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Design and development of photonic-based non-invasive hemoglobin level detector

AIP Conference Proceedings 2020年第1期2314卷

作者： Suryani Dyah Astuti Ikhsan Rino Wijaya Osmalina Nur Rahma Alfian Pramudita Putra Muhammad Fahmi Akif Rahmatillah Riries Rulaningtyas 1Biomedical Engineering Master Degree Department of Physics Faculty of Science and Technology Universitas Airlangga Surabaya Indonesia 2Department of Physics Faculty of Science and Technology Universitas Airlangga Surabaya Indonesia 3Biomedical Engineering Study Program Department of Physics Faculty of Science and Technology Universitas Airlangga Surabaya Indonesia

Hemoglobin is the protein molecule that binds oxygen in the blood. Hemoglobin level can be used as a benchmark of the human physiological condition, such as anemia, hypoxia, and postoperative bleeding. Generally, measurement of hemoglobin levels is performed by an invasive method that takes blood samples to be tested. This study offers a tele-monitoring system for measuring the hemoglobin level non-invasively, so it could reduce the possibility of infection or contamination to the body and can be monitored anywhere by using a website. This tele-monitoring device of non-invasive hemoglobin and oxygen saturation levels were designed by integrating the pulse oximetry sensor with signal conditioning circuit, Arduino Uno as a microcontroller, Ethernet module, an internet network, cloud server, and website. Pulse oximetry measured the oxygen saturation in the blood that indicate the vital state of human and became essential to determine the amount of hemoglobin level. The system performance in this study was tested on participants who had a good daily exercise and participants who never had daily activities to discover the correlation between hemoglobin levels with human physical activity and obtained 89% of accuracy. This system can be implemented as a personal device for monitoring the hemoglobin level and the oxygen saturation in daily used.

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Corrigendum to "Variations of oxidative potential of PM2.5 in a medium-sized residential city in South Korea measured using three different chemical assays" [920 (2024) 171053]

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The Science of the total environment 2024年 926卷 172075页

作者： Pyung-Rae Kim Sung-Won Park Young-Ji Han Myong-Hwa Lee Thomas M Holsen Cheol-Heon Jeong Greg Evans Agriculture and Life Sciences Research Institute Kangwon National University Chuncheon Gangwon-do 24341 Republic of Korea. Dept. of Interdisciplinary Graduate Program in Environmental and Biomedical Convergence Kangwon National University Chuncheon Gangwon-do 24341 Republic of Korea. Dept. of Environmental Science Kangwon National University Chuncheon Gangwon-do 24341 Republic of Korea Gangwon particle pollution research and management center Kangwon National University Chuncheon Gangwon-do 24341 Republic of Korea. Electronic address: youngji@kangwon.ac.kr. Gangwon particle pollution research and management center Kangwon National University Chuncheon Gangwon-do 24341 Republic of Korea Dept. of Environmental Engineering Kangwon National University Chuncheon Gangwon-do 24341 Republic of Korea. Dept. of Civil and Environmental Engineering Clarkson University Potsdam NY 13699 USA. Dept. of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario MS5 3E5 Canada.

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Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2

arXiv

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arXiv 2020年

作者： Law, Jeffrey N. Akers, Kyle Tasnina, Nure Della Santina, Catherine M. Deutsch, Shay Kshirsagar, Meghana Klein-Seetharaman, Judith Crovella, Mark Rajagopalan, Padmavathy Kasif, Simon Murali, T.M. Interdisciplinary Ph.D. Program in Genetics Bioinformatics and Computational Biology BlacksburgVA United States Department of Computer Science Virginia Tech BlacksburgVA United States Department of Biomedical Engineering Boston University BostonMA United States Department of Mathematics University of California Los AngelesCA United States AI for Good Lab Microsoft RedmondWA United States Department of Chemistry Colorado School of Mines GoldenCO United States Department of Computer Science Boston University BostonMA United States Department of Chemical Engineering Virginia Tech BlacksburgVA United States

