Article
Automation & Control Systems
Gang Sun, Zhu Xu, Hongfang Yu, Victor Chang
Summary: This article focuses on efficiently provisioning online SFC requests in NFV with 6G, introducing an efficient OSFCD algorithm that optimizes multiple performance indicators of online SFC deployment.
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS
(2021)
Article
Computer Science, Software Engineering
Pengzhan Zhao, Zhongtao Miao, Shuhan Lan, Jianjun Zhao
Summary: This paper proposes Bugs4Q, a benchmark suite of forty-two real, manually validated Qiskit bugs from GitHub, StackOverflow, and Stack Exchange. Bugs4Q provides interfaces for accessing the buggy and fixed versions of Qiskit programs, facilitating reproducible empirical studies and comparisons of Qiskit program debugging and testing tools. Bugs4Q is publicly available at https://github.com/Z-928/Bugs4Q-Framework.
JOURNAL OF SYSTEMS AND SOFTWARE
(2023)
Article
Multidisciplinary Sciences
Chin Ken Wong, Rebecca Y. Lai, Martina H. Stenzel
Summary: Polymersomes, as polymeric analogues of liposomes, have unique physical and chemical properties. However, their translation into clinical or industrial applications has been limited. This study presents a continuous flow methodology for the production of near-monodisperse polymersomes at scale, allowing for downstream polymersome manipulation.
NATURE COMMUNICATIONS
(2023)
Editorial Material
Engineering, Electrical & Electronic
Gunes Karabulut Kurt, Angeles Vazquez-Castro, Ejder Bastug
Summary: Only 63% of the global population is connected to the internet, but the emerging low Earth orbit satellite networks have the potential to bridge the digital divide and provide equal access to the internet through global coverage.
IEEE COMMUNICATIONS MAGAZINE
(2022)
Article
Computer Science, Information Systems
Eduardo Guerra, Antonio De Oliveira Dias, Luiz Gustavo D. O. Veras, Ademar Aguiar, Joelma Choma, Tiago Silva Da Silva
Summary: The Adaptive Object Model (AOM) is an architectural style that allows domain entity types to be changed at runtime for higher flexibility. This study proposes a model to reuse frameworks designed for classic object-oriented domain models in an AOM application, by using dynamically-generated adapters for AOM entities. The research shows that the proposed model can successfully be employed to use AOM entities with frameworks that were not originally designed for AOM applications, reducing the effort needed to adopt an AOM architecture.
Article
Health Care Sciences & Services
Alistair Ward, Matt Velinder, Tonya Di Sera, Aditya Ekawade, Sabrina Malone Jenkins, Barry Moore, Rong Mao, Pinar Bayrak-Toydemir, Gabor Marth
Summary: The primary goal of precision genomics is to identify disease-causing genetic variants in sequencing data. Currently, these findings are typically returned as text-based reports, which can make collaboration and discussion difficult. In order to address this issue, clin.iobio is a web-based solution that integrates various tools and allows diagnostic team members to easily review and contribute to the diagnostic process. It provides comprehensive genomic analysis, including data quality review, gene prioritization based on phenotype, variant prioritization, and exportable findings summary.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Engineering, Multidisciplinary
Zakaria Benomar, Francesco Longo, Giovanni Merlino, Antonio Puliafito
Summary: Thanks to advancements in hardware and software, the Internet of Things (IoT) is now expanding its usage to smaller and resource-constrained devices. However, the current IoT ecosystem is still fragmented due to different vertical solutions being used. To address this interoperability issue, this paper suggests a Cloud-based approach with a Dynamic Domain Name System (DDNS) mechanism that enables IoT devices to communicate seamlessly using the REST model.
IEEE TRANSACTIONS ON NETWORK SCIENCE AND ENGINEERING
(2022)
Article
Computer Science, Hardware & Architecture
Aditya Dhananjay, Kai Zheng, Marco Mezzavilla, Lorenzo Iotti, Dennis Shasha, Sundeep Rangan
Summary: This paper introduces the calibration procedures of the Pi-Radio v1 software-defined radio platform, showing that accurate calibration can be achieved without relying on expensive laboratory equipment. The demonstration of beamforming indicates that the SDR nodes have been calibrated correctly.
Article
Environmental Sciences
E. Garcia-Calvo, P. Cabezas-Sanchez, J. L. Luque-Garcia
Summary: The widespread use of quantum dots has led to potential emerging contaminants, necessitating evaluation of their potential toxicity and impact. Studies have shown that CdSe/ZnS quantum dots induce hypoxia and ROS generation in hepatic cells, leading to apoptosis through the TDP-43 pathway, as well as causing serious neural and developmental problems in developing organisms.
Article
Biotechnology & Applied Microbiology
Chenyi Li, Yusong Zou, Tian Jiang, Jianli Zhang, Yajun Yan
Summary: Dynamic regulation at gene replication level was explored to control gene expression in this study, and it showed great potential in engineering biosynthesis of valuable compounds in metabolic engineering.
