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Data analysis guidelines for single‑cell RNA‑seq in biomedical studies and clinical applications

Military Medical Research 2023年第4期10卷 529-553页

作者： Min Su Tao Pan Qiu‑Zhen Chen Wei‑Wei Zhou Yi Gong Gang Xu Huan‑Yu Yan Si Li Qiao‑Zhen Shi Ya Zhang Xiao He Chun‑Jie Jiang Shi‑Cai Fan Xia Li Murray J.Cairns Xi Wang Yong‑Sheng Li State Key Laboratory of Reproductive Medicine Nanjing Medical UniversityNanjing 211166China College of Biomedical Information and Engineering the First Affiliated Hospital of Hainan Medical UniversityHainan Medical UniversityHaikou 571199HainanChina College of Bioinformatics Science and Technology Harbin Medical UniversityHarbin 150081HeilongjiangChina Department of Immunology Nanjing Medical UniversityNanjing 211166China Department of Laboratory Medicine Women and Children’s Hospital of Chongqing Medical UniversityChongqing 401174China Baylor College of Medicine HoustonTX 77030USA Shenzhen Institute for Advanced Study University of Electronic Science and Technology of ChinaShenzhen 518110GuangdongChina School of Biomedical Sciences and Pharmacy Faculty of Health and Medicinethe University of NewcastleUniversity DriveCallaghanNSW 2308Australia Precision Medicine Research Program Hunter Medical Research InstituteNew Lambton HeightsNSW 2305Australia

The application of single-cell RNA sequencing(scRNA-seq)in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic *** the expansion of capacity for high-throughput scRNA-seq,including clinical samples,the analysis of these huge volumes of data has become a daunting prospect for researchers entering this ***,we review the workflow for typical scRNA-seq data analysis,covering raw data processing and quality control,basic data analysis applicable for almost all scRNA-seq data sets,and advanced data analysis that should be tailored to specific scientific *** summarizing the current methods for each analysis step,we also provide an online repository of software and wrapped-up scripts to support the *** and caveats are pointed out for some specific analysis tasks and *** hope this resource will be helpful to researchers engaging with scRNA-seq,in particular for emerging clinical applications.

关键词： Single-cell RNA-sequencing(scRNA-seq) Data analysis biomedical research Clinical applications

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Molecular dynamics simulation and purification of chimeric L1/L2 protein from human papillomavirus type 52 expressed in Escherichia coli BL21 (DE3)

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Journal of Immunoassay and Immunochemistry 2024年第5期45卷 395-414页

作者： Al Adawiah, Rabiyah Zaenal Mustopa, Apon Budiarti, Sri Nur Umami, Rifqiyah Hertati, Ai Irawan, Herman Ikramullah, Muh. Chaeril Arwansyah, Arwansyah Mamangkey, Jendri Kartikasari, Isti Salahudin Darusman, Huda Post Graduate Program of Microbiology IPB University Bogor Indonesia Research Center for Genetic Engineering National Research and Innovation Agency (BRIN) KST Soekarno Bogor Cibinong Indonesia Department of Biology IPB University Bogor Indonesia Biotechnology Study Program Postgraduate School of Universitas Gadjah Mada Yogyakarta Indonesia Department of Chemistry Education Tadulako University Palu Indonesia Department of Biology Education Faculty of Education and Teacher Training Universitas Kristen Indonesia Jakarta Indonesia Primate Animal Study Center IPB University Bogor Indonesia Department of Anatomy Physiology and Pharmacology School of Veterinary Medicine and Biomedical IPB University Bogor Indonesia Primate Animal Study Center Research Institution and Community Service (LPPM) IPB University Bogor Indonesia

The available prophylactic vaccines for human papillomavirus (HPV) in the market are only effective against specific types of HPV, rendering them ineffective for other types of HPV infections. The objective of this research is to investigate the stability of the recombinant protein constructed, namely chimeric L1/L2 protein from HPV type 52, with improved cross-neutralization ability. The 3D model, predicted using Alphafold, Robetta, I-Tasser, and refined with Galaxy Refinement, is validated using Ramachandran plot analysis. The stability is verified through molecular dynamics simulations, considering parameters such as RMSD, RMSF, Rg, and SASA, where stable conditions are observed. The chimeric L1/L2 protein from HPV type 52 is purified using affinity chromatography, and the His-tag is cleaved using SUMO protease to obtain pure chimeric protein with the size of ~ 55 kDa. Western blot analysis confirms binding to anti-L1 HPV type 52 polyclonal antibody. The obtained vaccine candidate can be utilized as an effective prophylactic vaccine against HPV. © 2024 Taylor & Francis.

