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Magnetized and quadratic convection based thermal transport in ternary radiative bio-nanofluid via intelligent neural networks: Two hidden layers mechanism

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Results in Physics 2024年 65卷

作者： Ayub, Assad Darvesh, Adil Shah, Syed Zahir Hussain Junjua, Moin-ud-Din Santos, Elizaldo Domingues dos Ahmad, Shabbir Hendy, Ahmed S. Ragab, Adham E. Department of Mathematics & Statistics Hazara University Manshera Pakistan School of Mathematical Sciences Zhejiang Normal University Zhejiang Jinhua 321004 China Programa de Pós-Graduação em Modelagem Computacional/LMCE Escola de Engenharia Universidade Federal do Rio Grande – FURG RS Rio Grande 96203900 Brazil FURG Escola de Engenharia RS Rio Grande Brazil Department of Basic Sciences and Humanities Muhammad Nawaz Sharif University of Engineering and Technology Multan 60000 Pakistan Department of Computational Mathematics and Computer Science Institute of Natural Sciences and Mathematics Ural Federal University 19 Mira St. Yekaterinburg 620002 Russian Federation Department of Industrial Engineering College of Engineering King Saud University P.O. Box 800 Riyadh 11421 Saudi Arabia Department of Mathematics Ghazi University Dera Ghazi Khan 32200 Pakistan Graduate Program of Ocean Engineering School of Engineering Universidade Federal do Rio Grande Italia Avenue km 8 96201-900 Rio Grande Brazil Department of Mechanics and Mathematics Western Caspian University Baku 1001 Azerbaijan

Significance: The thermal analysis of nanofluid in a vertical cylinder (artery) in a magnetized environment holds significant implications in physiological and thermal regulation networks. This research is significant in biomedical engineering with applications like medical diagnostics and treatment strategies. Motive: This study investigates the thermal behavior of a magnetized blood-based ternary Carreau nanofluid flowing through a vertically bounded artery with quadratic convection. Velocity and heat transfer analysis is conducted within the artery, utilizing thermal radiation and quadratic convection in a magnetized setting. The base fluid consists of blood, augmented with three nanoparticles: CuO, Al₂O₃, and TiO₂. The investigation centers on examining the properties of blood nanofluid, arterial geometry, and thermal dynamics. Methodology: The physical model generates a set of partial differential equations (PDEs) and similarities mechanism is utilized to fetch its non dimensional form in terms of ordinary differential equations (ODEs). Furthermore, numerical outcomes are obtained with Matlab function bvp4c and obtained data set is trained through robust scheme Levenberg-Marquardt neural network (LMNN) procedure to predict the solution. Findings: Velocity of blood is reduced with increased values of wiessenberg number, magnetic parameter and mixed convection parameter and velocity increases for Second-order convection parameter. Temperature profile decreases with curvature parameter, mixed convection parameter and permeability parameter. © 2024

关键词： Blood fluid Intelligent neural network Magnetized environment Ternary nanoparticles Thermal scrutiny

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Enriching and Characterizing T-Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products

arXiv

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arXiv 2022年

作者： Jivanjee, Tasneem Ibrahim, Samira Nyquist, Sarah K. James Gatter, G. Bromley, Joshua D. Jaiswal, Swati Berger, Bonnie Behar, Samuel M. Christopher Love, J. Shalek, Alex K. Institute for Medical Engineering & Science Department of Chemistry Massachusetts Institute of Technology CambridgeMA United States Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology CambridgeMA United States Ragon Institute of MGH MIT and Harvard CambridgeMA United States Broad Institute of MIT and Harvard CambridgeMA United States Massachusetts Institute of Technology CambridgeMA United States Program in Computational and Systems Biology Massachusetts Institute of Technology CambridgeMA United States Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology CambridgeMA United States Microbiology Graduate Program Massachusetts Institute of Technology CambridgeMA02139 United States Department of Microbiology and Physiological Systems University of Massachusetts Medical School WorcesterMA United States Department of Mathematics Massachusetts Institute of Technology CambridgeMA United States Department of Chemical Engineering Massachusetts Institute of Technology CambridgeMA United States

