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Exploration of dark chemical genomics space via portal learning: Applied to targeting the undruggable genome and COVID-19 anti-infective polypharmacology

arXiv

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arXiv 2021年

作者： Cai, Tian Xie, Li Chen, Muge Liu, Yang He, Di Zhang, Shuo Mura, Cameron Bourne, Philip E. Xie, Lei Ph.D. Program in Computer Science The Graduate Center The City University of New York New York10016 United States Department of Computer Science Hunter College The City University of New York New York10065 United States Master Program in Computer Science Courant Institute of Mathematical Sciences New York University United States School of Data Science Department of Biomedical Engineering University of Virginia VA22903 United States Helen and Robert Appel Alzheimer’s Disease Research Institute Feil Family Brain & Mind Research Institute Weill Cornell Medicine Cornell University New York10021 United States

Advances in biomedicine are largely fueled by exploring uncharted territories of human biology. Machine learning can both enable and accelerate discovery, but faces a fundamental hurdle when applied to unseen data with distributions that differ from previously observed ones—a common dilemma in scientific inquiry. We have developed a new deep learning framework, called Portal Learning, to explore dark chemical and biological space. Three key, novel components of our approach include: (i) end-to-end, step-wise transfer learning, in recognition of biology’s sequence-structure-function paradigm, (ii) out-of-cluster meta-learning, and (iii) stress model selection. Portal Learning provides a practical solution to the out-of-distribution (OOD) problem in statistical machine learning. Here, we have implemented Portal Learning to predict chemical-protein interactions on a genome-wide scale. Systematic studies demonstrate that Portal Learning can effectively assign ligands to unexplored gene families (unknown functions), versus existing state-of-the-art methods, thereby allowing us to target previously "undruggable" proteins and design novel polypharmacological agents for disrupting interactions between SARS-CoV-2 and human proteins. Portal Learning is general-purpose and can be further applied to other areas of scientific *** Codes 68T07 © 2021, CC BY.

关键词： Genes

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Electromyography digital input assistance as a muscle- computer interface device: A pilot study in development of stroke rehabilitation and assistive devices

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AIP Conference Proceedings 2023年第1期2634卷

作者： Eko Arisetijono Marhaendraputro Shelby Amrus Ernanda Muhammad Nayif Alan Hamada Faisal Mohammad Rifqi Aqil Fadhillah Randy Widiawan Melina Suhartono Muhammad Agil Wijaya Faradis Muhammad Refindo Azhar Bisma Dewanto Ari Prabowo Satriya Nur Firman Syah I. Made Bhayu Mahendra Merika Soraya Sabada Putra Rivan Tegar Syahriar 1Department of Neurology Faculty of Medicine Universitas Brawijaya Malang Indonesia 2Neurology Department Saiful Anwar Hospital Malang Indonesia 3Master Program in Biomedical Science Faculty of Medicine Universitas Brawijaya Malang Indonesia 4Medical Doctor Study Program Faculty of Medicine Universitas Brawijaya Malang Indonesia 5Independent Engineer and Researcher Bondowoso Indonesia

The rehabilitation therapy is essential for post stroke patients. However, rehabilitation facilities are not always accessible, due to distances or availability of vehicles and companion. This issue could be solved by utilizing portable Electromyograph (EMG)-like device that could communicate with a variety of smart devices (interfacing muscle and computer) and enabling remote monitoring by health care professionals. Hospital visit could be minimalized, reducing the risk to get an infectious disease, such as COVID-19. This device could become the foundation of an assistive device, since it can be connected to various Internet of Things (IoT). Thus, we developed a portable EMG-like device that has an interface with computers. We called this device Electromyography Digital Input Assistance (EDIA). EDIA could recognize 97% of the attempted contraction and 95% of the attempted relaxation. However, EDIA struggled to handle long duration muscle contraction. Whenever the user do a single long duration muscle contraction, EDIA might recognize and treat such input as multiple muscle contraction. Prior to the use of EDIA, training exercises for user should be performed to reduce error in the muscle states recognition. To use EDIA in clinical setting, further research and development is still needed.