Background: Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance tracing in this context, e.g., determining how much any experimental observation in the input contributes to the score of every prediction. Results: We design a network propagation framework with two novel components and apply it to predict human proteins that directly or indirectly interact with SARS-CoV-2 proteins. First, we trace the provenance of each prediction to its experimentally validated sources, which in our case are human proteins experimentally determined to interact with viral proteins. Second, we design a technique that helps to reduce the manual adjustment of parameters by users. We find that for every top-ranking prediction, the highest contribution to its score arises from a direct neighbor in a human protein-protein interaction network. We further analyze these results to develop functional insights on SARS-CoV-2 that expand on known biology such as the connection between endoplasmic reticulum stress, HSPA5, and anti-clotting agents. Conclusions: We examine how our provenance tracing method can be generalized to a broad class of network-based algorithms. We provide a useful resource for the SARS-CoV-2 community that implicates many previously undocumented proteins with putative functional relationships to viral infection. This resource includes potential drugs that can be opportunistically repositioned to target these proteins. We also discuss how our overall framework can be extended to other, newly-emerging viruses. © 2020, CC BY-NC-SA.

关键词： SARS

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Quality of internal representation shapes learning performance in feedback neural networks

arXiv

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arXiv 2020年

作者： Susman, Lee Mastrogiuseppe, Francesca Brenner, Naama Barak, Omri Interdisciplinary Program in Applied Mathematics Technion Israel Institute of Technology Haifa32000 Israel Network Biology Research Laboratories Technion Israel Institute of Technology Haifa32000 Israel Gatsby Computational Neuroscience Unit University College London London United Kingdom Dept. of Chemical Engineering Technion Israel Institute of Technology Haifa32000 Israel Rappaport Faculty of Medicine Technion Israel Institute of Technology Haifa32000 Israel

A fundamental feature of complex biological systems is the ability to form feedback interactions with their environment. A prominent model for studying such interactions is reservoir computing, where learning acts on low-dimensional bottlenecks. Despite the simplicity of this learning scheme, the factors contributing to or hindering the success of training in reservoir networks are in general not well understood. In this work, we study non-linear feedback networks trained to generate a sinusoidal signal, and analyze how learning performance is shaped by the interplay between internal network dynamics and target properties. By performing exact mathematical analysis of linearized networks, we predict that learning performance is maximized when the target is characterized by an optimal, intermediate frequency which monotonically decreases with the strength of the internal reservoir connectivity. At the optimal frequency, the reservoir representation of the target signal is high-dimensional, de-synchronized, and thus maximally robust to noise. We show that our predictions successfully capture the qualitative behaviour of performance in non-linear networks. Moreover, we find that the relationship between internal representations and performance can be further exploited in trained non-linear networks to explain behaviours which do not have a linear counterpart. Our results indicate that a major determinant of learning success is the quality of the internal representation of the target, which in turn is shaped by an interplay between parameters controlling the internal network and those defining the task. © 2020, CC BY.

关键词： Quality control

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Transfer learning with deep Convolutional Neural Network (CNN) for pneumonia detection using chest X-ray

arXiv

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arXiv 2020年

作者： Rahman, Tawsifur Chowdhury, Muhammad E.H. Khandakar, Amith Islam, Khandaker R. Islam, Khandaker F. Mahbub, Zaid B. Kadir, Muhammad A. Kashem, Saad Department of Biomedical Physics & Technology University of Dhaka Dhaka1000 Bangladesh Department of Electrical Engineering Qatar University Doha2713 Qatar Department of Orthodentics Bangabandhu Sheikh Mujib Medical University Dhaka1000 Bangladesh Department of Mathematics and Physics North South University Dhaka1229 Bangladesh Faculty of Robotics and Advanced Computing Qatar Armed Forces-Academic Bridge Program Qatar Foundation Doha24404 Qatar