关键词： HPV molecular dynamics purification vaccine

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Computational Study of Ventral Ankle-Foot Orthoses During Stance Phase for Post-surgery Spinal Tuberculosis Rehabilitation 1st

Computational Study of Ventral Ankle-Foot Orthoses During St...

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1st International Conference on Electronics, biomedical engineering, and Health Informatics, ICEBEHI 2020

作者： Putra, Alfian Pramudita Rahmatillah, Akif Pujiyanto Ain, Khusnul Rodiyah, Nur Khafidotur Pawana, I. Putu Alit Syahananta, Lolita Hapsari Dwi Dwiatma, Mohammad Rizki Hidayat, Arief Sofian Biomedical Engineering Study Program Department of Physics Faculty of Science and Technology Universitas Airlangga Surabaya60115 Indonesia Biomedical Signals and Systems Research Group Faculty of Science and Technology Universitas Airlangga Surabaya60115 Indonesia Department of Physics Faculty of Science and Technology Universitas Airlangga Surabaya60115 Indonesia Department of Physical Medicine and Rehabilitation Dr Soetomo General Academic Hospital Surabaya60286 Indonesia

ISBN: (纸本)9789813369252

Spinal Tuberculosis could cause abnormalities in the lower extremity, even after the surgery and can be treated with Ankle-Foot Orthoses (AFO). The patient with that condition has to stabilize their body because it tends to fall forward. Thus, a ventral AFO is needed to support them. This study aims to evaluate AFO design by using Finite Element Method (FEM) with two different thickness (2 and 4 mm). The material used was a Polyethylene Terephthalate (PET). Three subphases in the stance phase were simulated, namely initial contact, midstance, and terminal stance. The external force in the simulation was based on the patient’s weight (50 kg). The result showed that the highest stress was obtained from ventral AFO with a thickness of 2 mm at the terminal stance, 244.7 MPa. This value exceeded the Ultimate Tensile Strength (UTS) of PET which indicates the design would break. The ventral AFO with a thickness of 4 mm had lower stress than the UTS of PET. The strain of both designs was quite low with the maximum value of 0.019 from the ventral AFO with a thickness of 4 mm in the terminal stance. The deformation was also acceptable for both designs with the highest value of 39.67 mm from the ventral AFO with a thickness of 2 mm in the midstance. In conclusion, the ventral AFO with a thickness of 4 mm could be used for post-surgery spinal tuberculosis patient’s rehabilitation. © 2021, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Patient rehabilitation

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Undersampled Magnetic Resonance Image Reconstructions Based on a Combination of U-Nets and L1, L2, and TV Optimizations

Undersampled Magnetic Resonance Image Reconstructions Based ...

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IEEE International Workshop on Imaging Systems and Techniques (IST)

作者： Aline A.S. Thomaz Jonathan A.S. Lima Cristiano J. Miosso Mylé ne C.Q. Farias Andrey S. Krylov Yong Ding Department of Electrical Engineering University of Brasilia (UnB) Brasilia Brazil Biomedical Engineering Graduate Program University of Brasilia (UnB) Brasilia Brazil Faculty of Computational Mathematics and Cybernetics Lomonosov Moscow State University Moscow Russia College of Information Science and Electronic Engineering Zhejiang University Zhejiang China

Magnetic Resonance Imaging (MRI) plays a major role in the diagnosis of several diseases. However, the acquisition of measurements in the k-space domain, which is the basis for image reconstruction, takes a long time compared to other imaging modalities and is comparatively costly. In this context, undersampled MRI reconstruction is an approach for decreasing the acquisition duration and the exam's final cost. With this objective, both Compressed Sensing (CS) and Deep Learning (DL) provide techniques for generating good quality MRI images from undersampled measurements. In this paper, we combine CS and DL methods in order to investigate the potential increase in image quality over each isolated approach. We use reconstructions from from highly undersampled MRI signals using two CS approaches, the L1 and total minimizations, as inputs to a U-Net. We also use, for comparison, the reconstructions from the same undersampled signals using L2 minimization, and also test them as inputs to a U-net. The goal is to evaluate whether the the U-Net can improve the results of the CS reconstructions after learning from degraded and original image pairs. Our experimental results suggest that the combination of L1 or TV minimization with U-Nets can improve reconstruction, in terms of objective image quality, over each technique used in isolation.

