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Translational Bioinformatics to Enable Precision Medicine for All: Elevating Equity across Molecular, Clinical, and Digital Realms

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Yearbook of Medical Informatics 2022年第1期31卷 106-115页

作者： Tang, Alice Woldemariam, Sarah Roger, Jacquelyn Sirota, Marina Bakar Computational Health Sciences Institute UCSF San Francisco CA United States Graduate Program in Bioengineering UCSF San Francisco CA United States School of Medicine UCSF San Francisco CA United States Graduate Program in Biological and Medical Informatics UCSF San Francisco CA United States Department of Pediatrics UCSF San Francisco CA United States

Objectives: Over the past few years, challenges from the pandemic have led to an explosion of data sharing and algorithmic development efforts in the areas of molecular measurements, clinical data, and digital health. We aim to characterize and describe recent advanced computational approaches in translational bioinformatics across these domains in the context of issues or progress related to equity and inclusion. Methods: We conducted a literature assessment of the trends and approaches in translational bioinformatics in the past few years. Results: We present a review of recent computational approaches across molecular, clinical, and digital realms. We discuss applications of phenotyping, disease subtype characterization, predictive modeling, biomarker discovery, and treatment selection. We consider these methods and applications through the lens of equity and inclusion in biomedicine. Conclusion: Equity and inclusion should be incorporated at every step of translational bioinformatics projects, including project design, data collection, model creation, and clinical implementation. These considerations, coupled with the exciting breakthroughs in big data and machine learning, are pivotal to reach the goals of precision medicine for all. © 2022 IMIA and Georg Thieme Verlag KG.

关键词： Bioinformatics genomics health equity precision medicine

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Cartilage targeting cationic peptide carriers display deep cartilage penetration and retention in a rabbit model of post-traumatic osteoarthritis

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Osteoarthritis and Cartilage 2025年第6期33卷 721-734页

作者： Boyer, Timothy L. Chao, Olivia Hakim, Bill Childress, Luke Meslier, Quentin A. Iyengar, Suhasini M. Ondrechen, Mary Jo Porter, Ryan M. Bajpayee, Ambika G. Department of Bioengineering Northeastern University Boston MA United States Department of Biochemistry Northeastern University Boston MA United States Graduate Program for Interdisciplinary Biomedical Sciences UAMS Little Rock AR United States Department of Chemistry and Chemical Biology Northeastern University Boston MA United States Department of Internal Medicine UAMS Little Rock AR United States Department of Orthopaedic Surgery UAMS Little Rock AR United States

Objective: Drug delivery to cartilage is limited by its complex architecture and avascularity. Cationic peptide carriers (CPCs) have previously been optimized for improved cartilage transport and retention of drugs in vitro. In this study, we evaluated the kinetics, stability, and immunogenicity of CPCs after a single intra-articular injection using a rabbit knee injury model. Design: New Zealand White rabbits were administered a single dose of Cy5-labeled CPCs in knees receiving anterior cruciate ligament transection (ACLT) or Sham surgery. CPC biodistribution and retention within joint tissues and synovial fluid were evaluated 1 and 7 days after administration, and extra-articular kinetics were assessed in serum. Histology, immunohistochemistry, and reverse transcription quantitative polymerase chain reaction were performed to assess synovitis and protease activity. Proteolytic analysis of CPCs in the presence of arthritic enzymes was evaluated using synovial fluid size-exclusion filtration, Fluorescence Resonance Energy Transfer analysis, and computational molecular docking. Results: CPCs penetrated the full depth of sulfated glycosaminoglycan (sGAG)-rich tissues, notably cartilage, and were retained through the latest timepoint measured (one week) in both Sham and ACLT knees. Compared to ACLT, Sham knees had greater joint retention at Day 1 (1.6-fold) and Day 7 (1.8-fold). CPC intra-tissue concentration strongly correlated with tissue sGAG density, which did not considerably differ between surgical conditions at these timepoints. However, CPCs exhibited elevated vascular clearance and proteolytic fragmentation in inflammatory conditions. CPCs did not increase macrophage abundance, cytokine expression, or alter tissue morphology. Conclusion: CPCs target the deep layers of cartilage, even in inflamed joints, and can be utilized to substantially improve intra-joint bioavailability of therapeutics. © 2025 Osteoarthritis Research Society International

关键词： Cartilage penetration Cationic carriers Charge-based drug delivery Post-traumatic osteoarthritis Rabbit

