Article
Multidisciplinary Sciences
Jiseok Lee, Hobyeong Chae, KyungMin Kim, Hwa Soo Kim, TaeWon Seo
Summary: This paper proposes a method to detect and estimate the density of dust on translucent windows through image processing techniques. The method is easily applicable in outdoor conditions and only uses processing techniques that are not significantly restricted by global brightness and background.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Yancan Li, Jun Yao, Huiling Sang, Quangui Wang, Long Su, Xiaomeng Zhao, Zhenyu Xia, Feiran Wang, Kai Wang, Delong Lou, Guizhi Wang, Robert M. Waterhouse, Huihua Wang, Shudong Luo, Cheng Sun
Summary: In this study, a pan-genome approach was applied to map and explore genetic variations in populations of the Asian honeybee (Apis cerana). The research found that 31.32% of genes in the pan-genome were variable across populations, providing a broad gene pool for environmental adaptation. Structural variations were found to be closely associated with transposable elements, rather than single nucleotide polymorphisms. Additionally, a novel ecological group of A. cerana was identified using structural variations. The study also identified 44 structural variations likely to be associated with environmental adaptation. One of these structural variations, a deletion in the Atpalpha gene, was found to promote cold adaptation by altering gene expression.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Shangkun Jin, Zegang Han, Yan Hu, Zhanfeng Si, Fan Dai, Lu He, Yu Cheng, Yiqian Li, Ting Zhao, Lei Fang, Tianzhen Zhang
Summary: This study constructs a pan-genome based on structural variations in cotton and demonstrates their association with important agronomic traits through population structure analysis and genome-wide association studies. The findings highlight the importance of structural variations in speciation, domestication, and improvement of cultivated crop species.
Article
Engineering, Civil
Lukas Novak, Drahomir Novak
Summary: The paper focuses on efficient estimation of the coefficient of variation for functions of correlated and uncorrelated random variables. It shows that modifying Taylor series expansion for fully correlated random variables can significantly reduce the number of simulations. The concept of interval estimation is proposed and applied to numerical examples, with results corresponding to the theoretical conclusions.
Article
Genetics & Heredity
Haidong Yan, Min Sun, Zhongren Zhang, Yarong Jin, Ailing Zhang, Chuang Lin, Bingchao Wu, Min He, Bin Xu, Jing Wang, Peng Qin, John Pablo Mendieta, Gang Nie, Jianping Wang, Chris S. S. Jones, Guangyan Feng, Rakesh K. K. Srivastava, Xinquan Zhang, Aureliano Bombarely, Dan Luo, Long Jin, Yuanying Peng, Xiaoshan Wang, Yang Ji, Shilin Tian, Linkai Huang
Summary: A graph-based pan-genome, developed from ten pearl millet chromosomal genomes and one existing assembly, identifies 424,085 genomic structural variations. Comparative genomics and transcriptomics analyses highlight the role of RWP-RK transcription factors and endoplasmic reticulum (ER)-related genes in heat tolerance. Overexpression of an RWP-RK gene enhances plant heat tolerance and activates ER-related genes, indicating their importance in heat tolerance. Structural variations influence gene expression associated with heat tolerance and contribute to the adaptation of pearl millet during domestication. This study provides a comprehensive genomic resource for understanding heat tolerance and improving crop resilience to changing climates.
Editorial Material
Biochemical Research Methods
Mile Sikic
Summary: Although less studied, structural variation has been found to be linked to several human diseases. Three novel computational methods may provide insights into this poorly understood aspect of our genetic makeup.
Article
Computer Science, Theory & Methods
Hao Chen, Qiongfu Lian
Summary: With the rapid development of the Internet, personalized e-commerce platform recommendations are needed to enhance user shopping experience. Using clustering algorithms for behavioral data representation can effectively recommend commonly used e-commerce platforms.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
(2021)
Article
Multidisciplinary Sciences
Celia J. Hampton-Miller, Peter N. Neitlich, David K. Swanson
Summary: The Bering Land Bridge National Preserve and Cape Krusenstern National Monument in northwest Alaska are located along the Chukchi Sea, a fragile coastline with the increasing risk of oil spills due to the growth of marine vessel traffic. To prepare for potential spills and monitor changes, researchers have created a high-resolution coastal vegetation map using satellite images and classification models. The resulting map provides valuable baseline data and demonstrates the usefulness of the point-based method for incident preparedness and vegetation classification.