关键词： Image quality TV Magnetic resonance imaging Magnetic resonance Minimization Time measurement Sensors

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Genome-wide analysis of detoxification genes conferring diamide insecticide resistance in Spodoptera exigua identifies CYP9A40

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Chemosphere 2024年 367卷 143623页

作者： Han, Changhee Rahman, Md-Mafizur Kim, Juil Lueke, Bettina Nauen, Ralf Interdisciplinary Graduate Program in Smart Agriculture Kangwon National University Chuncheon24341 Korea Republic of Department Biotechnology and Genetic Engineering Faculty of Biological Science Islamic University Kushtia7003 Bangladesh Agriculture and Life Science Research Institute Kangwon National University Chuncheon24341 Korea Republic of Bayer AG Crop Science Division R&D Monheim40789 Germany

For over a decade, diamide insecticides have been effective against lepidopteran pests like beet armyworm, Spodoptera exigua (Hübner, 1808). However, the evolution of resistance poses a challenge to their sustainable use. We identified an I4790 M mutation in the S. exigua ryanodine receptor (RyR) gene, but its correlation with resistance varied across the field-collected Korean populations of S. exigua. RNA sequencing and differential gene expression analysis were performed to investigate other resistance mechanisms. Diamide-resistant and susceptible strains and F1 hybrids were compared by mapping RNA-seq reads to the S. exigua reference genome. CYP9A40 was identified as a critical gene in diamide resistance due to its high expression in the resistant strains. Synergist bioassays with piperonyl butoxide supported the role of P450s in diamide metabolic resistance in S. exigua. A strong positive correlation between CYP9A40 over-expression levels (up to 80-fold) and diamide LC50 values was obtained for field-collected populations uniformly showing a 100% frequency of the RyR I4790 M target-site resistance allele. To validate the function of CYP9A40 in diamide detoxification, we recombinantly expressed the gene and tested its ability to bind and degrade chlorantraniliprole as a substrate. The results confirmed its catalytic role in diamide metabolism. CYP9A40 has been identified and validated to confer metabolic resistance in Korean S. exigua populations. It works alongside the RyR target-site I4790 M mutation to enhance diamide resistance. These mechanisms offer insights for resistance monitoring and support insecticide resistance management programs to improve control strategies for S. exigua. © 2024 The Author(s)

关键词： Spodoptera exigua Diamide P450 CYP9A40 Heterologous expression RNA-Seq

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3D MR derived CT-like images of pelvic region from The Generative Adversarial Network (GAN)

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Journal of Medical Imaging and Radiation Sciences 2024年第3期55卷 101646-101646页

作者： Ina, Mr. Natee Rojchanaumpawan, Mr. Thirawut Thiangsook, Miss Wasinee Saleemee, Miss Saswanee Thongprajead, Miss Nannapas Cheewakul, Mr. Jongwat Radiological Technology Program Department of Radiology Faculty of Medicine Prince of Songkla University Hat Yai Songkhla Thailand Biomedical Engineering Program Department of Electrical Engineering Faculty of Engineering Prince of Songkla University Hat Yai Songkhla Thailand

BackgroundAlthough bone pathologies and lesions can be detected via CT images, patients may be exposed to radiation exposure. In contrast to CT, MRI does not subject the patient to radiation exposure; however, it is incapable of detecting cortical bone. CT-like images, on the other hand, can circumvent this limitation. GAN and U-net were utilized to generate CT-like images from 3D MR images for the purpose of comparing them to actual CT images. ObjectiveThis study aims to generate CT-like images from MRI images in three dimensions using fundamental deep learning methods. Materials and MethodsThe pelvic region real CT images and MR images of the same patients were obtained from the GOLD atlas public data set. A total of 6,236 images were utilized to train the model using the Python-based Spyder program. The model was then evaluated using 332 images to compare the quality of CT-like images to that of real CT images and to establish a comparison between the two models ResultsThe cGAN model generated CT-like images with smaller mean absolute error (MAE) and mean square error (MSE) values (0.0244 ± 0.0197 and 0.0032 ± 0.0040, respectively), and larger Pearson correlation coefficient (PCC) and peak signal-to-noise ratio (PSNR) values (27.1221 ± 3.9920 and 0.9283 ± 0.0389, respectively). ConclusionThis research illustrates the capability of GAN to produce CT-like images from MR data, which could potentially serve as a substitute for authentic CT images when assessing bone morphologies.

