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arXiv 2017年

作者： VanderWerf, Kyle Jin, Weiwei Shattuck, Mark D. O'Hern, Corey S. Department of Physics Yale University New HavenCT06520 United States Benjamin Levich Institute and Physics Department City College of New York New YorkNY10031 United States Department of Mechanics and Engineering Science Peking University Beijing100871 China Department of Mechanical Engineering & Materials Science Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States

We perform computational studies of static packings of a variety of nonspherical particles including circulo-lines, circulo-polygons, ellipses, asymmetric dimers, dumbbells, and others to determine which shapes form packings with fewer contacts than degrees of freedom (hypostatic packings) and which have equal numbers of contacts and degrees of freedom (isostatic packings), and to understand why hypostatic packings of nonspherical particles can be mechanically stable despite having fewer contacts than that predicted from naïve constraint counting. To generate highly accurate force- and torque-balanced packings of circulo-lines and -polygons, we developed an interparticle potential that gives continuous forces and torques as a function of the particle coordinates. We show that the packing fraction and coordination number at jamming onset obey a master-like form for all of the nonspherical particle packings we studied when plotted versus the particle asphericity A, which is proportional to the ratio of the squared perimeter to the area of the particle. Further, the eigenvalue spectra of the dynamical matrix for packings of different particle shapes collapse when plotted at the same A. For hypostatic packings of nonspherical particles, we verify that the number of "quartic" modes along which the potential energy increases as the fourth power of the perturbation amplitude matches the number of missing contacts relative to the isostatic value. We show that the fourth derivatives of the total potential energy in the directions of the quartic modes remain nonzero as the pressure of the packings is decreased to zero. In addition, we calculate the principal curvatures of the inequality constraints for each contact in circulo-line packings and identify specific types of contacts with inequality constraints that possess convex curvature. These contacts can constrain multiple degrees of freedom and allow hypostatic packings of nonspherical particles to be mechanically stable. C

关键词： Degrees of freedom (mechanics)

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Statistical analysis and data visualization of Indonesia and Malaysia SARS Cov-2 metadata

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AIP Conference Proceedings 2023年第1期2594卷

作者： D. Sudigyo A. Budiarto B. Pardamean Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

SARS CoV-2 is a fascinating topic to investigate, especially in Indonesia and Malaysia, which share similar racial demographics. However, statistical analysis of information on the SARS CoV-2 from a database, especially GISAID, does not contain specific customizations related to virus comparisons between selected countries. Therefore, the researchers conducted statistical analysis and data visualization using the Python programming language to describe and investigate SARS CoV-2 Indonesia and Malaysia from the GISAID database. SARS CoV-2 metadata from Indonesia (N=117) and Malaysia (N=250), which were gathered during 2020, were compared. This comparison was aimed to investigate the discrepancies of COVID-19 cases in closely related populations. Firstly, data visualization was conducted using the Python Matplotlib library to create bar charts for clades and mutation comparison. Additionally, a series of boxplots were generated to show age discrepancies stratified by gender. Furthermore, the statistical tests showed that only the dominant Malaysian (G and O) clades were found to be significantly different compared to Indonesian cases (p-value=0.016). The proportion of two major mutations (G614D and NSP12 P323L) were also significantly different in the two countries caused by the dominant clade differences (p-value=0.007). Lastly, the differences in the age distribution of COVID-19 cases between the two countries were significant only in the male group (p-value=0.017).

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Mrf-Former: A Multi-Scale Resolution Fusion Approach for Addressing Scale Discrepancies in Remote Sensing Image Change Detection

SSRN

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SSRN 2024年

作者： Yang, Hualin Ouyang, Jiarui Cheng, Junhao Zhang, Wen Li, Hui Li, Xiying Chen, Calvin Yu-Chian Artificial Intelligence Medical Research Center School of Intelligent Systems Engineering Shenzhen Campus of Sun Yat-sen University Guangdong Shenzhen518107 China - Preferred Program Peking University Shenzhen Graduate School Guangdong Shenzhen518055 China School of Electronic and Computer Engineering Peking University Shenzhen Graduate School Guangdong Shenzhen518055 China Department of Medical Research China Medical University Hospital Taichung40447 Taiwan Department of Bioinformatics and Medical Engineering Asia University Taichung41354 Taiwan Guangdong Provincial Key Laboratory of Intelligent Transportation System Sun Yat-sen University Guangzhou China School of Intelligent Systems Engineering Sun Yat-sen University Guangdong Shenzhen518107 China Institute of Artificial Intelligence Guangzhou University Guangzhou China

