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How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes

Genomics, Proteomics & Bioinformatics 2019年第1期17卷 91-105页

作者： Xiaoqing Jiang Xin Li Longshu Yang Chunhong Liu Qi Wang Weilai Chi Huaiqiu Zhu State Key Laboratory for Turbulence and Complex Systems Department of Biomedical Engineering College of Engineering Peking University Center for Quantitative Biology Peking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Biological (PTN) PhD Program and College of Life Sciences Peking University Center for Protein Science Peking University

Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction(FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage(AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping(CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.

关键词： Metagenomics Dynamics model Community structure Acid mine drainage Human gut microbiota

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OGC P14 A quantitative method to enhance endoscopic measurement

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British Journal of Surgery 2022年第SUPPLEMENT_9期109卷

作者： Safavian, Nazanin Lee, Prof Raymond Toh, Prof Simon Pani, Dr Martino PhD student in Biomedical engineering Portsmouth University Portsmouth United Kingdom PhD in Bioengineering and Professor of Biomechanics University Portsmouth United Kingdom England Consultant Surgeon Portsmouth Hospital NHS Trust Portsmouth United Kingdom Portsmouth University Portsmouth United Kingdom

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Development and Application of the Electrospun Microtube Array Membrane (MTAM) Substrate as a Potential Drug Encapsulation Platform for Continuous Drug Release Platform for Treatment of Elevated Intraocular Pressure (IOP) in Glaucoma Disease.

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Polymer 2025年

作者： Jou-Chen Huang Ching-Yu Lee Chee Ho Chew Wan-Ting Huang Shun-Chieh Chang Chien-Chung Chen Department of Ophthalmology Taipei Medical University Hospital Taipei Medical University Department of Ophthalmology School of Medicine College of Medicine Taipei Medical University Department of Orthopedics Taipei Medical University Hospital Taipei Medical University Department of Orthopedics School of Medicine College of Medicine Taipei Medical University Graduate Institute of Biomedical Materials and Tissue Engineering Taipei Medical University Taipei 11052 Taiwan International PhD Program for Cell Therapy and Regeneration Medicine College of Medicine Taipei Medical University Taipei 110 Taiwan The PhD Program for Translational Medicine Taipei Medical University Taipei 11052 Taiwan International Ph.D. Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei 110 Taiwan Ph.D Program in Biotechnology Research and Development College of Pharmacy Taipei Medical University Taipei 110 Taiwan

Glaucoma is the leading cause of blindness which is characterized by the elevation of intraocular pressure (IOP) which results in optic nerve damage. Clinically, the current mainstay of treatment which involves the use of anti-glaucoma agents delivered in the form of topical eye drops have limitations such as short drug retention times, pulsatile delivery and localized adverse effects. In this work, we strive to demonstrate the development of a novel drug encapsulation device, known as Microtube Array Membrane (MTAM) as a potential substrate for encapsulation of clinically available anti-glaucoma agent that is based on the materials Polysulfone (PSF) and poly(lactic acid) (PLA) and poly(glycolic acid) (PLA-PLGA) copolymer. The resulting MTAM variants demonstrated tunable microstructures, mechanical properties and drug release; where pore sizes ranging from from 0.24 ± 0.02 μm to 17.62 ± 4.62 μm was successfully fabricated, and with loading efficiency of Brimonidine Tartrate up to 90%. Sustained drug release was observed over 3 days under simulated tear physiological conditions, with the PLA-PLGA MTAM variants released the greatest amount of drug encapsulated within and sustained even in the presence of simulated tears turnover. Critically, the encapsulation of the drug within the respective MTAMs seemed to mitigate any toxicity effects that was largely reported in direct use of Brimonidine Tartrate. Potentially, with more research and development, the MTAM based drug encapsulation could effective be deployed as a novel drug release system in future localized and sustained drug delivery.

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Identification and Prevention of Glaucoma Through Digital Processing of biomedical Imaging by the Relationship Between Volume of Nerve Fibers and Intraocular Pressure

Identification and Prevention of Glaucoma Through Digital Pr...