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Thermography as a Supporting Tool for the Diagnosis of Patellar Tendon Dysfunctions: A Systematic Review

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Revista Brasileira de Ortopedia 2024年第5期59卷 e657-e662页

作者： de Barros, Sálvio Tadeu Correia Borba Neves, Eduardo Leal Brioschi, Marcos Universidade Federal de Alagoas (UFAL) AL Maceió Brazil Postgraduate Program in Biomedical Engineering Universidade Tecnológica Federal do Paraná (PPGEB/UTFPR) PR Curitiba Brazil Postgraduate Program in Medical Thermology and Thermography Faculty of Medicine Universidade de São Paulo (FMUSP) SP São Paulo Brazil

Objective The present study aimed to analyze the use of thermal images as a tool to aid in the diagnosis of dysfunctions in the patellar tendon. Methods A systematic review of the literature was carried out, following the PRISMA protocol with a search in international databases: Web of Science, SCOPUS, and Pubmed. Descriptors in English were used with the following combination ("thermal imaging" OR thermography OR "Infrared image" OR "Skin Temperature" OR "thermal image" OR "Infrared imaging") AND ("patellar tendon"). The evaluation of the methodological quality of the selected works was carried out by two evaluators independently, using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Results Six original articles were selected. Three papers evaluated changes in skin temperature in pathological situations. Two other works evaluated the reliability and reproducibility of thermography specifically in the patellar tendon region, and one article monitored skin temperature before and after two physical training protocols. Conclusion It can be concluded that the use of thermal images proved to be an excellent tool to support the diagnosis of dysfunctions in the patellar tendon region, as well as for monitoring the physiological changes in this region also in non-pathological conditions, such as during physical training. © 2024. The Author(s).

关键词： diagnosis knee patellar tendon thermography

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Predicting lipoabdominoplasty complications with infrared thermography: a delta-R analysis

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Archives of Plastic Surgery 2022年第5期48卷 553-558页

作者： Patricia Rodrigues Resende Marcos Leal Brioschi Franciele De Meneck Eduardo Borba Neves Manoel Jacobsen Teixeira Postgraduate Program in Thermology and Medical Thermography Hospital das Clínicas Faculty of Medicine University of São Paulo São Paulo School of Medicine Federal University of São Paulo São Paulo Graduate Program in Biomedical Engineering Federal Technological University of Paraná Curitiba

The diagnosis of the main complications resulting from lipoabdominoplasty has not yet been standardized. Infrared thermal imaging has been used to assess possible complications, such as necrosis and changes in micro- and macro-circulation, based on perforator mapping techniques, among others. The objective of this study was to present two clinical cases involving thermal imaging monitoring of the healing process of lipoabdominoplasty in the immediate postoperative evaluation and its preliminary results. Infrared thermography was performed 24 hours after the operation and on postoperative days 5, 25, and 27. In clinical case 1, it was found that the delta-R (∆T

关键词： Thermography Abdominoplasty Lipoabdominoplasty Postoperative complications Abdominal wall

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Toward a nomenclature consensus for diverse intelligent systems:Call for collaboration

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The Innovation 2024年第5期5卷 32-34页

作者： Brett J.Kagan Michael Mahlis Anjali Bhat Josh Bongard Victor MCole Phillip Corlett Christopher Gyngell Thomas Hartung Bianca Jupp Michael Levin Tamra Lysaght Nicholas Opie Adeel Razi Lena Smirnova Ian Tennant Peter Thestrup Wade Ge Wang Cortical Labs BrunswickVIC 3056Australia Wellcome Centre for Human Neuroimaging University College LondonLondon WC1N 3ARUK University of Vermont BurlingtonVT 05405USA Centre for Professional Communication Singapore Institute of TechnologySingapore 138683Singapore Department of Psychiatry Yale UniversityNew HavenCT 06511USA Murdoch Children’s Research Institute ParkvilleVIC 3052Australia Centre for Alternatives to Animal Testing(CAAT) Bloomberg School of Public Health and Whiting School of EngineeringJohns Hopkins UniversityDoerenkamp-Zbinden Chair for Evidence-based ToxicologyBaltimoreMD 21205USA CAAT-Europe University of Kostanz78464 KostanzGermany Department of Neuroscience Central Clinical SchoolMonash UniversityPrahranVIC 3004Australia Allen Discovery Centre at Tufts University MedfordMA 02155USA Yong Loo Lin School of Medicine National University of SingaporeSingapore 117597Singapore Faculty of Medicine and Health Sydney School of Public Health The University of SydneyCamperdownNSW 2050Australia Department of Medicine University of MelbourneParkvilleVIC 3010Australia Turner Institute for Brain and Mental Health Monash UniversityClaytonVIC 3168Australia Center for Alternatives to Animal Testing(CAAT) Bloomberg School of Public Health and Whiting School of EngineeringJohns Hopkins UniversityBaltimoreMD 21205USA Faculty of Engineering AgriTech and EnvironmentAnglia Ruskin UniversityPeterborough PE15BWUK Interacting Minds Centre Aarhus University8000 Aarhus CDenmark Department of Biomedical Engineering School of EngineeringBiomedical Imaging CenterCenter for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic InstituteTroyNY 12180USA Department of Biochemistry and Pharmacology University of MelbourneParkvilleVIC 3010Australia