Article
Biotechnology & Applied Microbiology
Birgit Kersten, Christian Rellstab, Hilke Schroeder, Sabine Brodbeck, Matthias Fladung, Konstantin V. Krutovsky, Felix Gugerli
Summary: In this study, the first mitogenome sequence of Abies alba was assembled and studied. The results revealed that the A. alba mitogenome has a complex and dynamic structure with high combinatorial variation. Comparative analysis also showed a moderate but significant positive correlation between mitogenome size and proportion of repetitive elements in gymnosperms. This research provides a basis for further understanding the structure, phylogeny, and evolution of A. alba.
Article
Biochemistry & Molecular Biology
Rong Zhou, Shang-Tong Li, Wen-Ye Yao, Chun-Di Xie, Zhiqiang Chen, Zhi-Jie Zeng, Di Wang, Kui Xu, Zhao-Ji Shen, Yulian Mu, Wenbin Bao, Wenkai Jiang, Ruiqiang Li, Qiqi Liang, Kui Li
Summary: This study assembled a high-quality genome for the Asian Meishan breed using a hybrid approach, revealing numerous structural variations between Asian and European pig breeds; Asian pig breeds share a common ancestor and possess a specific gene hotspot; Transcriptomics showed the transcriptional suppression roles of these variant genes in multiple tissues.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Cheng Quan, Hao Lu, Yiming Lu, Gangqiao Zhou
Summary: Population-scale studies of structural variation are expanding rapidly with the advancement of long-read sequencing technology. The reference bias poses challenges in large-scale genotyping. Academic efforts to improve genotype quality through graphical representation of reference and alternative alleles have shown promising results in large and diverse cohorts.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Genetics & Heredity
Jing Li, Rui Fan, Jintao Xu, Lisong Hu, Fan Su, Chaoyun Hao
Summary: This study performed chloroplast genome sequencing of poorly studied Piper species and compared them with black pepper. The examined species were similar in gene content but had significant structural differences. These structural variations can help evaluate phylogenetic relationships and provide an effective strategy for selecting chloroplast markers.
FRONTIERS IN GENETICS
(2022)
Article
Computer Science, Interdisciplinary Applications
Shun-Peng Zhu, Behrooz Keshtegar, Nguyen-Thoi Trung, Zaher Mundher Yaseen, Dieu Tien Bui
Summary: The study introduces a hybrid conjugate mean value (HCMV) method to enhance efficiency and robustness of RBDO. By dynamically utilizing CGA and AMV with a sufficient descent criterion for convex/concave constraints simplification, HCMV demonstrates superior efficiency and robustness in reliability and RBDO problems compared to other formulations.
ENGINEERING WITH COMPUTERS
(2021)
Article
Biotechnology & Applied Microbiology
Zhaowu Zhang, Rob van Treuren, Ting Yang, Yulan Hu, Wenhui Zhou, Huan Liu, Tong Wei
Summary: This study characterized a large number of SVs in the lettuce genome, uncovering potential causal SVs associated with agronomic traits like seed coat color and leaf anthocyanin content. The findings provide a valuable genomic resource for future lettuce breeding.
Article
Computer Science, Artificial Intelligence
Tsz Ching Ng, Siu Kai Choy, Shu Yan Lam, Kwok Wai Yu
Summary: This article presents a multi-phase image segmentation methodology based on fuzzy superpixel decomposition, aggregation, and merging. The proposed method achieves more accurate segmentation results through hierarchical aggregation of superpixels and multidimensional scaling. Comparative experiments demonstrate the superior performance of the proposed method compared to existing approaches.
PATTERN RECOGNITION
(2023)
Review
Physiology
Jack J. Scala, Ariel B. Ganz, Michael P. Snyder
Summary: By utilizing multi-modal biomarkers and advanced technologies, precision medicine has the potential to revolutionize psychiatric care by providing better diagnostics and treatment decisions. The emerging field of precision psychiatry aims to develop diagnostic tests, monitor treatment efficacy, and reduce ineffective treatments in order to mitigate challenges in mental health care. This narrative-style review summarizes the breakthroughs and challenges in applying precision medicine to mental health.
