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Polysaccharides from sea cucumbers are known for their biological activities, but little is known about those from sea cucumber viscera. The present study isolated a sulfated polysaccharide (SCVP-2) from the viscera of Apostichopus japonicas, which had a molecular weight of 209.1 kDa. SCVP-2 comprised 66.3 % total sugars, 2.1 % uronic acid, 4.5 % proteins, and 25.5 % sulfate groups, containing glucosamine, galactosamine, glucose, galactose, and fucose. FT-IR and NMR analyses identified SCVP-2 as a fucoidan sulfate with sulfation patterns of the fucose branches as Fuc2S, Fuc4S, and Fuc0S. SEM and AFM analyses showed irregular clusters and linear conformations. SCVP-2 demonstrated strong anti-inflammatory properties both in vitro and in vivo. In lipopolysaccharide (LPS)-induced inflammation in macrophage RAW264.7 cells, SCVP-2 significantly reduced nitric oxide (NO) and cytokine secretion (IL-1ß, IL-6, TNF-α). Additionally, it downregulated the expression of these cytokine genes. Furthermore, the anti-inflammatory mechanism of SCVP-2 was related to the inhibition of the MAPKs and NF-κB pathways. SCVP-2's anti-inflammatory capacity was confirmed in acute inflammation models, including xylene-induced ear swelling and acetic acid-induced peritoneal capillary permeability, and in high-fat diet-induced systemic low-grade chronic inflammation. In conclusion, SCVP-2 exhibits significant anti-inflammatory activity, suggesting its potential for development as a functional food ingredient or therapeutic agent for inflammation-related diseases.

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In marine ecosystems, communication among microorganisms is crucial since the distance is significant if considered on a microbial scale. One of the ways to reduce this gap is through the production of extracellular vesicles, which can transport molecules to guarantee nutrients to the cells. Marine bacteria release extracellular vesicles (EVs), small membrane-bound structures of 40 nm to 1 µm diameter, into their surrounding environment. The vesicles contain various cellular compounds, including lipids, proteins, nucleic acids, and glycans. EVs may contribute to dissolved organic carbon, thus facilitating heterotroph growth. This review will focus on marine bacterial EVs, analyzing their structure, composition, functions, and applications.

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BACKGROUND: Panax ginseng C. A. Mey is a precious medicinal resource that could be used to treat a variety of diseases. Saponins are the most important bioactive components of, and rare ginsenosides (Rg3, Rh2, Rk1 and Rg5, etc.) refer to the chemical structure changes of primary ginsenosides through dehydration and desugarization reactions, to obtain triterpenoids that are easier to be absorbed by the human body and have higher activity. PURPOSE: At present, the research of P. ginseng. is widely focused on anticancer related aspects, and there are few studies on the antibacterial and skin protection effects of rare ginsenosides. This review summarizes the rare ginsenosides related to bacterial inhibition and skin protection and provides a new direction for P. ginseng research. METHODS: PubMed and Web of Science were searched for English-language studies on P. ginseng published between January 2002 and March 2024. Selected manuscripts were evaluated manually for additional relevant references. This review includes basic scientific articles and related studies such as prospective and retrospective cohort studies. CONCLUSION: This paper summarizes the latest research progress of several rare ginsenosides, discusses the antibacterial effect of rare ginsenosides, and finds that ginsenosides can effectively protect the skin and promote wound healing during use, so as to play an efficient antibacterial effect, and further explore the other medicinal value of ginseng. It is expected that this review will provide a wider understanding and new ideas for further research and development of P. ginseng drugs.

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In this work, phosphorylated cellulosic fibers were functionalized with an aminosilane ((3-aminopropyl)triethoxysilane, APTES) using a simple and economical method. Several characterization were performed to determine the types of bonds between phosphorylated fibers and grafted APTES. The thermal behavior, hydrophobicity and surface charge variation as a function of pH of the multifunctional cellulose fibers were determined. Results demonstrate that APTES should proceed through Si-O-C, and possibly Si-O-P, covalent bonds with cellulose although the dimerization of silane through Si-O-Si bonds has also been observed. The terminal amino groups are expected to be partially involved in hydrogen bonds with phosphate hydroxyl groups found at phosphorylated cellulose fiber surface, causing a pulling in the configuration of the grafted APTES. The two chemical modifications proposed in this work do not significantly modify the morphology of cellulose fibers. XRD analysis also shows that the crystal structure of the phosphorylated fibers did not change after functionalization with APTES. The silylated phosphorylated fibers show potential flame-retardant properties with improved hydrophobicity. Furthermore, the functionalization of phosphorylated fibers with APTES changes the pH of zero charge point from 3.2 to 9.4 and providing a zwitterionic structure suitable for the simultaneous adsorption of both cationic and anionic species.