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Treatment with metal–organic frameworks (MOFs) elicits secondary metabolite accumulation in Aquilaria crassna (agarwood) callus culture

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Discover Plants 2025年第1期2卷 1-9页

作者： Overmans, Sebastian Alflayyeh, Yazan Gutiérrez, Sergio Aldlaigan, Yousef Lauersen, Kyle J. Bioengineering Program Biological and Environmental Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Jeddah Kingdom of Saudi Arabia Plant Tissue Culture & Biotechnology Center Ministry of Environment Water and Agriculture of Saudi Arabia (MEWA) Riyadh Kingdom of Saudi Arabia

Thymelaceaous trees are prized for accumulating fragrant resins composed of hundreds of secondary metabolites in their woody tissues. Slow growth and increasing consumer demand have stretched natural sources of agarwood trees to being endangered and alternative production modes, including silviculture and tissue culture, are currently being investigated. Dedifferentiated tissue culture of agarwood trees provides a means of cell propagation independent of environmental context. However, secondary metabolite accumulation, as found in fragrant resins, occurs largely in response to wounding. Here, we investigated the application of metal-organic frameworks (MOFs) as potential elicitors of secondary metabolite formation in Aquilaria crassna tissue culture. Callus cultures were exposed to five commercially available MOFs (UiO-67, MOF-808, HKUST-1, ZIF-67, and MOF-74) and ethanol extracts were analysed using GC-MS to quantify secondary metabolite accumulation in MOF-exposed cultures compared to untreated cultures. Samples that were exposed to either of the two Zr-based MOFs exhibited metabolite production profiles that were similar to each other, (trans-2-Carboxy-cyclo-hexyl)-acetic acid was reduced in the presence of all MOFs, the Cu-containing HKUST-1 MOF increased palmitic acid levels, and ZIF-67 (at 20 mg/L) was found to elicit the highest accumulation of secondary metabolites with potential fragrance applications. These results demonstrate the possibility of eliciting secondary metabolites from dedifferentiated agarwood tree cell culture and may provide an alternative means of sourcing fragrant specialty chemicals from these plants.

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SAME-CELL, SINGLE-CELL DETECTION OF PROTEIN ISOFORMS AND NUCLEIC ACIDS 25

SAME-CELL, SINGLE-CELL DETECTION OF PROTEIN ISOFORMS AND NUC...

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25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021

作者： Gomez Martinez, Ana E. Rosas-Canyelles, Elisabet Modzelewski, Andrew J. Geldert, Alisha Gopal, Anjali He, Lin Herr, Amy E. Department of Bioengineering University of California Berkeley BerkeleyCA United States UC Berkeley-UCSF Graduate Program in Bioengineering United States Division of Cellular and Developmental Biology Department of Molecular & Cell Biology University of California BerkeleyCA United States

ISBN: (纸本)9781733419031

Single-cell 'omics is advancing rapidly, but there are gaps in linking nucleic acids to proteins in their myriad forms. To surmount this gap, we describe a microfluidic device that reports information on nucleic acids and proteoforms, or proteins that arise from a variety of modifications to nucleic acids or proteins, which are detected by immunoblotting (triBlot). The triBlot fractionates nuclei from the cytoplasm, allowing analysis of cytoplasmic proteoforms. Then, nuclei-laden regions are laser excised to perform PCR/RT-qPCR. We correlate DNA, mRNA, and protein expression from the same few cells, a step forward in 'omics that measure diverse protein forms. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： Proteins

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Sweet–Bitter Taste Interactions in Binary Mixtures of Sweeteners: Relationship of Taste Receptor Activities with Sensory Perception

SSRN

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SSRN 2024年

作者： Choi, Yoonha Wong, RunRou Cha, Yeon Kyung Park, Tai Hyun Kim, Yuri Chung, Seo-Jin Department of Nutritional Science and Food Management Ewha Womans University Seoul03760 Korea Republic of Interdisciplinary Program in Bioengineering Seoul National University Seoul08826 Korea Republic of Graduate Program in System Health Science and Engineering Ewha Womans University Seoul03760 Korea Republic of

