Article
Multidisciplinary Sciences
Bowen Wang, Zhiheng Zhao, Michael Xiong, Rui Yan, Ke Xu
Summary: The endoplasmic reticulum (ER) is a versatile organelle with distinct forms of tubules, regulated by Rtn4 and Climp63, that together form a ribbon-like structure of well-defined width.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Microbiology
Ashley York
Summary: A recent study discovered that a small RNA released by the bioluminescent bacterium Vibrio fischeri can modulate crucial host responses in the Hawaiian bobtailed squid Euprymna scolopes, revealing a new mode of communication in beneficial animal-bacterial symbioses.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Oncology
Yilun Li, Li Ma
Summary: This study found a negative association between telomere length and the prognosis of breast cancer, particularly with ER- breast cancer. However, no significant correlation was found between telomere length and the prognosis of ER+ breast cancer.
FRONTIERS IN ONCOLOGY
(2022)
Article
Engineering, Marine
Chunping Wang, Shidong Fan, Yunan Yao, Jie Wu, Bin Wang, Liangyan Zheng
Summary: This study proposes an operational safety evaluation methodology for a tanker's cargo oil system, which uses data features and error analysis techniques to improve performance. The method has been applied to the cargo pump system, reflecting actual task safety conditions and providing new insights for tanker corporations' operational safety management.
Article
Oncology
Enuo Liu, Fan Zhang, Tiansheng Xu, Luyi Ye, Sean Si Qian Ma, Zai-Si Ji
Summary: This study revealed the association between microbiota transcriptional activity in breast tumors and the expression of carcinogenesis genes in ER-negative breast cancer. Changes in the breast tissue microbiota influenced by external factors may be a key factor in ER-negative breast cancer.
Article
Biochemistry & Molecular Biology
Duojiao Chen, Taylor M. Parker, Poornima Bhat-Nakshatri, Xiaona Chu, Yunlong Liu, Yue Wang, Harikrishna Nakshatri
Summary: Chromatin accessibility is critically important for gene expression, and in estrogen receptor-positive breast cancer cells, estradiol induces changes in chromatin accessibility for a subset of relevant genes. The open chromatin regions associated with estrogen-induced gene expression are enriched with certain elements, while surprising findings show that many E2-inducible gene promoters and enhancers display a closed chromatin configuration. Integration of ATAC-seq data with ER alpha ChIP-seq data reveals the complexity of ER-E2 interactions with nucleosomes, showing that closed chromatin configuration does not necessarily mean lack of gene expression.
Article
Chemistry, Medicinal
Jung-Chang Kung, Wei-Hsun Wang, Yu-Ching Chiang, Yuan-Ting Yang-Wang, Yueh-Ching Wang, Wen-Cheng Chen, Chi-Jen Shih
Summary: The study aimed to evaluate the remineralization and antibacterial effect of silver-containing mesoporous bioactive glass (MBG-Ag) sealing combined with Er:YAG laser irradiation on human demineralized dentin. Results showed that both MBG-Ag and Er:YAG laser have the ability to enhance remineralization and hydroxyapatite crystal precipitation, with superior treatment outcomes when combined.
Article
Computer Science, Artificial Intelligence
Bin Xu, Shuai Li, Zhaowu Zhang, Tongxin Liao
Summary: This article proposes a BERT-PAGG relationship extraction model that integrates entity location information into local features and combines it with the entity vector representation output by BERT. The model uses segmented convolution neural network to integrate entity location information with local features, captures more effective semantic features using attention mechanism, and regulates the transmission of information flow through gating mechanism. Experimental results show that the proposed method achieves the best results compared to other models on two open Chinese relation extraction datasets. Ablation experiments also demonstrate the effectiveness of the PAGG module, with a minimum increase of 2.82% in the model's Macro-F1 value.
PEERJ COMPUTER SCIENCE
(2023)
Article
Genetics & Heredity
Cuifen Li, Manli Xie, Weiwei Wang, Yanyan Liu, Dan Liao, Jingwen Yin, Hao Huang
Summary: This study is the first and most comprehensive investigation of the association between ERs and depression in women, and the findings support the concept that ERs participate in the etiology of sex heterogeneity in depression.
FRONTIERS IN GENETICS
(2022)
Review
Geriatrics & Gerontology
Chenxuan Zhao, Yong Liao, Abdul Rahaman, Vijay Kumar
Summary: The aberrant buildup of misfolded/unfolded proteins in the endoplasmic reticulum (ER) leads to biological stress, which is a key factor in many human neurodegenerative diseases. The unfolded protein response (UPR) serves as an integrated signal transduction pathway to adapt cells to ER stress. Both ER stress and UPR are important in the pathogenesis of ALS and TDP-43 pathology. Studies on in vitro and in vivo models of ALS help to understand the complex interplay between ER stress and UPR, and explore therapeutic strategies for controlling ALS pathogenesis.