Dealing with resolution variations in dual-temporal remote sensing images is challenging due to differences in sensor capabilities, altitudes, footprints, resampling, and data fusion. Conventional methods for different-resolution change detection struggle to effectively address these challenges, primarily due to insufficient consideration of global and local feature interactions. In this paper, we propose a novel change detection model that leverages the power of multi-scale resolution fusion(MRF). By incorporating the MRF-Block, our approach extracts hierarchical multi-scale features from the input data, enabling effective capture of contextual information at various granularities. This facilitates improved handling of resolution disparities and promotes interactions between global and local features. Experimental evaluations conducted on diverse datasets, demonstrate the effectiveness of our proposed model in achieving accurate change detection in dual-temporal remote sensing imagery, even in scenarios characterized by varying resolutions. Code is available on-line at https://***/yanghl1914/MRF-Former. © 2024, The Authors. All rights reserved.

关键词： Remote sensing

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Development of a respiratory sound labeling software for training a deep learning-based respiratory sound analysis model

arXiv

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arXiv 2021年

作者： Hsu, Fu-Shun Huang, Chao-Jung Kuo, Chen-Yi Huang, Shang-Ran Cheng, Yuan-Ren Wang, Jia-Horng Wu, Yi-Lin Huang, Chien-Wen Tzeng, Tzu-Ling Lai, Feipei Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan Heroic Faith Medical Science Corporation Limited New Taipei Taiwan National Taiwan University Stanford Joint Program Office of AI in Biotechnology Ministry of Science and Technology Joint Research Center for Artificial Intelligence Technology All Vista Healthcare Taipei Taiwan Department of Life Science College of Life Science National Taiwan University Taipei Taiwan Institute of Biomedical Sciences Academia Sinica Taipei Taiwan Department of Critical Care Far Eastern Memorial Hospital New Taipei City Taiwan

Respiratory auscultation can help healthcare professionals detect abnormal respiratory conditions if adventitious lung sounds are heard. The state-of-the-art artificial intelligence technologies based on deep learning show great potential in the development of automated respiratory sound analysis. To train a deep learning-based model, a huge number of accurate labels of normal breath sounds and adventitious sounds are needed. In this paper, we demonstrate the work of developing a respiratory sound labeling software to help annotators identify and label the inhalation, exhalation, and adventitious respiratory sound more accurately and quickly. Our labeling software integrates six features from MATLAB Audio Labeler, and one commercial audio editor, RX7. As of October, 2019, we have labeled 9,765 15-second-long audio files of breathing lung sounds, and accrued 34,095 inhalation labels,18,349 exhalation labels, 13,883 continuous adventitious sounds (CASs) labels and 15,606 discontinuous adventitious sounds (DASs) labels, which are significantly larger than previously published studies. The trained convolutional recurrent neural networks based on these labels showed good performance with F1-scores of 86.0% on inhalation event detection, 51.6% on CASs event detection and 71.4% on DASs event detection. In conclusion, our results show that our proposed respiratory sound labeling software could easily pre-define a label, perform one-click labeling, and overall facilitate the process of accurately labeling. This software helps develop deep learning-based models that require a huge amount of labeled acoustic data. Copyright © 2021, The Authors. All rights reserved.

关键词： Software design

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Implementation of online learning during the COVID-19 pandemic in primary schools

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AIP Conference Proceedings 2023年第1期2594卷

作者： A. Anugrahana E. Liswantiani D. Sudigyo T. Suparyanto B. Pardamean Elementary School Teacher Education Study Program (PGSD) Faculty of Teacher Training and Education Sanata Dharma University Yogyakarta Indonesia 55281 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

The COVID-19 pandemic requires face-to-face learning to shift to online or distance learning. Therefore, the elementary school, which is the most basic level of education affected by this phenomenon, where this research is carried out. This study aimed to analyze the process of implementing online learning, the supporting and inhibiting factors for teachers, students, and parents in implementing online learning during the COVID-19 pandemic. In addition, good practices for online learning were also analyzed in this study to understand these phenomena in elementary schools. The research method utilized descriptive qualitative research and was performed at a private primary school in Yogyakarta. The subjects consisted of teachers, students, and parents that were involved in the online learning process. Online questionnaires and interviews were used to collect data. The results of this study show the enormous impact of the COVID-19 pandemic on the learning process. Learning that is usually carried out face-to-face (conventional) has now been converted into online learning in elementary school.

