Article
Engineering, Environmental
Robert Sitzenfrei
Summary: A novel complex network analysis-based approach for high-computational efficiency water quality assessment in a water distribution system is developed and successfully applied in a design study. The proposed model can identify design solutions exceeding water quality thresholds with a computational efficiency significantly better than state-of-the-art models.
Article
Computer Science, Information Systems
Muhammad Awais Khan, Nadeem Javaid
Summary: This paper focuses on malicious attacks in scale-free Internet of Things (IoT) networks and aims to construct a robust network topology to support node functionality while reducing computational cost. Four solutions are presented, including a Smart Edge Swap Mechanism (SESM) to overcome excessive randomness, a threshold-based node removal method to reduce edge swap operation, correlation analysis of network measures, and the utilization of Heat Map Centrality (HMC) to find important nodes. Simulation results show the effectiveness of the proposed SESM mechanism, with better network robustness and reduced computational cost.
COMPUTER COMMUNICATIONS
(2022)
Article
Computer Science, Information Systems
Nadav Schweitzer, Amit Dvir, Ariel Stulman
Summary: This research proposes a method to maximize the profit of the wormhole attack and challenges the assumptions of the existing attack protocol. Simulating different combinations of network nodes and edges, it shows the effectiveness of an alternative attack method that does not require additional virtual links and decreases the chances of being detected by intrusion detection systems.
Article
Oncology
Young Eun Kim, Eun-Kyung Kim, Min-Jeong Song, Tae-Young Kim, Ho Hee Jang, Dukjin Kang
Summary: Resistance to oxaliplatin is a challenge in pancreatic cancer therapy, and the molecular mechanisms underlying this resistance remain unclear. This study aimed to identify changes in proteins associated with oxaliplatin resistance in pancreatic cancer cells. The findings revealed enrichment of multiple biological processes and highlighted the potential involvement of WLS and MARCKS in oxaliplatin resistance.
Review
Biochemical Research Methods
Mohammad Reza Karimi, Amir Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz
Summary: Holistic perspectives are crucial in understanding the complexity of tumors and current single-layer analysis has limitations. Integrative multilayer approaches are emerging as effective tools in achieving systemic views on cancer biology.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Mathematics, Applied
Qiuyan Shang, Bolong Zhang, Hanwen Li, Yong Deng
Summary: Identification of influential nodes in complex networks is crucial for addressing various problems in different disciplines. A proposed method based on network efficiency of edge weight updating effectively combines global and local information, ensuring accuracy of results and introducing dynamic information through iterative weight updating. Experiments on real-world data sets demonstrate the effectiveness and superiority of the proposed method.
Article
Computer Science, Artificial Intelligence
Kuang Gao, Guocai Yuan, Yang Yang, Ying Fan, Wenbin Hu
Summary: Immunization of social networks has gained attention, but most studies focus on individual node structures and ignore higher-order structures captured by network motifs. This paper proposes a new immunization algorithm that combines higher-order structures and edge-betweenness measure to select edges for immunization, showing improved effectiveness and reduced impact on the network structure.
KNOWLEDGE AND INFORMATION SYSTEMS
(2022)
Article
Computer Science, Artificial Intelligence
Martin Mirakyan
Summary: Betweenness-centrality is a popular measure in network analysis that describes the importance of nodes in a graph by accounting for the fraction of shortest paths passing through them. To speed up the computation, recent approaches have proposed using approximation algorithms and shallow graph convolutional networks. By employing a deep graph convolutional neural network with optimization techniques, the system achieves better results than current methods, showing a significant improvement in speed and resource efficiency.
PEERJ COMPUTER SCIENCE
(2021)
Article
Physics, Multidisciplinary
Michelle T. Cirunay, Rene C. Batac
Summary: In this study, the center-periphery structure of an urban road system is quantified based on the betweenness centrality of the nodes, and its spread over the evolution of the urban zone is measured using historical maps of Manila, Philippines. The results show temporal invariance of the betweenness centrality distributions, indicating the preservation of the planarity of the network. Despite the geographical expansion of the road network, there are topologically peripheral nodes in the geographical center, suggesting the presence of dendritic dead-ends that may affect traffic flow. The shortest paths among the topological periphery evolve towards a homogenized, grid-like structure for the entire network. Understanding peripheral connections is important for transport efficiency within the system.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2023)
Article
Computer Science, Information Systems
Sunil Kumar Maurya, Xin Liu, Tsuyoshi Murata
Summary: Graphs naturally occur in various contexts, and determining influential nodes is crucial for understanding the overall structure. Betweenness and closeness centrality are commonly used measures for identifying important nodes. Our proposed graph neural network (GNN) model improves upon current techniques for approximating betweenness and closeness centrality, showing superior performance in experiments.
ACM TRANSACTIONS ON KNOWLEDGE DISCOVERY FROM DATA
(2021)
Article
Physics, Multidisciplinary
Arsham Ghavasieh, Massimo Stella, Jacob Biamonte, Manlio De Domenico
Summary: Complex systems are large collections of entities that organize themselves into networks, and the study introduces network entanglement as a way to understand network robustness at different time scales. The entanglement between nodes and networks serves as a centrality measure, capturing the importance of nodes in information flow and network integration. Nodes with high entanglement centrality are critical for information dynamics and network integrity.
