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{"title":"Flipping the lab with AI support: a scalable model to address the theory-practice gap in analytical chemistry education.","authors":"Paulo R M Correia, Ian M Kinchin, Thiago R L C Paixão, David T Harvey","doi":"10.1007/s00216-025-05961-6","DOIUrl":"10.1007/s00216-025-05961-6","url":null,"abstract":"","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"4283-4290"},"PeriodicalIF":3.8,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144300865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Understanding the chemical stability of peptidomimetic therapeutics using high-resolution mass spectrometry: a study of terlipressin and its degradation products.","authors":"Ashwini Chawathe, Nitish Sharma","doi":"10.1007/s00216-025-05944-7","DOIUrl":"10.1007/s00216-025-05944-7","url":null,"abstract":"<p><p>Terlipressin, a synthetic 12-amino acid peptidomimetic of vasopressin, is a critical therapeutic agent for hepatorenal syndrome and oesophageal variceal hemorrhage. The inherent susceptibility of therapeutic peptides to hydrolytic and oxidative degradation necessitates thorough stability profiling. Conformational changes in the peptide, arising from hydrolysis and oxidative degradation, can hinder effective target binding and thereby diminish its capacity to elicit intended downstream effects, leading to reduced efficacy. For synthetic peptides, the most relevant stability testing principles are derived from the parent International Council for Harmonisation (ICH) stability testing guidelines Q1A(R2) and Q5C [1,2]. This study investigated the intrinsic degradation pathways of terlipressin under systematically varied stress conditions, including acidic, basic, neutral, and oxidative (H₂O₂) exposure at room temperature. Terlipressin exhibited sensitivity across all tested conditions, yielding a total of eleven distinct degradation products (DPs). To facilitate the separation of these DPs, a gradient reversed-phase high-performance liquid chromatography (RP-HPLC) method was developed utilizing an XSelect® CSH™ C18 (130 Å, 2.5 µm, 4.6 × 150 mm) column. The analytical assay method was validated according to ICH Q2(R1) guidelines. The intramolecular disulfide linkage between two cysteine residues presented a challenge for DP characterization. To address this, a chemical reduction strategy employing dithiothreitol (DTT) was integrated with ultra-high performance liquid chromatography-high resolution tandem mass spectrometry (UHPLC-HRMS/MS). This approach enabled the successful elucidation of the eleven DPs, revealing modifications such as truncation, deamidation, acetylation, and oxidation. The characterized fragmentation patterns and identified degradation products provide fundamental insights into the stability behavior of disulfide-containing therapeutic peptides, directly contributing to rational formulation design and development.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"4311-4329"},"PeriodicalIF":3.8,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144300866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Construction of a silver nanoparticle SERS aptamer-based sensor and its specific recognition of diazinon.","authors":"Xiaoying Yang, Qian Liu, Longhui Luo, Wei Tian, Chao Kang, Wanliang Yang, Tianxiang Li, Dongmei Chen, Xiufang Yan","doi":"10.1007/s00216-025-05956-3","DOIUrl":"10.1007/s00216-025-05956-3","url":null,"abstract":"<p><p>A novel biosensing strategy based on the synergy of aptamer molecular recognition and surface-enhanced Raman spectroscopy (SERS) has been developed to address the growing problem of groundwater and soil contamination by the organophosphorus pesticide diazinon (DZN). By combining a high-affinity aptamer with a plasmonic resonance-enhanced substrate, a SERS biosensing interface with single-molecule detection capability was successfully constructed, and the electrochemical surface-enhanced Raman spectroscopy (EC-SERS) method using AgNPs-modified screen-printed electrodes (SPEs) was also used for sensitive detection of DZN. The results showed that the constructed SERS aptamer sensor was able to specifically identify diazinon in the system where multiple interfering pesticides coexisted, and the detection limit of the sensor for diazinon was up to 5.33 × 10^-10 M. The intensity of the characteristic peaks (602 cm^-1) showed a good linear response with the concentration of DZN, which demonstrated very high detection sensitivity and specific identification function. The proposed EC-SERS method significantly improves the SERS signals of pesticides by potentiometrically modulating the plasmonic resonance coupling effect at the interface of AgNPs-modified electrodes, inducing an orientationally regularised arrangement of DZN molecules. The SERS aptasensor was used to detect diazinon in wastewater and subsurface soil with good recoveries (83.20%-117.78%), which were in good agreement with the results obtained by high-performance liquid chromatography. The results demonstrated that the SERS aptasensor has good sensitivity, stability, simplicity of operation, and specific identification, which provides a solution with ultra-sensitive response, rapid analysis, and strong anti-interference for the detection of trace pesticide.