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Tn5-FISH,a novel cytogenetic method to image chromatin interactions with sub-kilobase resolution

Journal of Genetics and Genomics 2020年第12期47卷 727-734页

作者： Jing Niu Xu Zhang Li Guipeng Pixi Yan Qing Yan Qionghai Dai Dayong Jin Xiaohua Shen Jichang Wang Michael QZhang Juntao Gao School of Medicine Tsinghua UniversityBeijing 100084China Department of Automation Tsinghua UniversityBeijing 100084China Beijing Institute of Collaborative Innovation Beijing 100094China Medi-X Institute SUSTech Academy for Advanced Interdisciplinary StudiesSouthern University of Science and TechnologyShenzhen 518055China Department of Biology Southern University of Science and TechnologyShenzhen 518055China MOE Key Laboratory of Bioinformatics Bioinformatics DivisionBNRistCenter for Synthetic&Systems BiologyTsinghua UniversityBeijing 100084China Institute for Biomedical Materials and Devices(IBMD) Faculty of ScienceUniversity of Technology SydneyNSW 2007Australia UTS-SUStech Joint Research Centre for Biomedical Materials and Devices Department of Biomedical EngineeringSouthern University of Science and TechnologyShenzhen 518055China Key Laboratory for Stem Cells and Tissue Engineering(Sun Yat-sen University) Ministry of EducationGuangzhou 510080China Department of histology and embryology Zhongshan School of MedicineSun Yat-sen UniversityGuangzhou 510080China Department of Biological Sciences Center for Systems BiologyThe University of TexasDallasTX 75080-3021USA

There is an increasing interest in understanding how three-dimensional(3D)organization of the genome is *** strategies have been employed to identify genome-wide chromatin ***,due to current limitations in resolving genomic contacts,visualization and validation of these genomic loci with sub-kilobase resolution remain unsolved to ***,we describe Tn5 transposase-based Fluorescencein situhybridization(Tn5-FISH),a PCR-based,cost-effective imaging method,which can co-localize the genomic loci with sub-kilobase resolution,dissect genome architecture,and verify chromatin interactions detected by chromatin configuration capture(3C)-derived *** validate this method,short-range interactions in keratin-encoding gene(KRT)locus in topologically associated domain(TAD)were imaged by triple-color Tn5-FISH,indicating that Tn5-FISH is very useful to verify short-range chromatin interactions inside the contact domain and ***,Tn5-FISH can be a powerful molecular tool for the clinical detection of cytogenetic changes in numerous genetic diseases such as cancers.

关键词： Fluorescencein situhybridization Chromatin interaction Cellular imaging Super resolution

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Measuring hand use in the home after cervical spinal cord injury using egocentric video

arXiv

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arXiv 2022年

作者： Bandini, Andrea Dousty, Mehdy Hitzig, Sander L. Craven, B. Catharine Kalsi-Ryan, Sukhvinder Zariffa, José KITE Research Institute Toronto Rehabilitation Institute University Health Network Canada The BioRobotics Institute Scuola Superiore Sant'Anna Pisa Italy Department of Excellence in Robotics and AI Scuola Superiore Sant'Anna Pisa Italy Institute of Biomedical Engineering University of Toronto TorontoON Canada Rehabilitation Sciences Institute Temerty Faculty of Medicine University of Toronto TorontoON Canada St. John's Rehab Research Program Sunnybrook Research Institute Sunnybrook Health Sciences Centre TorontoON Canada Department of Occupational Science & Occupational Therapy Temerty Faculty of Medicine University of Toronto TorontoON Canada Brain and Spinal Cord Rehabilitation Program Toronto Rehabilitation Institute University Health Network TorontoON Canada Division of Physical Medicine and Rehabilitation Department of Medicine Temerty Faculty of Medicine University of Toronto TorontoON Canada Department of Physical Therapy University of Toronto TorontoON Canada Edward S. Rogers Sr. Department of Electrical and Computer Engineering University of Toronto TorontoON Canada

