Article
Computer Science, Artificial Intelligence
Lifeng Zhang, Xiangwei Zheng, Xuanchi Chen, Xiuxiu Ren, Cun Ji
Summary: Facial expression recognition plays an important role in various applications, but not all extracted facial features are suitable. In this paper, a spatial-temporal fusion method with attention mechanism is proposed to improve accuracy. Experimental results show competitive performance compared to state-of-the-art methods.
NEURAL PROCESSING LETTERS
(2023)
Article
Biochemical Research Methods
Fuqing Jiang, Xin Zhou, Yingying Qian, Miao Zhu, Li Wang, Zhuxia Li, Qingmei Shen, Minhan Wang, Fangfang Qu, Guizhong Cui, Kai Chen, Guangdun Peng
Summary: The study describes a microfluidic indexing-based spatial assay (MISAR-seq) that combines spatial-ATAC-seq and RNA-seq to simultaneously profile chromatin accessibility and gene expression in the developing mouse brain. This method provides insights into tissue organization and spatiotemporal regulatory logics during brain development.
Article
Biochemistry & Molecular Biology
Shuang Gu, Chaoliang Wen, Junying Li, Honghong Liu, Qiang Huang, Jiangxia Zheng, Congjiao Sun, Ning Yang
Summary: This study selected four different breeds of chickens to investigate the temporal expression patterns of key regulatory genes during embryonic muscle development, providing a foundation for understanding the regulation mechanisms. The highest expression level of Myomaker, a crucial gene for myoblast fusion, occurred from embryonic days 13 to 15, with Cornish breed showing the highest expression level. The MYOD gene may play an important role after hatching. Histomorphology analysis suggested that the myofibers were largely complete by embryonic day 17 due to increased expression of MSTN and decreased expression of Myomaker.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Miguel Ramirez, Yuliya Badayeva, Joanna Yeung, Joshua Wu, Ayasha Abdalla-Wyse, Erin Yang, Brett Trost, Stephen W. Scherer, Daniel Goldowitz
Summary: This study identified active enhancers in the mouse cerebellum during embryonic and postnatal stages, revealing dynamic gene expression regulation during cerebellar development. The enhancers were enriched for neural transcription factor binding sites and showed cell-type specific expression regulation.
Article
Biochemical Research Methods
Britta Velten, Jana M. Braunger, Ricard Argelaguet, Damien Arnol, Jakob Wirbel, Danila Bredikhin, Georg Zeller, Oliver Stegle
Summary: MEFISTO is a flexible and versatile toolbox for modeling high-dimensional data with spatial or temporal dependencies, enabling spatio-temporally informed dimensionality reduction, interpolation, and separation of smooth and non-smooth patterns of variation. It can also integrate underlying patterns of variation in multiple related datasets in a data-driven manner.
Article
Computer Science, Artificial Intelligence
Jianing Teng, Dong Zhang, Wei Zou, Ming Li, Dah-Jye Lee
Summary: Typical Facial Expression Network (TFEN) proposes a new network structure to address the challenges in facial expression recognition. It uses two 2D CNNs to extract facial and expression features, and a facial feature decoupler to minimize the influence of individual facial characteristics. Experimental results show that TFEN achieves better recognition accuracy than state-of-the-art approaches on four popular dynamic FER datasets.
IEEE TRANSACTIONS ON AFFECTIVE COMPUTING
(2023)
Article
Plant Sciences
Pham Anh Tuan, Tran-Nguyen Nguyen, Parneet K. Toora, Belay T. Ayele
Summary: This study comprehensively analyzed the changes in the expression patterns of plant hormone metabolism genes and the levels of their bioactive forms during barley seed development. The results showed that the levels of plant hormones were generally high in the endosperm and embryo tissues at the early stage of seed filling, but decreased during seed filling, except for ABA. The level of ABA in the embryo increased during seed filling and peaked at physiological maturity, while the endospermic ABA remained stable during seed filling. After physiological maturity, most hormones in both tissues showed low levels, except for higher levels of jasmonoyl-isoleucine and SA detected at late stage.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Engineering, Biomedical
Weijun Gong, Yurong Qian, Weihang Zhou, Hongyong Leng
Summary: The recognition of dynamic facial expressions is challenging due to various factors, and obtaining discriminative expression features has been difficult. Traditional deep learning networks lack understanding of global and temporal expressions. This study proposes an enhanced spatial-temporal learning network to improve dynamic facial expression recognition.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2024)
Article
Computer Science, Artificial Intelligence
Weicong Chen, Dong Zhang, Ming Li, Dah-Jye Lee
Summary: In this article, an effective framework is proposed to address the challenge of capturing the dynamics of facial expression progression in video for facial expression recognition. It utilizes a C3D-based network architecture and a Spatial-Temporal and Channel Attention Module (STCAM) to extract spatial-temporal features and enhance them for more representative features. Experimental results demonstrate that the proposed method achieves better or comparable performance compared to the state-of-the-art approaches in dynamic facial expression recognition.
