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Reproducible brain-wide association studies require thousands of individuals (Mar, 10.1038/s41586-022-04492-9, 2022)

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NATURE 2022年第7911期605卷 E11-E11页

作者： Marek, Scott Tervo-Clemmens, Brenden Calabro, Finnegan J. Montez, David F. Kay, Benjamin P. Hatoum, Alexander S. Donohue, Meghan Rose Foran, William Miller, Ryland L. Hendrickson, Timothy J. Malone, Stephen M. Kandala, Sridhar Feczko, Eric Miranda-Dominguez, Oscar Graham, Alice M. Earl, Eric A. Perrone, Anders J. Cordova, Michaela Doyle, Olivia Moore, Lucille A. Conan, Gregory M. Uriarte, Johnny Snider, Kathy Lynch, Benjamin J. Wilgenbusch, James C. Pengo, Thomas Tam, Angela Chen, Jianzhong Newbold, Dillan J. Zheng, Annie Seider, Nicole A. Van, Andrew N. Metoki, Athanasia Chauvin, Roselyne J. Laumann, Timothy O. Greene, Deanna J. Petersen, Steven E. Garavan, Hugh Thompson, Wesley K. Nichols, Thomas E. Yeo, B. T. Thomas Barch, Deanna M. Luna, Beatriz Fair, Damien A. Dosenbach, Nico U. F. Department of Psychiatry Washington University School of Medicine St Louis MO USA Department of Neurology Washington University School of Medicine St Louis MO USA Department of Psychological and Brain Sciences Washington University in St Louis St Louis MO USA Department of Psychiatry Massachusetts General Hospital Harvard Medical School Boston MA USA Department of Psychology University of Pittsburgh Pittsburgh PA USA Department of Psychiatry University of Pittsburgh Pittsburgh PA USA Department of Bioengineering University of Pittsburgh Pittsburgh PA USA Department of Biomedical Engineering Washington University in St Louis St Louis MO USA Department of Radiology Washington University School of Medicine St Louis MO USA Department of Neurological Surgery Washington University School of Medicine St Louis MO USA Program in Occupational Therapy Washington University School of Medicine St Louis MO USA Department of Pediatrics Washington University School of Medicine St Louis MO USA University of Minnesota Informatics Institute University of Minnesota Minneapolis MN USA Department of Psychology University of Minnesota Minneapolis MN USA Masonic Institute for the Developing Brain University of Minnesota Medical School Minneapolis MN USA Department of Pediatrics University of Minnesota Medical School Minneapolis MN USA Department of Psychiatry Oregon Health and Science University Portland OR USA Minnesota Supercomputing Institute University of Minnesota Minneapolis MN USA Institute of Child Development University of Minnesota Medical School Minneapolis MN USA Department of Electrical and Computer Engineering National University of Singapore Singapore Singapore Centre for Sleep and Cognition National University of Singapore Singapore Singapore Centre for Translational MR Research National University of Singapore Singapore Singapore N.1 Institute for Health Institute for Digital Medicine National University of Singapore Singapore Sing

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Front Cover: Mechanism toward Turn-on of Polysaccharide-Porphyrin Complexes for Fluorescence Probes and Photosensitizers in Photodynamic Therapy in Living Cells (5/2021)

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ChemMedChem 2021年第5期16卷

作者： Shodai Hino Rikushi Funada Dr. Kouta Sugikawa Dr. Riku Kawasaki Prof. Kazuya Koumoto Dr. Toshio Suzuki Prof. Takeshi Nagasaki Prof. Atsushi Ikeda Applied Chemistry Program Graduate School of Advanced Science and Engineering Hiroshima University 1-4-1 Kagamiyama Higashi Hiroshima 739-8527 Japan Department of Nanobiochemistry Frontiers of Innovative Research in Science and Technology (FIRST) Konan University 7-1-20 Minatojima-Minamimachi Kobe Hyogo 650-0047 Japan Department of Applied Chemistry and Bioengineering Graduate School of Engineering Osaka City University 3-3-138 Sugimoto Sumiyoshi-ku Osaka 558-8585 Japan

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Peptide Amphiphile Mediated Co-assembly for Nanoplasmonic Sensing

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Angewandte Chemie 2022年第4期135卷

