Article
Pharmacology & Pharmacy
Jiyan Wang, Hongkai Chang, Meng Su, Huifang Zhao, Yaya Qiao, Yu Wang, Luqing Shang, Changliang Shan, Shuai Zhang
Summary: Network pharmacology, a novel approach utilizing bioinformatics to explore drug targets and interactions in cancer, provides insights into drug action and aids in drug discovery. This study utilized network pharmacology to investigate the role and mechanism of cinobufotalin in colon adenocarcinoma (COAD). The findings revealed that cinobufotalin inhibits the growth and proliferation of colon cancer cells and influences key networks involved in extracellular signal stimulation and transduction. Transcriptome sequencing results also indicated that cinobufotalin hinders the response of colon cancer cells to extracellular stimulation and induces cell apoptosis. Molecular docking further supported the potential of cinobufotalin as an anti-cancer therapeutic.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Elizabet Monteagudo-Cascales, Alvaro Ortega, Felix Velando, Bertrand Morel, Miguel A. Matilla, Tino Krell
Summary: Bacterial signal transduction systems are typically activated by the binding of signal molecules to receptor ligand binding domains (LBDs), such as the NIT LBD. The NIT domain is found in over 15,000 receptors from 30 bacterial phyla and 19 eukaryotic phyla, and it is a part of seven receptor families involved in transcription control, chemotaxis, or second messenger regulation.
MOLECULAR MICROBIOLOGY
(2023)
Article
Plant Sciences
Si-Yue Liu, Jin-Ge Xie, Xi-Wen Chen, De-Fu Chen
Summary: The possible mechanism by which Ds-26-16 gene regulates salt tolerance in Arabidopsis seedlings was revealed through phenotypic, physiological and proteomic analysis.
Review
Plant Sciences
Ning Li, Dejuan Euring, Joon Yung Cha, Zeng Lin, Mengzhu Lu, Li-Jun Huang, Woe Yeon Kim
Summary: Agriculture is heavily reliant on climate, making it vulnerable to climate change. High temperatures can lead to heat stress in plants, but plants have adaptive mechanisms involving plant hormones to cope with it.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Environmental Studies
Hongchang Hao, Zhe Ma, Anjian Wang, Wanli Xing, Hao Song, Pei Zhao, Jiangqiao Wei, Shuxian Zheng
Summary: Due to its importance in clean energy transition and low carbon economy, lithium is considered a critical mineral by many countries. International trade plays a crucial role in supplying lithium resources to consuming countries due to the uneven distribution and separation of production capacity. The robustness of the global lithium trading network system (LTNS) was analyzed under random and malicious attacks, revealing its vulnerabilities and the impact of key countries such as Australia, Chile, and China. This study provides valuable insights for policymakers to enhance the supply security of strategic raw materials.
Article
Microbiology
Ruojun Wang, Weipeng Zhang, Wei Ding, Zhicong Liang, Lexin Long, Wai Chuen Wong, Pei-Yuan Qian
Summary: This study analyzed signal transduction genes in marine biofilms and seawater microbial metagenomes, and found that the abundance of signal transduction-related genes in biofilm microbial communities was significantly higher than in seawater microbial communities. In addition, the dominant source microbes of signal transduction genes in marine biofilms were different from those in seawater samples. Co-occurrence network analysis revealed potential inter-phyla interactions between microorganisms from marine biofilms and seawater microbial communities.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Eshan Sharma, Akanksha Bhatnagar, Avantika Bhaskar, Susmita M. Majee, Martin Kieffer, Stefan Kepinski, Paramjit Khurana, Jitendra P. Khurana
Summary: The rice FB protein-coding gene OsFBX257 is differentially expressed under drought conditions and other abiotic stresses. It plays a significant role in modulating root architecture and improving drought stress tolerance in rice. OsFBX257 is a potential breeding target for alleviating drought stress-induced damage in rice.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Computer Science, Information Systems
Tianpei Xu, Ying Ma
Summary: With the advancement of 5G technology, the efficiency and security of signal modulation and demodulation in wireless communication systems become increasingly important. In this study, a classification network based on signal-to-noise ratio is proposed to enhance automatic modulation classification recognition. Experimental results show that the algorithm performs exceptionally well, achieving an accuracy of 81.6% when the modulation signal is 18 dB.
