IF 3.1

BioTech Pub Date : 2025-08-26 DOI: 10.3390/biotech14030065

Jagoš Golubović, Damjan Vučurović

{"title":"Biomaterials and Tissue Engineering in Neurosurgery: Current Innovations and Future Directions.","authors":"Jagoš Golubović, Damjan Vučurović","doi":"10.3390/biotech14030065","DOIUrl":"10.3390/biotech14030065","url":null,"abstract":"Neurosurgery is undergoing a significant transformation driven by advances in biomaterials and tissue engineering. These interdisciplinary innovations address challenges in repairing and regenerating neural tissues, integrating cranial and spinal implants, and improving patient outcomes. The incidence of neurological injuries such as traumatic brain injury and spinal cord injury remains high, underscoring the need for improved therapeutic strategies. This review provides a comprehensive overview of current biomaterial and tissue engineering approaches in neurosurgery, highlighting developments in neural tissue repair, cranial and spinal implants, spinal cord injury treatment, and peripheral nerve regeneration. Key challenges-such as ensuring biocompatibility, modulating the immune response, and bridging the gap between laboratory research and clinical application-are discussed. Emerging technologies including 3D bioprinting, nanotechnology (removing microfluidics), and microfluidics are examined for their potential to revolutionize neurosurgical treatments. The need for interdisciplinary collaboration among neurosurgeons, material scientists, and biologists is emphasized as critical for overcoming translational barriers and accelerating the clinical translation of these promising technologies.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"14 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12452776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Translocation of Insecticidal Bt Protein in Transgrafted Plants. Bt杀虫蛋白在移植物中的易位研究。

IF 3.1

BioTech Pub Date : 2025-08-25 DOI: 10.3390/biotech14030064

Arisa Ando, Hitomi Ohkubo, Hisae Maki, Takumi Nishiuchi, Takumi Ogawa, Tomofumi Mochizuki, Daisaku Ohta, Hiroaki Kodama, Taira Miyahara

{"title":"Translocation of Insecticidal Bt Protein in Transgrafted Plants.","authors":"Arisa Ando, Hitomi Ohkubo, Hisae Maki, Takumi Nishiuchi, Takumi Ogawa, Tomofumi Mochizuki, Daisaku Ohta, Hiroaki Kodama, Taira Miyahara","doi":"10.3390/biotech14030064","DOIUrl":"10.3390/biotech14030064","url":null,"abstract":"Transgrafting constitutes a technique involving the integration of genetically modified (GM) and non-GM plant organisms. Typically, edible components derived from non-GM scions are categorized as non-GM food products, attributed to the absence of exogenous genetic material within their respective genomes. Non-GM food status could be compromised if proteins translocated across the graft interface. We investigated the movement of insecticidal Bacillus thuringiensis (Bt) crystal proteins, widely utilized in GM crop species. Tobacco plants engineered to express the Cry1Ab gene exhibited trace levels of Cry1Ab protein accumulation. In transgrafted plants, translocated Cry1Ab protein originating from GM rootstocks was detectable within scion foliar tissues but not within the seeds obtained from the non-GM scion. This result unequivocally demonstrates the capacity for Bt protein translocation from rootstocks to scions yet indicates a constrained distribution confined to scion tissues relatively close to the graft junction. While regulatory considerations necessitate a thorough appraisal of potential risks associated with Bt proteins, the results shown here facilitate the commercialization of the edible components as non-GM food products.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"14 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12452608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145114273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhancing In Vitro Regeneration in Three Sweet Potato Genotypes: Interplay Between Disinfectant, Explant Age, and Genotype. 促进三种基因型甘薯离体再生：消毒剂、外植体年龄和基因型的相互作用

IF 3.1

BioTech Pub Date : 2025-08-19 DOI: 10.3390/biotech14030063

El Hadj Hussein Tapily, Kan Modeste Kouassi, Marius Konan Kouassi, John Steven S Seka, Fidèle Tiendrébéogo, Justin S Pita