作者： Dr. Zhicheng Jin Yi Li Dr. Ke Li Dr. Jiajing Zhou Justin Yeung Chuxuan Ling Wonjun Yim Tengyu He Dr. Yong Cheng Dr. Ming Xu Matthew N. Creyer Yu-Ci Chang Dr. Pavla Fajtová Dr. Maurice Retout Baiyan Qi Prof. Shuzhou Li Prof. Anthony J. O'Donoghue Prof. Jesse V. Jokerst Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA Institute of Materials Research and Engineering A*STAR (Agency for Science Technology and Research) Singapore 138634 Singapore School of Materials Science and Engineering Nanyang Technological University Singapore 639798 Singapore Department of Bioengineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA Materials Science and Engineering Program University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA Department of Radiology University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA

Aromatic interactions are commonly involved in the assembly of naturally occurring building blocks, and these interactions can be replicated in an artificial setting to produce functional materials. Here we describe a colorimetric biosensor using co-assembly experiments with plasmonic gold and surfactant-like peptides (SLPs) spanning a wide range of aromatic residues, polar stretches, and interfacial affinities. The SLPs programmed in DDD−(ZZ) x −FFPC self-assemble into higher-order structures in response to a protease and subsequently modulate the colloidal dispersity of gold leading to a colorimetric readout. Results show the strong aggregation propensity of the FFPC tail without polar DDD head. The SLPs were specific to the target protease, i.e., M pro , a biomarker for SARS-CoV-2. This system is a simple and visual tool that senses M pro in phosphate buffer, exhaled breath condensate, and saliva with detection limits of 15.7, 20.8, and 26.1 nM, respectively. These results may have value in designing other protease testing methods.

关键词： Aromatic Interactions Colorimetric Test Main Protease Peptide Amphiphile Saliva

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Determining sex differences in aortic valve myofibroblast responses to drug combinations identified using a digital medicine platform

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science advances 2025年第23期11卷 eadu2695页

作者： Brandon J Vogt Peter Wang Megan Chavez Peng Guo Edward Kai-Hua Chow Dean Ho Brian A Aguado Shu Chien-Gene Lay Department of Bioengineering University of California San Diego La Jolla CA 92093 USA. Sanford Consortium for Regenerative Medicine La Jolla CA 92037 USA. Department of Biomedical Engineering College of Design and Engineering National University of Singapore Singapore 117583 Singapore. Institute for Digital Medicine (WisDM) Yong Loo Lin School of Medicine National University of Singapore Singapore 117456 Singapore. The N.1 Institute for Health (N.1) National University of Singapore Singapore 117456 Singapore. Nikon Imaging Center Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA 92093 USA. Cancer Science Institute of Singapore National University of Singapore Singapore 117599 Singapore. Department of Pharmacology Yong Loo Lin School of Medicine National University of Singapore Singapore 117600 Singapore. The Bia-Echo Asia Centre for Reproductive Longevity and Equality (ACRLE) National University of Singapore Singapore 117456 Singapore. Program in Materials Science and Engineering University of California San Diego La Jolla CA 92093 USA.

Aortic valve stenosis (AVS) is a sexually dimorphic disease where aortic valve leaflets develop fibrosis and calcification, leading to heart failure if untreated. Sex differences in AVS progression depend on valvular interstitial cells (VICs) activating to myofibroblasts that drive aberrant extracellular matrix remodeling. To date, no treatment strategies have leveraged cellular sex differences to determine drug combinations that target VIC myofibroblast activation. Here, we harnessed ***, an artificial intelligence (AI)-derived platform, to optimize sex-biased synergistic drug combinations that may prevent and reverse VIC myofibroblast activation on hydrogel biomaterials. The results reveal that sex-specific drug response models can be used to predict sex biases in drug efficacy and combinatorial interactions. This study provides a framework for developing AVS treatments through the integration of high-throughput hydrogel cell culture platforms and AI-driven drug optimization. Designing targeted AVS drug combinations may help accelerate AVS drug development and address health disparities in AVS treatment outcomes.

