Article
Biochemical Research Methods
Benjamin A. Neely, Michael G. Janech, M. Brock Fenton, Nancy B. Simmons, Alison M. Bland, Daniel J. Becker
Summary: Bats are increasingly studied for their longevity model systems and their natural host abilities with virulent viruses. This study demonstrated the use of proteomics to overcome limitations in characterizing immune mechanisms of viral tolerance and quantifying infection dynamics in wild bats. By analyzing the serum proteome of vampire bats, the study identified various immunological and viral proteins, providing insights for wildlife immunology and pathogen surveillance.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Niema Moshiri, Tajana Rosing
Summary: Driven by technological advances, mass spectrometry (MS) proteomics experiments have greatly improved in throughput and cost. Spectral library searching is commonly used for annotating experimental mass spectra, but it has the disadvantage of only identifying known peptides. Open modification searching (OMS) is an increasingly popular approach to annotate modified peptides, but it suffers from large search spaces and long runtimes.
Article
Biochemical Research Methods
Chris D. McGann, William D. Barshop, Jesse D. Canterbury, Chuwei Lin, Wassim Gabriel, Jingjing Huang, David Bergen, Vlad Zabrouskov, Rafael D. Melani, Mathias Wilhelm, Graeme C. McAlister, Devin K. Schweppe
Summary: Sample multiplexed quantitative proteomics assays have improved instrument efficiency and quantitative accuracy through the development of intelligent data acquisition (IDA) strategies. The implementation of a real-time spectral library searching (RTLS) workflow enables intelligent scan triggering and peak selection in milliseconds, leading to improved quantitation of multiplexed samples. The RTLS method expands the IDA toolbox and allows for more efficient and accurate analysis of molecular phenotypes.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Brian C. Searle, Ariana E. Shannon, Damien Beau Wilburn
Summary: Scribe is a new library search engine that uses deep learning fragmentation prediction software to predict fragmentation and retention times for peptides in a FASTA database, outperforming traditional database searching tools in terms of sensitivity and quantitative precision.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Computer Science, Artificial Intelligence
Qianen He, Huisheng Zhang, Zhiqiang Mei, Xiuying Xu
Summary: Timely detection of swimming accidents is crucial for ensuring the safety of infants in pools. However, there is a lack of efficient, accurate, and comprehensive solutions for detecting infant drowning, due to the small and densely-distributed targets in complicated environments. To address this issue, a novel intelligent real-time framework using attention mechanism-integrated YOLOv5 and Single Shot Multi-box Detector (SSD) is proposed. Experimental results demonstrate that the framework achieves a Mean Average Precision (mAP) of 97.17% and a processing speed of 43 frames per second, surpassing previous networks and showing significant practical application value in infant drowning detection.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Ergonomics
Ananya Roy, Moinul Hossain, Yasunori Muromachi
Summary: The study introduces a real-time variable speed limit (VSL) system for urban expressways to improve safety, using a real-time crash prediction model (RTCPM) to assess crash risk and adjust traffic conditions. By employing a cell transmission model (CTM) and a dynamic Bayesian network (DBN), the proposed system reduced crash risk by 19% in busy segments of the Tokyo Metropolitan Expressway after several iterations.
ACCIDENT ANALYSIS AND PREVENTION
(2022)
Article
Biology
Koji Yonekura, Saori Maki-Yonekura, Hisashi Naitow, Tasuku Hamaguchi, Kiyofumi Takaba
Summary: This study introduces a machine learning-based real-time object locator yoneoLocr, which can rapidly and accurately locate carbon holes and crystals, facilitating automated single particle analysis or cryo-electron crystallography data collection.
COMMUNICATIONS BIOLOGY
(2021)
Article
Engineering, Chemical
Jianqin Zheng, Jian Du, Yongtu Liang, Bohong Wang, Miao Li, Qi Liao, Ning Xu
Summary: To improve the transport of different oil products and minimize contamination, a hybrid intelligent framework is proposed to track the real-time batch interface of multi-product pipelines. The framework includes a batch injection judgment module and a volume calculation model to accurately determine the location of each batch interface. A self-learning modified model is also introduced to compensate for tracking errors. The proposed model is verified using a real-world multi-product pipeline network in China and shows better performance compared to other methods.
