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An automatic classification method of testicular histopathology based on SC-YOLO framework. 基于 SC-YOLO 框架的睾丸组织病理学自动分类方法。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-12 DOI: 10.1080/07366205.2024.2393544
Jinggen Wu,Yao Sun,Yangbo Jiang,Yangcheng Bu,Chong Chen,Jingping Li,Lejun Li,Weikang Chen,Keren Cheng,Jian Xu
{"title":"An automatic classification method of testicular histopathology based on SC-YOLO framework.","authors":"Jinggen Wu,Yao Sun,Yangbo Jiang,Yangcheng Bu,Chong Chen,Jingping Li,Lejun Li,Weikang Chen,Keren Cheng,Jian Xu","doi":"10.1080/07366205.2024.2393544","DOIUrl":"https://doi.org/10.1080/07366205.2024.2393544","url":null,"abstract":"The pathological diagnosis and treatment of azoospermia depend on precise identification of spermatogenic cells. Traditional methods are time-consuming and highly subjective due to complexity of Johnsen score, posing challenges for accurately diagnosing azoospermia. Here, we introduce a novel SC-YOLO framework for automating the classification of spermatogenic cells that integrates S3Ghost module, CoordAtt module and DCNv2 module, effectively capturing texture and shape features of spermatogenic cells while reducing model parameters. Furthermore, we propose a simplified Johnsen score criteria to expedite the diagnostic process. Our SC-YOLO framework presents the higher efficiency and accuracy of deep learning technology in spermatogenic cell recognition. Future research endeavors will focus on optimizing the model's performance and exploring its potential for clinical applications.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142223432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
When is an SNP not an SNP? 什么时候 SNP 不是 SNP？
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-12 DOI: 10.1080/07366205.2024.2387993
Shapour Jalilzadeh,Valerie Walker,Gary P Leggatt,Eli Hatchwell
{"title":"When is an SNP not an SNP?","authors":"Shapour Jalilzadeh,Valerie Walker,Gary P Leggatt,Eli Hatchwell","doi":"10.1080/07366205.2024.2387993","DOIUrl":"https://doi.org/10.1080/07366205.2024.2387993","url":null,"abstract":"Genomic duplications are important sources of structural change and gene innovation. In humans, the most recent and highly identical sequences (>90% homology, >1 kb long) are known as segmental duplications (SDs). Single-nucleotide variants or single-nucleotide polymorphisms within SDs have not been systematically assessed due to limitations around mapping short-read sequencing data. Single-nucleotide variant rs62486260 was flagged in a study of familial renal stone disease but it was unclear whether it was real or an artifact resulting from the presence of a SD. We describe in silico and wet-lab approaches to investigate this, using segment-specific long-PCR assays, followed by short PCR for Sanger sequencing. Our conclusion was that rs62486260 is an artifact. Our approach can be generalized to deal with other such situations.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142223434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sampling and analysis methods of air-borne microorganisms in hospital air: a review. 医院空气中气载微生物的采样和分析方法：综述。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-12 DOI: 10.1080/07366205.2024.2372939
Xinyan Wei,Xuezheng Ma,Feng Tian,Zhaohui Wei,Liping Zhang,Kongxin Hu
{"title":"Sampling and analysis methods of air-borne microorganisms in hospital air: a review.","authors":"Xinyan Wei,Xuezheng Ma,Feng Tian,Zhaohui Wei,Liping Zhang,Kongxin Hu","doi":"10.1080/07366205.2024.2372939","DOIUrl":"https://doi.org/10.1080/07366205.2024.2372939","url":null,"abstract":"Pathogenic microorganisms can spread in the air as bioaerosols. When the human body is exposed to different bioaerosols, various infectious diseases may occur. As indoor diagnosis and treatment environments, hospitals are relatively closed and have a large flow rate of people. This indoor environment contains complex aerosol components; therefore, effective sampling and detection of microbial elements are essential in airborne pathogen monitoring. This article reviews the sampling and detection of different kinds of microorganisms in bioaerosols from indoor diagnostic and therapeutic settings, with a particular focus on microbial activity. This provides deeper insights into bioaerosols in diagnostic and therapeutic settings.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142177492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mito-kaede photoactivation and chase experiment for mitophagy: optimizing flux measurement via fluid exchange system. 有丝分裂的光激活和追逐实验：通过流体交换系统优化通量测量。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-11 DOI: 10.1080/07366205.2024.2372955
Hiroyuki Morinaga,Yoh Sugawara,Yoshinori Kitagawa,Jingyuan Chen,Nobuo Yasuda,Hiroki Ogata,Yoshihiro Yamaguchi,Masao Kaneki,Joseph A Jeevendra Martyn,Shingo Yasuhara