Egocentric video has recently emerged as a potential solution for monitoring hand function in individuals living with tetraplegia in the community, especially for its ability to detect functional use in the home environment. The aim of this study was to develop and validate a wearable vision-based system for measuring hand use in the home among individuals living with tetraplegia. Several deep learning algorithms for detecting functional hand-object interactions were developed and compared. The most accurate algorithm was used to extract measures of hand function from 65 hours of unscripted video recorded at home by 20 participants with tetraplegia. These measures were: the percentage of interaction time over total recording time (Perc);the average duration of individual interactions (Dur);the number of interactions per hour (Num). To demonstrate the clinical validity of the technology, egocentric measures were correlated with validated clinical assessments of hand function and independence (Graded Redefined Assessment of Strength, Sensibility and Prehension - GRASSP, Upper Extremity Motor Score - UEMS, and Spinal Cord Independent Measure - SCIM). Hand-object interactions were automatically detected with a median F1-score of 0.80 (0.67-0.87). Our results demonstrated that higher UEMS and better prehension were related to greater time spent interacting, whereas higher SCIM and better hand sensation resulted in a higher number of interactions performed during the egocentric video recordings. For the first time, measures of hand function automatically estimated in an unconstrained environment in individuals with tetraplegia have been validated against internationally accepted measures of hand function. Future work will necessitate a formal evaluation of the reliability and responsiveness of the egocentric-based performance measures for hand use. © 2022, CC BY-NC-ND.

关键词： Video recording

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Ginkgolide B facilitates muscle regeneration via rejuvenating osteocalcin-mediated bone-to-muscle modulation in aged mice

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Journal of cachexia, sarcopenia and muscle 2023年第3期14卷 1349-1364页

作者： Belle Yu-Hsuan Wang Yi-Fan Chen Allen Wei-Ting Hsiao Wan-Jing Chen Chien-Wei Lee Oscar Kuang-Sheng Lee Musculoskeletal Research Laboratory SH Ho Scoliosis Research Laboratory Department of Orthopaedics and Traumatology Faculty of Medicine The Chinese University of Hong Kong Hong Kong. Center for Neuromusculoskeletal Restorative Medicine CUHK InnoHK Centres Hong Kong Science Park Hong Kong. The Ph.D. Program for Translational Medicine College of Medical Science and Technology Taipei Medical University Taipei Taiwan. Graduate Institute of Translational Medicine College of Medical Science and Technology Taipei Medical University Taipei Taiwan. International Ph.D. Program for Translational Science College of Medical Science and Technology Taipei Medical University Taipei Taiwan. Master Program in Clinical Genomics and Proteomics School of Pharmacy Taipei Medical University Taipei Taiwan. Department of Orthopaedics and Traumatology Faculty of Medicine Prince of Wales Hospital The Chinese University of Hong Kong Hong Kong. Center for Translational Genomics & Regenerative Medicine Research China Medical University Hospital China Medical University Taichung Taiwan. Department of Biomedical Engineering China Medical University Taichung Taiwan. Department of Orthopedics China Medical University Hospital Taichung Taiwan. Institute of Clinical Medicine National Yang Ming Chiao Tung University Taipei Taiwan.

BACKGROUND:The progressive deterioration of tissue-tissue crosstalk with aging causes a striking impairment of tissue homeostasis and functionality, particularly in the musculoskeletal system. Rejuvenation of the systemic and local milieu via interventions such as heterochronic parabiosis and exercise has been reported to improve musculoskeletal homeostasis in aged organisms. We have shown that Ginkgolide B (GB), a small molecule from Ginkgo biloba, improves bone homeostasis in aged mice by restoring local and systemic communication, implying a potential for maintaining skeletal muscle homeostasis and enhancing regeneration. In this study, we investigated the therapeutic efficacy of GB on skeletal muscle regeneration in aged mice. METHODS:Muscle injury models were established by barium chloride induction into the hind limb of 20-month-old mice (aged mice) and into C2C12-derived myotubes. Therapeutic efficacy of daily administrated GB (12 mg/kg body weight) and osteocalcin (50 μg/kg body weight) on muscle regeneration was assessed by histochemical staining, gene expression, flow cytometry, ex vivo muscle function test and rotarod test. RNA sequencing was used to explore the mechanism of GB on muscle regeneration, with subsequent in vitro and in vivo experiments validating these findings. RESULTS:GB administration in aged mice improved muscle regeneration (muscle mass, P = 0.0374; myofiber number/field, P = 0.0001; centre nucleus, embryonic myosin heavy chain-positive myofiber area, P = 0.0144), facilitated the recovery of muscle contractile properties (tetanic force, P = 0.0002; twitch force, P = 0.0005) and exercise performance (rotarod performance, P = 0.002), and reduced muscular fibrosis (collagen deposition, P < 0.0001) and inflammation (macrophage infiltration, P = 0.03). GB reversed the aging-related decrease in the expression of osteocalcin (P < 0.0001), an osteoblast-specific hormone, to promote muscle regeneration. Exogenous osteocalcin supplementation was