Combining several low-calorie sweeteners in a food is a common strategy for reducing caloric sweeteners. The effects of binary sweetener mixtures on sweetness enhancement and sweet–bitter taste receptor interactions, specifically sensory perception and receptor activity, were investigated. Acesulfame K or saccharin was mixed with allulose, aspartame, erythritol, fructose, glucose, or sucrose to match a target sucrose sweetness. The effects of the mixtures on sweet and bitter taste receptors (expressed in HEK-293 cells) and sensory taste intensities were evaluated. Sweetness was enhanced in limited cases at the taste receptor level. Several monosaccharides reduced the bitter taste receptor activity triggered by acesulfame K or saccharin. The sweetness of acesulfame K and saccharin combined with any of the six sweeteners was perceptually enhanced, correlating with a reduction in their inherent bitterness. This finding suggested that sweetness perception likely increased because of the ability of monosaccharides to diminish bitter receptor activation by high-potency sweeteners. © 2024, The Authors. All rights reserved.

关键词： Binary mixtures

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Knowledge-Guided Multi-Task Learning for Breast Cancer Diagnosis Using Longitudinal Mammogram Images

Knowledge-Guided Multi-Task Learning for Breast Cancer Diagn...

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IEEE International Symposium on Biomedical Imaging

作者： Zhengbo Zhou Dooman Arefan Margarita Zuley Degan Hao Jules Sumkin Shandong Wu Intelligent Systems Program University of Pittsburgh Pittsburgh PA USA Department of Radiology University of Pittsburgh Pittsburgh PA USA Department of Biomedical Informatics and Department of Bioengineering University of Pittsburgh Pittsburgh PA USA

ISBN: (数字)9798350313338

ISBN: (纸本)9798350313345

In clinical detection and diagnosis of breast cancer, temporal analysis of mammogram images plays a crucial role. This study introduces a knowledge-guided multi-task learning approach that aims to elevate the accuracy of breast cancer diagnosis by incorporating the analysis of breast density changes over time. While breast cancer diagnosis is our main task, we construct the classification of breast density evolution over time as an auxiliary task that leverages crucial longitudinal tissue changes to enhance breast cancer diagnosis. Specifically, we propose a novel architecture that employs cross-view mechanisms and context-guided triplet loss to capture temporal changes and facilitate more effective learning. Our contributions include a customized multi-task model that integrates breast density categorization to capture temporal feature changes, and the application of context-guided triplet loss for faster convergence. We performed experiments on a cohort of 580 breast cancer patients (each has two sequential mammogram exams) in a case-control setting, and the proposed method achieved an AUC of 0.745, outperforming the several compared methods.

关键词： Accuracy Biological system modeling Multitasking Breast cancer Mammography Spatiotemporal phenomena Task analysis

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Tactile Displays Driven by Projected Light

arXiv

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arXiv 2024年

作者： Linnander, Max Goetz, Dustin Reardon, Gregory Kumar, Vijay Hawkes, Elliot Visell, Yon Department of Mechanical Engineering United States Department of Bioengineering United States Media Arts & Technology Program United States Department of Electrical and Computer Engineering University of California Santa Barbara United States

Tactile displays that lend tangible form to digital content could transform computing interactions. However, achieving the resolution, speed, and dynamic range needed for perceptual fidelity remains challenging. We present a tactile display that directly converts projected light into visible tactile patterns via a photomechanical surface populated with millimeter-scale optotactile pixels. The pixels transduce incident light into mechanical displacements through photostimulated thermal gas expansion, yielding millimeter scale displacements with response times of 2 to 100 milliseconds. Employing projected light for power transmission and addressing renders these displays highly scalable. We demonstrate optically driven displays with up to 1,511 addressable pixels – several times more pixels than any prior tactile display attaining comparable performance. Perceptual studies confirm that these displays can reproduce diverse spatiotemporal tactile patterns with high fidelity. This research establishes a foundation for practical, versatile high-resolution tactile displays driven by light. Copyright © 2024, The Authors. All rights reserved.

关键词： Light transmission

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Nanoconfinement effect of nanoporous carbon electrodes for ionic liquid-based aluminum metal anode

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Journal of Energy Chemistry 2022年第11期31卷 121-127,I0005页

作者： Juhee Yoon Seongbak Moon Son Ha Hyung-Kyu Lim Hyoung-Joon Jin Young Soo Yun Program in Environmental and Polymer Engineering Inha UniversityIncheon 22212South Korea Department of Polymer Science and Engineering Inha UniversityIncheon 22212South Korea KU-KIST Graduate School of Converging Science and Technology Korea UniversitySeoul 02841South Korea Division of Chemical Engineering and Bioengineering Kangwon National UniversityGangwon-do 24341South Korea Department of Integrative Energy Engineering Korea UniversitySeoul 02841South Korea

