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
Multidisciplinary Sciences
Yuanyuan Li, Guangyi Jin, Boyang Sun, Zhehao Cui, Bishun Lu
Summary: Border tourism between China and North Korea has a significant impact on international economic and cultural cooperation. This study examines the temporal and spatial distribution characteristics and influencing factors of travel demands to North Korea using Baidu Index. It reveals that the travel demands showed an initial increase followed by a decrease from 2011 to 2018, with significant seasonal and spatial differences. Holidays, population, GDP, per capita disposable income, internet penetration, and education are the main factors influencing tourism demand to North Korea.
Article
Neurosciences
Emilia Bergoglio, Ikuo K. Suzuki, Kazuya Togashi, Masato Tsuji, Shunsuke Takeuchi, Hiroyuki Koizumi, Kazuo Emoto
Summary: DCLK1 is an enzyme involved in brain development, with its different isoforms showing partially segregated localization in the developing mouse brain and suggesting distinct roles in brain development and function.
NEUROSCIENCE RESEARCH
(2021)
Review
Ecology
Melissa Ward, Tye L. Kindinger, Heidi K. Hirsh, Tessa M. Hill, Brittany M. Jellison, Sarah Lummis, Emily B. Rivest, George G. Waldbusser, Brian Gaylord, Kristy J. Kroeker
Summary: This study synthesizes the results from 56 studies on seagrass meadow metabolism and highlights the spatial and temporal variability in oxygen fluxes. The study finds that daytime net community production is generally positive and similar across seasons and geographies. The study also observes positive correlations between gross primary production and temperature, but these effects may vary between temperate and tropical ecosystems.
Article
Biotechnology & Applied Microbiology
Britta Lotstedt, Martin Strazar, Ramnik Xavier, Aviv Regev, Sanja Vickovic
Summary: This study presents a novel method called SHM-seq that captures tissue histology, RNA, and bacterial sequences simultaneously from tissues. Using this method, specific gene programs in gut cells related to host-microbe interactions were identified. This approach enhances the understanding of host-microbe interactions in health and disease.
NATURE BIOTECHNOLOGY
(2023)
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
Cell Biology
Aura Zelco, Vanja Borjesson, Jurrian K. de Kanter, Cristina Lebrero-Fernandez, Volker M. Lauschke, Eridan Rocha-Ferreira, Gisela Nilsson, Syam Nair, Pernilla Svedin, Mats Bemark, Henrik Hagberg, Carina Mallard, Frank C. P. Holstege, Xiaoyang Wang
Summary: The study provides a comprehensive transcriptional atlas of neonatal mouse meningeal leukocytes under normal conditions and after perinatal brain injury, highlighting the differences between neonatal and adult border-associated macrophages. The findings show the importance of meningeal leukocytes in early brain development and pathology, with implications for immune responses and inflammatory cascades after brain injury.
GENES & DEVELOPMENT
(2021)
Article
Neurosciences
Li Liang, Pengzheng Zhou, Chenfei Ye, Qi Yang, Ting Ma
Summary: Recent evidence suggests that white matter hyperintensities (WMHs) may contribute to cognitive dysfunction in Alzheimer's disease (AD) through their effects on brain networks. However, the vulnerability of specific neural connections related to WMHs in AD is not well understood. This study used a computational framework to assess the spatial-temporal patterns of WMH-related structural disconnectivity in AD. The results showed a specific pattern of brain disconnectome that predicted conversion from mild cognitive impairment (MCI) to dementia with high accuracy.
HUMAN BRAIN MAPPING
(2023)
Article
Biochemistry & Molecular Biology
Qi Liu, Chih-Yuan Hsu, Yu Shyr
Summary: The rapid growth of spatial omics technologies enables the profiling of genome-wide molecular events at molecular and single-cell resolution. SpaGene, a model-free method, is developed to discover spatial patterns rapidly in large-scale spatial omics studies. It outperforms existing methods in power and scalability, and is able to reconstruct unobserved tissue structures and discover ligand-receptor interactions through colocalization.
Article
Medicine, Research & Experimental
Daniel Kirschenbaum, Ehsan Dadgar-Kiani, Francesca Catto, Fabian F. Voigt, Chiara Trevisan, Oliver Bichsel, Hamid Shirani, K. Peter R. Nilsson, Karl J. Frontzek, Paolo Paganetti, Fritjof Helmchen, Jin Hyung Lee, Adriano Aguzzi
Summary: This study mapped the regional and temporal specificity of different anti-A beta treatments and found a striking dependence on the location and maturity of A beta plaques. Polythiophenes emerged as a potent anti-A beta compound.