Antigen-specific T cells play an essential role in immunoregulation and many diseases such as cancer. Characterizing the T cell receptor (TCR) sequences that encode T cell specificity is critical for elucidating the antigenic determinants of immunological diseases and designing therapeutic remedies. However, methods of obtaining single-cell TCR sequencing data are labor and cost intensive, typically requiring both cell sorting and full length single-cell RNA-sequencing (scRNA-seq). New high-throughput 3' cell-barcoding scRNA-seq methods can simplify and scale this process;however, they do not routinely capture TCR sequences during library preparation and sequencing. While 5' cell-barcoding scRNA-seq methods can be used to examine TCR repertoire at single-cell resolution, doing so requires specialized reagents which cannot be applied to samples previously processed using 3' cell-barcoding methods. Here, we outline a method for sequencing TCRα and TCRβ transcripts from samples already processed using 3' cell-barcoding scRNA-seq platforms, ensuring TCR recovery at a single-cell resolution. In short, a fraction of the 3' barcoded whole transcriptome amplification (WTA) product typically used to generate a massively parallel 3' scRNA-seq library is enriched for TCR transcripts using biotinylated probes, and further amplified using the same universal primer sequence from WTA. Primer extension using TCR V-region primers and targeted PCR amplification using a second universal primer results in a 3' barcoded single-cell CDR3-enriched library that can be sequenced with custom sequencing primers. Coupled with 3' scRNA-seq of the same WTA, this method enables simultaneous analysis of single-cell transcriptomes and TCR sequences which can help interpret inherent heterogeneity among antigen-specific T cells and salient disease biology. The method presented here can also be adapted readily to enrich and sequence other transcripts of interest from both 3' and 5' barcoded scRNA-seq

关键词： RNA

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Assessing the reliability of wind power operations under a changing climate with a non-Gaussian bias correction

arXiv

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arXiv 2020年

作者： Zhang, Jiachen Crippa, Paola Genton, Marc G. Castruccio, Stefano Department of Applied and Computational Mathematics and Statistics University of Notre Dame United States Department of Civid and Environmental Engineering and Geoscience University of Notre Dame United States Statistics Program King Abdullah University of Science and Technology Saudi Arabia

Facing increasing societal and economic pressure, many countries have established strategies to develop renewable energy portfolios, whose penetration in the market can alleviate the dependence on fossil fuels. In the case of wind, there is a fundamental question related to the resilience, and hence profitability, of future wind farms to a changing climate, given that current wind turbines have lifespans of up to thirty years. In this work we develop a new non-Gaussian method to adjust assimilated observational data to simulations and to estimate future wind, predicated on a trans-Gaussian transformation and a cluster-wise minimization of the Kullback-Leibler divergence. Future winds abundance will be determined for Saudi Arabia, a country with a recently established plan to develop a portfolio of up to 16 GW of wind energy. Further, we estimate the change in profits over future decades using additional high-resolution simulations, an improved method for vertical wind extrapolation and power curves from a collection of popular wind turbines. We find an overall increase in daily profit of $272,000 for the wind energy market for the optimal locations for wind farming in the country. Copyright © 2020, The Authors. All rights reserved.

关键词： Wind power

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Rapid identification and monitoring of cooking oil fume-based toxic volatile organic aldehydes in lung tissue for predicting exposure level and cancer risks

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Chemosphere 2023年第1期339卷 139704页

作者： Prakasham, Karthikeyan Gurrani, Swapnil Wu, Chia-Fang Wu, Ming-Tsang Hsieh, Tusty-Jiuan Peng, Chiung-Yu Huang, Po-Chin Krishnan, Anbarasu Tsai, Pei-Chien Lin, Yu-Chia Tsai, Bongee Lin, Yuan-Chung Ponnusamy, Vinoth Kumar Kaohsiung City807 Taiwan Kaohsiung City807 Taiwan International Master Program of Translational Medicine College of Engineering and Science National United University Miaoli Taiwan Kaohsiung City807 Taiwan Department of Public Health College of Health Sciences Kaohsiung Medical University Kaohsiung City807 Taiwan Miaoli County 35053 Taiwan Department of Computational Biology Institute of Bioinformatics Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Tamil Nadu Chennai602105 India Kaohsiung City807 Taiwan Corporation No.392 Yucheng Rd. Zuoying District. Kaohsiung City813 Taiwan Center for Emerging Contaminants Research National Sun Yat-Sen University Kaohsiung City804 Taiwan Institute of Environmental Engineering National Sun Yat-Sen University Kaohsiung City804 Taiwan Kaohsiung Medical University Kaohsiung City807 Taiwan Department of Medical Research China Medical University Hospital China Medical University Taichung Taiwan Department of Family Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan

Cooking oil fumes (COFs) comprised of a mixture of cancer-causing volatile organic aldehydes (VOAs), particularly trans, trans-2,4-decadienal (t,t-DDE), 4-hydroxy-hexenal (4-HHE), and 4-hydroxy-nonenal (4-HNE). Monitoring toxic VOAs levels in people exposed to different cooking conditions is vital to predicting the cancer risk. For this purpose, we developed a fast tissue extraction (FaTEx) technique combined with UHPLC-MS/MS to monitor three toxic VOAs in mice lung tissue samples. FaTEx pre-treatment protocol was developed by combining two syringes for extraction and clean-up process. The various procedural steps affecting the FaTEx sample pre-treatment process were optimized to enhance the target VOAs’ extraction efficiency from the sample matrix. Under the optimal experimental conditions, results exhibit good correlation coefficient values > 0.99, detection limits were between 0.5–3 ng/g, quantification limits were between 1–10 ng/g, and the matrix effect was © 2023 Elsevier Ltd

关键词： Diseases

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Hopper flows of deformable particles

arXiv

引用

arXiv 2022年

作者： Cheng, Yuxuan Treado, John D. Lonial, Ben Habdas, Piotr Weeks, Eric R. Shattuck, Mark D. O'Hern, Corey S. Department of Physics Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Physics Emory University AtlantaGA30322 United States Department of Physics Saint Joseph's University PhiladelphiaPA19131 United States Benjamin Levich Institute Physics Department The City College of New York New YorkNY10031 United States Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States

Numerous experimental and computational studies show that continuous hopper flows of granular materials obey the Beverloo equation that relates the volume flow rate Q and the orifice width w: Q ∼ (w/σavg − k)β, where σavg is the average particle diameter, kσavg is an offset where Q ∼ 0, the power-law scaling exponent β = d − 1/2, and d is the spatial dimension. Recent studies of hopper flows of deformable particles in different background fluids suggest that the particle stiffness and dissipation mechanism can also strongly affect the power-law scaling exponent β. We carry out computational studies of hopper flows of deformable particles with both kinetic friction and background fluid dissipation in two and three dimensions. We show that the exponent β varies continuously with the ratio of the viscous drag to the kinetic friction coefficient, λ = ζ/µ. β = d−1/2 in the λ → 0 limit and d− 3/2 in the λ → ∞ limit, with a midpoint λc that depends on the hopper opening angle θw. We also characterize the spatial structure of the flows and associate changes in spatial structure of the hopper flows to changes in the exponent β. The offset k increases with particle stiffness until k ∼ kmax in the hard-particle limit, where kmax ∼ 3.5 is larger for λ → ∞ compared to that for λ → 0. Finally, we show that the simulations of hopper flows of deformable particles in the λ → ∞ limit recapitulate the experimental results for quasi-2D hopper flows of oil droplets in water. © 2022, CC BY.

关键词： Stiffness

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Isotope effects on molecular structures and electronic properties of liquid water via deep potential molecular dynamics based on SCAN functional

arXiv

引用

arXiv 2020年

作者： Xu, Jianhang Zhang, Chunyi Zhang, Linfeng Chen, Mohan Santra, Biswajit Wu, Xifan Department of Physics Temple University PhiladelphiaPA19122 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States CAPT HEDPS College of Engineering Peking University Beijing100871 China Institute for Computational Molecular Science Temple University PhiladelphiaPA19122 United States

Feynman path-integral deep potential molecular dynamics (PI-DPMD) calculations have been employed to study both light (H2O) and heavy water (D2O) within the isothermal–isobaric ensemble. In particular, the deep neural network is trained based on ab initio data obtained from the strongly constrained and appropriately normed (SCAN) exchange-correlation functional. Because of the lighter mass of hydrogen than deuteron, the properties of light water is more influenced by nuclear quantum effect than those of heavy water. Clear isotope effects are observed and analyzed in terms of hydrogen-bond structure and electronic properties of water that are closely associated with experimental observables. The molecular structures of both liquid H2O and D2O agree well with the data extracted from scattering experiments. The delicate isotope effects on radial distribution functions and angular distribution functions are well reproduced as well. Our approach demonstrates that deep neural network combined with SCAN functional based ab initio molecular dynamics provides an accurate theoretical tool for modeling water and its isotope effects. Copyright © 2020, The Authors. All rights reserved.