IEEE TRANSACTIONS ON AFFECTIVE COMPUTING
(2023)
Article
Biochemistry & Molecular Biology
Katya L. Mack, Tyler A. Square, Bin Zhao, Craig T. Miller, Hunter B. Fraser
Summary: This study reveals the importance of gene regulatory evolution in the adaptation of threespine sticklebacks to freshwater habitats, especially concerning tissue-specific differences. The findings suggest that cis-regulatory changes play a significant role in gene divergence, with most of the differences occurring in specific tissues between freshwater and marine environments. The study also identified selective processes, particularly within the Wnt signaling pathway in dental tissues, indicating the role of specific genes in adaptation.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Cell Biology
Shenghuan Sun, Justin Torok, Christopher Mezias, Daren Ma, Ashish Raj
Summary: This study utilizes machine learning to model the relationship between cell type composition and connectivity, demonstrating a link between cell types and connectivity in both long-range and short-range connections.
Article
Multidisciplinary Sciences
Nuria Marti Gutierrez, Aleksei Mikhalchenko, Hong Ma, Amy Koski, Ying Li, Crystal Van Dyken, Rebecca Tippner-Hedges, David Yoon, Dan Liang, Tomonari Hayama, David Battaglia, Eunju Kang, Yeonmi Lee, Anthony Paul Barnes, Paula Amato, Shoukhrat Mitalipov
Summary: Cells can acquire mitochondrial DNA (mtDNA) from other cells without a parent-offspring relationship, and this acquisition can occur at high levels. The transfer of mtDNA may serve as a compensatory mechanism to restore compromised mitochondrial function. These findings have important implications for understanding mtDNA transfer and developing gene therapies.
Article
Biochemical Research Methods
F. William Townes, Barbara E. E. Engelhardt
Summary: Nonnegative matrix factorization (NMF) is a widely used method for analyzing high-dimensional count data, but it lacks the ability to incorporate known structure between observations. We present a new model called nonnegative spatial factorization (NSF) that addresses this limitation and achieves better accuracy and prediction performance than existing methods on spatial transcriptomics datasets. We also propose a hybrid extension of NSF that combines spatial and nonspatial components to quantify spatial importance. A TensorFlow implementation of NSF is available for researchers to use.
Article
Cell & Tissue Engineering
Shun He, Zhihou Guo, Mingshan Zhou, Haichang Wang, Zhuonan Zhang, Mengyang Shi, Xufeng Li, Xueying Yang, Lingjuan He
Summary: In this study, the authors used a proliferation recording system called ProTracer to investigate the spatial-temporal proliferation of hepatocytes during pregnancy. They found that hepatocyte proliferation during pregnancy starts in zone 1, then progresses to zone 2, and finally to zone 3, with the majority of new hepatocytes being generated in zone 2. Single-cell RNA sequencing analysis showed that Ccnd1 is highly enriched in zone 2 hepatocytes. Further experiments using genetic lineage tracing revealed that Ccnd1+ hepatocytes preferentially expand during pregnancy. Additionally, the authors demonstrated that estrogen-induced liver enlargement during pregnancy is dependent on Ccnd1. Overall, this study uncovers a unique spatial-temporal pattern of hepatocyte proliferation during pregnancy, with zone 2 Ccnd1+ hepatocytes being the major cellular source for hepatic enlargement.
Article
Plant Sciences
Alexandra Keren-Keiserman, Amit Shtern, Matan Levy, Daniel Chalupowicz, Chihiro Furumizu, John Paul Alvarez, Ziva Amsalem, Tzahi Arazi, Sharon Alkalai-Tuvia, Idan Efroni, Naomi Ori, John L. Bowman, Elazar Fallik, Alexander Goldshmidt
Summary: Tomato CLASS-II KNOX genes have antagonistic roles in regulating ripening at internal fruit domains and pericarp. These genes redundantly coordinate maturation in dry and fleshy fruits, and control the spatial patterns of fruit ripening through differential regulation of RIN activity at different fruit domains.