{"title":"Enhancing In Vitro Regeneration in Three Sweet Potato Genotypes: Interplay Between Disinfectant, Explant Age, and Genotype.","authors":"El Hadj Hussein Tapily, Kan Modeste Kouassi, Marius Konan Kouassi, John Steven S Seka, Fidèle Tiendrébéogo, Justin S Pita","doi":"10.3390/biotech14030063","DOIUrl":"10.3390/biotech14030063","url":null,"abstract":"Regenerating sweet potato from field-derived plant material requires careful management of several critical factors, including the effectiveness of the disinfectant, the age of the explant, and the genotype used. In this context, establishing a reliable aseptic protocol is essential for successful in vitro culture. This study aimed to assess the effects of two disinfectants (sodium hypochlorite and mercuric chloride), three sweet potato genotypes (Nakabo, Boyapleu, and Irene), and three explant ages (2, 3, and 4 weeks) on clean culture establishment and regeneration efficiency from nodal explants. The findings revealed that regeneration success is significantly influenced by the type and concentration of disinfectant, explant age, and genotype. Treatment with 10% sodium hypochlorite markedly reduced contamination, achieving clean culture and regeneration rates of 75.72 ± 3.36% and 86.83 ± 3.02%, respectively, regardless of explant age. In contrast, higher concentrations of mercuric chloride induced necrosis in the explants. The highest clean culture rate (93.82 ± 1.16%) was observed in 3-week-old explants, which also showed a regeneration rate of 54.93 ± 3.19%. Furthermore, the Boyapleu and Irene genotypes demonstrated good suitability for in vitro culture, whereas the Nakabo genotype performed poorly under the tested conditions.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"14 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144972281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effects of Glycerol and Phenolics on Myceliophthora heterothallica Endoxylanase Expressed in K. phaffii. 甘油和酚类物质对菲氏霉霉内生木聚糖酶表达的影响

IF 3.1

BioTech Pub Date : 2025-08-18 DOI: 10.3390/biotech14030062

Jéssica de Araujo Zanoni, Izabela Karolina Costa Zilli, Guilherme de Paula Pretto, Flavio Augusto Vicente Seixas, Marcela Marques de Freitas Lima, Eliana Gertrudes de Macedo Lemos, Eleni Gomes, Gabriel Zazeri, Gustavo Orlando Bonilla-Rodriguez

{"title":"Effects of Glycerol and Phenolics on Myceliophthora heterothallica Endoxylanase Expressed in K. phaffii.","authors":"Jéssica de Araujo Zanoni, Izabela Karolina Costa Zilli, Guilherme de Paula Pretto, Flavio Augusto Vicente Seixas, Marcela Marques de Freitas Lima, Eliana Gertrudes de Macedo Lemos, Eleni Gomes, Gabriel Zazeri, Gustavo Orlando Bonilla-Rodriguez","doi":"10.3390/biotech14030062","DOIUrl":"10.3390/biotech14030062","url":null,"abstract":"Industrial applications of xylanases in high-temperature settings are limited by enzyme instability. This study evaluated glycerol and phenolic compounds as modulators of the catalytic and structural properties of a recombinant Myceliophthora heterothallica endoxylanase (rMhXyn) expressed in Komagataella phaffii. Glycerol (20% v/v) significantly improved thermostability (5-fold increase in half-life at 55 °C), decreased the activation energy for catalysis, and enhanced structural rigidity as evidenced by molecular dynamics simulations (reduced RMSD and Rg). In contrast, phenolic acids provided only short-term stabilization at moderate temperatures and did not confer structural benefits. Enzyme kinetics revealed that glycerol enhanced catalytic turnover (↑Vmax), while phenolic compounds modified both K' and cooperativity (Hill coefficient). Thermodynamic analysis supported glycerol's stabilizing effect, with increased ∆H(D) and a positive shift in ∆S(D). These results suggest glycerol as a superior stabilizer for rMhXyn in high-temperature bioprocesses such as lignocellulosic biomass hydrolysis. These findings highlight the potential of targeted additives to improve enzyme performance for biotechnological applications.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"14 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144972331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rosemary Extract: Phytochemical Composition and Potential for Eliminating Polymicrobial Biofilm of Candida albicans and Multidrug-Resistant Bacteria. 迷迭香提取物：植物化学成分及其消除白色念珠菌和多重耐药细菌多微生物生物膜的潜力。

IF 3.1

BioTech Pub Date : 2025-08-13 DOI: 10.3390/biotech14030061

Tuana Mendonça Faria Cintra, Raquel Teles de Menezes, Lara Steffany de Carvalho, Leticia de Miguel Nazario, Leandro Wang Hantao, Maria Cristina Marcucci, Luciane Dias de Oliveira, Vanessa Marques Meccatti-Domiciano