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A Study of Eye Lens Radiation Dose Reduction During Head CT Scan Examination

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Journal of Medical Imaging and Radiation sciences 2022年第4期53卷 S25-S25页

作者： Nur Istiqomah, Anisa Dewi, Sofie Nornalita Mufida, Widya Radiology Study Program Faculty of Health Sciences Universitas ‘Aisyiyah Yogyakarta Sleman DI Yogyakarta 55292 Indonesia Biomedical Engineering Program Department of Electrical Engineering Faculty of Engineering Universitas Indonesia Depok West Java 16424 Indonesia Diagnostic Imaging Program Master of Applied Science Health Polytechnic of Semarang Semarang City Central Java 50268 Indonesia

BackgroundHead CT is the most frequently performed examination in every hospital in Indonesia. Considering of the large radiation dose of head CT produces and eye which is one of the most sensitive organs, radioprotection is should be done for every patient of head CT. The aim of this study is to determine the radiation dose of eye lens during head CT compared to the dose limit value determined by ICRP No. 87 of 2000 and provides recommendations for examination protocols that prioritize radiation protection in order to reducing eye lens radiation dose. MethodsRadiation dose measurement of eye lens were performed on 10 patient samples using two different scanograms for every 5 patients. The first five patients had a scanogram parallel to the Orbitomeatal line (OML) and the other 5 patients had a scanogram parallel to the Supraorbitomeatal line (SOML). Radiation dose measurement is done by placing the Thermoluminescent Dosimeter 100-chip on one of the patient's eyelid surfaces. The results of the radiation dose measurements are presented and compared with the standard dose CT scan according to ICRP No. 87 2000. ResultsThe research showed that the procedure using scanogram parallel to OML get eye lens radiation dose 53.889 mGy, 50.729 mGy, 60.407 mGy, 70.952 mGy, 70.952 mGy and the other procedure which is using scanogram parallel to SOML get eye lens radiation dose 7.265 mGy, 6.944 mGy, 8.747 mGy, 6.411 mGy, 6.944 mGy. ConclusionThe procedure using scanogram parallel to the OML produces a higher dose of eye lens and it exceeds the standard head CT eye lens dose according to ICRP No. 87 of 2000. While the another procedure using scanogram parallel to SOML produces a lower radiation dose. Head CT is advised to use a scanogram parallel to SOML to reduce the eye lens radiation dose.

关键词： Head CT scan Radiation Dose Orbitomeatal line Supraorbitomeatal line TLD

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Agar-altered foaming bacterial cellulose with carvacrol for active food packaging applications

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Food Packaging and Shelf Life 2024年 42卷

作者： Kusuma, Anita Chandra Chou, Yu-Chieh Hsieh, Chen-Che Santoso, Shella Permatasari Go, Alchris Woo Lin, Hong-Ting Victor Hsiao, I.-Lun Lin, Shin-Ping Master Program in Food Safety Taipei Medical University 250 Wu-Hsing Street Taipei 11031 Taiwan Ph.D. Program in Drug Discovery and Development Industry Taipei Medical University 250 Wu-Hsing Street Taipei 11031 Taiwan Institute of Biotechnology National Taiwan University 1 Roosevelt Rd. Section 4 Taipei 10617 Taiwan Department of Chemical Engineering Widya Mandala Surabaya Catholic University Kalijudan 37 Surabaya 60114 Indonesia Department of Chemical Engineering National Taiwan University of Science and Technology 43 Keelung Road Section 4 Taipei 10607 Taiwan Department of Food Science National Taiwan Ocean University No. 2 Pei-Ning Road Keelung 20224 Taiwan School of Food Safety Taipei Medical University 250 Wu-Hsing Street Taipei 11031 Taiwan TMU Research Center for Digestive Medicine Taipei Medical University 250 Wu-Hsing Street Taipei 11031 Taiwan Research Center of Biomedical Device Taipei Medical University 250 Wu-Hsing Street Taipei 11031 Taiwan

Bacterial cellulose (BC) is a biodegradable nanoscale film produced by microorganisms, which possesses great mechanical properties and biocompatibility. In this study, we produced foaming BC (FBC) utilizing foam medium with different concentrations of agar. In addition, carvacrol was loaded into the agar/FBC to establish active packaging material. Evaluation by characterization tests indicated that agar/FBC provided lower crystallinity (59.8%∼71.4%) and a high swelling ability (94.7%∼97.9%) compared to BC (92.2% and 96.1%). The 1.5% agar/FBC with carvacrol group exhibited the significantly highest antimicrobial properties against Escherichia coli and Staphylococcus aureus. Moreover, release measurements showed that greater agar addition contributed to higher protein and carvacrol release extents out of the film. Finally, a sea bass packaging test indicated that carvacrol with 1.5% agar/FBC presented a higher antimicrobial ability against Shewanella putrefaciens, great inhibition of lipid oxidation (67.5%), and a slower spoilage degree (49.8%) which suggested that agar/FBC with carvacrol has potential for active food packaging. © 2024 Elsevier Ltd

