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9th Asian Physics Symposium 2021, APS 2021

作者： Dini, Septian Ulan Nurafni, Sevi Fairuza, Achmad Zacky Taufik, Intan Master Program in Physics Faculty of Mathematics and Natural Science InstitutTeknologi Bandung Bandung40132 Indonesia Master Program in Computational Science Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Bandung40132 Indonesia Master Program in Nanotechnology Graduate School Institut Teknologi Bandung Bandung40132 Indonesia School of Life Science and Technology Institut Teknologi Bandung40132 Indonesia

Approximately 500-60,000 volvox cells constructed a colony with a spherical or elliptical hollow form. Each cell can use its flagella to move. For a colony of hundred cells to perform a direct motion, there must be a coordination of the flagella. In this work, we assume that the cells already form the spherical colony and can perform some simple motion types, i.e., translational (TRAN), roll (ROLL), spin (SPIN), and superposition of the motions, and neglect detail of each flagellum. It is possible to map each cell in the colony using angular positions with a constant radius R and different θ _i and φ_i, where i = 1, 2,..., N with N is the number of cells constructing a colony. The center of the colony is R = (x, y, z). The TRAN mode can be obtained, wherex(t) = x(0) + vxt, y(t) = y(0) + vyt, z(t) = z(0) +vzt, ROLLmode with θ(t) = ω(0) + ωθt and SPIN with φ(t) = ω(0) + ωφt. Through the available observation video, the model of volvox colony motion is also shown to have a qualitative agreement. © Published under licence by IOP Publishing Ltd.

关键词： Cells

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Strategies to Reduce Long-Term Drug Resistance by Considering Effects of Differential Selective Treatments 3rd

Strategies to Reduce Long-Term Drug Resistance by Considerin...

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3rd International Symposium on Mathematical and computational Oncology, ISMCO 2021

作者： Ghodsi Asnaashari, Tina Chang, Young Hwan Department of Biomedical Engineering and Computational Biology Program Oregon Health and Science University Portland United States

ISBN: (纸本)9783030912406

Despite great advances in modeling and cancer therapy using optimal control theory, tumor heterogeneity and drug resistance are major obstacles in cancer treatments. Since recent biological studies demonstrated the evidence of tumor heterogeneity and assessed potential biological and clinical implications, tumor heterogeneity should be taken into account in the optimal control problem to improve treatment strategies. Here, first we study the effects of two different treatment strategies (i.e., symmetric and asymmetric) in a minimal two-population model to examine the long-term effects of these treatment methods on the system. Second, by considering tumor adaptation to treatment as a factor of the cost function, the optimal treatment strategy is derived. Numerical examples show that optimal treatment decreases tumor burden for the long-term by decreasing rate of tumor adaptation over time. © 2021, Springer Nature Switzerland AG.

关键词： Tumors

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Evidence of electronic structural change at the metal-insulator transition in the perovskite NaOsO3

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Physical Review B 2023年第19期108卷 195115-195115页

作者： J.-S. Zhou X.-Y. Li M. D. Johannes Materials Science and Engineering Program Mechanical Engineering University of Texas at Austin Austin Texas 78712 USA Center for Computational Materials Science Naval Research Laboratory Washington D.C. 20375 USA

NaOsO3 exhibits an unusual metal-insulator transition (MIT) that has been touted as Slater type, though there are observations that do not entirely conform to this typing. Consistent with a Slater transition, the cell volume and crystal symmetry show no change on cooling through the transition, but both a and b axes in this Pbnm orthorhombic perovskite show a clear kink, and the splitting between them enlarges slightly. Since atomic positions, determined by fitting the intensity of state-of-the-art neutron diffraction data, exhibit no anomalies within the measurement uncertainty, the origin of the a−b splitting and the kink in the data have not yet been elucidated. Understanding the origin of these subtle structural changes across the transition temperature may provide understanding about the electronic behavior. In this paper, we connect local structural changes to changes in the lattice parameters through (1) well-established structural modeling and (2) density functional theory (DFT) calculations. This approach successfully reveals a subtle but significant change of the O-Os-O bond angle on cooling through TMIT. A Madelung energy calculation suggests that this bond angle change signals electron localization in the t2g orbital complex, and this is verified by DFT, which shows an electronic transition from itinerant to localized electronic behavior along with the bond angle shift. In this detailed structural study, we add an important though heretofore overlooked element in the microscopic picture of the MIT in NaOsO3.

