Article
Biochemical Research Methods
Jun Chen, Xianyang Zhang
Summary: Due to the sparsity and high dimensionality, microbiome data are often summarized into pairwise distances to capture compositional differences and gain biological insights through analyzing the distance matrix in relation to covariates. This study extends the traditional intraclass correlation coefficient (ICC) to distance measures, proposing a distance-based ICC (dICC) and demonstrating its effectiveness through the application of experimental data.
Article
Engineering, Multidisciplinary
Xueliang Gao, Ye Zhuang, Shu Liu
Summary: A novel method for measuring the rolling resistance coefficient of high-speed running tire is proposed, utilizing non-contact measurement and a high-speed stereo vision system to capture the transient deformation of the tire. By analyzing the relative displacement distribution and the relative flexible principal strain rate, the rolling resistance coefficient of high-speed running tire can be calculated.
Article
Materials Science, Multidisciplinary
Jacob A. Marks, Michael Schueler, Jan C. Budich, Thomas P. Devereaux
Summary: The study investigates charge pumping near order-obstructed topological phases where quantized charge pumping is still possible even in the presence of strong correlations and spontaneous symmetry breaking. The presence of orbital charge density wave order in the model's ordered phase assists in this quantized charge pumping, demonstrating the collective nature of this order. Additionally, the study shows that the Thouless pump scenario can be used to uncover the underlying topology of order-obstructed phases.
Article
Food Science & Technology
Alberto Gonzalez-Mohino, Antonio Jimenez, Montana Rufo, Jesus M. Paniagua, Lary S. Olegario, Sonia Ventanas
Summary: The relationship between sensory attributes and ultrasound parameters of pork loin samples cooked under different conditions was studied. The study found a strong and significant correlation between the physical properties of the samples and their sensory attributes, especially with parameters related to FFT and attenuation. Ultrasound inspection can be proposed as a viable tool for studying the correlation and prediction of sensory attributes.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Computer Science, Artificial Intelligence
Soeren Dittmer, Michael Roberts, Julian Gilbey, Ander Biguri, Ian Selby, Jacobus Preller, James H. F. Rudd, John A. D. Aston, Carola-Bibiane Schoenlieb
Summary: Data science systems are widely used in research and developed by people from various backgrounds, but the reproducibility of such systems is facing a crisis. Perverse incentives and a lack of software engineering skills contribute to this crisis. By analyzing the difficulties in software engineering and building complex systems, we propose applying software engineering methods to make data science systems more suitable for their purpose. We advocate for incremental growth and the use of two types of feedback loops in development - one for testing code correctness and another for evaluating code efficacy.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Biochemical Research Methods
Xinjun Li, Fan Feng, Hongxi Pu, Wai Yan Leung, Jie Liu
Summary: scHiCTools is an open-source computational toolbox implemented in Python, providing researchers with a collection of methods to comprehensively and efficiently analyze and visualize single-cell Hi-C data, including screening, smoothing, calculating similarity, embedding, clustering, and visualization.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Engineering, Electrical & Electronic
Meng Zhang, Ahmed Arafa, Ermin Wei, Randall Berry
Summary: The study investigates an information update system where a destination acquires fresh data updates from multiple sources, proposing an optimal mechanism to incentivize data sources to acquire new data and optimize performance related to data freshness. The research demonstrates that both the optimal and quantized mechanisms can lead to unbounded benefits under certain source cost distributions, particularly when there are few sources with heterogeneous sampling costs.
IEEE JOURNAL ON SELECTED AREAS IN COMMUNICATIONS
(2021)
Article
Engineering, Electrical & Electronic
Yuanbo Cheng, Xiaolei Shang, Jian Li, Petre Stoica
Summary: This paper investigates the problem of optimizing the quantization intervals of low-resolution ADCs using a metric based on the CRB. It presents the IDEA algorithm as a computationally efficient solution and discusses the application of optimized quantizers in signal compression. The equivalence between the Lloyd-Max quantizer and a low signal-to-noise ratio version of the IDEA quantizer is established, and numerical examples demonstrate the performance enhancement of using IDEA quantizers.
IEEE TRANSACTIONS ON SIGNAL PROCESSING
(2022)
Article
Computer Science, Information Systems
Dong-Jin Chang, Byeong-Gyu Nam, Seung-Tak Ryu
Summary: This paper introduces a design strategy for low-cost quantized neural networks, utilizing a large number of channels and incorporating a squeeze-and-excitation layer to maintain performance. Through analysis and simulations, a low-cost layer design strategy is proposed and a MixedNet network is successfully built, achieving high classification accuracy rates.