Pneumonia is a life threatening disease, which occurs in the lungs caused by either bacterial or viral infection. It can be life endangering if not acted upon in the right time and thus early diagnosis of pneumonia is vital. The aim of this paper is to automatically detect bacterial and viral pneumonia using the digital x-ray images. It provides a detailed report on advances made in making accurate detection of pneumonia and then presents the methodology adopted by the authors. Four different pre-trained deep Convolutional Neural Network (CNN): AlexNet, ResNet18, DenseNet201 and SqueezeNet were used for transfer learning. 5247 chest x-ray images consisting of bacterial, viral and normal chest x-rays were used and through preprocessing techniques, the modified images were trained for the transfer learning based classification task. In this work, the authors have reported three schemes of classifications: normal vs pneumonia, bacterial vs viral pneumonia and normal, bacterial and viral pneumonia. The classification accuracy of normal and pneumonia images, bacterial and viral pneumonia images, and normal, bacterial and viral pneumonia were 98%, 95% and 93.3% respectively. This is the highest accuracy in any scheme than the accuracies reported in the literature. Therefore, the proposed study can be useful in faster diagnosing pneumonia by the radiologist and can help in the fast airports screening of the pneumonia patients. Copyright © 2020, The Authors. All rights reserved.

关键词： Deep neural networks

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In-vitro characterization of 3D printed PLA scaffold with hydroxyapatite-chitosan coating for mandibula reconstruction

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AIP Conference Proceedings 2020年第1期2314卷

作者： Anis Fitria Wulandari Siti Zulaihah Ika Rachmadanti Aminatun 1Biomedical Engineering Program Department of Physics Faculty of Science and Technology Universitas Airlangga Surabaya 60115 Indonesia 2Physics Program Department of Physics Faculty of Science and Technology Universitas Airlangga Surabaya 60115 Indonesia

The mandibula is a part of the face that determines its shape as well as a place to attach the muscles of the mouth which has functions for chewing, swallowing, talking and yawning. Similar to other body organs, the mandibular bone can experience abnormalities, such as benign and malignant tumors. The tumor can potentially cause physiological and aesthetic disorders, so it needs to be resected in order to remove the infected part. This research was conducted to find out the potentials of 3D printed PLA scaffold with hydroxyapatite-chitosan coating for mandibula reconstructing through the contact angle test, the water absorption test and the biocompatibility test by in-vitro. The scaffold was made from polylactic acid (PLA) using 3D printing method of Fused Deposition Modelling (FDM) with a pore diameter of 1000 µm. Polylactic acid (PLA) is bioactive and hydrophobic filaments that needed to be coated with a bioactive material such as hydroxyapatite as well as a hydrophilic material such as chitosan. The composition variations of hydroxyapatite-chitosan which were used as the coating include A (70:30), B (60:40), C (50:50), D (40:60) and E (30:70). To determine the characteristics of the scaffold, several characterizations were carried out, namely the contact angle tests, the absorbency tests and the biocompatibility test. The characterization result from the contact angle test showed that PLA scaffold which has been coated with hydroxyapatite-chitosan is hydrophilic with contact angles of 45.7 - 71.3° in 25 minutes. The absorption test result showed a number of 4.15 - 9.34% from the first day to 9.57 - 12.90% on the seventh day which indicated that as the concentration of the chitosan increases, the water absorption also increases. Meanwhile, the biocompatibility test proved that scaffolds are non-toxic and safe for the body because they have a cell viability of 92.74 - 111.42%.

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Bilayer osteochondral graft in rabbit xenogeneic transplantation model comprising sintered 3D-printed bioceramic and human adipose-derived stem cells laden biohydrogel

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Journal of Biological engineering 2023年第1期17卷 74-74页