关键词： Agar Bacterial cellulose Carvacrol Foaming bacterial cellulose Food packaging Sea bass

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The effect of mango mistletoes (Dendrophthoe pentandra) leaves extract toward lmmunosenescence on old balb/c mice

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AIP Conference Proceedings 2023年第1期2634卷

作者： Kusworini Handono Mirza Zaka Pratama Maria Gabriela Yuniati Inmas Andi Sermoati Eviana Norahmawati Agustina Tri Endharti Yahya Irwanto Syaiful Hidayat Muhammad Badrus Solikhin Lilik Indahwati Fatmawati Fatmawati 1Department of Clinical Pathology Faculty of Medicine Universitas Brawijaya Malang Indonesia 3LAURA (Lupus Autoimmune Rheumatic and Allergy) Research Center Universitas Brawijaya Malang Indonesia 2Rheumatology and Immunology Division Department of Internal Medicine Faculty of Medicine Universitas Brawijaya Malang Indonesia 4Master Degree in Midwifery Faculty of Medicine Universitas Brawijaya Malang Indonesia 5Department of Anatomical Pathology Faculty of Medicine Brawijaya University Malang Indonesia 6Department of Parasitology Faculty of Medicine Brawijaya University Malang Indonesia 7Master Program in Biomedical Science Faculty of Medicine Brawijaya University Malang Indonesia 8Department of Obstetrics and Gynecology Faculty of Medicine Universitas Brawijaya Malang Indonesia 9Master Program in Biomedical Science Faculty of Medicine Universitas Brawijaya Malang Indonesia 10Bachelor of Midwifery Study Program Faculty of Medicine Universitas Brawijaya Malang Indonesia 11Midwife Professional Education Study Program Faculty of Medicine Universitas Brawijaya Malang Indonesia

Immunosenescence triggers increased morbidity in geriatrics; therefore, therapeutic intervention is required. This study aims to find out the effect of mango mistletoes/Dendrophthoe pentandra (MM/Dp) towards CD4/CD8 ratio, CD4+CD28- percentage, CD8+CD28− percentage, and IL-2 level on old female mice. The mango mistletoes leaves were extracted using ethanol 96%, and then administered orally once a day for 30 days (150, 300, and 600 mg/kgBW). CD4/CD8 ratio, and percentage of CD4+CD28- and CD8+CD28− were examined using flowcytometry on the spleen sample. ELISA was performed on the blood sample extracted from the heart to study the IL-2 level. MM/Dp could lower the percentage of CD4+CD28- significantly (p=0.001) (300 and 600 mg/kgBW), but statistically insignificant (p=0.121) in reducing the percentage of CD8+CD28- (but has positive trend). Although MM/Dp was insignificant in increasing the IL-2 level (p=0.124), there was an increase in trend at a dose of 600 mg/kgBW (2.53 pg/ml) compared to the control group (2.02 pg/ml). The administration of various doses had a strong correlation (r=0.496) with the decreasing CD4/CD8 ratio. MM/Dp has potentials in inhibiting immunosenescence that is signified by the decreasing percentage of CD4+CD28− and CD8+CD28-, as well as increasing the IL-2 level.

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POS0332 CD71 RECEPTOR APICAL EXPRESSION IN ILEUM IS RELATED WITH HIGH LEVELS OF SERUM SIgA AND ACTIVITY DISEASE IN SpA PATIENTS

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Annals of the Rheumatic Diseases 2022年 81卷 418-419页

作者： J. De Avila A. Ramos-Casallas D. Acero-M C. Florez V. Parra-Izquierdo L. Chila W. Bautista-Molano A. Beltrán D. Jaimes J.M. Bello-Gualtero C.F. Pacheco Tena P. Chalem C. Romero-Sánchez Universidad El Bosque Cellular and Molecular Immunology Group - INMUBO Bogotá D.C. Colombia Universidad El Bosque School of Science Biomedical Master Program Bogotá D.C. Colombia Grastroadvanced SAS Endoscopy Department Bogotá D.C. Colombia Universidad Militar Nueva Granada School of Medicine Clinical Immunology Group Bogotá D.C. Colombia Clínicos IPS Rheumatology Department Bogotá D.C. Colombia Hospital Militar Central Rheumatology and Immunology Department Bogotá D.C. Colombia Biomedicina de Chihuahua Rheumatology Department Chihuahua Mexico Fundacion Instituto de Reumatología Fernando Chalem Rheumatology Department Bogotá D.C. Colombia