关键词： Ginkgolide B aging osteocalcin rejuvenation skeletal muscle regeneration

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Comparison of Algebraic Reconstruction Technique Methods and Generative Adversarial Network in Image Reconstruction of Magnetic Induction Tomography (MIT)

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Journal of Physics: Conference Series 2021年第1期2071卷

作者： A J Lubis N F Mohd Nasir Z Zakaria M Jusoh M M Azizan M Z Zakaria M N F M Kazim S Rahman Faculty of Engineering and Computer Science Universitas Harapan Medan Medan Indonesia Computer Engineering Program Faculty of Electronic Engineering Technology Universiti Malaysia Perlis Perlis Malaysia Biomedical Electronic Engineering Program Faculty of Electronic Engineering Technology Universiti Malaysia Perlis Perlis Malaysia Sports Engineering Research Centre (SERC) Universiti Malaysia Perlis PerlisMalaysia Department of Electrical and Electronic Department Faculty of Engineering and Built Environment Universiti Sains Islam Malaysia Negeri Sembilan Malaysia Faculty of Mechanical Engineering Technology Universiti Malaysia Perlis Perlis Malaysia Mechatronic Engineering Program Faculty of Electrical Engineering Technology Universiti Malaysia Perlis Perlis Malaysia

Magnetic induction tomography (MIT) is a technique used for imaging electromagnetic properties of objects using eddy current effects. The non-linear characteristics had led to more difficulties with its solution especially in dealing with low conductivity imaging materials such as biological tissues. Two methods that could be applied for MIT image processing which is the Generative Adversarial Network (GAN) and the Algebraic Reconstruction Technique (ART). ART is widely used in the industry due to its ability to improve the quality of the reconstructed image at a high scanning speed. GAN is an intelligent method which would be able to carry out the training process. In the GAN method, the MIT principle is used to find the optimum global conductivity distribution and it is described as a training process and later, reconstructed by a generator. The output is an approximate reconstruction of the distribution's internal conductivity image. Then, the results were compared with the previous traditional algorithm, namely the regularization algorithm of BPNN and Tikhonov Regularization method. It turned out that GAN had able to adjust the non-linear relationship between input and output. GAN was also able to solve non-linear problems that cannot be solved in the previous traditional algorithms, namely Back Propagation Neural Network (BPNN) and Tikhonov Regularization method. There are several other intelligent algorithms such as CNN (Convolution Neural Network) and K-NN (K-Nearest Neighbor), but such algorithms have not been able to produce the expected image quality. Thus, further study is still needed for the improvement of the image quality. The expected result in this study is the comparison of these two techniques, namely ART and GAN to get the best results on the image reconstruction using MIT. Thus, it is shown that GAN is a better candidate for this purpose.

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The molecular characterization of complete mitochondrial genome of spotted snakehead fish,Channa punctata(Bloch 1793)

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Mitochondrial DNA Part B 2019年第1期4卷 547-548页

作者： Md. Jobaidul Alam Sapto Andriyono Sinar Pagi Sektiana Md. Mofizur Rahman Hyun-Woo Kim Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaDepartment of Fisheries Ministry of Fisheries and Livestock Dhaka Bangladesh Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaFisheries and Marine Faculty Universitas Airlangga Surabaya East Java Indonesia Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaAquaculture Technology Study Program Sekolah Tinggi Perikanan Jakarta Indonesia Department of Marine Biology Pukyong National University Busan Republic of KoreaDepartment of Fisheries and Marine Science Noakhali Science and Technology University Sonapur Noakhali Bangladesh Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaDepartment of Marine Biology Pukyong National University Busan Republic of Korea

The complete mitochondrial genome of spotted snakehead fish,Channa punctata(Bloch 1793) was determined by MiSeq platform. The genome was 16,409 bp in length, in which canonical 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region (D-Loop) were encoded. Relatively higher overall A + T contents (53.70%) was identified compared with G + C contents (46.30%). Among 13 protein-coding genes, only one unusual start condon (GTG) was identified in COX1, whereas six genes includingCOXII,COXIII,NAD2,NAD3,NAD4, andCytbwere ended with the incomplete stop codons (TA-/T–). Based on the currently identified mitogenomes of Channa fish species,C. punctatawas most closely related toChanna gachuawith 82% sequence identity.