COMMUNICATIONS PHYSICS
(2021)
Article
Biochemical Research Methods
Zi Gao, Preston Williams, Lin Li, Yinsheng Wang
Summary: DNA sequences with high G content have the potential to form G quadruplex structures, which can interact with specific proteins. Through quantitative proteomic experiments, a number of candidate G4-interacting proteins were identified, some of them being discovered for the first time. These findings highlight the complexity and importance of understanding the G4-interaction proteome in biology.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Computer Science, Theory & Methods
Cecile Daniel, Angelo Furno, Lorenzo Goglia, Eugenio Zimeo
Summary: The study introduces a fast algorithm for computing BC of undirected graphs by using clustering, which outperforms Brandes' algorithm and significantly improves known heuristics.
JOURNAL OF BIG DATA
(2021)
Article
Physics, Fluids & Plasmas
Barbara Benigni, Riccardo Gallotti, Manlio De Domenico
Summary: This study introduces a class of stochastic processes based on biased random walks, using a physical potential to drive agents through a network topology, allowing for interpolation between random walk and geodesic routing. It is demonstrated that there is no one-size-fits-all solution for efficient navigation, with network heterogeneity or modularity having measurable effects. The potential-driven random walks open up a wide range of analytical tools in methodological perspectives.
Article
Environmental Sciences
Orazio Giustolisi, Francesco Gino Ciliberti, Luigi Berardi, Daniele Biagio Laucelli
Summary: Complex Network Theory (CNT) is used to study reliability and vulnerability assessment in networked systems. This study proposes a new approach to analyze the importance of the Isolation Valve System (IVS) in Water Distribution Networks (WDNs) and finds that the classic CNT analyses may not be accurate in assessing reliability in WDNs.
WATER RESOURCES RESEARCH
(2022)
Article
Genetics & Heredity
Charlie F. Rowlands, Algy Taylor, Gillian Rice, Nicola Whiffin, Hildegard Nikki Hall, William G. Newman, Graeme C. M. Black, Raymond T. O'Keefe, Simon Hubbard, Andrew G. L. Douglas, Diana Baralle, Tracy A. Briggs, Jamie M. Ellingford
Summary: Variable gene expression levels between tissues complicate the use of RNA sequencing for delineating genomic variants impact. A gene and tissue-specific metric, MRSD, overcomes limitations of using expression values alone, estimating the required sequencing depth to achieve desired coverage. Fibroblasts are identified as the optimal RNA source using MRSD, demonstrating its utility in functional assessment of splicing aberrations, particularly in Mendelian genetic disorders context.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Plant Sciences
Helena A. Saunders, Pablo Calzadilla, Jean-Marc Schwartz, Giles N. Johnson
Summary: The accumulation of fumarate, catalyzed by the fumarase isoform FUM2, is necessary for photosynthetic acclimation in Arabidopsis. Using the Failure Mode and Effect Analysis (FMEA) technique, researchers have identified fumarate as a low-risk metabolite and malate as a high-risk metabolite that can cause system instability. FUM2 is suggested to provide a fail-safe mechanism to control malate concentration and maintain stability in a changing environment.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Dominic P. Byrne, Safal Shrestha, Leonard A. Daly, Vanessa Marensi, Krithika Ramakrishnan, Claire E. Eyers, Natarajan Kannan, Patrick A. Eyers
Summary: Pseudokinases lack conserved amino acids for catalytic activity and have diverse biological functions. Human PSKH2 is a pseudokinase closely related to the canonical kinase PSKH1. Species-level adaptations have led to the appearance of PSKH2 variants alongside PSKH1 in vertebrate genomes. PSKH2 lacks protein phosphotransferase activity and its N-terminal domain is required for stable expression and localization to the mitochondrial fraction. PSKH2 is part of a mitochondrial protein network and its expression is regulated through the HSP90/Cdc37 chaperone system.