Review
Physics, Particles & Fields
T. Basaglia, M. Bellis, J. Blomer, J. Boyd, C. Bozzi, D. Britzger, S. Campana, C. Cartaro, G. Chen, B. Couturier, G. David, C. Diaconu, A. Dobrin, D. Duellmann, M. Ebert, P. Elmer, J. Fernandes, L. Fields, P. Fokianos, G. Ganis, A. Geiser, M. Gheata, J. B. Gonzalez Lopez, T. Hara, L. Heinrich, M. Hildreth, K. Herner, B. Jayatilaka, M. Kado, O. Keeble, A. Kohls, K. Naim, C. Lange, K. Lassila-Perini, S. Levonian, M. Maggi, Z. Marshall, P. Mato Vila, A. Mecionis, A. Morris, S. Piano, M. Potekhin, M. Schroder, U. Schwickerath, E. Sexton-Kennedy, T. Simko, T. Smith, D. South, A. Verbytskyi, M. Vidal, A. Vivace, L. Wang, G. Watt, T. Wenaus
Summary: This document summarizes the status and importance of data preservation in high energy physics and discusses the experience and advances in this field over the past decade. It presents the current status of preserving data accumulated from large collider experiments and highlights efforts to ensure long-term analysis capabilities for ongoing and future experiments. Additionally, it introduces transverse projects inspired by open science and FAIR principles, and outlines a prospective and an action plan.
EUROPEAN PHYSICAL JOURNAL C
(2023)
Article
Public, Environmental & Occupational Health
Kelly Broen, Rob Trangucci, Jon Zelner
Summary: This study evaluated the impact of different data perturbation methods on spatial statistics and patient privacy, finding that random perturbation, donut masking, and Voronoi masking better maintained the validity of descriptive spatial statistics. However, none of the perturbation methods fully adhered to the HIPAA standard, suggesting further research is needed to explore alternate methods for balancing spatial data privacy and preservation of key patterns.
INTERNATIONAL JOURNAL OF HEALTH GEOGRAPHICS
(2021)
Article
Optics
Hongnan Xu, Yue Qin, Gaolei Hu, Hon ki Tsang
Summary: In this work, a scalable integrated spectrometer is proposed and demonstrated, achieving ultrahigh resolution and improved channel capacity. The spectrometer is based on a spatially reconfigurable multimode cavity formed by a waveguide array and delay lines, with enhanced mode mixing and random temporal speckles. Any arbitrary input spectrum can be computationally retrieved from the recorded output signal.
Article
Engineering, Multidisciplinary
Dan Zhang, Huiling Xu, Hui Wang, Xuefeng Chen
Summary: This paper investigates the stability analysis of interconnected systems and establishes a discontinuous Lyapunov functional to derive sufficient conditions for system stability. An optimization algorithm is proposed to reduce the total number of sampled data, demonstrating the effectiveness and applicability of the main results.
APPLIED MATHEMATICAL MODELLING
(2022)
Review
Geology
Behnam Sadeghi
Summary: This article introduces commonly used correlation coefficient (CC) methods in geochemical studies and discusses their advantages and limitations when dealing with different types of data. It then introduces a new correlation method, Chatterjee CC (CCC), which is simple, computationally efficient, and robust to various types of data. A Python package called TripleCpy was developed to apply CCC to datasets and its efficiency was demonstrated compared to traditional methods.
ORE GEOLOGY REVIEWS
(2022)
Article
Engineering, Multidisciplinary
Bart Lomiej Toron, Piotr Szperlich, Marian Nowak, Alicja Starczewska
Summary: This paper presents a novel method for directly measuring a material's piezoelectric coefficients based on fast gas decompression. The method is simple, fast, reliable, and easy to apply, allowing for the calculation of the coefficients from the measured output voltage and pressure change speed. Experimental results on quartz crystal, PZT ceramic, and antimony sulfoiodide single crystals show good agreement with literature values.
Article
Biotechnology & Applied Microbiology
Yanmei Dou, Minseok Kwon, Rachel E. Rodin, Isidro Cortes-Ciriano, Ryan Doan, Lovelace J. Luquette, Alon Galor, Craig Bohrson, Christopher A. Walsh, Peter J. Park
NATURE BIOTECHNOLOGY
(2020)
Article
Multidisciplinary Sciences
Sandrine Ettou, Youngsook L. Jung, Tomoya Miyoshi, Dhawal Jain, Ken Hiratsuka, Valerie Schumacher, Mary E. Taglienti, Ryuji Morizane, Peter J. Park, Jordan A. Kreidberg
Article
Biochemical Research Methods
Minseok Kwon, Soohyun Lee, Michele Berselli, Chong Chu, Peter J. Park
Summary: Visual inspection of read-level data remains crucial for accurate variant identification despite improvements in algorithms. BamSnap, an efficient BAM file viewer, can rapidly generate high-quality snapshots with customized tracks and layout, serving as a valuable tool in genome analysis.
Article
Neurosciences
Maxwell A. Sherman, Rachel E. Rodin, Giulio Genovese, Caroline Dias, Alison R. Barton, Ronen E. Mukamel, Bonnie Berger, Peter J. Park, Christopher A. Walsh, Po-Ru Loh
Summary: The contribution of mosaic copy number variants (mCNVs) to the risk of autism spectrum disorder (ASD) was investigated in a study, revealing that probands with ASD carry a significant burden of mCNVs compared to their unaffected siblings, particularly large mCNVs. Additionally, the severity of ASD symptoms correlated positively with the size of mCNVs, and no mosaic analogues of common short de novo CNVs associated with ASD were observed.