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"4407-4418"},"PeriodicalIF":3.8,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Navigating the participatory turn in agricultural and food research: Best practice from citizen science.","authors":"Raquel Ajates, Petra Benyei, Helen Avery, Egle Butkeviciene, Alexandra Czeglédi, Dominique Desclaux, Gerid Hager, Barbara Heinisch, Peter N Hoebe, Toos C G E van Noordwijk, Marco Barzman","doi":"10.1007/s13280-025-02151-7","DOIUrl":"10.1007/s13280-025-02151-7","url":null,"abstract":"<p><p>Food systems have enormous impacts on people and the planet, with agriculture and food research becoming strategic for many countries. However, the way this research is conducted and the rise of new agri-food technologies have ethical and socio-economic implications. To address these, many scholars are gaining interest in participatory methods, such as citizen science, but are unfamiliar with the latest debates on ethical and methodological issues surrounding non-academic stakeholder engagement. In this perspective paper, we revisit the European Citizen Science Association's (ECSA) Ten Principles of Citizen Science under the specific lens of agri-food research. The discussion presented is based on a review of the state of the art from academic literature, secondary data from agri-food citizen science projects, and the reflections of 11 scientist and practitioners, members of ECSA's Agri-Food Working Group. The findings reflect theoretical, methodological, and practical implications for navigating the participatory turn in agriculture and food research.</p>","PeriodicalId":461,"journal":{"name":"Ambio","volume":" ","pages":"1306-1317"},"PeriodicalIF":5.8,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12214145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Agonistic pluralism for enhancing the co-design of agri-environmental policy.","authors":"Charlotte-Anne Chivers, Lucy Barkley, Chris Short","doi":"10.1007/s13280-025-02158-0","DOIUrl":"10.1007/s13280-025-02158-0","url":null,"abstract":"<p><p>This study examines the role of agonistic pluralism in shaping policy co-design, including the development of agri-environment schemes. Embracing agonism may provide a democratic framework for deliberative co-design. By 'relinquishing all claims to finality, to happy endings', this involves embracing conflict rather than seeking consensus (McManus in Polity 40:509-525, 2008). By recognising and navigating power imbalances rather than eliminating them, it enhances co-design elements such as framing, facilitation, and ongoing negotiation. Although seemingly more time-consuming than less deliberative methods, this approach may prove efficient if it produces policies viewed as legitimate by diverse parties. In urgent contexts, adopting agonistic pluralism could foster rapid policy development by advancing 'good enough' ideas rather than pursuing unattainable consensus, particularly where complex challenges are being addressed. Furthermore, agonistic pluralism advocates for policies to remain flexible and continually evolve through meaningful negotiation, ensuring they are genuinely co-designed and adaptable to changing needs.</p>","PeriodicalId":461,"journal":{"name":"Ambio","volume":" ","pages":"1414-1430"},"PeriodicalIF":5.8,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12214143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and Validation of Biomarkers to Predict Early Diagnosis of Inflammatory Bowel Disease and Its Progression to Colorectal Cancer.","authors":"Farhat Khan, Naaziyah Abdulla, Thea-Leonie du Plessis, Kay Karlsson, Peter Barrow, Brendan Bebington, Liang Gu, Mandeep Kaur","doi":"10.1007/s10528-024-10917-z","DOIUrl":"10.1007/s10528-024-10917-z","url":null,"abstract":"<p><p>Inflammatory bowel disease (IBD) has become a common global health problem as prevalence continues to rise. It is often associated with increased risk of colorectal cancer (CRC) development. Limitations in current IBD biomarker-based diagnosis hinder the accuracy of early detection of CRC progression. Therefore, in this study, we proposed the use of transcription factor (TF)-based biomarkers that can potentially detect the transition of IBD to CRC. Various bioinformatic analysis and online database validations, and