Article
Meteorology & Atmospheric Sciences
Robert C. Gilliam, Jerold A. Herwehe, O. Russell Bullock, Jonathan E. Pleim, Limei Ran, Patrick C. Campbell, Hosein Foroutan
Summary: The U.S. EPA is using advanced meteorological modeling to develop an air quality modeling system for global to local consistency. By coupling the CMAQ modeling system within the MPAS global model, they are able to explore chemical transport modeling from global to local scales. MPAS compares well with WRF over the conterminous United States and shows potential for further improvements.
JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES
(2021)
Article
Medicine, General & Internal
Pindong Chen, Kun Zhao, Han Zhang, Yongbin Wei, Pan Wang, Dawei Wang, Chengyuan Song, Hongwei Yang, Zengqiang Zhang, Hongxiang Yao, Yida Qu, Xiaopeng Kang, Kai Du, Lingzhong Fan, Tong Han, Chunshui Yu, Bo Zhou, Tianzi Jiang, Yuying Zhou, Jie Lu, Ying Han, Xi Zhang, Bing Liu, Yong Liu
Summary: Using fMRI, researchers have found significant changes in global signal (GS) topography in patients with Alzheimer's disease (AD), which are associated with cognitive decline. These changes may disrupt functional network properties and are related to pathways associated with AD and neurodegenerative diseases.
Review
Medicine, General & Internal
Mohammad Reza Haeri
Summary: This study summarizes the molecular mechanisms involved in insulin secretion, the pathology of the insulin signaling pathway, and the mechanisms of drug interventions for hyperglycemia.
JOURNAL OF RESEARCH IN MEDICAL SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Archana Singh, Sahil Mehta, Sunita Yadav, Garima Nagar, Rajgourab Ghosh, Amit Roy, Amrita Chakraborty, Indrakant K. Singh
Summary: With the development of human civilization and global climate change, plants are exposed to a complex set of abiotic stresses, including oxidative stress. In this scenario, plants respond to these stresses through interaction between signaling molecules and maintain the balance of oxidative substances through antioxidants and enzymes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Anam Arif, Ameer A. Alameri, Umer Bin Tariq, Shakeel Ahmed Ansari, Hader Ibrahim Sakr, Maytham T. Qasim, Fadhil F. M. Aljoborae, Andres Alexis Ramirez-Coronel, Hijran Sanaan Jabbar, Gamal A. Gabr, Rasoul Mirzaei, Sajad Karampoor
Summary: Currently, cancer is the second leading cause of death worldwide, and the burden of cancer continues to increase. Understanding the molecular pathways involved in cancer initiation and development may lead to new treatments. Recent research suggests that TRIB3 plays a significant role in oncogenesis in various types of cancer.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Article
Microbiology
Zhichao Jiang, Zijia Lin, Qi Gan, Pengju Wu, Xuemei Zhang, Yuanxi Xiao, Qunxin She, Jinfeng Ni, Yulong Shen, Qihong Huang
Summary: Protein phosphorylation and its recognition by forkhead-associated (FHA) domain proteins play important roles in signal transduction in mammals. However, the functions of FHA proteins, especially in DNA damage response (DDR), in prokaryotes and archaea are less known. By studying an FHA protein (SisArnA) from an archaeon, it was found that SisArnA and its phosphorylated partner SisArnB repress the transcription of pili genes and facilitate DNA exchange and repair. SisArnA also regulates the expression of several genes involved in DDR, suggesting that the FHA/phosphorylation module may be an important signal transduction pathway in archaeal DDR.
Article
Physics, Multidisciplinary
Tatsuaki Tsuruyama
Summary: This study employed queuing network (QN) theory to model cell signal transduction and determined the process of signal transduction by analyzing the queuing and exchange of signal mediators in the cytoplasm. Experimental evidence supported the use of this method as a novel framework for analyzing signal transduction.
Article
Neurosciences
Michael Schoen, Anastasia Nosanova, Christian Jacob, Johann Michael Kraus, Hans A. Kestler, Benjamin Mayer, Simone Feldengut, Katrin Amunts, Kelly Del Tredici, Tobias M. Boeckers, Heiko Braak
Summary: The entorhinal cortex (EC) plays a crucial role in sensory data evaluation and processing for long-term memory consolidation. This study found that the presence of cellular islands in the pre-alpha layer of the EC is strongly related to cortical folding, brain and body weight, and neopallial volume. The absence of these cellular islands in lissencephalic cases suggests a potential role in the pathomechanism of developmental brain disorders.