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AHFE Virtual Conference on Human Factors and Ergonomics in Healthcare and Medical Devices, and the International Conference on Human Factors in Aging and Special Needs, 2020

作者： Pinos-Vélez, Eduardo Chazi, Marlon Cajamarca, Christian Robles-Bykbaev, Vladimir Chacón, Carlos Luis Ipanaqué, William Serpa-Andrade, Luis GIIATA Research Group on Artificial Intelligence and Assistive Technologies and GIIB Research Group on Biomedical Engineering Universidad Politécnica Salesiana Cuenca Ecuador GIIATA Research Group on Artificial Intelligence and Assistive Technologies Universidad Politécnica Salesiana Cuenca Ecuador Ecuadorian Society of Glaucoma Clinical Santa Lucía Quito Ecuador PhD of Engineering Computer Science and Control DICOP Universidad de Piura Piura Peru

ISBN: (纸本)9783030508371

Glaucoma is the second leading cause of blindness worldwide and the first in an irreversible way, many of the studies and investigations are concentrated in methods of control and treatment, however, there are few studies carried out in the areas of prevention and early detection of glaucoma, so, in this research presents the effect of increased intraocular pressure in the optic nerve, especially in damage caused in the layer of nerve fibers and their impact with the visual field, To do this, you work with background images of human eye, obtained from the Clinic "Santa Lucia", digital image processing to characterize parameters that determine a presumptive diagnosis of glaucoma suspect, the results are presented to specialists for a medical diagnosis. © 2020, The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Optical tomography

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Proposal for a Tool for the Calculation of Toric Intraocular Lens Using Multivariate Regression 1st

Proposal for a Tool for the Calculation of Toric Intraocular...

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1st International Conference on Advances in Emerging Trends and Technologies, ICAETT 2019

作者： Castillo-Cabrera, Johanna Pucha-Ortiz, Nataly Pinos-Velez, Eduardo Ipanque, William Chacón, Carlos Luis GIIATA Research Group on Artificial Intelligence and Assistive Technologies Universidad Politécnica Salesiana Cuenca Ecuador GIIATA Research Group on Artificial Intelligence and Assistive Technologies and GIIB Research Group on Biomedical Engineering at Universidad Politécnica Salesiana Cuenca Ecuador PhD of Engineering Computer Science and Control Universidad de Piura Piura Peru Board Member of the EcuadoRian Society of Glaucoma Clinical Santa Lucía Quito Ecuador

ISBN: (纸本)9783030320218

A common cause of loss of vision for humans is lens opacity, or cat aracts, which prevent patients from having a full field of vision and lower their visual acuities. Cataracts can be corrected for by replacing the opaque lens with a toric intraocular lens. The calculation for the placement of the toric lens is exceedingly important for the patient´s recovery of vision. Some houses, take date form medical equipment and perform the calculation, but more depends on the experience of the treating physician to ensure the desired effectiveness and efficiency, For this reason, in this investigation, the proposal is presented to perform the calculation, in addition, the approach to simulation of the placement of the lens inside the eye, especially in its axial length and depth in the anterior chamber, determinants for short, medium and long distance with an automatic focus and appropriate, in like manner, the results are exposed to the specialists of the clinic "Santa Lucia" in the city of Quito. © 2020, Springer Nature Switzerland AG.

关键词： Intraocular lenses

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Proposal for a Support Tool for the Study of Corneal Biomechanics and Its Influence in the Human Eye 1st

Proposal for a Support Tool for the Study of Corneal Biomech...

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1st International Conference on Advances in Emerging Trends and Technologies, ICAETT 2019

作者： Cordero, María Isabel Coronel, Roberto Pinos-Vélez, Eduardo Ipanque, William Chacón, Carlos Luis GIIATA Research Group on Artificial Intelligence and Assistive Technologies Universidad Politécnica Salesiana Cuenca Ecuador GIIATA Research Group on Artificial Intelligence and Assistive Technologies and GIIB Research Group on Biomedical Engineering at Universidad Politécnica Salesiana Cuenca Ecuador PhD of Engineering Computer Science and Control Universidad de Piura Piura Peru Board Member of the Ecuadorian Society of Glaucoma Clinical Santa Lucía Quito Ecuador

ISBN: (纸本)9783030320218

In search of more effective methods in the diagnosis vision and reduce the risk of post-operative ectasia, this article considers the importance of the biomechanical properties of the cornea and its close relationship with the development of corneal and possible conditions diseases in the human eye. For that reason, part of the literature is the review and analysis of the methods raised to remove accurate information from medical equipment, especially in the equipment Oculus Corvis and ORA from the Clinic "Santa Lucia" in the city of Quito. The corneal indices derived from these instruments can measure biomechanical parameters, but that is not accurate because of features such as geometry or thickness of the central corneal. The Young’s modulus corresponds to the elasticity of the corneal tissue. In addition, it is an important biomechanical feature that states different solutions for their extraction in vitro or in vivo through the use of numerical methods and/or modeling of complex systems of equations to simulate the real corneal tissue. There is also the obtaining of the elasticity of the cornea through processes of images of the human eye, which shows the action of the cornea at the time of using the tonometer. As a result, it demonstrate, in some cases, that the Young’s modulus relates only to the intraocular pressure, but also in other cases, it changes due to the increase of other factors such as age of people, corneal resistance, the central cornea thickness, etc. © 2020, Springer Nature Switzerland AG.