BIOCHEMICAL JOURNAL
(2023)
Article
Biochemical Research Methods
Martin Rusilowicz, David W. Newman, Declan R. Creamer, James Johnson, Kareena Adair, Victoria M. Harman, Chris M. Grant, Robert J. Beynon, Simon J. Hubbard
Summary: Protein quantitation via mass spectrometry requires the use of peptide proxies, and accurate quantitation often relies on the addition of an external standard. AlacatDesigner is a tool that assists in selecting suitable peptide candidates for recombinant protein standards. It considers factors such as target protein, existing databases, literature occurrence, potential post-translational modifications, and ionization potential within the mass spectrometer.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Martin D. Jennings, Priya Srivastava, Christopher J. Kershaw, David Talavera, Christopher M. Grant, Graham D. Pavitt
Summary: Cells respond to oxidative stress by reprogramming gene expression to enhance levels of antioxidant enzymes. In Saccharomyces cerevisiae, proteins Slf1 and Sro9 play a role in protein synthesis adaptation during stress. Slf1 is identified as a ribosome-associated translational modulator that promotes translation of highly-translated mRNAs, facilitating cell survival and adaptation to stress.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Jack Llewellyn, Venkatesh Mallikarjun, Ellen Appleton, Maria Osipova, Hamish T. J. Gilbert, Stephen M. Richardson, Simon J. Hubbard, Joe Swift
Summary: Cells respond to stress by producing chaperone proteins to maintain protein function, but aging leads to a disruption of protein balance and the formation of disease-related protein aggregates. Understanding the molecular causes of this proteostasis deterioration is important for disease interventions and cell health maintenance in regenerative medicine strategies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Leandro Xavier Neves, R. Alan Wilson, Philip Brownridge, Stephen W. W. Holman, Victoria M. M. Harman, Claire E. E. Eyers, Robert J. J. Beynon, William Castro-Borges
Summary: In this study, a detailed method for preserving the proteome of adult Schistosoma mansoni worms was described in order to enrich the tissues associated with the parasite's alimentary tract. The methodology employed label-free and QconCAT-based absolute quantification to detect S. mansoni oesophageal gland products. By stabilizing the proteome and minimizing sample degradation during dissection, the hidden proteome of target tissues, which are not readily available from total lysates due to their small volumes, could be accessed. This protocol can be used for the discovery of proteins with potential diagnostic and therapeutic utility in other Schistosoma species lacking quantitative proteomics characterization of specialized tissues.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Jana Schepers, Zorana Carter, Paraskevi Kritsiligkou, Chris M. Grant
Summary: This study reveals that methionine oxidation is a key factor in the formation of the yeast [PSI+] prion. By lacking methionine sulfoxide reductases, it is found that [PSI+] formation is increased, while lacking both isoenzymes of methionine sulfoxide reductases reduces [PSI+] formation.
Article
Biochemistry & Molecular Biology
Joanne Cunningham, Aristeidis P. Sfakianos, Paraskevi Kritsiligkou, Christopher J. Kershaw, Alan J. Whitmarsh, Simon J. Hubbard, Mark P. Ashe, Chris M. Grant
Summary: Translation initiation factor 4G (eIF4G) is crucial for translation initiation. In yeast, eIF4G1 is specifically required for the translational response to oxidative stress.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Omer F. Bay, Kelly S. Hayes, Jean-Marc Schwartz, Richard K. Grencis, Ian S. Roberts
Summary: Genome-scale metabolic model of Trichuris muris reveals the essential role of Thioredoxin Reductase (TrxR) enzyme for its survival, as well as the mechanism of glutathione reduction by TrxR enzyme. The model also predicts several essential amino acids that cannot be synthesized by T. muris.
NATURE COMMUNICATIONS
(2023)
Editorial Material
Genetics & Heredity
Olga Valenzuela, Francisco Ortuno, Alfredo Benso, Jean-Marc Schwartz, Alexandre G. de Brevern, Ignacio Rojas
Meeting Abstract
Pathology
Steven Woods, Nicola Bates, Stuart Cain, Paul Humphreys, Fabrizio Mancini, Antony Adamson, Peter Harley, Ian Donaldson, Geert Mortier, Kate Chandler, Clair Baldock, Jean-Marc Schwartz, Susan J. Kimber
INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY
(2023)
Article
Biochemical Research Methods
Leonard A. Daly, Dominic P. Byrne, Simon Perkins, Philip J. Brownridge, Euan Mcdonnell, Andrew R. Jones, Patrick A. Eyers, Claire E. Eyers
Summary: In this study, a MS-based workflow for sY-peptide characterization was developed, allowing systematic investigation of the sulfome. The key for distinguishing sulfated peptides from phosphopeptides was low collision energy-induced neutral loss. Applying this workflow identified 21 new sulfotyrosine-containing proteins and revealed new interplay between enzymes relevant to both protein and glycan sulfation.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Allen Po, Claire Eyers
Summary: Top-down proteomics aims to identify and analyze intact proteoforms extracted from biological samples. However, defining and pinpointing post-translational modifications on intact proteins remains a challenge. This is crucial for understanding the specific roles and structure-function relationships of proteins.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Chemistry, Multidisciplinary
Leonard A. Daly, Christopher J. Clarke, Allen Po, Sally O. Oswald, Claire E. Eyers
Summary: The article focuses on the application of mass spectrometry in the identification and quantification of protein modifications, specifically phosphorylation and sulfation. It discusses the challenges associated with discriminating and pinpointing the sites of these modifications on polypeptide chains. The article showcases various approaches for enrichment and site localisation of phosphorylated and sulfated peptides, as well as modification analysis in intact proteins. It also discusses the use of native ion-mobility MS to explore the effects of these modifications on protein structure and ligand binding. The article provides insights into the current strategies and future directions in studying phosphorylation and sulfation using mass spectrometry.
CHEMICAL COMMUNICATIONS
(2023)