METABOLIC ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Nikolaos A. Papanikolaou, Marios Nikolaidis, Grigorios D. Amoutzias, Ariadni Fouza, Maria Papaioannou, Akhilesh Pandey, Athanasios G. Papavassiliou
Summary: This study reveals for the first time the global changes in arginine protein mono- or dimethylation in proliferating myoblasts and differentiated myocytes, identifying differentially methylated protein families, enriched protein domains, and novel short linear motifs. These findings may be crucial for understanding the links between differentiation and cancer growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Mark Owusu Adjei, Huan Zhao, Xiaoguang Tao, Li Yang, Shuyue Deng, Xiyan Li, Xinjing Mao, Shujiang Li, Jianfeng Huang, Ruixiong Luo, Aiping Gao, Jun Ma
Summary: This study optimized the conditions of the protoplast isolation and transformation system, which can provide a lot of help in the gene expression regulation study of mango.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Peiran Zhang, Joseph Rufo, Chuyi Chen, Jianping Xia, Zhenhua Tian, Liying Zhang, Nanjing Hao, Zhanwei Zhong, Yuyang Gu, Krishnendu Chakrabarty, Tony Jun Huang
Summary: This study introduces acoustoelectronic nanotweezers, which combine the precision of electronic tweezers with the large-field dynamic control of acoustic tweezers, demonstrating complex patterning of sub-100nm objects.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Thanga Bhuvanesh, Yan Nie, Rainhard Machatschek, Nan Ma, Andreas Lendlein
Summary: In this study, self-assembly of laminin-111 into ultrathin films at the air-water interface is investigated. The films exhibit self-healing, self-renewal, growth, and mechanical support capabilities. Furthermore, the assembly of laminin-111 on preformed collagen-IV sheets results in a bilayer mimicking the basal lamina. These findings contribute to the understanding of the assembly, maintenance, and functioning of complex material systems in natural tissues.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Microbiology
Natan Nagar, Noa Ecker, Gil Loewenthal, Oren Avram, Daniella Ben-Meir, Dvora Biran, Eliora Ron, Tal Pupko
Summary: The degradation of intracellular proteins in Gram-negative bacteria is regulated through various cellular processes and serves as a mechanism for quality control. By employing a quantitative pulsed-SILAC method followed by mass spectrometry analysis, this study identified fast-degrading novel proteins and developed a machine learning classifier to discriminate them from the rest of the proteome. These findings expand the understanding of protein degradation in bacteria and have implications for protein engineering, potentially aiding in the identification of new antibacterial drug targets.
Article
Biochemical Research Methods
John S. Ramsey, Elizabeth L. Chin, Juan D. Chavez, Surya Saha, Darya Mischuk, Jaclyn Mahoney, Jared Mohr, Faith M. Robison, Elizabeth Mitrovic, Yimin Xu, Susan R. Strickler, Noe Fernandez, Xuefei Zhong, MaryLou Polek, Kris E. Godfrey, James J. Giovannoni, Lukas A. Mueller, Carolyn M. Slupsky, James E. Bruce, Michelle Heck
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Alexander Leitner, Alexandre M. J. J. Bonvin, Christoph H. Borchers, Robert J. Chalkley, Julia Chamot-Rooke, Colin W. Combe, Juergen Cox, Meng-Qiu Dong, Lutz Fischer, Michael Gotze, Fabio C. Gozzo, Albert J. R. Heck, Michael R. Hoopmann, Lan Huang, Yasushi Ishihama, Andrew R. Jones, Nir Kalisman, Oliver Kohlbacher, Karl Mechtler, Robert L. Moritz, Eugen Netz, Petr Novak, Evgeniy Petrotchenko, Andrej Sali, Richard A. Scheltema, Carla Schmidt, David Schriemer, Andrea Sinz, Frank Sobott, Florian Stengel, Konstantinos Thalassinos, Henning Urlaub, Rosa Viner, Juan A. Vizcaino, Marc R. Wilkins, Juri Rappsilber
Article
Multidisciplinary Sciences
Mukul K. Midha, David S. Campbell, Charu Kapil, Ulrike Kusebauch, Michael R. Hoopmann, Samuel L. Bader, Robert L. Moritz
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Malte Herold, Susana Martinez Arbas, Shaman Narayanasamy, Abdul R. Sheik, Luise A. K. Kleine-Borgmann, Laura A. Lebrun, Benoit J. Kunath, Hugo Roume, Irina Bessarab, Rohan B. H. Williams, John D. Gillece, James M. Schupp, Paul S. Keim, Christian Jaeger, Michael R. Hoopmann, Robert L. Moritz, Yuzhen Ye, Sujun Li, Haixu Tang, Anna Heintz-Buschart, Patrick May, Emilie E. L. Muller, Cedric C. Laczny, Paul Wilmes
NATURE COMMUNICATIONS
(2020)
Review
Spectroscopy
Juan D. Chavez, Sung-Gun Park, Jared P. Mohr, James E. Bruce
Summary: This review discusses the development and challenges in studying the interactome using chemical cross-linking and high-performance mass spectrometry technologies. It highlights the application of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and its potential for improving the visualization of the interactome. Further developments in parallel MS array capabilities are also discussed.