{"title":"Mito-kaede photoactivation and chase experiment for mitophagy: optimizing flux measurement via fluid exchange system.","authors":"Hiroyuki Morinaga,Yoh Sugawara,Yoshinori Kitagawa,Jingyuan Chen,Nobuo Yasuda,Hiroki Ogata,Yoshihiro Yamaguchi,Masao Kaneki,Joseph A Jeevendra Martyn,Shingo Yasuhara","doi":"10.1080/07366205.2024.2372955","DOIUrl":"https://doi.org/10.1080/07366205.2024.2372955","url":null,"abstract":"Modulating autophagy and mitophagy, vital cellular quality control systems, offer therapeutic potential for critical illnesses. However, limited drug screening options hinder progress. We present a novel assay using the photoswitchable fluorescent reporter, mito-Kaede, to quantify mitophagy flux. Mito-Kaede's superior UV-induced photoconversion and brightness post-conversion make it ideal for prolonged mitochondrial dynamics tracking. Its specificity in responding to mitophagy, confirmed by parkin-knockout cells, adds value. When coupled with a custom fluid exchange system, enabling efficient medium changes, precise mitophagy observations become feasible. This mitophagy assay, alongside our methodological insights, can decipher mitophagy's role in pathology and supports drug screening efforts.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142177493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Prioritizing privacy and presentation of supportable hypothesis testing in forensic genetic genealogy investigations. 在法医遗传系谱调查中优先考虑隐私和提出可支持的假设检验。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-08-09 DOI: 10.1080/07366205.2024.2386218
Bruce Budowle, Lee Baker, Antti Sajantila, Kristen Mittelman, David Mittelman
{"title":"Prioritizing privacy and presentation of supportable hypothesis testing in forensic genetic genealogy investigations.","authors":"Bruce Budowle, Lee Baker, Antti Sajantila, Kristen Mittelman, David Mittelman","doi":"10.1080/07366205.2024.2386218","DOIUrl":"10.1080/07366205.2024.2386218","url":null,"abstract":"<p><p>Investigative leads are not generated by traditional forensic DNA testing, if the source of the forensic evidence or a 1st degree relative of unidentified human remains is not in the DNA database. In such cases, forensic genetic genealogy (FGG) can provide valuable leads. However, FGG generated genetic data contain private and sensitive information. Therefore, it is essential to deploy approaches that minimize unnecessary disclosure of these data to mitigate potential risks to individual privacy. We recommend protective practices that need not impact effective reporting of relationship identifications. Examples include performing one-to-one comparisons of DNA profiles of third-party samples and evidence samples offline with an \"air gap\" to the internet and shielding the specific shared single nucleotide polymorphisms (SNP) states and locations by binning adjacent SNPs in forensic reports. Such approaches reduce risk of unwanted access to or reverse engineering of third-party individuals' genetic data and can give these donors greater confidence to support use of their DNA profiles in FGG investigation.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141905820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dual-mode detection of glucose based on pistol-like DNAzyme-mediated exonuclease-assisted signal cycle. 基于手枪式 DNA 酶介导的外切酶辅助信号循环的葡萄糖双模式检测。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-08-05 DOI: 10.1080/07366205.2024.2381403
Huiying Lu, Xiaofeng Wang
{"title":"Dual-mode detection of glucose based on pistol-like DNAzyme-mediated exonuclease-assisted signal cycle.","authors":"Huiying Lu, Xiaofeng Wang","doi":"10.1080/07366205.2024.2381403","DOIUrl":"https://doi.org/10.1080/07366205.2024.2381403","url":null,"abstract":"<p><p>Detecting glucose accurately and sensitively from clinical samples like tears and saliva is still difficult. We have created a sensor that can detect glucose with high sensitivity and accuracy by combining the use of glucose oxidase (GOx) to catalyze glucose, a pistol-like DNAzyme (PLDz) to transform the signal, gold nanoparticles (AuNPs) to enhance the optical properties and the exonuclease-III (Exo-III) to amplify the signal. As a result, the proposed method exhibits a low detection limit of 7.5 pM and a wide detection range covering seven orders of magnitude. The suggested dual-mode strategy provides a sensitive, precise and specific detection method for glucose. Another advantage is that the dual-mode technique significantly improves the precision and consistency of the measurements, demonstrating its immense potential for use in biomedical research and clinical diagnostics.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The environmental impact of AI in the lab: a double-edged sword? 实验室人工智能对环境的影响：一把双刃剑？
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-07-31 DOI: 10.1080/07366205.2024.2376459
Annie Coulson