Article
Biochemical Research Methods
Corinna Vehlow, David P. Kao, Michael R. Bristow, Lawrence E. Hunter, Daniel Weiskopf, Carsten Goerg
BMC BIOINFORMATICS
(2015)
Article
Biochemical Research Methods
Kevin M. Livingston, Michael Bada, William A. Baumgartner, Lawrence E. Hunter
BMC BIOINFORMATICS
(2015)
Article
Medicine, Research & Experimental
Jens Eberlein, Bennett Davenport, Tom Nguyen, Francisco Victorino, Kelsey Haist, Kevin Jhun, Anis Karimpour-Fard, Lawrence Hunter, Ross Kedl, Eric T. Clambey, Dirk Homann
JOURNAL OF CLINICAL INVESTIGATION
(2016)
Article
Mathematical & Computational Biology
Christopher S. Funk, K. Bretonnel Cohen, Lawrence E. Hunter, Karin M. Verspoor
JOURNAL OF BIOMEDICAL SEMANTICS
(2016)
Article
Biochemical Research Methods
Christopher Funk, William Baumgartner, Benjamin Garcia, Christophe Roeder, Michael Bada, K. Bretonnel Cohen, Lawrence E. Hunter, Karin Verspoor
BMC BIOINFORMATICS
(2014)
Article
Medicine, Research & Experimental
Mark Yarborough, Lawrence Hunter
CTS-CLINICAL AND TRANSLATIONAL SCIENCE
(2013)
Editorial Material
Computer Science, Software Engineering
Sheelagh Carpendale, Min Chen, Daniel Evanko, Nils Gehlenborg, Carsten Goerg, Larry Hunter, Francis Rowland, Margaret-Anne Storey, Hendrik Strobelt
IEEE COMPUTER GRAPHICS AND APPLICATIONS
(2014)
Article
Computer Science, Information Systems
Leslie A. Williams, Lynne M. Fox, Christophe Roeder, Lawrence Hunter
INFORMATION TECHNOLOGY AND LIBRARIES
(2014)
Article
Multidisciplinary Sciences
Haibin Liu, Lawrence Hunter, Vlado Keselj, Karin Verspoor
Article
Pathology
A. M. Frantz, A. L. Sarver, D. Ito, T. L. Phang, A. Karimpour-Fard, M. C. Scott, V. E. O. Valli, K. Lindblad-Toh, K. E. Burgess, B. D. Husbands, M. S. Henson, A. Borgatti, W. C. Kisseberth, L. E. Hunter, M. Breen, T. D. O'Brien, J. F. Modiano
VETERINARY PATHOLOGY
(2013)
Editorial Material
Biochemical Research Methods
Lawrence E. Hunter
PLOS COMPUTATIONAL BIOLOGY
(2013)
Article
Mathematical & Computational Biology
Kevin M. Livingston, Michael Bada, Lawrence E. Hunter, Karin Verspoor
JOURNAL OF BIOMEDICAL SEMANTICS
(2013)
Article
Biochemistry & Molecular Biology
David N. Nicholson, Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, Casey S. Greene
Summary: Preprints are a valuable tool for researchers to share their findings before they undergo peer review. This study examines the linguistic features of preprints in the bioRxiv repository and compares them to published biomedical text. The research reveals changes in typesetting and mentions of supporting information in preprints after peer review. Additionally, the study uses document embeddings to analyze scientific approaches, link preprints with peer-reviewed articles, and identify journals that publish similar papers. The findings show that preprints with more versions and textual changes take longer to publish. The study also introduces a web application that helps users identify linguistically similar journals and articles to preprints.
Proceedings Paper
Biotechnology & Applied Microbiology
Jason H. Moore, Steven F. Jennings, Casey S. Greene, Lawrence E. Hunter, Andy D. Perkins, Clarlynda Williams-Devane, Donald C. Wunsch, Zhongming Zhao, Xiuzhen Huang
PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017
(2017)
Review
Genetics & Heredity
Anis Karimpour-Fard, L. Elaine Epperson, Lawrence E. Hunter