关键词： Next generation sequencing Channa punctata mitochondrial genome phylogeny snakehead fish

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Melanoma Detection by AFM Indentation of Histological Specimens

Research Square

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Research Square 2021年

作者： Jeon, ByoungJun Jung, Hyo Gi Lee, Sang Won Lee, Gyudo Shim, Jung Hee Kim, Mi Ok Kim, Byung Jun Kim, Sang-Hyon Lee, Hyungbeen Lee, Sang Woo Yoon, Dae Sung Jo, Seong Jin Choi, Tae Hyun Lee, Wonseok Interdisciplinary Program for Bioengineering Seoul National University Seoul08826 Korea Republic of School of Biomedical Engineering Korea University Seoul02841 Korea Republic of Interdisciplinary Program in Precision Public Health Korea University Seoul02841 Korea Republic of Department of Biotechnology and Bioinformatics Korea University Sejong30019 Korea Republic of Department of Plastic and Reconstructive Surgery Research Services Seoul National University Bundang Hospital Seongnam13620 Korea Republic of Department of Plastic and Reconstructive Surgery Institute of Human Environment Interface Biology Seoul National University College of Medicine Seoul03087 Korea Republic of Department of Internal Medicine Keimyung University Dongsan Medical Center Daegu41931 Korea Republic of Department of Biomedical Engineering Yonsei University Wonju26493 Korea Republic of R&D Center of Curigin Ltd. Seoul04778 Korea Republic of Department of Dermatology Seoul National University College of Medicine Seoul03087 Korea Republic of Department of Electrical Engineering Korea National University of Transportation Chungju27469 Korea Republic of

Melanoma is visible unlike other types of cancer, but it is still challenging to diagnose correctly because of the difficulty in distinguishing between benign nevus and melanoma. We conducted a robust investigation of melanoma, identifying considerable differences in local elastic properties between nevus and melanoma tissues by using atomic force microscopy (AFM) indentation of histological specimens. Specifically, the histograms of the elasticity of melanoma displayed multimodal Gaussian distributions, exhibiting the heterogeneous mechanical properties, in contrast with the unimodal distributions of elasticity in the benign nevus. We identified this notable signature was consistent regardless of blotch incidence by sex, age, anatomical site (e.g., thigh, calf, arm, eyelid, and cheek), or cancer stage (I, IV, and V). In addition, we found that the non-linearity of the force-distance curves for melanoma is increased compared to benign nevus. We believe that AFM indentation of histological specimens may technically complement conventional histopathological analysis for earlier and more precise melanoma detection. © 2021, CC BY.

关键词： Elasticity

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Corrigendum to “Molecularly imprinted polymers for the detection of volatile biomarkers” [Trends Anal. Chem. 177 (2024) 117783]

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TrAC Trends in Analytical Chemistry 2025年 184卷

作者： Tomasz Wasilewski Sinem Orbay Nathália F. Brito Karol Sikora Ana Claudia A. Melo Matias E. Melendez Bartosz Szulczyński Amitav Sanyal Wojciech Kamysz Jacek Gębicki Department of Inorganic Chemistry Faculty of Pharmacy Medical University of Gdańsk Hallera 107 Gdańsk 80-416 Poland Biomedical Engineering Institute Boğaziçi University Çengelköy 34684 Istanbul Turkey Biomedical Engineering Erzincan Binali Yıldırım University Erzincan 24002 Turkey Program of Cell and Gene Therapy Brazilian National Cancer Institute Rio de Janeiro RJ 20231-050 Brazil Instituto de Química Universidade Federal do Rio de Janeiro Rio de Janeiro RJ 21941-909 Brazil Department of Process Engineering and Chemical Technology Chemical Faculty Gdańsk University of Technology Narutowicza 11/12 Gdańsk 80-233 Poland Department of Chemistry Boğaziçi University Bebek 34342 Istanbul Turkey

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Corrigendum to “Phosphazene-based covalent organic polymers as metal-free catalysts with improved H 2 generation from NaBH 4 in methanol with superior catalytic activity and re-generation ability” [J. Environ. Chem. Eng. 12 2 (2024) 112066]

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Journal of Environmental Chemical engineering 2024年第6期12卷