{"title":"The environmental impact of AI in the lab: a double-edged sword?","authors":"Annie Coulson","doi":"10.1080/07366205.2024.2376459","DOIUrl":"https://doi.org/10.1080/07366205.2024.2376459","url":null,"abstract":"<p><p>Computational tools, particularly AI, are becoming more ubiquitous in scientific research; but what impact do they have on the environment?[Formula: see text].</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modular probe-based colorimetric miRNA detection via polymerase/endonuclease assisted chain displacement. 通过聚合酶/内切酶辅助链置换进行基于探针的模块化比色 miRNA 检测。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-07-23 DOI: 10.1080/07366205.2024.2368394
Xialing Xu, Ping Zhang, Siyu Tao
{"title":"Modular probe-based colorimetric miRNA detection <i>via</i> polymerase/endonuclease assisted chain displacement.","authors":"Xialing Xu, Ping Zhang, Siyu Tao","doi":"10.1080/07366205.2024.2368394","DOIUrl":"https://doi.org/10.1080/07366205.2024.2368394","url":null,"abstract":"<p><p>Methods for sequence-specific microRNA (miRNA) analysis are crucial for miRNA research and guiding nursing strategies. We have devised a colorimetric technique for detecting miRNA using a dumbbell probe-based polymerase/endonuclease assisted chain displacement, along with silver ions (Ag<sup>+</sup>) aptamer assisted color reaction. The suggested approach enables precise measurement of miRNA-21 within the concentration range of 100 fM-5 nM, with a low detection limit of 45.32 fM. Additionally, it exhibits exceptional capability in distinguishing variations at the level of individual nucleotides. Furthermore, the detection technique may be utilized to precisely measure the amount of miRNA-21 in serum samples, demonstrating a high level of concordance with the findings obtained from a commercially available miRNA detection kit.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Adipocyte ABCA1 expression analysis using flow cytometry. 使用流式细胞仪分析脂肪细胞 ABCA1 的表达。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-07-17 DOI: 10.1080/07366205.2024.2376466
Sakshi Shukla, Ashutosh Bansal, Sandeep Aggarwal, Archna Singh
{"title":"Adipocyte ABCA1 expression analysis using flow cytometry.","authors":"Sakshi Shukla, Ashutosh Bansal, Sandeep Aggarwal, Archna Singh","doi":"10.1080/07366205.2024.2376466","DOIUrl":"https://doi.org/10.1080/07366205.2024.2376466","url":null,"abstract":"<p><p>Adipocyte characterization and assessing membrane proteins using flow cytometry has been proven to be challenging as adipocytes are fragile, especially in subjects with high BMI. We overcame these challenges through a protocol optimizing tissue digestion time by reducing intermediate steps to minimize adipocyte friction and breakage. We avoided requirement for specialized instrument configuration and used a modified gating strategy to prevent inclusion of lipid droplets during analysis. Up to 90% of the cell population were available in the gating area. We checked the expression level of ABCA1, a membrane protein reaffirming adipocyte selection. In summary, this protocol requires lesser tissue sample improving feasibility and cost efficiency. Thus, our flow cytometry method is an improvement for studying adipocyte membrane characteristics.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Novel buffer for long-term preservation of DNA in biological material at room temperature1. 用于在室温下长期保存生物材料中 DNA 的新型缓冲液。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-07-01 DOI: 10.1080/07366205.2024.2360813
Mohaimin Kasu, Peter G Ristow, Adria Michelle Burrows, Zafrir Kuplik, Mark J Gibbons, Maria E D'Amato
{"title":"Novel buffer for long-term preservation of DNA in biological material at room temperature<sup>1</sup>.","authors":"Mohaimin Kasu, Peter G Ristow, Adria Michelle Burrows, Zafrir Kuplik, Mark J Gibbons, Maria E D'Amato","doi":"10.1080/07366205.2024.2360813","DOIUrl":"10.1080/07366205.2024.2360813","url":null,"abstract":"<p><p>The collection and preservation of biological material before DNA analysis is critical for inter alia biomedical research, medical diagnostics, forensics and biodiversity conservation. In this study, we evaluate an in-house formulated buffer called the Forensic DNA Laboratory-buffer (FDL-buffer) for preservation of biological material for long term at room temperature. Human saliva stored in the buffer for 8 years, human blood stored for 3 years and delicate animal tissues from the jellyfish <i>Pelagia noctiluca</i> comb jelly <i>Beroe</i> sp., stored for 4 and 6 years respectively consistently produced high-quality DNA. FDL-buffer exhibited compatibility with standard organic, salting out and spin-column extraction methods, making it versatile and applicable to a wide range of applications, including automation.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141466005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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