EMBO MOLECULAR MEDICINE
(2023)
Article
Biology
Jiantao Guan, Zhenyu Wang, Shaoshuai Liu, Xingchen Kong, Fang Wang, Guoliang Sun, Shuaifeng Geng, Long Mao, Peng Zhou, Aili Li
Summary: This study provides a time-series transcriptome profile of developing wheat grain, revealing dynamic expressions of genes related to cell division, starch biosynthesis, and hormone metabolism. The study also identifies unbalanced expression patterns in genes involved in pivotal metabolic pathways. These findings deepen our understanding of wheat grain development and can contribute to improving wheat yield.
Article
Multidisciplinary Sciences
Shany Nivinsky Margalit, Hamutal Slovin
Summary: Optostimulation and electrical microstimulation are well-established techniques for artificial brain stimulation. However, there is less known about the activation patterns evoked by optostimulation compared to microstimulation. This study applied optostimulation and microstimulation in the barrel cortex of anesthetized rats and measured the membrane potential of neuronal populations using voltage-sensitive dye imaging. The results showed that longer optostimulation pulses evoked stronger and more widespread neural responses, and the effects of optostimulation depended on the expression time of opsins. Additionally, the spatial activation patterns of optostimulation were more similar to microstimulation in the long expression time condition.
SCIENTIFIC REPORTS
(2023)
Article
Computer Science, Artificial Intelligence
Jianwen Xie, Song-Chun Zhu, Ying Nian Wu
Summary: Video sequences contain rich dynamic patterns, and can be modeled and synthesized using an energy-based spatial-temporal generative ConvNet. The model can be learned from training video sequences and synthesize realistic dynamic patterns. The model is capable of handling incomplete training sequences and performing pattern completion simultaneously.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2021)
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
Cell Biology
Tiziana Sanavia, Chen Huang, Elisabetta Manduchi, Yanwen Xu, Prasanna K. Dadi, Leah A. Potter, David A. Jacobson, Barbara Di Camillo, Mark A. Magnuson, Christian J. Stoeckert, Guoqiang Gu
Summary: The study analyzed the global gene expression dynamics across six beta-cell developmental stages in mice, revealing the timing of important biological processes such as beta-cell developmental pathway deregulation, activation of molecular machineries for vesicle biosynthesis and transport, and glucose-induced Ca2+ influx. Temporal gene expression patterns were correlated with experimental GSIS, calcium influx, and insulin granule formation data, providing insights into the molecular components and biological mechanisms driving beta-cell maturation at different temporal stages. The findings suggest that genes associated with calcium-mediated processes show increased expression across beta-cell stages, indicating the temporal acquisition of proper GSIS.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Yen-Fu Chen, Hsiu-Chuan Lin, Kai-Neng Chuang, Chih-Hsu Lin, Hsueh-Chi S. Yen, Chen-Hsiang Yeang
PLOS COMPUTATIONAL BIOLOGY
(2017)
Article
Biotechnology & Applied Microbiology
Zing Tsung-Yeh Tsai, Huai-Kuang Tsai, Jen-Hao Cheng, Chih-Hsu Lin, Yuan-Fan Tsai, Daryi Wang
Article
Biotechnology & Applied Microbiology
Krishna B. S. Swamy, Chih-Hsu Lin, Ming-Ren Yen, Chuen-Yi Wang, Daryi Wang
Article
Biotechnology & Applied Microbiology
Chih-Hsu Lin, Zing Tsung-Yeh Tsai, Daryi Wang
Article
Biochemical Research Methods
Chih-Hsu Lin, Daniel M. Konecki, Meng Liu, Stephen J. Wilson, Huda Nassar, Angela D. Wilkins, David F. Gleich, Olivier Lichtarge
Article
Biochemical Research Methods
Minh Pham, Stephen Wilson, Harikumar Govindarajan, Chih-Hsu Lin, Olivier Lichtarge
Article
Biochemical Research Methods
Chih-Hsu Lin, Olivier Lichtarge
Summary: BioVNN, utilizing pathway knowledge, outperforms traditional neural networks in predicting cancer dependencies with faster convergence, and offers explainable dependency predictions by correlating with neuron output states.