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Non-isothermal crystallization kinetics of Nylon 10T and Nylon 10T/1010 copolymers:Effect of sebacic acid as a third comonomer

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Chinese Journal of Chemical engineering 2017年第7期25卷 963-970页

作者： Zhongqiang Wang Guosheng Hu Jingting Zhang Jiusheng Xu Wenbo Shi Institute of Macromolecules and Bioengineering School of Materials Science and EngineeringNorth University of ChinaTaiyuan 030051China Guongdong SinoplastAdvanced Material Co.Ltd. Dongguon 523860China

Nylon 10 T and Nylon 10T/1010 samples were synthesized by direct melt polymerization. The non-isothermal crystallization kinetics of Nylon 10 T and Nylon 10T/1010 was investigated by means of differential scanning calorimetry(DSC). Jeziorny equation and Mo equation were applied to describe the non-isothermal crystallization kinetics of the Nylon 10 T and the Nylon 10T/1010. The activation energies for non-isothermal crystallization were obtained by Vyazovkin's method and Friedman's method, respectively. These results showed that Jeziorny equation and Mo equation well described the non-isothermal crystallization kinetics of the Nylon 10 T and the Nylon 10T/1010. It was found that the values of the activation energy for non-isothermal crystallization of the Nylon 10T/1010 were lower than those of the Nylon 10 T at a given temperature or relative crystallinity degree,which revealed that crystallization ability of the Nylon 10T/1010 was higher. The crystal morphology was observed by means of a polarized optical microscope(POM) and X-ray diffraction(XRD). It was found that the addition of sebacic acid comonomer not only did not change the crystal form of the Nylon 10 T, but also significantly increased the number and decreased the size of spherulites. Comparing with the Nylon 10 T, the crystallization rate was increased with the addition of the sebacic acid comonomer.

关键词： Melt polymerization Nylon 10TNylon 10T/1010 Semiaromatic polyamides Crystallization kinetics Non-isothermal crystallization

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A mountable toilet system for personalized health monitoring via the analysis of excreta (vol 15, pg 561, 2020)

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NATURE BIOMEDICAL engineering 2020年第6期4卷 662-662页

作者： Park, Seung-min Won, Daeyoun D. Lee, Brian J. Escobedo, Diego Esteva, Andre Aalipour, Amin Ge, T. Jessie Kim, Jung Ha Suh, Susie Choi, Elliot H. Lozano, Alexander X. Yao, Chengyang Bodapati, Sunil Achterberg, Friso B. Kim, Jeesu Park, Hwan Choi, Youngjae Kim, Woo Jin Yu, Jung Ho Bhatt, Alexander M. Lee, Jong Kyun Spitler, Ryan Wang, Shan X. Gambhir, Sanjiv S. Department of Radiology Stanford University School of Medicine Stanford CA USA Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA USA Department of Surgery Seoul Song Do Hospital Seoul Republic of Korea Cancer Immunology Laboratory Seoul Song Do Hospital Seoul Republic of Korea Department of Surgery Leiden University Medical Center Leiden the Netherlands Department of Creative IT Engineering Pohang University of Science and Technology (POSTECH) Pohang Republic of Korea Precision Health and Integrated Diagnostic Center (PHIND) Stanford University School of Medicine Palo Alto CA USA Department of Materials Science and Engineering Stanford University Stanford CA USA Department of Bioengineering Stanford University Stanford CA USA Canary Center at Stanford for Cancer Early Detection Stanford University School of Medicine Palo Alto CA USA Salesforce Research Palo Alto CA USA Department of Urology Stanford University School of Medicine Stanford CA USA Department of Pharmacology Case Western Reserve University School of Medicine Cleveland OH USA Faculty of Medicine University of Toronto Toronto Ontario Canada Department of Electrical Engineering Stanford University Stanford CA USA College of Medicine The Catholic University of Korea Seoul Republic of Korea

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

关键词： Diagnosis

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Integrating Genomic & Transcriptomic Features for Noninvasive Detection, Characterization, and Monitoring of T-Cell Lymphomas

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Blood 2024年 144卷 454-454页

作者： Takeshi Sugio Monica Nesselbush Navika Shukla Andrea Garofalo Jurik A. Mutter Mohammad Shahrokh Esfahani Stefan K. Alig Shuyu Shi Troy Noordenbos Mark P. Hamilton Cedric Rossi Feng Tian Chih Long Liu Mari Olsen Xiaoman Kang David A Russler-Germain Steven Horwitz Koji Kato Ayumu Ito Makoto Yamagishi Ash A. Alizadeh Department of Medicine Divisions of Oncology and Hematology Stanford University Stanford CA Program in Cancer Biology Stanford School of Medicine Stanford CA Divisions of Oncology and Hematology Stanford University Stanford CA Department of Radiation Oncology Stanford University Stanford CA Dept. of Bioengineering Schools of Engineering and Medicine Stanford CA Division of Blood and Marrow Transplantation and Cellular Therapy Stanford University School of Medicine Palo Alto CA CHU Dijon DIJON France Department of Medicine Division of Oncology Stanford University Stanford CA Siteman Cancer Center Division of Oncology Washington University School of Medicine Saint Louis MO Lymphoma Service Department of Medicine Memorial Sloan Kettering Cancer Center New York NY Department of Medicine and Biosystemic Science Kyushu University Graduate School of Medicine Fukuoka Japan Department of Hematopoietic Stem Cell Transplantation National Cancer Center Hospital Tokyo Japan Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Tokyo JPN