CHEMICAL ENGINEERING RESEARCH & DESIGN
(2023)
Article
Computer Science, Artificial Intelligence
Ehsan Malekipour, Hazim El-Mounayri, Devon Hagedorn-Hansen
Summary: In this paper, a novel online thermography and closed-loop hybrid-control approach is introduced to modify the scan strategy in metal PBF real-time. The approach utilizes mathematical models to optimize printing sequence and uses artificial neural network to optimize energy density in order to control temperature distribution and mitigate thermal anomalies.
JOURNAL OF INTELLIGENT MANUFACTURING
(2023)
Article
Telecommunications
Huiyuan Fu, Jun Guan, Feng Jing, Chuanming Wang, Huadong Ma
Summary: This paper presents a new approach for intelligent traffic transportation in intelligent vehicular networks, focusing on collecting vehicles' information for autonomous driving. The proposed multi-vehicle tracking framework consists of three modules: detection, association, and miss-detected vehicle tracking, which have been proven effective through extensive experiments.
CHINA COMMUNICATIONS
(2021)
Article
Thermodynamics
Ningkang Yang, Shumin Ruan, Lijin Han, Hui Liu, Lingxiong Guo, Changle Xiang
Summary: This paper proposes a real-time energy management strategy for hybrid electric vehicles by incorporating reinforcement learning in a model predictive control framework. The strategy addresses the drawbacks of reinforcement learning and improves the real-time performance. The proposed strategy is compared with other methods, demonstrating its performance and adaptability, which is further validated through hardware-in-the-loop testing.
Article
Engineering, Electrical & Electronic
Chaoyang Zhang, Juchen Zhang, Weixi Ji, Wei Peng
Summary: Analyzing energy consumption and efficiency of machining processes in discrete manufacturing job shops is a significant challenge. This paper proposes a real-time energy consumption characteristic analysis method in intelligent workshops, which provides decision basis for energy data processing and energy-saving control.
Article
Biochemical Research Methods
Benjamin Furtwangler, Nil Uresin, Khatereh Motamedchaboki, Romain Huguet, Daniel Lopez-Ferrer, Vlad Zabrouskov, Bo T. Porse, Erwin M. Schoof
Summary: Improving global proteome characterization in single-cell proteomics is crucial, and this study demonstrates the effectiveness of real-time search and a new acquisition strategy in enhancing quantitative accuracy and proteome coverage.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Multidisciplinary Sciences
Isha Berry, Meghan O'Neill, Shelby L. Sturrock, James E. Wright, Kamal Acharya, Gabrielle Brankston, Vinyas Harish, Kathy Kornas, Nika Maani, Thivya Naganathan, Lindsay Obress, Tanya Rossi, Alison E. Simmons, Matthew Van Camp, Xiao Xie, Ashleigh R. Tuite, Amy L. Greer, David N. Fisman, Jean-Paul R. Soucy
Summary: The COVID-19 pandemic has highlighted the importance of real-time, open-access epidemiological information. In Canada, a volunteer-driven working group was established to collect and curate COVID-19 data at a sub-national scale, providing a reliable resource for researchers, journalists, and the general public.
Article
Chemistry, Analytical
Joana Costa, Catarina Silva, Miguel Santos, Telmo Fernandes, Sergio Faria
Summary: The use of intelligent data analytics system for swimmer performance, integrating wearable sensors and online pattern recognition, enables real-time feedback and support for coaches and swimmers, resulting in improved training outcomes. The experiments demonstrate the effectiveness of the proposed framework in monitoring swimmers' performance and providing immediate feedback based on real-time data analysis, with a Random Forest classifier achieving a macro-averaged F-1 of 95.02%.