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The macrophage to myofibroblasts transition (MMT) has been reported as a newly key target in renal fibrosis. Lycium barbarum L. is a traditional Chinese medicine for improving renal function, in which its polysaccharides (LBPs) are the mainly active components. However, whether the role of LBPs in treating renal fibrosis is related to MMT process remain unclear. The purpose of this study was to explore the relationship between the regulating effect on MMT process and the anti-fibrotic effect of LBPs. Initially, small molecular weight LBPs fractions (LBP-S) were firstly isolated via Sephadex G-100 column. Then, the potent inhibitory effect of LBP-S on MMT process was revealed on bone marrow-derived macrophages (BMDM) model induced by TGF-ß. Subsequently, the chemical structure of LBP-S was elucidated through monosaccharide, methylation and NMR spectrum analysis. In vivo biodistribution characteristics studies demonstrated that LBP-S exhibited effectively accumulation in kidney via intraperitoneal administration. Finally, LBP-S showed a satisfactory anti-renal fibrotic effect on unilateral ureteral obstruction operation (UUO) mice, which was significantly reduced following macrophage depletion. Overall, our findings indicated that LPB-S could alleviate renal fibrosis through regulating MMT process and providing new candidate agents for chronic kidney disease (CKD) related fibrosis treatment.

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Fe-N-C materials have been regarded as one of the potential candidates to replace traditional noble-metal-based electrocatalysts for the oxygen reduction reaction (ORR). It is believed that the structure of carbon support in Fe-N-C materials plays an essential role in highly efficient ORR. However, precisely designing the morphology and surface chemical structure of carbon support remains a challenge. Herein, we present a novel synthetic strategy for the preparation of porous carbon spheres (PCSs) with high specific surface area, well-defined pore structure, tunable morphology and controllable heteroatom doping. The synthesis involves Schiff-based polymerization utilizing octaaminophenyl polyhedral oligomeric silsesquioxane (POSS-NH2) and heteroatom-containing aldehydes, followed by pyrolysis and HF etching. The well-defined pore structure of PCS can provide the confinement field for ferroin and transform into Fe-N-C sites after carbonization. The tunable morphology of PCS can be easily achieved by changing the solvents. The surface chemical structure of PCS can be tailored by utilizing different heteroatom-containing aldehydes. After optimizing the structure of PCS, Fe-N-C loading on N,S-codoped porous carbon sphere (NSPCS-Fe) displays outstanding ORR activity in alkaline solution. This work paves a new path for fabrication of Fe-N-C materials with the desired morphology and well-designed surface chemical structure, demonstrating significant potential for energy-related applications.

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Integration of glycan-related databases between different research fields is essential in glycoscience. It requires knowledge across the breadth of science because most glycans exist as glycoconjugates. On the other hand, especially between chemistry and biology, glycan data has not been easy to integrate due to the huge variety of glycan structure representations. We have developed WURCS (Web 3.0 Unique Representation of Carbohydrate Structures) as a notation for representing all glycan structures uniquely for the purpose of integrating data across scientific data resources. While the integration of glycan data in the field of biology has been greatly advanced, in the field of chemistry, progress has been hampered due to the lack of appropriate rules to extract sugars from chemical structures. Thus, we developed a unique algorithm to determine the range of structures allowed to be considered as sugars from the structural formulae of compounds, and we developed software to extract sugars in WURCS format according to this algorithm. In this manuscript, we show that our algorithm can extract sugars from glycoconjugate molecules represented at the molecular level and can distinguish them from other biomolecules, such as amino acids, nucleic acids, and lipids. Available as software, MolWURCS is freely available and downloadable ( https://gitlab.com/glycoinfo/molwurcs ).

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Our previously reported HDAC6 inhibitor (HDAC6i) Marbostat-100 (4) has provided many arguments for further clinical evaluation. By the substitution of the acidic hydrogen of 4 for different carbon residues, we were able to generate an all-carbon stereocenter, which significantly improves the hydrolytic stability of the inhibitor. Further asymmetric synthesis has shown that the (S)-configured inhibitors preferentially bind to HDAC6. This led to the highly selective and potent methyl-substituted derivative S-29b, which elicited a long-lasting tubulin hyperacetylation in MV4-11 cells. Finally, a crystal structure of the HDAC6/S-29b complex provided mechanistic explanation for the high potency and stereoselectivity of synthesized compound series.