FRONTIERS IN AGING NEUROSCIENCE
(2022)
Article
Cell Biology
Junichi Inaba, Bo Min Kim, Yan Zhao, Andrew M. Jansen, Wei Wei
Summary: Phytoplasma infection disrupts ER homeostasis in tomato plants, leading to abnormal accumulation of ER-resident proteins, disrupted ER network structures, and formation of protein aggregates in the phloem. The ER stress and unfolded protein response (UPR) induced by Phytoplasma infection likely contribute to the host plant's defense mechanisms. Activation of UPR and induction of ER stress decrease phytoplasma titer, while suppression of the ER-resident protein BiP increases phytoplasma titer. Understanding the interactions between phytoplasmas and plant hosts at the subcellular level provides valuable insights for controlling phytoplasma diseases.
Article
Biology
Albert Perez-Marti, Suresh Ramakrishnan, Jiayi Li, Aurelien Dugourd, Martijn R. Molenaar, Luigi R. De la Motte, Kelli Grand, Anis Mansouri, Melanie Parisot, Soeren S. Lienkamp, Julio Saez-Rodriguez, Matias Simons
Summary: In diabetic patients, dyslipidemia is associated with organ damage such as diabetic kidney disease (DKD). A high-fat diet enriched with monounsaturated oleic acid (OA) was found to increase lipid storage in renal proximal tubular cells (PTCs) but cause less tubular damage compared to a butter diet with saturated palmitic acid (PA). The study identified endoplasmic reticulum (ER) stress as the main cause of PA-induced PTC injury and showed that OA can rescue cytotoxic effects by normalizing membrane order and promoting TAG and LD formation.
Article
Chemistry, Physical
Sitaram Ramakrishnan, Jinke Bao, Claudio Eisele, Bikash Patra, Minoru Nohara, Biplab Bag, Leila Noohinejad, Martin Tolkiehn, Carsten Paulmann, Achim M. Schaller, Toms Rekis, Surya Rohith Kotla, Andreas Schoenleber, Arumugam Thamizhavel, Bahadur Singh, Srinivasan Ramakrishnan, Sander van Smaalen
Summary: Ho2Ir3Si5 belongs to the family of 3D R2Ir3Si5 compounds. It exhibits a first-order charge-density-wave (CDW) transition accompanied by lattice distortion and superlattice reflections. The CDW is caused by Ir-Ir zigzag chains along c. Replacing Lu with magnetic Er or Ho decreases the CDW transition temperature. Ho2Ir3Si5 shows second-order superlattice reflections, indicating an anharmonic modulation wave. The CDW transition affects the magnetic moments of Ho3+ even in the paramagnetic state, and antiferromagnetic (AFM) ordering is suppressed in the single crystal.
CHEMISTRY OF MATERIALS
(2023)
Review
Biochemistry & Molecular Biology
Dong-Yong Hong, Dong-Hun Lee, Ji-Young Lee, Eun-Chae Lee, Sang-Won Park, Man-Ryul Lee, Jae-Sang Oh
Summary: This review summarizes the important role of low-density lipoprotein receptor in brain cholesterol metabolism and its association with cognitive deficits and neurodegenerative brain diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Eduardo Perez, Sebastian Ventura
Summary: Skin cancer, particularly melanoma, is a common and deadly disease. Recent attention has been given to automatic melanoma diagnosis from skin images within the machine learning community. While convolutional neural network models have been used to address this issue, they have limitations that hinder their application in real-world situations. The proposed Dynamic Routing between Capsules architecture aims to overcome these limitations and has shown promising results in outperforming existing models. Further research and validation are necessary to demonstrate the potential of this neural network architecture in other domains.