Background : Mature T-cell lymphoma (TCL) outcomes remain inferior to aggressive B-cell counterparts, and thus represent unmet need. Given high relapse rates after remissions induced by current regimens, more sensitive MRD methods are needed to personalize treatment. We tackled these questions by integrating distinct host and viral molecular features for noninvasive detection, risk profiling, and monitoring of diverse mature TCLs. Methods : We studied 132 patients diagnosed with diverse TCLs (PTCL-NOS n=21, ALCL n=13, TFH lymphoma n=21, ATLL n=54, ENKTL n=6, CTCL n=15, others n=2). 37% of pts had newly diagnosed TCL primarily treated with CHOP-based regimens, while 62% had relapsed/refractory disease treated with salvage chemotherapies (26%), nivolumab (5%), and/or allogeneic HSCT (31%). We molecularly profiled 530 specimens, including serial blood plasma samples drawn before, during, and at the end-of-therapy (EOT) (n=274), baseline tumor tissues (n=128), and matched normal cells (n=128). Plasma cfDNA for all cases were profiled to detect somatic mutations in 259 recurrently mutated TCL genes by CAPP-Seq, genome-wide CNVs by CANARy (Chabon 2020 Nature), clonotypic VDJ at all TCR/BCR loci by SABER, T/B-cell abundance by QUARTZ (Sugio ASH 2024 abstract #193441), and inferred expression of 381 TCL/immune-related genes by EPIC-Seq (Esfahani Nature biotechnology 2022). Viral load and genotyping for EBV and HTLV-1 were assessed by VirCAPP-Seq (Garofalo ASH2022). Plasma cfRNA expression was profiled using RARE-Seq, by targeting 6.8k coding genes (Nesselbush 2024 Cancer Research). Results : We found that mutation-based disease burden measurements in cfDNA by CAPP-Seq were significantly correlated with clonotypic cell-free TCR levels (cfTCR; R=0.95, p<0.001) across all patients and plasma HTLV-1 load in ATLL patients (R=0.84, p<0.001). When considering outcomes after CHOP-based regimens, detection of ctDNA-MRD at EOT predicted significantly higher relapse risk (p= 0.003), i

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Corrigendum to ‘Study of Carbon Supported CuPd Alloy Nanoparticles with Pd-Rich Surface for the Electrochemical Formate Oxidation and CO 2 Reduction’ [Electrochimica Acta, 387 (2021) 138531]

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Electrochimica Acta 2021年 389卷

作者： Wei Jyun Wang Sooyeon Hwang Taejin Kim Su Ha Louis Scudiero The Gene and Linda Voiland School of Chemical Engineering and Bioengineering Washington State University Wegner Hall Room 105 1505 NE Stadium Way Pullman WA 99164 Center for Functional Nanomaterial Brookhaven National Laboratory Upton NY 11973 Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook NY 11794 USA Chemistry Department and Materials Science and Engineering Program Washington State University PO Box 644630 Pullman WA 99164-4630

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Rewriting regulatory DNA to dissect and reprogram gene expression

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Cell 2025年第12期188卷 3349-3366.e23,26页