{"title":"Rosemary Extract: Phytochemical Composition and Potential for Eliminating Polymicrobial Biofilm of Candida albicans and Multidrug-Resistant Bacteria.","authors":"Tuana Mendonça Faria Cintra, Raquel Teles de Menezes, Lara Steffany de Carvalho, Leticia de Miguel Nazario, Leandro Wang Hantao, Maria Cristina Marcucci, Luciane Dias de Oliveira, Vanessa Marques Meccatti-Domiciano","doi":"10.3390/biotech14030061","DOIUrl":"10.3390/biotech14030061","url":null,"abstract":"Herbal medicines can be promising for the treatment of infections caused by multidrug-resistant microorganisms. This study aimed to evaluate Rosmarinus officinalis (Rosemary) hydroalcoholic extract (RHE) regarding its phytochemical composition and potential for eliminating polymicrobial biofilm of Candida albicans with multidrug-resistant bacteria (Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa). The extraction and quantification of the extract (flavonoids and phenols) were performed, and its antioxidant activity (DPPH) and the presence of bio-active compounds were investigated using high-performance liquid chromatography with Diode Array Detection (HPLC-DAD) and Gas Chromatography-Mass Spectrometry (GC-MS). The minimum inhibitory concentration (MIC) and minimum microbicidal concentration (MMC) were determined, and the extract's action on polymicrobial biofilms was evaluated using the MTT assay. Data were analyzed using one-way ANOVA and Tukey's tests, as well as Kruskal-Wallis and Dunn's tests, with a significance level of 5%. RHE showed compatible amounts of flavonoids and phenols, with an EC50 of 19.53 µg/mL. Through HPLC-DAD and GC-MS, biomolecules such as rosmarinic acid and α-Pinene were identified. The extract exhibited microbicidal activity and antibiofilm action, with reduction percentages of up to 69.6% (p < 0.05), showing superior performance compared to 0.12% chlorhexidine against C. albicans + A. baumannii. In conclusion, RHE may be a promising therapeutic agent against multidrug-resistant pathogens.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"14 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144972257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Influence of Nutrient Medium Composition on the Redistribution of Valuable Metabolites in the Freshwater Green Alga Tetradesmus obliquus (Chlorophyta) Under Photoautotrophic Growth Conditions. 营养液组成对光自养生长条件下淡水赤藻（Tetradesmus obliquus）有价代谢物再分配的影响

IF 3.1

BioTech Pub Date : 2025-08-11 DOI: 10.3390/biotech14030060

Elvira E Ziganshina, Ayrat M Ziganshin

{"title":"Influence of Nutrient Medium Composition on the Redistribution of Valuable Metabolites in the Freshwater Green Alga Tetradesmus obliquus (Chlorophyta) Under Photoautotrophic Growth Conditions.","authors":"Elvira E Ziganshina, Ayrat M Ziganshin","doi":"10.3390/biotech14030060","DOIUrl":"10.3390/biotech14030060","url":null,"abstract":"The study of microalgae has led to significant progress in recent decades. The current microalgal biomass yield is unsatisfactory, except for certain species that are cultivated for the nutraceutical and pharmaceutical industries. In this study, the growth efficiency and biochemical composition of Tetradesmus obliquus at high levels of nutrients were characterized. Increasing the NH4+-N content in the medium to 164 mg L-1 allowed the algae to steadily accumulate biomass (6.14 ± 0.28 g L-1) with a moderate content of starch. Optimizing the levels of N, P, and S allowed the biomass productivity to increase from the average 0.45 to 0.88 g L-1 day-1. A further increase of NH4+-N to 410 mg L-1 and other nutrients' concentration allowed the algae to accumulate biomass (7.50 ± 0.28 g L-1), enriched with protein and pigments. The algae cultivated with the high load of nutrients reached 100%, 84%, and 96% removal of N, P, and S, respectively. Adding the NaHCO3 to the photobioreactor for pH adjustment (instead of NaOH) did not significantly improve the growth parameters or affect the composition of the algal cells. In general, our study will improve the comprehensive understanding of culture-based approaches to study the perspective use of the alga T. obliquus.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"14 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144972318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effect of Ultrasonic Pretreatment on the Extraction Process of Essential Oils from Grapefruit (Citrus paradisi) By-Products. 超声波预处理对葡萄柚副产物精油提取工艺的影响。