关键词： Electronic properties

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Phenotype-guided subpopulation identification from single-cell sequencing data

Research Square

引用

Research Square 2021年

作者： Sun, Duanchen Guan, Xiangnan Moran, Amy E. Qian, David Z. Schedin, Pepper Dai, Mu-Shui Danilov, Alexey V. Alumkal, Joshi Adey, Andrew Spellman, Paul T. Xia, Zheng Computational Biology Program Oregon Health & Science University PortlandOR United States Department of Biomedical Engineering Oregon Health & Science University PortlandOR United States Department of Cell Developmental and Cancer Biology Oregon Health & Science University PortlandOR United States Knight Cancer Institute Oregon Health & Science University PortlandOR United States Department of Molecular and Medical Genetics Oregon Health & Science University PortlandOR United States City of Hope National Medical Center DuarteCA United States Department of Internal Medicine University of Michigan Ann ArborMI United States Department of Molecular Microbiology and Immunology Oregon Health & Science University PortlandOR United States

Single-cell sequencing yields novel discoveries by distinguishing cell types, states, and lineages within the context of heterogeneous tissues. However, interpreting complex single-cell data from highly heterogeneous cell populations remains challenging. Currently, most existing single-cell data analyses focus on cell type clusters defined by unsupervised clustering methods that cannot directly link cell clusters with specific biological and clinical phenotypes. Here we present Scissor, a novel approach that utilizes disease phenotypes to identify cell subpopulations from single-cell data that are most highly associated with the given phenotype. This "phenotype-to-cell" within a single-step strategy utilizes clinical information collected from bulk assays to identify the most highly phenotype-associated cell subpopulations. When applied to a lung cancer single-cell RNA-seq (scRNA-seq) dataset, Scissor identified a subset of cells associated with worse survival as well as another cell subpopulation associated with TP53 mutation. Furthermore, in a melanoma scRNA-seq dataset, Scissor discerned a T cell subpopulation with low PDCD1/CTLA4 and high TCF7 expressions, which is associated with a favorable immunotherapy response. Scissor also demonstrated its broad applicability and effectiveness in interpreting Facioscapulohumeral muscular dystrophy (FSHD) and Alzheimer’s disease scRNA-seq datasets. Thus, Scissor provides a novel framework to identify biologically and clinically relevant cell subpopulations from single-cell assays by leveraging the wealth of phenotype and bulk-omics datasets. © 2021, CC BY.

关键词： Data integration

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Transferable Learning of Reaction Pathways from Geometric Priors

arXiv

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arXiv 2025年

作者： Nam, Juno Steiner, Miguel Misterka, Max Yang, Soojung Singhal, Avni Gómez-Bombarelli, Rafael Department of Materials Science and Engineering Massachusetts Institute of Technology CambridgeMA02139 United States Energy Storage Research Alliance Argonne National Laboratory 9700 South Cass Avenue LemontIL60439 United States Department of Mathematics Massachusetts Institute of Technology CambridgeMA02139 United States Computational and Systems Biology Program Massachusetts Institute of Technology CambridgeMA02139 United States

Identifying minimum-energy paths (MEPs) is crucial for understanding chemical reaction mechanisms but remains computationally demanding. We introduce MEPIN, a scalable machine-learning method for efficiently predicting MEPs from reactant and product configurations, without relying on transition-state geometries or pre-optimized reaction paths during training. The task is defined as predicting deviations from geometric interpolations along reaction coordinates. We address this task with a continuous reaction path model based on a symmetry-broken equivariant neural network that generates a flexible number of intermediate structures. The model is trained using an energy-based objective, with efficiency enhanced by incorporating geometric priors from geodesic interpolation as initial interpolations or pre-training objectives. Our approach generalizes across diverse chemical reactions and achieves accurate alignment with reference intrinsic reaction coordinates, as demonstrated on various small molecule reactions and [3+2] cycloadditions. Our method enables the exploration of large chemical reaction spaces with efficient, data-driven predictions of reaction pathways. Copyright © 2025, The Authors. All rights reserved.