关键词： Density of states Jahn-Teller effect Spin-orbit coupling Mott insulators Strongly correlated systems

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Yale at "Discharge Me!": Evaluating Constrained Generation of Discharge Summaries with Unstructured and Structured Information 23

Yale at "Discharge Me!": Evaluating Constrained Generation o...

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23rd Meeting of the ACL Special Interest Group on Biomedical Natural Language Processing, BioNLP 2024

作者： Socrates, Vimig Huang, Thomas Ai, Xuguang Fereydooni, Soraya Chen, Qingyu Taylor, R. Andrew Chartash, David Department of Biomedical Informatics and Data Science Yale University School of Medicine United States Department of Emergency Medicine Yale School of Medicine United States Program of Computational Biology and Bioinformatics Yale University United States School of Medicine University College Dublin National University of Ireland Dublin Ireland

ISBN: (纸本)9798891761308

In this work, we propose our top-ranking (2nd place) pipeline for the generation of discharge summary subsections as a part of the BioNLP 2024 Shared Task 2: "Discharge Me!". We evaluate both encoder-decoder and state-of-the-art decoder-only language models on the generation of two key sections of the discharge summary. To evaluate the ability of NLP methods to further alleviate the documentation burden on physicians, we also design a novel pipeline to generate the brief hospital course directly from structured information found in the EHR. Finally, we evaluate a constrained beam search approach to inject external knowledge about relevant patient problems into the text generation process. We find that a BioBART model fine-tuned on a larger fraction of the data without constrained beam search outperforms all other models.. ©2024 Association for computational Linguistics.

关键词： Decoding

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M3D: Dual-Stream Selective State Spaces and Depth-Driven Framework for High-Fidelity Single-View 3D Reconstruction

arXiv

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arXiv 2024年

作者： Zhang, Luoxi Shrestha, Pragyan Zhou, Yu Xie, Chun Kitahara, Itaru Doctoral Program in Empowerment Informatics University of Tsukuba Japan Center for Computational Science University of Tsukuba Japan Department of Data Science and Artificial Intelligence The Hong Kong Polytechnic University China

The precise reconstruction of 3D objects from a single RGB image in complex scenes presents a critical challenge in virtual reality, autonomous driving, and robotics. Existing neural implicit 3D representation methods face significant difficulties in balancing the extraction of global and local features, particularly in diverse and complex environments, leading to insufficient reconstruction precision and quality. We propose M3D, a novel single-view 3D reconstruction framework, to tackle these challenges. This framework adopts a dual-stream feature extraction strategy based on Selective State Spaces to effectively balance the extraction of global and local features, thereby improving scene comprehension and representation precision. Additionally, a parallel branch extracts depth information, effectively integrating visual and geometric features to enhance reconstruction quality and preserve intricate details. Experimental results indicate that the fusion of multi-scale features with depth information via the dual-branch feature extraction significantly boosts geometric consistency and fidelity, achieving state-of-the-art reconstruction performance. Our code and dataset are publicly available at this URL. © 2024, CC BY-NC-ND.