IF 3.1

BioTech Pub Date : 2025-08-07 DOI: 10.3390/biotech14030059

Francisco Cadena-Cadena, Joe Luis Arias-Moscoso, Leandris Argentel-Martínez, Jony R Torres Velazquez, Dulce Alondra Cuevas-Acuña, Nydia Estrellita Buitimea Cantua, Bartolo Concha-Frías

{"title":"Effect of Ultrasonic Pretreatment on the Extraction Process of Essential Oils from Grapefruit (Citrus paradisi) By-Products.","authors":"Francisco Cadena-Cadena, Joe Luis Arias-Moscoso, Leandris Argentel-Martínez, Jony R Torres Velazquez, Dulce Alondra Cuevas-Acuña, Nydia Estrellita Buitimea Cantua, Bartolo Concha-Frías","doi":"10.3390/biotech14030059","DOIUrl":"10.3390/biotech14030059","url":null,"abstract":"This study evaluated the effect of ultrasonic pulse-assisted extraction on the yield and antioxidant activity of essential oils from grapefruit (Citrus paradisi) by-products using hydrodistillation and Soxhlet solvent extraction (hexane, acetone, ethanol). Ultrasound was applied at 40% amplitude for 20 min before extraction. Results showed that ultrasound significantly increased extraction yield with hexane (from 2.6 ± 0.58% to 7.6 ± 1.5%) and acetone (from 8.6 ± 0.96% to 12 ± 1.4%), while ultrasound-assisted hydrodistillation nearly doubled the yield (from 0.7 ± 0.03% to 1.5 ± 0.49%). In contrast, ultrasound decreased yield with ethanol by 3%. Antioxidant activity measured by TEAC assay was highest in acetone extracts without ultrasound (13,366.5 ± 7.66 mmol TE/g) and ethanol extracts (12,606.8 ± 0.51 mmol TE/g). However, ultrasound combined with ethanol increased DPPH scavenging activity from 1073.5 ± 1.07 µg/mL to 4933.3 ± 0.71 µg/mL and maintained high flavonoid content (9.41 ± 0.15 mg/mL) and phenolics (5.33 ± 0.09 mg/mL). Ultrasound-assisted hydrodistillation also enhanced antioxidant capacity, with DPPH values rising from 51.82 ± 5.56 µg/mL to 2413.03 ± 3.17 µg/mL. These findings demonstrate that ultrasound effectively enhances essential oil extraction and antioxidant activity depending on the solvent used, underscoring the potential of this clean technology for valorizing citrus by-products.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"14 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144972337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Pathway Analysis Interpretation in the Multi-Omic Era. 多基因组时代的路径分析解读。

IF 3.1

BioTech Pub Date : 2025-07-29 DOI: 10.3390/biotech14030058

William G Ryan V, Smita Sahay, John Vergis, Corey Weistuch, Jarek Meller, Robert E McCullumsmith

{"title":"Pathway Analysis Interpretation in the Multi-Omic Era.","authors":"William G Ryan V, Smita Sahay, John Vergis, Corey Weistuch, Jarek Meller, Robert E McCullumsmith","doi":"10.3390/biotech14030058","DOIUrl":"10.3390/biotech14030058","url":null,"abstract":"In bioinformatics, pathway analyses are used to interpret biological data by mapping measured molecules with known pathways to discover their functional processes and relationships. Pathway analysis has become an essential tool for interpreting large-scale omics data, translating complex gene sets into actionable experimental insights. However, issues inherent to pathway databases and misinterpretations of pathway relevance often result in \"pathway fails,\" where findings, though statistically significant, lack biological applicability. For example, the Tumor Necrosis Factor (TNF) pathway was originally annotated based on its association with observed tumor necrosis, while it is multifunctional across diverse physiological processes in the body. This review broadly evaluates pathway analysis interpretation, including embedding-based, semantic similarity-based, and network-based approaches to clarify their ideal use-case scenarios. Each method for interpretation is assessed for its strengths, such as high-quality visualizations and ease of use, as well as its limitations, including data redundancy and database compatibility challenges. Despite advancements in the field, the principle of \"garbage in, garbage out\" (GIGO) shows that input quality and method choice are critical for reliable and biologically meaningful results. Methodological standardization, scalability improvements, and integration with diverse data sources remain areas for further development. By providing critical guidance with contextual examples such as TNF, we aim to help researchers align their objectives with the appropriate method. Advancing pathway analysis interpretation will further enhance the utility of pathway analysis, ultimately propelling progress in systems biology and personalized medicine.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"14 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144972261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fetal Health Diagnosis Based on Adaptive Dynamic Weighting with Main-Auxiliary Correction Network. 基于主辅校正网络的自适应动态加权胎儿健康诊断。