Rechargeable aluminum batteries(RABs),which use earth-abundant and high-volumetric-capacity metal anodes(8040 m Ah cm-3),have great potential as next-generation power sources because they use cheaper resources to deliver higher energies,compared to current lithium ion ***,the mechanism of charge delivery in the newly developed,ionic liquid-based electrolytic system for RABs differs from that in conventional organic ***,targeted research efforts are required to address the large overpotentials and cycling decay encountered in the ionic liquid-based electrolytic *** this study,a nanoporous carbon(NPC)electrode with well-developed nanopores is used to develop a high-performance aluminum *** negatively charged nanopores can provide quenched dynamics of electrolyte molecules in the aluminum deposition process,resulting in an increased collision *** fast chemical equilibrium of anionic species induced by the facilitated anionic collisions leads to more favorable reduction reactions that form aluminum *** nanoconfinement effect causes separated nucleation and growth of aluminum nanoparticles in the multiple confined nanopores,leading to higher coulombic efficiencies and more stable cycling performance compared with macroporous carbon black and 2D stainless steel electrodes.

关键词： Nanoconfinement effect Nanoporous carbon Ionic liquid electrolyte Metal anode Aluminum batteries Multivalent batteries

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Technical artifacts in droplet-microfluidics-based single-nuclei RNA-sequencing 25

Technical artifacts in droplet-microfluidics-based single-nu...

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25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021

作者： Gupta, Anushka Streets, Aaron UC Berkeley-UC San Francisco Graduate Program in Bioengineering BerkeleyCA United States Chan Zuckerberg Biohub San FranciscoCA United States

ISBN: (纸本)9781733419031

Droplet microfluidic platforms have recently become a powerful tool for sequencing the transcriptomes of single nuclei in a ultrahigh-throughput format. However, single-nuclei RNA-sequencing (snRNA-seq) introduces severe sources of technical noise and transcript detection bias which distorts true biological heterogeneity. In this work, we performed a comparative study between droplet-based single-cell RNA-sequencing (scRNA-seq) and snRNA-seq on human preadipocytes to identify and characterize primary sources of technical artifacts associated with snRNA-seq, and propose strategies to account for these artifacts. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： RNA

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Development of an Application to Assess Quality of Life 27th

Development of an Application to Assess Quality of Life

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27th Brazilian Congress on Biomedical Engineering, CBEB 2020

作者： Oliveira, D.S. Santos, W.S. Ribeiro, L.M. Oliveira, G.S. Magalhães, D.S.F. Frade-Barros, A.F. Brazil University Bioengineering Department Rua A 208 Novo Jaçanã São Paulo Itabuna-Bahia Brazil Nutrition Department UniFTC Itabuna Brazil Graduate Program in Computational Modelling in Science and Technology State University of Santa Cruz Ilhéus Brazil

ISBN: (纸本)9783030706005

Quality of life (QOL) is how the individual perceives himself as having an impact on his physical-emotional integrity, functional capacity, and self-esteem. Quality of life assessment tools can be generic or specific. Generics evaluate various aspects of quality of life and health status, and can be useful for patients, regardless of disease or condition, and can also be used for healthy individuals. The Medical questionnaire Outcomes Study 36 (SF-36) is one of the main instruments used to assess the health-related quality of life. This study aimed to develop the first application software (APP) for assessing the quality of life in Portuguese. This is an experimental study, of analytical, observational, and transversal nature that seeks associations or correlations between variables of interest. The application was developed on the Unity Engine to facilitate port for Android and its graphical interface. The Sarcvida app contemplates the SF-36 questionnaire and the SARC-F+CC. The application has undergone structural and functional tests and the next step is the evaluation of the app by health professionals. Sarcvida app is composed of SF-36 QOL questionnaire, SARC-F+CC, and D-score. The application proved to be functional, corresponding to initial research expectations for the project. The app presented usability and functionality for the evaluation of QOL in the tests to which it has been submitted so far. In Brazil there are no applications composed of SF-36 QOL questionnaire, SARC-F+CC, and the D-score, therefore, this study is innovative, presenting the first Portuguese version available in the app. Besides, mobile technology developed here is a tool to help monitor patients by contributing health professionals in possible interventions for health promotion. © 2022, Springer Nature Switzerland AG.

关键词： Application programs

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