JOURNAL OF COMPARATIVE NEUROLOGY
(2022)
Article
Statistics & Probability
Sarah Friedrich, Gerd Antes, Sigrid Behr, Harald Binder, Werner Brannath, Florian Dumpert, Katja Ickstadt, Hans A. Kestler, Johannes Lederer, Heinz Leitgob, Markus Pauly, Ansgar Steland, Adalbert Wilhelm, Tim Friede
Summary: Statistics plays a significant role in both the theoretical and practical understanding of artificial intelligence (AI) and in its future development. It contributes to methodological development, planning and design of studies, assessment of data quality and data collection, differentiation of causality and associations, as well as evaluation of uncertainty in results. Integrating statistical aspects into AI teaching is crucial for schools and universities.
ADVANCES IN DATA ANALYSIS AND CLASSIFICATION
(2022)
Article
Biochemistry & Molecular Biology
Astrid K. Laut, Carmen Dorneburg, Axel Furstberger, Thomas F. E. Barth, Hans A. Kestler, Klaus-Michael Debatin, Christian Beltinger
Summary: CHD5, a tumor suppressor located at 1p36, is frequently lost or silenced in aggressive neuroblastoma and many adult cancers. Low expression of CHD5 is associated with stage 4 neuroblastoma and its forced expression inhibits key aspects of the metastatic cascade in vitro. Overexpression of CHD5 leads to reduced metastasis-related genes and gene sets, while known metastasis-suppressing genes are upregulated. Additionally, knockdown of PLCL1 and p53 reverses CHD5-induced inhibition of invasion and migration in vitro.
Article
Chemistry, Multidisciplinary
Peter Bellmann, Ludwig Lausser, Hans A. Kestler, Friedhelm Schwenker
Summary: Ordinal classification is a sub-discipline of multi-class classification where classes have an ordinal structure. It finds applications in various fields, including medicine. While the field has seen enhancements, there is a lack of a common mathematical definition for ordinal classification tasks. This research presents a general approach for defining ordinal class structures based on the corresponding feature space.
APPLIED SCIENCES-BASEL
(2022)
Article
Oncology
Mareike Waldenmaier, Lucas Schulte, Jonathan Schoenfelder, Axel Fuerstberger, Johann M. Kraus, Nora Daiss, Tanja Seibold, Mareen Morawe, Thomas J. Ettrich, Hans A. Kestler, Christoph Kahlert, Thomas Seufferlein, Tim Eiseler
Summary: PDAC has a poor prognosis, but personalized medicine and liquid biopsies may improve treatment outcomes through DNA profiling and actionable variant prediction. EvDNA shows advantages over cfDNA in SNV detection, suggesting potential for optimized treatment strategies.
Article
Cell Biology
Jana Krueger, Markus Breunig, Lino Pascal Pasquini, Mareen Morawe, Alexander Gross, Frank Arnold, Ronan Russell, Thomas Seufferlein, Ninel Azoitei, Hans A. Kestler, Cecile Julier, Sandra Heller, Meike Hohwieler, Alexander Kleger
Summary: In this study, human pluripotent stem cells were used to identify novel genes involved in early endodermal development. The findings provide important insights into human development and disease models.
Letter
Biochemical Research Methods
Felix M. Weidner, Julian D. Schwab, Silke D. Werle, Nensi Ikonomi, Ludwig Lausser, Hans A. Kestler
Article
Clinical Neurology
Sonja Schoenecker, Verena Hoffmann, Fady Albashiti, Reinhard Thasler, Marlien Hagedorn, Marie-Luise Louiset, Anna Kopczak, Jennifer Roesler, Enayatullah Baki, Silke Wunderlich, Florian Kohlmayer, Klaus Kuhn, Martin Boeker, Johannes Tuennerhoff, Sven Poli, Ulf Ziemann, Oliver Kohlbacher, Katharina Althaus, Susanne Mueller, Albert Ludolph, Hans A. Kestler, Ulrich Mansmann, Marianne Dieterich, Lars Kellert
Summary: This study aims to validate a prediction score for the 3-month functional outcome after juvenile stroke or transient ischemic attack (TIA) in a multi-center observational cohort study. The prediction score has been derived from a retrospective analysis and will be compared to observed clinical outcomes. The importance of this study lies in its potential to personalize counseling and treatment for juvenile stroke patients.