IF 3.1

BioTech Pub Date : 2025-07-28 DOI: 10.3390/biotech14030057

Haiyan Wang, Yanxing Yin, Liu Wang, Yifan Wang, Xiaotong Liu, Lijuan Shi

{"title":"Fetal Health Diagnosis Based on Adaptive Dynamic Weighting with Main-Auxiliary Correction Network.","authors":"Haiyan Wang, Yanxing Yin, Liu Wang, Yifan Wang, Xiaotong Liu, Lijuan Shi","doi":"10.3390/biotech14030057","DOIUrl":"10.3390/biotech14030057","url":null,"abstract":"Maternal and child health during pregnancy is an important issue in global public health, and the classification accuracy of fetal cardiotocography (CTG), as a key tool for monitoring fetal health during pregnancy, is directly related to the effectiveness of early diagnosis and intervention. Due to the serious category imbalance problem of CTG data, traditional models find it challenging to take into account a small number of categories of samples, increasing the risk of leakage and misdiagnosis. To solve this problem, this paper proposes a two-step innovation: firstly, we design a method of adaptive adjustment of misclassification loss function weights (MAAL), which dynamically identifies and increases the focus on misclassified samples based on misclassification rates. Secondly, a primary and secondary correction network model (MAC-NET) is constructed to carry out secondary correction for the misclassified samples of the primary model. Experimental results show that the method proposed in this paper achieves 99.39% accuracy on the UCI publicly available fetal health dataset, and also obtains excellent performance on other domain imbalance datasets. This demonstrates that the model is not only effective in alleviating the problem of category imbalance, but also has very high clinical utility.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"14 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144972340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Impact of Cattle Breed in scRNA-Seq Reference on Muscle Fiber Type Deconvolution from Bulk RNA-Seq: A Comparison of Software Tools. scRNA-Seq参考中牛品种对大量RNA-Seq中肌纤维类型反褶积的影响：软件工具的比较

IF 3.1

BioTech Pub Date : 2025-07-25 DOI: 10.3390/biotech14030056

Raphael P Moreira, Marcelo R Vicari, Henrique A Mulim, Theresa M Casey, Jacquelyn Boerman, Xing Fu, Hinayah R Oliveira

{"title":"Impact of Cattle Breed in scRNA-Seq Reference on Muscle Fiber Type Deconvolution from Bulk RNA-Seq: A Comparison of Software Tools.","authors":"Raphael P Moreira, Marcelo R Vicari, Henrique A Mulim, Theresa M Casey, Jacquelyn Boerman, Xing Fu, Hinayah R Oliveira","doi":"10.3390/biotech14030056","DOIUrl":"10.3390/biotech14030056","url":null,"abstract":"While bulk RNA sequencing provides a comprehensive view of transcriptomes, it lacks cell type specificity. Single-cell RNA sequencing (scRNA-seq) overcomes this limitation by providing detailed insights at the individual cell level, though it involves higher costs. Deconvolution methods can estimate cell type proportions in bulk RNA-seq data, but their results may vary based on the scRNA-seq reference data and software used. This study investigates the estimation of muscle fiber type proportions through deconvolution analysis of Longissimus dorsi muscle bulk RNA-seq data from late-gestation Holstein Friesian multiparous cows. Four software tools (i.e., CIBERSORTx, Cellanneal, DeconvR-NNLS, and DeconvR-RLM) were compared using scRNA-seq reference data from Brahman and Wagyu cattle breeds, which included proportions of types I, IIa, and IIx myofibers. Kruskal-Wallis and Dunn's tests revealed that the breed of reference data significantly influenced the proportions of type IIa and IIx muscle fibers across different deconvolution methods. To the best of our knowledge, this is the first study to show that the cattle breed used in reference scRNA-seq data can substantially impact deconvolution outcomes, highlighting a critical consideration for accurate cell type proportion estimation in livestock genomics. These findings suggest that future deconvolution studies should carefully consider breed compatibility between reference and target datasets.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"14 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144972292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

BioTech最新文献