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Probabilistic genotype-phenotype maps reveal mutational robustness of RNA folding, spin glasses, and quantum circuits

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Physical Review Research 2025年第1期7卷 013118-013118页

作者： Anna Sappington Vaibhav Mohanty Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Harvard-MIT Program in Health Sciences and Technology Harvard Medical School Boston Massachusetts 02115 USA and Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Harvard/MIT MD-PhD Program Harvard Medical School Boston Massachusetts 02115 USA and Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Department of Chemistry and Chemical Biology Harvard University Cambridge Massachusetts 02138 USA

Recent studies of genotype-phenotype maps have reported universally enhanced phenotypic robustness to genotype mutations, a feature essential to evolution. Virtually all of these studies make a simplifying assumption that each genotype—represented as a sequence—maps deterministically to a single phenotype, such as a discrete structure. Here we introduce probabilistic genotype-phenotype (PrGP) maps, where each genotype maps to a vector of phenotype probabilities, as a more realistic and universal language for investigating robustness in a variety of physical, biological, and computational systems. We study three model systems to show that PrGP maps offer a generalized framework which can handle uncertainty emerging from various physical sources: (1) thermal fluctuation in RNA folding, (2) external field disorder in the spin-glass ground state search problem, and (3) superposition and entanglement in quantum circuits, which are realized experimentally on IBM quantum computers. In all three cases, we observe a biphasic robustness scaling which is enhanced relative to random expectation for more frequent phenotypes and approaches random expectation for less frequent phenotypes. We derive an analytical theory for the behavior of PrGP robustness, and we demonstrate that the theory is highly predictive of empirical robustness.

关键词： Quantum computers

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Targeting multiple signaling pathways:the new approach to acute myeloid leukemia therapy

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Signal Transduction and Targeted Therapy 2021年第1期6卷 41-69页

作者： Jenna LCarter Katie Hege Jay Yang Hasini AKalpage Yongwei Su Holly Edwards Maik Hüttemann Jeffrey WTaub Yubin Ge Cancer Biology Graduate Program Wayne State University School of MedicineDetroitMIUSA MD/PhD Program Wayne State University School of MedicineDetroitMIUSA Department of Oncology Wayne State University School of MedicineDetroitMIUSA Molecular Therapeutics Program Barbara Ann Karmanos Cancer InstituteWayne State University School of MedicineDetroitMIUSA Center for Molecular Medicine and Genetics Wayne State University School of MedicineDetroitMIUSA National Engineering Laboratory for AIDS Vaccine Key Laboratory for Molecular Enzymology and EngineeringThe Ministry of EducationSchool of Life SciencesJilin UniversityChangchunChina Division of Pediatric Hematology/Oncology Children’s Hospital of MichiganDetroitMIUSA Department of Pediatrics Wayne State University School of MedicineDetroitMIUSA

Acute myeloid leukemia(AML)is the most common form of acute leukemia in adults and the second most common form of acute leukemia in *** this,very little improvement in survival rates has been achieved over the past few *** is partially due to the heterogeneity of AML and the need for more targeted therapeutics than the traditional cytotoxic chemotherapies that have been a mainstay in therapy for the past 50 *** the past 20 years,research has been diversifying the approach to treating AML by investigating molecular pathways uniquely relevant to AML cell proliferation and *** we review the development of novel therapeutics in targeting apoptosis,receptor tyrosine kinase(RTK)signaling,hedgehog(HH)pathway,mitochondrial function,DNA repair,and c-Myc *** has been an impressive effort into better understanding the diversity of AML cell characteristics and here we highlight important preclinical studies that have supported therapeutic development and continue to promote new ways to target AML *** addition,we describe clinical investigations that have led to FDA approval of new targeted AML therapies and ongoing clinical trials of novel therapies targeting AML survival *** also describe the complexity of targeting leukemia stem cells(LSCs)as an approach to addressing relapse and remission in AML and targetable pathways that are unique to LSC *** comprehensive review details what we currently understand about the signaling pathways that support AML cell survival and the exceptional ways in which we disrupt them.

关键词： myeloid approach approval

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Probabilistic Power Flow Analysis Based on Low Rank Approximation and Principle Component Analysis

Probabilistic Power Flow Analysis Based on Low Rank Approxim...