关键词： Elasticity

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Effect of Implant Scan Body type, Intraoral scanner and Scan Strategy on the accuracy and scanning time of a maxillary complete arch implant scans: an in vitro study

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Journal of Dentistry 2025年 159卷

作者： Grande, Francesco Mosca Balma, Alessandro Mussano, Federico Catapano, Santo PhD student Department of Mechanical and aerospace engineering Polytechnic University of Turin Turin Italy Biomedical Engineer Department of Surgical Sciences CIR Dental School University of Turin Turin Italy Department of Surgical Sciences CIR Dental School University of Turin Turin Italy and Department Head Department of Prosthodontics University of Ferrara Ferrara Italy

Objectives: This study aimed to investigate the influence of three Implant Scan Bodies (ISBs), four intraoral scanners (IOSs), and two scan strategies on the trueness of complete arch implant scans. Methods: A reference digital cast of an all-on-six maxillary rehabilitation was obtained using a coordinate measuring machine. Three ISBs - AQ (ISB-AQ), One-shot, Elos (ISB-PEEK) - four IOSs - Trios3POD (TRIOS), Medit i700 (MED), iTero Element 5D (iTe), Primescan (PRIME) - and two scan strategies - Zig-zag (ZZ), One-shot (OS) - were used for evaluation. For each group created by the combination of the different variables, 10 digital scans were taken by one operator (n = 240) under controlled temperature and lighting conditions. The positions of the ISB connections were compared to the standard tessellation language reference file by using the nurbs-to-nurbs method. The overall 3D linear and angular deviations of the ISBs connections between reference and test scans were evaluated by computing the Euler distances (α=0.05). Interimplant distance discrepancies were calculated at the ISB connection level. Scanning times were recorded. Results: Regarding linear and angular deviations, AQ had significantly higher trueness than the other ISBs (p < 0.01). TRIOS showed significantly higher trueness (p < 0.01). No significant differences for scan strategies were found (p > 0.05). ISB-OneSh, Primescan and ZZ method resulted in significant shortest scanning times (p<<0.01). Conclusions: ISB-AQ demonstrated higher trueness than One-Shot and PEEK. TRIOS performed better than the other IOSs. Scan strategy didn't influence the trueness. ISB-OneSh, Primescan, and ZZ strategy allowed the fastest scans. Clinical Significance: The choice of ISB and IOS significantly affects the accuracy of complete-arch implant scans. The scan strategy did not impact trueness but influenced the efficiency. As an in vitro study, results observed need confirmation in the clinical settings. © 2025 The Authors

关键词： Accuracy Angular deviation Implant scan body Interimplant discrepancy Intraoral scanner Scanning strategy Scanning time

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Statistical Power Analysis for Designing Bulk, Single-Cell, and Spatial Transcriptomics Experiments: Review, Tutorial, and Perspectives

arXiv

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arXiv 2023年

作者： Jeon, Hyeongseon Xie, Juan Jeon, Yeseul Jung, Kyeong Joo Gupta, Arkobrato Chang, Won Chung, Dongjun Department of Biomedical Informatics The Ohio State University ColumbusOH United States Pelotonia Institute for Immuno-Oncology The James Comprehensive Cancer Center The Ohio State University ColumbusOH43210 United States The Interdisciplinary PhD program in Biostatistics The Ohio State University ColumbusOH United States Department of Statistics and Data Science Yonsei University Seoul Korea Republic of Department of Applied Statistics Yonsei University Seoul Korea Republic of Department of Computer Science and Engineering The Ohio State University ColumbusOH United States Division of Statistics and Data Science University of Cincinnati CincinnatiOH United States

Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct characteristics. In order to guarantee biologically meaningful findings using transcriptomic experiments, it is important to consider various experimental factors in a systematic way through statistical power analysis. In this paper, we review and discuss the power analysis for three types of gene expression profiling technologies from a practical standpoint, including bulk RNA-seq, single-cell RNA-seq, and high-throughput spatial transcriptomics. Specifically, we describe the existing power analysis tools for each research objective for each of the bulk RNA-seq and scRNA-seq experiments, along with recommendations. On the other hand, since there are no power analysis tools for high-throughput spatial transcriptomics at this point, we instead investigate the factors that can influence power analysis. © 2023, CC BY-NC-ND.