Meeting Abstract
Biophysics
Joseph E. Faust, Tanvi Desai, Avani Verma, Idil Ulengin, Tzu-Lin Sun, Tyler J. Moss, Miguel A. Betancourt-Solis, Huey W. Huang, Tina Lee, James A. McNew
BIOPHYSICAL JOURNAL
(2016)
Review
Genetics & Heredity
Julia N. Bailey, Christopher Patterson, Laurence de Nijs, Reyna M. Duron, Viet-Huong Nguyen, Miyabi Tanaka, Marco T. Medina, Aurelio Jara-Prado, Iris E. Martinez-Juarez, Adriana Ochoa, Yolli Molina, Toshimitsu Suzuki, Maria E. Alonso, Jenny E. Wight, Yu-Chen Lin, Laura Guilhoto, Elza Marcia Targas Yacubian, Jesus Machado-Salas, Andrea Daga, Kazuhiro Yamakawa, Thierry M. Grisar, Bernard Lakaye, Antonio V. Delgado-Escueta
GENETICS IN MEDICINE
(2017)
Article
Cell Biology
James B. Summerville, Joseph F. Faust, Ethan Fan, Diana Pendin, Andrea Daga, Joseph Formella, Michael Stern, James A. McNew
JOURNAL OF CELL SCIENCE
(2016)
Article
Cell Biology
Shiyu Xu, Michael Stern, James A. McNew
JOURNAL OF CELL SCIENCE
(2017)
Article
Multidisciplinary Sciences
Wenting Zhang, Wenjie Zheng, Yukimatsu Toh, Miguel A. Betancourt-Solis, Jiagang Tu, Yanlin Fan, Vikram N. Vakharia, Jun Liu, James A. McNew, Meilin Jin, Yizhi J. Tao
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Genetics & Heredity
Michael F. Wangler, Yu-Hsin Chao, Vafa Bayat, Nikolaos Giagtzoglou, Abhijit Babaji Shinde, Nagireddy Putluri, Cristian Coarfa, Taraka Donti, Brett H. Graham, Joseph E. Faust, James A. McNew, Ann Moser, Marco Sardiello, Myriam Baes, Hugo J. Bellen
Article
Cell Biology
Tatiana Trevisan, Diana Pendin, Aldo Montagna, Sergio Bova, Anna Maria Ghelli, Andrea Daga
Article
Biochemistry & Molecular Biology
Miguel A. Betancourt-Solis, Tanvi Desai, James A. McNew
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Cell Biology
Eleni N. Tsakiri, Sentiljana Gumeni, Konstantinos Vougas, Diana Pendin, Issidora Papassideri, Andrea Daga, Vassilis Gorgoulis, Gabor Juhasz, Luca Scorrano, Ioannis P. Trougakos
Article
Multidisciplinary Sciences
Javier Espadas, Diana Pendin, Rebeca Bocanegra, Artur Escalada, Giulia Misticoni, Tatiana Trevisan, Ariana Velasco del Olmo, Aldo Montagna, Sergio Bova, Borja Ibarra, Peter Kuzmin, Pavel Bashkirov, Anna Shnyrova, Vadim A. Frolov, Andrea Daga
NATURE COMMUNICATIONS
(2019)
Article
Physiology
Nicola Vajente, Rosa Norante, Nelly Redolfi, Andrea Daga, Paola Pizzo, Diana Pendin
FRONTIERS IN PHYSIOLOGY
(2019)
Article
Neurosciences
Aldo Montagna, Nicola Vajente, Diana Pendin, Andrea Daga
FRONTIERS IN NEUROSCIENCE
(2020)
Article
Multidisciplinary Sciences
Kevin van der Graaf, Saurabh Srivastav, Pratibha Singh, James A. McNew, Michael Stern
Summary: The phi C31 integrase system is commonly used for transgene targeting in Drosophila melanogaster. AttP40, one of the popular docking sites, has been found to cause larval muscle nuclear clustering and decreased msp-300 transcript levels in third instar larvae. Furthermore, certain transgenic RNAi insertions into attP40 can lead to pupal or adult inviability, infertility, or dominant nuclear clustering effects in specific genetic backgrounds. These findings highlight the importance of considering the effects of attP40 and its insertion derivatives in data interpretation from attP40-bearing flies.
Article
Cell Biology
Saurabh Srivastav, Kevin van der Graaf, Pratibha Singh, Alloysius Budi Utama, Matthew D. Meyer, James A. Mcnew, Michael Stern
Summary: This study using a Drosophila model found that the absence of atlastin protein leads to muscle issues and affects the autophagy pathway and MTOR signaling. Therefore, the research suggests that mutations in the ATL1/SPG3A gene may cause pathological changes in patients with HSP.
Article
Biochemistry & Molecular Biology
Michael Stern, James A. McNew
Summary: The study discusses the changes in signaling pathways and their impact on cell degeneration in neurodegenerative and muscle degeneration disorders. It was found that TOR kinase and AMPK show reciprocal changes in activity during degeneration, and oxidative stress response may be a key factor in degeneration.
MOLECULAR PSYCHIATRY
(2021)