Background Currently, mucosal immunity research has been investigated whether the serum levels of SIgA reflects the over-activation immune system in gut associated lymphoid tissues (GALT) and if the antigenic stimuli in the mucosa are responsible for inducing and maintaining the inflammatory response in Spondyloartrhitis (SpA). Based on our previous results, variances on levels of SIgA might influence in disease activity. SIgA Reverse transcytosis (retrotranscytosis) has been demonstrated as a GALT mechanism which enhance systemic inflammation in some autoimmune pathologies such as celiac disease. Objectives This study proposes the evaluation of receptors associated with retrotranscytosis CD71 and Dectin-1 (Dec-1) in gut tissues from SpA without IBD patients to explore a possible mechanism responsible of gastrointestinal inflammatory imbalance. Methods In total, 180 patients with SpA (ASAS/criteria) were assessed by rheumatologists, of which (n=65, 36.1%) met the selection criteria and from them (n=41, 63.1%) by a gastroenterologist to perform digital chromoendoscopy with magnification for colon e ileum and histological analysis. Pregnant and lactating women, and cancer patients, patients with other autoinflammatory diseases, autoimmune diseases, immunodeficiency, chronic pancreatitis, or chronic liver disease, and those who had received antibiotic treatment in the last 3 months were excluded from the study. Furthermore, those patients with SpA and concomitant IBD were excluded. All included patients were between 18 and 65 years old. CD71 and Dec-1 apical expression were identified by indirect immunofluorescence. Fecal Calprotectin (FC), Serum SIgA in house and clinical indices BASDAI, BASFI, ASDAS-CRP, ASDAS-ESR were measured. The association were evaluated using the Chi-square or Fisher's exact test and a multiple correspondence discriminant analysis (MCDA) was performed including those variables with significant associations from bivariate analysis and some that

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Remodeling of the H3 nucleosomal landscape during mouse aging

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Translational Medicine of Aging 2020年 4卷 22-31页

作者： Chen, Yilin Bravo, Juan I. Son, Jyung Mean Lee, Changhan Benayoun, Bérénice A. Leonard Davis School of Gerontology University of Southern California Los Angeles 90089 CA United States Master of Science in Nutrition Healthspan and Longevity University of Southern California Los Angeles 90089 CA United States Graduate Program in the Biology of Aging University of Southern California Los Angeles 90089 CA United States USC Norris Comprehensive Cancer Center Epigenetics and Gene Regulation Los Angeles 90089 CA United States Biomedical Sciences Graduate School Ajou University Suwon 16499 South Korea USC Stem Cell Initiative Los Angeles 90089 CA United States

In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and deregulation of gene expression correlates with aging. A key layer in the study of gene regulation mechanisms lies at the level of chromatin: cellular chromatin states (i.e. the ‘epigenome’) can tune transcriptional profiles, and, in line with the prevalence of transcriptional alterations with aging, accumulating evidence suggests that the chromatin landscape is altered with aging across cell types and species. However, although alterations in the chromatin make-up of cells are considered to be a hallmark of aging, little is known of the genomic loci that are specifically affected by age-related chromatin state remodeling and of their biological significance. Here, we report the analysis of genome-wide profiles of core histone H3 occupancy in aging male mouse tissues (i.e. heart, liver, cerebellum and olfactory bulb) and primary cultures of neural stem cells. We find that, although no drastic changes in H3 levels are observed, local changes in H3 occupancy occur with aging across tissues and cells with both regions of increased or decreased occupancy. These changes are compatible with a general increase in chromatin accessibility at pro-inflammatory genes and may thus mechanistically underlie known shift in gene expression programs during aging. © 2020 The Authors

关键词： Aging Epigenome H3 Nucleosome

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#2685 SLC34A2 EXACERBATES TUBULAR INTERSTITIAL FIBROSIS VIA INDUCTION OF APOPTOSIS AND CELL CYCLE ARREST IN S PHASE

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Nephrology Dialysis Transplantation 2023年第SUPPLEMENT_1期38卷