作者： Sahin Demirci Mustafa Yildiz Nurettin Sahiner Department of Chemistry Faculty of Sciences and Nanoscience and Technology Research and Application Center (NANORAC) Canakkale Onsekiz Mart University Terzioglu Campus Canakkale 17100 Turkey Department of Ophthalmology Morsani College of Medicine University of South Florida Eye Institute 12901 Bruce B Down Blvd MDC 21 Tampa FL 33612 USA Department of Chemical & Biomedical Engineering Director Materials Science and Engineering Program University of South Florida Tampa FL 33620 USA

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Mechanical properties of poly-(hydroxybutyrate-co-valerate)/natural rubber/cellulose nanocrystal (PHBV/NR/CNC) nanocomposites prepared by using two-roll mill method

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AIP Conference Proceedings 2024年第1期2883卷

作者： K. C. Lim N. A. S. A. Halim S. N. S. Mahamud A. F. Osman M. H. M. Pisal A. Masa Faculty of Chemical Engineering Technology University Malaysia Perlis (UniMAP) Arau Perlis 02600 Malaysia. Biomedical and Nanotechnology Research Group Center of Excellence Geopolymer and Green Technology (CEGeoGTech) Universiti Malaysia Perlis 01000 Kangar Perlis Malaysia. Centre of Excellence for Biomass Utilization (CoEBU) Universiti Malaysia Perlis (UniMAP) 01000 Perlis Malaysia Rubber Engineering and Technology Program International College Prince of Songkla University Hat Yai Songkhla 90110 Thailand

Poly (hydroxybutyrate-co-valerate) (PHBV) was the ideal replacement for petroleum-based plastic, owing to its biocompatible, non-toxicity and naturally by bacteria. However, PHBV has high brittleness due to high crystallinity, becoming a major challenge for PHBV commercial production and limiting its use in molded products. Natural rubber (NR) and cellulose nanocrystal (CNC) created an excellent opportunity to enhance the modulus and minimize the effect of non-degradable materials utilized in the polymer matrix. This study demonstrates the formation of PHBV/NR/CNC ternary nanocomposites to obtain a commodity biomaterial with improved mechanical properties. The effects of CNC loadings (1, 3, 5 wt.%) on the mechanical properties and structure of the PHBV/NR/CNC nanocomposites were investigated. Based on the tensile test, the use of the CNC brought a more pronounced positive impact (especially 1wt.% CNC) to the PHBV/NR blend matrix, where it enhanced the tensile Young’s modulus of the PHBV/NR/CNC nanocomposites. Fourier transform infrared spectroscopy (FTIR) confirmed the success of peroxide crosslinking after the melt compounding process by using a heated two-roll mill.

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Correction to: 3D-printed microgels supplemented with dentin matrix molecules as a novel biomaterial for direct pulp capping

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Clinical oral investigations 2023年第4期27卷 1799-1800页

作者： Diana Cunha Nayara Souza Manuela Moreira Nara Rodrigues Paulo Silva Cristiane Franca Sivaporn Horsophonphong Ashley Sercia Ramesh Subbiah Anthony Tahayeri Jack Ferracane Pamela Yelick Vicente Saboia Luiz Bertassoni Post-Graduation Program in Dentistry Federal University of Ceara Fortaleza Ceara Brazil. School of Dentistry Faculty of Pharmacy Dentistry and Nursing Federal University of Ceara Fortaleza Ceara Brazil. School of Dentistry University of Fortaleza Fortaleza Ceara Brazil. Division of Biomaterials and Biomechanics Department of Restorative Dentistry School of Dentistry Oregon Health & Science University Portland OR USA. Department of Pediatric Dentistry Faculty of Dentistry Mahidol University Salaya Thailand. Department of Orthodontics School of Medicine School of Engineering Tufts University Boston MA 02111 USA. Department of Restorative Dentistry Faculty of Pharmacy Dentistry and Nursing Federal University of Ceara Fortaleza Ceara Brazil. Division of Biomaterials and Biomechanics Department of Restorative Dentistry School of Dentistry Oregon Health & Science University Portland OR USA. bertasso@ohsu.edu. Center for Regenerative Medicine School of Medicine Oregon Health & Science University Portland OR USA. bertasso@ohsu.edu. Department of Biomedical Engineering School of Medicine Oregon Health & Science University Portland OR USA. bertasso@ohsu.edu. Cancer Early Detection Advanced Research Center (CEDAR) Knight Cancer Institute Portland OR USA. bertasso@ohsu.edu.

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