Article
Nutrition & Dietetics
Francois Haddad, Xiao Li, Dalia Perelman, Everton Jose Santana, Tatiana Kuznetsova, Nicholas Cauwenberghs, Vincent Busque, Kevin Contrepois, Michael P. Snyder, Mary B. Leonard, Christopher Gardner
Summary: The study quantified the bias introduced by ratiometric scaling of resting energy expenditure (REE) using total body weight (BW) in obesity or weight loss intervention. Allometric scaling of REE based on lean body mass (LBM) and fat mass (FM) removed body composition biases and should be considered in obesity and weight-based intervention studies.
CLINICAL NUTRITION ESPEN
(2023)
Article
Allergy
Hesam Movassagh, Mary Prunicki, Abhinav Kaushik, Xiaoying Zhou, Diane Dunham, Eric M. M. Smith, Ziyuan He, German R. Aleman R. Muench, Minyi Shi, Annika K. K. Weimer, Shu Cao, Sandra Andorf, Amir Feizi, Michael P. P. Snyder, Pejman Soroosh, Elizabeth D. D. Mellins, Kari C. C. Nadeau
Summary: This study found that exposure to fine particulate matter (PM2.5) leads to specific alterations in monocytes, especially in children with asthma. Further mechanistic research revealed that fine particulate matter induces innate trained immunity in circulating monocytes, resulting in an enhanced inflammatory response. These findings suggest that the alterations of monocytes may serve as an immune signature for pediatric asthma, and pollution-induced trained immunity could be a potential therapeutic target for asthmatic children.
Editorial Material
Biochemistry & Molecular Biology
Mahdi Moqri, Michael Snyder
Summary: A multiorgan model has been developed to understand the aging network among different organs and predict the risks of chronic diseases and mortality.
Review
Gastroenterology & Hepatology
Matthias Zilbauer, Kylie James, Mandeep Kaur, Sebastian Pott, Zhixin Li, Albert Burger, Jay L. Thiagarajah, Joseph Burclaff, Frode L. Jahnsen, Francesca Perrone, Alexander D. Ross, Gianluca Matteoli, Nathalie Stakenborg, Tomohisa Sujino, Andreas Moor, Raquel Bartolome-Casado, Espen S. Baekkevold, Ran S. Zhou, Bingqing Xie, Ken T. Lau, Shahida Din, Scott T. Magness, Qiuming Yao, Semir Beyaz, Mark Arends, Alexandre Denadai-Souza, Lori A. Coburn, Jellert T. Gaublomme, Richard Baldock, Irene Papatheodorou, Jose Ordovas-Montanes, Guy Boeckxstaens, Anna Hupalowska, Sarah A. Teichmann, Aviv Regev, Ramnik J. Xavier, Alison Simmons, Michael P. Snyder, Keith T. Wilson
Summary: The number of single-cell profiling studies in the human gastrointestinal tract has significantly increased, presenting an opportunity to generate the first Human Gut Cell Atlas (HGCA). However, there are still major challenges that need to be addressed, including the need for structured and coordinated efforts globally. This Roadmap provides a comprehensive direction and overview of the challenges, as well as recommendations for future studies and the integration of the healthy gut atlas with diseases and gut organoids.
NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY
(2023)
Review
Computer Science, Artificial Intelligence
Lauren M. Sanders, Ryan T. Scott, Jason H. Yang, Amina Ann Qutub, Hector Garcia Martin, Daniel C. Berrios, Jaden J. A. Hastings, Jon Rask, Graham Mackintosh, Adrienne L. Hoarfrost, Stuart Chalk, John Kalantari, Kia Khezeli, Erik L. Antonsen, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Guillermo M. Delgado-Aparicio, Benjamin S. Glicksberg, Casey S. Greene, Melissa Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Christopher E. Mason, Mona Matar, George I. Mias, Jack Miller, Jerry G. Myers Jr, Charlotte Nelson, Jonathan Oribello, Seung-min Park, Patricia Parsons-Wingerter, R. K. Prabhu, Robert J. Reynolds, Amanda Saravia-Butler, Suchi Saria, Aenor Sawyer, Nitin Kumar Singh, Michael Snyder, Frank Soboczenski, Karthik Soman, Corey A. Theriot, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes
Summary: Deep space exploration missions require new technologies to support astronaut health systems and independent biological monitoring and research systems. A NASA workshop explores how artificial intelligence advances can address these challenges and discusses the intersection between artificial intelligence and space biology.