MASS SPECTROMETRY REVIEWS
(2022)
Article
Biochemical Research Methods
Vidur Kailash, Luis Mendoza, Robert L. Moritz, Michael R. Hoopmann
Summary: SPACEPro is a tool developed to evaluate the efficiency and reproducibility of protein cleavage in peptide samples, providing comprehensive information on sample processing to peptides at the PSM, peptide, and protein levels. It helps users understand the quality of sample processing efficiency and develop protocols for improvement with minimal effort.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Xiaoting Tang, Helisa H. Wippel, Juan D. Chavez, James E. Bruce
Summary: Protein structure is crucial for biological functions, and understanding it is fundamental in biological and biomedical research. Crosslinking mass spectrometry is an emerging technique that can capture transient information on protein interactions in their native environment. Combining XL-MS with traditional techniques has the potential to bridge the gap between structural biology and systems biology approaches.
Article
Microbiology
David W. Cobb, Heather M. Kudyba, Alejandra Villegas, Michael R. Hoopmann, Rodrigo P. Baptista, Baylee Bruton, Michelle Krakowiak, Robert L. Moritz, Vasant Muralidharan
Summary: The study revealed the essential role of Thioredoxin (Trx) superfamily proteins in the endoplasmic reticulum (ER) of Plasmodium falciparum for parasite survival. By identifying a small molecule inhibitor targeting the redox activities of Trx-domain proteins, the study provides a new direction for future antimalarial drug development.
Article
Medicine, Research & Experimental
Matthew A. Walker, Juan Chavez, Outi Villet, Xiaoting Tang, Andrew Keller, James E. Bruce, Rong Tian
Summary: One hallmark of impaired myocardial energetics in failing hearts is the downregulation of the creatine kinase (CK) system. A study found an inverse relationship between the activity and acetylation of CK muscle form (CKM) in human and mouse failing hearts, where hyperacetylation disrupted MM homodimer formation and reduced enzymatic activity. Deacetylation by sirtuin 2 improved dimer formation and restored CKM activity from failing heart tissue, suggesting a novel mechanism for improving high-energy phosphoryl transfer in heart failure.
Editorial Material
Biochemical Research Methods
Susan T. Weintraub, Michael R. Hoopmann, Magnus Palmblad
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Chemistry, Multidisciplinary
Juan D. Chavez, Helisa H. Wippel, Xiaoting Tang, Andrew Keller, James E. Bruce
Summary: Biological systems heavily rely on proteins for various functional roles, and recent advancements in mass spectrometry, chemical labeling, and informatics capabilities have provided insights into the structures of proteins, complexes, and networks within cells. These approaches, which benefit from the molecular detection specificity of mass spectrometry and proteomics, offer systems-level information about conformational changes and protein interactions in response to perturbations.
Review
Biochemistry & Molecular Biology
Helisa H. Wippel, Juan D. Chavez, Xiaoting Tang, James E. Bruce
Summary: This article provides an overview of recent technological developments and applications of qXL-MS, including the design and synthesis of cross-linkers, development of new liquid chromatography-MS methodologies, and computational developments for data interpretation.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Tara K. Bartolec, Joshua J. Hamey, Andrew Keller, Juan D. Chavez, James E. Bruce, Marc. R. Wilkins
Summary: This study investigates the function of histidine protein methyltransferase Hpm1p in yeast and confirms its association with diverse phenotypes, including sugar metabolism regulation, through techniques such as mass spectrometry analysis.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Helisa H. Wippel, Mariana Fioramonte, Juan D. Chavez, James E. Bruce
Summary: RNA-binding proteins (RBPs) interact with RNAs and other proteins to form ribonucleoprotein (RNP) complexes, which are involved in regulating various cellular processes. Heterogeneous nuclear ribonucleoproteins (hnRNPs) play a crucial role in transcription control and nuclear processing of transcripts, as well as in regulating alternative splicing of pre-mRNAs through spliceosome complex.
Article
Microbiology
Susana Martinez Arbas, Shaman Narayanasamy, Malte Herold, Laura A. Lebrun, Michael R. Hoopmann, Sujun Li, Tony J. Lam, Benoit J. Kunath, Nathan D. Hicks, Cindy M. Liu, Lance B. Price, Cedric C. Laczny, John D. Gillece, James M. Schupp, Paul S. Keim, Robert L. Moritz, Karoline Faust, Haixu Tang, Yuzhen Ye, Alexander Skupin, Patrick May, Emilie E. L. Muller, Paul Wilmes
Summary: The study found that CRISPR plays a more important role in defense against plasmids than phages, and the variability in plasmid abundance over time has a greater impact on community dynamics than phages. In addition, the enrichment of protospacers targeting genes involved in the transmission of iMGEs helps understand population fitness and devise control strategies.
NATURE MICROBIOLOGY
(2021)