RT-qPCR validations were performed to identify possible diagnostic TFs. RUNX1 was identified as a promising TF that regulates 106 IBD/CRC-related genes. The incorporation of RUNX1 in combination with currently known IBD biomarkers, FEV + NFKB1 + RELA, achieved a comparable sensitivity and specificity scores of 99% and 87%, respectively, while RUNX1 in combination with known CRC markers, CEA + TIMP1 + CA724 + CA199, achieved a sensitivity and specificity score of 97% and 99%, respectively. Furthermore, a small pilot RT-qPCR-based analysis confirmed a demarcated shift in expression profiles in CA724, CEA, RUNX1 and TIMP1 in IBD patients compared to CRC patients' tissue samples. Specifically, CA724 is noticeably elevated in IBD, while the levels of CEA, RUNX1 with TIMP1 are probable genes that may be employed in discerning IBD progression to CRC. Therefore, these preliminary results once validated in large patient cohorts could potentially have a significant impact on CRC disease stratification, resulting in a more precise prediction for treatment and treatment outcomes, especially in South African patients.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"3717-3743"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12271286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational screening of umami tastants using deep learning.","authors":"Prantar Dutta, Kishore Gajula, Nitu Verma, Deepak Jain, Rakesh Gupta, Beena Rai","doi":"10.1007/s11030-024-11006-4","DOIUrl":"10.1007/s11030-024-11006-4","url":null,"abstract":"<p><p>Umami, a fundamental human taste modality, refers to the savory flavors in meats and broths, often associated with monosodium glutamate and protein richness. With limited knowledge of umami molecules, the food industry seeks efficient approaches for identifying novel tastants. In this study, we have devised a virtual screening pipeline for identifying highly potent umami tastants from large molecular databases. We curated the most extensive classification dataset containing 439 umami and 428 non-umami molecules and trained a transformer-based architecture to differentiate between the two classes, achieving 93% accuracy. Additionally, we built a neural network model for predicting the potency of umami compounds, the first effort of its kind. The classification and potency prediction models were combined with similarity analysis and toxicity screening to build an end-to-end virtual framework for the rational discovery of novel tastants. We applied this framework to the FooDB database containing around 70,000 molecules as an illustrative use case for screening potent umami compounds. The screened molecules were validated using molecular docking with the umami taste receptor. This study demonstrates the potential of data-driven methods in discovering new tastants from structural and chemical features of molecules and proposes an efficient implementation for industrial applications.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":"2979-2993"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning models to identify lead compound and substitution optimization to have derived energetics and conformational stability through docking and MD simulations for sphingosine kinase 1.","authors":"Anantha Krishnan Dhanabalan, Velmurugan Devadasan, Jebiti Haribabu, Gunasekaran Krishnasamy","doi":"10.1007/s11030-024-10997-4","DOIUrl":"10.1007/s11030-024-10997-4","url":null,"abstract":"<p><p>Sphingosine kinases (SphKs) are a group of important enzymes that circulate at low micromolar concentrations in mammals and have received considerable attention due to the roles they play in a broad array of biological processes including apoptosis, mutagenesis, lymphocyte migration, radio- and chemo-sensitization, and angiogenesis. In the present study, we constructed three classification models by four machine learning (ML) algorithms including naive bayes (NB), support vector machine (SVM), logistic regression, and random forest from 395 compounds. The generated ML models were validated by fivefold cross validation. Five different scaffold hit fragments resulted from SVM model-based virtual screening and docking results indicate that all the five fragments exhibit common hydrogen bond interaction a catalytic residue of SphK1. Further, molecular dynamics (MD) simulations and binding free energy calculation had been carried out with the identified five fragment leads and three cocrystal inhibitors. The best 15 fragments were selected. Molecular dynamics (MD) simulations showed that among these compounds, 7 compounds have favorable binding energy compared with cocrystal inhibitors. Hence, the study showed that the present lead fragments could act as potential inhibitors against therapeutic target of cancers and neurodegenerative disorders.