作者： Lee, Chih-Yun Nedunchezian, Swathi Lin, Sung-Yen Su, Yu-Feng Wu, Che-Wei Wu, Shun-Cheng Chen, Chung-Hwan Wang, Chih-Kuang Ph.D. Program in Life Sciences College of Life Science Kaohsiung Medical University Kaohsiung 80708 Taiwan Regenerative Medicine and Cell Therapy Research Center Kaohsiung Medical University Kaohsiung 80708 Taiwan Orthopaedic Research Center College of Medicine Kaohsiung Medical University Kaohsiung 80708 Taiwan Department of Medicinal and Applied Chemistry College of Life Science Kaohsiung Medical University Kaohsiung 80708 Taiwan Departments of Orthopaedics School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung 80708 Taiwan Department of Orthopaedics Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung 80708 Taiwan Department of Orthopaedics Kaohsiung Municipal Ta-Tung Hospital Kaohsiung Medical University Kaohsiung 80145 Taiwan Faculty of Post-Baccalaureate Medicine College of Medicine Kaohsiung Medical University Kaohsiung 80756 Taiwan Department of Surgery Division of Neurosurgery Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung 80708 Taiwan Department of Nursing Asia University Taichung 41354 Taiwan Ph.D. Program in Biomedical Engineering College of Medicine Kaohsiung Medical University Kaohsiung 80708 Taiwan Graduate Institute of Medicine College of Medicine Kaohsiung Medical University Kaohsiung 80708 Taiwan

Reconstruction of severe osteochondral defects in articular cartilage and subchondral trabecular bone remains a challenging problem. The well-integrated bilayer osteochondral graft design expects to be guided the chondrogenic and osteogenic differentiation for stem cells and provides a promising solution for osteochondral tissue repair in this study. The subchondral bone scaffold approach is based on the developed finer and denser 3D β-tricalcium phosphate (β-TCP) bioceramic scaffold process, which is made using a digital light processing (DLP) technology and the novel photocurable negative thermo-responsive (NTR) bioceramic slurry. Then, the concave-top disc sintered 3D-printed bioceramic incorporates the human adipose-derived stem cells (hADSCs) laden photo-cured hybrid biohydrogel (HG + 0.5AFnSi) comprised of hyaluronic acid methacryloyl (HAMA), gelatin methacryloyl (GelMA), and 0.5% (w/v) acrylate-functionalized nano-silica (AFnSi) crosslinker. The 3D β-TCP bioceramic compartment is used to provide essential mechanical support for cartilage regeneration in the long term and slow biodegradation. However, the apparent density and compressive strength of the 3D β-TCP bioceramics can be obtained for ~ 94.8% theoretical density and 11.38 ± 1.72 MPa, respectively. In addition, the in vivo results demonstrated that the hADSC + HG + 0.5AFnSi/3D β-TCP of the bilayer osteochondral graft showed a much better osteochondral defect repair outcome in a rabbit model. The other word, the subchondral bone scaffold of 3D β-TCP bioceramic could accelerate the bone formation and integration with the adjacent host cancellous tissue at 12 weeks after surgery. And then, a thicker cartilage layer with a smooth surface and uniformly aligned chondrocytes were observed by providing enough steady mechanical support of the 3D β-TCP bioceramic scaffold. © 2023, The Author(s).

关键词： Bioceramic scaffold Digital light processing Gelatin methacryloyl Hyaluronic acid methacryloyl Osteochondral Tissue engineering

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Nano-enabled Quenching of Bacterial Communications for the Prevention of Biofilm Formation

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Angewandte Chemie 2023年第27期135卷

作者： Dr. Meng Gao Dr. Bolong Xu Dr. Yang Huang Jiayu Cao Lili Yang Dr. Xi Liu Alisher Djumaev Di Wu Moxichexra Shoxiddinova Xiaoming Cai Behruz Tojiyev Dr. Huizhen Zheng Prof. Xuehua Li Prof. Kunduz Normurodova Prof. Huiyu Liu Prof. Ruibin Li State Key Laboratory of Radiation Medicine and Protection School for Radiological and Interdisciplinary Sciences (RAD-X) Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions Suzhou Medical College Soochow University 215123 Suzhou Jiangsu China Beijing Advanced Innovation Center for Soft Matter Science and Engineering State Key Laboratory of Organic–Inorganic Composites Bionanomaterials & Translational Engineering Laboratory Beijing Key Laboratory of Bioprocess Beijing Laboratory of Biomedical Materials Beijing University of Chemical Technology 100029 Beijing China Key Laboratory of Industrial Ecology and Environmental Engineering School of Environmental Science and Technology Dalian University of Technology 116024 Dalian Liaoning China School of Public Health Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Soochow University 215123 Suzhou Jiangsu China Department of Microbiology and Biotechnology Faculty of Biology National University of Uzbekistan named after Mirzo Ulugbek 100174 Tashkent Uzbekistan