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2020 International Conference on Power, Energy and Innovations, ICPEI 2020

作者： Laowanitwattana, Jirasak Uatrongjit, Sermsak Chiang Mai University PhD's Degree Program in Electrical Engineering Faculty of Engineering Chiang Mai Thailand Chiang Mai University Faculty of Engineering Department of Electrical Engineering Chiang Mai Thailand

ISBN: (纸本)9781728172408

Probabilistic power flow (PPF) analysis is usually applied for evaluating the effects of uncertain parameters on power system performances. This paper presents a technique to enhance the arbitrary polynomial chaos expansion (aPCE) based PPF analysis technique when applying to system with many uncertain parameters. The proposed method represents a power system response as low rank approximation (LRA). In addition, the principle component analysis (PCA) is applied to reduce the number of uncertain parameters and also de-correlate them. This combination enables the proposed method to perform PPF of the power system having large number of uncertain parameters. Based on preliminary numerical results on the modified IEEE 57-bus system, it can be noticed that the proposed modified method is able to find accurate statistical characteristics of the responses but uses less computation time compared to the MCS based PPF analysis. © 2020 IEEE.

关键词： Uncertainty analysis

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Modifying BiVO4 as a photocatalyst for water oxidation using constant-duration alkaline-etched post treatments

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New Journal of Chemistry 2023年第2期48卷 569-577页

作者： Hsu, Chuan-Chih Chuang, Kai-Jie Huang, Hsiao-Wen Pan, Bo-Jin Chen, Hung-Ming Husain, Sadang Yougbaré, Sibidou Hsiao, Yu-Cheng Wu, Yung-Fu Lin, Lu-Yin Division of Cardiovascular Surgery Department of Surgery School of Medicine College of Medicine Taipei Medical University Taiwan Division of Cardiovascular Surgery Department of Surgery Taipei Medical University Hospital Taiwan Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei Taiwan Department of Chemical Engineering Ming Chi University of Technology New Taipei City24301 Taiwan Gingen Technology Co. Ltd. Rm. 7 10F. No. 189 Sec. 2 Keelung Rd. Xinyi Dist. Taipei11054 Taiwan Department of Physics Faculty of Mathematics and Natural Science Lambung Mangkurat University Banjarmasin70124 Indonesia /Nanoro Ouagadougou03 Burkina Faso International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Stanford Byers Center for Biodesign Stanford University CA94305-5428 United States Graduate Institute of Biomedical Optomechatronics College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Cell Physiology and Molecular Image Research Center Wan Fang Hospital Taipei Medical University Taipei11696 Taiwan

BiVO4 with suitable band edges and a small band gap is considered an efficient photocatalyst for the oxygen evolution reaction (OER), but short charge-transfer lengths limit its photocatalytic ability. Increasing active sites can essentially enhance oxidation reactions and photocatalytic ability. The alkaline etching technique can refine the surface properties of BiVO4 by introducing oxygen vacancies and possibly establishing a heterojunction, but suitable alkaline etching methods are rarely discussed. In this study, three alkaline etching methods, including hydrothermal, soaking, and electrodeposition processes, are first applied for a constant duration to tailor the surface properties of BiVO4 as a photocatalyst for the OER. Alkaline-etched BiVO4 prepared using hydrothermal and soaking processes shows better photocatalytic abilities due to the generation of additional oxygen vacancies, while poor photocatalytic ability is found for that fabricated using electrodeposition due to the formation of less photocatalytic VO2. The highest photocurrent density of 2.38 mA cm−2 is obtained at 1.23 V versus a reversible hydrogen electrode in an electrolyte without a hole scavenger for the BiVO4 etched in the hydrothermal process, while the untreated BiVO4 presents a photocurrent density of 0.58 mA cm−2. A photocurrent retention of 92.3% is achieved after 5000 seconds of continuous illumination. The study supplies blueprints for establishing effective alkaline etching methods for enhancing the photocatalytic ability of BiVO4, with the exception of time costs. © 2024 The Royal Society of Chemistry.

关键词： Charge transfer

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MIRROR: miRNA regulation-level differential network to study sex and ethnic disparities in cancer

MIRROR: miRNA regulation-level differential network to study...

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Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Caterina Alfano Marco Filetti Lorenzo Farina Manuela Petti Dept. of Experimental Medicine Sapienza University of Rome Rome Italy Phase 1 Unit Fondazione Policlinico Universitario A. Gemelli IRCCS Rome Italy Dept. of Computer Control and Management Engineering PhD Program in Network Oncology and Precision Medicine Sapienza University of Rome Rome Italy Dept. of Computer Control and Management Engineering Sapienza University of Rome Rome Italy

ISBN: (数字)9798350371499

ISBN: (纸本)9798350371505

Cancer disparities are adverse differences in cancer measures that exist among certain population groups. Given that the role they play not only in the disease prognosis but also in therapy response, there is an urgent need to understand what causes them. Most studies investigate these disparities by analyzing transcriptomic data and in particular miRNAs for their regulatory role, but only focusing on expression levels. To face this challenge we propose MIRROR, a new method which analyzes a differential co-expression network of miRNAs between patients’ cohorts, to study the role they play at the target genes’ level. Doing so, we can study the altered molecular mechanism that are linked to cancer disparities. The application of MIRROR to two different cases of cancer disparities has demonstrated its efficacy in identifying molecular players involved in the considered disparity, presenting itself as a viable option to approach this challenge.