Article
Cardiac & Cardiovascular Systems
Tatiana Kudryashova, Swati Dabral, Sreenath Nayakanti, Arnab Ray, Dmitry A. Goncharov, Theodore Avolio, Yuanjun Shen, Analise Rode, Andressa Pena, Lifeng Jiang, Derek Lin, Jeffrey Baust, Timothy N. Bachman, Johannes Graumann, Clemens Ruppert, Andreas Guenther, Mario Schmoranzer, Yann Grobs, Sarah Eve Lemay, Eve Tremblay, Sandra Breuils-Bonnet, Olivier Boucherat, Ana L. Mora, Horace DeLisser, Jing Zhao, Yutong Zhao, Sebastien Bonnet, Werner Seeger, Soni S. Pullamsetti, Elena A. Goncharova
Summary: This study uncovers a novel proproliferative/prosurvival role of MST1/2 in pulmonary arterial hypertension (PAH), which is mediated by interactions with IL-6 and BUB3, leading to abnormal proliferation and survival of pulmonary arterial vascular smooth muscle cells and pulmonary arterial adventitial fibroblasts. These findings suggest potential new target pathways for therapeutic intervention in PAH.
CIRCULATION RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Oleg Klykov, Mykhailo Kopylov, Bridget Carragher, Albert J. R. Heck, Alex J. Noble, Richard A. Scheltema
Summary: Combining diverse experimental methods, such as cryo-EM/ET and MS, allows for the construction of comprehensive molecular encyclopedias of biological systems. This approach provides valuable insights into protein structure and interactome determination.
Article
Biology
Danni A. Gadd, Robert F. Hillary, Daniel L. McCartney, Shaza B. Zaghlool, Anna J. Stevenson, Yipeng Cheng, Chloe Fawns-Ritchie, Cliff Nangle, Archie Campbell, Robin Flaig, Sarah E. Harris, Rosie M. Walker, Liu Shi, Elliot M. Tucker-Drob, Christian Gieger, Annette Peters, Melanie Waldenberger, Johannes Graumann, Allan F. McRae, Ian J. Deary, David J. Porteous, Caroline Hayward, Peter M. Visscher, Simon R. Cox, Kathryn L. Evans, Andrew M. McIntosh, Karsten Suhre, Riccardo E. Marioni
Summary: This study explores the relationship between DNA methylation and incident diseases using epigenome-wide data. By training and testing epigenetic scores, the researchers identified scores that are associated with various diseases. These scores can serve as valuable resources for disease prediction and risk stratification.
Article
Oncology
Mohamad K. Hammoud, Raimund Dietze, Jelena Pesek, Florian Finkernagel, Annika Unger, Tim Bieringer, Andrea Nist, Thorsten Stiewe, Aditya M. Bhagwat, Wolfgang Andreas Nockher, Silke Reinartz, Sabine Muller-Brusselbach, Johannes Graumann, Rolf Mueller
Summary: Survival of ovarian carcinoma is associated with immunosuppressed tumor-associated macrophages and high levels of arachidonic acid in the tumor microenvironment. The high expression of CD163 and CD206 in macrophages leads to an inhibition of cytokine signaling, which is further exacerbated by the presence of arachidonic acid. These findings may contribute to the development of new therapeutic approaches.
MOLECULAR ONCOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Michelle L. Woods, Astrid Weiss, Anna M. Sokol, Johannes Graumann, Thomas Boettger, Antje M. Richter, Ralph T. Schermuly, Reinhard H. Dammann
Summary: Silencing of the AATK gene has been observed in various cancers and is associated with decreased patient survival. In this study, we found that DNA methyltransferase inhibitors can reactivate AATK, while epigenetic targeting inhibits its expression. We also discovered that AATK is a Ser/Thr kinase that phosphorylates TP53, and its kinase activity is important for growth suppression and regulation of cell cycle regulators. These findings suggest that AATK acts as an epigenetically inactivated tumor suppressor gene.
CANCER GENE THERAPY
(2022)
Article
Oncology
Suresh Sivakumar, Sonja Lieber, Damiano Librizzi, Corinna Keber, Leah Sommerfeld, Florian Finkernagel, Katrin Roth, Silke Reinartz, Joerg W. Bartsch, Johannes Graumann, Sabine Mueller-Bruesselbach, Rolf Mueller
Summary: Different forms of BCAM protein are associated with metastasis and poor prognosis in ovarian cancer. The soluble form of BCAM inhibits tumor cell adhesion and migration, but promotes the dispersion and invasion of tumor cell spheroids. These findings provide new insights for the treatment of ovarian cancer.