Disagreements about language use are common both between and within *** interests require multidisciplinary collaboration or the field of research has the potential to impact society at large,it becomes critical to minimize these disagreements where *** development of diverse intelligent systems,regardless of the substrate(e.g.,silicon ***),is a case where both conditions are *** advancements have occurred in the development of technology progressing toward these diverse intelligence *** progress is silicon based,such as the use of large language models,or through synthetic biology methods,such as the development of organoids,a clear need for a community-based approach to seeking consensus on nomenclature is now ***,we welcome collaboration from the wider scientific community,proposing a pathway forward to achieving this intention,highlighting key terms and fields of relevance,and suggesting potential consensus-making methods to be applied.

关键词： seeking collaboration diverse

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Cigarette smoke-induced dysbiosis: comparative analysis of lung and intestinal microbiomes in COPD mice and patients

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Respiratory Research 2024年第1期25卷 1-14页

作者： Laiman, Vincent Chuang, Hsiao-Chi Lo, Yu-Chun Yuan, Tzu-Hsuen Chen, You-Yin Heriyanto, Didik Setyo Yuliani, Fara Silvia Chung, Kian Fan Chang, Jer-Hwa Department of Radiology Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada – Dr. Sardjito Hospital Yogyakarta Indonesia School of Respiratory Therapy College of Medicine Taipei Medical University 250 Wuxing Street Taipei 11031 Taiwan Division of Pulmonary Medicine Department of Internal Medicine Shuang Ho Hospital Taipei Medical University New Taipei Taiwan Cell Physiology and Molecular Image Research Center Wan Fang Hospital Taipei Medical University Taipei Taiwan National Heart and Lung Institute Imperial College London London United Kingdom The Ph.D. Program for Neural Regenerative Medicine College of Medical Science and Technology Taipei Medical University Taipei Taiwan Department of Health and Welfare College of City Management University of Taipei Taipei Taiwan Industrial Ph.D. Program of Biomedical Science and Engineering National Yang Ming Chiao Tung University Taipei Taiwan Department of Biomedical Engineering National Yang Ming Chiao Tung University Taipei Taiwan Department of Anatomical Pathology Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada – Dr. Sardjito Hospital Yogyakarta Indonesia Department of Pharmacology and Therapy Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada Yogyakarta Indonesia Division of Pulmonary Medicine Departments of Internal Medicine Wan Fang Hospital Taipei Medical University Taipei Taiwan Collaboration Research Center for Precision Oncology based Omics- PKR Promics Universitas Gadjah Mada Yogyakarta Indonesia

Background: The impact of cigarette smoke (CS) on lung diseases and the role of microbiome dysbiosis in chronic obstructive pulmonary disease (COPD) have been previously reported;however, the relationships remain unclear. Methods: Our research examined the effects of 20-week cigarette smoke (CS) exposure on the lung and intestinal microbiomes in C57BL/6JNarl mice, alongside a comparison with COPD patients’ intestinal microbiome data from a public dataset. Results: The study found that CS exposure significantly decreased forced vital capacity (FVC), thickened airway walls, and induced emphysema. Increased lung damage was observed along with higher lung keratinocyte chemoattractant (KC) levels by CS exposure. Lung microbiome analysis revealed a rise in Actinobacteriota, while intestinal microbiome showed significant diversity changes, indicating dysbiosis. Principal coordinate analysis highlighted distinct intestinal microbiome compositions between control and CS-exposed groups. In the intestinal microbiome, notable decreases in Patescibacteria, Campilobacterota, Defferibacterota, Actinobacteriota, and Desulfobacterota were observed. We also identified correlations between lung function and dysbiosis in both lung and intestinal microbiomes. Lung interleukins, interferon-ɣ, KC, and 8-isoprostane levels were linked to lung microbiome dysbiosis. Notably, dysbiosis patterns in CS-exposed mice were similar to those in COPD patients, particularly of Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage 4 patients. This suggests a systemic impact of CS exposure. Conclusion: In summary, CS exposure induces significant dysbiosis in lung and intestinal microbiomes, correlating with lung function decline and injury. These results align with changes in COPD patients, underscoring the important role of microbiome in smoke-related lung diseases. © The Author(s) 2024.

关键词： Cigarette smoke Emphysema Inflammation Intestine Lung Microbiome

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