关键词： Proteins Technological innovation Transcriptomics Medical treatment Focusing Mirrors Prostate cancer Prognostics and health management Faces Cancer

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Mississippi Burning: An Exploration of Community Noise Levels from a Rural Mississippi Community Grappling with Wood Pellet Production Manufacturing

SSRN

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SSRN 2024年

作者： Walker, Erica D. Franzen Lee, Nina Nica, C. Barnes, A. Graham, Barbara Martin, K. Community Noise Lab Department of Epidemiology Brown University School of Public Health ProvidenceRI02903 United States Environmental Science PhD Program College of Science Engineering and Technology Jackson State University JacksonMS39217 United States Greater Greener Gloster Project GlosterMS39638 United States

Wood pellets are being touted as a renewable and sustainable form of energy. As a result of this growing popularity, the global wood pellet market is expected to reach $16 billion by 2026. Currently, there are approximately 100 pellet manufacturing plants in the United States, with most of the production occurring in predominantly Black and poor communities in the rural South. At the request of residents concerned about the noise pollution emanating from wood pellet production plants in their community, we carried out a community noise exposure assessment. From August 2023 to March 2024, and working closely with a local community organization we measured a variety of noise metrics in Gloster, a wood pellet impacted city in rural Mississippi, comparing these noise pollution levels to a background community with no wood pellet industrial activity. We observed statistically significant higher levels of A-weighted, C-weighted, and Z-weighted sound in Gloster compared to Mendenhall. These differences persisted across different times of the day and days of the week. When examining the decibel levels for each of the center frequencies of the 1:3 octave band, this pattern persisted. Our preliminary findings suggest that a rural community’s soundscape can be negatively impacted by unchecked wood pellet manufacturing. We argue that the sound level differences in communities impacted by wood pellet manufacturing and those that are not, combined with the strategic placement of wood pellet plants in vulnerable communities in the rural south, may also be an environmental justice issue. © 2024, The Authors. All rights reserved.

关键词： Pelletizing

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Improving Transparency on Energy Transportation Losses through Digitalization Technologies

Improving Transparency on Energy Transportation Losses throu...

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International Scientific-Professional Conference on Information Technology (IT)

作者： Amir Farmanesh Irene Pereda Serrano Joaquín Ordieres-Meré Slobodan Bojanic Bojan Prlinčević PhD candidate from the Organizational Enginering Program at the Industrial Engineering School Universidad Politécnica de Madrid Madrid Spain Master student delivering her master thesis at the Industrial Engineering School Universidad Politécnica de Madrid Madrid Spain Full professor at the Industrial Engineering School Universidad Politécnica de Madrid Madrid Spain An associate professor at the Telecomunications Engineering School Universidad Politécnica de Madrid Madrid Spain Full professor at Academy of Applied Studies of Kosovo and Metohija Dostoje Obradoviq Leposaviq Kosovo

ISBN: (数字)9798331517649

ISBN: (纸本)9798331517656

Energy loss in power distribution networks remains a significant economic and environmental concern, often exacerbated by a lack of transparent data and limited realtime visibility. This paper introduces an Internet of Things (IoT) based monitoring system designed to capture, analyze, and securely store granular information on energy flow across a distribution grid. Through strategically and intervally placed sensors and a decentralized data ledger, the proposed system not only improves the spatial resolution of loss detection but also provide trust among stakeholders by preventing data tampering. Unlike traditional solutions reliant on centralized architectures, this approach combines lowcost hardware, scalable communication protocols, and immutable record, keeping to pinpoint inefficiencies in real time. A demonstration scenario validates its potential to identify localized anomalies, stemming from voltage drops, resistive heating, or other factors, more accurately than conventional methods, thereby enabling proactive maintenance and informed resource allocation. By striking a balance between affordability, security, and operational insight, the system lays the groundwork for more resilient and transparent energy distribution networks.