作者： Martyn, Gabriella E. Montgomery, Michael T. Jones, Hank Guo, Katherine Doughty, Benjamin R. Linder, Johannes Bisht, Deepa Xia, Fan Cai, Xiangmeng S. Chen, Ziwei Cochran, Kelly Lawrence, Kathryn A. Munson, Glen Pampari, Anusri Fulco, Charles P. Sahni, Nidhi Kelley, David R. Lander, Eric S. Kundaje, Anshul Engreitz, Jesse M. Department of Genetics Stanford University School of Medicine Stanford 94305 CA United States Basic Science and Engineering Initiative Stanford Children's Health Betty Irene Moore Children's Heart Center Stanford 94305 CA United States Calico Life Sciences LLC South San Francisco 94080 CA United States Department of Genitourinary Medical Oncology Division of Cancer Medicine The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Department of Genomic Medicine The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Houston 77230 TX United States Department of Bioengineering Stanford University Stanford 94305 CA United States Department of Computer Science Stanford University Stanford 94305 CA United States Novo Nordisk Foundation Center for Genomic Mechanisms of Disease Broad Institute of MIT and Harvard Cambridge 02142 MA United States Gene Regulation Observatory Broad Institute of MIT and Harvard Cambridge 02142 MA United States Broad Institute of MIT and Harvard Cambridge 02142 MA United States Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston 77230 TX United States Quantitative and Computational Biosciences Program Baylor College of Medicine Houston 77030 TX United States Department of Biology MIT Cambridge 02139 MA United States Department of Systems Biology Harvard Medical School Boston 02115 MA United States Stanford Cardiovascular Institute Stanford University Stanford 94305 CA United States

Regulatory DNA provides a platform for transcription factor binding to encode cell-type-specific patterns of gene expression. However, the effects and programmability of regulatory DNA sequences remain difficult to map or predict. Here, we develop variant effects from flow-sorting experiments with CRISPR targeting screens (Variant-EFFECTS) to introduce hundreds of designed edits to endogenous regulatory DNA and quantify their effects on gene expression. We systematically dissect and reprogram 3 regulatory elements for 2 genes in 2 cell types. These data reveal endogenous binding sites with effects specific to genomic context, transcription factor motifs with cell-type-specific activities, and limitations of computational models for predicting the effect sizes of variants. We identify small edits that can tune gene expression over a large dynamic range, suggesting new possibilities for prime-editing-based therapeutics targeting regulatory DNA. Variant-EFFECTS provides a generalizable tool to dissect regulatory DNA and to identify genome editing reagents that tune gene expression in an endogenous context. © 2025 Elsevier Inc.

关键词： CRISPR enhancers gene regulation high-throughput screening non-coding variants predictive models prime editing RNA FlowFISH sequence design transcription factors

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Preparation and optimization of antibacterial activity of graphene oxide silver nanocomposite

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AIP Conference Proceedings 2022年第1期2454卷

作者： An’amt Mohamed Noor Farah Amanina Mohd Zin Ahmad Muhsin Mohammad Fatin Setia Budi Muhammad Hafiz Abu Bakar Mohd Shaiful Sajab Mohamad Faiz Mohd Amin Sahid Mehmood 1Advanced Material Research Cluster Faculty of Bioengineering and Technology Universiti Malaysia Kelantan Jeli Campus Kelantan Malaysia 2Department of Chemistry Faculty of Mathematics and Natural Sciences Universitas Negeri Jakarta Indonesia 3Wireless and Photonic Network Research Centre Faculty of Engineering Universiti Putra Malaysia Serdang Selangor Malaysia 4Research Centre for Sustainable Process Technology Faculty of Engineering and Built Environment Universiti Kebangsaan Malaysia Bangi Malaysia 5Faculty of Earth Science Universiti Malaysia Kelantan Jeli Campus Kelantan Malaysia 6Center of Micro-Nano System School of Information Science and Technology Fudan University Shanghai China

Graphene oxide (GO) was prepared using simplified Hummer’s method, and GO-silver nanocomposite (GOAg) was prepared by microwave irradiation. The synthesis aims to decorate silver nanoparticles (AgNPs) on the surface of graphene oxide (GO) to enhance silver nanoparticle performances. The nanocomposite was characterized by using ultraviolet-visible spectrophotometry (UV-Vis) and fourier transform infrared (FTIR). Antibacterial activity of the nanocomposite was investigated using the disk diffusion method where several parameters such as GOAg loading (10%, 20%, and 30%), bacterial suspension concentration (1.5 and 3.0 × 108 CFU/ml ), and incubation temperature (30 and 35 °C) were varied. The antibacterial study was tested against one gram-negative bacteria, which is Escherichia coli ATCC 8739 (E. coli) and Gram-positive bacteria were Staphylococcus aureus (S. aureus) Lactobacillus Plantarum BD 8913C (L. Plantarum), and Bacillus subtilis (B. Subtilis). The results reveal that *** were more susceptible against GOAg nanocomposite at 30°C; meanwhile, ***, *** were more susceptible to incubation temperature at 35°C. The results also indicate that the GOAg nanocomposite also shows a promising inhibition zone with increasing bacterial suspension and disclosing its potential to be used in many other applications.

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