Molecular Docking Studies of 15‐Site Matrine Based Isatohydrazone Derivatives as Potential Anticancer Agents
Authors: Wu Yaqing , Kowah Jamal A. H. , Zhu Tianqi , Li Yufang , Wang Lisheng , Yu Haixia 
Published: October 2024

AbstractTo acquire matrine derivatives with enhanced anticancer activity, we designed and synthesized twenty‐one 15‐site matrine based isatohydrazone derivatives were designed and synthesized. The anti‐proliferative activity of all the compounds against human cervical cancer cells (HeLa), human colon cancer cells (HCT116), and non‐small cell lung cancer cells (A549) was examined by the MTT method. The majority of the compounds exhibited superior anticancer activity compared to matrine. Among them, compound 5a displayed the most potent anti‐proliferative activity, with IC50 values of 9.02±0.33 μM (HeLa), 10.49±1.09 μM (HCT116), and 15.23±0.12 μM (A549), respectively. Compound 5a can also induce cell cycle arrest in the G0/G1 phase and trigger apoptosis, as well as inhibit cell clonal formation and migration. Molecular docking experiments have demonstrated that compound 5a can form hydrogen bonds and hydrophobic interactions with EGFR‐related protein 7AEI.