NATURE NEUROSCIENCE
(2021)
Article
Multidisciplinary Sciences
Sara Bizzotto, Yanmei Dou, Javier Ganz, Ryan N. Doan, Minseok Kwon, Craig L. Bohrson, Sonia N. Kim, Taejeong Bae, Alexej Abyzov, Peter J. Park, Christopher A. Walsh
Summary: Through high-depth whole-genome sequencing and single-cell analysis, this study reveals the process of early cell division in human embryonic development and explores the asymmetric contributions of early progenitors to the formation of different organs and tissues.
Article
Multidisciplinary Sciences
Joshua H. Cook, Giorgio E. M. Melloni, Doga C. Gulhan, Peter J. Park, Kevin M. Haigis
Summary: Mutational activation of KRAS plays a key role in promoting cancer initiation and progression, with tissue-specific genetic interactions and dependencies driving the clinical consequences of mutant alleles. Genetic analysis reveals distinct signaling properties and comutation networks associated with different mutant KRAS alleles across multiple cancer types, highlighting the complexity underlying the genetic interactions of oncogenic KRAS mutations.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Cell Biology
Lovelace J. Luquette, Peter J. Park
Summary: The researchers have developed a new method to detect somatic mutations present in very few cells on a single molecule of DNA, and applied it to human tissues in different stages.
Article
Multidisciplinary Sciences
Chong Chu, Rebeca Borges-Monroy, Vinayak V. Viswanadham, Soohyun Lee, Heng Li, Eunjung Alice Lee, Peter J. Park
Summary: Identification of transposable element (TE) insertions from whole genome sequencing data remains challenging. However, the xTea tool developed by the authors provides a comprehensive solution for both short-read and long-read sequencing data, outperforming other methods and enabling creation of a catalogue of TE insertions.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Soohyun Lee, Clara Bakker, Carl Vitzthum, Burak H. Alver, Peter J. Park
Summary: With the increasing amount of 3D chromosomal interaction data, efficient storage and access to such data become crucial. Pairs is a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix is an open-source C application for indexing and querying Pairs files. Additionally, PairsQC is a collapsible HTML quality control report generator for Pairs files.
Review
Genetics & Heredity
Isidro Cortes-Ciriano, Doga C. Gulhan, Jake June-Koo Lee, Giorgio E. M. Melloni, Peter J. Park
Summary: This review provides an overview of key algorithmic developments, popular tools, and emerging technologies used in the bioinformatic analysis of cancer genomes. It also describes how such analysis can identify point mutations, copy number alterations, structural variations, and mutational signatures in cancer genomes.
NATURE REVIEWS GENETICS
(2022)
Article
Genetics & Heredity
Rebeca Borges-Monroy, Chong Chu, Caroline Dias, Jaejoon Choi, Soohyun Lee, Yue Gao, Taehwan Shin, Peter J. Park, Christopher A. Walsh, Eunjung Alice Lee
Summary: This study analyzed retrotransposon insertions in a cohort of 2288 ASD families using WGS data, identifying a large number of previously unreported polymorphic retrotransposon insertions and 158 de novo retrotransposition events. While the overall burden of de novo events was similar between ASD individuals and unaffected siblings, ASD cases showed an increased number of de novo L1 insertions compared to expectations in ASD genes.
Article
Multidisciplinary Sciences
Zijie Jin, Wenjian Huang, Ning Shen, Juan Li, Xiaochen Wang, Jigiao Dong, Peter J. Park, Ruibin Xi
Summary: The authors developed a computational tool called scFusion for detecting gene fusions in single-cell RNA sequencing data. Evaluation using simulated and real datasets showed that scFusion efficiently and sensitively detects fusions with low false discovery rate. The method was applied to study cellular heterogeneity and transcriptional impact of gene fusions at the single-cell level.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Dhawal Jain, Chong Chu, Burak Han Alver, Soohyun Lee, Eunjung Alice Lee, Peter J. Park
Summary: Hi-C data is used to detect mobile transposable element insertions across the entire genome. The HiTea pipeline utilizes clipped Hi-C reads and discordant read pairs to effectively detect TE insertions from three major families in humans, showing competitive performance with existing callers based on WGS data.
Article
Biotechnology & Applied Microbiology
Jae Won Yun, Lixing Yang, Hye-Young Park, Chang-Woo Lee, Hongui Cha, Hyun-Tae Shin, Ka-Won Noh, Yoon-La Choi, Woong-Yang Park, Peter J. Park
Article
Biotechnology & Applied Microbiology
Lixing Yang, Su Wang, Jake June-Koo Lee, Semin Lee, Eunjung Lee, Eve Shinbrot, David A. Wheeler, Raju Kucherlapati, Peter J. Park