Biofilm formation is a major threat to industry, the environment and human health. While killing of embedded microbes in biofilms may inevitably lead to the evolution of antimicrobial resistance (AMR), catalytic quenching of bacterial communications by lactonase is a promising antifouling approach. Given the shortcomings of protein enzymes, it is attractive to engineer synthetic materials to mimic the activity of lactonase. Herein, an efficient lactonase-like Zn−N x −C nanomaterial was synthesized by tuning the coordination environment around zinc atoms to mimic the active domain of lactonase for catalytical interception of bacterial communications in biofilm formation. The Zn−N x −C material could selectively catalyze 77.5 % hydrolysis of N-acylated-L-homoserine lactone (AHL), a critical bacterial quorum sensing (QS) signal in biofilm construction. Consequently, AHL degradation downregulated the expression of QS-related genes in antibiotic resistant bacteria and significantly prevented biofilm formation. As a proof of concept, Zn−N x −C-coated iron plates prevented 80.3 % biofouling after a month exposure in river. Overall, our study provides a nano-enabled contactless antifouling insight to avoid AMR evolution by engineering nanomaterials for mimicking the key bacterial enzymes (e.g., lactonase) functioning in biofilm construction.

关键词： Antibacterial Antimicrobial Resistance Biocatalysis Biofilm Nanozyme

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A disordered linker in the Polycomb protein Polyhomeotic tunes phase separation and oligomerization

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Molecular Cell 2025年第11期85卷 2128-2146.e15页

作者： Gemeinhardt, Tim M. Regy, Roshan M. Phan, Tien M. Pal, Nanu Sharma, Jyoti Senkovich, Olga Mendiola, Andrea J. Ledterman, Heather J. Henrickson, Amy Lopes, Daniel Kapoor, Utkarsh Bihani, Ashish Sihou, Djamouna Kim, Young C. Jeruzalmi, David Demeler, Borries Kim, Chongwoo A. Mittal, Jeetain Francis, Nicole J. Montreal Clinical Research Institute (IRCM) Montreal QC Canada Division of Experimental Medicine McGill University Montreal QC Canada Artie McFerrin Department of Chemical Engineering Texas A&M University College Station TX United States Department of Biochemistry and Molecular Medicine University of Montreal Montreal QC Canada Department of Biochemistry and Molecular Genetics Midwestern University Glendale AZ United States Department of Chemistry and Biochemistry The University of Lethbridge Lethbridge AB Canada Department of Chemistry and Biochemistry City College of New York New York NY United States Department of Chemical and Biomedical Engineering University of Wyoming Laramie WY United States Center for Materials Physics and Technology Naval Research Laboratory Washington DC United States Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New York NY United States Ph.D. Program in Biology The Graduate Center of the City University of New York New York NY United States Ph.D. Program in Chemistry The Graduate Center of the City University of New York New York NY United States Department of Chemistry and Biochemistry University of Montana Missoula MT United States Department of Chemistry Texas A&M University College Station TX United States Interdisciplinary Graduate Program in Genetics and Genomics Texas A&M University College Station TX United States

Biomolecular condensates are increasingly recognized as key regulators of chromatin organization, yet how their formation and properties arise from protein sequences remains incompletely understood. Cross-species comparisons can reveal both conserved functions and significant evolutionary differences. Here, we integrate in vitro reconstitution, molecular dynamics simulations, and cell-based assays to examine how Drosophila and human variants of Polyhomeotic (Ph)—a subunit of the PRC1 chromatin regulatory complex—drive condensate formation through their sterile alpha motif (SAM) oligomerization domains. We identify divergent interactions between SAM and the disordered linker connecting it to the rest of Ph. These interactions enhance oligomerization and modulate both the formation and properties of reconstituted condensates. Oligomerization influences condensate dynamics but minimally impacts condensate formation. Linker-SAM interactions also affect condensate formation in Drosophila and human cells and growth in Drosophila imaginal discs. Our findings show how evolutionary changes in disordered linkers can fine-tune condensate properties, providing insights into sequence-function relationships. © 2025 The Author(s)