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To facilitate the application of rhamnogalacturonan-I (RG-I)-enriched pectins (RGPs) as novel, healthy, and gelling food additives, this study compared the structural characteristics and gelling properties of RGPs extracted from citrus peel via four methods (alkali: AK, high-temperature/pressure: TP, citric acid: CA, and enzyme-assisted: EA extractions). AK and CA yielded pectins with the highest RG-I proportions (54.8 % and 51.9 %, respectively) by disrupting the homogalacturonan region; TP and EA increased the RG-I proportions by ~10 %. Among the four methods, AK induced the lowest degree of esterification (DE) (6.7 %) and longer side chains that form strong entanglement, contributing to its highest gel hardness. The relatively low DE (18.5 %) of CA RGP facilitated stable gel formation. Notably, its highly branched RG-I region afforded more intramolecular hydrophobic interactions, making a more highly cross-linked gel network of better gel resilience. In contrast, TP induced the highest DE (57 %) and curved molecular chains; it inhibited Ca2+ binding, entanglement, and intramolecular hydrophobic interactions, and thus no gel formed. EA RGP was associated with the lowest molecular size, rendering it more difficult for Ca2+ to form links, which resulted no gel. These findings offer insights into the relationship among the extraction methods, molecular structures, and gelling properties of RGPs.

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Opioids are small-molecule agonists of µ-opioid receptor (µOR), while reversal agents such as naloxone are antagonists of µOR. Here, we developed machine learning (ML) models to classify the intrinsic activities of ligands at the human µOR based on the SMILES strings and two-dimensional molecular descriptors. We first manually curated a database of 983 small molecules with measured Emax values at the human µOR. Analysis of the chemical space allowed identification of dominant scaffolds and structurally similar agonists and antagonists. Decision tree models and directed message passing neural networks (MPNNs) were then trained to classify agonistic and antagonistic ligands. The hold-out test AUCs (areas under the receiver operator curves) of the extra-tree (ET) and MPNN models are 91.5 ± 3.9% and 91.8 ± 4.4%, respectively. To overcome the challenge of a small data set, a student-teacher learning method called tritraining with disagreement was tested using an unlabeled data set comprised of 15,816 ligands of human, mouse, and rat µOR, κOR, and δOR. We found that the tritraining scheme was able to increase the hold-out AUC of MPNN models to as high as 95.7%. Our work demonstrates the feasibility of developing ML models to accurately predict the intrinsic activities of µOR ligands, even with limited data. We envisage potential applications of these models in evaluating uncharacterized substances for public safety risks and discovering new therapeutic agents to counteract opioid overdoses.

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Gastrodia elata Blume (G. elata), listed as one of the 34 precious Chinese medicines, servers a dual purpose as both a medicinal herb and a food source. Polysaccharide is the main active ingredient in G. elata, which has pharmacological activities such as immune regulation, anti-oxidation, anti-cancer, anti-aging, neuroprotection and antibacterial activity and so on. The biological activities of G. elata polysaccharide (GPs) is closely related to its chemical structures. However, no a review has synthetically summarized the chemical structures and pharmacological activities of GPs. This study delves into the chemical structures, pharmacological action of GPs, offering insights for the future development an application of these compounds.

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Accurate recognition of hand-drawn chemical structures is crucial for digitising hand-written chemical information in traditional laboratory notebooks or facilitating stylus-based structure entry on tablets or smartphones. However, the inherent variability in hand-drawn structures poses challenges for existing Optical Chemical Structure Recognition (OCSR) software. To address this, we present an enhanced Deep lEarning for Chemical ImagE Recognition (DECIMER) architecture that leverages a combination of Convolutional Neural Networks (CNNs) and Transformers to improve the recognition of hand-drawn chemical structures. The model incorporates an EfficientNetV2 CNN encoder that extracts features from hand-drawn images, followed by a Transformer decoder that converts the extracted features into Simplified Molecular Input Line Entry System (SMILES) strings. Our models were trained using synthetic hand-drawn images generated by RanDepict, a tool for depicting chemical structures with different style elements. A benchmark was performed using a real-world dataset of hand-drawn chemical structures to evaluate the model's performance. The results indicate that our improved DECIMER architecture exhibits a significantly enhanced recognition accuracy compared to other approaches. SCIENTIFIC CONTRIBUTION: The new DECIMER model presented here refines our previous research efforts and is currently the only open-source model tailored specifically for the recognition of hand-drawn chemical structures. The enhanced model performs better in handling variations in handwriting styles, line thicknesses, and background noise, making it suitable for real-world applications. The DECIMER hand-drawn structure recognition model and its source code have been made available as an open-source package under a permissive license.