关键词： Reaction intermediates

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Current Progress and Challenges in Large-scale 3D Mitochondria Instance Segmentation

TechRxiv

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TechRxiv 2023年

作者： Franco-Barranco, Daniel Lin, Zudi Jang, Won-Dong Wang, Xueying Shen, Qijia Yin, Wenjie Fan, Yutian Li, Mingxing Chen, Chang Xiong, Zhiwei Xin, Rui Liu, Hao Chen, Huai Li, Zhili Zhao, Jie Chen, Xuejin Pape, Constantin Conrad, Ryan De Folter, Jozefus Nightingale, Luke Jones, Martin L. Liu, Yanling Ziaei, Dorsa Huschauer, Stephan Arganda-Carreras, Ignacio Pfister, Hanspeter Wei, Donglai The Department of Computer Science and Artificial Intelligence University of the Basque Country Donostia-San Sebastian Spain San Sebastian Spain Ikerbasque Basque Foundation for Science Bilbao Spain Biofisika Institute CSIC UPV/EHU Bilbao Spain Harvard University All-ston MA United States The Department of Molecular and Cellular Biology Harvard University CambridgeMA United States The Wellcome Centre for Integrative Neuroimaging FMRIB Nuffield Department of Clinical Neurosciences University of Oxford Oxford United Kingdom University of Science and Technology of China Anhui China The Institute of Image Processing and Pattern Recognition Department of Automation Shanghai Jiao Tong University Shanghai China The National Engineering Laboratory for Brain-inspired Intelligence Technology and Application University of Science and Technology of China Anhui China The Georg-August University Goettingen Germany The Center for Molecular Microscopy Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda United States The Cancer Research Technology Program Frederick National Laboratory for Cancer Research Frederick United States The Francis Crick Institute London United Kingdom The Advanced Biomedical Computational Science Group Frederick National Laboratory for Cancer Research FrederickMD United States The Computer Science Department Boston College Chestnut Hill MA United States

In this paper, we present the results of the MitoEM challenge on mitochondria 3D instance segmentation from electron microscopy images, organized in conjunction with the IEEE-ISBI 2021 conference. Our benchmark dataset consists of two large-scale 3D volumes, one from human and one from rat cortex tissue, which are 3,600 times larger than previously used datasets. At the time of paper submission, 257 participants had registered for the challenge, 14 teams had submitted their results, and six teams participated in the challenge workshop. Here, we present eight top-performing approaches from the challenge participants, along with our own baseline strategies. Posterior to the challenge, annotation errors in the ground truth were corrected without altering the final ranking. Additionally, we present a retrospective evaluation of the scoring system which revealed that (1) the challenge metric was permissive with the false positive predictions and (2) the size-based grouping of instances did not correctly categorize mitochondria of interest. Thus, we propose a new scoring system that better reflects the correctness of the segmentation results. Although several of the top methods are compared favorably to our own baselines, substantial errors remain unsolved for mitochondria with challenging morphologies. Thus, the challenge remains open for submission and automatic evaluation, with all volumes available for download. © 2023, CC BY.

关键词： Electron microscopy

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Design and Performance Evaluation of a P4 based Load Balancer 8

Design and Performance Evaluation of a P4 based Load Balance...

引用

8th International Conference on Innovation, Communication and engineering, ICICE 2019

作者： Hsu, Shih-Jung Ke, Chih-Heng Chen, Yeong-Sheng Hung, Cheng-Feng Lo, Yu-Wen Master Degree Program of Computational Intelligence and Applications National Quemoy University Taiwan National Taipei University of Education Department of Computer Science Taiwan Master of Information Technology and Application National Quemoy University Taiwan National Quemoy University Department of Computer Science and Information Engineering Taiwan

ISBN: (纸本)9781728158396

Being increasingly dense and mature in layout, Internet has become an infrastructure for a state. The traditional single server can no longer bear the network traffic in rapid growth. For example, once the booking service for concert tickets is made available to the public, we are always prompted when clicking into the booking system that the server is busy. And when the system is finally restored normal, the tickets have been sold out. The load issue puzzling the ticket system also occurs in the transportation section every time when a long holiday is coming. Even though the system is updated on a yearly basis, net- work congestion still happens frequently. Therefore, there is still great space for the development of the ways and mechanisms of load balance in traditional multi-servers. Evaluation of the mech- anism and efficacy of load balance through P4Switch is proposed in this paper in the hope to achieve more efficient server load balance. © 2019 IEEE.

关键词： loadbalance openflow p4switch sdn

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