NATURE MACHINE INTELLIGENCE
(2023)
Review
Computer Science, Artificial Intelligence
Ryan T. Scott, Lauren M. Sanders, Erik L. Antonsen, Jaden J. A. Hastings, Seung-min Park, Graham Mackintosh, Robert J. Reynolds, Adrienne L. Hoarfrost, Aenor Sawyer, Casey S. Greene, Benjamin S. Glicksberg, Corey A. Theriot, Daniel C. Berrios, Jack Miller, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Stuart Chalk, Guillermo M. Delgado-Aparicio, Melissa Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, John Kalantari, Kia Khezeli, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Hector Garcia Martin, Christopher E. Mason, Mona Matar, George I. Mias, Jerry G. Myers Jr, Charlotte Nelson, Jonathan Oribello, Patricia Parsons-Wingerter, R. K. Prabhu, Amina Ann Qutub, Jon Rask, Amanda Saravia-Butler, Suchi Saria, Nitin Kumar Singh, Michael Snyder, Frank Soboczenski, Karthik Soman, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes
Summary: Deep-space exploration requires new technologies for astronaut health systems and autonomous biomonitoring. This article discusses the vision for precision space health based on the findings from a NASA workshop on artificial intelligence and machine learning.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Immunology
Summer Mengelkoch, Sophia Miryam Schuessler-Fiorenza Rose, Ziv Lautman, Jenna C. Alley, Lydia G. Roos, Benjamin Ehlert, Daniel P. Moriarity, Samuel Lancaster, Michael P. Snyder, George M. Slavich
Summary: The field of psychoneuroimmunology (PNI) has grown in importance and relevance over the past 40 years. However, most PNI studies are limited to a small number of analytes. To advance this field, adopting a multi-omics approach can provide a more comprehensive understanding of biological functions and their relationship to clinical and behavioral outcomes. This article provides an overview of multi-omics research and its potential applications in PNI.
BRAIN BEHAVIOR AND IMMUNITY
(2023)
Article
Biochemistry & Molecular Biology
Mahdi Moqri, Chiara Herzog, Jamie Justice, Daniel W. Belsky, Albert Higgins-Chen, Alexey Moskalev, Georg Fuellen, Alan A. Cohen, Ivan Bautmans, Martin Widschwendter, Jingzhong Ding, Alexander Fleming, Joan Mannick, Jing-Dong Jackie Han, Alex Zhavoronkov, Nir Barzilai, Matt Kaeberlein, Steven Cummings, Brian K. Kennedy, Luigi Ferrucci, Steve Horvath, Eric Verdin, Andrea B. Maier, Michael P. Snyder, Vittorio Sebastiano, Vadim N. Gladyshev
Summary: This study discusses the terminology, characterization, and potential clinical applications of biomarkers of aging, and proposes a framework for their further development and validation. The framework sets the stage for the development of valid biomarkers of aging and their utilization in clinical trials and practice.
Review
Endocrinology & Metabolism
Arvind Veluvali, Michael Snyder
Summary: Studies have shown that dietary fiber deficiency is associated with an increased risk of MetS. The main mechanisms by which dietary fiber may reduce the risk of MetS include reduction of cholesterol levels, improvement of blood sugar control, reduction of inflammation, and promotion of weight loss.
CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE
(2023)
Correction
Multidisciplinary Sciences
Waihay J. Wong, Connor Emdin, Alexander G. Bick, Seyedeh M. Zekavat, Abhishek Niroula, James Pirruccello, Laura Dichtel, Gabriel Griffin, Md Mesbah E. Uddin, Christopher Gibson, Veronica T. Kovalcik, Amy Lin, Marie McConkey, Amelie Vromman, Rob Sellar, Peter Kim, Mridul Agrawal, Joshua Weinstock, Michelle Long, Bing Yu, Rajarshi Banerjee, Rowan Nicholls, Andrea Dennis, Matt Kelly, Po-Ru Loh, Steve McCarroll, Eric Boerwinkle, Ramachandran Vasan, Siddhartha Jaiswal, Andrew Johnson, Raymond Chung, Kathleen Corey, Daniel Levy, Christie Ballantyne, Benjamin Ebert, Pradeep Natarajan
Article
Multidisciplinary Sciences
John W. Hickey, Winston R. R. Becker, Stephanie A. A. Nevins, Aaron Horning, Almudena Espin Perez, Chenchen Zhu, Bokai Zhu, Bei Wei, Roxanne Chiu, Derek C. C. Chen, Daniel L. L. Cotter, Edward D. D. Esplin, Annika K. K. Weimer, Chiara Caraccio, Vishal Venkataraaman, Christian M. M. Schurch, Sarah Black, Maria Brbic, Kaidi Cao, Shuxiao Chen, Weiruo Zhang, Emma Monte, Nancy R. R. Zhang, Zongming Ma, Jure Leskovec, Zhengyan Zhang, Shin Lin, Teri Longacre, Sylvia K. K. Plevritis, Yiing Lin, Garry P. P. Nolan, William J. J. Greenleaf, Michael Snyder
Summary: The intestine is a complex organ with various functions including digestion, immune surveillance, and maintaining symbiotic relationships with microbiota. It has differences in structure and function along its over nine-meter length. Through multiplexed imaging and single-cell assays, this study reveals substantial differences in cell compositions across different regions of the intestine, highlighting distinct immunological niches. The findings also suggest a regulatory differentiation cascade and associate specific cell types with intestinal disease heritability. This research provides an important reference map for understanding human biology and disease.
Article
Biotechnology & Applied Microbiology
Shuxiao Chen, Bokai Zhu, Sijia Huang, John W. Hickey, Kevin Z. Lin, Michael Snyder, William J. Greenleaf, Garry P. Nolan, Nancy R. Zhang, Zongming Ma
Summary: This article introduces a cross-modal data integration method called MaxFuse, which utilizes iterative coembedding, data smoothing, and cell matching to achieve high-quality integration even with weakly linked features. The method is modality-agnostic and demonstrates high robustness and accuracy in the weak linkage scenario, achieving a relative improvement of 20% to 70% over existing methods on benchmarking datasets.
NATURE BIOTECHNOLOGY
(2023)
Article
Biology
Yashvardhan Jain, Leah L. L. Godwin, Yingnan Ju, Naveksha Sood, Ellen M. M. Quardokus, Andreas Bueckle, Teri Longacre, Aaron Horning, Yiing Lin, Edward D. D. Esplin, John W. W. Hickey, Michael P. P. Snyder, Nathan Heath Patterson, Jeffrey M. M. Spraggins, Katy Borner
Summary: The Human BioMolecular Atlas Program (HuBMAP) aims to create a Human Reference Atlas (HRA) for the healthy adult body at the cellular level. To achieve this, accurate and efficient machine-learning algorithms are needed for the segmentation of functional tissue units (FTUs). A Kaggle competition was organized to develop such algorithms and the winning algorithm, Tom, outperformed others in an expanded study. Tom has been implemented in the HuBMAP infrastructure for large-scale kidney FTU segmentation, showcasing the value of Kaggle competitions in advancing research.
COMMUNICATIONS BIOLOGY
(2023)
Article
Endocrinology & Metabolism
Daniel Hornburg, Si Wu, Mahdi Moqri, Xin Zhou, Kevin Contrepois, Nasim Bararpour, Gavin M. Traber, Baolong Su, Ahmed A. Metwally, Monica Avina, Wenyu Zhou, Jessalyn M. Ubellacker, Tejaswini Mishra, Sophia Miryam Schussler-Fiorenza Rose, Paula B. Kavathas, Kevin J. Williams, Michael P. Snyder
Summary: This study reports over 800 lipid species and their roles in health-to-disease transitions, such as in diabetes, ageing, and inflammation. Longitudinal lipidomic profiling of plasma samples from 112 participants revealed dynamic changes in the plasma lipidome during respiratory viral infection, insulin resistance, and ageing, highlighting the potential roles of lipids in immune homoeostasis and inflammation regulation.