关键词： 3D reconstruction

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EEG analysis for surprise in VR traffic environment 15

EEG analysis for surprise in VR traffic environment

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15th Asia-Pacific Workshop on Mixed and Augmented Reality, APMAR 2023

作者： Tayama, Yuto Kameda, Yoshinari Master’s program in Intelligent and Mechanical Interacion Systems University of tsukuba 1-1-1 Tennoudai Ibaraki Tsukuba305-8573 Japan Center for Computational Science University of Tsukuba 1-1-1 Tennoudai Ibaraki Tsukuba305-8573 Japan

On the assessment of user experience in VR traffic environments, a method to evaluate the mental state of subjects is required to measure the effects of dynamic events in the traffic environments. EEG is one of the promising devices for measuring the subject mental status. We propose to analyze EEG responses against traffic scenes, including traffic accidents, for the evaluation of the surprise feelings of subjects in VR traffic environments by a set of HMD and an EEG device. Throughout the experiments, we examined whether EEG can evaluate subjects’ emotional states in response to the events in VR space. Three traffic scenes and 10 subjects were prepared for the experiment. The EEG analysis was made on beta frequency band power related to surprise response. © 2023 Copyright for this paper by its authors.

关键词： Accidents

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A Multi-phase Deep Learning Approach for Predicting HCC Response to TACE using Complete Computed Tomography

A Multi-phase Deep Learning Approach for Predicting HCC Resp...

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2023 IEEE EMBS Special Topic Conference on Data science and Engineering in Healthcare, Medicine and Biology, IEEECONF 2023

作者： Chang, Shun Cheng Liu, Chien Fu Misztal, Marta Hsieh, Yi Hsien Lin, Che Taiwan School of Electronic Engineering and Computer Science Queen Mary University of London United Kingdom Department of Electrical Engineering Ntu Taiwan Center for Computational and Systems Biology Center for Biotechnology Ntu Taiwan Smart Medicine and Health Informatics Program Ntu Taiwan

ISBN: (纸本)9798350383386

In this research study, we compare the predictive performance of two advanced deep learning-based models in order to provide a solution to TACE (Transarterial Chemoembolization) response prediction in HCC (Hepatocellular Carcinoma) patients. Using entire abdominal CT scans enabled a broader perspective available for the model, eliminating the need for segmentation during the preprocessing. Making use of both single-phase and multi-phase CT imaging, we have used DenseNet121 and have obtained an accuracy of 80% for the multi-phase *** Relevance: The ability to predict the effectiveness of TACE treatment prior to its administration makes it possible to provide a better decision-making aid for physicians and patients. © 2023 IEEE.

关键词： Computerized tomography

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Understanding the binding of the same ligand to GPCRs of different families

Understanding the binding of the same ligand to GPCRs of dif...

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2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021

作者： Dankwah, Kwabena Owusu Mohl, Jonathon E Begum, Khodeza Leung, Ming-Ying The University of Texas at El Paso Computational Science Program El Paso United States The University of Texas at El Paso Bioinformatics Program Computational Science Program Dept. of Mathematical Sciences El Paso United States The University of Texas at El Paso Bioinformatics Program Border Biomedical Research Center El Paso United States

ISBN: (纸本)9781665401265

G protein-coupled receptors (GPCRs) are the largest class of cell-surface receptor proteins with important functions in signal transduction and often serve as therapeutic drug targets. With the rapidly growing public data on three dimensional (3D) structures of GPCRs and GPCR-ligand interactions, computational prediction of GPCR ligand binding becomes a convincing option to high throughput screening and other experimental approaches during the beginning phases of ligand discovery. Such predictions are cost-efficient and can be important aides for planning wet lab experiments to help elucidate signaling pathways and expedite drug discovery. There are existing computational tools for GPCR ligand binding prediction using various sequence and structural derived features. However, these methods have been typically tested on specific families of GPCRs and none has focused on features that characterize binding of a single ligand to multiple GPCR families. In this work, we set out to uncover and understand the binding of the same ligand to multiple GPCRs of different families. As expected only a few GPCRs share a conserved sequence motif. We observed local 3D structural similarities and local sequence similarities. We also observed that the GPCRs within the same family share similar binding pockets for the ligand. Molecular docking revealed that a ligand can bind to GPCRs of different families with different poses but similar conformations. Finally, the ligands bind to similar pockets with similar electrostatic and solvation properties and share similar residues. These findings can be exploited to improve protein function inference, drug repurposing and drug toxicity prediction, and accelerate the development of new drugs. © 2021 IEEE.