关键词： RNA

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Assessment of circulating extracellular vesicles from calorie-restricted mice and humans in ischaemic injury models

Journal of Extracellular Biology

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Journal of Extracellular Biology 2023年第5期2卷 e86页

作者： Jaimes, Manuel S. V. Liao, Chia-Te Chen, Max M. Czosseck, Andreas Lee, Tsung-Lin Chou, Yu-Hsiang Chen, Yung-Ming Lin, Shuei-Liong Lai, James J. Lundy, David J. Graduate Institute of Biomedical Materials & Tissue Engineering Taipei Medical University Taipei Taiwan Division of Nephrology Department of Internal Medicine Shuang Ho Hospital Taipei Medical University New Taipei Taiwan Division of Nephrology Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei Taiwan TMU Research Center of Urology and Kidney (TMU-RCUK) Taipei Medical University Taipei Taiwan Division of Nephrology Department of Internal Medicine National Taiwan University Hospital College of Medicine National Taiwan University Taipei Taiwan Graduate Institute of Physiology College of Medicine National Taiwan University Taipei Taiwan Department of Bioengineering University of Washington Seattle WA United States Department of Materials Science and Engineering National Taiwan University of Science and Technology Taipei Taiwan International PhD Program in Biomedical Engineering Taipei Medical University Taipei Taiwan Center for Cell Therapy Taipei Medical University Hospital Taipei Taiwan

Calorie restriction (CR) and fasting affect lifespan, disease susceptibility and response to acute injury across multiple animal models, including ischaemic injuries such as myocardial infarction or kidney hypoxia. The cargo and function of circulating extracellular vesicles (EV) respond to changes in host physiology, including exercise, injury, and other interventions. Thus, we hypothesised that EVs induced following CR may reflect some of the beneficial properties of CR itself. In a pilot study, EVs were isolated from mice following 21 days of 30 % CR, and from eight human donors after 72 h water-only fasting. EV size, concentration and morphology were profiled by NTA, western blot and cryoEM, and their function was assessed using multiple assays related to ischaemic diseases. We found that EVs from post-fasting samples better protected cardiac cells from hypoxia/reperfusion (H/R) injury compared to pre-fasting EVs. However, there was no difference when used to treat H/R-injured kidney epithelial cells. Post-fasting derived EVs slowed the rate of fibroblast migration and slightly reduced macrophage inflammatory gene expression compared to pre-fasting derived EVs. Lastly, we compared miRNA cargos of pre- and post-fasting human serum EVs and found significant changes in a small number of miRNAs. We conclude that fasting appears to influence EV cargo and function, with varied effects worthy of further exploration. © 2023 The Authors. Journal of Extracellular Biology published by Wiley Periodicals, LLC on behalf of the International Society for Extracellular Vesicles.

关键词： calorie restriction cardiomyocyte diet extracellular vesicle fasting hypoxia ketone macrophage microRNA serum

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Genomic data processing with GenomeFlow

arXiv

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arXiv 2025年

作者： Park, Junseok Maury, Eduardo A. Oh, Changhoon Shin, Donghoon Denisko, Danielle Lee, Eunjung Alice Division of Genetics and Genomics Boston Children’s Hospital 3 Blackfan Circle BostonMA United States Department of Pediatrics Harvard Medical School 25 Shattuck St BostonMA United States Bioinformatics Integrative Genomics Program Harvard/MIT MD-PHD Program Harvard Medical School BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard CambridgeMA United States Graduate School of Information Yonsei University 50 Yonsei-ro Seodaemun-gu Seoul Korea Republic of Department of Human Centered Design and Engineering University of Washington SeattleWA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States

Advances in genome sequencing technologies generate massive amounts of sequence data that are increasingly analyzed and shared through public repositories. On-demand infrastructure services on cloud computing platforms enable the processing of such large-scale genomic sequence data in distributed processing environments with a significant reduction in analysis time. However, parallel processing on cloud computing platforms presents many challenges to researchers, even skillful bioinformaticians. In particular, it is difficult to design a computing architecture optimized to reduce the cost of computing and disk storage as genomic data analysis pipelines often employ many heterogeneous tools with different resource requirements. To address these issues, we developed GenomeFlow, a tool for automated development of computing architecture and resource optimization on Google Cloud Platform, which allows users to process a large number of samples at minimal cost. We outline multiple use cases of GenomeFlow demonstrating its utility to significantly reduce computing time and cost associated with analyzing genomic and transcriptomic data from hundreds to tens of thousands of samples from several consortia. Here, we describe a step-by-step protocol on how to use GenomeFlow for a common genomic data processing task. We introduce this example protocol geared toward a bioinformatician with little experience in cloud computing. © 2025, CC BY.

关键词： Cloud platforms

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