Article
Computer Science, Interdisciplinary Applications
Matthias Ganzinger, Max Blumenstock, Axel Fuerstberger, Leonard Greulich, Hans A. Kestler, Michael Marschollek, Christian Niklas, Tim Schneider, Cord Spreckelsen, Erik Tute, Julian Varghese, Martin Dugas
Summary: Structured documentation of findings is important in clinical research and patient care. Integration of electronic case report forms (eCRF) with electronic health records (EHR) is challenging when researchers from different institutions collaborate. To address this issue, a novel architecture for a federated electronic data capture system (fEDC) was proposed.
JOURNAL OF BIOMEDICAL INFORMATICS
(2023)
Article
Virology
Alan Bareiss, Gunalp Uzun, Marco Mikus, Matthias Becker, Karina Althaus, Nicole Schneiderhan-Marra, Axel Fuerstberger, Julian D. D. Schwab, Hans A. A. Kestler, Martin Holderried, Peter Martus, Katja Schenke-Layland, Tamam Bakchoul
Summary: This study investigates self-reported side effects after COVID-19 vaccination and finds that the frequency of local and systemic side effects differs significantly between mRNA and vector-based vaccines, and is associated with vaccine type, age, and gender.
Article
Medicine, General & Internal
Una Ebong, Susanne Martina Buettner, Stefan A. Schmidt, Franziska Flack, Patrick Korf, Lynn Peters, Beate Gruener, Steffen Stenger, Thomas Stamminger, Hans Kestler, Meinrad Beer, Christopher Kloth
Summary: This study implemented an AI-based software prototype for the detection of COVID-19 pneumonia and differentiation between other types of pneumonia in lung CT datasets. The software achieved a sensitivity of 80.8% and a specificity of 50% for detecting COVID-19, but the human radiologist achieved a higher specificity of 97.2%.
Article
Computer Science, Artificial Intelligence
Felix M. Weidner, Julian D. Schwab, Sabine Woelk, Felix Rupprecht, Nensi Ikonomi, Silke D. Werle, Steve Hoffmann, Michael Kuehl, Hans A. Kestler
Summary: The dynamics of cellular mechanisms can be studied through network analysis. Logic-based models are a popular and simple modeling strategy, but their simulation complexity grows exponentially instead of linearly with the number of nodes. This study applies logic modeling to quantum computing to simulate cellular networks and demonstrates the benefits, such as complexity reduction and quantum algorithms for systems biology tasks. A model of mammalian cortical development is implemented to showcase the applicability of this approach, and results from quantum processing units and a noisy simulator are presented, along with discussions on current technical challenges.
Article
Computer Science, Interdisciplinary Applications
Axel Fuerstberger, Nensi Ikonomi, Angelika M. R. Kestler, Ralf Marienfeld, Julian D. Schwab, Peter Kuhn, Thomas Seufferlein, Hans A. Kestler
Summary: AMBAR is an interactive web application developed to support personalized decision-making in Molecular Tumor Boards (MTBs), improving the analysis and documentation of patients' data for therapeutic interventions.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2023)
Article
Cell Biology
Gaojie Zhu, Fatima Khalid, Danhui Zhang, Zhouli Cao, Pallab Maity, Hans A. Kestler, Donata Orioli, Karin Scharffetter-Kochanek, Sebastian Iben
Summary: Mutations in various genes can cause the childhood disorder TTD, which is classified as a DNA repair disease or a transcription syndrome. Knockout/knockdown of TTDN1 and RNF113A resulted in consistent effects on ribosomal biogenesis and performance. Interference with these TTD factors led to downregulation of RNA polymerase I transcription, disrupted rRNA processing, reduced rRNA 18S backbone, impaired protein translation decoding, and accumulation of misfolded and carbonylated proteins, suggesting loss of protein homeostasis. This study proposes that ribosomal dysfunction is a common underlying mechanism in TTD.
Article
Biochemical Research Methods
Felix M. Weidner, Mirko Rossini, Joachim Ankerhold, Hans A. Kestler
Summary: This article presents a protocol for implementing Boolean network dynamics as quantum circuits. It provides steps for accessing cloud-based quantum processing units offered by IBM and IonQ, parsing logic for gene regulatory networks, performing simulations of quantum circuits on local devices, and visualizing measurement results. For complete details on the use and execution of this protocol, please refer to Weidner et al.1.