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A new polysaccharide, named SP40015A01, was obtained from Saposhnikoviae Radix by water extraction, isolation and purification. SP40015A01 (9.7 × 105 Da) is composed of Rhamnose (Rha), Galacturonic acid (GalA), Galactose (Gal), and Arabinose (Ara) with the proportion of 1.6:85.6:5.8:7.6. The backbone of SP40015A01 is composed of 3-α-GalAp, 2-α-GalAp, 2,3-ß-GalAp and 2,3-ß-Galp, and branched at C3 of 2,3-ß-GalAp, C3 of 2,3-ß-Galp. Zebrafish experiments were used to explore the immunomodulatory activity of SP40015A01. Results showed that SP40015A01 could significantly improve the neutrophils density of immunocompromised zebrafish and reduce the content of nitric oxide (NO) and interleukin-1ß (IL-1ß). This study demonstrated that SP40015A01 has significant immunomodulatory activity, which can improve the neutrophils density and reduce inflammatory factor content, suggesting SP40015A01 may be a potential immunomodulator in Saposhnikoviae Radix (SR) for treatment of hypoimmunity related disease. This study supplemented the research on the polysaccharide components in traditional Chinese medicine and provided a scientific explanation for the development and clinical applications of SR.

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Microbial colonization on plastic polymers has been extensively explored, however the temporal dynamics of biofilm community in Antarctic environments are almost unknown. As a contribute to fill this knowledge gap, the structural characteristics and microbial diversity of the biofilm associated with polyvinyl chloride (PVC) and polyethylene (PE) panels submerged at 5 m of depth and collected after 3, 9 and 12 months were investigated in four coastal sites of the Ross Sea. Additional panels placed at 5 and 20 m were retrieved after 12 months. Chemical characterization was performed by FTIR-ATR and Raman (through Surface-Enhanced Raman Scattering, SERS) spectroscopy. Bacterial community composition was quantified at a single cell level by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) and Confocal Laser Scanning Microscopy (CLSM); microbial diversity was assessed by 16S rRNA gene sequencing. This multidisciplinary approach has provided new insights into microbial community dynamics during biofouling process, shedding light on the biofilm diversity and temporal succession on plastic substrates in the Ross Sea. Significant differences between free-living and microbial biofilm communities were found, with a more consolidated and structured community composition on PVC compared to PE. Spectral features ascribable to tyrosine, polysaccharides, nucleic acids and lipids characterized the PVC-associated biofilms. Pseudomonadota (among Gamma-proteobacteria) and Alpha-proteobacteria dominated the microbial biofilm community. Interestingly, in Road Bay, close to the Italian "Mario Zucchelli" research station, the biofilm growth - already observed during summer season, after 3 months of submersion - continued afterwards leading to a massive microbial abundance at the end of winter (after 12 months). After 3 months, higher percentages of Gamma-proteobacteria in Road Bay than in the not-impacted site were found. These observations lead us to hypothesize that in this site microbial fouling developed during the first 3 months could serve as a starter pioneering community stimulating the successive growth during winter.

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OBJECTIVES: Sometimes clinical efficacy and potential risk of therapeutic and toxic agents are difficult to predict over a long period of time. Hence there is need for literature search with a view to assessing cause of toxicity and less efficacy of drugs used in clinical practice. METHOD: Hence literatures were searched for physicochemical properties, chemical formulas, molecular masses, pH values, ionization, receptor type, agonist and antagonist, therapeutic, toxic and structure-activity relationship of chemical compounds with pharmacophore and toxicophore, with a view to identifying high efficacious and relative low toxic agents. Inclusion criteria were manuscripts published on PubMed, Scopus, Web of Science, PubMed Central, Google Scholar among others, between 1960 and 2023. Keywords such as pharmacophore, toxicophore, structure-activity-relationship and disease where also searched. The exclusion criteria were the chemicals that lack pharmacophore, toxicophore and manuscripts published before 1960. RESULTS: Findings have shown that pharmacophore and toxicophore functional groups determine clinical efficacy and safety of therapeutics, but if they overlap therapeutic and toxicity effects go concurrently. Hence the functional groups, dose, co-administration and concentration of drugs at receptor, drug-receptor binding and duration of receptor binding are the determining factors of pharmacophore and toxicophore activity. Molecular mass, chemical configuration, pH value, receptor affinity and binding capacity, multiple pharmacophores, hydrophilic/lipophilic nature of the chemical contribute greatly to functionality of pharmacophore and toxicophore. CONCLUSION: Daily single therapy, avoidance of reversible pharmacology, drugs with covalent adduct, maintenance of therapeutic dose, and the use of multiple pharmacophores for terminal diseases will minimize toxicity and improve efficacy.