关键词： analytical ultracentrifugation biochemistry biomolecular condensates CRISPR Drosophila gene regulation intrinsically disordered regions molecular dynamics simulations oligomerization phase separation Polycomb sterile alpha motif

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FLAIR MRI biomarkers of the Normal-Appearing Brain Matter (NABM) are related to APOE-4 status and CSF markers Aβ42 and Tau

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Alzheimer's & Dementia 2023年第S3期19卷

作者： Karissa Chan Corinne E. Fischer Houman Khosravani Sandra E. Black Pascal Tyrrell Pejman Jabehdar Maralani Alan R. Moody April Khademi Electrical Computer and Biomedical Engineering Department Ryerson University Toronto ON Canada St. Michael’s Hospital Toronto ON Canada University of Toronto Toronto ON Canada Keenan Research Centre for Biomedical Science St. Michael’s Hospital Toronto ON Canada Faculty of Medicine Department of Psychiatry University of Toronto Toronto ON Canada Institute of Medical Sciences University of Toronto Toronto ON Canada Keenan Research Centre for Biomedical Science the Li Ka Shing Knowledge Institute St. Michael’s Hospital Toronto ON Canada Division of Neurology Department of Medicine University of Toronto Toronto ON Canada Heart and Stroke Foundation Canadian Partnership for Stroke Recovery Toronto ON Canada Sunnybrook Research Institute Toronto ON Canada Hurvitz Brain Sciences Program Sunnybrook Research Institute Toronto ON Canada Toronto Dementia Research Alliance Toronto ON Canada LC Campbell Cognitive Neurology Research Unit Sunnybrook Research Institute Toronto ON Canada Department of Statistical Science University of Toronto Toronto ON Canada Department of Medical Imaging University of Toronto Toronto ON Canada Keenan Research Centre for Biomedical Research the Li Ka Shing Knowledge Institute St. Michael’s Hospital Toronto ON Canada Ryerson University IAMLAB Department of Electrical Computer and Biomedical Engineering Toronto ON Canada

Background Reduced amyloid-beta-42 (Aβ42) and elevated total tau (t-tau) protein concentrations in the CSF are characteristic of Alzheimer’s disease (AD) pathology [1]. Aβ42 contributes to extracellular plaque formation between neurons [2]. The total level of tau, a microtubule-stabilizer in neuron axons [3], is associated with neuronal death [1]. Additionally, presence of ApoE4 (ε4) alleles is an established identifier for increased risk of AD [4]. Non-invasive imaging-based correlates of the CSF markers are lacking. This study examines correlations of novel FLAIR texture, intensity, and volume biomarkers, along with white matter lesion (WML) burden, with Aβ42, t-tau, and ε4 status. Method FLAIR volumes (n = 4044) from the ADNI database were used for analysis with CSF biomarkers. A subset (n = 921) was used for ε4 analysis based on available data. Normal-appearing brain matter (NABM) was obtained by removing CSF and WML. Macrostructural damage (MAD), microstructural damage (MID), and integrity (MII) texture biomarkers [5] were extracted from each NABM volume (Fig. 1), along with median intensity, NABM/ICV ratio, and normalized WML volume [5]. Relationships between FLAIR biomarkers and AD markers were described using parametric statistical analyses. Statistical significance was set at p<0.05. Result All FLAIR biomarkers were statistically significantly correlated with CSF Aβ42 levels. All features except MID and WML burden were significantly correlated with CSF t-tau levels (Table 1). MAD, MID, and WML burden showed negative correlations with Aβ42, while MAD showed a positive correlation with t-tau. Opposite trends were seen with MII, intensity, and NABM/ICV (Fig. 2). Significant differences between groups without and with one ε4 allele were found in all FLAIR biomarkers except WML burden. Significant differences in MAD, MII and NABM/ICV were found between groups with one and two ε4 alleles (Table 2). Conclusion FLAIR biomarkers were inversely associated with CSF Aβ

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