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Article
Cell Biology
Reem Alkhayer, Viviane Ponath, Miriam Frech, Till Adhikary, Johannes Graumann, Andreas Neubauer, Elke Pogge von Strandmann
Summary: This study identifies the transcription factor KLF4 as associated with the MICA promoter, and demonstrates that pharmacological activation of KLF4 leads to increased expression of MICA in AML cells. The small compound APTO253, which activates KLF4, also inhibits MYC expression and causes DNA damage in AML cells. The induction of MICA expression renders AML cells more susceptible to NK cell-mediated killing, suggesting a potential therapeutic approach for targeting AML cells.
CELL COMMUNICATION AND SIGNALING
(2023)
Article
Multidisciplinary Sciences
Rui Li, Jingchen Shao, Young-June Jin, Haruya Kawase, Yu Ting Ong, Kerstin Troidl, Qi Quan, Lei Wang, Remy Bonnavion, Astrid Wietelmann, Francoise Helmbacher, Michael Potente, Johannes Graumann, Nina Wettschureck, Stefan Offermanns
Summary: The authors found that the protein FAT1, when present in endothelial cells, inhibits the growth and formation of new blood vessels by promoting degradation of two co-activators called YAP and TAZ. They showed that FAT1 interacts with an enzyme called Mind Bomb-2 (MIB2), which leads to the degradation of YAP and TAZ. Without FAT1, the levels of YAP and TAZ increase, leading to increased blood vessel growth. Their findings suggest that FAT1 and MIB2 play a critical role in regulating blood vessel formation.
NATURE COMMUNICATIONS
(2023)
Article
Medicine, General & Internal
Sara Voelkel, Thomas S. Tarawneh, Laura Sacher, Aditya M. Bhagwat, Ihab Karim, Hildegard I. D. Mack, Thomas Wiesmann, Bjoern Beutel, Joachim Hoyer, Christian Keller, Harald Renz, Andreas Burchert, Andreas Neubauer, Johannes Graumann, Chrysanthi Skevaki, Elisabeth K. M. Mack
Summary: This study found that COVID-19-ARDS patients who received Ruxolitinib treatment showed significant changes in the serum proteome, involving biological processes such as T-cell response, humoral immune response, and complement activation. In addition, Ruxolitinib regulates the NRF2 pathway and SARS-CoV-2 signaling.
FRONTIERS IN MEDICINE
(2023)
Article
Multidisciplinary Sciences
Aina Lluch, Jessica Latorre, Angela Serena-Maione, Isabel Espadas, Estefania Caballano-Infantes, Jose M. Moreno-Navarrete, Nuria Oliveras-Canellas, Wifredo Ricart, Maria M. Malagon, Alejandro Martin-Montalvo, Walter Birchmeier, Witold Szymanski, Johannes Graumann, Maria Gomez-Serrano, Elena Sommariva, Jose M. Fernandez-Real, Francisco J. J. Ortega
Summary: This study reveals that levels of Plakophilin-2 (PKP2) steadily increase during fat cell differentiation, but are compromised in the presence of inflammation. Expression of PKP2 in subcutaneous adipose tissue diminishes in patients with obesity and normalizes upon weight loss. The impaired PKP2 leads to cell cycle dysfunction and premature senescence in adipocytes.
NATURE COMMUNICATIONS
(2023)
Article
Cell & Tissue Engineering
Maria Angeles de Pedro, Esther Lopez, Francisco Manuel Gonzalez-Nuno, Maria Pulido, Veronica Alvarez, Ana Maria Marchena, Christian Preusser, Witold Szymanski, Elke Pogge von Strandmann, Johannes Graumann, Francisco Miguel Sanchez-Margallo, Javier G. G. Casado, Maria Gomez-Serrano
Summary: The study investigates the effects of different preconditioning conditions on the therapeutic potential of extracellular vesicles (EVs) released by menstrual blood-derived stromal cells (MenSCs). The results show that priming MenSCs under proinflammatory and hypoxic conditions alters the cargo proteome of EVs, leading to different therapeutic properties. This highlights the importance of further exploring and defining MSC-derived bioproducts.