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Small interfering RNAs (siRNAs) are revolutionizing the treatment of liver-associated indications. Yet, robust delivery to extrahepatic tissues remains a challenge. Conjugating lipids (e.g., docosanoic acid [DCA]) to siRNA supports extrahepatic delivery, but tissue accumulation remains lower than that achieved in liver by approved siRNA therapeutics. Early evidence suggests that functionalizing DCA with a head group (e.g., phosphatidylcholine [PC]) may enhance delivery to certain tissues. Here, we report the first systematic evaluation of the effect of PC head group chemistry on the extrahepatic distribution of DCA-conjugated siRNAs. We show that functionalizing DCA with a PC head group enhances siRNA accumulation in heart, muscle, lung, pancreas, duodenum, urinary bladder, and fat. Varying the size of the linker between the phosphate and choline moiety of the PC head group altered the extrahepatic accumulation of siRNA, with the optimal linker length being different for different tissues. Increasing PC head group valency also improved extrahepatic accumulation in a tissue-specific manner. This study demonstrates the structural impact of the PC moiety on the biodistribution of lipid-conjugated siRNA and introduces multiple novel PC variants for the chemical optimization of DCA-conjugated siRNA. These chemical variants can be used in the context of other lipids to increase the repertoire of conjugates for the extrahepatic distribution of siRNAs.

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Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.

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Chemokines, also known as chemotactic cytokines, stimulate the migration of immune cells. These molecules play a key role in the pathogenesis of inflammation leading to atherosclerosis, neurodegenerative disorders, rheumatoid arthritis, insulin-resistant diabetes, and cancer. Moreover, they take part in inflammatory bowel disease (IBD). The main objective of our research was to determine the activity of methyl-derivatives of flavanone, namely, 2'-methylflavanone (5B), 3'-methylflavanone (6B), 4'-methylflavanone (7B), and 6-methylflavanone (8B), on the releasing of selected cytokines by RAW264.7 macrophages activated by LPS. We determined the concentration of chemokines belonging to the CC chemokine family, namely, MCP-1, MIP-1ß, RANTES, and eotaxin, using the Bio-Plex Magnetic Luminex Assay and the Bio-PlexTM 200 System. Among the tested compounds, only 5B and 6B had the strongest effect on inhibiting the examined chemokines' release by macrophages. Therefore, 5B and 6B appear to be potentially useful in the prevention of diseases associated with the inflammatory process.

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Cyclosporine A (CyA) holds significant importance as a strategic immunosuppressive drug for organ transplant patients. In this study, we aimed to produce pure and cost-effective Cyclosporine A (CyA) by fermenting a culture medium containing dairy sludge, using Tolypocladium inflatum PTCC 5253. Following the fermentation stage, ethyl acetate extraction and fast protein liquid chromatography were employed for sample purification. The initial evaluation of the effectiveness of CyA obtained from these processes was performed through bioassay, wherein the antimicrobial clear zone diameter was found to be larger compared to the sample obtained from the fermentation culture. The concentration of CyA was determined using high-performance liquid chromatography, yielding values of 334 mg/L, 456 mg/L, and 578 mg/L for the fermented, extracted, and purified samples, respectively. Further analysis utilizing liquid chromatography tandem mass spectrometry (LC/MS/MS) confirmed a purity of 91.9% and proper agreement with the standard sample based on the ion intensity of Z/m 1205. To validate the structure of CyA, nuclear magnetic resonance spectroscopy, Fourier-transform infrared (FT-IR), and Raman spectroscopy were employed. X-ray diffraction and differential scanning calorimetry analyses demonstrated that the purified CyA exhibited a crystal structure similar to the standard sample, characterized by two broad peaks at 2θ = 9° and 20°, and comparable glass transition temperatures (57-68 °C for the purified sample; 53-64 °C for the standard sample). Dynamic light scattering analysis confirmed a uniform particle size distribution in both the purified and standard samples. The zeta potentials of the purified and standard samples were determined to be - 25.8 ± 0.16 and - 23.63 ± 0.12 mV, respectively. Our results demonstrate that dairy sludge can serve as a suitable culture medium for the production of (CyA).

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