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Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees

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Current Protocols in bioinformatics 2018年第1期62卷 e49-e49页

作者： Ricketts, Camir Popic, Victoria Toosi, Hosein Hajirasouliha, Iman Tri-I Computational Biology & Medicine Graduate Program Cornell University New York NY United States Institute for Computational Biomedicine Department of Physiology and Biophysics Weill Cornell Medicine New York NY United States Illumina Inc. Illumina Mission Bay San Francisco CA United States Department of Bioinformatics Institute for Biochemistry and Biophysics University of Tehran Iran Englander Institute for Precision Medicine The Meyer Cancer Center Weill Cornell Medicine New York United States

The reconstruction of cancer phylogeny trees and quantifying the evolution of the disease is a challenging task. LICHeE and BAMSE are two computational tools designed and implemented recently for this purpose. They both utilize estimated variant allele fraction of somatic mutations across multiple samples to infer the most likely cancer phylogenies. This unit provides extensive guidelines for installing and running both LICHeE and BAMSE. © 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

关键词： cancer phylogeny deep sequencing next-generation sequencing somatic variations tumor heterogeneity

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Identifying topologically associating domains using differential kernels

arXiv

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arXiv 2023年

作者： Maisuradze, Luka King, Megan C. Surovtsev, Ivan V. Mochrie, Simon G.J. Shattuck, Mark D. O’Hern, Corey S. Department of Molecular Biophysics and Biochemistry Yale University New HavenCT United States Department of Cell Biology Yale School of Medicine New HavenCT United States Department of Physics Yale University New HavenCT United States Benjamin Levich Institute Physics Department The City College of New York New YorkNY United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT United States

Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional (3D) structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture techniques generate Hi-C maps that can provide insight into the 3D structure of chromatin. Hi-C maps can be represented as a symmetric matrix Aij, where each element represents the average contact probability or number of contacts between chromatin loci i and j. Previous studies have detected topologically associating domains (TADs), or self-interacting regions in Aij within which the contact probability is greater than that outside the region. Many algorithms have been developed to identify TADs within Hi-C maps. However, most TAD identification algorithms are unable to identify nested or overlapping TADs and for a given Hi-C map there is significant variation in the location and number of TADs identified by different methods. We develop a novel method to identify TADs, KerTAD, using a kernel-based technique from computer vision and image processing that is able to accurately identify nested and overlapping TADs. We benchmark this method against state-of-the-art TAD identification methods on both synthetic and experimental data sets. We find that the new method consistently has higher true positive rates (TPR) and lower false discovery rates (FDR) than all tested methods for both synthetic and manually annotated experimental Hi-C maps. The TPR for KerTAD is also largely insensitive to increasing noise and sparsity, in contrast to the other methods. We also find that KerTAD is consistent in the number and size of TADs identified across replicate experimental Hi-C maps for several organisms. Thus, KerTAD will improve automated TAD identification and enable researchers to better correlate changes in TADs to biological phenomena, such as enhancer-promoter interactions and disease states. © 2023, CC BY.

关键词： Topology

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Accuracy Enhancement of L-Band EPR Tooth Dosimetry by Implementing Multiple Harmonic Detection

SSRN

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SSRN 2024年

作者： Oh, Jeonghun Koo, Chang Uk Park, Jong In Choi, Kwon Lee, Junyoung Hirata, Hiroshi Ye, Sung-Joon Program in Biomedical Radiation Sciences Graduate School of Convergence Science and Technology Seoul National University Seoul08826 Korea Republic of Ionizing Radiation Metrology Group Korea Research Institute of Standards and Science Daejeon34113 Korea Republic of Research Institute for Convergence Science Seoul National University Seoul08826 Korea Republic of Division of Bioengineering and Bioinformatics Faculty of Information Science and Technology Hokkaido University Sapporo060–0814 Japan Department of Applied Bioengineering Graduate School of Convergence Science and Technology Seoul National University Seoul08826 Korea Republic of Advanced Institute of Convergence Technology Seoul National University Suwon16629 Korea Republic of Biomedical Research Institute Seoul National University Hospital Seoul03080 Korea Republic of