作者： Hu, Liang-Shuan Chang, Sheng-Cheng Tsai, Chia-Hui Wu, Chun-Ching Nguyen, Phuong Thao Hoang Chang, Wei-Che Chang, Wei-Ya Yang, Ya-Chien Jao, Tzu-Ming National Taiwan University College of Medicine International Joint Degree Master's Program in Agro-Biomedical Science in Food and Health Taipei Taiwan Rep. of China Kaohsiung Veterans General Hospital Department of Medical Education and Research Kaohsiung Taiwan Rep. of China National Taiwan University College of Medicine Department of Clinical Laboratory Sciences and Medical Biotechnology Taipei Taiwan Rep. of China

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Personal health records - Potential one-stop approach in polypharmacy

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Computer Methods and programs in Biomedicine Update 2022年 2卷

作者： Chen, Ya-Lin Satria, Fauzi Budi Jamshed, Shazia Babar, Zaheer-Ud-Din Mukherjee, Nilesh Yang, Hsuan-Chia Li, Yu-Chuan Iqbal, Usman Graduate Institute of Biomedical Informatics College of Medical Science and Technology Taipei Medical University Taipei Taiwan PhD Program in Global Health & Health Security College of Public Health Taipei Medical University Taipei Taiwan Department of Pharmacy Practice Faculty of Pharmacy UniSZA Kuala Terengganu Malaysia Qualitative Research-Methodological Application in Health Sciences Research Group Kulliyyah of Pharmacy International Islamic University Malaysia Kuantan Malaysia Centre for Pharmaceutical Policy and Practice Research Department of Pharmacy University of Huddersfield Huddersfield United Kingdom Master of Science in Systems Biology Manipal School of Life Sciences Manipal Academy of Higher Education Manipal India International Center for Health Information Technology (ICHIT) Taipei Medical University Taipei Taiwan

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Improvement of extracellular polysaccharides production from Cordyceps militaris immobilized alginate beads in repeated-batch fermentation

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LWT 2024年 193卷

作者： Hou, Shi-Jing Cheng, Kuan-Chen Lin, Shyh-Hsiang Hsiao, I-Lun Santoso, Shella Permatasari Singajaya, Stephanie Chou, Yu-Chieh Lin, Shin-Ping Master Program in Food Safety Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Institute of Biotechnology National Taiwan University 1 Roosevelt Rd. Sec. 4 Taipei10617 Taiwan Graduate Institute of Food Science and Technology National Taiwan University 1 Roosevelt Rd. Sec. 4 Taipei10617 Taiwan Department of Medical Research China Medical University Hospital China Medical University 91 Hsueh-Shih Rd. Taichung40402 Taiwan Department of Optometry Asia University 500 Lioufeng Rd. Wufeng Taichung41354 Taiwan School of Nutrition and Health Sciences Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan School of Food Safety Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Department of Chemical Engineering Widya Mandala Surabaya Catholic University Kalijudan 37 East Java Surabaya60114 Indonesia Collaborative Research Center for Sustainable and Zero Waste Industries Kalijudan 37 East Java Surabaya60114 Indonesia Ph.D. Program in Drug Discovery and Development Industry Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Research Center of Biomedical Device Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan TMU Research Center for Digestive Medicine Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan

Cordyceps militaris (C. militaris) is a unique medicinal fungus of the genus Cordyceps. It has high economic value due to various biological functions from the extracellular polysaccharides (EPSs) it produces. The aim of this study was to establish a mycelium-immobilization system for EPS production in a bubble column system. First, EPS production was optimized by 90.2% (from 0.72 to 1.37 g/L) using response surface methodology under an alginate-immobilized mycelium system with 6 days of cultivation. The highest EPS production was obtained (5.3 g/L) in a flask system through elongation to 15 days of cultivation. EPS production subsequently further increased to 10.42 g/L utilizing a bubble column reactor. Furthermore, the system can be reused for at least three rounds. In the EPS characteristics analysis, the produced EPSs were mainly composed of glucose and galactose. They presented strong antibacterial activity against Staphylococcus aureus. In terms of antioxidant activity, respective the EPS concentration that caused 50% scavenging of DPPH and ABTS free radicals values (IC50) were 4.65 and 7.92 mg/mL. In summary, these findings should be helpful for establishing a suitable industrial fermentation system for C. militaris and can be studied in the food and medical industries in future work. © 2024 The Authors

关键词： Mycelium

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