STEM CELL RESEARCH & THERAPY
(2023)
Article
Respiratory System
Debby Ngo, Katherine A. Pratte, Claudia Flexeder, Hans Petersen, Hong Dang, Yanlin Ma, Michelle J. Keyes, Yan Gao, Shuliang Deng, Bennet D. Peterson, Laurie A. Farrell, Victoria M. Bhambhani, Cesar Palacios, Juweria Quadir, Lucas Gillenwater, Hanfei Xu, Claire Emson, Christian Gieger, Karsten Suhre, Johannes Graumann, Deepti Jain, Matthew P. Conomos, Russell P. Tracy, Xiuqing Guo, Yongmei Liu, W. Craig Johnson, Elaine Cornell, Peter Durda, Kent D. Taylor, George J. Papanicolaou, Stephen S. Rich, Jerome I. Rotter, Steven I. Rennard, Jeffrey L. Curtis, Prescott G. Woodruff, Alejandro P. Comellas, Edwin K. Silverman, James D. Crapo, Martin G. Larson, Ramachandran S. Vasan, Thomas J. Wang, Adolfo Correa, Mario Sims, James G. Wilson, Robert E. Gerszten, George T. O'Connor, R. Graham Barr, David Couper, Josee Dupuis, Ani Manichaikul, Wanda K. O'Neal, Yohannes Tesfaigzi, Holger Schulz, Russell P. Bowler
Summary: This study identifies and validates novel protein markers and pathways associated with lung function impairment in a diverse population. The findings highlight the potential for risk assessment and treatment of COPD based on these biomarkers.
ANNALS OF THE AMERICAN THORACIC SOCIETY
(2023)
Article
Medicine, Research & Experimental
Karla Rubio, Addi J. Romero-Olmedo, Pouya Sarvari, Guruprasadh Swaminathan, Vikas P. Ranvir, Diana G. Rogel-Ayala, Julio Cordero, Stefan Guenther, Aditi Mehta, Birgit Bassaly, Peter Braubach, Malgorzata Wygrecka, Stefan Gattenloehner, Achim Tresch, Thomas Braun, Gergana Dobreva, Miguel N. Rivera, Indrabahadur Singh, Johannes Graumann, Guillermo Barreto
Summary: A study revealed that non-canonical ITGB2 signaling activates EGFR and RAS/MAPK/ERK signaling in small cell lung cancer (SCLC), providing a potential target for therapy independent of EGFR mutations.
Article
Medicine, Research & Experimental
Kaire Ojasalu, Sonja Lieber, Anna M. Sokol, Andrea Nist, Thorsten Stiewe, Imke Bullwinkel, Florian Finkernagel, Silke Reinartz, Sabine Mueller-Bruesselbach, Robert Grosse, Johannes Graumann, Rolf Mueller
Summary: Lysophosphatidic acid (LPA) species accumulate in the ascites of ovarian high-grade serous cancer (HGSC) and are associated with short relapse-free survival. LPA supports metastatic spread of cancer cells by activating multiple signaling pathways. However, a systematic analysis of the LPA-regulated signal transduction network in ovarian cancer cells has not been reported.
Article
Multidisciplinary Sciences
Anna Mary Steitz, Clarissa Schroeder, Isabel Knuth, Corinna U. Keber, Leah Sommerfeld, Florian Finkernagel, Julia M. Jansen, Uwe Wagner, Sabine Muller-Bruesselbach, Thomas Worzfeld, Magdalena Huber, Vanessa M. Beutgen, Johannes Graumann, Elke Pogge von Strandmann, Rolf Mueller, Silke Reinartz
Summary: In ovarian high-grade serous carcinoma (HGSC), disruption of the protective peritoneal mesothelium is a crucial requirement for metastasis formation. This study discovered that tumor-associated NK cells induce TRAIL-dependent apoptosis in mesothelial cells via death receptors DR4 and DR5 when encountering activated T cells. The upregulation of TRAIL expression in NK cells and enhanced cytotoxicity towards mesothelial cells are primarily driven by T-cell-derived TNFa. Apoptotic mesothelial cells were found in the peritoneal fluid of HGSC patients, indicating a cooperative action of T and NK cells in breaching the mesothelial barrier.