In a large-scale radiation accident, the swift classification of individuals exposed to high levels of radiation is crucial to minimize casualties. In-vivo tooth dosimetry using L-band electron paramagnetic resonance (EPR) spectroscopy is a promising method for this purpose, as it can estimate individual exposure levels rapidly and non-invasively. However, the accuracy of dose estimation associated with this technique remains a great challenge. To enhance the accuracy, digital multiple harmonic detection (MHD) was incorporated into a home-built L-band EPR spectrometer. This approach enabled the utilization of information present in higher harmonics of EPR signals, which has been often discarded in traditional EPR spectroscopy. Acquired multiple harmonic spectra were reconstructed to the first derivative spectrum to merge information and mitigate the signal broadening. The modulation amplitude varied in a range of 0.3 to 0.7 mT to maximize the accuracy. In a 0.5-minute measurement at 0.6 mT, the standard error of inverse prediction (SEIP) was reduced to 0.57 Gy from 0.71 Gy. The statistical significancy of the enhancement was validated. In conclusion, the accuracy enhanced by this MHD can contribute to improving the efficiency of triage systems in the aftermath of a mass radiation accident. © 2024, The Authors. All rights reserved.

关键词： Paramagnetic resonance

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A Bayesian model for SNP discovery based on next-generation sequencing data

A Bayesian model for SNP discovery based on next-generation ...

引用

IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

作者： Yanxun Xu Xiaofeng Zheng Yuan Yuan Marcos R Estecio Jean-Pierre Issa Yuan Ji Shoudan Liang Department of Statistics Rice University Houston TX USA Department of Bioinformatics and Computational Biology University of Texas M.D. Anderson Cancer Center Houston TX USA Graduate Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine Houston TX USA Department of Biochemistry and Molecular Biology University of Texas M.D. Anderson Cancer Center Houston TX USA Fels Institute for Cancer Research and Molecular Biology Temple University Philadelphia PA USA CCRI NorthShore University HealthSystem Chicago IL USA

ISBN: (纸本)9781467352345

A single-nucleotide polymorphism (SNP) is a single base change in the DNA sequence and is the most common polymorphism. Since some SNPs have a major influence on disease susceptibility, detecting SNPs plays an important role in biomedical research. To take fully advantage of the next-generation sequencing (NGS) technology and detect SNP more effectively, we propose a Bayesian approach that computes a posterior probability of hidden nucleotide variations at each covered genomic position. The position with higher posterior probability of hidden nucleotide variation has a higher chance to be a SNP. We apply the proposed method to detect SNPs in two cell lines: the prostate cancer cell line PC3 and the embryonic stem cell line H1. A comparison between our results with dbSNP database shows a high ratio of overlap (≥95 %). The positions that are called only under our model but not in dbSNP may serve as candidates for new SNPs.

关键词： comparison candidates generation Single nucleotide polymorphism sequence number protection a posteriori probability DNA Sequence Bayesian inference Disease Susceptibility Analyses, Sequence

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Meteorological parameters for PV installations in Indonesia

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AIP Conference Proceedings 2024年第1期3026卷

作者： Joko Pebrianto Trinugroho Alam Ahmad Hidayat Reza Rahutomo Bens Pardamean Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Information System Department School of Information Systems Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

Many countries are still dependent on fossil fuels as their primary energy supply. However, there is a growing concern about the sustainability and the environmental issue of fossil fuels. Therefore, it is important to utilize renewable resources as the energy supply, such as solar energy. As a country with a tropical climate, Indonesia has a great potential to use solar energy, due to the abundance of sunlight exposure. The present study aims to analyze several meteorological parameters for the installation of photovoltaic (PV) technology in Jakarta, Indonesia. The meteorological data provided by the Ministry of Environment and Forestry, Indonesia from 2008-2021 were used at three different locations in Jakarta. Data visualizations were used to show the difference between each variable in different locations. In addition, the statistical difference between the variables in the three locations was also examined using the Mann-Whitney U test. The test shows that all parameters are evenly distributed in the three locations except for a moderate difference in air temperature in the two locations. Furthermore, the monthly analysis of the parameters also indicates that the dry season, especially from August to September, would be the optimal time to utilize PV technology. Hence, this study would be useful to give preliminary insight regarding a site-specified assessment of PV plants in Jakarta based on local meteorological data.

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