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":"2945-2977"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Drug repurposing to identify potential FDA-approved drugs targeting three main angiogenesis receptors through a deep learning framework.","authors":"Mohammadreza Torabi, Soroush Sardari, Alejandro Rodríguez-Martínez, Nooshin Arabi, Horacio Pérez-Sánchez, Fahimeh Ghasemi","doi":"10.1007/s11030-025-11214-6","DOIUrl":"10.1007/s11030-025-11214-6","url":null,"abstract":"<p><p>Tumor cell survival depends on the presence of oxygen and nutrients provided by existing blood vessels, particularly when cancer is in its early stage. Along with tumor growth in the vicinity of blood vessels, malignant cells require more nutrients; hence, capillary sprouting occurs from parental vessels, a process known as angiogenesis. Although multiple cellular pathways have been identified, controlling them with one single biomolecule as a multi-target inhibitor could be an attractive strategy for reducing medication side effects. Three critical pathways in angiogenesis have been identified, which are activated by the vascular endothelial growth factor receptor (VEGFR), fibroblast growth factor receptor (FGFR), and epidermal growth factor receptor (EGFR). This study aimed to develop a methodology to discover multi-target inhibitors among over 2000 FDA-approved drugs. Hence, a novel ensemble approach was employed, comprising classification and regression models. First, three different deep autoencoder classifications were generated for each target individually. The top 100 trained models were selected for the high-throughput virtual screening step. After that, all identified molecules with a probability of more than 0.9 in more than 70% of the models were removed to ensure accurate consideration in the regression step. Since the ultimate aim of virtual screening is to discover molecules with the highest success rate in the pharmaceutical industry, various aspects of the molecules in different assays were considered by integrating ten different regression models. In conclusion, this paper contributes to pharmaceutical sciences by introducing eleven diverse scaffolds and eight approved drugs that can potentially be used as inhibitors of angiogenesis receptors, including VEGFR, FGFR, and EGFR. Considering three target receptors simultaneously is another central concept and contribution used. This concept could increase the chance of success, while reducing the possibility of resistance to these agents.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":"3637-3659"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Left coronary artery biomechanics: a characterization study using fluid structure interaction simulations.","authors":"Marina Fandaros, Chloe Kwok, Zachary Wolf, Michael Shearer, Johnathan Scheiner, Yulee Li, J Jane Cao, Wei Yin","doi":"10.1007/s10237-025-01974-3","DOIUrl":"10.1007/s10237-025-01974-3","url":null,"abstract":"<p><p>Patient-specific coronary artery biomechanics studies often have limited sample size. The goals of this study were: (1) To develop more patient-specific FSI models to expand current research effort in characterizing hemodynamic and biomechanical conditions within the coronary arteries; (2) to compare some of our model outputs, especially FSI model-generated vFFR values, to those provided by HeartFlow, to evaluate the clinical relevance of our model results. Ten healthy LCA geometries were used to develop patient-specific FSI models using COMSOL Multiphysics. The hemodynamic and biomechanical environment in the arterial wall were assessed, along the proximal, mid, and distal portions of the left anterior descending coronary artery (LAD). The FSI model-calculated vFFR was compared to the matched HeartFlow reports. All FSI models indicated healthy perfusion. There was a good agreement with the HeartFlow calculation in the proximal LAD. The FSI model results indicated that the wall stresses were below the rupture thresholds. However, variations were observed along the arterial length in the von-Mises stress and strains. The FSI models offered improved physiological relevance for LCA simulation by including a large field of view. The biomechanical parameters were minimally related to geometric features, necessitating this procedure. This FSI modeling approach presented a few limitations. More work is needed to address these limitations and improve the physiological relevance of FSI modeling, so it can serve as a non-invasive method to assess the biomechanics of the coronary arteries, to support clinician's decision making.</p>","PeriodicalId":489,"journal":{"name":"Biomechanics and Modeling in Mechanobiology","volume":" ","pages":"1385-1400"},"PeriodicalIF":3.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}