关键词： Transportation Voltage Sensor systems Real-time systems Sensors Internet of Things Stakeholders Security Resource management Spatial resolution

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Desalination Alternative Technology in Conjunction with Membrane Capacitive Deionization (MCDI): A Literature Review Article

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Journal of Environmental Protection 2021年第3期12卷 218-236页

作者： Ahmed J. Aldalou Yunes K. Mogheir Water Technology PhD Program Islamic University of Gaza & AL-Azhar University Gaza Palestine Civil and Environmental Engineering Department Islamic University of Gaza Gaza Palestine

Water and energy shortages came due to rapid population growth, living standards and rapid development in the agriculture and industrial sectors. Desalination tends to be one of the most promising water solutions;however, it is a process of intense energy. Membrane Capacitive Deionization (MCDI) has received considerable interest as a promising desalination technology, and MCDI research has increased significantly over the last 10 years. In addition, there are no guidelines for the design of Capacitive Deionization (CDI) implementation strategies for individual applications. This study, therefore;provides an alternative of CDI’s recent application developments, with emphasis placed on hybrid systems to address the technological needs of different relevant fields. The MCDI’s energy consumption is compared with the reverse osmosis literature data based on experimental data from laboratory-scale system. The study demonstrates that MCDI technology is a promising technology in the next few years with an extreme competition in water recovery, energy consumption and salt removal for reverse osmosis.

关键词： Capacity Deionization Membrane Capacitive Deionization Desalination Reverse Osmosis (RO)

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Segmenting Alzheimer's Disease MRI Slices for Hippocampal Volume Calculation

Segmenting Alzheimer's Disease MRI Slices for Hippocampal Vo...

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IEEE International Conference on Consumer Electronics-Taiwan (ICCE-TW)

作者： Hsiao-Chuan Tan Gilang Titah Ramadhan Wei-Cheng Shen Wen-Thong Chang Chih-Yang Lin Ben-Yi Liau Yih-Kuen Jan Yori Pusparani Chi-Wen Lung Department of Artificial Intelligence PhD Program Asia University Taichung Taiwan Department of Computer Science and Information Engineering Asia University Taichung Taiwan Department of Creative Product Design Asia University Taichung Taiwan Department of Mechanical Engineering National Central University Taoyuan Taiwan Department of Automatic Control Engineering Feng Chia University Taichung Taiwan Department of Kinesiology and Community Health University of Illinois Urbana America Department of Digital Media Design Asia University Taichung Taiwan

ISBN: (数字)9798350386844

ISBN: (纸本)9798350386851

Alzheimer's is a neurodegenerative disease that quietly steals human memory. This study analyzed hippocampal volume in Alzheimer's Disease (AD), Mild Cognitive Impairment (MCI), and Normal Cognition (NC) using MRI image slices from the ADNI database and YOLOv8 instance segmentation. We used 300 images to segment the left and right hippocampal. This study focused on volume calculation from five MRI image slices. The results showed 0.98 (AD), 0.92 (MCI), and 0.90 (NC) and revealed significant volumetric differences showed in the NC class (P = 0.045). This suggests early neuroanatomical changes can occur without cognitive symptoms, highlighting the potential of deep learning in the early detection of neurodegenerative diseases.

关键词： Instance segmentation Deep learning Accuracy Databases Magnetic resonance imaging Cognition Alzheimer's disease

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Medical Image Segmentation by Improved Nested Unet 2nd

Medical Image Segmentation by Improved Nested Unet

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2nd International Conference on Intelligent Systems and Data Science, ISDS 2024

作者： Tran, Song-Toan Le, Minh-Hai Nguyen, Thai-Son Nghi, Vinh-Khanh Nguyen, Thanh-Nguyen School of Engineering and Technology Tra Vinh University Tra Vinh87000 Viet Nam Resource Development Institute Tra Vinh University Tra Vinh87000 Viet Nam PhD program in Computer Science Tra Vinh University Tra Vinh87000 Viet Nam Facilities Management Department Tien Giang University Tien Giang84000 Viet Nam

ISBN: (纸本)9789819796120

Deep learning is revolutionizing the field of medical image segmentation. The U-shaped (Unet) model, with its encoder-decoder architecture and skip connections, has become the dominant architecture for this task. However, variations like Nested-Unet are necessary to address the challenge of adapting network size for datasets of varying scales. This study proposes a novel model based on a multilayer Unet architecture that leverages all output features within nodes of a Nested Unet network. We evaluate the proposed model on four key medical image datasets: electron microscopy (EM), nuclei, polyps (CVC-ClinicDB), and skin lesions. The model achieves impressive Dice scores: 94.08% for EM, 92.68% for nuclei, 87.20% for skin lesions, and 93.02% for the CVC-ClinicDB dataset. These outstanding results demonstrate the superior performance of our proposed model compared to recent advancements in the field. Remarkably, the model achieves this performance while maintaining a size that is half that of a traditional Unet model. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2025.

关键词： Image segmentation

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