关键词： Ligands

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Effect of Pentaclethra macrophyla Benth. Leaf on expression of P53, IRS, HsD17β2, FTO, and CYP11a genes in letrozole-induced polycystic ovarian syndrome rats

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Comparative Clinical Pathology 2024年第3期33卷 355-366页

作者： Ogunlakin, Akingbolabo Daniel Ojo, Oluwafemi Adeleke Osagie, Precious Oreoluwa Ubogu, Oghenetega Adegoke, Adeyemi Abdullahi Ogunlakin, Oluwaseun A. Bowen University SDG 03 (Good Health and Wellbeing Research Cluster) Iwo 232101 Nigeria Phytomedicine Molecular Toxicology and Computational Biochemistry Research Laboratory (PMTCB-RL) Department of Biochemistry Bowen University Iwo 232101 Nigeria Department of Pharmacognosy Faculty of Pharmacy University of Ibadan Ibadan Nigeria Agricultural Science Program Bowen University Iwo 232101 Nigeria

Hyperandrogenism and menstruation difficulties are the hallmarks of polycystic ovarian syndrome (PCOS), a disorder affecting women in their reproductive years. The purpose of this study is to determine if Pentaclethra macrophylla leaf extract is beneficial in treating letrozole-induced PCOS rats. To ascertain the antioxidant characteristics of the plant extract, in vitro tests including the hydroxyl radical scavenging assay, FRAP, DPPH radical scavenging assay, and iron chelating assay were performed. A toxicology study was also conducted. Following PCOS induction, the standard and plant extract groups received treatment for 12 days with Clomiphene citrate (standard;1 mg/kg) and Pentaclethra macrophylla (100 and 250 mg/kg). Vaginal cytology was performed daily before the administration of treatment orally by gavage. The rats were euthanized after the treatment period, and their ovaries and blood were taken. Luteinizing hormone, follicle-stimulating hormone, testosterone, and estradiol were measured using ELISA, and P53, IRS, HsD17β2, FTO, and CYP11a gene expression were quantified in the ovary. P. macrophylla effectively restored the hormonal balance and enhanced follicular development in the letrozole-induced rats, compared to the untreated group. In addition, the ovary of PCOS rats with methanol extract showed normalization of P53, insulin receptor substrate (IRS), fat mass and obesity-associated (FTO), and 11a-hydroxylase/17,20-desmolase (CYP11a) genes, except type 2 17-HSD (17-HSD) gene. Overall, in rats with polycystic ovarian syndrome, Pentaclethra macrophylla leaf showed overall ameliorative effects, indicating potential as an effective PCOS therapy strategy. © 2024, The Author(s), under exclusive licence to Springer-Verlag London Ltd., part of Springer Nature.

关键词： Gene expression In vitro assays In vivo assay Pentaclethra macrophylla Polycystic ovarian syndrome

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Antithetic Multilevel Particle Filters

arXiv

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arXiv 2023年

作者： Jasra, Ajay Maama, Mohamed Ombao, Hernando Applied Mathematics and Computational Science Program United States Statistics Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia

In this paper we consider the filtering of partially observed multi-dimensional diffusion processes that are observed regularly at discrete times. This is a challenging problem which requires the use of advanced numerical schemes based upon time-discretization of the diffusion process and then the application of particle filters. Perhaps the state-of-the-art method for moderate dimensional problems is the multilevel particle filter of [12]. This is a method that combines multilevel Monte Carlo and particle filters. The approach in that article is based intrinsically upon an Euler discretization method. We develop a new particle filter based upon the antithetic truncated Milstein scheme of [10]. We show that for a class of diffusion problems, for ϵ > 0 given, that the cost to produce a mean square error (MSE) in estimation of the filter, of O(ϵ2) is O(ϵ−2 log(ϵ)2). In the case of multidimensional diffusions with non-constant diffusion coefficient, the method of [12] has a cost of O(ϵ−2.5) to achieve the same MSE. We support our theory with numerical results in several examples. Copyright © 2023, The Authors. All rights reserved.

关键词： Mean square error

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